bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous Septic Arthritis of Canine Elbows: Twenty-One Cases
Authors: Mielke Ben , Comerford Eithne , English Kate , Meeson Richard 
Published: October 2018

Objective This study provides information on clinical features, diagnosis, treatment and associated risk factors of spontaneous septic elbow arthritis in the dog.
Methods Medical records between March 2007 and June 2015 were searched for cases of spontaneous septic elbow arthritis with a diagnosis based on clinical signs, arthrocentesis, cytological and microbiological analysis of elbow joint synovial fluid, radiography and outcome following treatment.
Results Twenty-one cases of septic arthritis were identified. Pre-existing osteoarthritis was present in 14/15 elbows for which diagnostic imaging was available. Although all cases had increased neutrophil count on synovial fluid cytology, culture was only positive in 12/21. Despite initial improvement in lameness scores (pre-treatment 9/10 [range: 1–10] versus post-treatment 3/10 [range: 1–5]), 11/12 had residual long-term lameness. Recurrence of infection was noted in 3/12 elbows for which long-term (>8 weeks) follow-up was available. There was an acute mortality rate of 2/21 associated with severe systemic sepsis.
Clinical Significance Septic arthritis, even in the absence of pyrexia, should be considered as a major differential diagnosis in middle aged, large breed dogs, with pre-existing elbow arthritis, that suffer an acute onset lameness, with elbow joint effusion and discomfort. Antibiotic therapy alone was effective for treatment with high initial response rates. Chronic lameness post-treatment was common, and a high rate of recurrence was seen with 3/12 dogs suffering more than one episode.
Clinical and Radiographic Evaluation of Mineral Trioxide Aggregate Pulpotomy in Permanent Teeth
Authors: Verma Neha , Kaur Avninder , Acharya Shivesh , Sharma Sunila 
Published: October 2018

Abstract
Aim and objective: The aim of the present study was to evaluate clinical and radiographic outcome of MTA as a pulpotomy agent in permanent teeth as an alternative to conventional root canal treatment. Materials and Methods: Ten permanent teeth with symptoms of irreversible pulpitis with vital pulp were selected for the study. MTAPulpotomy procedure was done in all the cases using standard protocol. Teeth were evaluated for various clinical and radiographic parameters at 3, 6, 9 and 12 months of follow up. Results: None of the patients reported any kind of clinical discomfort or radiographic abnormality during the follow up period of 3, 6, 9 and 12 months. All the teeth responded positive on electric pulp test at all successive follow ups. Conclusions: MTA Pulpotomy may be used as an alternative treatment modality to root canal treatment in permanent teeth with irreversible pulpitis, if future research continues to show promising results.
Chronic social stress-induced hyperglycemia in mice couples individual stress susceptibility to impaired spatial memory
Authors: van der Kooij Michael A. , Jene Tanja , Treccani Giulia , Miederer Isabelle , Hasch Annika , Voelxen Nadine , Walenta Stefan , Müller Marianne B. 
Published: October 2018

Significance
Stress-associated mental disorders and diabetes pose an enormous socio-economic burden. Glucose dysregulation occurs with both psychosocial and metabolic stress. While cognitive impairments are common in metabolic disorders such as diabetes and are accompanied by hyperglycemia, a causal role for glucose has not been established. We show that chronic social defeat (CSD) stress induces lasting peripheral and central hyperglycemia and impaired glucose metabolism in a subgroup of mice. Animals exhibiting hyperglycemia early post-CSD display spatial memory impairments that can be rescued by the antidiabetic empagliflozin. We demonstrate that individual stress vulnerability to glucose homeostasis can be identified early after insult and that stress-induced hyperglycemia directly impinges on cognitive integrity. Our findings further bridge the gap between stress-related pathologies and metabolic disorders.
Highly disordered histone H1−DNA model complexes and their condensates
Authors: Turner Abigail L. , Watson Matthew , Wilkins Oscar G. , Cato Laura , Travers Andrew , Thomas Jean O. , Stott Katherine 
Published: October 2018

Significance
DNA is a stiff polymer that is condensed in vivo by polyamines and cationic proteins, many of which are intrinsically disordered. In eukaryotes, where DNA is packaged as chromatin, condensation of internucleosomal (linker) DNA is effected by the C-terminal tail of histone H1. Its structure and DNA binding are poorly understood, as is the link between H1 phosphorylation and chromatin structural changes during the cell cycle. Here we present a model system, with which we show that H1 binds tightly to DNA but retains a high level of disorder. Phase-separated condensates form, containing higher-order structures that are highly sensitive to the phosphorylation state of H1, suggesting a mechanism by which condensation of the chromatin fiber and other assemblies might be regulated.
Why large icosahedral viruses need scaffolding proteins
Authors: Li Siyu , Roy Polly , Travesset Alex , Zandi Roya 
Published: October 2018

Significance
Despite a plethora of experimental data on the role of scaffolding proteins in the structure of viral shells, no theoretical/numerical explanations have been put forward to decipher the indisputable need of large shells for scaffolding proteins. This paper explains the underlying physical mechanisms for the formation of large viral shells and elucidates the “universal” role of scaffolding proteins in the formation of large spherical crystals.
Nonproteinogenic deep mutational scanning of linear and cyclic peptides
Authors: Rogers Joseph M. , Passioura Toby , Suga Hiroaki 
Published: October 2018

Significance
The 20 proteinogenic amino acids have physicochemical properties that allow peptides and proteins to fold and bind. However, there are numerous unnatural, nonproteinogenic amino acids that may be equally good, or even better, at folding and binding. Exploration of these alternative peptide building blocks has been limited by slow, one-at-a-time synthesis and testing. We describe how, in a single experiment, multiple nonproteinogenic amino acids can be trialed at all positions in a peptide sequence, with thousands of modifications tested in parallel. This permits detailed analysis of how chemical structure relates to function and allows for systematic comparisons of proteinogenic and nonproteinogenic chemistry. Such analysis can guide the improvement of drug-candidate peptides, including the therapeutically promising class of cyclic peptides.
Word order as a subject test in Old Icelandic
Authors: Jónsson Jóhannes Gísli 
Published: October 2018

Abstract
The main claim of this article is that word order can be used to diagnose subjecthood in Old Icelandic if the relative order of subjects and objects in clauses where both arguments follow the finite verb is examined. The subject always precedes the object in such cases unless (i) the object is moved by Pronominal Object Scrambling, (ii) the subject is moved by Heavy/Indefinite Subject Shift, or (iii) the object contains a reflexive possessive which precedes its binder, a distributive subject. This means that a pronominal subject will always precede an object following the finite verb. It is also shown that these facts strongly support the existence of oblique subjects in Old Icelandic since oblique subjects behave exactly like nominative subject in that they must precede objects under the same conditions as nominative subjects.
Forty years in the search of a/the subject
Authors: Malchukov Andrej L. 
Published: October 2018

Abstract
The present short discussion piece presents my personal view of the studies of the topics related to the notion of subject, oblique subject and non-canonical subject marking over the last years. The presentation is of course subjective insofar as it reflects my range of interests in this field. Equally subjective is the selected timeframe mentioned in the title (“forty years”) which is meant to refer to the time when the notion of subject has been in the spotlight of typological interest.
Plural inflection in North Sea Germanic languages
Authors: Versloot Arjen P. , Adamczyk Elżbieta 
Published: October 2018

Abstract
The present study explores the variation in the plural inflection of eight varieties of Frisian and English, focusing on irregular plural formations. The aim of the study is to identify and assess the significance of the factors which contributed to the preservation and emergence of irregular plural patterns in the investigated varieties. Multivariate regression analysis, which was employed to weigh the significance of individual factors, reveals that the retention and emergence of irregular plural patterns is primarily determined by a combination of three major factors: relative frequency, absolute frequency and salience. These factors can be reduced to underlying cognitive processes, including the storage and retrieval of linguistic information in the human brain. Another relevant factor, semantics, affects the lemma frequency profile, but can gain momentum as a factor in its own right due to analogical co-activation in language processing.
Shifting of air pollutants distribution during car free day event
Authors: Huboyo H S , Wardhana I W , Sutrisno E , Budisulistiorini S H 
Published: October 2018

Abstract
According to Decree of Semarang Mayor No. 22/2011, car free day activities is addressed to give clean air for facilitating citizens activities. This car free day event is held every Sunday in the morning in the city center of Semarang i.e. located at Simpang Lima square. This research is aimed at identifying the shifting of pollutant during car fee day event by comparing ambient air pollutant concentration represented by carbon monoxide during car free day event and non-car free day event. About 14 streets had been measured its ambient CO concentration during Saturday (non-car free day event) and Sunday (car free day event). We also modeled (using Caline4) the CO dispersion at the certain area on those streets to know the spatial distribution of concentration during those two events. The ambient CO concentration, in general, during car free day event were somewhat increase for certain roads. The emission load of vehicles emission during CFD event was 1.37 times of non-CFD event. Nevertheless, based on spatial distribution of ambient CO concentration at the area of roads of interest, its concentrations were below the ambient CO concentration standard (PP.41/99).
PlateDesigner: a web-based application for the design of microplate experiments
Authors: Suprun Maria , Suárez-Fariñas Mayte 
Published: October 2018

Abstract

Summary
In biological assays, systematic variability, known as a batch effect, can often confound the effects of true biological conditions and has been well documented for a variety of high-throughput technologies. In microplate-based multiplex experiments, such as Luminex or OLINK assays, researchers need to consider both position and plate effects. Those effects can be easily accounted for if the experiments are properly designed, which includes randomization of the samples across multiple experimental runs. However, doing the ad hoc randomization becomes challenging when handling multiple samples. PlateDesigner is the first web-based application that provides randomization for microplate experiments, ensuring that the main principles of the experimental design, such as grouping samples from the same biological units and balancing the distribution of experimental conditions, are applied. Creating randomizations with PlateDesigner is simple and the results can be exported in a variety of formats, and easily integrated with microplate readers and statistical analysis software.

Availability and implementation
PlateDesigner is written in R/Shiny and is hosted online by the Center of Biostatistics at the Icahn School of Medicine at Mount Sinai. This application is freely available at platedesigner.net.
RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling
Authors: Zhao Dengke , Baez William D , Fredrick Kurt , Bundschuh Ralf 
Published: October 2018

Abstract

Motivation
Ribosome profiling has been widely used to study translation in a genome-wide fashion. It requires deep sequencing of ribosome protected mRNA fragments followed by mapping of fragments to the reference genome. For applications such as identification of ribosome pausing sites, it is not enough to map a fragment to a given gene, but the exact position of the ribosome represented by the fragment must be identified for each mRNA fragment. The assignment of the correct ribosome position is complicated by the broad length distribution of the ribosome protected fragments caused by the known sequence bias of micrococcal nuclease (MNase), the most widely used nuclease for digesting mRNAs in bacteria. Available mapping algorithms suffer from either MNase bias or low accuracy in characterizing the ribosome pausing kinetics.

Results
In this paper, we introduce a new computational method for mapping the ribosome protected fragments to ribosome locations. We first develop a mathematical model of the interplay between MNase digestion and ribosome protection of the mRNAs. We then use the model to reconstruct the ribosome occupancy profile on a per gene level. We demonstrate that our method has the capability of mitigating the sequence bias introduced by MNase and accurately locating ribosome pausing sites at codon resolution. We believe that our method can be broadly applied to ribosome profiling studies on bacteria where codon resolution is necessary.

Availability and implementation
Source code implementing our approach can be downloaded under GPL3 license at http://bioserv.mps.ohio-state.edu/RiboProP.

Supplementary information
Supplementary data are available at Bioinformatics online.
CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis
Authors: Badgeley Marcus A , Liu Manway , Glicksberg Benjamin S , Shervey Mark , Zech John , Shameer Khader , Lehar Joseph , Oermann Eric K , McConnell Michael V , Snyder Thomas M , Dudley Joel T 
Published: October 2018

Abstract

Motivation
Radiologists have used algorithms for Computer-Aided Diagnosis (CAD) for decades. These algorithms use machine learning with engineered features, and there have been mixed findings on whether they improve radiologists’ interpretations. Deep learning offers superior performance but requires more training data and has not been evaluated in joint algorithm-radiologist decision systems.

Results
We developed the Computer-Aided Note and Diagnosis Interface (CANDI) for collaboratively annotating radiographs and evaluating how algorithms alter human interpretation. The annotation app collects classification, segmentation, and image captioning training data, and the evaluation app randomizes the availability of CAD tools to facilitate clinical trials on radiologist enhancement.

Availability and implementation
Demonstrations and source code are hosted at (https://candi.nextgenhealthcare.org), and (https://github.com/mbadge/candi), respectively, under GPL-3 license.

Supplementary information
Supplementary material is available at Bioinformatics online.
TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction
Authors: Chen Li , Wang Ye , Yao Bing , Mitra Amit , Wang Xu , Qin Xiao 
Published: October 2018

Abstract

Summary
Predicting genetic regulatory variants, most of which locate in non-coding genomic regions, still remain a challenge in genetic research. Among all non-coding regulatory variants, cis-eQTL single nucleotide variants (SNVs) are of particular interest for their crucial role in regulating gene expression. Since different gene expression patterns are believed to contribute to the etiologies of different phenotypes, it is desirable to characterize the impact of cis-eQTL SNVs in a context-specific manner. Though computational methods for predicting the potential of variants being pathogenic or deleterious are well-established, methods for annotating and predicting cis-eQTL SNVs are under-developed. Here, we present TIVAN (TIssue-specific Variant ANnotation and prediction), an ensemble method of decision trees, to predict tissue-specific cis-eQTL SNVs. TIVAN is trained based on a comprehensive collection of features, including genome-wide genomic and epigenomic profiling data. As a result, TIVAN has been shown to accurately discriminate cis-eQTL SNVs from non-eQTL SNVs and perform favorably to other methods by obtaining higher five-fold cross-validation AUC values (CV-AUC) and Leave-One-Chromosome-Out predicted AUC values (LOCO-AUC) across 44 different tissues belonging to 27 different tissue classes. Finally, TIVAN consistently maintains top performance on an independent testing dataset, which includes 7 tissues in 11 studies.

Availability and implementation
TIVAN software is available at https://github.com/lichen-lab/TIVAN.

Supplementary information
Supplementary data are available at Bioinformatics online.
Characterization of cell fusion in an experimental mouse model of endometriosis†
Authors: Tal A , Tal R , Shaikh S , Gidicsin S , Mamillapalli R , Taylor H S 
Published: October 2018

Abstract
Cell fusion is involved in the development of some adult organs, is implicated in the pathogenesis of specific types of cancer, and is known to participate in repair/regeneration processes mediated by bone-marrow-derived cells (BMDCs). Endometriosis is a disease characterized by growth of functional endometrial tissue outside of the uterine cavity. Endometriosis shares some molecular properties with cancer and BMDCs home to endometriosis lesions in a mouse model. Our objective was to determine if cell fusion can occur in endometriosis and establish whether bone-marrow-derived cells participate in cell fusion events in lesions. We employed a Cre-Lox system to identify cell fusion events in a mouse model of endometriosis. Fused cells were detected in endometriotic lesions, albeit at a low frequency (∼1 in 400 cells), localized to the stromal compartment, and displayed restricted proliferation. Using 5-fluorouracil-based nongonadotoxic bone marrow transplantation model, we demonstrate that bone marrow cells represent a principal cell source for fusion events in lesions. Cell fusion progeny uniformly lacked expression of selected markers of hematopoietic, endothelial, and epithelial markers, though they expressed the mesenchymal/stromal markers Sca-1 and CD29. This study is the first to describe the phenomenon of cell fusion in endometriosis and points to a mesenchymal population derived from cell fusion events with limited proliferative activity, properties previously attributed to endometrial stem cells. Their putative role in the pathogenesis of the disease remains to be elucidated.
Featured Article: Bidirectional Effects of Sleep and Sedentary Behavior Among Toddlers: A Dynamic Multilevel Modeling Approach
Authors: Armstrong Bridget , Covington Lauren B , Unick George J , Black Maureen M 
Published: October 2018

Abstract

Objective
To examine the bidirectional effects of objectively measured nighttime sleep and sedentary activity among toddlers.

Method
Actical accelerometer data were analyzed for 195 toddlers participating in an obesity prevention trial (mean age = 27 months). Toddlers wore the accelerometers for up to 7 consecutive days. Nighttime sleep was defined as the number of minutes asleep between the hours of 8 pm and 8 am the following morning. Sedentary behavior (in minutes) was defined using previously established Actical cut points for toddlers. Variables were lagged and parsed into latent within- and between-person components, using dynamic structural equation modeling (DSEM).

Results
Toddlers spent an average of 172 min (∼3 hr) in sedentary activity and slept an average of 460 min (∼8 hr) per night. An autoregressive cross-lagged multilevel model revealed significant autoregression for both sleep and sedentary activity. Cross-lagged values revealed that decreased sleep predicted increased next-day sedentary activity, and sedentary activity predicted that night’s sleep. For 89% of the sample, the within-person standardized cross-lagged effects of sleep on sedentary were larger than the cross-lagged effects of sedentary on sleep.

Conclusions
Results suggest that, on average, nighttime sleep is a stronger predictor of subsequent sedentary behavior (compared with the reverse), and this is the case for the majority of toddlers. Findings highlight the importance of interindividual associations between sleep and sedentary activity. The present study is an example of how DSEM methods can be used to ask questions about Granger-causal cross-lagged relations between variables, both within and between individuals.
Applications of chemical imaging techniques in paleontology
Authors: Pan Yanhong , Hu Liang , Zhao Tao 
Published: October 2018

Abstract
Chemical imaging techniques, based on a combination of microscopy and spectroscopy, are designed to analyse the composition and spatial distribution of heterogeneous chemical complexes within a sample. Over the last few decades, it has become an increasingly popular tool for characterizing trace elements, isotopic information and organic biomarkers (molecular biosignatures) found in fossils. Here, we introduce the analytical principle of each technique and the interpretation of the chemical signals, followed by a review of the main applications of these techniques in paleontology. We also demonstrate that each technique is associated with pros and cons, and the current limitations and obstacles associated with the use of each specific technique should be taken into account before being applied to fossil samples. Finally, we propose that, due to the rapid advances in the available technology and overall trends towards more multi-disciplinary studies in paleontology, chemical imaging techniques can be expected to have broader applications in paleontology in the near future.
Gender Wage Inequalities Between Historical Heritage and Structural Adjustments: A German–German Comparison Over Time
Authors: Minkus Lara , Busch-Heizmann Anne 
Published: October 2018

AbstractWhile research on the gender pay gap (GPG) is growing, there is little evidence on the stability or convergence of GPGs against the backdrop of sudden historical changes. Taking advantage of German reunification, after which western male-breadwinner policies were superimposed on the hitherto gender egalitarian East, we illuminate this research gap. Using decompositions on the Socio-economic Panel, we examine how historically grown gender arrangements influence the GPG in eastern and western Germany 1990–2013. We find support for the concept of a stalled gender revolution and a continued influence of pre-unification gender arrangements on the German GPG.