bluuebunny/crossref_metadata_2025_split huggingface dataset:
admixturegraph: an R package for admixture graph manipulation and fitting
Authors: Leppälä Kalle , Nielsen Svend V , Mailund Thomas 
Published: January 2017

Abstract

Summary
Admixture graphs generalize phylogenetic trees by allowing genetic lineages to merge as well as split. In this paper we present the R package admixturegraph containing tools for building and visualizing admixture graphs, for fitting graph parameters to genetic data, for visualizing goodness of fit and for evaluating the relative goodness of fit between different graphs.

Availability and Implementation
GitHub: https://github.com/mailund/admixture_graph and CRAN: https://cran.r-project.org/web/packages/admixturegraph.
Bayesian network–response regression
Authors: Wang Lu , Durante Daniele , Jung Rex E , Dunson David B 
Published: January 2017

Abstract

Motivation
There is increasing interest in learning how human brain networks vary as a function of a continuous trait, but flexible and efficient procedures to accomplish this goal are limited. We develop a Bayesian semiparametric model, which combines low-rank factorizations and flexible Gaussian process priors to learn changes in the conditional expectation of a network-valued random variable across the values of a continuous predictor, while including subject-specific random effects.

Results
The formulation leads to a general framework for inference on changes in brain network structures across human traits, facilitating borrowing of information and coherently characterizing uncertainty. We provide an efficient Gibbs sampler for posterior computation along with simple procedures for inference, prediction and goodness-of-fit assessments. The model is applied to learn how human brain networks vary across individuals with different intelligence scores. Results provide interesting insights on the association between intelligence and brain connectivity, while demonstrating good predictive performance.

Availability and Implementation
Source code implemented in R and data are available at https://github.com/wangronglu/BNRR

Supplementary information
Supplementary data are available at Bioinformatics online.
NSSRF: global network similarity search with subgraph signatures and its applications
Authors: Zhang Jiao , Kwong Sam , Jia Yuheng , Wong Ka-Chun 
Published: January 2017

Abstract

Motivation
The exponential growth of biological network database has increasingly rendered the global network similarity search (NSS) computationally intensive. Given a query network and a network database, it aims to find out the top similar networks in the database against the query network based on a topological similarity measure of interest. With the advent of big network data, the existing search methods may become unsuitable since some of them could render queries unsuccessful by returning empty answers or arbitrary query restrictions. Therefore, the design of NSS algorithm remains challenging under the dilemma between accuracy and efficiency.

Results
We propose a global NSS method based on regression, denotated as NSSRF, which boosts the search speed without any significant sacrifice in practical performance. As motivated from the nature, subgraph signatures are heavily involved. Two phases are proposed in NSSRF: offline model building phase and similarity query phase. In the offline model building phase, the subgraph signatures and cosine similarity scores are used for efficient random forest regression (RFR) model training. In the similarity query phase, the trained regression model is queried to return similar networks. We have extensively validated NSSRF on biological pathways and molecular structures; NSSRF demonstrates competitive performance over the state-of-the-arts. Remarkably, NSSRF works especially well for large networks, which indicates that the proposed approach can be promising in the era of big data. Case studies have proven the efficiencies and uniqueness of NSSRF which could be missed by the existing state-of-the-arts.

Availability and Implementation
The source code of two versions of NSSRF are freely available for downloading at https://github.com/zhangjiaobxy/nssrfBinary and https://github.com/zhangjiaobxy/nssrfPackage.

Supplementary information
Supplementary data are available at Bioinformatics online.
Automated cell type discovery and classification through knowledge transfer
Authors: Lee Hao-Chih , Kosoy Roman , Becker Christine E , Dudley Joel T , Kidd Brian A 
Published: January 2017

Abstract

Motivation
Recent advances in mass cytometry allow simultaneous measurements of up to 50 markers at single-cell resolution. However, the high dimensionality of mass cytometry data introduces computational challenges for automated data analysis and hinders translation of new biological understanding into clinical applications. Previous studies have applied machine learning to facilitate processing of mass cytometry data. However, manual inspection is still inevitable and becoming the barrier to reliable large-scale analysis.

Results
We present a new algorithm called Automated Cell-type Discovery and Classification (ACDC) that fully automates the classification of canonical cell populations and highlights novel cell types in mass cytometry data. Evaluations on real-world data show ACDC provides accurate and reliable estimations compared to manual gating results. Additionally, ACDC automatically classifies previously ambiguous cell types to facilitate discovery. Our findings suggest that ACDC substantially improves both reliability and interpretability of results obtained from high-dimensional mass cytometry profiling data.

Availability and Implementation
A Python package (Python 3) and analysis scripts for reproducing the results are availability on https://bitbucket.org/dudleylab/acdc.

Supplementary information
Supplementary data are available at Bioinformatics online.
Salsamenta pictavensium: Gastronomy and Medicine in Twelfth-Century England
Authors: Gasper Giles E.M. , Wallis Faith 
Published: January 2017

Abstract
This article presents a collection of culinary recipes from a manuscript produced in England from the later twelfth century. The suite of ten recipes for ‘Poitou sauces’ or ‘Poitou relishes’ (salsamenta pictavensium—literally ‘of the Poitevins’) to garnish various kinds of meat, fish and fowl are introduced and analysed, with an appended edition and translation. These are, to date, the oldest extant medieval recipes for such sauces, and in their role as gastronomic enhancements, the earliest surviving medieval culinary recipes. The historical and cultural contexts for the recipes at Durham Cathedral Priory are explored: the nature of the community for whom the recipes were written, its choices of library acquisition, its relationships with the bishopric, and attitudes within the community towards food and medicine in a monastic setting. The Poitevin designation of the sauces is also considered. Above all the article investigates the question of the relationship between gastronomy and medicine in the twelfth century, and seeks to demonstrate that any distinction between medical and culinary recipes suggests a false dichotomy, particularly in the case of salsamenta. The authors argue against the position that medieval cuisine is, in its origins and essence, applied dietetics, and suggest that in the twelfth century salsamenta belonged in the first instance to gastronomy, but were in the process of being appropriated as medicines by the authors of the new literature of therapeutics.
More than a fair share of good luck
Authors: Jobling Malcolm 
Published: January 2017

This article deals with reflections on a career as a fish biologist that has spanned 40 + years. I provide insights into lessons I have learned over the years, describe some research successes and failures, and end by drawing the conclusion that variety in teaching and research is the spice of academic life. The lessons I have learned might be a guide for those at an early stage of their scientific career:
You should try to recognize where your talents lie and what your weaknesses are: play to your strengths, but do not try to hide your weaknesses.
Collaboration with perceptive colleagues and receptive associates is the foundation upon which an academic career is built.
Research should be designed to address a problem, not apply a technique; use the technology, and do not submit to the temptation of letting it use you.
The most rewarding pieces of research are often those that produce unexpected results; you learn more from having your preconceived ideas challenged than by having them confirmed.
It is important to know who your readers are, and to select the most appropriate channel for publication of your work. It is not necessary to publish in high impact factor journals to get your work read and cited.
You are likely to shift your focus many times during your career; you must continue to grow to remain fresh and enthusiastic.
Your students are your scientific legacy; nurture them well because there is nothing more satisfying than to see them succeed.
I offer a final piece of advice: Should teaching and research cease to be fascinating and fun, move on; do not risk becoming a square peg in a round hole.
Decrease in unnecessary vitamin D testing using clinical decision support tools: making it harder to do the wrong thing
Authors: Felcher Andrew H , Gold Rachel , Mosen David M , Stoneburner Ashley B 
Published: January 2017

Abstract
Objective:To evaluate the impact of clinical decision support (CDS) tools on rates of vitamin D testing. Screening for vitamin D deficiency has increased in recent years, spurred by studies suggesting vitamin D’s clinical benefits. Such screening, however, is often unsupported by evidence and can incur unnecessary costs.
Materials and Methods:We evaluated how rates of vitamin D screening changed after we implemented 3 CDS tools in the electronic health record (EHR) of a large health plan: (1) a new vitamin D screening guideline, (2) an alert that requires clinician acknowledgement of current guidelines to continue ordering the test (a “hard stop”), and (3) a modification of laboratory ordering preference lists that eliminates shortcuts. We assessed rates of overall vitamin D screening and appropriate vitamin D screening 6 months pre- and post-intervention.
Results:Vitamin D screening rates decreased from 74.0 tests to 24.2 tests per 1000 members (P &lt; .0001). The proportion of appropriate vitamin D screening tests increased from 56.2% to 69.7% (P &lt; .0001), and the proportion of inappropriate screening tests decreased from 43.8% pre-implementation to 30.3% post-implementation (P &lt; .0001).
Discussion:To our knowledge, this is the first demonstration of how CDS can reduce rates of inappropriate vitamin D screening. We used 3 straightforward, inexpensive, and replicable CDS approaches. We know of no previous research on the impact of removing options from a preference list.
Conclusion:Similar approaches could be used to reduce unnecessary care and decrease costs without reducing quality of care.
Prevalence and significance of plasma Epstein-Barr Virus DNA level in nasopharyngeal carcinoma
Authors: Prayongrat Anussara , Chakkabat Chakkapong , Kannarunimit Danita , Hansasuta Pokrath , Lertbutsayanukul Chawalit 
Published: January 2017

Abstract
Epstein-Barr virus (EBV) DNA has been recognized as a promising tumor marker for nasopharyngeal carcinoma (NPC). This study aims to demonstrate the prevalence of plasma EBV DNA and its temporal correlation with treatment outcomes in the modern era. A total of 204 patients with Stage I–IVB NPC treated with intensity-modulated radiotherapy (IMRT) were enrolled. Quantitative plasma EBV DNA measurement was performed before treatment (pre-IMRT), on the fifth week of radiation (mid-IMRT), at 3 months after radiation (post-IMRT), then every 6 months until disease relapse. Progression-free survival (PFS) and overall survival (OS) were analyzed using the Kaplan–Meier method. Plasma EBV DNA was detected in 110 patients (53.9%), with a median pre-IMRT EBV DNA level of 8005 copies/ml. Significant correlation was noted between pre-IMRT EBV DNA level and disease stage, but not between pre-IMRT EBV DNA level and World Health Organization classification. With a median follow-up time of 35.1 months, the 3-year PFS and OS rates were higher in the group with undetectable pre-IMRT EBV DNA level compared with in the group in which it was detectable. When classified according to disease stage and pre-IMRT EBV DNA, patients with early disease and detectable pre-IMRT EBV DNA experienced poorer survival than those with locally advanced disease and undetectable pre-IMRT EBV DNA. According to the dynamic changes in EBV DNA level between pre-IMRT and mid/post IMRT, survival was significantly higher in patients who achieved an undetectable level following treatment. On multivariate analysis, post-IMRT EBV DNA level was the strongest predictor of all treatment outcomes (P &lt; 0.001). Our study demonstrated the clinical significance of the plasma EBV DNA level at specific time points, as well as of the dynamic changes in the EBV DNA level. Disappearance of plasma EBV DNA after treatment was associated with better survival.
Credit Expansion and Neglected Crash Risk*
Authors: Baron Matthew , Xiong Wei 
Published: January 2017

Abstract
By analyzing 20 developed economies over 1920–2012, we find the following evidence of overoptimism and neglect of crash risk by bank equity investors during credit expansions: (i) bank credit expansion predicts increased bank equity crash risk, but despite the elevated crash risk, also predicts lower mean bank equity returns in subsequent one to three years; (ii) conditional on bank credit expansion of a country exceeding a 95th percentile threshold, the predicted excess return for the bank equity index in subsequent three years is −37.3%; and (iii) bank credit expansion is distinct from equity market sentiment captured by dividend yield and yet dividend yield and credit expansion interact with each other to make credit expansion a particularly strong predictor of lower bank equity returns when dividend yield is low.
Product Standards and Firms’ Export Decisions
Authors: Fernandes Ana M , Ferro Esteban , Wilson John S 
Published: January 2017

Abstract
Two novel datasets are used to estimate the effect of product standards on firms’ export decisions. The first covers all exporting firms in 42 developing countries. The second covers pesticide standards for 243 agricultural and food products in 80 importing countries over 2006–2012. The analysis shows that product standards affect significantly foreign market access. An increase in the stringency of standards in the destination country, relative to the exporting country, lowers firms’ probability of exporting, deters exporters from entering new markets, and fosters exit from existing markets. Smaller exporters are more affected in their market entry and exit decisions by the relative stringency of destination standards than larger exporters. Networks of other exporters from the same country can help overcome the negative effects of the relative stringency of destination standards on exporter entry and exit.
Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)
Authors: Dolotovskaya Sofya , Torroba Bordallo Juan , Haus Tanja , Noll Angela , Hofreiter Michael , Zinner Dietmar , Roos Christian 
Published: January 2017

Abstract
Complete mitochondrial (mtDNA) genomes have proved to be useful in reconstructing primate phylogenies with higher resolution and confidence compared to reconstructions based on partial mtDNA sequences. Here, we analyse complete mtDNA genomes of African green monkeys (genus Chlorocebus), a widely distributed primate genus in Africa representing an interesting phylogeographical model for the evolution of savannah species. Previous studies on partial mtDNA sequences revealed nine major clades, suggesting several cases of para- and polyphyly among Chlorocebus species. However, in these studies, phylogenetic relationships among several clades were not resolved, and divergence times were not estimated. We analysed complete mtDNA genomes for ten Chlorocebus samples representing major mtDNA clades to find stronger statistical support in the phylogenetic reconstruction than in the previous studies and to estimate divergence times. Our results confirmed para- and polyphyletic relationships of most Chlorocebus species, while the support for the phylogenetic relationships between the mtDNA clades increased compared to the previous studies. Our results indicate an initial west–east division in the northern part of the Chlorocebus range with subsequent divergence into north-eastern and southern clades. This phylogeographic scenario contrasts with that for another widespread African savannah primate genus, the baboons (Papio), for which a dispersal from southern Africa into East and West Africa was suggested.
Grid cells show field-to-field variability and this explains the aperiodic response of inhibitory interneurons
Authors: Dunn Benjamin , Wennberg Daniel , Huang Ziwei , Roudi Yasser 
Published: January 2017

AbstractResearch on network mechanisms and coding properties of grid cells assume that the firing rate of a grid cell in each of its fields is the same. Furthermore, proposed network models predict spatial regularities in the firing of inhibitory interneurons that are inconsistent with experimental data. In this paper, by analyzing the response of grid cells recorded from rats during free navigation, we first show that there are strong variations in the mean firing rate of the fields of individual grid cells and thus show that the data is inconsistent with the theoretical models that predict similar peak magnitudes. We then build a two population excitatory-inhibitory network model in which sparse spatially selective input to the excitatory cells, presumed to arise from e.g. salient external stimuli, hippocampus or a combination of both, leads to the variability in the firing field amplitudes of grid cells. We show that, when combined with appropriate connectivity between the excitatory and inhibitory neurons, the variability in the firing field amplitudes of grid cells results in inhibitory neurons that do not exhibit regular spatial firing, consistent with experimental data. Finally, we show that even if the spatial positions of the fields are maintained, variations in the firing rates of the fields of grid cells are enough to cause remapping of hippocampal cells.
Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture
Authors: Schreiber Jacob , Libbrecht Maxwell , Bilmes Jeffrey , Noble William Stafford 
Published: January 2017

AbstractRecently, Hi-C has been used to probe the 3D chromatin architecture of multiple organisms and cell types. The resulting collections of pairwise contacts across the genome have connected chromatin architecture to many cellular phenomena, including replication timing and gene regulation. However, high resolution (10 kb or finer) contact maps remain scarce due to the expense and time required for collection. A computational method for predicting pairwise contacts without the need to run a Hi-C experiment would be invaluable in understanding the role that 3D chromatin architecture plays in genome biology. We describe Rambutan, a deep convolutional neural network that predicts Hi-C contacts at 1 kb resolution using nucleotide sequence and DNaseI assay signal as inputs. Specifically, Rambutan identifies locus pairs that engage in high confidence contacts according to Fit-Hi-C, a previously described method for assigning statistical confidence estimates to Hi-C contacts. We first demonstrate Rambutan’s performance across chromosomes at 1 kb resolution in the GM12878 cell line. Subsequently, we measure Rambutan’s performance across six cell types. In this setting, the model achieves an area under the receiver operating characteristic curve between 0.7662 and 0.8246 and an area under the precision-recall curve between 0.3737 and 0.9008. We further demonstrate that the predicted contacts exhibit expected trends relative to histone modification ChlP-seq data, replication timing measurements, and annotations of functional elements such as promoters and enhancers. Finally, we predict Hi-C contacts for 53 human cell types and show that the predictions cluster by cellular function. [NOTE: After our original submission we discovered an error in our calling of statistically significant contacts. Briefly, when calculating the prior probability of a contact, we used the number of contacts at a certain genomic distance in a chromosome but divided by the total number of bins in the full genome. When we corrected this mistake we noticed that the Rambutan model, as it curently stands, did not outperform simply using the GM12878 contact map that Rambutan was trained on as the predictor in other cell types. While we investigate these new results, we ask that readers treat this manuscript skeptically.]
Radiative energy budgets of phototrophic surface-associated microbial communities and their photosynthetic efficiency under diffuse and collimated light
Authors: Lichtenberg Mads , Brodersen Kasper Elgetti , Kühl Michael 
Published: January 2017

AbstractWe investigated the radiative energy budgets of a heterogeneous photosynthetic coral reef sediment and a compact uniform cyanobacterial biofilm on top of coastal sediment. By combining electrochemical, thermocouple and fiber-optic microsensor measurements of O2, temperature and light, we could calculate the proportion of the absorbed light energy that was either dissipated as heat or conserved by photosynthesis. We show, across a range of different incident light regimes, that such radiative energy budgets are highly dominated by heat dissipation constituting up to 99.5% of the absorbed light energy. Highest photosynthetic energy conservation efficiency was found in the coral sediment under light-limiting conditions and amounted to ~13% of the absorbed light energy. Additionally, the effect of light directionality, i.e., diffuse or collimated light, on energy conversion efficiency was tested on the two surface-associated systems. The effects of light directionality on the radiative energy budgets of these phototrophic communities were not unanimous but, resulted in local spatial differences in heat-transfer, gross photosynthesis and light distribution. The light acclimation index, Ekwas >2 times higher in the coral sediment compared to the biofilm and changed the pattern of photosynthetic energy conservation under light-limiting conditions. At moderate to high incident 45 irradiances, the photosynthetic conservation of absorbed energy was highest in collimated light; a tendency that changed in the biofilm under sub-saturating incident irradiances, where higher photosynthetic efficiencies were observed under diffuse light. Our results suggest that the optical properties and the structural organization of phytoelements are important traits affecting the photosynthetic efficiency of biofilms and sediments.