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32.4: Further Reading - Biology

32.4: Further Reading - Biology


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32.4: Further Reading

Francesco Redi

Francesco Redi (18 February 1626 – 1 March 1697) was an Italian physician, naturalist, biologist and poet. [1] He is referred to as the "founder of experimental biology", [2] [3] and as the "father of modern parasitology". [4] [5] He was the first person to challenge the theory of spontaneous generation by demonstrating that maggots come from eggs of flies. [6] [7]

Having a doctoral degree in both medicine and philosophy from the University of Pisa at the age of 21, he worked in various cities of Italy. A rationalist of his time, he was a critic of verifiable myths, such as spontaneous generation. [8] His most famous experiments are described in his magnum opus Esperienze intorno alla generazione degl'insetti (Experiments on the Generation of Insects), published in 1668. He disproved that vipers drink wine and could break glasses, and that their venom was poisonous when ingested. He correctly observed that snake venoms were produced from the fangs, not the gallbladder, as was believed. He was also the first to recognize and correctly describe details of about 180 parasites, including Fasciola hepatica and Ascaris lumbricoides. He also distinguished earthworms from helminths (like tapeworms, flukes, and roundworms). He possibly originated the use of the control, the basis of experimental design in modern biology. A collection of his poems first published in 1685 Bacco in Toscana ("Bacchus in Tuscany") is considered among the finest works of 17th-century Italian poetry, and for which the Grand Duke Cosimo III gave him a medal of honor.


Image Credits

Tuna swimming courtsey of Wild Muse's Blog.

Four Questions image courtsey of Suzy Renn's Bio 342 website.

Adaptive Value

Diving depth of bluefin tuna. Diagram courtsey of Tag-A-Giant Foundation.

Caught bluefin tuna image courtsey of Four Packs for Oggies.

Mechanism

Migration tracking of bluefin tuna in the Atlantic. Diagram courtsey of Tag-A-Giant Foundation.

Bluefin tuna swimming image courtsey of Start An Animal Sanctuary.

Ontogeny

Juvenile Bluefin tuna's red muscle temperature being tested. Courtsey of Kubo et al. 2008.


32.3 Carrying out a chi-square contingency table test in R

Walk through example

You should work through the example in this section.

Let’s carry on with the ladybird colour and habitat type example. You need to download three data sets to work through this section: LADYBIRDS1.CSV, LADYBIRDS2.CSV, and LADYBIRDS3.CSV. These all contain the same information—it is just organised differently in each case.

Carrying out a (chi^<2>) contingency table test in R is very simple: we use the chisq.test function again. The only slight snag is that we have to ensure the data is formatted correctly before it can be used. Whenever we read data into R using read.csv or read_csv we end up with a data frame. Unfortunately, the chisq.test function is one of the few statistical functions not designed to work with data frames. This means we first have to use a function called xtabs to construct something called a contingency table object. 33 . The xtabs function does categorical ‘cross tabulation’ 34 , i.e., it sums up the number of occurrences of different combinations of categories among variables.

We’ll look at how to use xtabs before running through the actual test…

32.3.1 Step 1. Getting the data into the correct format

It is not difficult to use, but the precise usage of xtabs depends upon how the raw data are organised. We’ll examine the three main cases in turn.

Data suitable for analysis with a (chi^<2>) contingency table test are often represented in a data set with one column per categorical variable, and one row per observation. The LADYBIRDS1.CSV file contains the data in this format. Read it into an R data frame:

We called the data lady_bird_df to emphasise that they are stored in a data frame at this point. We can use glimpse , head and tail to get a sense of how the data are organised:

We only showed you the first and last 10 values—you should take a full look at the data with the View function. You will see that the data frame contains 300 rows—one for each ladybird—and two variables ( Habitat and Colour ). The two variables obviously contain the information about the categorisation of each ladybird in the sample.

We require a two-way table that contains the total counts in each combination of categories. This is what xtabs does. It takes two arguments: the first is a formula (involving the

symbol) that specifies the required contingency table the second is the name of the data frame containing the raw data. When working with data in the above format—one observation per row—we use a formula that only contains the names of the categorical variables on the right hand side of the

When used like this, xtabs will sum up the number of observations with different combinations of Habitat and Colour . We called the output lady_bird_table to emphasise that the data from xtabs are now stored in a contingency table. When we print this to the console we see that lady_bird_table does indeed refer to something that looks like a 2 x 2 contingency table of counts.

Sometimes data suitable for analysis with a (chi^<2>) contingency table test are partially summarised into counts. For example, imagine that we had visited five rural sites and five urban sites and recorded the numbers of red and black colour forms found at each site. Data in this format are stored in the LADYBIRDS2.CSV file. Read this into an R data frame and examine this with the View function:

This time we printed at the whole dataset (it’s easier to use View , but that won’t render in this book). The counts at each site are in the Number variable, and the site identities are in the Site variable. We need to sum over the sites to get the total number within each combination of Habitat and Colour . We use xtabs again, but this time we have to tell it which variable to sum over:

When working with data in this format—more than one observation per row—we use a formula where the name of the variable containing the counts is on left hand side of the

, and the names of the categorical variables to sum over are on the right hand side of the

Habitat + Colour ). When used like this xtabs will sum up the counts associated with different combinations of Habitat and Colour . The lady_bird_table object produced by xtabs is no different than before. Good! These are the same data.

Data suitable for analysis with a (chi^<2>) contingency table test are sometimes already summarised into total counts. Data in this format are stored in the LADYBIRDS3.CSV file. Read this into an R data frame and print it to the console (it’s very small, so there’s no need to use View ):

The total counts are already in the Number variable so there is no real need to sum over anything to get the total for each combination of Habitat and Colour . However, we still need to convert the data from a data frame to a contingency table. There are various ways to do this, but it is easiest to use xtabs . The R code is identical to the previous case:

In this case xtabs doesn’t change the data at all because it’s just ‘summing’ over one value in each combination of categories. We’re just using xtabs to convert it from a data frame to a contingency table. The resulting lady_bird_table object is the same as before.

32.3.2 Step 2. Doing the test

Once we have the data in the form of a contingency table the associated (chi^<2>) test of independence between the two categorical variables is easy to carry out with chisq.test :

That’s all we have to do. Just pass one argument to chisq.test : the contingency table.

This output should make sense in the light of what we saw in the previous chapter. R first prints a reminder of the test employed ( Pearson's Chi-squared test with Yates' continuity correction ) and the data used ( data: lady_bird_table ). We’ll come back to the “Yates’ continuity correction” bit in a moment. R then summarises the (chi^<2>) value, the degrees of freedom, and the p-value: X-squared = 19.103, df = 1, p-value = 1.239e-05 The p-value is highly significant (p<0.001) indicating that the colour type frequency varies among the two kinds of habitats. 35

Degrees of freedom for a (chi^<2>) contingency table test

We need to know the degrees of freedom associated with the test: in a two-way (chi^<2>) contingency table test these are ((n_A-1) imes (n_B-1)) , where (n_A-1) is the number of categories in the first variable, and (n_B-1) is the number of categories in the second variable. So if we’re working with a 2 x 2 table the d.f. are 1, if we’re working with a 2 x 3 table the d.f. are 2, if we’re working with a 3 x 3 table the d.f. are 4, and so on.

What was that “Yates’ continuity correction” all about? The reasoning behind using this correction is a bit beyond this course, but in a nutshell, it generates more reliable p-values under certain circumstances. By default, the chisq.test function applies this correction to all 2 x 2 contingency tables. We can force R to use the standard calculation by setting correct = FALSE if we want to:

Both methods give similar results in this example, though they aren’t exactly the same—the (chi^<2>) value calculated when correct = FALSE is very slightly higher than the value found when using the correction.

Don’t use the correct = FALSE option! The default correction is a safer option for 2 x 2 tables.

32.3.3 Summarising the result

We have obtained the result so now we need to write the conclusion. As always, we go back to the original question to write the conclusion. In this case the appropriate conclusion is:

There is a significant association between the colour of Adalia bipunctata individuals and habitat, such that black individuals are more likley to be found in industrial areas ( (chi^<2>) = 19.1, d.f. = 1, p < 0.001).

Notice that we summarised the nature of the association alongside the statistical result. This is easy to do in the text when describing the results of a 2 x 2 contingency table test. It’s much harder to summarise the association in written form when working with larger tables. Instead, we often present a table or a bar chart showing the observed counts.


Primary lung cancers detected by LDCT are at lower risk of brain metastases

(Denver)-Patients with primary lung cancer detected using low-dose computed tomography screening are at reduced risk of developing brain metastases after diagnosis, according to a study published in the Journal of Thoracic Oncology.

JTO is an official journal of the International Association for the Study of Lung Cancer. The full study is available here: Impact of Low-Dose Computed Tomography Screening for Primary Lung Cancer on Subsequent Risk of Brain Metastasis - Journal of Thoracic Oncology (jto.org)

The researchers, led by Summer Han, PhD, from Stanford University School of Medicine in Palo Alto, Calif., used the National Lung Screening Trial data to identify 1502 participants who were diagnosed with lung cancer between 2002 to 2009 and have follow-up data for brain metastases.

Of 1502 participants, 41.4% had lung cancer detected through LDCT screening versus 58.6% detected through other methods, for example, chest radiograph or incidental detection. Patients whose lung cancer was detected with LDCT screening had a significantly lower three-year incidence of brain metastases (6.5%) versus those without (11.9%), with a cause-specific hazard ratio (HR) of 0.53 (p = 0.001), adjusting for age at lung cancer diagnosis, stage, histology, and smoking status. This significant reduction in brain metastases risk among patients with lung cancer detected through LDCT screening persisted in subgroups of participants with early-stage primary lung cancer (HR = 0.47, p = 0.002) and those who underwent surgery (HR = 0.37, p = 0.001).

To investigate potential explanations for an association between brain metastases risk and lung cancer detected by LDCT screening, the researchers explored LDCT imaging data using a subset of patients (n = 552) who were randomized to the LDCT arm and have LDCT imaging data available. The researchers then compared the characteristics of the nodules that were LDCT screen-detected versus those that were missed by LDCT screening among the patients who were interval detected in the LDCT screening arm.

Given the observed high rate of brain metastases among patients with lung cancer in stage I in NLST (32.4%), the research group further evaluated and compared the characteristics of the nodules of the patients who developed brain metastases (n = 12) versus those who did not develop brain metastases (n = 350) within the patients whose lung cancer was LDCT screen detected in stage I (n = 362).

"This reduction in risk for brain metastases among LDCT screen-detected lung cancer--which persisted in subgroup analyses of patients with early-stage lung cancer and those who underwent surgery for lung cancer--may not be fully explained by stage shift nor curative treatment for PLC," said Han. "The reduction in brain metastases risk may be because of a potentially different tumor biology of the tumors detected by LDCT screening that are less aggressive and slow growing, which needs to be confirmed by further investigation."

"To the best of our knowledge, our study presents the first effort investigating the potential impact of LDCT lung screening on subsequent risk of metastasis," said Han. She pointed out that using the NLST data with a long follow up period provided sufficient time to observe the development of brain metastases.

About the IASLC: The International Association for the Study of Lung Cancer (IASLC) is the only global organization dedicated solely to the study of lung cancer and other thoracic malignancies. Founded in 1974, the association's membership includes nearly 7,500 lung cancer specialists across all disciplines in over 100 countries, forming a global network working together to conquer lung and thoracic cancers worldwide. The association also publishes the Journal of Thoracic Oncology, the primary educational and informational publication for topics relevant to the prevention, detection, diagnosis, and treatment of all thoracic malignancies. Visit http://www. iaslc. org for more information.

About the JTO: The Journal of Thoracic Oncology (JTO), the official journal of the International Association for the Study of Lung Cancer, is the primary educational and informational publication for topics relevant to the prevention, detection, diagnosis, and treatment of all thoracic malignancies. JTO emphasizes a multidisciplinary approach and includes original research reviews and opinion pieces. The audience includes epidemiologists, medical oncologists, radiation oncologists, thoracic surgeons, pulmonologists, radiologists, pathologists, nuclear medicine physicians, and research scientists with a special interest in thoracic oncology.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.


Discussion

The main objective of this study was to fully characterize the nature of the relation between objective cortical measures of SiN processing and reading abilities in elementary school children. Results demonstrate that some cortical measures of SiN processing relate to reading performance and reading strategy. First, phrasal nCTS in babble (i.e., informational) noise relates to the ability to read irregular but not pseudowords, which in the dual-route cascaded model indicates maturation of the lexical route. Second, the ability to leverage visual speech to boost phrasal nCTS in babble noise relates to reading speed (but not accuracy). Third, the ability to leverage visual speech to boost syllabic nCTS in noise relates to global reading abilities. Fourth, classical behavioral predictors of reading abilities (RAN, phonological memory, and phonological awareness) relate to global reading performance and not strategy. Importantly, behavioral scores and the two features of phrasal CTS in babble noise explained a different part of the variance in reading abilities. Finally, the features of nCTS underlying the first and third relations uncovered in typical readers (phrasal nCTS in babble noise and visual modulation in syllabic nCTS) were significantly altered in dyslexia in comparison with aged-matched but not reading-level–matched typically developing children. However, within the population with dyslexia, nCTS measures of the ability to deal with babble noise were negatively related to reading speed and positively related to the compromise between reading precision and reading speed.

Significant associations were found between reading abilities and some features of phrasal and syllabic nCTS. There is evidence that CTS at phrasal rate (here taken as 0.2–1.5 Hz) partly reflects parsing or chunking of words, phrases, and sentences [71]. Indeed, the brain tracks phrase and sentence boundaries even when speech is devoid of prosody but only if it is comprehensible [41], and the phase of brain oscillations below 4 Hz modulates perception of ambiguous sentences [39]. CTS at phrasal/sentential rate would help align neural excitability with syntactic information to optimize language comprehension [38]. In contrast, CTS at syllable rate (here taken as 2–8 Hz) would reflect low-level auditory processing [71]. In light of the above, our results highlight that associations between SiN perception and reading abilities build on their shared reliance on both language processing and low-level auditory processing.

Robustness of cortical speech representation to babble noise indexes the degree of development of the lexical route

Our results indicate that an objective cortical measure of the ability to deal with babble noise relates to the maturation of the lexical route. Technically, the informational modulation in phrasal nCTS correlated significantly positively with the reading score on irregular but not pseudowords. Reading score on irregular words indeed provided unique information about the informational modulation in nCTS. Also, the two reading scores in synergy provided some additional information about the informational modulation in nCTS. Furthermore, the result that the informational modulation in nCTS correlated more with the reading strategy index than the score on the irregular words suggests that the key elements at the basis of this relation are the processes needed to read irregular words that are not needed to read pseudowords.

The relation between the degree of development of the lexical route and the level of phrasal nCTS in babble noise could be explained by a positive influence of good SiN abilities on reading acquisition. Let us take as an example the situation of being faced for the first time with a written word that is read by a teacher while some classmates are making noise. SiN abilities will naturally determine the odds of hearing that word properly and hence the odds of building up the orthographic lexicon. When again reading the word alone, only children with good SiN abilities will have the opportunity to train their lexical route for that specific word. Of course, the same chain of action could be posited for the training of grapheme–phoneme correspondence. But there are many more words than phonemes and syllables, so good SiN abilities might be more important to successfully learning the correspondence between irregular words’ orthographic and phonological representations. Indeed, grapheme–phoneme correspondence is intensively trained when learning to read. Children are repeatedly exposed to examples of successful grapheme–phoneme correspondence, some with noise and some without noise. Accordingly, no matter what children’s SiN abilities are, they will learn the grapheme–phoneme correspondence and develop their sublexical route provided that they have adequate phonological awareness. Supporting this, phonological awareness does not predict SiN abilities in typical readers [21].

Alternatively, the relation between the ability to read irregular words (which tags the degree of development of the lexical route) and nCTS in babble noise could be mediated by the degree of maturation of the mental lexicon [72,73]. The mental lexicon integrates and binds the orthographic, semantic, and phonological representations of words. Its proper development is important for reading acquisition. Indeed, reading acquisition entails creating a new orthographic lexicon and binding it to the preexisting semantic and phonological lexicons [74]. Development of such binding (1) is indispensable for reading irregular words [75], (2) benefits reading of regular words, and (3) does not contribute to reading pseudowords. The proper degree of development of the mental lexicon is also important for SiN comprehension. Indeed, SiN comprehension strongly depends on lexical knowledge [21,76–78]. And the level of CTS in noise relates to the listeners’ level of comprehension [37,42,43]. This therefore suggests that the robustness of CTS to babble noise depends on the level of comprehension, which in turn depends on how developed the mental lexicon is. The degree of development of the mental lexicon could therefore be the hidden factor mediating the relation between SiN and lexical reading ability. This is also perfectly in line with our result that altered phrasal nCTS in babble noise in dyslexia may result from reduced reading experience. In brief, reading difficulties in dyslexia would reduce their reading experience, which would impair building up the mental lexicon and in turn impede SiN perception. Still, future studies on the association between SiN processing and reading should include measures of the degree of development of the mental lexicon to carefully analyze the interrelation between SiN perception, reading abilities, and the degree of development of the mental lexicon.

Our results in dyslexia support the existence of a relation between reading abilities and cortical measures of the ability to deal with SiN, but they bring important nuances. First, phrasal nCTS in nonvisual babble noise conditions was altered in children with dyslexia compared with age-matched but not reading-level–matched controls, indicating that such alteration could be due to variability in reading experience. Second, within the children with dyslexia, phrasal nCTS was globally and negatively correlated with reading speed, and the informational modulation in phrasal nCTS was positively correlated with the contrast between reading accuracy and reading speed. These two relations could be explained by compensatory attentional mechanisms so that children with severe dyslexia developed enhanced attentional abilities at the basis of improved SiN abilities and more accurate—despite still slower—reading (compared with children with a mild dyslexia). Hence, such relations might hold only in children with dyslexia free of attentional disorder, as was the case with our participants. Also, it should be remembered that these relations were found in a relatively small sample of children with dyslexia (n = 26) and should be confirmed by future studies.

Audiovisual integration and reading abilities

We found significant relations between reading abilities and the ability to leverage visual speech to maintain phrasal and syllabic CTS in noise. Visual speech cues (articulatory mouth and facial gestures) are well known to benefit SiN comprehension [61] and CTS in noise [79–83]. Obviously, the auditory signal carries much more fine-grained information about the phonemic content of speech than the visual signal. But the effect of audiovisual speech integration is quite evident in SiN conditions, in which it affords a substantial comprehension benefit [61,62,84,85]. Mirroring this perceptual benefit, it is already well documented that phrasal and syllabic CTS in noise is boosted in adults when visual speech information is available [79–83,86–89].

We found that the visual modulation in phrasal nCTS correlated globally and positively with reading speed (significantly so for the pseudowords) but not accuracy. However, our children with dyslexia (compared with both control groups) did not have any alteration in their phrasal nCTS in babble noise when visual speech was provided. Instead, they successfully relied on visual speech information to restore their phrasal CTS in babble noise (which was altered without visual speech information). In other words, reliance on lipreading to maintain appropriate phrasal CTS in babble noise appeared as a protection factor in our group of children with dyslexia.

We also found that the visual modulation in syllabic nCTS correlated globally and positively with reading abilities. More interestingly, our children with dyslexia (compared with both control groups) did not have any significant alteration in their syllabic nCTS in noise when visual speech was not provided. However, compared with age-matched typically developing children, they benefited significantly less from visual speech to boost syllabic CTS in noise. Instead, they behaved more like reading-level–matched typically developing children. Accordingly, our results cannot argue against the view that poor audiovisual integration in dyslexia is caused by reduced reading experience [63,90,91]. Notwithstanding, the pattern of results (see Fig 4B left) is even suggestive of an alteration in dyslexia in comparison with reading-level–matched children. More statistical power would be needed to confirm/disprove the trend.

Our result that audiovisual integration abilities correlate with reading abilities is in line with existing literature. Indeed, individuals with dyslexia benefit less from visual cues to perceive SiN than typical readers [92–96]. Audiovisual integration and reading could be altered in dyslexia simply because both rely on similar mechanisms. Indeed, reading relies on the ability to bind visual (graphemic) and auditory (phonemic) speech representations [97,98]. And according to some authors, suboptimal audiovisual integration mechanisms could reduce reading fluency [99]. Importantly, the finding that individuals with dyslexia benefit normally from visual speech to boost phrasal but not syllabic CTS in noise brings important information about the nature of the audiovisual integration deficit in dyslexia. Following the functional roles attributed to CTS, individuals with dyslexia would properly integrate visual speech information to optimize processing of syntactic information [38] but not to support acoustic/phonemic processing [71]. This could be explained by their preserved ability to extract and integrate the temporal dynamics of visual speech but not the lip configuration [96], two aspects of audiovisual speech integration currently thought to be supported by distinct neuronal pathways [100]. This inability to rely on lip configuration to improve auditory phonemic perception in SiN conditions may be caused by a supramodal phonemic categorization deficit, as already proposed for children with specific language impairment [101]. Finally, the fact that the visual modulation in syllabic nCTS brought a limited amount of unique information about reading with respect to classical behavioral predictors of reading, but that all of them brought more information in synergy, suggests that a broad set of low-level processing abilities contribute to determining reading abilities and alterations in dyslexia [102,103].

Classical behavioral predictors related to global reading abilities

Our results confirm that classical behavioral predictors of reading (RAN, phonological memory, and metaphonological abilities) are directly related to the global reading level rather than reading strategy. We draw this conclusion because the optimal model for reading score contained a common slope for all reading subtests. This means that the model was not significantly improved by optimizing the slope for each of the five reading subtests separately. Accordingly, univariate correlation coefficients presented in Table 4 were roughly similar across the five reading scores.

Phonological memory (assessed with forward digit span) was significantly positively correlated with the global reading level. That phonological memory relates to global reading abilities rather than reading strategy is well documented [4]. Poor readers, regardless of their reading profile, typically perform poorly on phonological memory tests involving digits, letters [104,105], or words [106].

Performance on the RAN task was also related to the global reading level, in line with existing literature [6–8,107–110]. RAN performance indeed has a moderate to strong relationship with all classical reading measures alike, including word, nonword, and text reading, as well as text comprehension [107]. It is a consistent predictor of reading fluency in various alphabetic orthographies independent of their complexity [111]. RAN performance even predicts reading performance similarly well at an interval of 2 years [112] for reading performance assessed with tasks tagging lexical and sublexical routes. It is thought that RAN and reading performances correlate because they involve serial processing and oral production [110], two processes that are common to both reading routes.

Finally, phonological awareness assessed with phoneme suppression and fusion tasks was significantly related to reading abilities. However, the information it brought about reading was less and essentially redundant with that brought by RAN and phonological memory. This is not surprising given that children tested in the present study had at least 1 year of reading experience. Phonological awareness indeed plays a key role in the early stages of reading acquisition, i.e., when learning grapheme-to-phoneme conversion [113–115], and undergoes a substantial maturation during that period [116].

Phonological awareness

Our results indicate that, in typical readers, phonological awareness mediates at best part of the relation between the cortical processing of SiN and reading abilities. Indeed, the information about reading brought by phonological awareness was redundant with that brought by the visual modulation in syllabic nCTS but not with that brought by the informational and visual modulations in phrasal nCTS. This finding illustrates the importance of separating the different processes involved in SiN processing and reading to seek associations. It also provides a potential reason why contradictory reports exist on the topic [19–21].

Nevertheless, the role of phonological awareness might have been underestimated in the present study because of a lack of sensitivity in our phonological awareness subtests. Indeed, phonological awareness tasks turned out to be too easy for older participants, leading to ceiling effects (about half of the participants reached the maximum score on phoneme fusion and suppression tasks). This could explain the weak relation observed between reading abilities and phonological awareness skills. In contrast, there was no ceiling effect for the RAN, which may explain the strong correlation between this score and reading abilities.

Further discussion

In S1 Discussion, we discuss considerations related to the fact that (1) only one acoustic signal-to-noise ratio was studied, (2) regression models to estimate CTS in a given condition were trained on all other conditions, (3) occipital sensors were included in regression models to estimate CTS, and (4) the study was conducted in French. We also discuss the potential yield of future studies in illiterate adults.

Conclusion

Overall, these results significantly further our understanding of the nature of the relation between SiN processing abilities and reading abilities. They demonstrate that cortical processing of SiN and reading abilities are related in several specific ways and that some of these relations translate into alterations in dyslexia that are attributable to reading experience. However, within children with dyslexia, these relations appeared changed or even reversed, potentially owing to compensatory attentional mechanisms. Our results also demonstrate that classical behavioral predictors of reading (including phonological awareness) mediate relations involving the processing of acoustic/phonemic but not syntactic information in natural SiN conditions. This contrasts with the classically assumed mediating role of phonological awareness. Instead, the ability to process speech syntactic content in babble noise (indexed by phrasal nCTS) could directly modulate skilled reading acquisition. Finally, the information about reading abilities brought by cortical markers of syntactic processing of SiN was complementary to that provided by classical behavioral predictors of reading. This implies that such markers of SiN processing could serve as novel electrophysiological markers of reading abilities.


Fundamentals of Molecular Evolution*

Supratim Choudhuri , in Bioinformatics for Beginners , 2014

2.3.4.1.D Horizontal Gene Transfer

Horizontal gene transfer , also known as lateral gene transfer, refers to nonsexual transmission of genetic material between unrelated genomes hence, horizontal gene transfer involves gene transfer across species boundaries. The phenomenon of horizontal gene transfer throws a wrench in the concepts of last common ancestor, syntenic relationship between genomes, phylogeny and the evolution of discrete species units, taxonomic nomenclature, etc. m The majority of examples of horizontal gene transfer are known in prokaryotes. In bacteria, three principal mechanisms can mediate horizontal gene transfer: transformation (uptake of free DNA), conjugation (plasmid-mediated transfer), and transduction (phage-mediated transfer). In plants, introgression can mediate horizontal gene transfer this means gene flow from one gene pool to another gene pool—that is, from one species to another species by repeated backcrossing between an interspecific hybrid and one of its parent species. Therefore, introgression depends on the extent of reproductive isolation between the two species. Introgression has also been reported between duck species, between butterfly species involved in mimicry, and between human and Neanderthal. 41

Horizontal gene transfer in animals is not common, but there are some reports. For example, Acuña et al. 42 identified the gene HhMAN1 from the coffee berry borer beetle, Hypothenemus hampei, which shows clear evidence of horizontal gene transfer from bacteria. HhMAN1 encodes the enzyme mannanase, which hydrolyzes galactomannan. Phylogenetic analyses of the mannanase from both prokaryotes and eukaryotes revealed that mannanases from plants, fungi, and animals formed a distinct eukaryotic clade, but HhMAN1 was most closely related to prokaryotic mannanases, grouping with the Bacillus clade. HhMAN1 was not detected in the closely related species H. obscurus, which does not colonize coffee beans. The authors hypothesized that the acquisition of the HhMAN1 gene from bacteria was likely an adaptation in response to need in a specific ecological niche.

There are also some examples of horizontal gene transfer from fungi to arthropods, such as aphids (insects) and mites (arachnids). Phylogenetic analysis revealed the evidence of horizontal transfer of genes encoding carotenoid desaturase and carotenoid cyclase–carotenoid synthase from fungi to pea aphid, 43 and to spider mite. 44 Notably, the fused carotenoid cyclase–carotenoid synthase gene is characteristic of fungi but not of plants or bacteria. The authors discussed the possible mechanism of such gene transfer. Gene transfer into a single arthropod ancestor of both spider mites and aphids is not likely because it would require subsequent loss of these genes in most other living arthropod taxa. The most likely scenario is the transfer of these genes through symbiosis, which probably occurred independently in both aphids and spider mites. It has been suggested that the frequent association of mites with viruses makes them ideal horizontal gene transfer vectors, including incorporation of mobile genes into their own genomes.


About the Author

Dagmar Bruß graduated at RWTH University Aachen, Germany, and received her PhD in theoretical particle physics from the University of Heidelberg in 1994. As a research fellow at the University of Oxford she became interested in quantum information. Another European fellowship at ISI Torino, Italy, followed. While being a research assistant at the University of Hannover she completed her habilitation. Since 2004 Professor Bruß has been holding a chair at the Institute of Theoretical Physics at Heinrich-Heine-University Düsseldorf, Germany. Her research pertains to theoretical aspects of quantum information processing.


1. Phosphoproteomic dissection of PRR-triggered immunity

Several studies indicated that distinct PRRs share downstream components to induce defence responses. To identify crucial components for PRR-triggered immunity (PTI), we have been monitoring phosphoproteome dynamics upon different MAMP treatments.

One of the key requirements for successful posttranslational modification (PTM)-oriented proteomics is the establishment of efficient enrichment methods for posttranslationally modified peptides. We have developed a posttranslational modification (PTM)-oriented proteomics platform, with an emphasis on phosphorylation as this plays a significant role in early events of plant immune responses.

References and further reading

Li X, Sanagi M, Lu Y, Nomura Y, Stolze SC, Yasuda S, Saijo Y, Schulze WX, Feil R, Stitt M, Lunn JE, Nakagami H, Sato T, Yamaguchi J, “Protein phosphorylation dynamics under identification of a cell death-related receptor-like kinase in Arabidopsis”, Frontiers in Plant Science, Apr 311:377 (2020)

Kimura S, Hunter K, Vaahtera L, Tran HC, Citterico M, Vaattovaara A, Rokka A, Stolze SC, Harzen A, Meißner L, Tabea Wilkens MMT, Hamann T, Toyota M, Nakagami H, Wrzaczek M, “CRK2 and C-terminal phosphorylation of NADPH oxidase RBOHD regulate ROS production in Arabidopsis”, The Plant Cell, 32(4):1063-1080 (2020)

Matsui H, Nomura Y, Egusa M, Hamada T, Hyon GS, Kaminaka H, Watanabe Y, Ueda T, Trujillo M, Shirasu K, Nakagami H, “The GYF domain protein PSIG1 dampens the induction of cell death during plant-pathogen interactions”, PLoS Genetics, 13(10):e1007037 (2017)

Nakagami H, StageTip-based HAMMOC, an efficient and inexpensive phosphopeptide enrichment method for plant shotgun phosphoproteomics, Methods in Molecular Biology "Methods in Plant Proteomics", 1072:595-607 (2014)

Nakagami H, Sugiyama N, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K, Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants, Plant Physiology, 153(3):1161-74 (2010)

Sugiyama N, Nakagami H, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y, Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis, Molecular Systems Biology, 4:193 (2008)


B.2 The structure of a scientific report

The normal scientific report has a standard structure (parts in parentheses are optional):

B.2.1 Title

Although not really a section of the paper, it is worth giving the title some thought. Aim for something that gives a fairly specific description of the topic of the paper, and possibly the essential result, but without being too long:

Diurnal changes in the depth distribution of copepods in lakes with and without planktivorous fish: evidence of a predator avoidance mechanism?

An experimental study of the effect of food supply on laying date in the coot.

The distribution and altitudinal limits of bracken (Pteridium aquilinum) in the North York Moors National Park.

Reverse transcription-PCR detection of LaCrosse virus in mosquitoes and comparison with enzyme immunoassay and virus isolation.

The important thing to note is that the titles contain a good deal of specific information—we have a pretty good idea what the paper is about before we read it. Avoid vague titles such as…

A study of damselfly behaviour

…when in fact we have looked at is the mating and oviposition behaviour of damselflies of a particular species in relation to the current speed in different areas of the river and what we want to say is:

The influence of river flow rate on mating behaviour and oviposition in the damselfly Calopteryx splendens

Don’t put irrelevant specific information in the title. It might be irrelevant to say that we carried out a study in a particular river—that detail is probably not important for the question we’re asking . The reference to the North York Moors above, however, is relevant because the study is of an area-specific problem (the study is primarily of use to people who want to know about bracken in that area).

B.2.2 Abstract or Summary

The purpose of an abstract is to present a factual summary of the main purpose, results and conclusions of the report which is short and makes sense on its own. Often it is best (and some journals require it) to do this as 3-6 numbered points comprising some, or all, the following:

The scope and purpose of the study

Methods (not always necessary)

  • The territorial behaviour, mating frequency and oviposition of Calopteryx splendens (Charpentier) (Odonata: Calopterygidae) were studied in relation to the water flow rate in the territories (weed patches) of individual males.
  • Weed patches with faster flow rates appeared to be preferentially selected by males, and more vigorously defended. Weed patches in slow or still water were often unoccupied. Experimental reduction of flow rate in individual patches caused males to desert previously defended territories.
  • Males had greater mating success on territories with higher flow rates and more ovipositions were observed in these patches.
  • It is not known why weed patches with faster flows seem to be better quality sites for Calopteryx oviposition, but possible reasons include higher oxygen levels for developing eggs and better protection from egg parasitoids.

B.2.3 Introduction

set the background to the question, using the literature (Why is it interesting? Why is it important?).

state the question, hypotheses and predictions. (What is it that we’re actually investigating?)

briefly state what the study does (What is in this paper?)

Start with brief general statements to put the study into its broader context:

Oviposition site selection by female insects can be a critical factor in offspring survival, and hence fitness (Smith 1981). In some insects, notably many of the Odonata, males occupy or defend oviposition sites and mate with arriving females before allowing them to oviposit at that site. Males in such systems benefit in two ways from defending high quality sites: mating with all females ovipositing at the site ensures their offspring will have higher survival, and by occupying high quality sites, they will have access to more females (Jones 1976).

Then move on to more specific detail about the type of system:

In calopterygid damselflies females oviposit in the submerged stems of aquatic plants in streams and small rivers (Hines 1956, Norman 1968). Males defend patches of weed…

Then develop the question:

It has been repeatedly observed that many weed patches are always occupied and are the subject of much territorial dispute amongst males, whilst others remain unoccupied or uncontested (Gateman and Nunn 1978, Speake 1982, Mollison 1987). This suggests substantial differences in patch quality, but the basis of this difference is not known. Since the larvae may disperse after hatching, the underwater environment of a weed patch seems most likely to be important for survival and development of the eggs. One important physical factor which could influence the environment in a weed patch, and which may vary considerably in different parts of the river channel, is flow rate. We therefore hypothesised that flow rates could be an important determinant of patch quality.

Say what the study actually does:

In this study we investigated the physico-chemical differences between ‘good’ and ‘poor’ quality patches of weed as defined by the behaviour of the damselfly Calopteryx virgo Linnaeus. We also tested the assumption that males on more vigorously defended patches have greater mating success.

Don’t separate out the question, hypothesis and predictions as special statements in bold or whatever, or put them under separate headings. Although they provide vitally important context to a study they should simply appear where necessary as part of the normal text.

B.2.4 Methods

The Methods section should provide enough information about how the study was carried out to enable the reader to evaluate the validity of the results.

Where (usually necessary for field work) ?

When (may be necessary for seasonally dependent studies) ?

Why (may be necessary to justify the use of a particular approach) ?

It is often said that we should write the methods so that someone could repeat what we’ve have done exactly. This is OK in principle, but often takes an excessive amount of space and shouldn’t be the overriding principle. The emphasis should be on giving the reader sufficient information to evaluate the results of a study. Focus on the important detail: i.e., it doesn’t matter that we sorted our sample into Petri dishes, or which make of microscope we used, but it does matter that we worked at 20x magnification, because that may determine how likely it is that we missed very small items. The main exception to this is if we’re reporting a novel technique that other people are likely to want to use. In that case more detail than normal will be required.

Be concise. There is no need to explain the details of standard procedures. If we’re using a procedure described by someone else then summarise the essential features and just cite the reference for the method. In the Methods it is not necessary to state which statistical tests were used unless they are non-standard or require particular discussion (e.g. it is useful to state that the data were transformed before analysis). Similarly, we don’t need to state what statistics package were used for standard statistical procedures. Avoid ‘padding’ sentences that just waste space, such as:

The data were analysed statistically and by plotting graphs to see what the results were.

The standard style in scientific reports is to write in the third person (“Experimental plots were marked out” rather than “We marked out experimental plots”). This an area where the accepted conventions vary between different areas of biology. In some the use of the first person, where it enhances readability of the text, is permitted and even encouraged. Judicious use of ‘I’ or ‘we’ can improve the clarity and readability of text and should be used where appropriate. Just keep in mind that the use of the first person is not accepted in some disciplines. If in doubt it is safest to stick with the third person approach.

Also try to use the active voice, i.e., avoid this style…

It was found that males always defended single weed patches.

… and and use this style instead:

Males always defended single weed patches.

A final point is that when a study is made up of several experiments, or sets of observations, it is a good idea to use appropriate subheadings to make it easier for the reader to follow, both within a particular section (such as the Methods) but then also using the equivalent subheadings to organise the Results and possibly the Discussion. e.g.,

MATERIALS AND METHODS

Study site

Territory occupancy by males

Oviposition behaviour

Experimental manipulations of flow rate

B.2.5 Results

The central goal of a results section is to provide a clear account of the material factual findings of the investigation, using a combination of text, summarised data, and figures. If different parts of the study are covered under different subheadings in the Methods, then use the same subheadings (where relevant) to organize the Results.

The Results section should focus on explaining clearly what the results are, but should not contain discussion of the biological implications of the results.

Results are presented in a variety of different ways:

Text. The text part is important. This must include clear statements of the results. No result should just be presented just as a figure or a table with no corresponding statement in the text. It is important to lead the reader through the information, bringing out the important features. This does not mean that we should duplicate information in text and figures, or tables, but if a figure is used then there should be a reference to that figure in the text, which summarizes the result.

Data. Numerical data are normally presented in tables (see below), but sometimes ‘stand-alone’ simple numerical results can be given in the text. In either case the data is normally be presented in summarised form only (e.g. means and standard deviations).

Presenting raw data may be appropriate if there are very few data, or there is a legitimate need to discuss the values of specific data points, but this is rarely the case. Don’t include big tables of raw data. If we want include the raw data (usually only the case if the data set may be of use to others as a basis for further analyses), they should go in as an appendix. Alternatively, if our goal is to share our data with the rest of the world we might consider using an online data repository like Figshare.

Statistical summaries. The results should be where most or all of the statistical results appear. There are three places to include summaries of statistics:

In tables. If there are large numbers of tests to present which would clutter the text, e.g. the analysis involves 10 regressions of the same kinds of variables, for a number of different taxa, then it may be convenient to summarise the slopes, intercepts and significance of the relationships in a table rather than trying to put all ten in the text (although a figure would be even better).

Be sure to report statistical results in full: include the test statistic, degrees of freedom (both of them, when reporting an F-test), and the p-value.

Figures and Tables. Any type of graphical presentation is a figure. A table has just text and numbers. All figures and tables must be referred to in the text of the Results (or elsewhere).

contain just text and numbers

have the legend at the top

use just horizontal lines as separators

are labelled: Table 1, Table 2, etc.

have a legend at the bottom

should be labelled: Figure 1, Figure 2, etc.

can comprise a single graph or diagram, but a single figure can also comprise several graphs – in which case each should be labelled: a, b, c, etc.

Preparing a manuscript for publication

Word processing software makes it easy to incorporate tables and figures directly into a document. When writing a report which is not going to be typeset, then this allows the production of very professional looking documents. However, if the material is for publication, then the printers will usually require the text and figures (and sometimes tables) on separate pages. If sending a manuscript for publication, then the figures and tables should be put at the end of the document (after all the text and references), but in a normal document if a table or figure occurs on a separate page then the page should immediately follow the first point at which the figure is referred to in the text.

B.2.6 Discussion

The function of the discussion is to consider the meaning of the results and the light they throw on the original question to assess the results in the context of other studies and, if appropriate, to consider the limitations of the work and future directions for study. The exact structure and content of the Discussion will vary somewhat depending on the particular study and what the results show, but usually the following components should be included.

It is usually helpful to start the discussion with a short paragraph, or so, summarizing the key results. e.g.,

Calopteryx females exhibit a distinct preference for weed beds in faster flowing water as oviposition sites. Males recognise such good quality sites and occupy and defend them against other males, ignoring weed beds in slower water. This results in more copulations for males which occupy the fast flowing sites. The assessment and response of males to flow rate changes can occur within a few hours

Next, we usually consider the whether the results support the hypothesis or suggest it requires modification or rejection. e.g.,

The male damselflies’ preferential occupancy and vigorous defence of weed patches with faster flow rates, combined with a clear positive relationship between flow rate and oviposition frequency, provides strong support for the view that the underwater environment is an important determinant of oviposition site quality.

It may be important to discuss the limitations of the study and the appropriate direction for further work, but these are not always required. Don’t pad out the discussion with endless text considering every possible wrinkle in the study. When appropriate, a discussion of the limitations should be brief and to the point.

Although the results do implicate flow rate as a determinant of oviposition site, it is not clear whether females are responding directly to flow rate, or whether males are assessing flow rate and females are selecting the higher quality males (presumably those that occupy the best patches) assessed in some other way. This would require a separate experiment where females were allowed to select oviposition sites in the absence of males.

Don’t just grumble and don’t make stock criticisms without good reason (e.g., don’t automatically say it would have been better to have a larger sample size—this may be true, but it may not—large sample sizes don’t solve everything). There may be unresolved, or unsolvable, problems. Be honest about these, but also be positive: if the author don’t seem to be sure that a study is worth reporting, how will anyone else be convinced? A report does not require a section headed ‘Experimental Error.’ Similarly don’t attribute any problems that can’t be explained to experimental error everyone knows measurements aren’t perfect so it doesn’t explain anything.

Finally, bring out the wider implications (but be realistic about the significance of the work) and future directions, e.g.

These results indicate selection of oviposition sites, by females, on the basis of flow rate, but the reasons for such selectivity are not known. Flow rate has been implicated in other studies of aquatic insects as being of importance for preventing low oxygen conditions developing (a stress to which developing eggs may be particularly sensitive) (Armherst 1989). High flow may also reduce the ability of egg parasitoids to search the plants (Girton and Jenner 1976). A critical part of assessing the basis of site choice, and evaluating the role of the underwater environment will be measurement of egg and larval survival in weed beds of different flow rates.

It seems likely that the patterns observed in Calopteryx in a single section of the river may also be important in determining choice of habitat between different river sections or even different rivers with high or flow rates. This also raises the unwelcome possibility that quite subtle changes in flow caused by water abstraction and river regulation (a problem on a neighbouring stream to the study site) could cause marked interference with Calopteryx breeding and even loss of the species from a river system.

The Discussion should not contain new results (except occasionally for small additional analyses of the data that have arisen as a direct consequence of interpretation of the main results - and that shed light upon the questions in the paper). Also avoid over-extending the implications of what was found. A slight trend in the results from one particular experiment may not be an entirely sound basis from which to challenge the fundamental tenets of evolutionary biology. (On the other hand it just could be the skill is in spotting the few occasions when it is!).

Overall, keep the focus of the discussion firmly on the results, don’t wander off into ten pages of philosophical discourse on the state of the field in general. And keep the volume and depth of the discussion in proportion to the rest of the paper, and to the significance (biological rather than statistical) of the results.

B.2.7 Acknowledgements

This is the place to acknowledge persons or organizations who have made significant contributions to the execution of the work. For example: funding bodies, people who have contributed ideas or assisted with some of the actual work, landowners giving access to sites, specialists who have made identifications and people who have read and commented on the manuscript. Don’t get carried away—there’s no need to thank every friend, relation and loved one for general help through life’s little crises.

B.2.8 Literature cited / References

This section should provide a complete listing of all, and only, references cited in the text of the report. There are three things to consider here:

How to cite it in the text

How to construct a reference list

B.2.8.1 What to cite

We should cite appropriate references wherever a point of substance (fact, or opinion) is made that is not our own or may not be regarded as common knowledge. e.g.

Several species in the genus Calopteryx perform a complex `wing floating’ display as part of the courtship behaviour (Malmquist 1956)

This behaviour is generally considered to be a display of male quality (Fredenholm 1978, Summers 1991).

Absence of citation is taken to indicate either the author’s own view or a result generated by the present study:

The function of this behaviour may be to signal the flow rate, and hence quality of a patch, to a female.

…or something sufficiently well known to be regarded as common knowledge:

Damselflies are predatory both in the larval and adult stages.

B.2.8.2 Styles of citation

If writing a manuscript for publication in a scientific journal, obviously use the style of the journal in question (exactly—including punctuation). When writing any other type of report, we can choose our own style, but if in doubt the easiest approach is probably to follow the style of a major journal in the appropriate subject area. There are two main styles in widespread use:

The most common (and most straightforward) cites references in the text using names and dates, and lists all references alphabetically in the reference list.

Wide fluctuations in temperature reduce egg viability (Smith 1987).

Smith (1987) found that wide variations in temperature reduced egg viability.

And in the reference list:

Smith, A. J. (1987) The effect of temperature on egg development and survival in the damselfly Calopteryx virgo. J. Zool. (Lond.) 47: 231-243.

Note that the necessary information about the journal is the: journal title, the volume number (47) and the pages of the article (231-243). Journals often also have a part number, e.g., volume 47(2). There is no to include this in the citation the page numbers should be sufficient.

The list should be in alphabetical order by first author. If there is more than one reference by the same author then order them by date. If there are papers with the same first author but different second/third authors then these come after the single author papers by the first author, and in alphabetical order by second, third, etc. authors, e.g.,

Smith A J (1987)…
Smith A J (1989)…
Smith A J, Girton S and Mackay R H (1984)…
Smith A J and Wallis K C (1983)…
Smith A J and Wallis K C (1985)…

If several citations by the same author in the same year are in the list, then denote them with letters e.g.

Smith, A. J. (1987a) The effect of temperature on egg development and survival in the damselfly Calopteryx virgo. J. Zool. (Lond.) 47: 231-243 Smith, A. J. (1987b) The oviposition behaviour of Calopteryx virgo (Odonata: Zygoptera). Anim. Behav. 27: 197-209

The other main style is to use numerical superscripts (or equivalent) in the text, numbering the references in the order in which they are mentioned in the text, and ordering the final reference list in the same way, e.g.

Wide fluctuations in temperature reduce egg viability 23 . Smith 23 found that wide variations in temperature reduced egg viability.

  1. Wilcove H, Papapangiotou L A and Lu, X (1978) Mating strategies in a calopterygid damselfly. Anim. Behav. 16:21-30
  2. Smith A J (1987) The effect of temperature on egg development and survival in the damselfly Calopteryx virgo. J. Zool. (Lond.) 47:231-243
  3. Morris L L (1991) A model of territory switching behaviour. Am. Nat. 230:390-395

In many journals using this system, the titles of the references in the list are also omitted e.g.

This is done purely to save space, so unless we are specifically asked to do this it is best to include the complete reference. Although such numerical systems usually require the reference list to be ordered by number, it is possible (and much more convenient) to use an alphabetical listing even if numbers are used in the text (alphabetically ordered references are numbered in order and then the numbers used in the text instead of names). The advantage to a numbering system is that is saves space in the text, the disadvantage is that the numbers don’t tell a reader which paper is being referred to as they read—they have to keep looking them up in the list.

Some final points to bear in mind about references and their citation: 1) every reference cited in the text must appear in the reference list, and every reference in the list must appear in the text 2) we should never cite something we’ve not seen. If we need to cite something we have seen discussed or cited somewhere else, but haven’t seen our self (and cannot get hold of) we should make it clear that we’re citing someone else’s interpretation of the original reference, e.g.,

In the list we should then give the full citation for Smith (1987), not Jones (1928).

There are standard abbreviations for journal names. These are often given in the journal itself, and are available on a list in the Library, or can be found by looking up the journal on Biological Abstracts. If we don’t know what the standard abbreviation is, and it is not obvious, then it’s best to use the full name rather than making up a new abbreviation.

Use a reference manager!

Managing citations and generating reference lists can be a painful process, especially when everything is done ‘manually’ (cut and paste, cut and paste, cut and paste…). These days a number of reasonably good reference managers (software packages) are available to help with the process of managing references, inserting citations, formatting, and generating reference lists. Endnote, Mendeley and Papers are probably the most popular, but there are many different options. Choose one, and learn how to use it. This will save a huge amount of effort in the long run.

B.2.9 Appendices

Use appendices for large amounts of raw data, long species lists, detailed mathematical or laboratory working, of a non-standard method, or (short) program listings, but only where the inclusion of such information markedly enhances the usefulness of the paper. Normally such appendices are not required. Avoid using them just to show how much work went into a study!


An Introduction to Bayesian Data Analysis for Cognitive Science

Load the following data. These data are from Experiment 1 in a set of reading studies on Persian (Safavi, Husain, and Vasishth 2016) . This is a self-paced reading study on particle-verb constructions, with a (2 imes 2) design: distance (short, long) and predictability (predictable, unpredictable). The data are from a critical region in the sentence. All the data from the Safavi, Husain, and Vasishth (2016) paper are available from https://github.com/vasishth/SafaviEtAl2016.

  • Distance=short and Predictability=unpredictable
  • Distance=short and Predictability=predictable
  • Distance=long and Predictability=unpredictable
  • Distance=long and Predictability=predictable

The researcher wants to do the following sets of hypothesis tests:

Compare the condition labeled Distance=short and Predictability=unpredictable with each of the following conditions:

  • Distance=short and Predictability=predictable
  • Distance=long and Predictability=unpredictable
  • Distance=long and Predictability=predictable
  • Which contrast coding is needed for such a comparison?
  • First, define the relevant contrast coding. Hint: You can do it by creating a condition column labeled a,b,c,d and then use a built-in contrast coding function.
  • Then, use the hypr library function to confirm that your contrast coding actually does the hypothesis tests you need.
  • Fit a simple linear model with the above contrast coding and display the slopes, which constitute the relevant comparisons.
  • Now, compute each of the four conditions’ means and check that the slopes from the linear model correspond to the relevant differences between means that you obtained from the data.

The data come from an eyetracking study in German reported in Vasishth et al. (2008) . The experiment is a reading study involving six conditions. The sentences are in English, but the original design was involved German sentences. In German, the word durchaus (certainly) is a positive polarity item: in the constructions used in this experiment, durchaus cannot have a c-commanding element that is a negative polarity item licensor. Here are the conditions:

  • Negative polarity items
      1. Grammatical: No man who had a beard was ever thrifty.
      1. Ungrammatical (Intrusive NPI licensor): A man who had no beard was ever thrifty.
      1. Ungrammatical: A man who had a beard was ever thrifty.
      1. Ungrammatical: No man who had a beard was certainly thrifty.
      1. Grammatical (Intrusive NPI licensor): A man who had no beard was certainly thrifty.
      1. Grammatical: A man who had a beard was certainly thrifty.

    We will focus only on re-reading time in this data-set. Subset the data so that we only have re-reading times in the data-frame:

    The comparisons we are interested in are:

    • What is the difference in reading time between negative polarity items and positive polarity items?
    • Within negative polarity items, what is the difference between grammatical and ungrammatical conditions?
    • Within negative polarity items, what is the difference between the two ungrammatical conditions?
    • Within positive polarity items, what is the difference between grammatical and ungrammatical conditions?
    • Within positive polarity items, what is the difference between the two grammatical conditions?

    Use the hypr package to specify the comparisons specified above, and then extract the contrast matrix. Finally, specify the contrasts to the condition column in the data frame. Fit a linear model using this contrast specification, and then check that the estimates from the model match the mean differences between the conditions being compared.

    • How many comparisons can one make in a single model when there is a single factor with four levels? Why can we not code four comparisons?
    • How many comparisons can one code in a model where there are two factors, one with 3 levels and one with 2 levels?
    • How about a model for a 2 x 2 x 3 design?

    References

    Safavi, Molood Sadat, Samar Husain, and Shravan Vasishth. 2016. “Dependency Resolution Difficulty Increases with Distance in Persian Separable Complex Predicates: Implications for Expectation and Memory-Based Accounts.” Frontiers in Psychology 7 (403).

    Vasishth, Shravan, Sven Bruessow, Richard L. Lewis, and Heiner Drenhaus. 2008. “Processing Polarity: How the Ungrammatical Intrudes on the Grammatical.” Cognitive Science 32 (4, 4): 685–712.


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