bluuebunny/crossref_metadata_2025 huggingface dataset:
Language Contact in Cape Verdean Creole
Authors: Baptista Marlyse , Veiga Manuel , Soares da Costa Sérgio , Robalo Lígia Maria Herbert Duarte Lopes
Published: February 2020

This chapter examines bidirectional influences in the speech of bilingual speakers of Portuguese and Cape Verdean Creole in the Cape Verde islands, in two modalities (oral and written). All the data are drawn from two main sources: Costa (2013) that documents the influences of Portuguese onto Cape Verdean Creole and from Herbert Robalo (2013) from Cape Verdean Creole onto Portuguese. The observed contact effects include code-switching strategies and transfer in the domains of gender marking, number agreement, verb morphology, complementizers, and prepositions. One of the main findings is that although speakers practice insertional, alternational code-switching and congruent lexicalization, congruent lexicalization clearly emerges as the dominant pattern and the keystone behind speakers’ choices of code-switching sites in both the oral and written modes. Speakers preferentially switch on the sites that happen to be structurally isomorphic between Cape Verdean Creole and Portuguese.
Language Contact in Celtic and Early Irish
Authors: Hickey Raymond
Published: February 2020

There is little doubt that the early stages of the subgroups of the Indo-European language family involved extensive contact. The movements of early groups of speakers across large stretches of land in Euroasia meant that these people came into contact with others who spoke genetically unrelated languages. This contact is responsible for the non Indo-European lexis in Indo-European languages and may also be the source of non-inherited grammatical features. Establishing the precise source of such lexis and grammar is a daunting task, given the great time-depth involved and the dearth of textual records that could provide helpful data for reconstructing the sources of borrowings external to this language family. But there was also contact within the orbit of the Indo-European languages when members of different subgroups came into close geographical proximity with each other due to repeated migrations. This fact accounts for borrowings across Indo-European subgroups (e.g. from Celtic into Germanic). This chapter examines cases of contact and probable borrowing both within the Indo-European language family and at its external interface to languages from other families, inasmuch as this can be established with reasonable certainty. The focus for this treatment is on early stages both of Celtic and of the Irish language as one of the main members of this group. The consideration of contact effects in Irish is limited to the language as it developed up to the late Middle Ages.
Language Contact Considering Signed Language
Authors: Quinto-Pozos David , Adam Robert
Published: February 2020

Language contact of various kinds is the norm in Deaf communities throughout the world, and this allows for exploration of the role of the different kinds of modality (be it spoken, signed or written, or a combination of these) and the channel of communication in language contact. Drawing its evidence largely from instances of American Sign Language (ASL) this chapter addresses and illustrates several of these themes: sign-speech contact, sign-writing contact, and sign-sign contact, examining instances of borrowing and bilingualism between some of these modalities, and compares these to contact between hearing users of spoken languages, specifically in this case American English.
Semantic Borrowing in Language Contact
Authors: Mott Brian , Laso Natalia J.
Published: February 2020

After providing a general introduction to loan phenomena, which may be phonological, grammatical and syntactic, morphological or lexical, and commenting on the degree to which various different languages have borrowed elements from other languages, this chapter concentrates on the main types of semantic change triggered by language contact, and underlines the frequency of these processes. First, loanwords are distinguished from loan creations, which are new coinages made from loan material. Then pure loanwords are contrasted with loanblends. Pure loanwords are adopted wholesale, with little phonological or morphological change, while loanblends adopt only part of the form of a foreign lexical item. Loanshifts borrow the meaning, but the form is native. These include pure loan translations (calques), where the original morphemes are translated item by item. The more fanciful among these are called loan renditions, in which the translation of the foreign word is freer and less than literal. In semantic loan (semantic calque), a native word undergoes extension of its meaning on the model of a foreign counterpart. The second half of the chapter deals with the causes of semantic borrowing, and shows that it is often induced by formal similarity of cognates. In this section, attention is paid to pressure from the native language in second language acquisition, and the influence exerted on dialect by the standard language, or vice versa. The chapter ends with some examples of pragmatic borrowing.
First- and Second-Language Acquisition and CILC
Authors: Eppler Eva Duran , Ozón Gabriel
Published: February 2020

This chapter explores the contested role of L1 and L2 acquisition in contact-induced linguistic change (CILC). We first identify three factors underlying these controversies (field of research; theoretical approach; and methodological limitations/advances), before discussing two elements language change and language acquisition have in common (i.e., isolated individuals cannot accomplish either, and both have to be studied through natural language data, with its attendant high degree of variation). We go on to define key terms and concepts for the role of L1 and L2 acquisition in contact-induced language change, including first and second language acquisition (L1A and L2A), bilingual first language acquisition, language variation and change, language contact and contact-induced language change. In the main section we discuss the role of L1A and L2A in CILC, and examine different language-acquisition scenarios, in particular their potential for leading to CILC. We use these different language-acquisition types as testing grounds for the motivations behind (i.e., causes for, and triggers of) language change, and arrive at tentative conclusions about which of these language-acquisition scenarios is more likely to play a role in CILC, and why.
A Systematic Literature Review of Brain Neurostimulation Therapies for the Treatment of Pain
Authors: Deer Timothy R , Falowski Steven , Arle Jeff E , Vesper Jan , Pilitsis Julie , Slavin Konstantin V , Hancu Maria , Grider Jay S , Mogilner Alon Y
Published: February 2020

Objective

To conduct a systematic literature review of brain neurostimulation for pain.

Design

Grade the evidence for deep brain neurostimulation (DBS).

Methods

An international, interdisciplinary work group conducted a literature search for brain stimulation. Abstracts were reviewed to select studies for grading. Randomized controlled trials (RCTs) meeting inclusion/exclusion criteria were graded by two independent reviewers. General inclusion criteria were prospective trials (RCTs and observational) that were not part of a larger or previously reported group. Excluded studies were retrospective or existed only as abstracts. Studies were graded using the modified Interventional Pain Management Techniques–Quality Appraisal of Reliability and Risk of Bias Assessment, the Cochrane Collaborations Risk of Bias assessment, and the United States Preventative Services Task Force level-of-evidence criteria.

Results

Two high-quality RCTs and three observational trials supported DBS, resulting in Level II (moderate) evidence.

Conclusion

Moderate evidence supports DBS to treat chronic pain. Additional Level I RCTs are needed to further the strength of the evidence in this important area of medicine, but the current evidence suggests that DBS should be considered as an option in treating complex pain cases.
On Tangency in Equisingular Families of Curves and Surfaces
Authors: Giles Flores Arturo , Silva O N , Snoussi J
Published: February 2020

We study the behavior of limits of tangents in topologically equivalent spaces. In the context of families of generically reduced curves, we introduce the $s$-invariant of a curve and we show that in a Whitney equisingular family with the property that the $s$-invariant is constant along the parameter space, the number of tangents of each curve of the family is constant. In the context of families of isolated surface singularities, we show through examples that Whitney equisingularity is not sufficient to ensure that the tangent cones of the family are homeomorphic. We explain how the existence of exceptional tangents is preserved by Whitney equisingularity but their number can change.
The Effect of Cash Injections: Evidence from the 1980s Farm Debt Crisis
Authors: Bergman Nittai K , Iyer Rajkamal , Thakor Richard T
Published: February 2020

What is the effect of cash injections during financial crises? Exploiting county-level variation arising from random weather shocks during the 1980s Farm Debt Crisis, we analyze and measure the effect of local weather-driven cash flow shocks on the real and financial sectors. We show that such cash flow shocks significantly affect a host of economic outcomes, including land values, loan delinquency rates, the probability of bank failure, employment, and wages. Estimates of the effect of local cash flow shocks on county income levels during the financial crisis yield a multiplier of 1.63.
Happiness in Hard Times: Does Religion Buffer the Negative Effect of Unemployment on Happiness?
Authors: Hastings Orestes P , Roeser Kassandra K
Published: February 2020

Two well-known findings are that the religious are happier than the non-religious, and people are less happy when they lose their job. We investigate a link between these by asking whether religion buffers against the negative effect of unemployment on happiness. Although theorized or implicitly assumed in many studies, empirical demonstrations of a causal, moderating effect of religion have been infrequent and often not strong methodologically. We conduct individual-level fixed effects models to test for the buffering effect in the US context using recent panel data from the 2006–2014 General Social Surveys. Religious service attendance, belief in life after death, and trying to carry one’s religious beliefs over into other dealings in life all substantially buffered the effect of unemployment on happiness. Praying daily, believing God exists, identifying as a religious person, and having a religious affiliation did not. We discuss these results in the context of prior work and existing theory. To further support a causal interpretation of these findings, we also conduct a secondary analysis showing that unemployment does not appear to increase or decrease religiousness. This paper makes an important sociological contribution to the growing field of happiness research and to our understanding of how religion matters to people during hard times.
Race, Racism, and the Cool Pose: Exploring Black and White Male Masculinity
Authors: Unnever James D , Chouhy Cecilia
Published: February 2020

Scholars argue that racial oppression uniquely causes Black males to construct a definition of their masculinity—the “Cool Pose”—that is different from White male masculinity. In this paper, using a nationally representative survey conducted in 2018, we examined whether young Black males were more likely than White male youths to feel greater pressure to conform to the Cool Pose. We analyzed six measures of the Cool Pose. We found no evidence that young Black males were more likely than White male youths to feel greater pressure to use violence if provoked. However, we found that young Black males were more likely than White male youths to feel greater pressure to be physically and emotionally strong, play sports, and to dominate or control others. We conclude that research needs to move beyond idiosyncratic accounts of Black males’ cultural adaptations in order to explicate the developmental processes that affect how Black males living in a systemically racist society express their masculinity.
Leishmanial selenoproteins and the host immune system: towards new therapeutic strategies?
Authors: Rashidi Sajad , Kalantar Kurosh , Nguewa Paul , Hatam Gholamreza
Published: February 2020

Optimum levels of selenoproteins are essential for starting and managing the host immune responses against pathogens. According to the expression of selenoproteins in Leishmania parasites, and since high levels of selenoproteins lead to adverse effects on immune cells and their functions, Leishmania parasites might then express selenoproteins such as selenomethionine in their structure and/or secretions able to challenge the host immune system. Finally, this adaptation may lead to evasion of the parasite from the host immune system. The expression of selenoproteins in Leishmania parasites might then induce the development of infection. We therefore suggest these molecules as new therapeutic candidates for the treatment of leishmaniasis.
A review of applications of visual inspection technology based on image processing in the railway industry
Authors: Liu Scarlett , Wang Quandong , Luo Yiping
Published: February 2020

In order to ensure the safety of railway transportation, it is necessary to regularly check for faults and defects in the railway system. Visual inspection technology is conducive to improving the low efficiency, poor economy and inaccurate detection results of traditional detection methods. This paper introduces the research and contribution of various scholars in the field of visual inspection, summarizes the application and development of visual inspection technology in the railway industry, and finally forecasts the future research direction of visual inspection technology.
Arabidopsis Response Regulator 6 (ARR6) Modulates Plant Cell-Wall Composition and Disease Resistance
Authors: Bacete Laura , Mélida Hugo , López Gemma , Dabos Patrick , Tremousaygue Dominique , Denancé Nicolas , Miedes Eva , Bulone Vincent , Goffner Deborah , Molina Antonio
Published: February 2020

The cytokinin signaling pathway, which is mediated by Arabidopsis response regulator (ARR) proteins, has been involved in the modulation of some disease-resistance responses. Here, we describe novel functions of ARR6 in the control of plant disease-resistance and cell-wall composition. Plants impaired in ARR6 function (arr6) were more resistant and susceptible, respectively, to the necrotrophic fungus Plectosphaerella cucumerina and to the vascular bacterium Ralstonia solanacearum, whereas Arabidopsis plants that overexpress ARR6 showed the opposite phenotypes, which further support a role of ARR6 in the modulation of disease-resistance responses against these pathogens. Transcriptomics and metabolomics analyses revealed that, in arr6 plants, canonical disease-resistance pathways, like those activated by defensive phytohormones, were not altered, whereas immune responses triggered by microbe-associated molecular patterns were slightly enhanced. Cell-wall composition of arr6 plants was found to be severely altered compared with that of wild-type plants. Remarkably, pectin-enriched cell-wall fractions extracted from arr6 walls triggered more intense immune responses than those activated by similar wall fractions from wild-type plants, suggesting that arr6 pectin fraction is enriched in wall-related damage-associated molecular patterns, which trigger immune responses. This work supports a novel function of ARR6 in the control of cell-wall composition and disease resistance and reinforces the role of the plant cell wall in the modulation of specific immune responses.
Host identity and symbiotic association affects the taxonomic and functional diversity of the clownfish-hosting sea anemone microbiome
Authors: Titus Benjamin M. , Laroche Robert , Rodríguez Estefanía , Wirshing Herman , Meyer Christopher P.
Published: February 2020

All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly linked physical interactions that characterize many macroscopic symbioses create opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species of clownfish-hosting sea anemones that co-occur on coral reefs in the Maldives. We test the importance of evolutionary history, clownfish symbiont association, and habitat on the taxonomic and predicted functional diversity of the microbiome, and explore signals of microbiome convergence in anemone taxa that have evolved symbioses with clownfishes independently. Our data indicate that host identity and clownfish association shapes the majority of the taxonomic diversity of the clownfish-hosting sea anemone microbiome, and predicted functional microbial diversity analyses demonstrate a convergence among host anemone microbiomes, which reflect increased functional diversity over individuals that do not host clownfishes. Further, we identify upregulated predicted microbial functions that are likely affected by clownfish presence. Taken together our study potentially reveals an even deeper metabolic coupling between clownfishes and their host anemones, and what could be a previously unknown mutualistic benefit to anemones that are symbiotic with clownfishes.
Cuttlefish show flexible and future-dependent foraging cognition
Authors: Billard Pauline , Schnell Alexandra K. , Clayton Nicola S. , Jozet-Alves Christelle
Published: February 2020

Some animals optimize their foraging activity by learning and memorizing food availability, in terms of quantity and quality, and adapt their feeding behaviour accordingly. Here, we investigated whether cuttlefish flexibly adapt their foraging behaviour according to the availability of their preferred prey. In Experiment 1, cuttlefish switched from a selective to an opportunistic foraging strategy (orvice versa) when the availability of their preferred prey at night was predictable versus unpredictable. In Experiment 2, cuttlefish exhibited day-to-day foraging flexibility, in response to experiencing changes in the proximate future (i.e. preferred prey available on alternate nights). In Experiment 1, the number of crabs eaten during the day decreased when shrimp (i.e. preferred food) were predictably available at night, while the consumption of crabs during the day was maintained when shrimp availability was unpredictable. Cuttlefish quickly shifted from one strategy to the other, when experimental conditions were reversed. In Experiment 2, cuttlefish only reduced their consumption of crabs during the daytime when shrimps were predictably available the following night. Their daytime foraging behaviour appeared dependent on shrimps' future availability. Overall, cuttlefish can adopt dynamic and flexible foraging behaviours including selective, opportunistic and future-dependent strategies, in response to changing foraging conditions.
DNA preserved in jetsam whale ambergris
Authors: Macleod Ruairidh , Sinding Mikkel-Holger S. , Olsen Morten Tange , Collins Matthew J. , Rowland Steven J.
Published: February 2020

Jetsam ambergris, found on beaches worldwide, has always been assumed to originate as a natural product of sperm whales (Physeteroidea). However, only indirect evidence has ever been produced for this, such as the presence of whale prey remains in ambergris. Here, we extracted and analysed DNA sequences from jetsam ambergris from beaches in New Zealand and Sri Lanka, and sequences from ambergris of a sperm whale beached in The Netherlands. The lipid-rich composition of ambergris facilitated high preservation-quality of endogenous DNA, upon which we performed shotgun Illumina sequencing. Alignment of mitochondrial and nuclear genome sequences with open-access reference data for multiple whale species confirms that all three jetsam samples derived originally from sperm whales (
Physeter macrocephalus
). Shotgun sequencing here also provides implications for metagenomic insights into ambergris-preserved DNA. These results demonstrate significant implications for elucidating the origins of jetsam ambergris as a prized natural product, and also for the understanding of sperm whale metabolism and diet, and the ecological mechanisms underlying these coproliths.
Fluid and solute transport across the retinal pigment epithelium: a theoretical model
Authors: Dvoriashyna Mariia , Foss Alexander J. E. , Gaffney Eamonn A. , Repetto Rodolfo
Published: February 2020

The retina is composed of two main layers—the neuroretina and the retinal pigment epithelium (RPE)—that are separated by a potential gap termed the sub-retinal space (SRS). Accumulation of fluid in the SRS may result in a retinal detachment. A key function of the RPE is to prevent fluid accumulation in the SRS by actively pumping fluid from this space to the choroid. We have developed a mathematical model of this process that incorporates the transport of seven chemical species: Na
+
, K
+
, Cl
−
,

HCO
3
−

, H
+
, CO
2
and H
2
CO
3
. This allows us to estimate solute and water fluxes and to understand the role of the different membrane ion channels. We have performed a global sensitivity analysis using the extended Fourier amplitude sensitivity test to investigate the relative importance of parameters in generating the model outputs. The model predicts that flow across the RPE is driven by an osmotic gradient in the cleft gap between adjacent cells. Moreover, the model estimates how water flux is modified in response to inhibition of membrane ion channels and carbonic anhydrase (CA). It provides a possible explanation for how CA inhibitors, which are used clinically to prevent fluid accumulation in the SRS, may be acting.
Exploring the visual world of fossilized and modern fungus gnat eyes (Diptera: Keroplatidae) with X-ray microtomography
Authors: Taylor Gavin J. , Hall Stephen A. , Gren Johan A. , Baird Emily
Published: February 2020

Animal eyes typically possess specialized regions for guiding different behavioural tasks within their specific visual habitat. These specializations, and evolutionary changes to them, can be crucial for understanding an animal's ecology. Here, we explore how the visual systems of some of the smallest flying insects, fungus gnats, have adapted to different types of forest habitat over time (approx. 30 Myr to today). Unravelling how behavioural, environmental and phylogenetic factors influence the evolution of visual specializations is difficult, however, because standard quantitative techniques often require fresh tissue and/or provide data in eye-centric coordinates that prevent reliable comparisons between species with different eye morphologies. Here, we quantify the visual world of three gnats from different time periods and habitats using X-ray microtomography to create high-resolution three-dimensional models of the compound eyes of specimens in different preservation states—fossilized in amber, dried or stored in ethanol. We present a method for analysing the geometric details of individual corneal facets and for estimating and comparing the sensitivity, spatial resolution and field of view of species across geographical space and evolutionary time. Our results indicate that, despite their miniature size, fungus gnats do have variations in visual properties across their eyes. We also find some indication that these visual specializations vary across species and may represent adaptations to their different forest habitats. Overall, the findings demonstrate how such investigations can be used to study the evolution of visual specializations—and sensory ecology in general—across a range of insect taxa from different geographical locations and across time.
The interpretation of urban scaling analysis in time
Authors: Bettencourt Luís M. A. , Yang Vicky Chuqiao , Lobo José , Kempes Christopher P. , Rybski Diego , Hamilton Marcus J.
Published: February 2020

Scaling is a general analytical framework used by many disciplines—from physics to biology and the social sciences—to characterize how population-averaged properties of a collective vary with its size. The observation of scale invariance over some range identifies general system types, be they ideal gases, ecosystems or cities. The use of scaling in the analysis of cities quantifies many of their arguably fundamental general characteristics, especially their capacity to create interrelated economies of scale in infrastructure and increasing returns to scale in socio-economic activities. However, the measurement of these effects, and the relationship of observable parameters to theory, hinge on how scaling analysis is used empirically. Here, we show how two equivalent approaches to urban scaling—cross-sectional and temporal—lead to the measurement of different mixtures of the same fundamental parameters describing pure scale and pure temporal phenomena. Specifically, temporal exponents are sensitive to the intensive growth of urban quantities and to circumstances when population growth vanishes, leading to instabilities and infinite divergences. These spurious effects are avoided in cross-sectional scaling, which is more common and closer to theory in terms of quantitative testable expectations for its parameters.
DNA topoisomerase IIIβ promotes cyst generation by inducing cyst wall protein gene expression in
Giardia lamblia
Authors: Sun Chin-Hung , Weng Shih-Che , Wu Jui-Hsuan , Tung Szu-Yu , Su Li-Hsin , Lin Meng-Hsuan , Lee Gilbert Aaron
Published: February 2020

Giardia lamblia
causes waterborne diarrhoea by transmission of infective cysts. Three cyst wall proteins are highly expressed in a concerted manner during encystation of trophozoites into cysts. However, their gene regulatory mechanism is still largely unknown. DNA topoisomerases control topological homeostasis of genomic DNA during replication, transcription and chromosome segregation. They are involved in a variety of cellular processes including cell cycle, cell proliferation and differentiation, so they may be valuable drug targets.
Giardia lamblia
possesses a type IA DNA topoisomerase (TOP3β) with similarity to the mammalian topoisomerase IIIβ. We found that TOP3β was upregulated during encystation and it possessed DNA-binding and cleavage activity. TOP3β can bind to the
cwp
promoters
in vivo
using norfloxacin-mediated topoisomerase immunoprecipitation assays. We also found TOP3β can interact with MYB2, a transcription factor involved in the coordinate expression of
cwp1-3
genes during encystation. Interestingly, overexpression of TOP3β increased expression of
cwp1
-
3
and
myb2
genes and cyst formation. Microarray analysis confirmed upregulation of
cwp1-3
and
myb2
genes by TOP3β. Mutation of the catalytically important Tyr residue, deletion of C-terminal zinc ribbon domain or further deletion of partial catalytic core domain reduced the levels of cleavage activity,
cwp1-3
and
myb2
gene expression, and cyst formation. Interestingly, some of these mutant proteins were mis-localized to cytoplasm. Using a CRISPR/Cas9 system for targeted disruption of
top3β
gene, we found a significant decrease in
cwp1-3
and
myb2
gene expression and cyst number. Our results suggest that TOP3β may be functionally conserved, and involved in inducing
Giardia
cyst formation.
Differential equation-based minimal model describing metabolic oscillations in
Bacillus subtilis
biofilms
Authors: Garde Ravindra , Ibrahim Bashar , Kovács Ákos T. , Schuster Stefan
Published: February 2020

Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in
Bacillus subtilis
biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
Flexibility in reaction time analysis: many roads to a false positive?
Authors: Morís Fernández Luis , Vadillo Miguel A.
Published: February 2020

In the present article, we explore the influence of undisclosed flexibility in the analysis of reaction times (RTs). RTs entail some degrees of freedom of their own, due to their skewed distribution, the potential presence of outliers and the availability of different methods to deal with these issues. Moreover, these degrees of freedom are usually not considered part of the analysis itself, but preprocessing steps that are contingent on data. We analysed the impact of these degrees of freedom on the false-positive rate using simulations over real and simulated data. When several preprocessing methods are used in combination, the false-positive rate can easily rise to 17%. This figure becomes more concerning if we consider that more degrees of freedom are awaiting down the analysis pipeline, potentially making the final false-positive rate much higher.
European and Asian contribution to the genetic diversity of mainland South American chickens
Authors: Herrera Michael B. , Kraitsek Spiridoula , Alcalde Jose A. , Quiroz Daniel , Revelo Herman , Alvarez Luz A. , Rosario Millor F. , Thomson Vicki , Jianlin Han , Austin Jeremy J. , Gongora Jaime
Published: February 2020

Chickens (Gallus gallus domesticus) from the Americas have long been recognized as descendants of European chickens, transported by early Europeans since the fifteenth century. However, in recent years, a possible pre-Columbian introduction of chickens to South America by Polynesian seafarers has also been suggested. Here, we characterize the mitochondrial control region genetic diversity of modern chicken populations from South America and compare this to a worldwide dataset in order to investigate the potential maternal genetic origin of modern-day chicken populations in South America. The genetic analysis of newly generated chicken mitochondrial control region sequences from South America showed that the majority of chickens from the continent belong to mitochondrial haplogroup E. The rest belongs to haplogroups A, B and C, albeit at very low levels. Haplogroup D, a ubiquitous mitochondrial lineage in Island Southeast Asia and on Pacific Islands is not observed in continental South America. Modern-day mainland South American chickens are, therefore, closely allied with European and Asian chickens. Furthermore, we find high levels of genetic contributions from South Asian chickens to those in Europe and South America. Our findings demonstrate that modern-day genetic diversity of mainland South American chickens appear to have clear European and Asian contributions, and less so from Island Southeast Asia and the Pacific Islands. Furthermore, there is also some indication that South Asia has more genetic contribution to European chickens than any other Asian chicken populations.
Mechanistic investigations on Pinnick oxidation: a density functional theory study
Authors: Hussein Aqeel A. , Al-Hadedi Azzam A. M. , Mahrath Alaa J. , Moustafa Gamal A. I. , Almalki Faisal A. , Alqahtani Alaa , Shityakov Sergey , Algazally Moaed E.
Published: February 2020

A computational study on Pinnick oxidation of aldehydes into carboxylic acids using density functional theory (DFT) calculations has been evaluated with the (SMD)-M06-2X/aug-pVDZ level of theory, leading to an important understanding of the reaction mechanism that agrees with the experimental observations and explaining the substantial role of acid in driving the reaction. The DFT results elucidated that the first reaction step (FRS) proceeds in a manner where chlorous acid reacts with the aldehyde group through a distorted six-membered ring transition state to give a hydroxyallyl chlorite intermediate that undergoes a pericyclic fragmentation to release the carboxylic acid as a second reaction step (SRS).
1
H NMR experiments and simulations showed that hydrogen bonding between carbonyl and
t
-butanol is unlikely to occur. Additionally, it was found that the FRS is a rate-determining and thermoneutral step, whereas SRS is highly exergonic with a low energetic barrier due to the Cl(III) → Cl(II) reduction. Frontier molecular orbital analysis, intrinsic reaction coordinate, molecular dynamics and distortion/interaction analysis further supported the proposed mechanism.
Dramatic decline of northern bat
Eptesicus nilssonii
in Sweden over 30 years
Authors: Rydell Jens , Elfström Marcus , Eklöf Johan , Sánchez-Navarro Sonia
Published: February 2020

We monitored northern bat
Eptesicus nilssonii
(Keyserling & Blasius, 1839) acoustically along a 27 km road transect at weekly intervals in 1988, 1989 and 1990, and again in 2016 and 2017. The methodology of data collection and the transect were the same throughout, except that the insect-attracting mercury-vapour street-lights along parts of the road were replaced by sodium lights between the two survey periods. Counts along sections of the transect with and without street-lights were analysed separately. The frequency of bat encounters in unlit sections showed an average decline of 3.0% per year, corresponding to a reduction of 59% between 1988 and 2017. Sections with street-lights showed an 85% decline over the same period (6.3% per year). The decline represents a real reduction in the abundance of bats rather than an artefact of changed distribution of bats away from roads. Our study conforms with another long-term survey of the same species on the Baltic island of Gotland. Our results agree with predictions based on climate change models. They also indicate that the decline was caused directly by the disuse of the insect-attracting mercury-vapour street-lights, which may have resulted in lower availability of preferred prey (moths). In the 1980s,
E. nilssonii
was considered the most common bat in Sweden, but the subsequent decline would rather qualify it for vulnerable or endangered status in the national Red List of Threatened Species.
Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts
Authors: Zou Hong , Jakovlić Ivan , Zhang Dong , Hua Cong-Jie , Chen Rong , Li Wen-Xiang , Li Ming , Wang Gui-Tang
Published: February 2020

The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome ofAsotana magnifica(Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.
Migrating birds rapidly increase constitutive immune function during stopover
Authors: Eikenaar Cas , Hessler Sven , Hegemann Arne
Published: February 2020

Migratory flight is physiologically highly demanding and has been shown to negatively affect multiple parameters of constitutive immune function (CIF), an animal's first line of physiological defence against infections. In between migratory flights, most birds make stopovers, periods during which they accumulate fuel for the next flight(s). Stopovers are also commonly thought of as periods of rest and recovery, but what this encompasses is largely undefined. Here, we show that during stopover, northern wheatears
Oenanthe oenanthe,
a long-distance migratory bird, can rapidly increase constitutive innate immune function. We caught and temporarily caged birds under ad libitum food conditions at a stopover site in autumn. Within 2 days, most birds significantly increased complement activity and their ability to kill microbes. Changes in immune function were not related to the birds' food intake or extent of fuel accumulation. Our study suggests that stopovers may not only be important to refuel but also to restore immune function. Additionally, the increase in CIF could help migrating birds to deal with novel pathogens they may encounter at stopover sites.
Substrate use drives the macroevolution of mammalian tail length diversity
Authors: Mincer Sarah T. , Russo Gabrielle A.
Published: February 2020

External length is one of the most conspicuous aspects of mammalian tail morphological diversity. Factors that influence the evolution of tail length diversity have been proposed for particular taxa, including habitat, diet, locomotion and climate. However, no study to date has investigated such factors at a large phylogenetic scale to elucidate what drives tail length evolution in and across mammalian lineages. We use phylogenetic comparative methods to testa priorihypotheses regarding proposed factors influencing tail length, explore possible interactions between factors using evolutionary best-fit models, and map evolutionary patterns of tail length for specific mammalian lineages. Across mammals, substrate use is a significant factor influencing tail length, with arboreal species maintaining selection for longer tails. Non-arboreal species instead exhibit a wider range of tail lengths, secondarily influenced by differences in locomotion, diet and climate. Tail loss events are revealed to occur in the context of both long and short tails and influential factors are clade dependent. Some mammalian groups (e.g.Macaca; primates) exhibit elevated rates of tail length evolution, indicating that morphological evolution may be accelerated in groups characterized by diverse substrate use, locomotor modes and climate.
Circulating tumor DNA in neoadjuvant treated breast cancer reflects response and survival
Authors: Magbanua Mark Jesus M. , Brown-Swigart Lamorna , Wu Hsin-Ta , Hirst Gillian L. , Yau Christina , Wolf Denise M. , Tin Antony , Salari Raheleh , Shchegrova Svetlana , Pawar Hemant , Delson Amy L. , DeMichele Angela , Liu Minetta C. , Chien A. Jo , Asare Smita , Lin Cheng-Ho J. , Billings Paul , Aleshin Alexey , Sethi Himanshu , Louie Maggie , Zimmermann Bernhard , Esserman Laura J. , van ’t Veer Laura J.
Published: February 2020

Pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) is strongly associated with favorable outcome. We examined the utility of serial circulating tumor DNA (ctDNA) testing for predicting pCR and risk of metastatic recurrence in 84 high-risk early breast cancer patients treated in the neoadjuvant I-SPY 2 TRIAL. Cell-free DNA (cfDNA) was isolated from 291 plasma samples collected at pretreatment (T0), 3 weeks after initiation of paclitaxel (T1), between paclitaxel and anthracycline regimens (T2), or prior to surgery (T3). A personalized ctDNA test was designed to detect 16 patient-specific mutations (from whole exome sequencing of pretreatment tumor) in cfDNA by ultra-deep sequencing. At T0, 61 of 84 (73%) patients were ctDNA-positive, which decreased over time (T1-35%; T2-14%; T3-9%). Patients who remained ctDNA-positive at T1 were significantly more likely to have residual disease after NAC (83% non-pCR) compared to those who cleared ctDNA (52% non-pCR; OR 4.33, P=0.012). After NAC, all patients who achieved pCR were ctDNA-negative (n=17, 100%). For those who did not achieve pCR (n=43), ctDNA-positive patients (14%) had significantly increased risk of metastatic recurrence (HR 10.4; 95% CI, 2.3–46.6); interestingly, patients who did not achieve pCR but were ctDNA-negative (86%) had excellent outcome, similar to those who achieved pCR (HR 1.4; 95% CI, 0.15–13.5). Lack of ctDNA clearance was a significant predictor of poor response and metastatic recurrence, while clearance was associated with improved survival regardless of pCR status. Personalized monitoring of ctDNA during NAC may aid in real-time assessment of treatment response and help fine-tune pCR as a surrogate endpoint of survival.
Network-based Drug Repurposing for Human Coronavirus
Authors: Zhou Yadi , Hou Yuan , Shen Jiayu , Huang Yin , Martin William , Cheng Feixiong
Published: February 2020

Human Coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle east respiratory syndrome coronavirus (MERS-CoV), and 2019 novel coronavirus (2019-nCoV), lead global epidemics with high morbidity and mortality. However, there are currently no effective drugs targeting 2019-nCoV. Drug repurposing, represented as an effective drug discovery strategy from existing drugs, could shorten the time and reduce the cost compared to de novo drug discovery. In this study, we present an integrative, antiviral drug repurposing methodology implementing a systems pharmacology-based network medicine platform, quantifying the interplay between the HCoV-host interactome and drug targets in the human protein-protein interaction network. Phylogenetic analyses of 15 HCoV whole genomes reveal that 2019-nCoV has the highest nucleotide sequence identity with SARS-CoV (79.7%) among the six other known pathogenic HCoVs. Specifically, the envelope and nucleocapsid proteins of 2019-nCoV are two evolutionarily conserved regions, having the sequence identities of 96% and 89.6%, respectively, compared to SARS-CoV. Using network proximity analyses of drug targets and known HCoV-host interactions in the human protein-protein interactome, we computationally identified 135 putative repurposable drugs for the potential prevention and treatment of HCoVs. In addition, we prioritized 16 potential anti-HCoV repurposable drugs (including melatonin, mercaptopurine, and sirolimus) that were further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. Finally, we showcased three potential drug combinations (including sirolimus plus dactinomycin, mercaptopurine plus melatonin, and toremifene plus emodin) captured by the ‘Complementary Exposure’ pattern: the targets of the drugs both hit the HCoV-host subnetwork, but target separate neighborhoods in the human protein-protein interactome network. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations toward future clinical trials for HCoVs.
Specific ACE2 Expression in Cholangiocytes May Cause Liver Damage After 2019-nCoV Infection
Authors: Chai Xiaoqiang , Hu Longfei , Zhang Yan , Han Weiyu , Lu Zhou , Ke Aiwu , Zhou Jian , Shi Guoming , Fang Nan , Fan Jia , Cai Jiabin , Fan Jue , Lan Fei
Published: February 2020

A newly identified coronavirus, 2019-nCoV, has been posing significant threats to public health since December 2019. ACE2, the host cell receptor for severe acute respiratory syndrome coronavirus (SARS), has recently been demonstrated in mediating 2019-nCoV infection. Interestingly, besides the respiratory system, substantial proportion of SARS and 2019-nCoV patients showed signs of various degrees of liver damage, the mechanism and implication of which have not yet been determined. Here, we performed an unbiased evaluation of cell type specific expression of ACE2 in healthy liver tissues using single cell RNA-seq data of two independent cohorts, and identified specific expression in cholangiocytes. The results indicated that virus might directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes. This finding suggested the liver abnormalities of SARS and 2019-nCoV patients may not be due to hepatocyte damage, but cholangiocyte dysfunction and other causes such as drug induced and systemic inflammatory response induced liver injury. Our findings indicate that special care of liver dysfunction should be installed in treating 2019-nCoV patients during the hospitalization and shortly after cure.
Habitat selection drives dietary specialisation inSorex minutus
Authors: Ware Roselyn L. , Booker Annie L. , Allaby Francesca R. , Allaby Robin G.
Published: February 2020

To meet their demand for food, Eurasian pygmy shrews (Sorex minutus) require large territories, normally in fields, woodlands, and meadows. Their high metabolism and food requirement often leads to high mortality during winter. However, evidence of shrews in the roof voids of residential buildings has recently been observed, contrary to ecological expectations. Here, five faecal samples collected from different locations were studied by metagenomic analysis to gain information about the shrew’s diets and environments. Two of the samples were collected from novel indoor locations, while the other three were from outdoors in ‘traditional’ habitats. Distinct differences were observed between the diets of the two populations, suggesting a commensal niche expansion has occurred inS. minutus.We found thatS. minutusexploit man-made spaces for foraging, potentially at the cost of a greater parasite burden.