bluuebunny/crossref_metadata_2025_split huggingface dataset:
A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities
Authors: Kleiner Manuel , Dong Xiaoli , Hinzke Tjorven , Wippler Juliane , Thorson Erin , Mayer Bernhard , Strous Marc 
Published: January 2018

AbstractMeasurements of the carbon stable isotope ratio (δ13C) are widely used in biology to address major questions regarding food sources and metabolic pathways used by organisms. Measurement of these so called stable carbon isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals have led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide limited taxonomic resolution, such as with the use of lipid biomarkers, or are limited in throughput, such as NanoSIMS imaging of single cells.Here we present “direct Protein-SIF” and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we show that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria-animal symbiosis showed that direct Protein-SIF confirms previous physiological hypotheses and can provide unexpected new insights into the symbionts’ metabolism. This confirms the usefulness of this new approach to accurately determine δ13C values for different species in microbial community samples.SignificanceTo understand the roles that microorganisms play in diverse environments such as the open ocean and the human intestinal tract, we need an understanding of their metabolism and physiology. A variety of methods such as metagenomics and metaproteomics exist to assess the metabolism of environmental microorganisms based on gene content and gene expression. These methods often only provide indirect evidence for which substrates are used by a microorganism in a community. The direct Protein-SIF method that we developed allows linking microbial species in communities to the environmental carbon sources they consume by determining their stable carbon isotope signature. Direct Protein-SIF also allows assessing which carbon fixation pathway is used by autotrophic microorganisms that directly assimilate CO2.
An entropic barriers diffusion theory of decision-making in multiple alternative tasks
Authors: Fernandez Slezak Diego , Sigman Mariano , Cecchi Guillermo A. 
Published: January 2018

AbstractWe present a theory of decision-making in the presence of multiple choices that departs from traditional approaches by explicitly incorporating entropic barriers in a stochastic search process. We analyze response time data from an on-line repository of 15 million blitz chess games, and show that our model fits not just the mean and variance, but the entire response time distribution (over several response-time orders of magnitude) at every stage of the game. We apply the model to show that (a) higher cognitive expertise corresponds to the exploration of more complex solution spaces, and (b) reaction times of users at an on-line buying website can be similarly explained. Our model can be seen as a synergy between diffusion models used to model simple two-choice decision-making and planning agents in complex problem solving.
Long read sequencing reveals Poxvirus evolution through rapid homogenization of gene arrays
Authors: Sasani Thomas A. , Cone Kelsey R. , Quinlan Aaron R. , Elde Nels C. 
Published: January 2018

AbstractLarge DNA viruses rapidly evolve to defeat host defenses. Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same locus, yet how these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to immune blocks is unknown. We performed experimental evolution with a vaccinia virus population harboring a SNV in a gene actively undergoing copy number amplification. Comparisons of virus genomes using the Oxford Nanopore Technologies sequencing platform allowed us to phase SNVs within large gene copy arrays for the first time, and uncovered a mechanism of adaptive SNV homogenization reminiscent of gene conversion, which is actively driven by selection. Our work reveals a new mechanism for the fluid gain of beneficial mutations in genetic regions undergoing active recombination in viruses, and illustrates the value of long read sequencing technologies for investigating complex genome dynamics in diverse biological systems.
The abnormal, mis-localizated HR bmh protein associates with members of the protein processing machinery in the cytoplasm
Authors: Folco Eric G. , Brancaz-Bouvier Maud-Virginie , Belly Agnès , Nonchev Stefan 
Published: January 2018

AbstractWe have recently mapped a 296 bp deletion at the mouse hairless locus that causes the mutation hairless rhino bald Mill Hill, (Hrrhbmh), (ID:MGI:3039558; J:89321), removing the stop codon and generating a larger mutant protein HR bmh with an additional sequence of 117 amino acids. The mutanthairlessgene mRNA is expressed during the embryonic and post-natal development of the hair follicle. A mutant HR protein was identified in bmh mouse skin at different stages of development by a specific antibody. We demonstrated that the HR bmh protein is able to interact with the vitamin D receptor, but is not able to repress VDR-mediated transactivation. Immunofluorescence analysis revealed that HR bmh protein displays an abnormal cellular localization in transfected cell lines, as well as in the epidermis and hair follicle of bmh mutant mice. Here we analyse the patterns of HR bmh extra-nuclear localization in cell transfection experiments. Using a candidate approach, double transfection experiments, immunofluorescent staining and IP protocols we established that HR bmh co-localizes specifically with the proteins HDAC6 in the cytoplasm is able to physically interact with it. Blast analysis allowed to show that HDAC6 and share high sequence homologies with specific motifs of HR bmh. We studied the association of these potential interactors with various cytoplasmic compartments. We discuss the relevance of the mutant hairless protein mis-localization in endosomal processing and in proteasome related pathways with respect to the specific skin phenotype of mouse hairless mutants.
In silico design of ligand triggered RNA switches
Authors: Findeiß Sven , Hammer Stefan , Wolfinger Michael T. , Kühnl Felix , Flamm Christoph , Hofacker Ivo L. 
Published: January 2018

AbstractThis contribution sketches a work flow to design an RNA switch that is able to adapt two structural conformations in a ligand-dependent way. A well characterized RNA aptamer, i. e., knowing its Kd and adaptive structural features, is an essential ingredient of the described design process. We exemplify the principles using the well-known theophylline aptamer throughout this work. The aptamer in its ligand-binding competent structure represents one structural conformation of the switch while an alternative fold that disrupts the binding-competent structure forms the other conformation. To keep it simple we do not incorporate any regulatory mechanism to control transcription or translation. We elucidate a commonly used design process by explicitly dissecting and explaining the necessary steps in detail. We developed a novel objective function which specifies the mechanistics of this simple, ligand-triggered riboswitch and describe an extensive in silico analysis pipeline to evaluate important kinetic properties of the designed sequences. This protocol and the developed software can be easily extended or adapted to fit novel design scenarios and thus can serve as a template for future needs.
Septal Secretion of Protein A inStaphylococcus aureusRequires SecA and Lipoteichoic Acid Synthesis
Authors: Yu Wenqi , Missiakas Dominique , Schneewind Olaf 
Published: January 2018

AbstractSurface proteins ofStaphylococcus aureusare secreted across septal membranes for assembly into the bacterial cross-wall. This localized secretion requires the YSIRK/GXXS motif signal peptide, however the mechanisms supporting precursor trafficking are not known. We show here that the signal peptide of staphylococcal protein A (SpA) is cleaved at the YSIRK/GXXS motif. A signal peptide mutant defective for cleavage can be crosslinked to SecA, SecDF and LtaS. SecA depletion blocks precursor targeting to septal membranes, whereas deletion ofsecDFdiminishes SpA secretion into the cross-wall. Depletion of LtaS blocks lipoteichoic acid synthesis and promotes precursor trafficking to peripheral membranes. We propose a model whereby SecA directs SpA precursors to lipoteichoic acid-rich septal membranes for YSIRK/GXXS motif cleavage and secretion into the cross-wall.
A conserved function for pericentromeric satellite DNA
Authors: Jagannathan Madhav , Cummings Ryan , Yamashita Yukiko M. 
Published: January 2018

AbstractA universal and unquestioned characteristic of eukaryotic cells is that the genome is divided into multiple chromosomes and encapsulated in a single nucleus. However, the underlying mechanism to ensure such a configuration is unknown. Here we provide evidence that pericentromeric satellite DNA, which is often regarded as junk, is a critical constituent of the chromosome, allowing the packaging of all chromosomes into a single nucleus. We show that the multi AT-hook satellite DNA binding proteins, D. melanogaster D1 and mouse HMGA1, play an evolutionarily conserved role in bundling pericentromeric satellite DNA from heterologous chromosomes into ‘chromocenters’, a cytological association of pericentromeric heterochromatin. Defective chromocenter formation leads to micronuclei formation due to budding off of interphase nucleus and cell death. We propose that chromocenter and satellite DNA serves a fundamental role to achieve the universal characteristic of eukaryotic cells: full complement of the genome within a single nucleus.
CENP-B dynamics at centromeres is regulated by a SUMOylation/ubiquitination and proteasomal-dependent degradation mechanism involving the SUMO-targeted ubiquitin E3 ligase RNF4
Authors: Maalouf Jhony El , Texier Pascale , Erliandri Indri , Cohen Camille , Corpet Armelle , Catez Frédéric , Boutell Chris , Lomonte Patrick 
Published: January 2018

AbstractCentromeric protein B (CENP-B) is a major constituent of the centromere. It is a DNA binding protein that recognizes a specific 17-nt sequence present in the centromeric alphoid satellite repeats. CENP-B importance for centromere stability has only been revealed recently. In addition to its DNA binding properties, CENP-B interacts with the histone H3 variant CENP-A and CENP-C. These interactions confer a mechanical strength to the kinetochore that enables accurate sister chromatids segregation to avoid aneuploidy. Therefore, understanding the mechanisms that regulate CENP-B stability at the centromere is a major unresolved issue for the comprehension of centromere function. In this study, we demonstrate that lysine K402 of CENP-B is a substrate for SUMO post-translational modifications. We show that K402 regulates CENP-B stability at centromeres through a SUMOylation/ubiquitination and proteasomal-dependent degradation mechanism involving the SUMO-Targeted Ubiquitin E3 Ligase RNF4/SNURF. Our study describes SUMOylation of CENP-B as a major post-translational modification involved in centromere dynamics.
Evaluation of a Chlamydia trachomatis-specific, commercial, real-time PCR for use with ocular swabs
Authors: Pickering H , Holland MJ , Last AR , Burton MJ , Burr SE 
Published: January 2018

AbstractBackgroundChlamydia trachomatis (Ct) is the most common bacterial sexually transmitted infection and the causative organism of trachoma, the leading infectious cause of blindness worldwide. Trachoma is diagnosed clinically by observation of conjunctival inflammation and/or scarring, however, there is evidence that monitoring Ct infection may be required for elimination programs. There are many commercial and ‘in-house’ nucleic acid amplification tests for the detection of Ct DNA, but the vast majority have not been validated for use with ocular swabs. This study evaluated a commercial assay, the Fast-Track Vaginal swab kit, using conjunctival samples from two trachoma-endemic areas. An objective, biostatistical-based method for binary classification of continuous PCR data was also developed, to limit potential user-bias in diagnostic settings.ResultsThe Fast-Track Vaginal swab assay was run on 210 ocular swab samples from Guinea-Bissau and Tanzania. Fit of individual amplification curves to exponential or sigmoid models, derivative and second derivative of the curves and final fluorescence value were examined for utility in thresholding for determining positivity. The results from the Fast-Track Vaginal swab assay were evaluated against a commercial test (Amplicor CT/NG) as well as a non-commercial test (in-house ddPCR) both of whose performance has previously been evaluated.Significant evidence of exponential amplification (R2 > 0.99) and final fluorescence > 0.15 were combined for thresholding. This objective approach identified a population of positive samples, however there were a subset of samples that amplified towards the end of the cycling protocol (at or later than 35 cycles), which were less clearly defined. The Fast-Track Vaginal swab assay showed good sensitivity against the commercial (95.71) and non-commercial (97.18) tests. Specificity was lower against both tests (90.00 and 96.55 respectively).ConclusionsThis study defined a simple, automated protocol for binary classification of continuous, real time qPCR data, for use in an end-point diagnostic test. This method identified a population of positive samples, however, as with manual thresholding, a subset of samples that amplified towards the end of the thermal cycling program were less easily classified. When used with ocular swabs, the Fast-Track Vaginal swab assay had good sensitivity but for Ct detection lower specificity than the commercial and non-commercial assays it was evaluated against, possibly leading to false positives.
Collicular circuits for flexible sensorimotor routing
Authors: Duan Chunyu A. , Pagan Marino , Piet Alex T. , Kopec Charles D. , Akrami Athena , Riordan Alexander J. , Erlich Jeffrey C. , Brody Carlos D. 
Published: January 2018

SUMMARYHistorically, cognitive processing has been thought to rely on cortical areas such as prefrontal cortex (PFC), with the outputs of these areas modulating activity in lower, putatively simpler spatiomotor regions, such as the midbrain superior colliculus (SC). Using a rat task in which subjects switch rapidly between task contexts that demand changes in sensorimotor mappings, we report a surprising role for the SC in non-spatial cognitive processes. Before spatial response choices could be formed, neurons in SC encoded task context more strongly than neurons in PFC, and bilateral SC silencing impaired behavioral performance. Once spatial choices could begin to be formed, SC neurons encoded the choice faster than PFC, while bilateral SC silencing no longer impaired choices. A set of dynamical models of the SC replicates our findings. Our results challenge cortically-focused views of cognition, and suggest that ostensibly spatiomotor structures can play central roles in non-spatiomotor cognitive processes.
A variational model for 3D tolerance analysis with manufacturing signature and operating conditions
Authors: Corrado Andrea , Polini Wilma , Moroni Giovanni , Petrò Stefano 
Published: January 2018

Purpose
The purpose of this work is to present a variational model able to deal with form tolerances and assembly conditions. The variational model is one of the methods proposed in literature for tolerance analysis, but it cannot deal with form tolerances and assembly conditions that may influence the functional requirements of mechanical assemblies.

Design/methodology/approach
This work shows how to manage the actual surfaces generated by the manufacturing process and the operating conditions inside the variational model that has been modified to integrate the manufacturing signature left on the surfaces of the parts and the operating conditions that arise during an actual assembly, such as gravity and friction. Moreover, a geometrical model was developed to numerically simulate what happens in a real assembly process and to give a reference value.

Findings
The new variational model was applied to a three-dimensional case study. The obtained results were compared to those of the geometrical model and to those of the variational model to validate the new model and to show the improvements.

Research limitations/implications
The proposed approach may be extended to other models of literature. However, its limitation is that it is able to deal with a sphere–plane contact.

Practical implications
Tolerance analysis is a valid tool to foresee geometric interferences among the components of an assembly before getting the physical assembly. It involves a decrease in the manufacturing costs.

Originality/value
The main contributions of the study are the insertion of a systematic pattern characterizing the features manufactured by a process, assembly operating conditions and development of a geometrical model to reproduce what happens in a real assembly process.
Anxiety and self-efficacy as sequential mediators in US college students’ career preparation
Authors: Deer LillyBelle K. , Gohn Kelsey , Kanaya Tomoe 
Published: January 2018

Purpose
Current college students in the USA are reporting higher levels of anxiety over career planning than previous generations, placing pressure on colleges to provide effective career development opportunities for their students. Research has consistently found that increasing career-related self-efficacy is particularly effective at increasing career-related behaviors among college students. These studies, however, do not account for the potentially negative impact of anxiety on cognitive, mediational pathways, including self-efficacy. Therefore, the purpose of this paper is to determine if anxiety plays a sequentially mediating role in the relationship between self-efficacy and job search intentions among college students.

Design/methodology/approach
Participants who were currently looking for a job or an internship were recruited to participate in an online study regarding career development preparation. Participants completed a job search behaviors “quiz” and were randomly assigned to either a “no feedback/control” condition or a “false-positive feedback/experimental” condition. Their career decision-making self-efficacy and state-trait anxiety were then assessed, as well as their intentions to engage in job search behaviors. A sequential mediational pathway analysis was performed to determine whether anxiety plays a mediational role in the relationship between self-efficacy and job search behaviors.

Findings
The hypothesized sequential mediational model was statistically significant. More specifically, participants who were randomly assigned to receive positive feedback experienced significantly lower levels of anxiety than participants in the control condition. In turn, lower levels of anxiety led to significantly higher levels of self-efficacy and significantly higher levels of job search intentions.

Practical implications
These findings have immediate implications for practitioners and educators who work with college students or any population that may be facing anxiety regarding the job search process. More specifically, these underscore the importance of lowering anxiety in order to lead to significantly higher levels of engagement in the career preparation process.

Originality/value
Currently, few studies (if any) have examined the potential mediating impact of anxiety on career-related self-efficacy and career development. Furthermore, no study has incorporated experimental methodology to test multiple pathways between anxiety, self-efficacy, and career preparation.
“The cut and thrust of industrial relations” – bullying by another name?
Authors: Drake Pat 
Published: January 2018

Purpose
The purpose of this paper is to offer a feminography, that is a “narration of a female self in a feminist age” (Abrams, 2017) by presenting a conceptual analysis, derived from experience, of email providing a form of discourse – that the author calls finger-speak – through which unexamined gender positioning caricatures a person’s identity. In so doing, the paper provides an illustrative case of a female manager being positioned through email to “know her place, perform it and feel it” (Hey, 2011).

Design/methodology/approach
An analysis of email foregrounds “finger-speak” as a form of digital conversation and through which people in universities may be positioned publicly but without their consent in relation to unexamined norms and assumptions. For women, it is argued, these norms are ageist and sexist. In this paper, fragments of finger-speak are collated to provide a reading of how mixing gendered norms with apparent differences of opinion constructs, via unexamined sexism, a public identity and then undermines it.

Findings
Through the case presented, the author argues that, because of a shared but unarticulated shadow over women as leaders, email lays the ground for subsequent scapegoating in such a manner that the woman takes responsibility for structural challenges that rightly belong to the organisation.

Originality/value
The contribution that email makes to constructing female identity in public is new, complementing other work that publicly characterises women leaders, through film (Ezzedeen, 2015), and through published writing such as autobiography (Kapasi et al., 2016). Emotional work undertaken by women in university leadership is so far under-represented in public, and email is a site through which this work becomes visible.
When the scars begin to heal: narratives of obstetric violence in Chiapas, Mexico
Authors: Murray de Lopez Jenna 
Published: January 2018

Purpose
The purpose of this paper is to examine how obstetric violence is embodied and understood by the women who experience it, how it impacts on maternal subjectivity and what the long-term health implications may be.

Design/methodology/approach
This paper is a qualitative, non-clinical analysis of women’s experiences of obstetric violence in Mexico. Data sources are derived from ethnographic interviews, participant observation and an extensive revision of public reports and policy.

Findings
Local ideas and beliefs over what one must endure to become a “good mother” contribute to how acts of obstetric violence are treated and interpreted by professionals, the community and the individual alike. The ways in which women interpret violence in relation to the wider context of their everyday lives have significant implications for evaluating the effectiveness of approaches to reproductive and maternal health.

Social implications
Situating women’s narratives within an ecological framework of gender-based violence reveals not only the conditions under which obstetric violations occur, but also the forms of resilience and coping mechanisms that women develop. This provides a deeper understanding for the long-term health implications of iatrogenic trauma during pregnancy and birth.

Originality/value
This paper discusses obstetric violence from the perspective of women who experience it and contextualises it within the wider life course approach to personhood and maternal transformation.