bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symbolic emblems of the Levantine Aurignacians as a regional entity identifier (Hayonim Cave, Lower Galilee, Israel)
Authors: Tejero José-Miguel , Belfer-Cohen Anna , Bar-Yosef Ofer , Gutkin Vitaly , Rabinovich Rivka 
Published: April 2018

SignificanceThe emergence and diffusion of Upper Paleolithic (UP) typo-technical traditions are among the most debated topics related to anatomically modern humans’ colonization of and establishment in Eurasia. The Levantine Aurignacian represents one of the UP cultural entities in the Near East, and its origins, spread, and interrelationships with other UP entities are central to the understanding of local UP dynamics. The data we present demonstrate that the notched bones from Hayonim Cave stratum D are unquestionably anthropic marks constituting an emblem of the Levantine Aurignacian. Assessment of data from Middle Stone Age and UP sites of Africa and Europe as well as other UP sites in the Levant supports the notion that this is indeed a unique feature of the Levantine Aurignacian.
Symbiotic polydnavirus of a parasite manipulates caterpillar and plant immunity
Authors: Tan Ching-Wen , Peiffer Michelle , Hoover Kelli , Rosa Cristina , Acevedo Flor E. , Felton Gary W. 
Published: April 2018

Significance
The role of herbivore-associated microbes in mediating plant–herbivore interactions has gained recent attention. We show that a parasitoid associated with its caterpillar host not only suppresses the immune system of the caterpillar but also suppresses the induced defenses of the caterpillar’s host plant. Parasitoids inject eggs into their hosts but also inject polydnaviruses that suppress the caterpillar’s immunity. Immunosuppression enables eggs to hatch and develop as larvae within caterpillars. Additionally, the polydnavirus reduces salivary glucose oxidase, the primary elicitor found in the caterpillar’s oral secretions. Caterpillars injected with polydnavirus induce lower plant defenses than untreated caterpillars. Our results reveal a dimension to the complexity of plant–herbivore interactions indicating that polydnaviruses mediate the phenotypes of the parasitoid, herbivore, and plant.
Tertiary structure of apolipoprotein A-I in nascent high-density lipoproteins
Authors: Pourmousa Mohsen , Song Hyun D. , He Yi , Heinecke Jay W. , Segrest Jere P. , Pastor Richard W. 
Published: April 2018

Significance
High-density lipoprotein (HDL), popularly known as “good cholesterol,” is an assembly of lipids and proteins that is protective against cardiovascular diseases. HDL begins to develop when two copies of the protein apolipoprotein A-I (APOA1) mediate the removal of excess lipids from peripheral cells and form a nanodisc. How the proteins adjust their structures as the nanodisc increases in diameter, mediates the conversion of cholesterol to cholesteryl esters, and becomes spherical is crucial to understanding HDL maturation and relevant pathologies. This study combines multimicrosecond atomistic molecular dynamics simulations, molecular modeling, and cross-linking experiments to reveal APOA1 structure in two nascent HDLs. The structures provide a mechanistic understanding for HDL maturation and revise previous models of nascent HDL.
Hidden collapse is driven by fire and logging in a socioecological forest ecosystem
Authors: Lindenmayer David B. , Sato Chloe 
Published: April 2018

SignificanceAlmost all descriptions of ecosystem collapse are made after it has occurred and not during the process of collapse. We describe the process of collapse in the iconic Australian Mountain Ash ecosystem. We uncovered empirical evidence for hidden collapse, which occurs when an ecosystem superficially appears to be intact but a prolonged period of decline coupled with long lag times for recovery mean that collapse is almost inevitable. This is because key ecosystem components continue to decline for long periods even after drivers of collapse are removed. Hidden collapse suggests a need for actions well before managers perceive they are required. Long-term monitoring targeting different classes of state variables can be used to provide early warnings of impending collapse.
HCMV glycoprotein B subunit vaccine efficacy mediated by nonneutralizing antibody effector functions
Authors: Nelson Cody S. , Huffman Tori , Jenks Jennifer A. , Cisneros de la Rosa Eduardo , Xie Guanhua , Vandergrift Nathan , Pass Robert F. , Pollara Justin , Permar Sallie R. 
Published: April 2018

Significance
The CDC estimates that every hour, a child is born in the United States with permanent neurologic disability resulting from human cytomegalovirus (HCMV) infection—more than is caused by Down syndrome, fetal alcohol syndrome, and neural tube defects combined. A maternal vaccine to block transmission of HCMV to the developing fetus is a necessary intervention to prevent these adverse outcomes. The gB/MF59 vaccine is the most successful tested clinically to date, achieving 50% reduction in HCMV acquisition. This manuscript establishes the function and epitope specificity of the humoral response stimulated by this vaccine that may explain the partial vaccine efficacy. Understanding the mechanism of gB/MF59-elicited protective immune responses will guide rational design and evaluation of the next generation of HCMV vaccines.
Unexpected slowdown of US pollutant emission reduction in the past decade
Authors: Jiang Zhe , McDonald Brian C. , Worden Helen , Worden John R. , Miyazaki Kazuyuki , Qu Zhen , Henze Daven K. , Jones Dylan B. A. , Arellano Avelino F. , Fischer Emily V. , Zhu Liye , Boersma K. Folkert 
Published: April 2018

SignificanceEmissions of nitrogen oxides (NOx) have a large impact on air quality and climate change as precursors in the formation of ozone and secondary aerosols. We find that NOxemissions have not been decreasing as expected in recent years (2011–2015) when comparing top-down estimates from satellites and surface NO2measurements to the trends predicted from the US Environmental Protection Agency’s emission inventory data. The discrepancy can be explained by the growing relative contribution of industrial, area, and off-road mobile sources of emissions, decreasing relative contribution of on-road gasoline vehicles, and slower than expected decreases in on-road diesel NOxemissions, with implications for air-quality management.
Histone demethylase JMJD1A promotes alternative splicing of AR variant 7 (AR-V7) in prostate cancer cells
Authors: Fan Lingling , Zhang Fengbo , Xu Songhui , Cui Xiaolu , Hussain Arif , Fazli Ladan , Gleave Martin , Dong Xuesen , Qi Jianfei 
Published: April 2018

Significance
Formation of androgen receptor splicing variant 7 (AR-V7), a constitutively active form of AR, plays a key role in the resistance of prostate cancer to hormone therapy. However, the mechanisms that regulate AR-V7 generation are poorly understood. Here, we identified a new role for histone demethylase JMJD1A (Jumonji domain containing 1A) in the formation of AR-V7 in prostate cancer cells. We found that JMJD1A facilitated recruitment of a splicing factor, heterogeneous nuclear ribonucleoprotein F, for alternative splicing and generation of AR-V7. The findings suggest that targeting JMJD1A may provide new therapeutic opportunity for prostate cancer.
Real self-respect and its social bases
Authors: Schemmel Christian 
Published: April 2018

AbstractMany theories of social justice maintain that concern for the social bases of self-respect grounds demanding requirements of political and economic equality, as self-respect is supposed to be dependent on continuous just recognition by others. This paper argues that such views miss an important feature of self-respect, which accounts for much of its value: self-respect is a capacity for self-orientation that is robust under adversity. This does not mean that there are no social bases of self-respect that such theories ought to incorporate. It means that they are different: they consist of the motivational and epistemic resources needed to develop and maintain such robustness.
Direct bioethanol production from brown macroalgae by co-culture of two engineered Saccharomyces cerevisiae strains
Authors: Sasaki Yusuke , Takagi Toshiyuki , Motone Keisuke , Shibata Toshiyuki , Kuroda Kouichi , Ueda Mitsuyoshi 
Published: April 2018

ABSTRACT
A co-culture platform for bioethanol production from brown macroalgae was developed, consisting of two types of engineered Saccharomyces cerevisiae strains; alginate- and mannitol-assimilating yeast (AM1), and cellulase-displaying yeast (CDY). When the 5% (w/v) brown macroalgae Ecklonia kurome was used as the sole carbon source for this system, 2.1 g/L of ethanol was produced, along with simultaneous consumption of alginate, mannitol, and glucans.
Extraction of ECG signal with adaptive filter for hearth abnormalities detection
Authors: Turnip Mardi , Saragih Rijois. I. E. , Dharma Abdi , Kusumandari Dwi Esti , Turnip Arjon , Sitanggang Delima , Aisyah Siti 
Published: April 2018

Abstract
This paper demonstrates an adaptive filter method for extraction ofelectrocardiogram (ECG) feature in hearth abnormalities detection. In particular, electrocardiogram (ECG) is a recording of the heart's electrical activity by capturing a tracingof cardiac electrical impulse as it moves from the atrium to the ventricles. The applied algorithm is to evaluate and analyze ECG signals for abnormalities detection based on P, Q, R and S peaks. In the first phase, the real-time ECG data is acquired and pre-processed. In the second phase, the procured ECG signal is subjected to feature extraction process. The extracted features detect abnormal peaks present in the waveform. Thus the normal and abnormal ECG signal could be differentiated based on the features extracted.
Particle Concentrations in Occupational Settings Measured with a Nanoparticle Respiratory Deposition (NRD) Sampler
Authors: Stebounova Larissa V , Gonzalez-Pech Natalia I , Park Jae Hong , Anthony T Renee , Grassian Vicki H , Peters Thomas M 
Published: April 2018

Abstract
There is an increasing need to evaluate concentrations of nanoparticles in occupational settings due to their potential negative health effects. The Nanoparticle Respiratory Deposition (NRD) personal sampler was developed to collect nanoparticles separately from larger particles in the breathing zone of workers, while simultaneously providing a measure of respirable mass concentration. This study compared concentrations measured with the NRD sampler to those measured with a nano Micro Orifice Uniform-Deposit Impactor (nanoMOUDI) and respirable samplers in three workplaces. The NRD sampler performed well at two out of three locations, where over 90% of metal particles by mass were submicrometer particle size (a heavy vehicle machining and assembly facility and a shooting range). At the heavy vehicle facility, the mean metal mass concentration of particles collected on the diffusion stage of the NRD was 42.5 ± 10.0 µg/m3, within 5% of the nanoMOUDI concentration of 44.4 ± 7.4 µg/m3. At the shooting range, the mass concentration for the diffusion stage of the NRD was 5.9 µg/m3, 28% above the nanoMOUDI concentration of 4.6 µg/m3. In contrast, less favorable results were obtained at an iron foundry, where 95% of metal particles by mass were larger than 1 µm. The accuracy of nanoparticle collection by NRD diffusion stage may have been compromised by high concentrations of coarse particles at the iron foundry, where the NRD collected almost 5-fold more nanoparticle mass compared to the nanoMOUDI on one sampling day and was more than 40% different on other sampling days. The respirable concentrations measured by NRD samplers agreed well with concentrations measured by respirable samplers at all sampling locations. Overall, the NRD sampler accurately measured concentrations of nanoparticles in industrial environments when concentrations of large, coarse mode, particles were low.
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs
Authors: Stocks Matthew B , Mohorianu Irina , Beckers Matthew , Paicu Claudia , Moxon Simon , Thody Joshua , Dalmay Tamas , Moulton Vincent 
Published: April 2018

Abstract

Motivation
RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential.

Results
We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses.

Availability and implementation
The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk. The source code is available at: https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench

Supplementary information
Supplementary data are available at Bioinformatics online.
Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation
Authors: Usmanova Dinara R , Bogatyreva Natalya S , Ariño Bernad Joan , Eremina Aleksandra A , Gorshkova Anastasiya A , Kanevskiy German M , Lonishin Lyubov R , Meister Alexander V , Yakupova Alisa G , Kondrashov Fyodor A , Ivankov Dmitry N 
Published: April 2018

Abstract

Motivation
Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.

Results
Here we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here.

Availability and implementation
All calculations were implemented by in-house PERL scripts.

Supplementary information
Supplementary data are available at Bioinformatics online.

Note
The article 10.1093/bioinformatics/bty348, published alongside this paper, also addresses the problem of biases in protein stability change predictions.
Applying graph theory to protein structures: an Atlas of coiled coils
Authors: Heal Jack W , Bartlett Gail J , Wood Christopher W , Thomson Andrew R , Woolfson Derek N 
Published: April 2018

AbstractMotivationTo understand protein structure, folding and function fully and to design proteins de novo reliably, we must learn from natural protein structures that have been characterized experimentally. The number of protein structures available is large and growing exponentially, which makes this task challenging. Indeed, computational resources are becoming increasingly important for classifying and analyzing this resource. Here, we use tools from graph theory to define an Atlas classification scheme for automatically categorizing certain protein substructures.ResultsFocusing on the α-helical coiled coils, which are ubiquitous protein-structure and protein–protein interaction motifs, we present a suite of computational resources designed for analyzing these assemblies. iSOCKET enables interactive analysis of side-chain packing within proteins to identify coiled coils automatically and with considerable user control. Applying a graph theory-based Atlas classification scheme to structures identified by iSOCKET gives the Atlas of Coiled Coils, a fully automated, updated overview of extant coiled coils. The utility of this approach is illustrated with the first formal classification of an emerging subclass of coiled coils called α-helical barrels. Furthermore, in the Atlas, the known coiled-coil universe is presented alongside a partial enumeration of the ‘dark matter’ of coiled-coil structures; i.e. those coiled-coil architectures that are theoretically possible but have not been observed to date, and thus present defined targets for protein design.Availability and implementationiSOCKET is available as part of the open-source GitHub repository associated with this work (https://github.com/woolfson-group/isocket). This repository also contains all the data generated when classifying the protein graphs. The Atlas of Coiled Coils is available at: http://coiledcoils.chm.bris.ac.uk/atlas/app.
PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence
Authors: Iqbal Sumaiya , Hoque Md Tamjidul 
Published: April 2018

Abstract

Motivation
Machine learning plays a substantial role in bioscience owing to the explosive growth in sequence data and the challenging application of computational methods. Peptide-recognition domains (PRDs) are critical as they promote coupled-binding with short peptide-motifs of functional importance through transient interactions. It is challenging to build a reliable predictor of peptide-binding residue in proteins with diverse types of PRDs from protein sequence alone. On the other hand, it is vital to cope up with the sequencing speed and to broaden the scope of study.

Results
In this paper, we propose a machine-learning-based tool, named PBRpredict, to predict residues in peptide-binding domains from protein sequence alone. To develop a generic predictor, we train the models on peptide-binding residues of diverse types of domains. As inputs to the models, we use a high-dimensional feature set of chemical, structural and evolutionary information extracted from protein sequence. We carefully investigate six different state-of-the-art classification algorithms for this application. Finally, we use the stacked generalization approach to non-linearly combine a set of complementary base-level learners using a meta-level learner which outperformed the winner-takes-all approach. The proposed predictor is found competitive based on statistical evaluation.

Availability and implementation
PBRpredict-Suite software: http://cs.uno.edu/~tamjid/Software/PBRpredict/pbrpredict-suite.zip.

Supplementary information
Supplementary data are available at Bioinformatics online.
Strangers in the Frame: Inside and Outside the
Cent Nouvelles nouvelles
Authors: Emerson Catherine 
Published: April 2018

Abstract

This article examines the way in which tales of the Burgundian
Cent Nouvelles nouvelles
are interpreted differently by different reading publics. Taking a neglected tale in the corpus,
nouvelle
66, as a starting point, the article argues that this
nouvelle
exemplifies tendencies observable throughout the collection, particularly in regard to surprising physical characteristics of outgroup members such as women and clerics. Viewed in the context of the tales’ original readership, such stories cement ingroup solidarity amongst a group of elite men who, whilst sharing some characteristics, were reasonably diverse in a number of ways. However, the original reading context is not fully reconstructable because it is unclear as to what the narrative frame actually represents. Once the tales move beyond this frame, the court of Philippe le Bon becomes a spectacle itself, and this is reflected in a number of readings which censure the original audience. The article argues that this reaction is present in the very first edition and is indeed inherent in the narrative frame of the
Cent Nouvelles nouvelles
.
Confucian Values as a Buffer Against Age-Based Stereotype Threat for Chinese Older Adults
Authors: Tan Shyuan Ching , Barber Sarah J 
Published: April 2018

AbstractObjectivesResearch has shown that stereotype threat can impair older adults’ memory in Western cultures. We tested whether this also occurs for older adults from the East Asian Chinese culture. We also tested whether an intervention that highlighted Confucian principles would protect Chinese older adults from stereotype threat’s detrimental effects.MethodCulturally-Chinese older adults residing in the United States completed a memory test either under age-based stereotype threat about cognitive decline or not. Prior to this, some participants were also reminded of Confucian traditions of filial piety and were assured these values had been transmitted to the younger generation.ResultsStereotype threat impaired Chinese older adults’ memory performance. However, our intervention was effective in eliminating this deficit. When the Chinese participants were reminded of the Confucian principle of filial piety they did not exhibit stereotype threat effects.DiscussionConfirming that younger adults have an obligation to respect their elders can eliminate the social-evaluative pressure of stereotype threat for Chinese older adults. These findings are noteworthy since population aging is happening at an unprecedented pace in East Asia. Although our results suggest that stereotype threat can adversely affect older adults’ cognitive performance in these societies, we also identify a culturally-based intervention to alleviate this impairment.
Mincle: 20 years of a versatile sensor of insults
Authors: Lu Xiuyuan , Nagata Masahiro , Yamasaki Sho 
Published: April 2018

AbstractMacrophage-inducible C-type lectin, better known as Mincle, is a member of the C-type lectin receptor family and is encoded by Clec4e. Mincle was an orphan receptor for a long time after having been discovered as a lipopolysaccharide-induced protein, yet later an adjuvant glycolipid in mycobacteria—trehalose dimycolate—was identified as a ligand. Ligands for Mincle were also found existing in bacteria, fungi and even mammals. When confronted with foreign elements, Mincle can recognize characteristic pathogen-associated molecular patterns, mostly glycolipids, from Mycobacterium tuberculosis and other pathogens, and thus induce immune responses against infection. To maintain self-homeostasis, Mincle can recognize lipid-based damage-associated molecular patterns, thereby monitoring the internal environment. The mechanism by which Mincle functions in the immune system is also becoming more clear along with the identification of its ligands. Being expressed widely on antigen-presenting cells, Mincle activation leads to the production of cytokines and chemokines, neutrophil infiltration and other inflammatory responses. Besides, Mincle can induce acquired immunity such as antigen-specific T-cell responses and antibody production as an adjuvant receptor. In this review, we will retrospectively sketch the discovery and study of Mincle, and outline some current work on this receptor.