bluuebunny/crossref_metadata_2025_split huggingface dataset:
Misassembly detection using paired-end sequence reads and optical mapping data
Authors: Muggli Martin D. , Puglisi Simon J. , Ronen Roy , Boucher Christina 
Published: June 2015

Abstract
Motivation: A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method called misSEQuel that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. Our method also fulfills the critical need for open source computational methods for analyzing optical mapping data. We apply our method to various assemblies of the loblolly pine, Francisella tularensis, rice and budgerigar genomes. We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar.
Results: Our results demonstrate that we detect more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine. Using the real optical mapping data, we correctly identified 75% of extensively misassembled contigs and 100% of locally misassembled contigs in rice, and 77% of extensively misassembled contigs and 80% of locally misassembled contigs in budgerigar.
Availability and implementation: misSEQuel can be used as a post-processing step in combination with any genome assembler and is freely available at http://www.cs.colostate.edu/seq/.
Contact: muggli@cs.colostate.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Genome-wide detection of intervals of genetic heterogeneity associated with complex traits
Authors: Llinares-López Felipe , Grimm Dominik G. , Bodenham Dean A. , Gieraths Udo , Sugiyama Mahito , Rowan Beth , Borgwardt Karsten 
Published: June 2015

Abstract
Motivation: Genetic heterogeneity, the fact that several sequence variants give rise to the same phenotype, is a phenomenon that is of the utmost interest in the analysis of complex phenotypes. Current approaches for finding regions in the genome that exhibit genetic heterogeneity suffer from at least one of two shortcomings: (i) they require the definition of an exact interval in the genome that is to be tested for genetic heterogeneity, potentially missing intervals of high relevance, or (ii) they suffer from an enormous multiple hypothesis testing problem due to the large number of potential candidate intervals being tested, which results in either many false positives or a lack of power to detect true intervals.
Results: Here, we present an approach that overcomes both problems: it allows one to automatically find all contiguous sequences of single nucleotide polymorphisms in the genome that are jointly associated with the phenotype. It also solves both the inherent computational efficiency problem and the statistical problem of multiple hypothesis testing, which are both caused by the huge number of candidate intervals. We demonstrate on Arabidopsis thaliana genome-wide association study data that our approach can discover regions that exhibit genetic heterogeneity and would be missed by single-locus mapping.
Conclusions: Our novel approach can contribute to the genome-wide discovery of intervals that are involved in the genetic heterogeneity underlying complex phenotypes.
Availability and implementation: The code can be obtained at: http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/sis.html.
Contact: felipe.llinares@bsse.ethz.ch
Supplementary information : Supplementary data are available at Bioinformatics online.
PAGER: constructing PAGs and new PAG–PAG relationships for network biology
Authors: Yue Zongliang , Kshirsagar Madhura M. , Nguyen Thanh , Suphavilai Chayaporn , Neylon Michael T. , Zhu Liugen , Ratliff Timothy , Chen Jake Y. 
Published: June 2015

Abstract
In this article, we described a new database framework to perform integrative “gene-set, network, and pathway analysis” (GNPA). In this framework, we integrated heterogeneous data on pathways, annotated list, and gene-sets (PAGs) into a PAG electronic repository (PAGER). PAGs in the PAGER database are organized into P-type, A-type and G-type PAGs with a three-letter-code standard naming convention. The PAGER database currently compiles 44 313 genes from 5 species including human, 38 663 PAGs, 324 830 gene–gene relationships and two types of 3 174 323 PAG–PAG regulatory relationships—co-membership based and regulatory relationship based. To help users assess each PAG’s biological relevance, we developed a cohesion measure called Cohesion Coefficient (CoCo), which is capable of disambiguating between biologically significant PAGs and random PAGs with an area-under-curve performance of 0.98. PAGER database was set up to help users to search and retrieve PAGs from its online web interface. PAGER enable advanced users to build PAG–PAG regulatory networks that provide complementary biological insights not found in gene set analysis or individual gene network analysis. We provide a case study using cancer functional genomics data sets to demonstrate how integrative GNPA help improve network biology data coverage and therefore biological interpretability. The PAGER database can be accessible openly at http://discovery.informatics.iupui.edu/PAGER/.
Contact: jakechen@iupui.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Using collective expert judgements to evaluate quality measures of mass spectrometry images
Authors: Palmer Andrew , Ovchinnikova Ekaterina , Thuné Mikael , Lavigne Régis , Guével Blandine , Dyatlov Andrey , Vitek Olga , Pineau Charles , Borén Mats , Alexandrov Theodore 
Published: June 2015

Abstract
Motivation: Imaging mass spectrometry (IMS) is a maturating technique of molecular imaging. Confidence in the reproducible quality of IMS data is essential for its integration into routine use. However, the predominant method for assessing quality is visual examination, a time consuming, unstandardized and non-scalable approach. So far, the problem of assessing the quality has only been marginally addressed and existing measures do not account for the spatial information of IMS data. Importantly, no approach exists for unbiased evaluation of potential quality measures.
Results: We propose a novel approach for evaluating potential measures by creating a gold-standard set using collective expert judgements upon which we evaluated image-based measures. To produce a gold standard, we engaged 80 IMS experts, each to rate the relative quality between 52 pairs of ion images from MALDI-TOF IMS datasets of rat brain coronal sections. Experts’ optional feedback on their expertise, the task and the survey showed that (i) they had diverse backgrounds and sufficient expertise, (ii) the task was properly understood, and (iii) the survey was comprehensible. A moderate inter-rater agreement was achieved with Krippendorff’s alpha of 0.5. A gold-standard set of 634 pairs of images with accompanying ratings was constructed and showed a high agreement of 0.85. Eight families of potential measures with a range of parameters and statistical descriptors, giving 143 in total, were evaluated. Both signal-to-noise and spatial chaos-based measures performed highly with a correlation of 0.7 to 0.9 with the gold standard ratings. Moreover, we showed that a composite measure with the linear coefficients (trained on the gold standard with regularized least squares optimization and lasso) showed a strong linear correlation of 0.94 and an accuracy of 0.98 in predicting which image in a pair was of higher quality.
Availability and implementation: The anonymized data collected from the survey and the Matlab source code for data processing can be found at: https://github.com/alexandrovteam/IMS_quality.
Contact: theodore.alexandrov@embl.de
SoloDel: a probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data
Authors: Kim Junho , Kim Sanghyeon , Nam Hojung , Kim Sangwoo , Lee Doheon 
Published: June 2015

Abstract
Motivation: Finding somatic mutations from massively parallel sequencing data is becoming a standard process in genome-based biomedical studies. There are a number of robust methods developed for detecting somatic single nucleotide variations However, detection of somatic copy number alteration has been substantially less explored and remains vulnerable to frequently raised sampling issues: low frequency in cell population and absence of the matched control samples.
Results: We developed a novel computational method SoloDel that accurately classifies low-frequent somatic deletions from germline ones with or without matched control samples. We first constructed a probabilistic, somatic mutation progression model that describes the occurrence and propagation of the event in the cellular lineage of the sample. We then built a Gaussian mixture model to represent the mixed population of somatic and germline deletions. Parameters of the mixture model could be estimated using the expectation-maximization algorithm with the observed distribution of read-depth ratios at the points of discordant-read based initial deletion calls. Combined with conventional structural variation caller, SoloDel greatly increased the accuracy in classifying somatic mutations. Even without control, SoloDel maintained a comparable performance in a wide range of mutated subpopulation size (10–70%). SoloDel could also successfully recall experimentally validated somatic deletions from previously reported neuropsychiatric whole-genome sequencing data.
Availability and implementation: Java-based implementation of the method is available at http://sourceforge.net/projects/solodel/
Contact: swkim@yuhs.ac or dhlee@biosoft.kaist.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
The expanding family of regulatory B cells
Authors: Mauri Claudia , Menon Madhvi 
Published: June 2015

Abstract
Over the last decade it has become evident that in addition to producing antibody, B cells activate the immune system by producing cytokines and via antigen presentation. In addition, B cells also exhibit immunosuppressive functions via diverse regulatory mechanisms. This subset of B cells, known as regulatory B cells (Bregs), contributes to the maintenance of tolerance, primarily via the production of IL-10. Studies in experimental animal models, as well as in patients with autoimmune diseases, have identified multiple Breg subsets exhibiting diverse mechanisms of immune suppression. In this review, we describe the different Breg subsets identified in mice and humans, and their diverse mechanisms of suppression in different disease settings.
A weak lensing comparability study of galaxy mergers that host AGNs
Authors: Harvey D. , Courbin F. 
Published: June 2015

Abstract
We compared the total mass density profiles of three different types of galaxies using weak gravitational lensing: (i) 29 galaxies that host quasars at $\bar{z}\sim 0.32$ that are in a post-starburst quasar (PSQ) phase with high star formation indicating recent merger activity, (ii) 22 large elliptical galaxies from the Sloan Lens ACS Survey (SLACS) sample that do not host a quasar at $\bar{z}\sim 0.23$, and (iii) 17 galaxies that host moderately luminous quasars at $\bar{z}\sim 0.36$ powered by disc instabilities, but with no intense star formation. In an initial test we found no evidence for a connection between the merger state of a galaxy and the profile of the halo, with the PSQ profile comparable to that of the other two samples and consistent with the Leauthaud et al. study of moderately luminous quasars in Cosmic Evolution Survey (COSMOS). Given the compatibility of the two quasar samples, we combined these and found no evidence for any connection between black hole activity and the dark matter halo. All three mass profiles remained compatible with isothermality given the present data.
Cosmic ray penetration in diffuse clouds
Authors: Morlino G. , Gabici S. 
Published: June 2015

Abstract
Cosmic rays are a fundamental source of ionization for molecular and diffuse clouds, influencing their chemical, thermal, and dynamical evolution. The amount of cosmic rays inside a cloud also determines the gamma-ray flux produced by hadronic collisions between cosmic rays and cloud material. We study the spectrum of cosmic rays inside and outside of a diffuse cloud by solving the stationary transport equation for cosmic rays including diffusion, advection, and energy losses due to ionization of neutral hydrogen atoms. We found that the cosmic ray spectrum inside a diffuse cloud differs from the one in the interstellar medium (ISM) for energies smaller than Ebr ≈ 100 MeV, irrespective of the model details. Below Ebr, the spectrum is harder (softer) than that in the ISM if the latter is a power law ∝p−s with s larger (smaller) than ∼0.42.
Use of Simulation to Test Systems and Prepare Staff for a New Hospital Transition
Authors: Adler Mark D. , Mobley Bonnie L. , Eppich Walter J. , Lappe Molly , Green Michaeleen , Mangold Karen 
Published: June 2015

Objective
To describe the development and key outcomes arising from the use of simulation as a method to test systems and prepare staff for a transition to a new hospital.

Methods
We describe a simulation program developed by key parties with the goal of reducing latent safety threats present at the opening of a new hospital and to train staff in new workflows. Issues identified were collected and reported to leadership. Outcomes included the number of learners reached, issues identified (grouped by theme), and results of a postmove survey of hospital-based staff.

Results
Approximately 258 hours of simulation were conducted, impacting 514 participants. We conducted 64 hours of system testing and 196 hours of training during the main orientation process. Approximately 641 unique issues were identified (175 equipment, 136 code alarm, 174 barriers to care, and 156 incorrect signage). In a hospital-wide survey, 38% reported simulation as part of their training (39% of nurses and 23% of physicians). 43% of survey respondents reported multidisciplinary simulations; 55% of simulation attendees felt that the simulation was helpful and eased their transition to the new hospital.

Conclusions
Systems testing and education using simulation can play a meaningful role in new facility training. Key lessons included early planning, allocation of resources to the effort, flexibility to adapt to changes, and planned integration with other training activities. A formal a priori plan to address issues identified during the process is necessary.
Additional Medical Costs Due to Hospital-Acquired Falls
Authors: Hirose Masahiro , Nakabayashi Narue , Fukuda Seiji , Yamaguchi Shuhei , Igawa Mikio , Egami Koichi , Honda Junichi , Shima Hiroji 
Published: June 2015

Objectives
To explore the additional medical costs (AMCs) due to hospital-acquired falls (falls), as well as their impact on clinical services within hospitals under the nationally uniform universal health insurance system in Japan.

Methods
With the use of administrative profiling data based on accounting systems linked with the Japanese social insurance medical fee schedule, we analyzed data from 2 teaching hospitals: Shimane University Hospital (SUH) and St. Mary's Hospital (SMH). We extracted 588 fall cases from 4669 incident reports in SUH and 1168 fall cases from 7717 incident reports in SMH that potentially incurred AMCs.

Results
Additional medical costs were 364 ± 2129 USD for minor injuries and 4336 ± 3645 USD for major injuries at SUH (P < 0.001) and 114 ± 124 USD for minor injuries and 2267 ± 2811 USD for major injuries at SMH (P < 0.001). Among the clinical services provided, imaging services were the most frequently used, with 89.9% (n = 205) of 228 minor injuries at SUH and 86.7% (n = 339) of 391 minor injuries at SMH; imaging services were used in all major injury cases at both hospitals. Although the number of cases using additional procedure/surgery services was lower than those using imaging services at both hospitals, AMCs for procedure/surgery services accounted for the highest proportions of total AMCs in both hospitals.

Conclusions
Although falls with minor injuries outnumbered falls with major injuries, fall-related AMCs for the latter were higher at both teaching hospitals because procedure/surgery services were required for cases with major injuries such as femoral neck and trochanteric fractures. The findings suggest that hospital administrators and policy makers have to take appropriate measures to prevent major injuries inpatients due to hospital-acquired falls.
Critical Value Reporting at Egyptian Laboratories
Authors: Mosallam Rasha , Ibrahim Samaa Zenhom 
Published: June 2015

Objectives
To examine critical value reporting policies and practices and to identify critical value ranges for selected common laboratory assays at inpatient division of laboratories of Alexandria hospitals.

Methods
A cross-sectional descriptive study design was used. Subjects were from inpatient division of all laboratories of Alexandria hospitals (40 laboratories). Data were collected using a questionnaire composed of 4 sections. The first section explored hospital and laboratory characteristics. The second section assessed policies and procedures of critical value reporting. The third section explored the reporting process. The fourth section explored critical value ranges for selected common laboratory assays.

Results
Written procedure for reporting of critical values was present in 77.5% of laboratories and a comprehensive list of critical values in 72.55%. For laboratories having a critical value list, the number of tests in the list ranged from 7 to 40. Three-fifths of laboratories had a policy for assessing the timeliness of reporting and 3 quarters stated that the laboratory policy requires feedback (60.0% and 75.0%, respectively). The hospital laboratory physician was responsible for critical value reporting followed by the laboratory technician (75.0% and 50.0%, respectively). The call is received mainly by nurses and physicians ordering the test (67.5% and 55.0%, respectively) and the channel of reporting is mainly the telephone or through sending test report to the ward (67.5% and 50.0%, respectively). Wireless technologies are used in reporting in only 10.0% of hospitals. The cutoff limits for reporting different assays showed considerable interlaboratory variation.

Conclusions
Critical value policies and practices showed interinstitutional variation with deficiencies in some reporting practices. Selection of critical assays for notification and setting the limits of notification exhibited wide variation as well.
Improving Adherence to Practice Guidelines for Anticoagulation in Patients Receiving Neuraxial Anesthesia Using an Electronic Order Entry Alert System
Authors: Jajosky Jessica , Howell Stephen M. , Honaker John , Moriarty Allison , Shea Joy Marie 
Published: June 2015

Objectives
Epidural analgesia is frequently used to alleviate postoperative pain. Though rare, epidural hematoma continues to be a feared complication of neuraxial analgesia. The risk of epidural hematoma is likely increased when certain regimens are used for prophylaxis/treatment of venous thromboembolism. To help decrease the risk, we developed an alert in our electronic medical record to assist providers with adherence to published guidelines addressing neuraxial analgesia and anticoagulation.

Methods
Patient data were collected retrospectively 3 months before and 3 months after the initiation of the computerized alert to assess the effectiveness of the alert. Patients were included if they had a procedure code associated with epidural analgesia. Pregnant patients and children were excluded. Type and frequency of antithrombotic medications were recorded for comparison to published practice guidelines.

Results
Using Poisson regression to describe the data, patients with epidurals after the best practice alert observed a 61% decrease in the expected number of days of exposure to inappropriate doses of anticoagulation versus patients treated before implementation of the alert.

Conclusion
Unapproved antithrombotic administration was significantly reduced after initiation of the alert system. This simple electronic alert was found to have a protective effect for patients receiving both anticoagulation and epidural analgesia.
A Systematic Review of Systemic Cobaltism After Wear or Corrosion of Chrome-Cobalt Hip Implants
Authors: Gessner Bradford D. , Steck Thomas , Woelber Erik , Tower Stephen S. 
Published: June 2015

Objectives
We sought to synthesize data on systemic arthroprosthetic cobaltism, a recently described syndrome that results from wear or corrosion of chrome-cobalt hip components.

Methods
We conducted a systematic literature review to identify all reported cases of systemic arthroprosthetic cobaltism. To assess the epidemiologic link between blood cobalt levels (B[Co]), we developed a symptom scoring tool that evaluated 9 different symptom categories and a category of medical utilization.

Results
We identified 25 patients reported between 2001 and 2014 with a substantial increase in case reports over the past 3 years. Symptoms were diverse and involved the hip (84%), cardiovascular system (60%), audiovestibular system (52%), peripheral motor-sensory system (48%), thyroid (48%), psychological functioning (32%), visual system (32%), and the hematological, oncological, or immune system (20%). The mean latency from implantation to presentation or revision was 41 months (range, 9–99 months). The mean B[Co] was 324 μg/L and 4 patients had levels less than 20 μg/L. The B[Co] but not blood chromium level was highly associated with a quantitative measure of overall symptom severity (r
2, 0.81; P < 0.001). Mean B[Co] and symptom scores were substantially higher in patients with revisions of failed ceramic-on-ceramic prostheses than those with primary metal-on-metal prostheses.

Conclusions
Systemic arthroprosthetic cobaltism is an increasingly recognized complication of wear or corrosion of chrome-cobalt hip implants, may involve a large number of organ systems, and may occur with relatively low B[Co]. There is an urgent need to better define the overall scope of the problem and to develop screening and management strategies.
MERS-CoV recombination: implications about the reservoir and potential for adaptation
Authors: Dudas Gytis , Rambaut Andrew 
Published: June 2015

AbstractRecombination is a process that unlinks neighbouring loci allowing for independent evolutionary trajectories within genomes of many organisms. If not properly accounted for, recombination can compromise many evolutionary analyses. In addition, when dealing with organisms that are not obligately sexually reproducing, recombination gives insight into the rate at which distinct genetic lineages come into contact. Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has caused 1106 laboratory-confirmed infections, with 421 MERS-CoV associated deaths as of April 16, 2015. Although bats are considered as the likely ultimate source of zoonotic betacoronaviruses, dromedary camels have been consistently implicated as the source of current human infections in the Middle East. In this paper we use phylogenetic methods and simulations to show that MERS-CoV genome has likely undergone numerous recombinations recently. Recombination in MERS-CoV implies frequent co-infection with distinct lineages of MERS-CoV, probably in camels given the current understanding of MERS-CoV epidemiology.