bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Consensus Between UK Renal Clinicians on Listing for Kidney Transplantation: A Modified Delphi Study
Authors: Tonkin-Crine Sarah , Pruthi Rishi , Taylor Dominic M. , Leydon Geraldine M. , Calestani Melania , Oniscu Gabriel C. , Bradley J. Andrew , Tomson Charles R. , Bradley Clare , Dudley Christopher , Watson Christopher J.E. , Draper Heather , Johnson Rachel J. , Metcalfe Wendy , Fogarty Damian G. , Ravanan Rommel , Roderick Paul 
Published: April 2018

Background
It is well recognized that there is significant variation between centers in access to kidney transplantation. In the absence of high-grade evidence, it is unclear whether variation is due to patient case mix, other center factors, or individual clinician decisions. This study sought consensus between UK clinicians on factors that should influence access to kidney transplantation.

Methods
As part of the Access to Transplantation and Transplant Outcome Measures project, consultant nephrologists and transplant surgeons in 71 centers were invited to participate in a Delphi study involving 2 rounds. During rounds 1 and 2, participants rated their agreement to 29 statements covering 8 topics regarding kidney transplantation. A stakeholder meeting was used to discuss statements of interest after the 2 rounds.

Results
In total, 122 nephrologists and 16 transplant surgeons from 45 units participated in rounds 1 and 2. After 2 rounds, 12 of 29 statements reached consensus. Fifty people participated in the stakeholder meeting. After the stakeholder meeting, a further 4 statements reached agreement. Of the 8 topics covered, consensus was reached in 6: use of a transplant protocol, patient age, body mass index, patient compliance with treatment, cardiac workup, and use of multidisciplinary meetings. Consensus was not reached on screening for malignancy and use of peripheral Doppler studies.

Conclusions
The Delphi process identified factors upon which clinicians agreed and areas where consensus could not be achieved. The findings should inform national guidelines to support decision making in the absence of high quality evidence and to guide areas that warrant future research.
Isolation, Detection and Characterization of Aerobic Bacteria from Honey Samples of Bangladesh
Authors: Saha Sarbojoy 
Published: April 2018

AbstractHoney is a sweet substance made from the nectar of flowers and other chemical secretions from the bees’ bodies who collect nectar from the flowers and bring it to their hives to transform it to the thick, golden and sweet liquid that we call honey. The benefits of honey are not just limited to its basic use as a natural sweetener, but also its medicinal properties. The purpose of this study was to identify the bacteria that are present in honey commonly found in Bangladesh, which can tolerate the antimicrobial conditions of honey and survive in it. Fortunately, such bacteria could be detected, isolated and characterized by morphological and biochemical tests. The predominant type of bacteria commonly found in both raw and commercial honeys of Bangladesh are gram positive cocci such as streptococci, staphylococci, micrococci, bacilli and lactobacilli. Few gram negative bacteria were also isolated like Escherichia coli (8%) and Klebsiella pneumonia (8%) and some gram negative/gram variable Micrococcus luteus (75%). Hopefully, such knowledge would benefit people in the future as they will know more about the microorganisms present in honey and about the safety and quality of the honey they are about to buy or consume.
MaSS-Simulator: A highly configurable MS/MS simulator for generating test datasets for big data algorithms
Authors: Awan Muaaz Gul , Saeed Fahad 
Published: April 2018

AbstractMass Spectrometry (MS) based proteomics has become an essential tool in the study of proteins. The big data from MS machines has led to the development of novel serial and parallel algorithmic tools. However, the absence of data benchmarks and ground truth makes the algorithmic integrity testing and reproducibility a challenging problem. To this end, we present MaSS-Simulator, which is an easy to use simulator and can be configured to generate MS/MS datasets for a wide variety of conditions with known ground truths. MaSS-Simulator offers a large number of configuration options to simulate control datasets with desired properties thus enabling rigorous and large scale algorithmic testing. We assessed 8,031 spectra generated by MaSS-Simulator by comparing them against the experimentally generated spectra of same peptides. Our results showed that MaSS-Simulator generated spectra were very close to the real-experimental spectra and had a relative-error distribution centered around 25%. In contrast the theoretical spectra for same peptides had relative-error distribution centered around 150%. Source code, executables and a user manual can be downloaded from https://github.com/pcdslab/MaSS-Simulator
STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data
Authors: Chen Huidong , Albergante Luca , Hsu Jonathan Y , Lareau Caleb A , Bosco Giosue` Lo , Guan Jihong , Zhou Shuigeng , Gorban Alexander N , Bauer Daniel E , Aryee Martin J , Langenau David M , Zinovyev Andrei , Buenrostro Jason D , Yuan Guo-Cheng , Pinello Luca 
Published: April 2018

AbstractSingle-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.
Phylogenetically novel uncultured microbial cells dominate Earth microbiomes
Authors: Lloyd Karen G. , Ladau Joshua , Steen Andrew D. , Yin Junqi , Crosby Lonnie 
Published: April 2018

AbstractTo unequivocally determine a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029(81%) and 2.2 × 1029(25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.
Beaked and Killer Whales Show How Collective Prey Behaviour Foils Acoustic Predators
Authors: Aguilar de Soto Natacha , Visser Fleur , Madsen Peter , Tyack Peter , Ruxton Graeme , Arranz Patricia , Alcazar Jesús , Johnson Mark 
Published: April 2018

ABSTRACTAnimals aggregate to obtain a range of fitness benefits, but a common cost of aggregation is increased detection by predators. Here we show that, in contrast to visual and chemical signallers, aggregated acoustic signallers need not face higher predator encounter rate. This is the case for prey groups that synchronize vocal behaviour but have negligible signal time-overlap in their vocalizations. Beaked whales tagged with sound and movement loggers exemplify this scenario: they precisely synchronize group vocal and diving activity but produce non-overlapping short acoustic cues. They combine this with acoustic hiding when within reach of eavesdropping predators to effectively annul the cost of aggregation for predation risk from their main predator, the killer whale. We generalize this finding in a mathematical model that predicts the key parameters that social vocal prey, which are widespread across taxa and ecosystems, can use to mitigate detection by eavesdropping predators.
Automated analysis of small RNA datasets with RAPID
Authors: Karunanithi Sivarajan , Simon Martin , Schulz Marcel H. 
Published: April 2018

AbstractSummary: Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2. RAPID is available under MIT license at https://github.com/SchulzLab/RAPID. We recommend using it as a conda environment available from https://anaconda.org/bioconda/rapid.
Thrombocytopenia Microcephaly Syndrome - a novel phenotype associated withACTBmutations
Authors: Latham Sharissa L. , Ehmke Nadja , Reinke Patrick Y.A. , Taft Manuel H. , Lyons Michael J. , Friez Michael J , Lee Jennifer A. , Hecker Ramona , Frühwald Michael C. , Becker Kerstin , Neuhann Teresa M. , Horn Denise , Schrock Evelin , Sarnow Katharina , Grützmann Konrad , Gawehn Luzie , Klink Barbara , Rump Andreas , Chaponnier Christine , Knöfler Ralf , Manstein Dietmar J. , Di Donato Natalia 
Published: April 2018

Introductory paragraphUntil recently missense germ-line mutations inACTB, encoding the ubiquitously expressed β-cytoplasmic actin (CYA), were exclusively associated with Baraitser-Winter Cerebrofrontofacial syndrome (BWCFF), a complex developmental disorder1,2. Here, we report six patients with previously undescribed heterozygous variants clustered in the 3’-coding region ofACTB. These patients present with clinical features different from BWCFF, including thrombocytopenia, microcephaly, and mild developmental disability. Patient derived cells are morphologically and functionally distinct from controls. Assessment of cytoskeletal constituents identified a discrete filament population altered in these cells, which comprises force generating and transmitting actin binding proteins (ABP) known to be associated with thrombocytopenia3–8.In silicomodelling and molecular dynamics (MD)-simulations support altered interactions between these ABP and mutant β-CYA. Our results describe a new clinical syndrome associated withACTBmutations with a distinct genotype-phenotype correlation, identify a cytoskeletal protein interaction network crucial for thrombopoiesis, and provide support for the hypomorphic nature of these actinopathy mutations.
Identification of co-evolving temporal networks
Authors: Elhesha Rasha , Sarkar Aisharjya , Boucher Christina , Kahveci Tamer 
Published: April 2018

AbstractMotivationBiological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time. In this paper, we consider the problem of identifying co-evolving pair of temporal networks, which aim to capture the evolution of molecules and their interactions over time. Although this problem shares some characteristics of the well-known network alignment problems, it differs from existing network alignment formulations as it seeks a mapping of the two network topologies that is invariant to temporal evolution of the given networks. This is a computationally challenging problem as it requires capturing not only similar topologies between two networks but also their similar evolution patterns.ResultsWe present an efficient algorithm,Tempo, for solving identifying coevolving subnetworks with two given temporal networks. We formally prove the correctness of our method. We experimentally demonstrate that Tempo scales efficiently with the size of network as well as the number of time points, and generates statistically significant alignments—even when evolution rates of given networks are high. Our results on a human aging dataset demonstrate that Tempo identifies novel genes contributing to the progression of Alzheimer’s, Huntington’s and Type II diabetes, while existing methods fail to do so.AvailabilitySoftware is available online (https://www.cise.ufi.edu/∼relhesha/temporal.zip).Contactrelhesha@ufi.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Sapropterin Treatment Prevents Congenital Heart Defects Induced by Pregestational Diabetes in Mice
Authors: Engineer Anish , Saiyin Tana , Lu Xiangru , Kucey Andrew S. , Urquhart Brad L. , Drysdale Thomas A. , Norozi Kambiz , Feng Qingping 
Published: April 2018

ABSTRACTAimsTetrahydrobiopterin (BH4) is a co-factor of endothelial nitric oxide synthase (eNOS), which is critical to embryonic heart development. We aimed to study the effects of sapropterin (Kuvan®), an orally active synthetic form of BH4 on eNOS uncoupling and congenital heart defects (CHDs) induced by pregestational diabetes in mice.MethodsAdult female mice were induced to pregestational diabetes by streptozotocin and bred with normal males to produce offspring. Pregnant mice were treated with sapropterin or vehicle during gestation. CHDs were identified by histological analysis. Cell proliferation, eNOS dimerization and reactive oxygen species (ROS) production were assessed in the fetal heart.ResultsPregestational diabetes results in a spectrum of CHDs in their offspring. Oral treatment with sapropterin in the diabetic dams significantly decreased the incidence of CHDs from 59% to 27% and major abnormalities, such as atrioventricular septal defect and double outlet right ventricle were absent in the sapropterin treated group. Lineage tracing reveals that pregestational diabetes results in decreased commitment of second heart field progenitors to the outflow tract, endocardial cushions, and ventricular myocardium of the fetal heart. Notably, decreased cell proliferation and cardiac transcription factor expression induced by maternal diabetes were normalized with sapropterin treatment. Furthermore, sapropterin administration in the diabetic dams increased eNOS dimerization and lowered ROS levels in the fetal heart.ConclusionsSapropterin treatment in the diabetic mothers improves eNOS coupling, increases cell proliferation and prevents the development of CHDs in the offspring. Thus, sapropterin may have therapeutic potential in preventing CHDs in pregestational diabetes.
An optimal kernel-based method for gene set association analysis
Authors: He Tao , Li Shaoyu , Zhong Ping-Shou , Cui Yuehua 
Published: April 2018

ABSTRACTSingle-variant based genome-wide association studies have successfully detected many genetic variants that are associated with many complex traits. However, their power is limited due to weak marginal signals and ignoring potential complex interactions among genetic variants. Set-based strategy was proposed to provide a remedy where multiple genetic variants in a given set (e.g., gene or pathway) are jointly evaluated, so that the systematic effect of the set is considered. Among many, the kernel-based testing (KBT) framework is one of the most popular and powerful methods in set-based association studies. Given a set of candidate kernels, method has been proposed to choose the one with the smallest p-value. Such a method, however, can yield inflated type I error, especially when the number of variants in a set is large. Alternatively one can get p-values by permutations which, however, could be very time consuming. In this work, we proposed an efficient testing procedure that can not only control type I error rate but also generate power close to the one obtained under the optimal kernel. Our method is built upon the KBT framework and is based on asymptotic results under a high-dimensional setting. Hence it can efficiently deal with the case where the number of variants in a set is much larger than the sample size. Both simulation and real data analysis demonstrate the advantages of the method compared with its counterparts.
Spatio-temporally specific transcranial magnetic stimulation to test the locus of perceptual decision making in the human brain
Authors: Luber Bruce , Jangraw David C. , Appelbaum Greg , Harrison Austin , Hilbig Susan , Beynel Lysianne , Jones Tristan , Sajda Paul , Lisanby Sarah H. 
Published: April 2018

AbstractPrevious research modeling EEG, fMRI and behavioral data has identified three spatially distributed brain networks that activate in temporal sequence, and are thought to enable perceptual decision-making during face-versus-car categorization. These studies have linked late activation (>300ms post stimulus onset) in the lateral occipital cortex (LOC) to object discrimination processes. We applied paired-pulse transcranial magnetic stimulation (ppTMS) to LOC at different temporal latencies with the specific prediction, based on these studies, that ppTMS beginning at 400ms after stimulus onset would slow reaction time (RT) performance. Thirteen healthy adults performed a two-alternative forced choice task selecting whether a car or face was present on each trial amidst visual noise pre-titrated to approximate 79% accuracy. ppTMS, with pulses separated by 50ms, was applied at one of five stimulus onset asynchronies: -200, 200, 400, 450, or 500ms, and a sixth no-stimulation condition. As predicted, TMS at 400ms resulted in significant slowing of RTs, providing causal evidence in support of LOC contribution to perceptual decision processing. In addition, TMS delivered at -200ms resulted in faster RTs, indicating early stimulation may result in performance enhancement. These findings build upon correlational EEG and fMRI observations and demonstrate the use of TMS in predictive validation of psychophysiological models.
Customer orientation and SME performance: the role of networking ties
Authors: Neneh Brownhilder Ngek 
Published: April 2018

Purpose
The purpose of this paper is to examine the moderating effect of networking ties on the relationship between customer orientation and firm performance.

Design/methodology/approach
This study adopted a survey approach to collect data from 251 respondents in the Mangaung Metropolitan Municipality in the Free State province, South Africa. Scales for data collection were operationalised from prior studies. A hierarchical regression analysis was used to examine the moderating effect of networking ties on the relationship between customer orientation and firm performance.

Findings
The results showed that customer orientation had a significant positive association with firm performance, thus supporting the existing calls for examining the unique contributions of customer orientation to firm performance. Furthermore, this study hypothesised that business, political, and social network ties positively moderated this association. However, the results showed that only business and social network ties had a positive and significant moderating effect, with the influence of customer orientation on firm performance being more pronounced for firms with high as opposed to low business and social network ties. Nevertheless, all the three types of network ties showed a positive and significant direct relationship with firm performance, thus supporting the consolidated literature on the positive impact of network ties on firm performance.

Practical implications
The practical implications are twofold. First, it encourages business owners to develop a customer-oriented approach as a key strategic objective in their pursuit for optimal business performance. Second, business owners and managers should increasingly exploit their business and social network ties to accumulate vital resources for effectively exploiting their customer-oriented capabilities as a means to improve their performance.

Originality/value
Even though customer orientation is a valuable internal strategic capability, its benefit on firm performance might be limited in small and medium enterprises (SMEs) when the businesses are unable to respond quickly to customer needs. This is more common when the SME is faced with resource limitations required for exploiting the new market opportunities. However, this study showed that SMEs can mitigate this issue by depending on their business and social network ties for valuable resources to effectively exploit opportunities that emerge from identified customer needs.
Career boundaries and boundary-crossing by public sector employees
Authors: Dafou Efthimia 
Published: April 2018

PurposeThe purpose of this paper is to provide a boundary-focused analysis of career patterns in Greek public education.Design/methodology/approachA descriptive, interpretive design from the naturalistic paradigm was chosen for the study, based on narratives of 27 public education employees who used decision-making models for outlining their career plans.FindingsThis study depicted career-related boundaries and intentions of employees to develop their career within their domain or crossing particular boundaries, namely, the public-private boundary, the public education to higher education boundary, the occupational and other less salient boundaries.Research limitations/implicationsThe delimitation of the study on public education employees studying for a postgraduate diploma might limit the scope of inter-occupational mobility.Practical implicationsThis study highlights the subject of the first degree as the most critical determinant of career development, and identifies the role of structural constraints, especially of promotion systems, in “bounding” graduate careers.Originality/valueThis study developed a typology of career paths of public education employees and associated them with the identification of two main employee profiles, related to the subject of their first degree.