bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes
Authors: Fernandes Daniel , Sirak Kendra , Novak Mario , Finarelli John A. , Byrne John , Connolly Edward , Carlsson Jeanette E. L. , Ferretti Edmondo , Pinhasi Ron , Carlsson Jens 
Published: January 2017

AbstractThomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison’s grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent’s DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as “forced homozygote approach”. The results were confirmed using simulated data for different relatedness classes. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.
Implication of dorsostriatal D3 receptors in motivational processes: a potential target for neuropsychiatric symptoms in Parkinson’s disease
Authors: Favier Mathieu , Carcenac Carole , Drui Guillaume , Vachez Yvan , Boulet Sabrina , Savasta Marc , Carnicella Sebastien 
Published: January 2017

AbstractBeyond classical motor symptoms, motivational and affective deficits are frequently observed in Parkinson’s disease (PD), dramatically impairing the quality of life of patients. Using bilateral 6-hydroxydopamine (6-OHDA) lesions of the substantia nigra pars compacta (SNc) in rats, we have been able to reproduce these neuropsychiatric/non-motor impairments. The present study describes how bilateral 6-OHDA SNc lesions affect the function of the main striatal dopaminergic (DA) receptor subtypes. Autoradiography was used to measure the levels of striatal DA receptors, and operant sucrose self-administration and neuropharmacological approaches were combined to investigate the causal implication of specific DA receptors subtypes in the motivational deficits induced by a dorsostriatal DA denervation. We found that D3 receptors (D3R) exclusively are down-regulated within the dorsal striatum of lesioned rats. We next showed that infusion of a D3R antagonist (SB-277011A) in non-lesioned animals specifically disrupts preparatory, but not consummatory behaviors. Our findings reveal an unexpected involvement of dorsostriatal D3R in motivational processes. They strongly suggest an implication of dorsostriatal D3R in the neuropsychiatric symptoms observed in PD, highlighting this receptor as a potential target for pharmacological treatment.
Discorrelated quantum states
Authors: Meyer-Scott Evan , Tiedau Johannes , Harder Georg , Shalm Lynden K. , Bartley Tim J. 
Published: January 2017

AbstractThe statistical properties of photons are fundamental to investigating quantum mechanical phenomena using light. In multiphoton, two-mode systems, correlations may exist between outcomes of measurements made on each mode which exhibit useful properties. Correlation in this sense can be thought of as increasing the probability of a particular outcome of a measurement on one subsystem given a measurement on a correlated subsystem. Here, we show a statistical property we call “discorrelation”, in which the probability of a particular outcome of one subsystem is reduced to zero, given a measurement on a discorrelated subsystem. We show how such a state can be constructed using readily available building blocks of quantum optics, namely coherent states, single photons, beam splitters and projective measurement. We present a variety of discorrelated states, show that they are entangled, and study their sensitivity to loss.
Whole-transcriptome sequence analysis of differentially expressed genes in Phormium tenax under drought stress
Authors: Bai Zhen-yu , Wang Tong , Wu Yin-huan , Wang Ke , Liang Qian-yu , Pan Yuan-zhi , Jiang Bei-bei , Zhang Lei , Liu Guang-li , Jia Yin , Liu Qing-lin 
Published: January 2017

AbstractPhormium tenax is a kind of drought resistant garden plant with its rich and colorful leaves. To clarify the molecular mechanism of drought resistance in Phormium tenax, transcriptome was sequenced by the Illumina sequencing technology under normal and drought stress, respectively. A large number of contigs, transcripts and unigenes were obtained. Among them, only 30,814 unigenes were annotated by comparing with the protein databases. A total of 4,380 genes were differentially expressed, 2,698 of which were finally annotated under drought stress. Differentially expression analysis was also performed upon drought treatment. In KEGG pathway, the mechanism of drought resistance in Phormium tenax was explained from three aspects of metabolism and signaling of hormones, osmotic adjustment and reactive oxygen species metabolism. These results are helpful to understand the drought tolerance mechanism of Phormium tenax and will provide a precious genetic resource for drought-resistant vegetation breeding and research.
Synchronized purification and immobilization of his-tagged β-glucosidase via Fe3O4/PMG core/shell magnetic nanoparticles
Authors: Zhou Yang , Yuan Shaofei , Liu Qian , Yan Dandan , Wang Yun , Gao Li , Han Juan , Shi Haifeng 
Published: January 2017

AbstractIn this paper, an efficient and convenient Fe3O4/PMG/IDA-Ni2+ nanoparticles that applied to purify and immobilize his-tagged β-glucosidase was synthesized, in which, Fe3O4/PMG (poly (N, N’-methylenebisacrylamide-co-glycidyl methacrylate) core/shell microspheres were synthesized firstly using distillation-precipitation polymerization, then iminodiacetic acid (IDA) was used to open epoxy rings on the shell of microspheres to the combination of Ni2+. The gene of β-glucosidase that was from Coptotermes formosanus Shiraki was amplified, cloned into the expression vector pET28a with an N-terminal His-tag, and expressed in E.coli BL21. The nanoparticles showed the same purification efficiency as commercial nickel column which was a frequently used method in the field of purifying his-tagged proteins from crude cell lysates. The results indicated that Fe3O4/PMG/IDA-Ni2+ nanoparticles can be considered as an excellent purification material. β-glucosidase was immobilized on the surface of Fe3O4/PMG/IDA-Ni2+ to form Fe3O4/PMG/IDA-β-glucosidase by means of covalent bound with imidazolyl and Ni2+. The immobilized β-glucosidase exhibited excellent catalytic activity and stabilities compared with free β-glucosidase. In addition, immobilized β-glucosidase can be recycled for many times and retain more than 65% of the original activity. The materials display enormous potential in the aspect of purifying and immobilizing enzyme.
Poly(carboxylate ether)-based superplasticizer achieves workability retention in calcium aluminate cement
Authors: Akhlaghi Omid , Menceloglu Yusuf Ziya , Akbulut Ozge 
Published: January 2017

AbstractCalcium aluminate cement (CAC) suffers from loss of workability in less than an hour (~15 minutes) after first touch of water. Current superplasticizers that are utilized to modify the viscosity of cement admixtures are designed to target ordinary Portland cement (OPC). The high affinity between these superplasticizers and cement particles were found to be detrimental in CAC systems. Utilization of a monomer that, instead, facilitates gradual adsorption of a superplasticizer provides workability retention. For the first time in literature, we report a superplasticizer that caters to the properties of CAC such as high rate of surface development and surface charge. While neat CAC was almost unworkable after 1 hour, with the addition of only 0.4% of the optimized superplasticizer, 90% fluidity retention was achieved.
Back Pain in Adolescent Athletes: Results of a Biomechanical Screening
Authors: Mueller Steffen , Mueller Juliane , Stoll Josefine , Cassel Michael , Hirschmüller Anja , Mayer Frank 
Published: January 2017

AbstractThe aim was to use a short biomechanical test battery to screen adolescent athletes with and without back pain to reveal relevant and possibly preventable deficits. 1 559 adolescent athletes (m/f 945/614; 13.2±1.6y) were included. Back pain was assessed (1–5: 1=no pain; 5=maximum pain) for dichotomous categorization into back pain (BP: pain>2, n=113), healthy (NBPAll: pain=1, n=1 213) and matched healthy (NBPmatched: pain=1, n=113) athletes. Athletes performed stability, performance (jumps) and trunk strength testing. The center of pressure displacement [mm], jump height [cm], peak force [N], contact time [ms] and peak torque of the trunk [Nm] were analyzed. Analysis showed a statistically significant influence of trunk strength on back pain (BP/NBPALL). Nevertheless, after including co-variables (anthropometrics, gender and training volume), there were no significant variables detectable any longer. ANOVA identified no group differences (BP/NBPmatched) in the outcome measurement for the biomechanical tests (p>0.05). This short biomechanical screening shows no sufficient differentiation in adolescent athletes for back pain. Therefore, age, training load and gender has greater relevance than strength deficits or postural control. This is challenging for further understanding of the complex conditions in young athletes with back pain.
“Today I know, we know, that these sacrifices are heavy, but necessary”
Authors: Polymeneas George 
Published: January 2017

Abstract
This study attempts an analysis of political discourse during the current Greek debt crisis at the beginning of 2010, when the size of the debt became apparent. It draws upon both the critical discourse analysis tradition and corpus linguistics in order to examine the relationship between discourse and group “knowledge” in speeches of the then Prime Minister, George Papandreou, and the Minister of Finance, George Papakonstantinou. It is argued that political knowledge on the crisis is a matter of “truth” between contesting political groups. The Greek government talked and wrote about the crisis so as to establish their “truth”, by transforming their beliefs and interpretations on how the crisis can be converted into knowledge.
Golden Dawn in the media during the Greek crisis
Authors: Mouka Effie , Saridakis Ioannis E. 
Published: January 2017

Abstract
This is a corpus-driven study of the perception of Golden Dawn and its discourse by the Greek and European mainstream Press. More specifically, we examine the main traits attributed to Golden Dawn by eleven Greek and European newspapers, the causes to which its rise is linked, expecially with respect to the current crisis, and the suggested ways of addressing the phenomenon. Key lexemes are analysed and their co-articulation into meaningful discourse units is critically and contrastively discussed in the journalistic corpus. Overall, the study attempts to address the question of how the traits and political aims of Golden Dawn, as well as its discourse, are perceived by society through media.
Making sense of the Greek crisis
Authors: Goutsos Dionysis , Hatzidaki Ourania 
Published: January 2017

Abstract
The epilogue to this volume summarizes its relevance and contribution as far as the synergy between critical discourse analysis and corpus linguistics is concerned. It further discusses the issue of quantification, which seems to be the critical parameter in this synergy, and proposes the concept of discourse-driven quantification to complement the conventional corpus-driven quantification usually followed in corpus studies. Finally, it draws several conclusions on the basis of the individual chapters of the volume, which mainly concern the importance of genre as well as the viewpoint of various agents (discourse producers and receivers) as to how the Greek crisis is construed in diverse kinds of texts.
Grounds and ‘Grounds’
Authors: Rettler Bradley 
Published: January 2017

AbstractIn this paper, I offer a new theory of grounding. The theory has is that grounding is a job description that is realized by different properties in different contexts. Those properties play the grounding role contingently, and grounding is the property that plays the grounding role essentially. On this theory, grounding is monistic, but ‘grounding’ refers to different relations in different contexts. First, I argue against Kit Fine’s monist univocalism. Next, I argue against Jessica Wilson’s pluralist multivocalism. Finally, I introduce monist multivocalism, explicate three versions of it, and show its advantages.
Electrodeposition of multilayer Ni–W and Ni–W–alumina nanocomposite coatings
Authors: Allahyarzadeh M. , Aliofkhazraei M. , Rouhaghdam A. S. , Torabinejad V. 
Published: January 2017

Multilayer Ni–W and Ni–W–Al2O3 coatings with intermittent low and high concentrations of tungsten and alumina were electrodeposited through alternative variation of pulse parameters. Microstructural studies and elemental analyses of the coatings were carried out using scanning electron microscopy and energy dispersive X-ray spectroscopy, respectively. Profilometry and atomic force microscopy were employed to investigate the surface roughness at two different scales. Pin-on-disc wear test was used to evaluate the tribological properties. The corrosion resistance was also studied using potentiodynamic polarisation and electrochemical impedance spectroscopy methods. Results revealed that at lower duty cycles, more incorporation of alumina and more co-deposition of tungsten are achieved. Results indicated variable and alternative microhardness values corresponding to the different concentrations of tungsten and alumina in each specific layers. Wear tests demonstrated the descending trend of the wear rate as a function of sliding distance. It was found that alumina nanoparticles enhanced the corrosion resistance. GRAPHICAL ABSTRACT
The Impact of Broadband on U.S. Agriculture: An Evaluation of the USDA Broadband Loan Program
Authors: Kandilov Amy M.G. , Kandilov Ivan T. , Liu Xiangping , Renkow Mitch 
Published: January 2017

AbstractWe evaluate the impact that the USDA’s low‐cost broadband loan programs have on the U.S. agricultural sector. The broadband loan programs increase access to high‐speed Internet in recipient communities, which can raise farm sales by increasing both farm output and prices received by producers. Further, high‐speed Internet may drive down costs by providing information on cheaper inputs and better management practices, leading to an overall improvement in farm profits. Using U.S. county‐level data on farm sales and expenditures in 2000 and 2007, we employ an inverse probability weighting technique to control for endogenous selection in an econometric model that also accounts for spatial dependence. We find that the two USDA broadband loan programs have had positive causal impacts on farm sales, expenditures, and profits in a subset of rural counties—those adjacent to metropolitan counties—but not in other types of counties.
Addressing Participant Inattention in Federal Programs: A Field Experiment with the Conservation Reserve Program
Authors: Wallander Steven , Ferraro Paul , Higgins Nathaniel 
Published: January 2017

AbstractVoluntary land conservation programs depend upon the willingness of land owners to participate. Since participation requires commitment to long‐term contracts, most studies on participation focus on changes to the pecuniary incentives facing land owners. This study presents a large‐scale field experiment within the USDA's Conservation Reserve Program (CRP) that examines whether informational outreach, including behavioral nudges, could improve land owners’ willingness to participate. The experiment evaluates the impact of three types of reminder letters on the rate at which land is offered into the CRP. We find that for the most well‐informed group, farms with expiring CRP contracts, the reminder letters did improve participation. We interpret this result as evidence of inattentive behavior. We do not detect any differences in the estimated treatment effects among the basic reminder letter and the letters augmented with peer comparisons and social norm messaging, nor do we detect any treatment effect among currently unenrolled farms. From a policy perspective, these results imply that the USDA can generate additional CRP offers among farms with expiring contracts at an average cost of $39 per additional offer. Assuming a twenty‐five million acre program, reminder letters sent during every sign‐up period would result in re‐enrollment offers from an additional 420,000 acres. Using simulations based on offers from prior CRP sign‐ups, we estimate that these additional offers in the CRP auction would reduce program costs. Depending on the year of simulation, the outreach effort achieves a benefit‐cost ratio of between 20:1 and 90:1.
Tools for the Precision Medicine Era: How to Develop Highly Personalized
Treatment Recommendations From Cohort and Registry Data Using Q-Learning
Authors: Krakow Elizabeth F , Hemmer Michael , Wang Tao , Logan Brent , Arora Mukta , Spellman Stephen , Couriel Daniel , Alousi Amin , Pidala Joseph , Last Michael , Lachance Silvy , Moodie Erica E M 
Published: January 2017

Abstract
Q-learning is a method of reinforcement learning that employs backwards stagewise estimation to identify sequences of actions that maximize some long-term reward. The method can be applied to sequential multiple-assignment randomized trials to develop personalized adaptive treatment strategies (ATSs)—longitudinal practice guidelines highly tailored to time-varying attributes of individual patients. Sometimes, the basis for choosing which ATSs to include in a sequential multiple-assignment randomized trial (or randomized controlled trial) may be inadequate. Nonrandomized data sources may inform the initial design of ATSs, which could later be prospectively validated. In this paper, we illustrate challenges involved in using nonrandomized data for this purpose with a case study from the Center for International Blood and Marrow Transplant Research registry (1995–2007) aimed at 1) determining whether the sequence of therapeutic classes used in graft-versus-host disease prophylaxis and in refractory graft-versus-host disease is associated with improved survival and 2) identifying donor and patient factors with which to guide individualized immunosuppressant selections over time. We discuss how to communicate the potential benefit derived from following an ATS at the population and subgroup levels and how to evaluate its robustness to modeling assumptions. This worked example may serve as a model for developing ATSs from registries and cohorts in oncology and other fields requiring sequential treatment decisions.
Recent Advances in Immunity and Hypertension
Authors: Lopez Gelston Catalina A. , Mitchell Brett M. 
Published: January 2017

AbstractPersistent immune system activation plays an important role in the development of various forms of hypertension. Activation of the innate immune system, inflammation, and subsequent adaptive immune system response causing end-organ injury and dysfunction ultimately leads to hypertension and its associated sequelae including coronary artery disease, heart failure, stroke, and chronic kidney disease. In this review, we will provide updates on the innate and adaptive immune cells involved in hypertension, the current understanding of how the immune system gets activated, and examine the recently discovered mechanisms involved in several forms of experimental hypertension.
Correlated mutations select misfolded from properly folded proteins
Authors: Wozniak P P , Vriend G , Kotulska M 
Published: January 2017

Abstract

Motivation
The recently developed direct coupling analysis (DCA) method has greatly improved the accuracy with which residue–residue contacts can be predicted from multiple sequence alignments. Contact prediction accuracy, though, is still often not sufficient for complete ab initio protein structure prediction. DCA can, however, support protein structure studies in several ways.

Results
We show that DCA can select the better structure from among properly folded and misfolded variants. This idea was tested by comparing obsolete PDB files with their more correctly folded successors and by the comparison of structures with deliberately misfolded decoy models from the Decoys ′R′ Us database. The DCA method systematically predicts more contacts for properly folded structures than for misfolded ones. The method works much better for X-ray structures than for NMR structures.

Availability and Implementation
All data are available from http://comprec-lin.iiar.pwr.edu.pl/dcaVSmisfolds/ and http://swift.cmbi.ru.nl/dcaVSmisfolds/.

Supplementary information
Supplementary data are available at Bioinformatics online.
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq
Authors: Tang Xing , Srivastava Arunima , Liu Huayang , Machiraju Raghu , Huang Kun , Leone Gustavo 
Published: January 2017

Abstract

Summary
We developed annoPeak, a web application to annotate, visualize and compare predicted protein-binding regions derived from ChIP-seq/ChIP-exo-seq experiments using human and mouse cells. Users can upload peak regions from multiple experiments onto the annoPeak server to annotate them with biological context, identify associated target genes and categorize binding sites with respect to gene structure. Users can also compare multiple binding profiles intuitively with the help of visualization tools and tables provided by annoPeak. In general, annoPeak will help users identify patterns of genome wide transcription factor binding profiles, assess binding profiles in different biological contexts and generate new hypotheses.

Availability and Implementation
The web service is freely accessible through URL: https://apps.medgen.iupui.edu/rsc/content/19/. Source code is available at https://github.com/XingTang2014/annoPeak.

Supplementary information
Supplementary data are available at Bioinformatics online.
HIPred: an integrative approach to predicting haploinsufficient genes
Authors: Shihab Hashem A , Rogers Mark F , Campbell Colin , Gaunt Tom R 
Published: January 2017

Abstract

Motivation
A major cause of autosomal dominant disease is haploinsufficiency, whereby a single copy of a gene is not sufficient to maintain the normal function of the gene. A large proportion of existing methods for predicting haploinsufficiency incorporate biological networks, e.g. protein-protein interaction networks that have recently been shown to introduce study bias. As a result, these methods tend to perform best on well-studied genes, but underperform on less studied genes. The advent of large genome sequencing consortia, such as the 1000 genomes project, NHLBI Exome Sequencing Project and the Exome Aggregation Consortium creates an urgent need for unbiased haploinsufficiency prediction methods.

Results
Here, we describe a machine learning approach, called HIPred, that integrates genomic and evolutionary information from ENSEMBL, with functional annotations from the Encyclopaedia of DNA Elements consortium and the NIH Roadmap Epigenomics Project to predict haploinsufficiency, without the study bias described earlier. We benchmark HIPred using several datasets and show that our unbiased method performs as well as, and in most cases, outperforms existing biased algorithms.

Availability and Implementation
HIPred scores for all gene identifiers are available at: https://github.com/HAShihab/HIPred.

Supplementary information
Supplementary data are available at Bioinformatics online.