bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of the sun as a heading indicator when caching and recovering in a wild rodent
Authors: Samson Jamie , Manser Marta B. 
Published: September 2016

AbstractA number of diurnal species have been shown to use directional information from the sun to orientate. The use of the sun in this way has been suggested to occur in either a time-dependent (relying on specific positional information) or a time-compensated manner (a compass that adjusts itself over time with the shifts in the sun’s position). However, some interplay may occur between the two where a species could also use the sun in a time-limited way, whereby animals acquire certain information about the change of position, but do not show full compensational abilities. We tested whether Cape ground squirrels (Xerus inauris) use the sun as an orientation marker to provide information for caching and recovery. This species is a social sciurid that inhabits arid, sparsely vegetated habitats in Southern Africa, where the sun is nearly always visible during the diurnal period. Due to the lack of obvious landmarks, we predicted that they might use positional cues from the sun in the sky as a reference point when caching and recovering food items. We provide evidence that Cape ground squirrels use information from the sun’s position while caching and reuse this information in a time-limited way when recovering these caches.
Case Report of Posttraumatic Middle Cerebral Artery Territory Infarct
Authors: Unnithan Ajaya 
Published: September 2016

A 27-year-old man had severe diffuse brain injury. The patient developed malignant right MCA territory infarction on second day. Emergency decompressive craniectomy was done. He was ventilated. He developed subdural hygroma on the opposite side that was drained. He improved slowly. He had hydrocephalus. VP shunt was done. He became conscious but dependent. PEG was done for feeding. Cranioplasty was done for syndrome of trephined. The patent improved to a state of good cognition with residual motor aphasia and left hemiplegia.Posttraumatic cerebral infarction is an indicator of poor prognosis. Vasospasm, intimal dissection, and thrombosis are the mechanisms. MCA territorial infarction is rare. Usual mechanism is impact of rotational forces on relatively fixed M1 segment on the posterior margin of lower wing of sphenoid, resulting in arterial dissection or intimal damage.
De novo DNA methylation by DNA methyltransferase 3a controls early effector CD8+T-cell fate decisions following activation
Authors: Ladle Brian H. , Li Kun-Po , Phillips Maggie J. , Pucsek Alexandra B. , Haile Azeb , Powell Jonathan D. , Jaffee Elizabeth M. , Hildeman David A. , Gamper Christopher J. 
Published: September 2016

SignificanceUpon activation and proliferation, CD8+T cells uniformly differentiate first into an early effector cell stage. This is followed by divergent differentiation into a mix of memory precursor and terminal effector cells. The contributing factors to the fate decisions during the early effector cell stage continue to be deciphered. Here we report the critical role of the de novo DNA methyltransferase 3a (DNMT3a) in restricting the development of memory precursor cells and allowing normal terminal effector cell differentiation. Importantly, the effects of DNMT3a-mediated DNA methylation occur during the early effector cell stage of CD8+T-cell differentiation.
Atom–atom interactions around the band edge of a photonic crystal waveguide
Authors: Hood Jonathan D. , Goban Akihisa , Asenjo-Garcia Ana , Lu Mingwu , Yu Su-Peng , Chang Darrick E. , Kimble H. J. 
Published: September 2016

Significance
In recent years, there has been considerable effort to bring ultracold atoms into the realm of nanophotonics. Nanoscopic dielectric devices offer unprecedented opportunities to engineer novel capabilities for the control of atom–photon interactions. In particular, photonic crystals are periodic dielectric structures that display a photonic bandgap where light cannot propagate and provide a new setting for coherent photon-mediated interactions between atoms with tunable range. Here, we report the initial observation of cooperative atom–atom interactions around the band edge of a photonic crystal waveguide. Our experiment opens the door to fascinating scenarios, such as exploring many-body physics with large spin exchange energies and low dissipation.
Non-Faith-Based Arguments against Physician-Assisted Suicide and Euthanasia
Authors: Sulmasy Daniel P. , Travaline John M. , Mitchell Louise A. , Ely E. Wesley 
Published: September 2016

This article is a complement to “A Template for Non-Religious-Based Discussions Against Euthanasia” by Melissa Harintho, Nathaniel Bloodworth, and E. Wesley Ely which appeared in the February 2015 Linacre Quarterly. Herein we build upon Daniel Sulmasy's opening and closing arguments from the 2014 Intelligence Squared debate on legalizing assisted suicide, supplemented by other non-faith-based arguments and thoughts, providing four nontheistic arguments against physician-assisted suicide and euthanasia: (1) “it offends me”; (2) slippery slope; (3) “pain can be alleviated”; (4) physician integrity and patient trust. Lay Summary: Presented here are four non-religious, reasonable arguments against physician-assisted suicide and euthanasia: (1) “it offends me,” suicide devalues human life; (2) slippery slope, the limits on euthanasia gradually erode; (3) “pain can be alleviated,” palliative care and modern therapeutics more and more adequately manage pain; (4) physician integrity and patient trust, participating in suicide violates the integrity of the physician and undermines the trust patients place in physicians to heal and not to harm.
Correlations of polyploidy and apomixis with elevation and associated environmental gradients in an alpine plant
Authors: Schinkel Christoph C. F. , Kirchheimer Bernhard , Dellinger Agnes S. , Klatt Simone , Winkler Manuela , Dullinger Stefan , Hörandl Elvira 
Published: September 2016

AbstractApomictic plants expand their geographical distributions more to higher elevations compared to their sexual progenitors. It was so far unclear whether this tendency is related to mode of reproduction itself or represents a side effect of polyploidy. Apomixis is advantageous for range expansions as no mating partners and pollinators are needed (Baker’s rule). Polyploidy is thought to infer fitness advantages and a higher vigour that would enable plants to adjust better to more extreme climatic conditions. However, little is known about actual performance of plants at higher elevations. We analyzed 81 populations of Ranunculus kuepferi from the whole distribution area in the European Alps to quantify apomictic versus sexual seed formation via flow cytometric seed screening. Seed set and vegetative growth were measured as fitness parameters. All parameters were correlated to geographical distribution, elevation, temperature and precipitation. Flow cytometric seed screening revealed predominantly obligate sexuality (88.9 %) and facultative apomixis in diploid populations, while tetraploid populations are predominantly facultative (65.4 %) to obligate apomictic. Apomictic seed formation correlated significantly to higher elevations, which explains also the observed niche shift to lower temperatures. However, within the tetraploid range, there is no apparent correlation of degree of facultative apomixis to geographical distance. Apomixis appeared in diploids three times independently in separated, otherwise sexual populations in the southwestern refugial areas of the Alps. Diploid apomixis was not successful in range expansions, and obligate sexual polyploids were not observed. Polyploidy may relate to cold tolerance as an adaptation to conditions at high elevations, where diploid sexuals have no fitness advantage. Instead, facultative apomixis may have aided colonization of higher elevations and range expansions in the Alps without mate and pollinator limitation, but did not necessarily involve long-distance dispersal. A direct influence of low temperatures on unreduced gamete formation cannot be ruled out.
Information-optimal genome assembly via sparse read-overlap graphs
Authors: Shomorony Ilan , Kim Samuel H , Courtade Thomas A , Tse David N C 
Published: September 2016

Abstract

Motivation
In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits. In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence?

Results
Based on insights from this information feasibility question, we present an algorithm—the Not-So-Greedy algorithm—to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50.

Availability
Available at github.com/samhykim/nsg

Contact
courtade@eecs.berkeley.edu or dntse@stanford.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
Assemble CRISPRs from metagenomic sequencing data
Authors: Lei Jikai , Sun Yanni 
Published: September 2016

Abstract

Motivation
Clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) allows more specific and efficient gene editing than all previous genetic engineering systems. These exciting discoveries stem from the finding of the CRISPR system being an adaptive immune system that protects the prokaryotes against exogenous genetic elements such as phages. Despite the exciting discoveries, almost all knowledge about CRISPRs is based only on microorganisms that can be isolated, cultured and sequenced in labs. However, about 95% of bacterial species cannot be cultured in labs. The fast accumulation of metagenomic data, which contains DNA sequences of microbial species from natural samples, provides a unique opportunity for CRISPR annotation in uncultivable microbial species. However, the large amount of data, heterogeneous coverage and shared leader sequences of some CRISPRs pose challenges for identifying CRISPRs efficiently in metagenomic data.

Results
In this study, we developed a CRISPR finding tool for metagenomic data without relying on generic assembly, which is error-prone and computationally expensive for complex data. Our tool can run on commonly available machines in small labs. It employs properties of CRISPRs to decompose generic assembly into local assembly. We tested it on both mock and real metagenomic data and benchmarked the performance with state-of-the-art tools.

Availability and Implementation
The source code and the documentation of metaCRISPR is available at https://github.com/hangelwen/metaCRISPR.

Contact
yannisun@msu.edu
Large-scale inference of conjunctive Bayesian networks
Authors: Montazeri Hesam , Kuipers Jack , Kouyos Roger , Böni Jürg , Yerly Sabine , Klimkait Thomas , Aubert Vincent , Günthard Huldrych F , Beerenwinkel Niko ,   The Swiss HIV Cohort Study
Published: September 2016

Abstract
The continuous time conjunctive Bayesian network (CT-CBN) is a graphical model for analyzing the waiting time process of the accumulation of genetic changes (mutations). CT-CBN models have been successfully used in several biological applications such as HIV drug resistance development and genetic progression of cancer. However, current approaches for parameter estimation and network structure learning of CBNs can only deal with a small number of mutations (&lt;20). Here, we address this limitation by presenting an efficient and accurate approximate inference algorithm using a Monte Carlo expectation-maximization algorithm based on importance sampling. The new method can now be used for a large number of mutations, up to one thousand, an increase by two orders of magnitude. In simulation studies, we present the accuracy as well as the running time efficiency of the new inference method and compare it with a MLE method, expectation-maximization, and discrete time CBN model, i.e. a first-order approximation of the CT-CBN model. We also study the application of the new model on HIV drug resistance datasets for the combination therapy with zidovudine plus lamivudine (AZT + 3TC) as well as under no treatment, both extracted from the Swiss HIV Cohort Study database.

Availability and implementation
The proposed method is implemented as an R package available at https://github.com/cbg-ethz/MC-CBN.

Contact
niko.beerenwinkel@bsse.ethz.ch

Supplementary information
Supplementary data are available at Bioinformatics online.
L 1 regularization facilitates detection of cell type-specific parameters in dynamical systems
Authors: Steiert Bernhard , Timmer Jens , Kreutz Clemens 
Published: September 2016

AbstractMotivationA major goal of drug development is to selectively target certain cell types. Cellular decisions influenced by drugs are often dependent on the dynamic processing of information. Selective responses can be achieved by differences between the involved cell types at levels of receptor, signaling, gene regulation or further downstream. Therefore, a systematic approach to detect and quantify cell type-specific parameters in dynamical systems becomes necessary.ResultsHere, we demonstrate that a combination of nonlinear modeling with L1 regularization is capable of detecting cell type-specific parameters. To adapt the least-squares numerical optimization routine to L1 regularization, sub-gradient strategies as well as truncation of proposed optimization steps were implemented. Likelihood-ratio tests were used to determine the optimal regularization strength resulting in a sparse solution in terms of a minimal number of cell type-specific parameters that is in agreement with the data. By applying our implementation to a realistic dynamical benchmark model of the DREAM6 challenge we were able to recover parameter differences with an accuracy of 78%. Within the subset of detected differences, 91% were in agreement with their true value. Furthermore, we found that the results could be improved using the profile likelihood. In conclusion, the approach constitutes a general method to infer an overarching model with a minimum number of individual parameters for the particular models.Availability and ImplementationA MATLAB implementation is provided within the freely available, open-source modeling environment Data2Dynamics. Source code for all examples is provided online at http://www.data2dynamics.org/.Contactbernhard.steiert@fdm.uni-freiburg.de
CoLoRMap: Correcting Long Reads by Mapping short reads
Authors: Haghshenas Ehsan , Hach Faraz , Sahinalp S Cenk , Chauve Cedric 
Published: September 2016

Abstract

Motivation
Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.

Results
We introduce CoLoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.

Availability and Implementation
The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormap

Contact
ehaghshe@sfu.ca or cedric.chauve@sfu.ca

Supplementary information
Supplementary data are available at Bioinformatics online.
LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs
Authors: Äijö Tarmo , Yue Xiaojing , Rao Anjana , Lähdesmäki Harri 
Published: September 2016

Abstract

Motivation
5-methylcytosine (5mC) is a widely studied epigenetic modification of DNA. The ten-eleven translocation (TET) dioxygenases oxidize 5mC into oxidized methylcytosines (oxi-mCs): 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). DNA methylation modifications have multiple functions. For example, 5mC is shown to be associated with diseases and oxi-mC species are reported to have a role in active DNA demethylation through 5mC oxidation and DNA repair, among others, but the detailed mechanisms are poorly understood. Bisulphite sequencing and its various derivatives can be used to gain information about all methylation modifications at single nucleotide resolution. Analysis of bisulphite based sequencing data is complicated due to the convoluted read-outs and experiment-specific variation in biochemistry. Moreover, statistical analysis is often complicated by various confounding effects. How to analyse 5mC and oxi-mC data sets with arbitrary and complex experimental designs is an open and important problem.

Results
We propose the first method to quantify oxi-mC species with arbitrary covariate structures from bisulphite based sequencing data. Our probabilistic modeling framework combines a previously proposed hierarchical generative model for oxi-mC-seq data and a general linear model component to account for confounding effects. We show that our method provides accurate methylation level estimates and accurate detection of differential methylation when compared with existing methods. Analysis of novel and published data gave insights into to the demethylation of the forkhead box P3 (Foxp3) locus during the induced T regulatory cell differentiation. We also demonstrate how our covariate model accurately predicts methylation levels of the Foxp3 locus. Collectively, LuxGLM method improves the analysis of DNA methylation modifications, particularly for oxi-mC species.

Availability and Implementation
An implementation of the proposed method is available under MIT license at https://github.org/tare/LuxGLM/

Contact
taijo@simonsfoundation.org or harri.lahdesmaki@aalto.fi

Supplementary information
Supplementary data are available at Bioinformatics online.
Rail-RNA: scalable analysis of RNA-seq splicing and coverage
Authors: Nellore Abhinav , Collado-Torres Leonardo , Jaffe Andrew E , Alquicira-Hernández José , Wilks Christopher , Pritt Jacob , Morton James , Leek Jeffrey T , Langmead Ben 
Published: September 2016

Abstract

Motivation
RNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. Current spliced alignment software is designed to analyze each sample separately. Consequently, no information is gained from analyzing multiple samples together, and it requires extra work to obtain analysis products that incorporate data from across samples.

Results
We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners. We use Rail-RNA to align 667 RNA-seq samples from the GEUVADIS project on Amazon Web Services in under 16 h for US$0.91 per sample. Rail-RNA outputs alignments in SAM/BAM format; but it also outputs (i) base-level coverage bigWigs for each sample; (ii) coverage bigWigs encoding normalized mean and median coverages at each base across samples analyzed; and (iii) exon–exon splice junctions and indels (features) in columnar formats that juxtapose coverages in samples in which a given feature is found. Supplementary outputs are ready for use with downstream packages for reproducible statistical analysis. We use Rail-RNA to identify expressed regions in the GEUVADIS samples and show that both annotated and unannotated (novel) expressed regions exhibit consistent patterns of variation across populations and with respect to known confounding variables.

Availability and Implementation
Rail-RNA is open-source software available at http://rail.bio.

Supplementary information
Supplementary data are available at Bioinformatics online.
A systematic review of the types and causes of prescribing errors generated from using computerized provider order entry systems in primary and secondary care
Authors: Brown Clare L , Mulcaster Helen L , Triffitt Katherine L , Sittig Dean F , Ash Joan S , Reygate Katie , Husband Andrew K , Bates David W , Slight Sarah P 
Published: September 2016

Objective: To understand the different types and causes of prescribing errors associated with computerized provider order entry (CPOE) systems, and recommend improvements in these systems.
Materials and Methods: We conducted a systematic review of the literature published between January 2004 and June 2015 using three large databases: the Cumulative Index to Nursing and Allied Health Literature, Embase, and Medline. Studies that reported qualitative data about the types and causes of these errors were included. A narrative synthesis of all eligible studies was undertaken.
Results: A total of 1185 publications were identified, of which 34 were included in the review. We identified 8 key themes associated with CPOE-related prescribing errors: computer screen display, drop-down menus and auto-population, wording, default settings, nonintuitive or inflexible ordering, repeat prescriptions and automated processes, users’ work processes, and clinical decision support systems. Displaying an incomplete list of a patient’s medications on the computer screen often contributed to prescribing errors. Lack of system flexibility resulted in users employing error-prone workarounds, such as the addition of contradictory free-text comments. Users’ misinterpretations of how text was presented in CPOE systems were also linked with the occurrence of prescribing errors.
Discussion and Conclusions: Human factors design is important to reduce error rates. Drop-down menus should be designed with safeguards to decrease the likelihood of selection errors. Development of more sophisticated clinical decision support, which can perform checks on free-text, may also prevent errors. Further research is needed to ensure that systems minimize error likelihood and meet users’ workflow expectations.