bluuebunny/crossref_metadata_2025 huggingface dataset:
Hearing the voice of Donbas: art and literature as forms of cultural protest during war
Authors: Ilchuk Yuliya
Published: December 2016

This paper analyzes literary, visual, and street art works of writers and artists from Eastern Ukraine produced during 2014. Two Donetsk artists, Serhii Zakharov and Anzhela Dzherikh, and two Luhansk writers, Serhii Zhadan and Olena Stepova, play with the myth of the proletarian Donbas, on the one hand, and debunk the popular perception of Donbas people as being in consent with the politics of the self-proclaimed Donetsk and Luhansk People's Republics, on the other. They explore familiar tropes and images of Donbas and use guerrilla tactics (shock effects, provocativeness, and deception) to initiate public reaction to the war. Their works are united by their search for a shared communication space and direct access to the audience on occupied territories. These artists challenge the accepted perception of Donbas as a free but uncivilized space and participate in the creation of a new Donbas text. The interaction between politics, art, and activism makes their voices and vision powerful and infectious and can help achieve civic consolidation in Donbas.
A Comparison of Sampling Gears for Capturing Juvenile Silver Carp in River–Floodplain Ecosystems
Authors: Collins Scott F. , Diana Matthew J. , Butler Steven E. , Wahl David H.
Published: December 2016

Effective management and monitoring programs require confidence regarding basic biological sampling. Gear comparisons are often required to determine the most effective techniques. Such is the case for populations of invasive Asian carps Hypophthalmichthys spp., which have recently occurred in large numbers throughout sections of the Mississippi River basin. We tested five gears (mini-fyke nets, beach seine, purse seine, pulsed-DC electrofishing, and gill net) that targeted juvenile (age 0) Silver Carp H. molitrix at sites along the Illinois River during 2014 and 2015 to determine the most effective ones for age-0 Silver Carp. We considered the most cost-effective gear to be the one that provided the largest catch at a minimal expenditure of labor. Mini-fyke nets were the most effective at collecting large numbers of age-0 Silver Carp, followed in decreasing order by beach seines, pulsed-DC electrofishing, purse seines, and gill nets. The smallest Silver Carp were caught in beach seines and the largest were caught in gill nets, and there was considerable variation in size distributions among gears. However, when we considered cost-effectiveness in terms of labor hours for each gear, both beach seines and mini-fyke nets had similar and overlapping labor expenditures. Gill nets and purse seines were not cost-effective, as they required more labor and had lower overall catch rates.

Received May 23, 2016; accepted September 19, 2016Published online December 21, 2016
Beyond forceful measures: Tanzania’s ‘war on poaching’ needs diversified strategies more than militarised tactics
Authors: Mabele Mathew Bukhi
Published: December 2016

This Briefing looks at the existing strategies to confront poaching in Tanzania. With militarised strategies becoming dominant, the Briefing argues for diversified tactics to counter ‘poaching’, suggesting that bureaucrats and conservationists must put more efforts into addressing root causes of poaching through strategies that go beyond coercive measures.
Floral Mimicry
Authors: Johnson Steven D. , Schiestl Florian P.
Published: December 2016

Mimicry is a classic example of adaptation through natural selection. The traditional focus of mimicry research has been on defense in animals (protective mimicry), but there is now also a highly developed and rapidly growing body of research on floral mimicry in plants. Being literally rooted to one spot, plants generally have to use food bribes to cajole animals into acting as couriers for their pollen. Plants that lack these food rewards often deploy elaborate color and scent signals in order to mimic food sources, oviposition sites, or mating partners of particular animals, and thereby exploit these animals for the purposes of pollination. This book addresses the question of whether the evolutionary and ecological principles that were developed for protective mimicry in animals also apply to floral mimicry in plants. Visual, olfactory, and tactile signals can all be important in floral mimicry systems. The traditional focus has been on visual cues, but there is increasing evidence that some forms of mimicry, notably sexual and oviposition-site mimicry, are largely based on chemical cues. The molecular basis for these signals, their role in cognitive misclassification of flowers by pollinators, and the implications of these signals for plant speciation are among the topics covered in the book. The chapters of this book are designed to highlight particular systems of floral mimicry and to integrate them into the broader theory of mimicry.
How Many Fasces?
Authors: Syme Ronald
Published: December 2016

This paper provides a discussion of the concept of imperium between late Republic and Augustan period, which is developed through the study of a specific problem: the number of fasces that Roman magistrates were allowed to display in the performance of their duties, both in Rome and outside the city, and Augustus’s choice to display twelve fasces. The detailed exploration of this issue leads to a number of further remarks on the nature of Augustus’s power, on its constitutional and religious definition, and on the development of the notion of imperium between the late Republic and the early Principate. The difference between consular and proconsular imperium is given special consideration, and is singled out as an important feature of Augustus’s constitutional arrangements.
Objects of Thought
Authors: Priest Graham
Published: December 2016

Chapter 3 provides a semantics for intentional predicates. The semantics proceeds in terms of objects which may or may not exist. An appendix discusses accounts of intentionality in Medieval Logic.
Phenomenological Pointing
Authors: Priest Graham
Published: December 2016

Chapter 11 takes up the issue of purely phenomenological pointing. Many have claimed that such a notion is philosophically incoherent. Several reasons why one might suppose it to be so are disentangled, and all of them may be rebuffed.
Neighbourhood Semantics
Authors: Priest Graham
Published: December 2016

Chapter 15 concerns a quite different semantics for intentional operators, neighbourhood semantics. This is similar to the neighbourhood semantics for modal logics. Such a semantics is presented, and its ramifications explored
Family and Business During the Industrial Revolution
Authors: Barker Hannah
Published: December 2016

Small businesses were at the heart of the economic growth and social transformation that characterized the Industrial Revolution in Britain. In towns across north-west England, shops and workshops dominated the streetscape, and helped to satisfy an increasing desire for consumer goods. Yet, despite their significance, we know surprisingly little about these firms and the people who ran them, for, while those engaged in craft-based manufacturing, retailing, and allied trades constituted a significant proportion of the urban population, they have been generally overlooked by historians. Instead, our view of the world of business is more usually taken up by narratives of particularly successful firms, and especially those involved in new modes of production. By examining some of the forgotten businesses of the Industrial Revolution, and the men and women who worked in them, this book presents a largely unfamiliar commercial world. Its approach, which spans economic, social, and cultural history, as well as encompassing business history and the histories of the emotions, space, and material culture, alongside studies of personal testimony, testatory practice, and property ownership, tests current understandings of gender, work, family, class, and power in the late eighteenth and early nineteenth centuries. It provides us with new insights into the lives of ordinary men and women in trade, whose relatively mundane lives are easily overlooked, but who were central to the story of a pivotal period in British history.
Metallicity-dependent kinematics and morphology of the Milky Way bulge
Authors: Athanassoula E. , Rodionov S. A. , Prantzos N.
Published: December 2016

We use N-body chemo-dynamic simulations to study the coupling between morphology, kinematics and metallicity of the bar/bulge region of our Galaxy. We make qualitative comparisons of our results with available observations and find very good agreement. We conclude that this region is complex, since it comprises several stellar components with different properties – i.e. a boxy/peanut bulge, thin and thick disc components, and, to lesser extents, a disky pseudo-bulge, a stellar halo and a small classical bulge – all cohabiting in dynamical equilibrium. Our models show strong links between kinematics and metallicity, or morphology and metallicity, as already suggested by a number of recent observations. We discuss and explain these links.
GABA (γ-Aminobutyric Acid) Uptake Via the GABA Permease GabP Represses Virulence Gene Expression inPseudomonas syringaepv. tomato DC3000
Authors: McCraw S. L. , Park D. H. , Jones R. , Bentley M. A. , Rico A. , Ratcliffe R. G. , Kruger N. J. , Collmer A. , Preston G. M.
Published: December 2016

The nonprotein amino acid γ-aminobutyric acid (GABA) is the most abundant amino acid in the tomato (Solanum lycopersicum) leaf apoplast and is synthesized by Arabidopsis thaliana in response to infection by the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (hereafter called DC3000). High levels of exogenous GABA have previously been shown to repress the expression of the type III secretion system (T3SS) in DC3000, resulting in reduced elicitation of the hypersensitive response (HR) in the nonhost plant tobacco (Nicotiana tabacum). This study demonstrates that the GABA permease GabP provides the primary mechanism for GABA uptake by DC3000 and that the gabP deletion mutant ΔgabP is insensitive to GABA-mediated repression of T3SS expression. ΔgabP displayed an enhanced ability to elicit the HR in young tobacco leaves and in tobacco plants engineered to produce increased levels of GABA, which supports the hypothesis that GABA uptake via GabP acts to regulate T3SS expression in planta. The observation that P. syringae can be rendered insensitive to GABA through loss of gabP but that gabP is retained by this bacterium suggests that GabP is important for DC3000 in a natural setting, either for nutrition or as a mechanism for regulating gene expression.

[Formula: see text] Copyright © 2016 The Author(s). This is an open access article distributed under the CC BY Attribution 4.0 International license .
Evaluation of Plant Health Programs Using Outcome Mapping
Authors: Testen Anna L. , Mamiro Delphina P. , Nahson Jackson , Mtui Hosea D. , Miller Sally A.
Published: December 2016

Evaluation is a necessary component of plant health programs designed for and implemented in research, extension, and international development settings. Outcome Mapping is a method of program planning, observation, and assessment in which changes in behavior, relationships, or actions of the target groups (boundary partners) are evaluated during program implementation. Outcome Mapping was used to evaluate stakeholder participation in participatory variety selection trials for tomato and soil health training for tomato farmers in Tanzania. Boundary partner participation varied between the three villages evaluated and predicted adoption of new varieties assessed one year later. Outcome Mapping was valuable in tracking progress during program implementation and can indicate long-term impacts of the program.

Accepted for publication 21 November 2016.
Pelvic Floor Ultrasound: A Review
Authors: DIETZ HANS PETER
Published: December 2016

Female pelvic floor dysfunction encompasses a number of prevalent conditions and includes pelvic organ prolapse, urinary and fecal incontinence, obstructed defecation, and sexual dysfunction. In most cases neither etiology nor pathophysiology are well understood. Imaging has great potential to enhance both research and clinical management capabilities, and to date this potential is underutilized. Of the available techniques such as x-ray, computed tomography, magnetic resonance imaging, and ultrasound, the latter is generally superior for pelvic floor imaging, especially in the form of perineal or translabial imaging. The technique is safe, simple, cheap, easily accessible and provides high spatial and temporal resolutions.
Barriers to Universal Prescribing of Antiretroviral Therapy by HIV Care Providers in the United States, 2013–2014
Authors: Weiser John , Brooks John T. , Skarbinski Jacek , West Brady T. , Duke Christopher C. , Gremel Garrett W. , Beer Linda
Published: December 2016

Introduction:

HIV treatment guidelines recommend initiating antiretroviral therapy (ART) regardless of CD4 cell (CD4) count, barring contraindications or barriers to treatment. An estimated 6% of persons receiving HIV care in 2013 were not prescribed ART. We examined reasons for this gap in the care continuum.

Methods:

During 2013–2014, we surveyed a probability sample of HIV care providers, of whom 1234 returned surveys (64.0% adjusted response rate). We estimated percentages of providers who followed guidelines and their characteristics, and who deferred ART prescribing for any reason.

Results:

Barring contraindications, 71.2% of providers initiated ART regardless of CD4 count. Providers less likely to initiate had caseloads ≤20 vs. >200 patients [adjusted prevalence ratios (aPR) 0.69, 95% confidence interval (CI): 0.47 to 1.02, P = 0.03], practiced at non–Ryan White HIV/AIDS Program-funded facilities (aPR 0.85, 95% CI: 0.74 to 0.98, P = 0.02), or reported pharmaceutical assistance programs provided insufficient medication to meet patients' needs (aPR 0.79, 95% CI: 0.65 to 0.98, P = 0.02). In all, 17.0% never deferred prescribing ART, 69.6% deferred for 1%–10% of patients, and 13.3% deferred for >10%. Among providers who had deferred ART, 59.4% cited patient refusal as a reason in >50% of cases, 31.1% reported adherence concerns because of mental health disorders or substance abuse, and 21.4% reported adherence concerns because of social problems, eg, homelessness, as factors in >50% of cases when deferring ART.

Conclusions:

An estimated 29% of HIV care providers had not adopted recommendations to initiate ART regardless of CD4 count, barring contraindications, or barriers to treatment. Low-volume providers and those at non–Ryan White HIV/AIDS Program-funded facilities were less likely to follow this guideline. Among all providers, leading reasons for deferring ART included patient refusal and adherence concerns.
Neuropsychological Testing in Pathologically Verified Alzheimer Disease and Frontotemporal Dementia
Authors: Ritter Aaron R. , Leger Gabriel C. , Miller Justin B. , Banks Sarah J.
Published: December 2016

Background/Aims:

Differences in cognition between frontotemporal dementia (FTD) and Alzheimer disease (AD) are well described in clinical cohorts, but have rarely been confirmed in studies with pathologic verification. For emerging therapeutics to succeed, determining underlying pathology early in the disease course is increasingly important. Neuropsychological evaluation is an important component of the diagnostic workup for AD and FTD. Patients with FTD are thought to have greater deficits in language and executive function while patients with AD are more likely to have deficits in memory.

Objectives:

To determine if performance on initial cognitive testing can reliably distinguish between patients with frontotemporal lobar degeneration (FTLD) and AD neuropathology. In addition, are there other factors of the neuropsychological assessment that can be used to enhance the accuracy of underlying pathology?

Methods:

Using a logistic regression we retrospectively compared neurocognitive performance on initial evaluation of 106 patients with pathologically verified FTLD (pvFTLD), with 558 pathologically verified AD (pvAD) patients from the National Alzheimer’s Coordinating Center using data from the Uniform Data Set (UDS) and the neuropathology data set.

Results:

As expected, pvFTLD patients were younger, demonstrated better memory performance, and had more neuropsychiatric symptoms than pvAD patients. Other results were less predictable: pvFTLD patients performed better on one test of executive function (trail making test part B) but worse on another (digit span backward). Performance on language testing did not strongly distinguish the 2 groups. To determine what factors led to a misdiagnosis of AD in patients with FTLD, we further analyzed a small group of pvFTLD patients. These patients demonstrated older age and lower Neuropsychiatric Inventory Questionnaire counts compared with accurately diagnosed cases.

Conclusions:

Other than memory, numerical scores of neurocognitive performance on the UDS are of limited value in differentiating FTLD from AD at the initial visit. These results highlight the difficulty of obtaining an accurate early diagnosis of FTLD and argue for adding supplemental tests to those included in the UDS to assess cognition in FTD and AD patients.
Micropyle number is associated with elevated female promiscuity in Lepidoptera
Authors: Iossa Graziella , Gage Matthew J. G. , Eady Paul E.
Published: December 2016

In the majority of insects, sperm fertilize the egg via a narrow canal through the outer chorion called the micropyle. Despite having this one primary function, there is considerable unexplained variation in the location, arrangement and number of micropyles within and between species. Here, we examined the relationship between micropyle number and female mating pattern through a comparative analysis across Lepidoptera. Three functional hypotheses could explain profound micropylar variation: (i) increasing micropyle number reduces the risk of infertility through sperm limitation in species that mate infrequently; (ii) decreasing micropyle number reduces the risk of pathological polyspermy in species that mate more frequently; and (iii) increasing micropyle number allows females to exert greater control over fertilization within the context of post-copulatory sexual selection, which will be more intense in promiscuous species. Micropyle number was positively related to the degree of female promiscuity as measured by spermatophore count, regardless of phylogenetic signal, supporting the hypothesis that micropyle number is shaped by post-copulatory sexual selection. We discuss this finding in the context of cryptic female choice, sperm limitation and physiological polyspermy.
Genetic colour polymorphism is associated with avian malarial infections
Authors: Gangoso Laura , Gutiérrez-López Rafael , Martínez-de la Puente Josué , Figuerola Jordi
Published: December 2016

Individual genetic diversity is predicted to influence host–parasite interactions. Together with the genes directly associated with immune responses, variation in genes regulating vertebrate melanin-based pigmentation may play an important role in these interactions, mainly through the pleiotropic effects that affect colour-specific physiology, behaviour and immunity. Here, we test the hypothesis that the prevalence of avian malarial parasites differs between phenotypes in a raptor species in which the genetic basis of colour polymorphism and its pleiotropic effects over immune functions are known. We found that dark morphs had a higher prevalence of
Plasmodium
parasites than pale ones but detected no such association for
Haemoproteus
. This pattern may be associated with unequal exposure to vectors or, as suggested by our circumstantial evidence, to a differential ability to mount an immune response against blood parasites.
Intensity-based axial localization approaches for multifocal plane microscopy
Authors: Velmurugan Ramraj , Chao Jerry , Ram Sripad , Ward E. Sally , Ober Raimund J.
Published: December 2016

Multifocal plane microscopy (MUM) can be used to visualize biological samples in three dimensions over large axial depths and provides for the high axial localization accuracy that is needed in applications such as the three-dimensional tracking of single particles and superresolution microscopy. This report analyzes the performance of intensity-based axial localization approaches as applied to MUM data using Fisher information calculations. In addition, a new non-parametric intensity-based axial location estimation method, Multi-Intensity Lookup Algorithm (MILA), is introduced that, unlike typical intensity-based methods that make use of a single intensity value per data image, utilizes multiple intensity values per data image in determining the axial location of a point source. MILA is shown to be robust against potential bias induced by differences in the sub-pixel location of the imaged point source. The method's effectiveness on experimental data is also evaluated.
FlashPCA2: principal component analysis of biobank-scale genotype datasets
Authors: Abraham Gad , Qiu Yixuan , Inouye Michael
Published: December 2016

Motivation

Principal component analysis (PCA) is a crucial step in quality control of genomic data and a common approach for understanding population genetic structure. With the advent of large genotyping studies involving hundreds of thousands of individuals, standard approaches are no longer computationally feasible. We present FlashPCA2, a tool that can perform PCA on 1 million individuals faster than competing approaches, while requiring substantially less memory.

Availability

https://github.com/gabraham/ashpca

Contact

gad.abraham@unimelb.edu.au
A dense brown trout (Salmo trutta) linkage map reveals recent chromosomal rearrangements in theSalmogenus and the impact of selection on linked neutral diversity
Authors: Leitwein Maeva , Guinand Bruno , Pouzadoux Juliette , Desmarais Erick , Berrebi Patrick , Gagnaire Pierre-Alexandre
Published: December 2016

High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socio-economically important species heavily impacted by human activities. A total of 3,977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison betweenS. truttaand its sister speciesSalmo salarrevealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after theS.salar/S.truttaspeciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate inS.truttaat 3,721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high density linkage map provides a useful genomic resource for future aquaculture, conservation and eco-evolutionary studies in brown trout.
DataMed: Finding useful data across multiple biomedical data repositories
Authors: Ohno-Machado L , Sansone SA , Alter G , Fore I , Grethe J , Xu H , Gonzalez-Beltran Alejandra , Rocca-Serra Philippe , Soysal Ergin , Zong Nansu , Kim H
Published: December 2016

The value of broadening searches for data across multiple repositories has been identified by the biomedical research community. As part of the NIH Big Data to Knowledge initiative, we work with an international community of researchers, service providers and knowledge experts to develop and test a data index and search engine, which are based on metadata extracted from various datasets in a range of repositories. DataMed is designed to be, for data, what PubMed has been for the scientific literature. DataMed supports Findability and Accessibility of datasets. These characteristics - along with Interoperability and Reusability - compose the four FAIR principles to facilitate knowledge discovery in today’s big data-intensive science landscape.
Quantifying the relationship between pollinator behavior and plant reproductive isolation
Authors: Hopkins Robin
Published: December 2016

Pollinator behavior is an important contributor to reproductive isolation in plants. Despite hundreds of years of empirical research, we lack a quantitative framework for evaluating how variation in pollinator behavior causes variation in reproductive isolation in plants. Here I present a model describing how two aspects of pollinator behavior – constancy and preference – lead to reproductive isolation in plants. This model is motivated by two empirical observations: most co-occurring plants vary in frequency over space and time and most plants have multiple pollinators that differ in behavior. These two observations suggest a need to understand how plant frequency and pollinator frequency influence reproductive isolation between co-occurring plants. My model predicts how the proportion of heterospecific matings varies over plant frequencies given pollinator preference and constancy. I find that the shape of this relationship is dependent on the strength of pollinator behavior. Additionally, my model incorporates multiple pollinators with different behaviors to predict the proportion of heterospecific matings across pollinator frequencies. I find that when two pollinators display different strength constancy the total proportion of heterospecific matings is simply the average proportion of heterospecific matings predicted for each pollinator. When pollinators vary in their preference the pollinator with the stronger preference disproportionally contributes to the predicted proportion of total heterospecific matings. I apply this model to examples of pollinator-mediated reproductive isolation inPhloxand inMimulusto predict relationships between plant and pollinator frequency and reproductive isolation in natural systems.
Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks
Authors: Baryshnikova Anastasia
Published: December 2016

Summary/Abstract

Spatial Analysis of Functional Enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network regions that are statistically overrepresented for functional groups or quantitative phenotypes of interest, and provides an intuitive visual representation of their relative positioning within the network. In doing so, SAFE determines which functions are represented in a network, which parts of the network they are associated with and how they are potentially related to one another.

Here, I provide a detailed stepwise description of how to perform a SAFE analysis. As an example, I use SAFE to annotate the genome-scale genetic interaction similarity network fromSaccharomyces cerevisiaewith Gene Ontology (GO) biological process terms. In addition, I show how integrating GO with chemical genomic data in SAFE can recapitulate known modes-of-action of chemical compounds and potentially identify novel drug mechanisms.
An Integrated Risk Predictor for Pulmonary Nodules
Authors: Kearney Paul , Li Xiao-Jun , Porter Alex , Springmeyer Steve , Mazzone Peter
Published: December 2016

It is estimated that over 1.5 million lung nodules are detected annually in the United States. Most of these are benign but frequently undergo invasive and costly procedures to rule out malignancy. A risk predictor that can accurately differentiate benign and malignant lung nodules could be used to more efficiently route benign lung nodules to non-invasive observation by CT surveillance and route malignant lung nodules to invasive procedures. The majority of risk predictors developed to date are based exclusively on clinical risk factors, imaging technology or molecular markers. Assessed here are the relative performances of previously reported clinical risk factors and proteomic molecular markers for assessing cancer risk in lung nodules. From this analysis an integrated model incorporating clinical risk factors and proteomic molecular markers is developed and its performance assessed on a previously reported prospective collection of lung nodules that enrolled 475 patients from 12 sites with lung nodules between 8 and 30mm in diameter. In this analysis it is found that the molecular marker is most predictive. However, the integration of clinical and molecular markers is superior to both clinical and molecular markers separately.

Clinical Trial Registration: Registered at ClinicalTrials.gov (NCT01752101).
Cohesin dependent compaction of mitotic chromosomes
Authors: Schalbetter Stephanie A. , Goloborodko Anton , Fudenberg Geoffrey , Belton Jon M. , Miles Catrina , Yu Miao , Dekker Job , Mirny Leonid , Baxter Jon
Published: December 2016

Structural Maintenance of Chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply-conserved SMC complexes, organize chromosomes in budding yeast. The canonical role of cohesins is to co-align sister chromatids whilst condensins generally compact mitotic chromosomes. We find strikingly different roles in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosomes arms, independent of and in addition to its role in sister-chromatid cohesion. Cohesin dependent mitotic chromosome compaction can be fully accounted for throughcis-looping of chromatin by loop extrusion. Second, condensin is dispensable for compaction along chromosomal arms and instead plays a specialized role, structuring rDNA and peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that SMC-dependent looping is readily deployed in a range of contexts to functionally organize chromosomes.

Highlights

Cohesin compacts mitotic chromosomes independently of sister chromatid cohesion.

Formation ofcis-loops by loop extrusion fully accounts for cohesin-mediated compaction.

Condensin is not required for mitotic chromosome compaction of yeast chromosome arms

Condensin has a focused pre-anaphase role at centromeres and rDNA in yeast
In culture cross-linking of bacterial cells reveals proteome scale dynamic protein-protein interactions at the peptide level
Authors: de Jong Luitzen , de Koning Edward A. , Roseboom Winfried , Buncherd Hansuk , Wanner Martin J. , Dapic Irena , Jansen Petra J. , van Maarseveen Jan H. , Corthals Garry L. , Lewis Peter J. , Hamoen Leendert W. , de Koster Chris G.
Published: December 2016

Identification of dynamic protein-protein interactions at the peptide level on a proteomic scale is a challenging approach that is still in its infancy. We have developed a system to cross-link cells directly in culture with the special lysine cross-linker bis(succinimidyl)-3-azidomethyl-glutarate (BAMG). We used the Gram positive model bacteriumBacillus subtilisas an exemplar system. Within 5 min extensive intracellular cross-linking was detected, while intracellular cross-linking in a Gram-negative species,Escherichia coli, was still undetectable after 30 min, in agreement with the low permeability in this organism for lipophilic compounds like BAMG. We were able to identify 82 unique inter-protein cross-linked peptides with less than a 1% false discovery rate by mass spectrometry and genome-wide data base searching. Nearly 60% of the inter-protein cross-links occur in assemblies involved in transcription and translation. Several of these interactions are new, and we identified a binding site between the δ and β′ subunit of RNA polymerase close to the downstream DNA channel, providing a clue into how δ might regulate promoter selectivity and promote RNA polymerase recycling. Our methodology opens new avenues to investigate the functional dynamic organization of complex protein assemblies involved in bacterial growth.
poRe GUIs for parallel and real-time processing of MinION sequence data
Authors: Stewart Robert , Watson Mick
Published: December 2016

Motivation

Oxford Nanopore’s MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs.

Results

We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets. Both GUIs are capable of extracting sequence- and meta- data from large MinION datasets via a friendly point-and-click interface using commodity hardware.

Availability

The GUIs are packaged within poRe which is available on SourceForge:https://source-forge.net/projects/rpore/files/. Documentation is available on GitHub:https://github.com/mw55309/poRe_docs
Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest
Authors: Dangerfield Cody R. , Nadkarni Nalini M. , Brazelton William J.
Published: December 2016

Trees of temperate rainforests host a large biomass of epiphytes, living plants associated with soils formed in the forest canopy. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different species-level operational taxonomic units. A field experiment was conducted to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, connection to the living tree is an important factor in the ecology of canopy soil bacteria. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

IMPORTANCE

Temperate rainforests host large accumulations of epiphytes, plants that live on the branches of trees. This study provides a first look at the unique nature of bacterial communities in soil that is formed by the decomposition of epiphytes in the canopy of a temperate rainforest. Falling of epiphytic material results in the transfer of significant amounts of carbon and nutrients from the canopy to the forest floor. This study also experimentally documented how soil bacterial communities are affected by their movement from the canopy to the forest floor. The bacterial composition of canopy soil was altered by the severing of the epiphytic material from the living tree, even when the epiphytes remained in the canopy. Therefore, the unique nature of canopy soil bacteria is determined in part by the living host tree and not only by the physical environmental conditions associated with the canopy.
Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean
Authors: Chen Minmin , Fontaine Michael C. , Ben Chehida Yacine , Zheng Jinsong , Labbe Frédéric , Mei Zhigang , Hao Yujiang , Wang Kexiong , Wu Min , Zhao Qingzhong , Wang Ding
Published: December 2016

Understanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size (≤92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.
Universal scaling of maximum speed with body mass - Why the largest animals are not the fastest
Authors: Hirt Myriam R. , Jetz Walter , Rall Bjöern C. , Brose Ulrich
Published: December 2016

Speed is the fundamental constraint on animal movement, yet there is no general consensus on the determinants of maximum speed itself. Here, we provide a universal scaling model of maximum speed with body mass, which holds across locomotion modes, ecosystem types and taxonomic groups. In contrast to traditional power-law scaling, we predict a hump-shaped relationship due to a finite acceleration time for animals. This model is strongly supported by extensive empirical data (470 species with body masses ranging from 5.7×10−8to 108,000 kg) from terrestrial as well as aquatic ecosystems. Our approach offers a novel concept of what determines the upper limit of animal movement, thus enabling a better understanding of realized movement patterns in nature and their multifold ecological consequences.
Helical reconstruction in RELION
Authors: He Shaoda , Scheres Sjors H.W.
Published: December 2016

We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users. Although our implementation does not solve the problem that grossly incorrect structures can be obtained when the wrong helical symmetry is imposed, we show for four different test cases that it is capable of reconstructing structures to near-atomic resolution.

Abbreviations

CARD

Caspase Activation and Recruitment Domain

EM

Electron Microscopy

FSC

Fourier Shell Correlation

IHRSR

Iterative Helical Real-Space Reconstruction

MAVS

Mitochondrial Antiviral Signaling Protein

TMV

Tobacco Mosaic Virus
Quantifying the Heat Dissipation from Molecular Motor’s Transport Properties in Nonequilibrium Steady States
Authors: Hwang Wonseok , Hyeon Changbong
Published: December 2016

Theoretical analysis, which maps single molecule time trajectories of a molecular motor onto unicyclic Markov processes, allows us to evaluate the heat dissipated from the motor and to elucidate its dependence on the mean velocity and diffusivity. Unlike passive Brownian particles in equilibrium, the velocity and diffusion constant of molecular motors are closely inter-related to each other. In particular, our study makes it clear that the increase of diffusivity with the heat production is a natural outcome of active particles, which is reminiscent of the recent experimental premise that the diffusion of an exothermic enzyme is enhanced by the heat released from its own catalytic turnover. Compared with freely diffusing exothermic enzymes, kinesin-1 whose dynamics is confined on one-dimensional tracks is highly efficient in transforming conformational fluctuations into a locally directed motion, thus displaying a significantly higher enhancement in diffusivity with its turnover rate. Putting molecular motors and freely diffusing enzymes on an equal footing, our study offers thermodynamic basis to understand the heat enhanced self-diffusion of exothermic enzymes.
Computational Pharmacogenetics of P-Glycoprotein Mediated Antiepileptic Drug Resistance
Authors: Palaniappan Ashok , Varghese Sindhu
Published: December 2016

The treatment of epilepsy using antiepileptogenic drugs is complicated by drug re-sistance, resulting in treatment failure in more than one-third of cases. Human P-glycoprotein (hPGP;MDR1) is a known epileptogenic mediator. Given that experimental investigations have suggested a role for pharmacogenetics in this treatment failure, it would be of interest to study hPGP polymorphisms that might contribute to the emergence of drug resistance. Changes in protein functional activity could result from point mutations as well as altered abundance. Bioinformatics approaches were used to assess and rank the functional impact of 20 missense MDR1 polymorphisms and the top five were selected. The structures of the wildtype and mutant hPGP were modelled based on the mouse PGP structure. Docking studies of the wildtype and mutant hPGP with four standard anti-epileptic drugs were carried out. Our results revealed that the drug binding site with respect to the wildtype protein was uniform. However the mutant hPGP proteins displayed a repertoire of binding sites with stronger binding affinities towards the drug. Our studies indicated that specific polymorphisms in MDR1 could drive conformational changes of PGP structure, facilitating altered contacts with drug-substrates and resulting in drug extrusion. This suggests that MDR1 polymorphisms could play an active role in modifying drug bioavailability, leading to pharmacoresistance in antiepileptic chemotherapy.
Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease
Authors: Patrick Ellis , Rajagopal Sathyapriya , Wong Hon-Kit Andus , McCabe Cristin , Xu Jishu , Tang Anna , Imboywa Selina H. , Schneider Julie A. , Pochet Nathalie , Krichevsky Anna M. , Chibnik Lori B. , Bennett David A. , De Jager Philip L.
Published: December 2016

Background

Given multiple studies of brain microRNA (miRNA) in relation to Alzheimer’s disease (AD) with few consistent results and the heterogeneity of this disease, the objective of this study was to explore their mechanism by evaluating their relation to different elements of Alzheimer’s disease pathology, confounding factors and mRNA expression data from the same subjects in the same brain region.

Results

We report analyses of expression profiling of miRNA (n=700 subjects) and lincRNA (n=540 subjects) from the dorsolateral prefrontal cortex of individuals participating in two longitudinal cohort studies of aging. Evaluating well-established (miR-132, miR-129), we confirm their association with pathologic AD in our dataset, and then characterize their in disease role in terms of neuritic β-amyloid plaques and neurofibrillary tangle pathology. Additionally, we identify one new miRNA (miR-99) and four lincRNA that are associated with these traits. Many other previously reported associations of microRNA with AD are associated with the confounders quantified in our longitudinal cohort. Finally, by performing analyses integrating both miRNA and RNA sequence data from the same individuals (525 samples), we characterize the impact of AD associated miRNA on human brain expression: we show that the effects of miR-132 and miR-129-5b converge on certain genes such as EP300 and find a role for miR200 and its target genes in AD using an integrated miRNA/mRNA analysis.

Conclusions

Overall, miRNAs play a modest role in human AD, but we observe robust evidence that a small number of miRNAs are responsible for specific alterations in the cortical transcriptome that are associated with AD.
Benchmarking BarraCUDA on Epigenetic DNA and nVidia Pascal GPUs
Authors: Langdon W. B.
Published: December 2016

Typically BarraCUDA uses CUDA graphics cards to map DNA reads to the human genome. Previously its software source code was genetically miproved for short paired end next generation sequences. On longer, 150 base paired end noisy Cambridge Epigsnetix’s data, a Pascal GTX 1080 proc esses about 10000 strings per second, comparable with twin nVidia Tesla K40.
Single-molecule theory of enzymatic inhibition predicts the emergence of inhibitor-activator duality
Authors: Robin Tal , Reuveni Shlomi , Urbakh Michael
Published: December 2016

The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules—called inhibitors—on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace with the single-molecule revolution that is sweeping through the sciences. Here, we take the single enzyme perspective and rebuild the theory of enzymatic inhibition from the bottom up. We find that accounting for multi-conformational enzyme structure and intrinsic randomness cannot undermine the validity of classical results in the case of competitive inhibition; but that it should strongly change our view on the uncompetitive and mixed modes of inhibition. There, stochastic fluctuations on the single-enzyme level could give rise to inhibitor-activator duality—a phenomenon in which, under some conditions, the introduction of a molecule whose binding shuts down enzymatic catalysis will counter intuitively work to facilitate product formation. We state—in terms of experimentally measurable quantities—a mathematical condition for the emergence of inhibitor-activator duality, and propose that it could explain why certain molecules that act as inhibitors when substrate concentrations are high elicit a non-monotonic dose response when substrate concentrations are low. The fundamental and practical implications of our findings are thoroughly discussed.