bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-Scale Skin Resurfacing of the Upper Extremity in Pediatric Patients Using a Pre-Expanded Intercostal Artery Perforator Flap
Authors: Wei Jiao , Herrler Tanja , Gu Bin , Yang Mei , Li Qingfeng , Dai Chuanchang , Xie Feng 
Published: February 2018

Background:
The repair of extensive upper limb skin lesions in pediatric patients is extremely challenging due to substantial limitations of flap size and donor-site morbidity. We aimed to create an oversize preexpanded flap based on intercostal artery perforators for large-scale resurfacing of the upper extremity in children.

Method:
Between March 2013 and August 2016, 11 patients underwent reconstructive treatment for extensive skin lesions in the upper extremity using a preexpanded intercostal artery perforator flap. Preoperatively, 2 to 4 candidate perforators were selected as potential pedicle vessels based on duplex ultrasound examination. After tissue expander implantation in the thoracodorsal area, regular saline injections were performed until the expanded flap was sufficient in size. Then, a pedicled flap was formed to resurface the skin lesion of the upper limb. The pedicles were transected 3 weeks after flap transfer. Flap survival, complications, and long-term outcome were evaluated.

Result:
The average time of tissue expansion was 133 days with a mean final volume of 1713 mL. The thoracoabdominal flaps were based on 2 to 6 pedicles and used to resurface a mean skin defect area of 238 cm2 ranging from 180 to 357 cm2. In all cases, primary donor-site closure was achieved. Marginal necrosis was seen in 5 cases. The reconstructed limbs showed satisfactory outcome in both aesthetic and functional aspects.

Conclusion:
The preexpanded intercostal artery perforator flap enables 1-block repair of extensive upper limb skin lesions. Due to limited donor-site morbidity and a pedicled technique, this resurfacing approach represents a useful tool especially in pediatric patients.
Locally Aggressive Fibrous Dysplasia Mimicking Malign Calvarial Lesion
Authors: Ogul Hayri , Keskin Emine 
Published: February 2018

Abstract
Fibrous dysplasia is an unusual benign bone tumor. It is divided into 3 groups as monostotic, polyostotic, and craniofacial form. The authors reported an unusual patient with fibrous dysplasia with an aggressive radiologic appearance.
Trauma Hemostasis and Oxygenation Research Network position paper on the role of hypotensive resuscitation as part of remote damage control resuscitation
Authors: Woolley Thomas , Thompson Patrick , Kirkman Emrys , Reed Richard , Ausset Sylvain , Beckett Andrew , Bjerkvig Christopher , Cap Andrew P. , Coats Tim , Cohen Mitchell , Despasquale Marc , Dorlac Warren , Doughty Heidi , Dutton Richard , Eastridge Brian , Glassberg Elon , Hudson Anthony , Jenkins Donald , Keenan Sean , Martinaud Christophe , Miles Ethan , Moore Ernest , Nordmann Giles , Prat Nicolas , Rappold Joseph , Reade Michael C. , Rees Paul , Rickard Rory , Schreiber Martin , Shackelford Stacy , Skogran Eliassen Håkon , Smith Jason , Smith Mike , Spinella Philip , Strandenes Geir , Ward Kevin , Watts Sarah , White Nathan , Williams Steve 
Published: February 2018

ABSTRACT
The Trauma Hemostasis and Oxygenation Research (THOR) Network has developed a consensus statement on the role of permissive hypotension in remote damage control resuscitation (RDCR). A summary of the evidence on permissive hypotension follows the THOR Network position on the topic. In RDCR, the burden of time in the care of the patients suffering from noncompressible hemorrhage affects outcomes. Despite the lack of published evidence, and based on clinical experience and expertise, it is the THOR Network’s opinion that the increase in prehospital time leads to an increased burden of shock, which poses a greater risk to the patient than the risk of rebleeding due to slightly increased blood pressure, especially when blood products are available as part of prehospital resuscitation.
The THOR Network’s consensus statement is, “In a casualty with life-threatening hemorrhage, shock should be reversed as soon as possible using a blood-based HR fluid. Whole blood is preferred to blood components. As a part of this HR, the initial systolic blood pressure target should be 100 mm Hg. In RDCR, it is vital for higher echelon care providers to receive a casualty with sufficient physiologic reserve to survive definitive surgical hemostasis and aggressive resuscitation. The combined use of blood-based resuscitation and limiting systolic blood pressure is believed to be effective in promoting hemostasis and reversing shock”
Somatic aberrations of BRCA1 gene are associated with progressive and stem cell-like phenotype of prostate cancer
Authors: Omari Aleksandra , Nastały Paulina , Bałabas Aneta , Dąbrowska Michalina , Bielińska Beata , Huss Sebastian , Pantel Klaus , Semjonow Axel , Eltze Elke , Brandt Burkhard , Bednarz-Knoll Natalia 
Published: February 2018

AbstractBackgroundBRCA1 is a pivotal tumor suppressor. Its dysfunction is known to play a role in different tumor entities. Among others, BRCA1 germline mutations account for higher risk and more aggressive course of prostate cancer (PCa). In addition, somatic BRCA1 gene loss was demonstrated to be a signature of PCa dissemination to regional lymph nodes and peripheral blood, and indicate worse clinical outcome. In order to substantiate the data for BRCA1 gene loss in PCa and to reveal its phenotypical background, BRCA1 gene status was assessed in a large cohort of PCa patients and compared to different molecular factors.MethodsBRCA1 gene dosage was assessed in 2398 tumor samples from 1199 PCa patients using fluorescent in situ hybridization. It was compared to clinic-pathological parameters, patients’ outcome as well as selected proteins (Ki-67, apoptosis marker, cytokeratins, vimentin, E- and N-cadherin, ALDH1 and EGFR) examined by immunohistcohemistry.ResultsBRCA1 losses were found in 10%, whereas gains appeared in 7% of 603 informative PCa patients. BRCA1 losses correlated to higher T status (p=0.027), Gleason score (p=0.039), shorter time to biochemical recurrence in patients with Gleason score >7 independently of other factors (multivariate analysis, p=0.005) as well as expression of proteins regulating stemness and epithelial-mesenchymal transition i.e. ALDH1 (p=0.021) and EGFR (p=0.011), respectively. BRCA1 gains correlated to shorter time to metastasis (p=0.012) and expression of ALDH1 (p=0.014).ConclusionsThe presented results support the assumption that BRCA1 gene losses contribute to a progressive and stem cell-like phenotype of PCa. Furthermore, they reveal that also BRCA1 gain might mark more invasive tumors.
bpRNA: Large-scale Automated Annotation and Analysis of RNA Secondary Structure
Authors: Danaee Padideh , Rouches Mason , Wiley Michelle , Deng Dezhong , Huang Liang , Hendrix David 
Published: February 2018

ABSTRACTWhile RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, “bpRNA-1m”, of over 100,000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.
Oxygen diffusion in ellipsoidal tumour spheroids
Authors: Grimes David Robert , Currell Frederick J. 
Published: February 2018

AbstractOxygen plays a central role in cellular metabolism, in both healthy and tumour tissue. The presence and concentration of molecular oxygen in tumours has a substantial effect on both radiotherapy response and tumour evolution, and as a result the oxygen micro-environment is an area of intense research interest. Multicellular tumour spheroids closely mimic real avascular tumours, and in particular they exhibit physiologically relevant heterogeneous oxygen distribution. This property has made them a vital part of in vitro experimentation. For ideal spheroids, their heterogeneous oxygen distributions can be predicted from theory, allowing determination of cellular oxygen consumption rate (OCR) and anoxic extent. However, experimental tumour spheroids often depart markedly from perfect sphericity. There has been little consideration of this reality. To date, the question of how far an ellipsoid can diverge from perfect sphericity before spherical assumptions breakdown remains unanswered. In this work we derive equations governing oxygen distribution (and more generally, nutrient and drug distribution) in both prolate and oblate tumour ellipsoids, and quantify the theoretical limits of the assumption that the spheroid is a perfect sphere. Results of this analysis yield new methods for quantifying OCR in ellipsoidal spheroids, and how this can be applied to markedly increase experimental throughput and quality.Author summaryMulticellular tumour spheroids (MCTS) are an increasingly important tool in cancer research, exhibiting non-homogeneous oxygen distributions and central necrosis. These are more similar to in situ avascular tumours than conventional 2D biology, rendering them exceptionally useful experimental models. Analysis of spheroids can yield vital information about cellular oxygen consumption rates, and the heterogeneous oxygen contribution. However, such analysis pivots on the assumption of perfect sphericity, when in reality spheroids often depart from such an ideal. In this work, we construct a theoretical oxygen diffusion model for ellipsoidal tumour spheroids in both prolate and oblate geometries. With these models established, we quantify the limits of the spherical assumption, and illustrate the effect of this assumption breaking down. Methods of circumventing this breakdown are also presented, and the analysis here suggests new methods for expanding experimental throughput to also include ellipsoidal data.
Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose
Authors: Bartoli Kristen M. , Schaening Cassandra , Carlile Thomas M. , Gilbert Wendy V. 
Published: February 2018

SUMMARYNon-coding RNAs contain dozens of chemically distinct modifications, of which only a few have been identified in mRNAs. The recent discovery that certain tRNA modifying enzymes also target mRNAs suggests the potential for many additional mRNA modifications. Here, we show that conserved tRNA 2′-O-methyltransferases Trm3, 7,13 and 44, and rRNA 2′-O-methyltransferase Spb1, interact with specific mRNA sites in yeast by crosslinking immunoprecipitation and sequencing (CLIP-seq). We developed sequencing of methylation at two prime hydroxyls (MeTH-seq) for transcriptome-wide mapping of 2′-O-methyl ribose (Nm) with single-nucleotide resolution, and discover thousands of potential Nm sites in mRNAs. Genetic analysis identified hundreds of mRNA targets for the Spb1 methyltransferase, which can target both mRNA and non-coding RNA for environmentally regulated modification. Our work identifies Nm as a prevalent mRNA modification that is likely to be conserved and provides methods to investigate its distribution and regulation.HIGHLIGHTSMeTH-seq identifies 2′-O-methylribose genome-wide at single-nucleotide resolutionFive conserved methyltransferases interact with yeast mRNASpb1 is a major mRNA 2′-O-methyltransferase, and targets most ribosomal protein mRNAsSPB1 expression is required to maintain normal levels of Spb1 target mRNAs
Ratiometric assays of autophagic flux in zebrafish for analysis of familial Alzheimer’s disease-like mutations
Authors: Jiang Haowei , Newman Morgan , Ratnayake Dhanushika , Lardelli Michael 
Published: February 2018

AbstractProtein aggregates such as those formed in neurodegenerative diseases can be degraded via autophagy. To assess changes in autophagic flux in zebrafish models of familial Alzheimer’s disease (fAD) mutations, we first developed a transgene, polyQ80-GFP-v2A-GFP, expressing equimolar amounts of aggregating polyQ80-GFP and a free GFP internal control in zebrafish embryos and larvae. This assay detects changes in autophagic flux by comparing the relative strength of polyQ80-GFP and free GFP moiety signals on western immunoblots probed with an antibody detecting GFP. However, the assay’s application is limited by the toxicity of polyQ80-GFP, and because aggregation of this protein may, itself, induce autophagy. To overcome these issues, we subsequently developed a similar ratiometric assay where expression of a GFP-Lc3a-GFP transgene generates initially equimolar amounts of GFP-Lc3a (directed to autophagic degradation) and a free GFP internal control. The sensitivity of this latter assay is reduced by a cellular protease activity that separates Lc3a from GFP-Lc3a, thus contributing to the apparent free GFP signal and somewhat masking decreases in autophagic flux. Nevertheless, the assay demonstrates significantly decreased autophagic flux in zebrafish lacking presenilin2 gene activity supporting that the Presenilin2 protein, like human PRESENILIN1, plays a role(s) in autophagy. Zebrafish heterozygous for a typical fAD-like, reading-frame-preserving mutation in psen1 show decreased autophagic flux consistent with observations in mammalian systems. Unexpectedly, a zebrafish model of the only confirmed reading-frame-truncating fAD mutation in a human PRESENILIN gene, the K115Efs mutation of human PSEN2, shows possibly increased autophagic flux in young zebrafish (larvae).
Improved sgRNA design in bacteria via genome-wide activity profiling
Authors: Guo Jiahui , Wang Tianmin , Guan Changge , Liu Bing , Luo Cheng , Xie Zhen , Zhang Chong , Xing Xin-Hui 
Published: February 2018

AbstractCRISPR/Cas9 is a promising tool in prokaryotic genome engineering, but its success is limited by the widely varying on-target activity of single guide RNAs (sgRNAs). Based on the association of CRISPR/Cas9-induced DNA cleavage with cellular lethality, we systematically profiled sgRNA activity by co-expressing a genome-scale library (~70,000 sgRNAs) with Cas9 or its specificity-improved mutant in E. coli. Based on this large-scale dataset, we constructed a comprehensive and high-density sgRNA activity map, which enables selecting highly active sgRNAs for any locus across the genome in this model organism. We also identified ‘resistant’ genomic loci with respect to CRISPR/Cas9 activity, notwithstanding the highly accessible DNA in bacterial cells. Moreover, we found that previous sgRNA activity prediction models that were trained on mammalian cell datasets were inadequate when coping with our results, highlighting the key limitations and biases of previous models. We hence developed an integrated algorithm to accurately predict highly effective sgRNAs, aiming to facilitate the design of CRISPR/Cas9-based genome engineering or screenings in bacteria. We also isolated the important sgRNA features that contribute to DNA cleavage and characterized their key differences among wild type Cas9 and its mutant, shedding light on the biophysical mechanisms of the CRISPR/Cas9 system.
Numerical solutions for the Robin time-fractional partial differential equations of heat and fluid flows based on the reproducing kernel algorithm
Authors: Abu Arqub Omar 
Published: February 2018

Purpose
The purpose of this study is to introduce the reproducing kernel algorithm for treating classes of time-fractional partial differential equations subject to Robin boundary conditions with parameters derivative arising in fluid flows, fluid dynamics, groundwater hydrology, conservation of energy, heat conduction and electric circuit.

Design/methodology/approach
The method provides appropriate representation of the solutions in convergent series formula with accurately computable components. This representation is given in the W(Ω) and H(Ω) inner product spaces, while the computation of the required grid points relies on the R(y,s) (x, t) and r(y,s) (x, t) reproducing kernel functions.

Findings
Numerical simulation with different order derivatives degree is done including linear and nonlinear terms that are acquired by interrupting the n-term of the exact solutions. Computational results showed that the proposed algorithm is competitive in terms of the quality of the solutions found and is very valid for solving such time-fractional models.

Research limitations/implications
Future work includes the application of the reproducing kernel algorithm to highly nonlinear time-fractional partial differential equations such as those arising in single and multiphase flows. The results will be published in forthcoming papers.

Practical implications
The study included a description of fundamental reproducing kernel algorithm and the concepts of convergence, and error behavior for the reproducing kernel algorithm solvers. Results obtained by the proposed algorithm are found to outperform in terms of accuracy, generality and applicability.

Social implications
Developing analytical and numerical methods for the solutions of time-fractional partial differential equations is a very important task owing to their practical interest.

Originality/value
This study, for the first time, presents reproducing kernel algorithm for obtaining the numerical solutions of some certain classes of Robin time-fractional partial differential equations. An efficient construction is provided to obtain the numerical solutions for the equations, along with an existence proof of the exact solutions based upon the reproducing kernel theory.
Developing fraud prevention model in regional public hospital in West Sulawesi Province
Authors: Kartini Kartini 
Published: February 2018

Purpose
This paper aims to reveal the empirical facts of pressure, rationalization, effect on opportunity and fraud prevention and accountability to fraud prevention in Rumah Sakit Umum Daerah (RSUD; local public hospitals in English) in West Sulawesi Province.

Design/methodology/approach
This research is explanatory in nature, with a time horizon from January to July 2016. The research objects were selected from local public hospitals (RSUD) in West Sulawesi Province. The population in this study is employees working at regional general hospitals in West Sulawesi Province. While sample is determined based on cluster sampling technique, the analysis tool used is structural equation modeling.

Findings
The variables of pressure and rationalization are found to have a positive and significant effect on opportunity, so improvements in the variables pressure and rationalization will create improvements in the variable opportunity. Pressure, rationalization and opportunity variables have a positive and significant effect on fraud prevention, so improvements in pressure, rationalization and opportunity variables will create improvements in variable fraud prevention. Accountability variables have a negative and significant effect on fraud prevention, so a high value of accountability will decrease the value of fraud prevention.

Originality/value
Originality of this paper shows built developing fraud prevention model in regional public hospital in West Sulawesi Province with five variables, namely, pressure, rationalization, opportunity, accountability and fraud prevention.
Corporate governance code comparison for South Asian emerging economies
Authors: Qurashi Mubashir Hassan 
Published: February 2018

Purpose
The purpose of this study is to compare the corporate governance (CG) codes of Pakistan, India and Bangladesh with the CG guide of United Nations (UN) and to identify the similar points of these codes with the requirements of Combined Code (CC) that are not included in the CG guide of UN.

Design/methodology/approach
This study is based on the qualitative data, while content analysis is used for the analysis. For this exploratory research, different documents have been reviewed and consulted and qualitative data are collected from those. A multiple case study approach is adopted because the codes of three countries (four CG codes used for the analysis) have been reviewed.

Findings
This study has presented that the Pakistani and Bangladeshi (issued by Bangladesh Enterprise Institute) CG code has approximately 77 per cent convergence (40 out of 52), Indian CG code has 50 per cent convergence (26 out of 52), whereas the Bangladeshi (issued by Bangladesh Security and Exchange Commission) CG code has approximately 41 per cent convergence (21 out of 52) to CG guide of UN. Seven similar points to CC have been found out in all four or few of the codes that were used in this study.

Originality/value
This study has explored the convergence of CG codes of Pakistan, Bangladesh and India with the CG guide of UN. Furthermore, this study has highlighting the similar mechanisms presented in CC and the codes of selected countries so international investors get clear information about the quality of these codes and take informed investment decision.
The factors affecting the implementation of OpenFreedom information policy and public service performance
Authors: Hutahaen John Fresly , Gani Abdul Yuli Andi , Saleh Choirul , Sarwono Sarwono 
Published: February 2018

Purpose
This study aims to examine and explain the effect of the influence of public leadership role through the implementation of open information disclosure on the performance of public services in the Daerah Khusus Ibukota Jakarta or Capital Special Region of Jakarta (DKI Jakarta) Provincial Government which is divided into five areas of the administrative city and one administrative district.

Design/methodology/approach
The population is the entire community in Jakarta, which already have ID cards is as much as 6,980,584 people with a sample of 228 respondents. The duration for this research is January-March 2017. Methods of data analysis in this research using descriptive analysis and inferential statistical analysis using the structural equation modeling (SEM).

Findings
The role of the public leaders influences the implementation of education but has no direct influence on the public service performance but indirectly through the implementation of OpenFreedom of information.

Originality/value
Originality in this research shows that never been testing this kind of relation in Jakarta, Indonesian.