## Sample exercises and tests

This page contains a list of all the exercises provided throughout this website. The exercises are organized by topic and are assigned a reference number (e.g. Lit-3) so that you may more easily direct your students to a specific exercise on the site.

## Aud – Audience and purpose

Exercises from “How do I get started?

Aud-1: Practice exercise

## Compare the sentences in each set given. What do you think is the purpose and intended audience for each sentence? Think about what kinds of clues in the language led you to these conclusions.

1.  a. Porosity was determined using the following method: samples were dried in an oven at 40 °C; sample dimensions and dry mass were recorded; samples were blotted and weighted to obtain saturated mass.

b. Determine porosity using the following method: 1. Dry samples in an oven at 40 ˚C overnight. 2. Record the dimensions and the dry mass of each sample. 3. Blot each sample using MMX Oval paper. 4. Weigh each sample and record its saturated mass.

2. (Adapted from Costanza-Robinson and Brusseau 2002)

a. Although several methods for measuring air-water interfacial area have been proposed, each with associated advantages and disadvantages, it is not clear that the methods yield consistent information. It is possible that the various methods probe different physical interfacial domains within the soil, although studies have not specifically examined this phenomenon in detail.

b.The current study was conducted to evaluate in greater detail one of the proposed methods for measuring the air-water interface, a gas-phase interfacial tracer method.

3. a. Isotope 136Xe exhibits very high transition energy Q = 2457.8 keV, and the probability of decay by the neutrinoless channel is proportional to ~Q5. (Adapted from Belov et al. 2012)

b. Xenon (Xe) has over 30 unstable isotopes. 136Xe, which is the longest-lived with a half-life of 2 x 1021 years, undergoes double beta decay, a process that involves a nucleus releasing 2 beta particles.

4. a. Here, subglacial ice velocity is well correlated with moulin hydraulic head but is out of phase with that of nearby (0.3–2 kilometres away) boreholes. (Adapted from Andrews et al. 2014)

b. Our boreholes display high mean hydraulic head (close to or above overburden) and low-amplitude diurnal variability (less than 25 m or <5% of overburden).

#### Possible solutions

1. a. Audience: scientists, especially those who want to be able to conduct a similar experiment. Purpose: to convey how a study was conducted.
b. Audience: students. Purpose: to instruct on how to conduct an experiment.
2. a. Audience: scientists, especially professionals interested in air-water interfacial areas. Purpose: to explain what hasn’t been done yet.
b. Audience: scientists, especially professionals interested in air-water interfacial areas. Purpose: to describe how the “current study” addresses a poorly-understood topic.
3. a. Audience: scientists who are well-versed in isotope decay and its associated terminology. Purpose: to inform about the decay properties of 136Xe.
b. Audience: students. Purpose: teach about the decay properties of 136Xe.
4. a. Audience: scientists interested in subglacial ice velocity. Purpose: to describe experimental results.
b. Audience: professional glacial scientists. Purpose: to describe experimental results.

As you can see, sometimes similar-sounding information can address 2 entirely different audiences and/or purposes, while different purposes can be achieved with the same audiences in mind. The vocabulary, level of detail, and amount of explanation you use can all help tailor information to your intended audience and purpose.

Aud-2: Test yourself

## What genre would be most appropriate for the following scientific audiences and purposes?

1. To request funding from the National Science Foundation for a new research project
2. To share your summer research findings with people at your school
3. To share your summer research findings with people in your department
4. To share your summer research findings with the national scientific community in your discipline
5. To record what you did step by step in your research for other students to use for replicating your experiments

### Solutions

1. A research proposal
2. A poster
3. A poster or presentation
4. A journal article
5. A lab notebook

Aud-3.1: Test yourself

Based on the kinds of details used, which audience (expert, scientist, or student) do each of the following statements seem to be most addressing?

## Aud 3.1 – Biology

1. Measure 140 mg ammonium sulfate into a 15-mL conical vial. Add 4.0 mL cell lysate preparation and rotate at room temperature for 30 min.
2. The testosterone assay is based on a four-position tritium competitor and an antiserum raised against testosterone-11-BSA. Hydrolysed urine samples were extracted twice in diethyl ether prior to assay, with recoveries individually monitored by the addition of trace amounts of tritiated testosterone (Muller and Wrangham 2004).
3. In plants, miRNAs base pair with messenger RNA targets by precise or nearly precise complementarity, and direct cleavage and destruction of the target mRNA through a mechanism involving the RNA interference machinery (adapted from Ambros 2004).
4. MicroRNAs pair to the messages of genes that code for proteins to prevent them from allowing the synthesis of these proteins. (adapted from Ambros 2004).

## Solutions

1) student; this is the kind of detailed procedural instructions that would be found in a lab manual or notebook.
2) expert; enough important detail (such as “extracted twice in diethyl ether”)  is given in scientific terms that an expert could replicate the project, but the nitty-gritty of the benchwork (like the volume of the urine samples) is left out.
3) scientist; this description of miRNAs is a little more in-depth than could probably be given to a student all at once, yet it helps more sophisticated scientists grasp the background of the project.
4) student; this is a much more surface description of miRNAs that requires only minimal knowledge of biology.

## Aud 3.2 – Chemistry

1. The appropriate function of insulin-producing pancreatic β-cells is crucial for the regulation of glucose homeostasis, and its impairment leads to diabetes mellitus, the most common metabolic disorder in man (Leibiger, Leibiger, and Berggren 2008).
2. Thermal cycling conditions were set as follows: initial denaturation step at 50°C for 2 minutes and 95°C for 10 minutes, followed by 40 cycles at 95°C for 15 seconds and 60°C for 1 minute (Mitani et al. 2009).
3. Although the mechanisms of its antitumor effects remain unclear, it appears that cell cycle arrest and apoptosis induction via various regulatory pathways may play fundamental roles (Mitani et al. 2009).
4. The most performing ligand architectures are based on tetra-arylporphyrins (N4), Schiff bases (N4), salens/salphens and related ligands (N2O2), substituted phenols (N2O) or complex bridged bisphenols (N4O2) (Adolph et al. 2015).

## Solutions

1) student; this statement includes a simple explanation of what diabetes is but doesn’t go greatly into detail about the chemistry of β-cell function.
2) expert; the details of exactly how the PCR was conducted would mostly be of interest to an expert trying to replicate the experiment.
3) scientist; suggestions of possible mechanisms would help scientists better understand the direction of the field but wouldn’t necessarily help a student learn more about how the molecule functions.
4) scientist; the statement lists the types of structures that are functional but doesn’t go into detail about why they work, making it somewhat less useful for an expert.

## Aud 3.3 – Physics

Which audience (expert, scientist, or student) do each of the following statements seem to be most addressing?

1. It describes the coherent exchange of energy between a quantized electromagnetic field and a quantum two-level system at a rate g/2π, which is observable if g is much larger than the decoherence rates κ and γ (Wallraff et al. 2004).
2. In order to identify the sources of turbulence in astronomical systems, it is also important to determine the behavior of velocity and magnetic field correlations on larger spatial scales (adapted from McKee and Ostriker 2007).
3. Two electrical components are in series if they are joined together at one end each; electric current flowing through the first component has nowhere to go but through the second component as well (Ratcliff 2014).
4. Although chaotic communication experiments with electronic circuits have typically demonstrated information transmission at bandwidths of tens of kilohertz or less, the fast dynamics of optical systems offers the possibility of communication at bandwidths of hundreds of megahertz or higher (adapted from VanWiggeren and Roy 1998).

## Solutions

1) expert; “g/2π” and “the decoherence rates κ and γ” are so specific that they would likely only be of interest to someone with prior knowledge of quantum physics.
2) scientist; “turbulence in astronomical systems” is somewhat specific to the area of study but is not so detailed that a non-physicist couldn’t understand it.
3) student; this a clear and simple explanation that requires no prior knowledge of physics.
4) scientist; telling us the orders of magnitude of bandwidth is necessary to understand a key difference between electronics and optics, yet the overall statement only involves fairly basic scientific concepts.

## Aud 3.4 – Geology

Which audience (expert, scientist, or student) do each of the following statements seem to be most addressing?

1. Extracellular polymeric substances, widely produced by microbes for attachment and protection, are important in facilitating sediment trapping in cave and soil environments (adapted from Riding 2000).
2. Sandstone composition is influenced by source rock composition, climate, relief, slope, vegetation, and characteristics of the depositional environment (adapted from Johnsson, Stallard, and Meade 1988).
3. Sands were cemented with epoxy, and standard thin sections were stained for both potassium feldspar and plagioclase (adapted from Johnsson, Stallard, and Meade 1988).
4. Grain surfaces of first-cycle sands from the lowland shield are typically densely covered with dissolution etch pits and are frequently deeply embayed, features that are rare on the surfaces of first-cycle sands from the elevated shield (adapted from Johnsson, Stallard, and Meade 1988).

## Solutions

1) scientist; understanding this statement requires some scientific background to understand such phrases as “extracellular polymeric substances,” but none of the details require highly specific knowledge about geology.
2) student; the details used would be accessible to someone with minimal scientific background and are used to teach fundamental knowledge about sandstone.
3) scientist (or expert); this level of methodological detail would be useful to any scientist trying to better understand your project (but could also be used by someone trying to replicate the experiment).
4) expert; such detail would be of little interest or use to someone who did not already understand the implications of “first-cycle sands” and want to know extremely specific information about grain surfaces.

Aud-4: Practice exercise

## Re-write the following statements to make them more formal.

1. When I first mixed the dried cell extract into the solution, it didn’t dissolve. After I stirred it for a while, it finally did.
2. The oscilloscope said that the frequency wasn’t above 25 Hz.
3. DNA, or deoxyribonucleic acid, packs a lot of genetic information into a relatively tiny molecule.
4. When the sediment collected downstream after the storm event from the week previous to the week that this study happened, buildup caused troubles for the water to flow from the stream into the main lake.

## Possible solutions

1. The dried cell extract dissolved completely after continual stirring.
2. Using an oscilloscope, the frequency was determined to be less than 25 Hz.
3. Genetic information is compactly stored in cells using DNA. [“DNA” usually does not have to be spelled out, as it is common knowledge[link].]
4. Sediment accumulation from a storm event the week previous hindered drainage from the stream into the main lake.

Note that by using formal language, your writing will also become more concise!

Aud-5: Test yourself

## Which genre or section of a particular genre should you use to achieve the following purposes?

1. Make sure a student in your lab could repeat an experiment later.
2. Quickly inform your audience what the subject of your study was.
3. Share your findings with members of your school who may or may not be part of your scientific discipline.
4. Formally share your findings with biologists across the nation.
5. Convince the NSF to fund your next research endeavor.
6. Recognize the research that formed the conceptual basis for your current project.

## Solutions

1. Lab notebook
2. Title of a poster or paper
3. Poster
4. Journal article
5. Research proposal
6. Literature cited (if said research is published)

Aud-6: Test yourself

## Each pair of sentences has one audience, given in bold. Compare the formality, level of detail, and conciseness of each sentence in the pair to determine what its purpose is.

1. Student audience
• a) After the purge completes, allow the system to run at about 1 mL/min for about 1 minute to equilibrate the pressure. To set the flow rate, use the arrow keys to highlight the flow box and type “1.” Press enter.
• b) In HPLC, pump pressures allow for consistent flow rates. Equilibration is necessary to prepare the column for interaction with the desired molecule.
2. Expert audience
• a) Coherent quantum effects have been recently observed in several superconducting circuits, making these systems well suited for use as quantum bits (qubits) for quantum information processing (Wallraff et al. 2004).
• b) The anti-crossing between the single photon resonator state and the first excited qubit state was observed by tuning the qubit into and out of resonance with a gate charge near n = 1 and measuring the transmission spectrum (see Fig. 4c).
3. Scientific audience
• a) Methane (CH4) emission by carbon-rich cryosols at the high latitudes in Northern Hemisphere has been studied extensively. In contrast, data on the CH4 emission potential of carbon-poor cryosols is limited, despite their spatial predominance (Lau et al. 2015).
• b) In situ CH4 fluxes were measured in July 2011–2013 using a Picarro soil CO2-CH4 gas analyzer (Picarro Inc., Santa Clara, CA, USA) or Los Gatos Fast Methane Analyzer (Los Gatos Research Inc., Mountain View, CA, USA).

## Solutions

1. Student audience
• a) to instruct on use of the instrument
• b) to teach the theory behind using the instrument in this way
2. Expert audience
• a) to teach about quantum information processing
• b) to present new findings about qubit states
3. Scientific audience
• a) to introduce the state of CH4 emissions research
• b) to inform about how CH4 emissions were measured

Note that in addition to knowing your audience, you need to know your purpose before you can know what to write about! The reverse is also true.

## Lit – Literature, citations, and references

Exercises from “How can I find and use the literature?” and sub-pages.

Lit-1: Test yourself

## If you got information from one of the following sources, what is the best way for it to be cited? Choose either A, B, or C: A) Information should be paraphrased and cited. B) Information should be paraphrased and not cited. C) Information should be tracked to its original source before determining A or B.

1. The abstract of a primary research article published in Nature
2. A datum from a review article published in Physical Review C
3. A graph from the Results section of a research article published in Analytical Chemistry
4. An article on Wikipedia
5. A chapter from your textbook Introduction to Mineralogy
6. Your Biology 145 lab manual
7. Information from a data table in a metastudy published in Science.
8. The Vermont Agency of Agriculture Regulations for Control of Pesticides

## Solutions

1. C – The information should be found in the body of the text before citing so that you fully understand the context of the data. Learn more about abstracts here.
2. C – Although the information from a review can give you a good understanding of the state of a field or topic, try citing the papers that originated the data when comparing it to your own results.
3. A – Graphs are often a great summary of information that can be referenced in your paper.
4. C – Some of the information may be from primary sources, which you can locate using footnote chasing and then cite the original work. However, much of the information on Wikipedia will not be, so you will have to find another source for the information.
5. B – This is a general knowledge work.
6. B – This is not a primary source and thus should not be cited in professional documents. Note: Some classes may require the citation of their manuals for work submitted in that class. Be sure to check with your professor for his or her expectations!
7. A – Metastudies are great resources for finding information from lots of research compiled in one place. Because the analysis of all the data is usually new and different than in the original research, metastudies are considered to contribute something original to the scientific literature and are therefore primary resources.
8. A – Regulatory documents and permits are considered primary sources and should always be cited.

Lit-2: Practice exercise

## Paraphrase each of the following by changing both the wording and structure of the passage while retaining the important scientific information.

1. HCN emission, which is very strong in most ultraluminous galaxies, originates in the high-density extreme starburst regions similar to A and B. These regions do not produce most of the CO luminosity, but they do emit most of the HCN luminosity (adapted from Downes and Solomon 1998).
2. The dynamic nature of drinking water treatment processes exerts a strong influence on removal of pathogens from raw waters. Pathogen removal efficiency in a conventional treatment plant is affected even with a slight variation in influent water quality or influent water conditions (adapted from Upadhyayula et al. 2009).
3. Dendrimers are highly branched macromolecules having precisely defined molecular structures with nanoscale size. Complexes containing dendritic ligands are also soluble in many common solvents and can be separated from the products by precipitation, membrane or nanofiltration techniques (Fan, Li, and Chan 2002).

## Possible solutions

All solutions should attempt to both alter the organization of the original passage and be in your own words. Remember that the original source will still need to be cited.

1. High-density starburst regions such as A and B are responsible for most of the HCN luminosity (but not CO luminosity), as in most ultraluminous galaxies.13
2. Minor variations in the quality of influent water can significantly affect the processes required for efficient pathogen removal in drinking water treatment plants.4
3. Precipitation, membrane and nanofiltration are all techniques capable of separating dendritic ligand complexes from the products.7

Some of these example solutions may seem to cut out important information. The key is to know what information is critical for you to use and to cut out anything else.

Lit-3: Practice exercise

## Look at the figures and tables in the examples below and ask yourself:

1. Why did the author(s) choose this particular reference style?
2. In what other ways, if any, could the authors have clearly referenced the data shown?

Adapted from Armstrong et al. (2005)

The undergraduate thesis of Alison Maxwell (Middlebury College)

Vecchi et al. (2015)

Costanza-Robinson and Brusseau (2002)

Costanza-Robinson and Brusseau (2002)

Lit-4: Test yourself

1.  a)

b)

2. a)

b)

## Solutions

1. B is preferred because repeating “From Rubart et al. 2000” in (a) is redundant and therefore less concise. Figure B also looks less cluttered, which aids interpretation of the graph.
2. A is preferred because labeling each datum with a separate reference makes it obvious what information came from what source. The technique in (b) is unclear.

## Org – Broad and fine writing organization, including move structures

Exercises from “How do I organize my writing?

Org-1: Test yourself

## Read the abstract given and identify which sentences comprise each of the major moves (1, 2 and 3) made by the authors. The beginning of each sentence is numbered, such as [1], for easier reference in the solutions.

1. [1] Sexual reproduction in fungi is controlled by genes present at the mating type (MAT) locus, which exists as two alternative idiomorphs in ascomycetous fungi. [2] The gene content of this locus determines whether a fungus is heterothallic (self-sterile) or homothallic (self-fertile). [3] Recently, a unique sub-class of homothallism has been described in fungi, where individuals possessing a single MAT idiomorph can reproduce sexually in the absence of a partner. [4] Using various mycological, molecular and bioinformatic techniques, we investigated the sexual strategies and characterized the MAT loci in two tree wound-infecting fungi, Huntiella moniliformis and Huntiella omanensis. [5] H. omanensis was shown to exhibit a typically heterothallic sexual reproductive cycle, with isolates possessing either the MAT1-1 or MAT1-2 idiomorph. [6] This was in contrast to the homothallism via unisexual reproduction that was shown in H. moniliformis, where only the MAT1-2-1 gene was present in sexually reproducing cultures. [7] While the evolutionary benefit and mechanisms underpinning a unisexual mating strategy remain unknown, it could have evolved to minimize the costs, while retaining the benefits, of normal sexual reproduction. (Adapted from Wilson et al. 2015).

1. [1] Seasonal acceleration of the Greenland Ice Sheet is influenced by the dynamic response of the subglacial hydrologic system to variability in meltwater delivery to the bed via crevasses and moulins (vertical conduits connecting supraglacial water to the bed of the ice sheet). [2] As the melt season progresses, the subglacial hydrologic system drains supraglacial meltwater more efficiently, decreasing basal water pressure and moderating the ice velocity response to surface melting. [3] However, limited direct observations of subglacial water pressure mean that the spatiotemporal evolution of the subglacial hydrologic system remains poorly understood. [4] In this study, we simultaneously measured moulin and borehole hydraulic head and ice velocity in the Paakitsoq region of western Greenland. [5] We show that ice velocity is well correlated with moulin hydraulic head but is out of phase with that of nearby (0.3-2 kilometres away) boreholes, indicating that moulins connect to an efficient, channelized component of the subglacial hydrologic system, which exerts the primary control on diurnal and multi-day changes in ice velocity. [6] Furthermore, show that decreasing trends in ice velocity during the latter part of the melt season cannot be explained by changes in the ability of moulin-connected channels to convey supraglacial melt. [7] Instead, these observations suggest that decreasing late-season ice velocity may be caused by changes in connectivity in unchannelized regions of the subglacial hydrologic system. [8] Understanding this spatiotemporal variability in subglacial pressures is increasingly important because melt-season dynamics affect ice velocity beyond the conclusion of the melt season. (Adapted from Andrews et al. 2014).

1. [1] Isomeric 4′- and 5′-substituted phosphinooxazoline (PHOX) ligands are used to probe the electronic origins of enantioselective nucleophilic additions to (1,3-diphenylallyl)palladium PHOX ligand complexes. [2] Hammett analysis of the 13C NMR chemical shifts of the allyl C-1 and C-3 carbons shows that the major exo diastereomer is less susceptible to differential changes at C-1 and C-3 and that the location of the substituent has a smaller impact on these changes. [3] In contrast, the minor endo diastereomer is more susceptible to differential 13C NMR changes at C-1 and C-3 and the location of the substituent has a greater impact on these changes. The endo diastereomer exhibits a pronounced “cis effect” by the ligating nitrogen and phosphorus atoms across the palladium center that explains its lower reactivity and, therefore, how the enantioselectivity typically obtained with PHOX ligands exceeds the approximately 8/1 ratio of exo to endo intermediates. [4] Swain-Lupton analysis reveals the importance of both resonance and field effects by the substituents regardless of their location and supports the overall electronic control model for enantioselection by PHOX ligands. [5] For rational chiral ligand design and electronic tuning of ligand properties, these results suggest that the overall electronic impact of a remote substituent generally depends more on its identity than on its location within the ligand. (Adapted from Armstrong et al. 2012).

## Solutions

1. Move 1: Sentences 1 – 3
Move 2: Sentence 4
Move 3: Sentences 5 – 7

1. Move 1: Sentences 1 – 3
Move 2: Sentence 4
Move 3: Sentences 5 – 8

1. Move 1: Sentence 1
Move 2: Only parts of sentences 2 and 4. (“Hammett analysis of the 13C NMR chemical shifts of the allyl C-1 and C-3 carbons” and “Swain-Lupton analysis.”)
Move 3: Sentences 2 – 5

Org-2: Test yourself

## Each of the following sentences are taken out of context from journal article abstracts. Identify the move associated with each statement.

1. The recoveries of the eight synthetic colorants in four matrices ranged from 93.2 to 108.3%. (Ma et al. 2006)
2. Here we use P-to-S (compressional-to-shear) converted teleseismic waves observed on several temporary networks in the Central Andes to image the deep structure associated with these tectonic processes. (Yuan et al. 2000)
3. Dental restorative composites are activated by visible light and the polymerization process, known as direct technique, is initiated by absorbing light in a specific wavelength range (450–500 nm). (Campos et al. 2015)
4. The effect of repeated treatments with lead on hepatic cell proliferation was investigated in male Wistar rats. (Ledda-Columbano, Columbano, and Pani 1983)
5. The same conditions were also effective for the synthesis of two trans-porphyrins derived from 5-(2,6-dichlorophenyl)dipyrromethane. (Littler, Ciringh, and Lindsey 1999)
6. These weak processes are evaluated in an approach which consists of one-nucleon and two-nucleon meson-exchange currents and nuclear wave functions generated by a high precision nucleon-nucleon potential. (Nasu et al. 2015)

## Solutions

1. Move 3 (Summarize your results)
2. Move 2 (Describe your methods)
3. Move 1 (Describe your project)
4. Move 1
5. Move 3
6. Move 2

Org-3: Test yourself

## In the following examples, identify the gap statement. Then, identify the fill. Notice if there are any specific words or phrases used to signal either of these moves.

1. Adapted from Costa, Robertson, and Quilliam (2015):

Paralytic shellfish poisoning occurs worldwide, and harmful algal blooms, including those responsible for PSP, appear to be increasing in frequency and intensity. PSP outbreaks in Portuguese waters have been associated with blooms of Gymnodinium caenatum in the late 1980s to early 1990s, then again after 2005. According to the national monitoring program in Portugal, G. catenatum were not reported along the Portuguese coast during the 10-year period from 1995 to 2005. The aims of this study were to fully characterize the toxin profile of G. catenatum strains isolated from the NW Portuguese coast before and after the 10-year absence of blooms to
determine changes and potential implications for the region. Hydrophilic interaction liquid
chromatography tandem mass spectrometry (HILIC-MS/MS) was utilized to determine the presence of any known and emerging PSTs in sample extracts.

2. Adapted from Littler, Ciringh, and Lindsey (1999):

The exchange process frequently observed in polypyrrane condensations is proposed to occur by the acid-catalyzed fragmentation of a polypyrrane 1 into pyrrolic 2 and azafulvene 3 components.15 As illustrated in Scheme 2, recombination of 2 and 3 can form a new polypyrrane 4 that cannot be formed by direct condensation of the dipyrromethane and aldehyde. Ultimately this process leads to the production of a scrambled mixture of porphyrins. The factors that promote the scrambling process in MacDonald-type 2 + 2 condensations are poorly understood, but suppression of scrambling is essential for preparing large quantities of pure trans-porphyrins. In this paper we describe a study of a wide range of reaction conditions for the 2 + 2 condensation that has led to refined synthetic procedures for the preparation of trans-porphyrins.

3. Adapted from Pukhov and Meyer-ter-Vehn (2002):

In the present paper, we focus on laser wake field acceleration in a new, highly non-linear regime. It occurs for laser pulses shorter than λ(p) but for relativistic intensities high enough to break the plasma wave after the first oscillation. In the present relativistic regime, one should notice that the plama wave fronts are curved and first break new the wave axis and for lower values than the plane-wave limit. This has been studied in 2D geometry in [14-17]. Here, we present 3D PIC simulations of two representative cases. The case (I) is just marginally above and the case (II) is far above the breaking threshold.

## Solutions

Good gap and fill signaling phrases are italicized.

1. Gap statement: “The factors that promote the scrambling process in MacDonald-type 2 + 2 condensations are poorly understood….”

Fill: In this paper we describe a study of a wide range of reaction conditions for the 2 + 2 condensation that has led to refined synthetic procedures for the preparation of trans-porphyrins.”

2. This question is a little trickier! The authors use “In the present paper…,” then, “In the present regime…,” and finally, “Here…,” all of which sound like signaling words for filling the gap. But where is the gap? We have to look closely at what exactly is being said. It is true that the first statement appears to be somewhat of a gap fill, although they haven’t yet given us a gap statement. The authors go on to say “This has been studied in 2D geometry,” which brings us back to move 1(iii), identifying critical evidence from the literature.

Thus, the gap statement is not explicit. It is a combination of stating that this concept has been studied in 2D, followed by announcement that the authors will study it in 3D.
Fill: “Here, we present 3D PIC simulations of two representative cases.”

Although the first sentence (“… we focus on laser wake field acceleration…”) could also be considered part of the fill, because it comes before the gap statement and is also less descriptive, it functions more as an introduction to these moves.

3. Gap statement: “According to the national monitoring program in Portugal, G. catenatum were not reported along the Portuguese coast during the 10-year period from 1995 to 2005.”

Fill: “The aims of this study were to fully characterize the toxin profile of G. catenatum strains isolated from the NW Portuguese coast before and after the 10-year absence of blooms to
determine changes and potential implications for the region.”

Org-4: Practice exercise

## Find 3-4 primary research articles (not reviews) from reputable journals in your field. Underline the gap statement and circle the gap fill. Remember that not all papers follow this exact move structure, so if you can’t seem to find either of these moves, you might have to look carefully at different parts of the introduction and ask yourself:

• What concept are the authors trying to better understand? (This might point to a gap statement.)
• What did the authors try to accomplish in the paper, in summary? (This might point to a fill.)

Org-5: Test yourself

## Each of the following sentences are taken out of context from journal article abstracts. Identify the move associated with each statement.

1. To a suspension of 50 × 10-3 mol of NaH (80% in oil) in dry 100 ml of THF, 0.1 mol of dialkyl malonate was added dropwise over 30 min. (Trabelsi, Szönyi, and Geribaldi 2001)
2. The porous medium used in these experiments was spherical glass beads (Particle Technology Ltd., Hatton, Derbyshire, UK) in a size range of 300-425 μm, with a mean diameter of 355 μm. (Lecoanet, Bottero, and Wiesner 2004)
3. The detector operates at atmospheric pressure and has two drift gaps, so that the highvoltage electrodes are attached to the upper and lower planes of the detector. (Belov et al. 2012)
4. Genomic DNA was digested with these enzymes, self-ligated, and used as template in inverse PCR reactions with primer sets derived from known regions. (Yun et al. 2000)
5. The fry survival rate was analysed by the Proc GLIMMIX procedure (version 9.2, SAS
Institute) for differences between control and treatments. (Straus et al. 2012)
6. For several runs, we also performed velocity measurements with an 8 MHz ultrasonic Doppler velocity profiler (UDVP). (Weill et al. 2014)
7. Samples #10 and 11 were deposited on a 1000-mesh copper-grid with no carbon film directly from a drop of the DMF suspension, in order to prevent any misinterpretation due to the occurrence of byproducts origination from the alteration of a carbon film by the DMF. (Monthioux et al. 2001)
8. For each numerical electron, we integrate over time from 0 to t to obtain the gain components Γz to Γ. (Pukhov and Meyer-ter-Vehn 2002)
9. In this area are 156 stations, but we remove stations with instrumental timing errors using a time symmetry argument for noise cross correlations as introduced by Ref. 4. (Obermann et al. 2014)

## Solutions

1. Move 2 (Describe experimental methods)
2. Move 1 (Describe materials)
3. Move 1
4. Move 2
5. Move 3 (Describe numerical methods)
6. Move 2
7. Move 2
8. Move 3
9. Move 1

Org-6: Practice exercise

## In a paper by Emerson and Moyer (1997), the authors describe an experiment in which they attempt to grow two different iron-oxidizing bacterial strains, ES-1 and ES-2, on various mediums . Below is an excerpt from this paper with an accompanying figure. Read the excerpt and answer the following questions:

1. How do the authors organize this portion of their Results section?
2. How early and how frequently do the authors refer to the figures?
3. Which of the three submoves (describe important trends, highlight key findings, identify unexpected results) do the authors utilize? Why do you think they didn’t include the other move(s)?
4. What trends or data in the figure do the authors also describe in the text? What do the authors note in the text that they don’t include in a figure or table? (Note that we don’t include Figure 4 here, although it contains the same types of information as in Figure 5)

The growth curves of strains ES-1 and ES-2 are shown in Fig. 4 and 5, respectively. ES-1 grew on FeS with a doubling time of approximately 8 h. The addition of acetate to the growth medium did not appear to stimulate the growth of ES-1 above that of Fe2+ alone. When ES-1 was grown in the presence of agarose alone it did not show any sign of growth (Fig. 4). When it was grown in the presence of acetate, pyruvate, or glucose without added iron, there was no visible sign of growth.

Strain ES-2 grew on FeS with a doubling time of approximately 12.5 h and had a comparable doubling time when grown on FeCO3 (Fig. 5). It too did not grow with acetate, pyruvate, or glucose as a C source, nor did it show any indication of oxygen consumption in the presence of these substrates. ES-2 also did not grow on Mn2+, sulfide, or thiosulfate. The cell yield of ES-2 was not as high, 5 × 107 cells/ml, as that of ES-1, which reached a cell density of 108 cells/ml.

Both strains required vitamins for growth; when the vitamins were omitted their growth diminished markedly after two or three transfers. If bicarbonate was omitted from the medium and 10 mM HEPES buffer was substituted as a buffer at pH 6.5, it also appeared that the growth of the strains was diminished, as judged by the slower than normal formation of a growth band.

## Possible solutions

1.  First they presented the growth attributes of ES-1. Then they mimicked the structure of this paragraph to present ES-2. Finally they gave the results that applied regardless of strain number.
2. They refer to the figures in the first sentence. They then refer back to the figures for each respective strain, too (to make the figure references more clear).
3. They describe important trends (e.g. increasing accumulation of Fe in Fig. 5). They also highlight key findings by including them both in the figure and the text (e.g. growth of ES-2 with FeS alone but not acetate + FeS). They don’t identify unexpected results, probably because the authors were not sure what to expect when starting the project.
4. In a figure and in the text: Growth of ES-2 with FeS; growth of ES-2 with FeS + acetate. Not included in a figure/table: Data showing all of the mediums with which the strains did not grow; the curve for ES-2 grown with FeCO3; a figure showing that growth of both strains diminished when vitamins were omitted from the growth medium or when HEPES was used as a buffer.

Org-7: Test yourself

## Each of the following sentences are taken out of context from journal article Results sections. Identify the move associated with each statement. Also try to identify the sub-move, if you can!

1. To illustrate the effect of a changing temperature or sea level on the evolution of the AIS, we performed a simulation with a constant LGM temperature from the Fuji ice-core record and one with a constant LGM sea level from the SPECMAP sea level record (I0S and IF0 in Fig. 6b respectively). (Maris et al. 2015)
2. Under these conditions mono-alkylation is the main reaction, and only low percentages of dialkylation and elimination products are observed in GC. (Trabelsi, Szönyi, and Geribaldi 2001)
3. As shown in representative examples (Figure 3), heptane breakthrough curves exhibit relatively sharp and symmetric arrival and elution waves, indicating relatively ideal transport. (Costanza-Robinson and Brusseau 2002)
4. The hydrogen bonding in the Gua–Cyt base pairs decreases significantly by 35 as compared to only 6 in the Ade–Thy base pairs. (Kattie et al. 2015)
5. The measured distributions in the energy of each electron and the total energy of two electrons differ in shape from the expected distributions for the 2ν2β decay of  136Xe. (Belov et al. 2012)
6. Four preparations of Boza beverage (named 1, 2, 3 and 4) with different cereal contents (Table 1) were analyzed for pH, total titratable acidity (TTA) and water activity (aw). (Caputo et al. 2012)

## Solutions

1. Move 1(i and ii)
2. Move 2 (identify key findings)
3. Move 1(ii) followed by Move 2 (describe trends)
4. Move 2 (describe trends)
5. Move 2 (identify unexpected results)
6. Move 1(i)

Org-8: Test yourself

## Each of the following excerpts are taken out of context from journal article Discussion sections. Assuming each excerpt as a whole accomplishes Move 2, identify which of the four sub-moves is accomplished by each sentence. Note that not every excerpt will contain all of the sub-moves. (Sentences are numbered with italicised superscript numerasl for reference in the Solutions.)

1. Adapted from Steelman, Kennedy, and Parker (2015):

1 The riverbed along the Eramosa River is an intermittently-exposed bedrock surface, where groundwater and surface water are variably connected through networks of open and sediment-filled discrete fractures and conduits. 2 The identification of epikarst partially covered by fluvial sediment and its relationship to the formation open and exposed fracture conduit networks and suspected sinkholes, advanced our understanding of hydraulic and temperature responses in the shallow bedrock aquifer. 3 Our ability to estimate physical properties of the bulk rock formation to 15–20 m depth using GPR resulted in a better understanding of hydraulic conditions and aquifer properties across the study area, improving our understanding of spatial variability of advective pathways along this river system. 4 The approach used in this study could be used to construct larger-scale 2D layer models of shallow groundwater aquifers enhancing the development of local flow models capable of assessing groundwater–surface water dynamics.

5 While our geophysical approach was effective in detecting the position and frequency of vertical and subvertical fracture zones and exploring the general characteristics of a bedrock river system, it did not provide direct evidence of the mechanisms governing spatial variations in bedrock riverbed features (e.g., buried channels, fractures and conduits, sinkholes) or their hydrogeologic significant to the local flow system. 6 Based on the available geophysical, hydrogeological and geological information, we suspect that lateral variations in erosion-resistant layering (e.g., fine-grained, well-cemented, thinly-laminated rock) are likely controlling channel morphology, as well as the occurrence and development of discrete fracture networks and conduits which transiently control surface water–groundwater connectivity from low to high stage periods. 7Nevertheless, this initial work represents a basis for future studies aimed at characterizing groundwater–surface water exchange patterns in a bedrock river environment.

2. Adapted from Mottaleb, Woo, and Kim (2001):

1 In ELCAD-AES analysis, a stable glow discharge plasma could be obtained by applying 1-2 kV in an atmospheric air pressure and a several mm discharge gap between the Pt rod anode and electrolyte solution cathode. 2 Spectrum emitted from waters contained basic atomic lines of dissolved metals and OH bands peaks. 3 The intensity of spectral lines depends on the operating parameters such as pH of the electrolytes, discharge current and discharge gap. 4 The LOD values of Hg, Pb, Cd, Cu, Na and K were found in the range of 0.001-0.08 mg/l. 5 The LOD values of Hg, Pb, Cd and Cu were improved by more than one order of magnitude compared to closed-type ECLAD. 6 The applicability of ELCAD-AES has been assessed for fresh milk analysis. 7 The concentrations of different metals such as Cu, Pb, Fe, Mn, Ca, Zn, Mg, Na and K found in drinking water and fresh milk support the WHO and Korean Environmental Protection Agency guidelines. 8 Finally, this technique could have potential and effectively be used for analysis of other liquid samples such seawater, fruit juices, etc.

3. Adapted from Stensvold et al. (2015):

1 Future studies should monitor the prevalence, distribution, and host specificity of Babesia in ticks from different geographical regions in Denmark and neighbouring countries in order to increase awareness and to enable assessment of the potential public health risk of contracting babesiosis in this region where infections may be emerging. 2 Furthermore, it should be investigated, to which extent patients with Lyme disease are seropositive for Babesia. 3 Low diagnostic sensitivity related to traditional diagnosis of acute babesiosis can be overcome by the use of Babesia-specific PCR, suitable for direct detection of the pathogen in blood samples from patients with relevant exposure and unexplained fever.

Conclusion

4 This study is the first to detect of B. microti in Danish ticks. We confirmed the presence of B. microti in I. ricinus collected at multiple locations in Denmark. 5 Our data evinces endemic occurrence of potentially zoonotic Babesia in Denmark and confirms I. ricinus as a vector of multiple pathogens of public health concern. 6 Awareness of the potential impact of Babesia on public health in Scandinavia could be increased by monitoring the prevalence, distribution, and host specificity of Babesia in ticks.

4. Adapted from Pukhov and Meyer-ter-Vehn (2002):

1 In this work we have considered the wake field acceleration of electrons in the broken-wave regime. 2 This kinetic and highly non-linear regime is difficult to treat analytically, and therefore we have studied it numerically. 3 We find that the 3D wave breaking of the laser wake field can produce electron bunches with unique properties. 4 A sub-10-fs laser pulse with only 20-mJ energy is able to accelerate 109 electrons with a flat spectrum reaching 50-MeV energy. 5 A spectrum sharply peaked in energy is obtained for a 12-J, 30-fs laser pulse. 6 In this case the laser is intense enough to expel all background electrons from the first wake trough, forming a solitary cavity and a completely broken wake field further downstream. 7 Propagating through plasma, this cavity continuously traps a small portion of background electrons and generates an almost mono-energetic beam of 3 × 1010 electrons at 300 MeV.

8 These new results call for experimental verification. 9 At present we have to rely on our 3D PIC simulations. 10 However, we recall that PIC simulations have been very successful in reproducing existing experiments [12, 14, 34]. 11 The fast development of laser technology suggests that the laser pulses with corresponding parameters will be available in the near future.

## Solutions

1.    Sentences 1-3: Move 2(i)

Sentence 3: Move 2(iii)

Sentence 4: Move 2(iv)

Sentences 5-6: Move 2(ii) –although sentence 6 isn’t exactly identifying a limitation of the project, it is further explaining the limitation identifyed in sentence 5.

Sentences 7: Move 2(iii)

2.    Sentences 1-5: Move 2(i)

Sentences 6-8: Move 2(iii)

3.    Sentences 1-3: Move 2(iv)

Sentence 4: Move 2(i)

Sentence 5: Move 2(iii)

Sentence 6: Move 2(iv) –yes, again! Here they decided to sum up the future work in one concise, overarching statement, which helps broaden their discussion back out at the very end of their paper.

4.    Sentences 1-7: Move 2(i)

Sentence 8: Move 2(iv)

Sentence 9: Move 2(ii)

Sentence 10-11: The end to this paper is unconventional. The authors make an effort to further validify their results by explaining the accuracy of the method. This kind of discussion might be better suited to earlier in the discussion (as part of Move 1), but nonetheless somewhat implies Move 2(iv) by referring to the future of this type of project and therefore succeeds in broadening the scope of the end of the paper.

Note how none of these papers use all of the available moves or use them in the same order! The most important thing is to use the moves that make the most sense for your project and what you are trying to accomplish.

## Pro – Conciseness, visuals, clarity, objectivity, and accuracy

Pro-1 and 2 are practices in conciseness.

Pro-1: Practice exercise

## Revise the following paragraphs for conciseness by crossing out any unnecessary words and replacing any wordy phrases with shorter ones.

1. Unfortunately, inferred mass changes using the gravity field solutions obtained by the groups we previously mentioned do not agree to a level that is considered truly acceptable. (Adapted from Lemoine et al. 2007)
2. Kokubun et al. [7], Terasawa et al. [8], and Blom et al. [9] obtained through analytical methods the damping ratio of a vacuum gauge resonator by modelling the resonator as a sphere or, alternatively, a string of spheres, as shown in previous studies. (Adapted from Hosaka, Itao, and Kuroda 1995).
3. At some point in the future, the incredible field of research known as molecular dynamics simulations could be used in this way for use with plant DNA and nanoparticles to potentially provide an insight into changes observed here in plant health and output. (Adapted from Katti et al. 2015)
4. It is interesting to note that our results show that the topological states are remarkably robust and that their dispersion has the capacity to be tuned in the range that we explored here (m=03; n=1) as well as in bulk Sb. (Adapted from Johannsen et al. 2015)
5. Experiments performed using reverse transcriptase-polymerase chain reaction obviously demonstrated that the hTRT mRNA originated from the cDNA that had been transfected and not the endogenous gene. (Adapted from Bodnar et al. 1998)
6. Immediately after decapitation, the livers were first removed, then placed in cold 0.9% NaCl solution, and then sliced in a careful manner. Next, imprints on glass slides very freshly prepared from the liver slices were fixed in cold 4% paraformaldehyde for 10 min before they were rinsed three times in cold phosphate-buffered saline for 5 min each. The samples were then permeabilized with 0.2% Triton X-100 in phosphate-buffered-saline buffer, after which they were blocked with 5% fetal bovine serum in phosphate-buffered-saline. (Adapted from Ghiraldini, Crispim, and Mello 2013)

## Possible Solutions

1. Inferred mass changes using the gravity field solutions obtained by aforementioned groups do not agree to an acceptable level.
2. Analytical methods [7-9] have obtained the damping ratio of a vacuum gauge resonator by modelling it as a sphere or a string of spheres.
3. Molecular dynamics simulations of plant DNA and nanoparticles could provide an insight into changes observed in plant health and output.
4. Our results show that the topological states are remarkably robust and that their dispersion can be tuned in the explored range ( m=03; n=1) and in bulk Sb.
5. Reverse transcriptase-polymerase chain reaction experiments demonstrated that the hTRT mRNA originated from the transfected cDNA and not the endogenous gene.
6. Immediately after decapitation, the livers were removed, placed in cold 0.9% NaCl solution, and sliced. Imprints on glass slides freshly prepared from the liver slices were fixed in cold 4% paraformaldehyde for 10 min and rinsed three times in cold phosphate-buffered saline (PBS) for 5 min each. The samples were permeabilized with 0.2% Triton X-100 in PBS buffer and blocked
with 5% fetal bovine serum in PBS.

Pro-2: Practice exercise

## Using all of the techniques you have learned in this section, rewrite the following sentences to be as concise as possible (without omitting seemingly important content!).

1. A ventral curling phenotype was actually observed for five of the subunits we tested here, as can be seen in Figures 2A-2F and the table within. The subunits that showed this phenotype were med7, med12, med17, med19, and med27. (Adapted from Burrows, Pearson, and Scott 2015)
2. On the ligand side, the most highly performing architectures include tetraarylporphyrins [12] and Schiff bases [13], both of which involve N4 structures. Salens/salphens in addition to ligands that are related to salens or salphens  have N2O2 architecture and also have high performance [14]. Some ligands that also involve oxygen have also been shown to have useful architectures, specifically substituted phenols (N2O) [15] or also complex bridged bisphenols (N4O2) [16]. (Adapted from Adolph et al. 2015)
3. At our primary field site located at precisely 69˚ 27′ N and 49˚ 53′ W, which is in the ablation zone of Sermeq Avannarleq in western Greenland as shown in Figure 1, we drilled seven boreholes to the bed using a hot water drill in 2011. That same year, we instrumented three of these boreholes with pressure transducers. (Adapted from Andrews et al. 2014)
4. Four mouse groups were used in this study. One that was used was from 8-week-old normoglycemic young adult NOD mice. NOD adult mice that were hyperglycemic instead of normoglycemic were also used. Another group was also normoglycemic and young and 8 weeks old, but was a BALB/c adult variety. Finally, normoglycemic adult mice that were acutually 56 weeks old and of the BALBcAnUnib variety were used as one group for study. (Adapted from Ghiraldini, Crispim, and Mello 2013)
5. By measuring noise we were able to show that the detector’s noise equivalent power has the ability to be substantially further improved by what we calculated to be two orders of magnitude. Managing to deplete the surface states using an infrared flood exposure technique was shown to four-fold enhance the measured sensitivity of the detector. (Adapted from Neubauer et al. 2015)

## Possible solutions

1.  A ventral curling phenotype was observed for five subunits tested: med7, med12, med17, med19, and med27 (Figures 2A–2F and table within).
2. On the ligand side, the most performing architectures are based on tetraarylporphyrins (N4) [12], Schiff bases (N4) [13], salens/salphens and related ligands (N2O2) [14], substituted phenols (N2O) [15] or complex bridged bisphenols (N4O2) [16].
3. At our primary field site in the ablation zone of Sermeq Avannarleq in western Greenland (Fig. 1; 69˚ 27′ N, 49˚ 53′ W; Extended Data Table 1), we drilled seven boreholes to the bed using a hot water drill and instrumented three of these with pressure transducers in 2011.
4. Four mouse groups were used in this study: 1) normoglycemic young (8-wk-old) NOD adults, 2) normoglycemic young (8-wk-old) BALB/c adults, 3) severe hyperglycemic NOD adults, and 4) normoglycemic 56-wk-old BALB/cAnUnib mice.
5. Noise measurements show that the detector’s noise equivalent power can be further improved by two orders of magnitude. Depletion of the surface states using infrared flood exposure was shown to four-fold enhance the detector sensitivity.

Pro-3, 4 and 5 are for practicing professional use of visuals.

Pro-3: Test yourself

## In each of the following instances, decide if it would be most appropriate to present the data using a figure, a scheme, a table, or words alone.

1. The accuracy of a 5-point calibration curve you constructed to verify the lead content in a series of water samples
2. Population size and sex ratios for 4 different organisms grouped by habitat types to convey more detailed information about each organism
3. The positive correlation of population size to sex ratios for 3 different organisms in your study
4. The result that seed production was higher in a direct-sunlight condition than in a filtered-light condition
5. The effect of 2 different temperatures on the failure impact threshold (in Joules) of steel
6. The relative amounts (in percent yield) of each of 4 compounds in a reaction
7. The 4 steps in a proposed reaction mechanism
8. The surface features and average hardness and size of 18 different rock samples
9. The location of a lake where random water samples were taken to generally understand what kind of algae grows in that lake
10. The location of 6 different sediment samples in each of 4 major regions of interest in a stream for which you want to identify how contaminant levels vary at key points
11. A proposed autophagy signaling pathway involving 8 steps and 14 total proteins

## Solutions

1. Words: a calibration curve is only a verification of your method and almost never warrants more than a quick mention in your paper.
2. Table: there isn’t necessarily any pattern of relationship among these data, but there is enough of it to where words alone could become confusing.
3. Figure (graph): in this case, there is a relationship between population size and sex ratios, which will be most clearly presented in a figure.
4. Words: there is a relationship between seed production and sunlight type, but because there are only 2 total data points, it is not enough information to warrant a graph.
5. Words: again, although you may want to show the relationship here, it will be equally clear using words alone.
6. Words: now we have 4 data points (without a trend), but this is still not enough for a table; it would be more concise in words alone. For example: “The relative abundances of compounds A, B, C, and D were 44.3%, 12.9%, 16.8%, and 26.0%.”
7. Scheme: steps in a reaction are best shown in a scheme, although some disciplines and journals may prefer a diagram or equation instead.
8. Table: this is 18×3=54 total data points! That is definitely enough for a table.
9. Words: from the description, it doesn’t seem as though the exact location of the water samples is necessary; instead, you could just say, “Samples were taken from 6 locations in Lake X.”
10. Figure (map): The exact locations of these samples are important, so a map would likely be the most useful.
11. Figure (diagram): although a scheme may seem appropriate, diagrams are generally used for biological pathways in order to better depict the ways in which proteins (or other components) will physically interact, which is often the goal of such an experiment.

Pro-4: Practice exercise

## Possible solution

There are a few key things very wrong with the above figure:

• Numerous different fonts and font sizes used, including the font size of the y-axis which is far too large relative to the size of the text
• Use of color is meaningless and would be incomprehensible once photocopied into black and white
• Curves and error bars are too cluttered to understand
• Scale of Y axis is misleading
• No units are given for the X axis
• The box around the graph and key and the horizontal lines within the graph make the graph extra cluttered
• The X axis labels do not match up with the tick marks
• The figure title is not descriptive
• The legend provides no additional information to help the reader better understand the figure.
• Overall, the figure is not understandable on its own (without supporting text).

One possible alternative we devised is:

Note: In the original graph, all of the formatting (except for the axis labels, legend, and box around the key) was generated automatically by Excel. So be careful! When Excel creates a chart for you, you will always need to do a fair bit of formatting yourself before it is of publishable quality.

Pro-5: Practice exercise

## Possible solution

Here is one way to re-format the example above:

Although there are many ways to format this table correctly, the critical changes we made were to:

• get rid of the boxes around the data in favor of minimal horizontal lines.
• remove the redundant column “Depth” and put this information somewhere that makes it clear that it applies to the whole table
• change the table identifier from “Table A” to “Table 1.”
• change the meaningless sample sample names to something more straightforward, such as “1,” “2,” etc.
• move the units of the source coefficient to the column heading.
• remove the excess formatting from the column headings.

In addition, we also chose to:

• align the “source coefficient” data by decimal point, to make it easier to see the differences between data.
• place the “depth” data in the caption, although it also could go in a footnotes section.

Pro-6 through …

Pro-6: Test yourself

## Which of the following sentences use personal nouns and pronouns appropriately in the context of professional scientific writing? For any that don’t, rewrite them to be more objective.

1. We prepared palladium complexes 2af from the corresponding chiral ligands (1af) and 1,3-diphenylallylpalladium chloride dimer by reaction with silver tetrafluoroborate in acetone (Scheme 1). (Adapted from Armstrong et al. 2005)
2. Howat et al. (2007) recently reported a rapid and large increase of flow velocity and ice loss for several outlet glaciers and described as dynamic thinning, particularly along the NW and E coasts. (Adapted from Frezzotti and Orombelli 2013).
3. Thus, in the present work we isolated and identified the mycobiota of four different preparations of Boza, spontaneously fermented, and characterized the dominant yeasts for their biotechnological properties. (Adapted from Caputo et al. 2012)
4. In light of the underground hydrological system that facilitates drainage of snowmelt, we therefore expect the acidic mineral surface cryosols at our upland site to stay dry during summer. (Adapted from Lau et al. 2015)
5. When looking more closely at the conserved matches for the miRNAs that do not have a U at position 9, we found an overabundance of a conserved A forming a mismatch to this nucleotide. (Adapted from Lewis, Burge, and Bartel 2005)
6. The terminology for the structure of molecular clouds is not fixed; here we follow the discussion in Williams, Blitz & McKee (2000). (Adapted from McKee and Ostriker 2007)
7. To test the wavelength scaling, we measured the nonlinear response for different pump wavelengths. (Adapted from O’Brien et al. 2015)

## Solutions

1. Palladium complexes 2a–f were prepared from the corresponding chiral ligands…
2. A rapid and large increase of flow velocity and ice loss has been recently reported for
several outlet glaciers and described as dynamic thinning, particularly along the NW and E coasts (Howat et al. 2007).
3. Correct, assuming this passage “fills the gap” in the Introduction
4. Correct, because an “expectation” involves the scientists explicitly
5. Upon more careful inspection of the conserved matches for the miRNAs that do not have a U at position 9, an overabundance of conserved A forming a mismatch to this nucleotide was found.
6. Correct, in most cases, because “we” signals a deliberate choice in terminology, while the authors referenced are useful since people familiar with the field might recognize the names and therefore instantly become familiar with the terminology in question.
7. To test the wavelength scaling, the nonlinear response was measured for different pump wavelengths.

Pro-7: Practice exercise

## Choose any primary research article and read its discussion section. Underline all hedging words and phrases and note the contexts in which they are used.

Pro-8: Test yourself

## Which of the following statements are inaccurately ascribing animate qualities to inanimate objects? Re-write any such statements to avoid this error.

1. The acid wash cleaned the glassware.
2. A probe sonicator lysed the cells.
3. Data were analyzed by Harmonic Analysis Software.
4. Soil temperatures were measured by LiCOR thermistor.
5. Syringe pumps were operated at a flow of 1 mL/min during particle injection.
6. This condition requires that samples undergo purification prior to analysis.
7. The oven heated samples to 55 ˚C.

## Solutions

1. Inaccurate. The glassware was cleaned using an acid wash.
2. Inaccurate. A probe sonicator was used to lyse the cells.
3. Inaccurate. Data were analyzed using Harmonic Analysis Software.
4. Accurate: an instrument can measure something.
5. Accurate
6. Accurate: something can be “required” or made necessary by the mere conditions of a situation.
7. Inaccurate. Samples were heated to 55 ˚C using an oven.

Pro-9: Practice exercise

## Make each of the following sentences more fluid by replacing any colloquial words or phrases with more formal ones.

1. Both strains had to have vitamins for growth.
2. The high sensitivity is achieved by getting a big gain for the “on” state. (Adapted from Neubauer et al. 2015)
3. Ground deformation monitors like GPS turn out accurate readings of fault movement that can be used to reconstruct the detailed structure of the earthquake source. (Adapted from Wei et al. 2014)
4. The most astonishing things found out were carbon nanotubes holding in C60 molecules or elongated fullerenes (Fig. 27). (Adapted from Monthioux et al. 2001)
5. These borehole and moulin hydraulic heads are put together with coincident measurements of
surface ice velocity, bed separation, and air temperature to get to know relationships between ice dynamics and the subglacial hydrologic system. (Adapted from Andrews et al. 2014)
6. The present experiment talks about two new bacteria isolated from a groundwater-fed iron seep that look like they grow lithotropically on ferrous iron. (Adapted from Emerson and Moyer 1997)
7. The idea of circuit quantum electrodynamics can also be put to use for quantum information processing and quantum communication and may bring on new ways of single photon generation and detection. (Adapted from Vučković et al. 2003)
8. The typical ways to do restriction endonuclease digestion and agarose electrophoresis were done like they are described in Sambrook et al., 1989. (Adapted from Yun et al. 2000)

## Possible Solutions

1. Both strains had to have required vitamins for growth.
2. The high sensitivity is achieved by getting obtaining a big large gain for the “on” state.
3. Ground deformation monitors like such as GPS turn out provide accurate readings measurements of fault movement that can be used to reconstruct the detailed structure of the earthquake source.
4. The most astonishing things objects found out discovered were carbon nanotubes holding in containing C60 molecules or elongated fullerenes (Fig. 27).
5. These borehole and moulin hydraulic heads are put together coupled with coincident measurements of surface ice velocity, bed separation, and air temperature to get to know characterize relationships between ice dynamics and the subglacial hydrologic system.
6. The present experiment study talks about describes two new bacteria isolated from a groundwater-fed iron seep that look like they appear to grow lithotropically on ferrous iron.
7. The idea concept of circuit quantum electrodynamics can also be put to use utilized for quantum information processing and quantum communication and may bring on lead to new ways of approaches for single photon generation and detection.
8. The typical Standard ways to do procedures for restriction endonuclease digestion and agarose electrophoresis were done carried out like they are described in (Sambrook et al., 1989).

Pro-10: Practice exercise

## Re-write each of the following sentences using parallelism and, if appropriate, the word “respectively.”

1. The dry limit is represented by BC and the wet limit by AB in Figure 1. (Adapted from Zhang, Dawes, and Walker 2001)
2. The probe hybridized to a single XhoI fragment that was approximately 2.5 kb in size, as well as a KpnI fragment (~3.7 kb length) and a 5.8-kb EcoRI fragment. (Adapted from Yun et al. 2000)
3. Other solid-state analogues of strong coupling cavity QED have been envisaged for superconductor systems13–20, in systems involving semiconductors21,22, and even micro-mechanical systems23. (Adapted from Wallraff et a. 2004)
4. The two main synthesis approaches used are: 1) the in-situ technique, in which the NPs are generated in the presence of polymer and (2) Ex-situ technique: dispersion of separately prepared NPs to the polymer matrix. (Adapted from Tripathi, Kaur, and Jyoti 2015)
5. CuO is an important industrial material and has been widely used, such as in gas sensors, electrode materials, magnetic ceramics, hydrogen storage materials, solar cells, photo-catalysis, and ZnO selectivity enhancement in hydration and dehydration reactions. (Adapted from Subhan et al. 2015)
6. Excitation at 370 nm provided PL peaks at 406, 430, and 455 nm, whereas 390-nm excitation resulted in peaks appearing at 428, 456 nm. (Adapted from Subhan et al. 2015)
7.  A. Topography Evolution
b. The influence of bed slope
c. Influence of mass flux.
8. The distribution function for the case that the splitting probability is given by K(Φ) = k0Φ with unipolarity is shown in panel a. Panel B shows the distribution function if the flux ratio is 2:1, wheras panel (c) shows the situation that the fluxes are equal. (Adapted from Schrijver et al. 1997)
9. All runs produced the same morphological units, which were (1) rhomboid patterns on the sediment bed extending over the entire width of the unconfined gravity current, (2) a straight-channel run of constant width and depth from the injection point to the slope break; (3) retrogressive erosion patterns at the slope break; and a sediment lobe on the elevated floor associated with the channel progression. (Adapted from Weill et al. 2014)

## Possible solutions

1. The dry and wet limits are represented in Figure 1 by BC and AB, respectively.
2. The probe hybridized to single XhoI, KpnI, and EcoRI fragments (~2.5, 3.7, and 5.8 kb in size, respectively).
3. Other solid-state analogues of strong coupling cavity QED have been envisaged in superconducting13–20, semiconducting21,22, and even micro-mechanical systems23.
4. The two main synthesis approaches used are: (1) in-situ technique: generation of NPs in the presence of polymer and (2) ex-situ technique: dispersion of separately prepared NPs to the polymer matrix.
5. CuO, which can enhance the selectivity of ZnO in hydration and dehydration reactions, is an important industrial material and has been widely used, such as in gas sensors, electrode materials, magnetic ceramics, hydrogen storage materials, solar cells, and photo-catalysis.
6. Excitation at 370 and 390 nm provided PL peaks at 406, 430, 455 nm and 428, 456 nm, respectively.
7.  A. Evolution of topography
B. Influence of bed slope
C. Influence of mass flux
8. Panels a, b, and c show distribution functions for the case that the splitting probability is given by K(Φ) = k0Φ for three situations: the unipolar case, a flux ratio of 2:1 and equal fluxes, respectively.
9. All runs produced the same morphological units: rhomboid patterns on the sediment bed extending over the entire width of the unconfined gravity current; a straight channel of constant width and depth running from the injection point to the slope break; retrogressive erosion patterns appearing at the slope break; and a sediment lobe on the elevated floor associated with the channel progression.

Pro 11 – Practice exercise

## Re-write any awkward sentences below so that they are more fluid by changing some of the parts of speech used. Keep in mind that transforming the part of speech of a term will also require that you change the sentence structure in other ways.

1. A variety of PCR methods were used to enable us to detect DNA from different pathogens (Table 1). (Adapted from Stensvold et al. 2015)
2. This is probably the case for the Puna plateau, in accord with a suggestion of strong lithospheric delamination for this region15. (Adapted from Yuan et al. 2000)
3. The ability of the azobenzene strap to photoisomerize undergoes a transformation, when the Fc pivot moves angularly, into the blade zinc porphyrins being able to move such that they are open or closed. (Adapted from Vecchi et al. 2015)
4. After the inner vesicle fuses, it degrades in a way that is dependent on a series of lysosomal/vacuolar acid hydrolases. (Adapted from from He and Klionsky 2009)
5. Adding an excess of potassium carbonate and an excess of the starting active methylene compound to the reaction mixture allows complete conversion of the halide. (Adapted from Trabelsi, Szönyi, and Geribaldi 2001)
6. In order to investigate other possible causes of observed radial velocity variations such as the pulsing of the star and its rotational modulation rather than it moving orbitally, spectral line shape analysis was performed with the use of high-resolution stellar template spectra. (Adapted from Sato et al. 2013)

## Possible solutions

1. A variety of PCR methods were used to enable detection of DNA from different pathogens (Table 1).
2. This is probably the case for the Puna plateau, in accord with strong lithospheric delamination suggested for this region15.
3. The photoisomerization of the azobenzene strap is transformed, through angular motion of the Fc pivot, into an open-close motion of the blade zinc porphyrins.
4. After fusion, degradation of the inner vesicle is dependent on a series of lysosomal/vacuolar acid hydrolases.
5. This sentence is fine as is; “Addition of excess …” would also be acceptable.
6. In order to investigate other possible causes of observed radial velocity variations such as star pulsation and rotational modulation rather than orbital motion, spectral line shape
was analyzed with the use of high-resolution stellar template spectra.

## Mec – Language, grammar, and punctuation

Exercises from “Common errors to watch out for.

Mec-1: Test yourself

## Correct the mistakes, if there are any, in the way that the numbers and units are written in the following statements.

1. The ball traveled .35 m per s across the table.
2. The rock formation originated 3.2 Ga. ago.
3. 6, 8, and 10 measurements were taken, respectively.
4. Two hundred micrograms per milliliter of zeocin was used to culture the cells.
5. The experiment was repeated 7 times.
6. Basalt samples had errors of 0.08 Ma–0.13 Ma.
7. 2’5′-ADP Sepharose was used in the column purification.
8. Sixteen K was found to be the minimum allowable temperature.
9. Tests were conducted from 200 to 300 meV.

## Solutions

1. The ball traveled 0.35 m/s across the table.
2. The rock formation originated 3.2 Ga ago. (Ga is a unit of time, so 3.2 is not written out.)
3. Six, 8, and 10 measurements were taken, respectively.
4. Although this is technically correct, writing the whole number and unit out should be avoided by writing something like the following: “The cells were cultured in zeocin (200 μg/mL).”
5. The experiment was repeated seven times.
6. Basalt samples had errors of 0.08–0.13 Ma.
7. This statement is written correctly, but starting the sentence with a number should still be avoided.
8. Sixteen Kelvin was found to be the minimum allowable temperature. This statement would be even better and more concise if it was rearranged to say: “The minimum allowable temperature was found to be 16 K.”
9. Correct.

Mec-2: Test yourself

## Correct the mistakes, if there are any, in the way that the following statements are punctuated, spaced, and/or capitalized.

1. The reaction was conducted at 98˚ C.
2. There was a significant decrease in the amount of denaturation when the temperature was decreased from 65 to 55 ˚C (p <0.01).
3. QND’s were performed in the non-resonant condition.
4. The Second Law of Thermodynamics states that the entropy of an isolated system increases over time.
5. From the lorentzian line the photon decay rate of the resonator was determined as κ/2π=0.8 MHz.
6. The observed decrease of the cathode fall with decreasing pH was explained by a model that uses two different electron emission processes near the electrolyte cathode: an emission coupled with hydrated electrons is prominent below pH 2.5 while a proton independent emission of poor efficiency operates above 3 (adapted from Mottaleb, Woo, and Kim 2001).
7. trans-2,3-dibromo-2-butene (0.2 g) was slowly added to the mixture.
8. The charging energy was determined as EC = 5.2 (±0.1) GHz.
9. Heat–producing elements are elements that generate heat as a results of their rapid radioactive decay (adapted from Rudnick and Fountain 1995).

## Solutions

1. The reaction was conducted at 98 ˚C.
2. There was a significant decrease in the amount of denaturation when the temperature was decreased from 65 to 55 ˚C (p < 0.01).
3. QNDs were performed in the non-resonant condition.
4. The second law of thermodynamics states that the entropy of an isolated system increases over time.
5. From the lorentzian line the photon decay rate of the resonator was determined as κ/2π = 0.8 MHz.
6. The observed decrease of the cathode fall with decreasing pH was explained by a model that uses two different electron emission processes near the electrolyte cathode; an emission coupled with hydrated electrons is prominent below pH 2.5 while a proton independent emission of poor efficiency operates above 3.
7. trans-2,3-Dibromo-2-butene
8. Correct.
9. Heat-producing elements are elements that generate heat as a results of their rapid radioactive decay.

Mec-3: Test yourself

## Is the grammar in each of the following sentences correct? If not, what word should be changed, and in what way?

1. The analysis were performed in succession using specialized software.
2. The lithospheric mantle is the part of the Earth’s mantle which lies immediately under the crust.
3. The blank spectra was produced side-by-side with the sample spectra, which showed different elements spiked in the tap water.
4. This data shows a significant decrease in retention with the addition of Compound E.
5. The LOD values of Hg, Pb, and Cu were improved by more then one order of magnitude.
6. The phases were marked at less than 1 s.
7. Ellen et al. (2008) has shown support for this conclusion through work with the human liver.
8. Coexistence of species at intermediate frequencies of disturbance is thought to require
trade-offs among competitive ability and disturbance tolerance (adapted from Yuan et al. 2000).
9.  A relationship between diversity, genotype, and disturbance frequency was generated in heterogeneous, but not in homogeneous, environments (adapted from Yuan et al. 2000).
10. In the case of standard electrocatalytic electrodes only formation of hydrogen peroxide was observed, while electrodes additionally modified with graphene can convert oxygen into water via four-electron process.
11. Surprisingly, while closely spaced, these compounds exhibit the simultaneous oxidation of Fc groups, , indicating a negligible interaction between the organometallic fragments (adapted from Vecchi et al. 2015).
12. Less final orbits were observed after field gravity stabilization.
13. The solutions are much less effected by artifacts, such as North–South streaking patterns, than earlier global solutions due to the constraint (adapted from Lemoine et al. 2007).
14. Electrochemical data for ferrocenyl-containing phthalocyanines and their analogs is summarized in Table 2 (adapted from Vecchi et al. 2015).

## Solutions

1. The analyses were performed…
2. …the Earth’s mantle that lies…
3. The blank spectrum was produced…
4. …more than one order…
5. These data show
6. Correct
7. Ellen et al. (2008) have shown…
8. …trade-offs between competitive ability and disturbance tolerance.
9. Correct
10. Correct, although any ambiguity could be solved by using “although” instead.
11. although closely spaced… – Using “while” here creates ambiguity and makes the statement sound like the oxidation might only happen when the compounds are closely spaced.
12. Fewer final orbits…
13. …are much less affected by artifacts…
14. Electrochemical data…are summarized in Table 2.