bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring orthologous gene regulatory networks using interspecies data fusion
Authors: Penfold Christopher A. , Millar Jonathan B. A. , Wild David L. 
Published: June 2015

Abstract
Motivation: The ability to jointly learn gene regulatory networks (GRNs) in, or leverage GRNs between related species would allow the vast amount of legacy data obtained in model organisms to inform the GRNs of more complex, or economically or medically relevant counterparts. Examples include transferring information from Arabidopsis thaliana into related crop species for food security purposes, or from mice into humans for medical applications. Here we develop two related Bayesian approaches to network inference that allow GRNs to be jointly inferred in, or leveraged between, several related species: in one framework, network information is directly propagated between species; in the second hierarchical approach, network information is propagated via an unobserved ‘hypernetwork’. In both frameworks, information about network similarity is captured via graph kernels, with the networks additionally informed by species-specific time series gene expression data, when available, using Gaussian processes to model the dynamics of gene expression.
Results: Results on in silico benchmarks demonstrate that joint inference, and leveraging of known networks between species, offers better accuracy than standalone inference. The direct propagation of network information via the non-hierarchical framework is more appropriate when there are relatively few species, while the hierarchical approach is better suited when there are many species. Both methods are robust to small amounts of mislabelling of orthologues. Finally, the use of Saccharomyces cerevisiae data and networks to inform inference of networks in the budding yeast Schizosaccharomyces pombe predicts a novel role in cell cycle regulation for Gas1 (SPAC19B12.02c), a 1,3-beta-glucanosyltransferase.
Availability and implementation: MATLAB code is available from http://go.warwick.ac.uk/systemsbiology/software/.
Contact: d.l.wild@warwick.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Integrative random forest for gene regulatory network inference
Authors: Petralia Francesca , Wang Pei , Yang Jialiang , Tu Zhidong 
Published: June 2015

Abstract
Motivation: Gene regulatory network (GRN) inference based on genomic data is one of the most actively pursued computational biological problems. Because different types of biological data usually provide complementary information regarding the underlying GRN, a model that integrates big data of diverse types is expected to increase both the power and accuracy of GRN inference. Towards this goal, we propose a novel algorithm named iRafNet: integrative random forest for gene regulatory network inference.
Results: iRafNet is a flexible, unified integrative framework that allows information from heterogeneous data, such as protein–protein interactions, transcription factor (TF)-DNA-binding, gene knock-down, to be jointly considered for GRN inference. Using test data from the DREAM4 and DREAM5 challenges, we demonstrate that iRafNet outperforms the original random forest based network inference algorithm (GENIE3), and is highly comparable to the community learning approach. We apply iRafNet to construct GRN in Saccharomyces cerevisiae and demonstrate that it improves the performance in predicting TF-target gene regulations and provides additional functional insights to the predicted gene regulations.
Availability and implementation: The R code of iRafNet implementation and a tutorial are available at: http://research.mssm.edu/tulab/software/irafnet.html
Contact: zhidong.tu@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Predictors of 2010–2011 Michigan Medicaid Beneficiary Adverse E-Code Health Care Encounters
Authors: Corser William D. , Huebner Marianne , Zhu Qi 
Published: June 2015

Abstract
To inform Medicaid medication management and public health policymaking, the authors analyzed the major predictive factors influencing program-approved therapeutic use or poisoning E-coded encounters leading to emergency department visits and hospital admission for the totality of Michigan Medicaid beneficiaries during a 12-month 2010–2011 period. The analytic cohort was composed of 26,134 approved E-code encounters submitted for 19,865 discrete Michigan Medicaid beneficiaries.
More than 1% of all beneficiaries experienced at least one adverse medication/agent-related E-code encounter during the period. More such encounters and costlier approved encounters were recorded female subjects, African Americans, dually eligible adults, urban elderly, those with fee-for-service Medicaid coverage, and those residing in urban-density counties.
Especially notably for patient safety policymakers, more than 9% of total E-coded encounters for children and adults were primarily attributed by providers to likely preventable poisoning causes such as exposure to household cleaning agents/gases, cosmetic products, illicit drug/alcohol, or secondary tobacco smoke. Encounter costs for the total sample totaled $37 million but ranged considerably up to more than a quarter million dollars.
In view of the future expanding Medicaid-covered beneficiary cohorts, the authors propose several key patient safety/public health policy implications for researchers and policymakers striving to serve lower-income health care consumer groups.
Exploring Health Care Professionals' Perceptions of Incidents and Incident Reporting in Rehabilitation Settings
Authors: Espin Sherry , Carter Celina , Janes Nadine , McAllister Mary 
Published: June 2015

Objectives
Research exploring patient safety in rehabilitation settings is limited. This study's aim was to describe team members' perceptions of incidents and incident reporting in rehabilitation settings.

Methods
Semistructured interviews were conducted with 18 health care professionals from multiple rehabilitation units (medical, neurological, and orthopedic) at 2 inner-city rehabilitation centers. Five hypothetical scenarios were presented to participants during the interviews. Participants were asked to classify the scenarios and whether they would report any identified incidents. Data were analyzed using a descriptive thematic approach.

Results
Participants classified events based on 2 parameters: the nature of the outcome and deviation from professional practice. Factors influencing participants' decisions to file incident reports included their classification of the events in the scenarios (i.e., events classified as critical incidents were more often reported than those classified as incident or near miss); the severity of the impact on the client; and their profession's perceived role in reporting specific incidents. When participants said they would report incidents, all agreed that they would report only objective facts.

Conclusions
The study findings demonstrate gaps between incident-reporting policy and practice, and opportunities to address these gaps. Organizational leaders can work with all health care professions to support their roles in reporting. Interprofessional team building, focused on valuing all team members, may improve interprofessional communication and reporting. Setting standards for classifying events could increase consistency in reporting. Ultimately, encouraging reporting of near misses and incidents can create a culture of learning focused on problem solving and improved patient safety.
Research Priorities in the Field of Patient Safety in Iran: Results of a Delphi Study
Authors: Ravaghi Hamid , Sajadi Haniye Sadat 
Published: June 2015

Abstract
There is inadequate evidence to direct and support patient safety practice. Therefore, identifying research priorities in this field is relevant for many stakeholders. This study, which was built on the World Health Organization work, aimed to identify and prioritize research topics for patient safety in Iran. A 3-round Modified Delphi process was used. We purposefully recruited a panel of 45 policy makers, planners, health care managers and staff, and academic members with experience or expertise in patient safety research. A review of the literature was used to develop the first questionnaire, including 24 research topics. Respondents were asked to rate their agreement with each research topic and propose new topics. Based on the results of round 1, the second questionnaire was developed and the respondents were requested to rate 45 research topics and also put similar research topics in the same groups. Given the responses of round 2, the third questionnaire including a list of 45 research priorities categorized in 4 groups was developed. Respondents were asked to reflect their opinions. Content analysis was used to analyze round 1 data and descriptive statistics for round 2 and round 3 data. Forty-five identified research topics in round 1 prioritized and grouped in subsequent rounds. Among 4 research groups, the extent and epidemiology threatening patient safety group received the highest priority; and among research topics, adverse drug events and its epidemiology were the top-ranked research priorities. In addition to the priorities identified in previous work, more research priorities that reflect important and needed issue related to patient safety, especially in Iran, were recognized. This priority research list, which most stakeholders agree with it, can serve as a blueprint for patient safety research.
Probing the fabric of the rare biosphere
Authors: Crespo Bibiana G. , Wallhead Philip J. , Logares Ramiro , Pedrós-Alió Carlos 
Published: June 2015

AbstractThe relatively recent development of high-throughput sequencing (HTS) techniques has revealed a wealth of novel sequences found in very low abundance: the rare biosphere. Today, most studies of diversity of microorganisms are carried out almost exclusively with HTS techniques. However, culturing seems indispensable for diversity studies especially if the aim is exploring the rare biosphere. We have carried out a deep (1 million sequences per sample) pyrosequencing analysis of two marine bacterial samples and isolated a culture collection from one of them. We have shown that the collectors curves of the pyrosequencing data were close to reaching an asymptote. We have estimated the total richness of the samples and the sequencing effort necessary to obtain the total estimated richness experimentally. Comparing the pyrosequencing data and the isolates sequences we have found that isolation retrieves some of the rarest taxa and that the composition of rare taxa follows an annual succession. We have shown that increasing the number of tags sequenced would slowly uncover the isolated bacteria. However, even if the whole bacterial diversity was found by increasing the sampling depth, culturing would still be essential for the study of marine bacterial communities, especially if the target is the rare biosphere.
The Nature, Extent, and Consequences of Genetic Variation in theopaRepeats ofNotchinDrosophila
Authors: Rice Clinton , Beekman Danielle , Liu Liping , Erives Albert 
Published: June 2015

ABTRACTPolyglutamine (pQ) tracts are abundant in many proteins co-interacting on DNA. The lengths of these pQ tracts can modulate their interaction strengths. However, pQ tracts > 40 residues are pathologically prone to amyloidogenic self-assembly. Here, we assess the extent and consequences of variation in the pQ-encodingoparepeats ofNotch(N) inDrosophila melanogaster. We use Sanger sequencing to genotypeopasequences (5’-CAX repeats), which have resisted assembly using short sequence reads. While the majority ofNsequences pertain to referenceopa31(Q13HQ17) andopa32(Q13HQ18) allelic classes, several rare alleles encode tracts > 32 residues:opa33a(Q14HQ18),opa33b(Q15HQ17),opa34(Q16HQ17),opa35a1/opa35a2(Q13HQ21),opa36(Q13HQ22), andopa37(Q13HQ23). Only one rare allele encodes a tract < 31 residues:opa23(Q13–Q10). Thisopa23allele shortens the pQ tract while simultaneously eliminating the interrupting histidine. Homozygotes for the short and longopaalleles have defects in sensory bristle organ specification, abdominal patterning, and embryonic survival. Inbred stocks with wild-typeopa31alleles become more viable when outbred, while an inbred stock with the longeropa35becomes less viable after outcrossing to different backgrounds. In contrast, an inbred stock with the shortopa23allele is semi-viable in both inbred and outbred genetic backgrounds. Thisopa23 Notchallele also produces notched wings when recombined out of the X chromosome. Importantly,wa-linked X balancers carry theNalleleopa33band suppressAS-Cinsufficiency caused by thesc8inversion. Our results demonstrate potent pQ variation and epistatic sensitivity for theNlocus, and the need for long read genotyping of key repeat variables underlying gene regulatory networks.
Sentinel lymph node biopsy for 102 patients with primary cutaneous melanoma at a single Japanese institute
Authors: Otsuka Masaki , Yamasaki Osamu , Kaji Tatsuya , Iwatsuki Keiji , Asagoe Kenji 
Published: June 2015

AbstractSentinel lymph node biopsy (SLNB) is a widely accepted standard procedure for patients with clinically localized melanoma. Melanoma prevalence and Clark's subtype differ between Asians and Caucasians. Here, we evaluated our experience on SLNB for cutaneous melanoma in a Japanese population. SLNB was performed for patients with melanoma between July 2000 and June 2014. We retrospectively analyzed 102 patients regarding association of clinicopathological features with sentinel lymph node (SLN) status, melanoma‐specific survival (MSS) and disease‐free survival (DFS). A positive SLN was significantly associated with primary Breslow thickness. Compared with 43 patients with negative SLN, 59 patients with positive SLN had significantly shorter MSS (5‐year survival rate, 94.3% vs 63.2%; P = 0.0002) and DFS (5‐year survival rate, 92.7% vs 63.4%; P = 0.0004). According to our subgroup analyses, nine patients with positive non‐SLN had significantly shorter MSS compared with 32 patients with negative non‐SLN (5‐year survival rate, 32.4% vs 68.5%; P = 0.0273). The survival of 51 Japanese patients with acral lentiginous melanoma (ALM) was not inferior to the survival of patients with other Clark's subtype. Breslow thickness is an important factor for both MSS and DFS, and the status of SLN is the most predictive prognostic factor in Japanese patients with clinically localized melanomas, as in case of Caucasians. Features of ALM may be different between Asians and Caucasians.
Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity
Authors: Cheng Tao , Xu Chao , Lei Li , Li Changhao , Zhang Yu , Zhou Shiliang 
Published: June 2015

AbstractThe internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant‐specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant‐specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common‐used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant‐specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
Compensation in the Post‐FIN 48 Period: The Case of Contracting on Tax Performance and Uncertainty
Authors: Brown Jennifer L. , Drake Katharine D. , Martin Melissa A. 
Published: June 2015

AbstractAcademic and anecdotal evidence indicates that incentive systems often provide short‐term payouts without regard for long‐term consequences. New detailed disclosures mandated by FIN No. 48, Accounting for Uncertainty in Income Taxes, enable us to use a tax setting to investigate whether boards adjust performance‐based pay for uncertainty. We find managers’ bonus payouts are positively associated with tax performance; however, bonus payouts are lower when measures of ex ante tax uncertainty are higher. Our results are robust to tests of alternative explanations including financial reporting aggressiveness, overall firm risk, and other forms of compensation. Further, we document that the relation between bonus compensation and tax performance has changed in the post‐FIN No. 48 period. Specifically, we identify a significant association between bonus payout and GAAP ETR only in the pre‐FIN No. 48 period and a significant association between bonus payout and cash ETR only in the post‐FIN No. 48 period, suggesting that the relation between compensation and tax avoidance should be examined carefully with particular attention to the post‐FIN No. 48 period.
Weight loss and low age are associated with intensity of rooting behaviours in newborn infants
Authors: Takahashi Yuki , Jonas Wibke , Ransjö‐Arvidson Anna‐Berit , Lidfors Lena , Uvnäs Moberg Kerstin , Nissen Eva 
Published: June 2015

AbstractAimLittle is known about the developing breastfeeding behaviour of newborn infants. This study describes infants' prebreastfeeding behaviour during the second day of life and explores possible associations with infant characteristics.MethodsWe studied 13 mothers and healthy full‐term infants after normal births. At 24–48 hours of life, the newborns were placed in skin‐to‐skin contact with their mothers for breastfeeding and were video‐filmed. The order, frequency and duration of predefined infant prefeeding behaviours and suckling were coded and analysed using computer‐based video software.ResultsPrefeeding behaviours occurred in the following order: rooting, hand to mouth movements, licking of the nipple and hand to breast to mouth movements. The infants started to suckle at a median of one to two minutes. Rooting was the most common behaviour, observed in 12 infants. The duration of rooting movements during the last minute before breastfeeding was inversely related to neonatal age (p ≤ 0.001) and positively related to neonatal weight loss (p = 0.02) after birth.ConclusionInfants exhibited a distinct sequence of prefeeding behaviours during the second day of life, and our findings suggest that rooting movements were governed by mechanisms involved in the regulation of food intake and weight gain.
Effects of simulated historical tree litter raking on the understorey vegetation in a central European forest
Authors: Vild Ondřej , Kalwij Jesse M. , Hédl Radim 
Published: June 2015

AbstractQuestionsWhat is the impact of simulated historical tree litter removal on understorey plants and soil properties in a temperate deciduous forest? What is the role of seasonal timing of tree litter removal on understorey plants?LocationPodyjí National Park, Czech Republic.MethodsWe conducted an experiment in a randomized complete block design of 45 plots (5 × 5 m). Each block (N = 15) consisted of one plot for each of the three treatments. Treatments consisted of (1) tree litter removal during spring, (2) tree litter removal during autumn, or (3) no litter removal as control treatment. These treatments were repeated over 4 yr. In each plot we recorded the understorey plant species composition and collected soil samples prior to treatment (year 0) and in each subsequent year (years 1–4). Temporal trends in species richness were analysed using repeated measures ANOVAs. The impact of the treatments on vegetation composition over time was analysed using principal response curves.ResultsTotal species richness per plot significantly changed over time, but this was not related to treatment. Annual species richness increased significantly, but only for the autumn treatment. Annual species also showed the highest inter‐annual variation. Endangered species were not affected. When compared to the control treatment, the effect of autumn raking on species composition was stronger than the effect of spring raking. Although the amount of removed nutrients substantially exceeded ambient nitrogen input, no changes in soil conditions were detected.ConclusionsThe season in which tree litter removal took place had a small but significant impact on the understorey vegetation, in particular affecting the germination and establishment of annual species. The large inter‐annual variation in species richness calls for a long‐term field experiment. The removal of nutrients via litter raking greatly exceeds atmospheric nutrient deposition, warranting a further investigation of litter raking as a potential tool for forest conservation.
Does vegetation in restored salt marshes equal naturally developed vegetation?
Authors: Van Loon‐Steensma Jantsje M. , Van Dobben Han F. , Slim Pieter A. , Huiskes Hendrik P.J. , Dirkse Gerard M. 
Published: June 2015

AbstractQuestionDo low stone dams built to prevent erosion and to restore salt marshes through increased sedimentation affect plant species composition?LocationDutch Wadden Sea area (ca. 53°N 5°E).MethodsRelevés (N = 170) were made of the vegetation of two restored salt marsh sites on the barrier islands Terschelling (Grië) and Ameland (Neerlands Reid). Existing relevés of salt‐marsh vegetation (N = 6198) made along the entire Dutch Wadden Sea coast (both the mainland and the barrier islands) were used as a reference. The vegetation of the two restored sites (Grië NLR data) was compared with the reference by (1) simple species‐by‐species analysis based on frequencies in both data sets, and by (2) ordination, where relevés of the restored sites were projected into a multivariate space defined by the species' abundances in the reference relevés.ResultsOut of the 37 species that are common (i.e. have a frequency >5%) in either the Grië NLR data or the reference data, 31 have frequencies that differ by less than a factor of five, and 23 differ by less than a factor of two. Furthermore, the Grië NLR data occupy a space that is well in the centre of the ordination space defined by the reference data.ConclusionsThere are no conspicuous differences between salt‐marsh vegetation behind low dams and the vegetation that has naturally developed on unprotected mudflats. We conclude that measures targeting salt marsh development in view of flood protection do not interfere with nature conservation.