bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preferential Amplification of Pathogenic Sequences
Authors: Ge Fang , Parker Jayme , Chul Choi Sang , Layer Mark , Ross Katherine , Jilly Bernard , Chen Jack 
Published: June 2015

AbstractThe application of next generation sequencing (NGS) technology in the diagnosis of human pathogens is hindered by the fact that pathogenic sequences, especially viral, are often scarce in human clinical specimens. This known disproportion leads to the requirement of subsequent deep sequencing and extensive bioinformatics analysis. Here we report a method we called “Preferential Amplification of Pathogenic Sequences (PATHseq)” that can be used to greatly enrich pathogenic sequences. Using a computer program, we developed 8-, 9- and 10-mer oligonucleotides called “non-human primers” that do not match the most abundant human transcripts, but instead selectively match transcripts of human pathogens. Instead of using random primers in the construction of cDNA libraries, the PATHseq method recruits these short non-human primers, which in turn, preferentially amplifies non-human, presumably pathogenic sequences. Using this method, we were able to enrich pathogenic sequences up to 200-fold in the final sequencing library. This method does not require prior knowledge of the pathogen or assumption of the infection; therefore, it provides a fast and sequence-independent approach for detection and identification of human viruses and other pathogens. The PATHseq method, coupled with NGS technology, can be broadly used in identification of known human pathogens and discovery of new pathogens.
Genome-wide single-nucleotide polymorphism analysis revealed SUFU suppression of acute graft-versus-host disease through downregulation of HLA-DR expression in recipient dendritic cells
Authors: Bari Rafijul , Hartford Christine , Chan Wing Keung , Vong Queenie , Li Ying , Gan Kwan , Zhou Yinmei , Cheng Cheng , Kang Guolian , Shurtleff Sheila , Turner Victoria , Pui Ching-Hon , Downing James R. , Leung Wing 
Published: June 2015

AbstractGraft-versus-host disease (GVHD) is a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (HSCT). To identify recipient risk factors, a genome-wide study was performed including 481,820 single-nucleotide polymorphisms (SNPs). Two GVHD susceptibility loci (rs17114803 and rs17114808) within the SUFU gene were identified in the discovery cohort (p = 2.85 × 10−5). The incidence of acute GVHD among patients homozygous for CC at SUFU rs17114808 was 69%, which was significantly higher than the 8% rate observed in CT heterozygous patients (p = 0.0002). In an independent validation cohort of 100 patients, 50% of the patients with the CC genotype developed GVHD compared to 8% of the patients with either CT or TT genotype (p = 0.01). In comparison to CC dendritic cells, those from CT expressed higher levels of SUFU mRNA and protein, had lower levels of surface HLA-DR and induced less allogeneic mixed leukocyte response (MLR). Ectopic expression of SUFU in THP-1 derived DCs reduced HLA-DR expression and suppressed MLR, whereas silencing of SUFU enhanced HLA-DR expression and increased MLR. Thus our findings provide novel evidence that recipient SUFU germline polymorphism is associated with acute GVHD and is a novel molecular target for GVHD prevention and treatment.
Next-generation sequencing for molecular diagnosis of lung adenocarcinoma specimens obtained by fine needle aspiration cytology
Authors: Qiu Tian , Guo Huiqin , Zhao Huan , Wang Luhua , Zhang Zhihui 
Published: June 2015

AbstractIdentification of multi-gene variations has led to the development of new targeted therapies in lung adenocarcinoma patients and identification of an appropriate patient population with a reliable screening method is the key to the overall success of tumor targeted therapies. In this study, we used the Ion Torrent next-generation sequencing (NGS) technique to screen for mutations in 89 cases of lung adenocarcinoma metastatic lymph node specimens obtained by fine-needle aspiration cytology (FNAC). Of the 89 specimens, 30 (34%) were found to harbor epidermal growth factor receptor (EGFR) kinase domain mutations. Seven (8%) samples harbored KRAS mutations and three (3%) samples had BRAF mutations involving exon 11 (G469A) and exon 15 (V600E). Eight (9%) samples harbored PIK3CA mutations. One (1%) sample had a HRAS G12C mutation. Thirty-two (36%) samples (36%) harbored TP53 mutations. Other genes including APC, ATM, MET, PTPN11, GNAS, HRAS, RB1, SMAD4 and STK11 were found each in one case. Our study has demonstrated that NGS using the Ion Torrent technology is a useful tool for gene mutation screening in lung adenocarcinoma metastatic lymph node specimens obtained by FNAC and may promote the development of new targeted therapies in lung adenocarcinoma patients.
Five Decades of Research in Speech Motor Control: What Have We Learned, and Where Should We Go From Here?
Authors: Perkell Joseph S. 
Published: June 2015

Purpose
The author presents a view of research in speech motor control over the past 5 decades, as observed from within Ken Stevens's Speech Communication Group (SCG) in the Research Laboratory of Electronics at MIT.

Method
The author presents a limited overview of some important developments and discoveries. The perspective is based largely on the research interests of the Speech Motor Control Group (SMCG) within the SCG; thus, it is selective, focusing on normal motor control of the vocal tract in the production of sound segments and syllables. It also covers the particular theories and models that drove the research. Following a brief introduction, there are sections on methodological advances, scientific advances, and conclusions.

Results
Scientific and methodological advances have been closely interrelated. Advances in instrumentation and computer hardware and software have made it possible to record and process increasingly large, multifaceted data sets; introduce new paradigms for feedback perturbation; image brain activity; and develop more sophisticated, computational physiological and neural models. Such approaches have led to increased understanding of the widespread variability in speech, motor-equivalent trading relations, sensory goals, and the nature of feedback and feedforward neural control mechanisms.

Conclusions
Some ideas about important future directions for speech research are presented.
Several Types of Similarity Solutions for the Hunter–Saxton Equation*
Authors: Baxter Mathew , Van Gorder Robert A. , Vajravelu Kuppalapalle 
Published: June 2015

Abstract
We study separable and self-similar solutions to the Hunter–Saxton equation, a nonlinear wave equation which has been used to describe an instability in the director Geld of a nematic liquid crystal (among other applications). Essentially, we study solutions which arise from a nonlinear inhomogeneous ordinary differential equation which is obtained by an exact similarity transform for the Hunter–Saxton equation. For each type of solution, we are able to obtain some simple exact solutions in closed-form, and more complicated solutions through an analytical approach. We find that there is a whole family of self-similar solutions, each of which depends on an arbitrary parameter. This parameter essentially controls the manner of self-similarity and can be chosen so that the self-similar solutions agree with given initial data. The simpler solutions found constitute exact solutions to a nonlinear partial differential equation, and hence are also useful in a mathematical sense. Analytical solutions demonstrate the variety of behaviors possible within the wider family of similarity solutions. Both types of solutions cast light on self-similar phenomenon arising in the Hunter–Saxton equation.
Modified Kadomtsev–Petviashvili Equation in (3+1) Dimensions: Multiple Front-Wave Solutions
Authors: Wazwaz A.M. , Xu Gui-Qiong 
Published: June 2015

Abstract
A modified Kadomtsev–Petviashvili (mKP) equation in (3+1) dimensions is presented. We reveal multiple front-waves solutions for this higher-dimensional developed equation, and multiple singular front-wave solutions as well. The constraints on the coefficients of the spatial variables, that assure the existence of these multiple front-wave solutions are investigated. We also show that this equation fails the Painlevé test, and we conclude that it is not integrable in the sense of possessing the Painlevé property, although it gives multiple front-wave solutions.
Electrostatic Nonplanar Positron-Acoustic Shock Waves in Superthermal Electron-Positron-Ion Plasmas
Authors: Uddin M.J. , Alam M.S. , Mamun A.A. 
Published: June 2015

AbstractThe basic properties of the nonlinear propagation of the nonplanar (cylindrical and spherical) positron-acoustic (PA) shock waves (SHWs) in an unmagnetized electron-positron-ion (e-p-i) plasma containing immobile positive ions, mobile cold positrons, and superthermal (kappa distributed) hot positrons and electrons are investigated both analytically and numerically. The modified Burgers equation (mBE) is derived by using the reductive perturbation method. The basic features of PA SHWs are significantly modified by the cold positron kinematic viscosity (η), superthermal parameter of electrons (κe), superthermal parameter of hot positrons (κp), the ratio of the electron temperature to hot positron temperature (σ), the ratio of the electron number density to cold positron number density and the ratio of the hot positron number density to cold positron number density (μph). This study could be useful to identify the basic properties of nonlinear electrostatic disturbances in dissipative space and laboratory plasmas.
EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data
Authors: Wijetunge Chalini D. , Saeed Isaam , Boughton Berin A. , Spraggins Jeffrey M. , Caprioli Richard M. , Bacic Antony , Roessner Ute , Halgamuge Saman K. 
Published: June 2015

Abstract
Motivation: Matrix Assisted Laser Desorption Ionization-Imaging Mass Spectrometry (MALDI-IMS) in ‘omics’ data acquisition generates detailed information about the spatial distribution of molecules in a given biological sample. Various data processing methods have been developed for exploring the resultant high volume data. However, most of these methods process data in the spectral domain and do not make the most of the important spatial information available through this technology. Therefore, we propose a novel streamlined data analysis pipeline specifically developed for MALDI-IMS data utilizing significant spatial information for identifying hidden significant molecular distribution patterns in these complex datasets.
Methods: The proposed unsupervised algorithm uses Sliding Window Normalization (SWN) and a new spatial distribution based peak picking method developed based on Gray level Co-Occurrence (GCO) matrices followed by clustering of biomolecules. We also use gist descriptors and an improved version of GCO matrices to extract features from molecular images and minimum medoid distance to automatically estimate the number of possible groups.
Results: We evaluated our algorithm using a new MALDI-IMS metabolomics dataset of a plant (Eucalypt) leaf. The algorithm revealed hidden significant molecular distribution patterns in the dataset, which the current Component Analysis and Segmentation Map based approaches failed to extract. We further demonstrate the performance of our peak picking method over other traditional approaches by using a publicly available MALDI-IMS proteomics dataset of a rat brain. Although SWN did not show any significant improvement as compared with using no normalization, the visual assessment showed an improvement as compared to using the median normalization.
Availability and implementation: The source code and sample data are freely available at http://exims.sourceforge.net/.
Contact: awgcdw@student.unimelb.edu.au or chalini_w@live.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Maspin-related Orchestration of Aggressiveness of Gastric Cancer
Authors: Gurzu Simona , Kadar Zoltan , Sugimura Haruhiko , Orlowska Janina , Bara Tivadar , Bara Tivadar , Szederjesi Janos , Jung Ioan 
Published: June 2015

Background and Study Aim:
Although some hypotheses have been postulated on the genesis of gastric cancer (GC), the origin of this disease remains unclear. The aim of this study was to develop a hypothesis about gastric carcinogenesis based on our experience in the field of GC and on published reports on about 28 studies in the field of subcellular maspin expression in GC. In 180 cases of GC, the clinicopathologic features were correlated with the results obtained after paired immunohistochemical stains (tumor/normal mucosa) with 15 antibodies: E-cadherin, HER-2, VEGF, CD31, CD105, COX-2, maspin, bax, bcl-2, p53, Ki67, MLH-1, MSH-2, Mena protein, and vimentin.

Results:
Cytoplasmic maspin was observed in foveolar cells with intestinal metaplasia, whereas mixed (combined nuclear-cytoplasmic) expressions were more characteristic of the intramucosal foci of signet-ring cells and dysplastic cells. The tumor cells that expressed cytoplasmic maspin were mostly intestinal type bax/COX-2/Mena/E-cadherin-positive differentiated adenocarcinomas with nodular growth and more superficial invasion. The nuclear shift of maspin was more frequent in HER-2/p53-positive intestinal type adenocarcinomas with diffuse architecture at the invasion front, as well as for node-positive poorly cohesive carcinomas. Loss of maspin expression induced a higher risk of distant metastases, without differences in the survival rate.

Conclusions:
In GC with associated metaplasia, cytoplasmic maspin is predominant; the nuclear shift induces local aggressiveness and risk of node metastases, whereas total loss can indicate a risk of distant metastases. In GC without associated metaplasia, nuclear expression of maspin is retained, indicating a more aggressive behavior.
Prevalence of Implanted Medical Devices in Medicine Inpatients
Authors: Kuder Margaret , Gelman Amanda , Zenilman Jonathan M. 
Published: June 2015

Abstract
Implanted medical devices (IMDs) are extremely common, yet they are not systematically documented on hospital admission. Through structured patient interviews, we determined the prevalence of IMDs in hospital inpatients. Using medical record review, we evaluated the sensitivity of the medical record reporting of IMDs on an academic medical inpatient service. Fifty-eight percent of 191 interviewees reported 1 or more IMDs. Participants who reported greater than 1 IMD were older and had more frequent hospitalizations. The most common devices reported were surgical mesh, screws, plates, or wires (n = 47); intravascular stents (n = 25); and prosthetic joint replacements (n = 17). Forty-six patients (24%) reported greater than 1 IMD that had not been recorded in their admission history and physical examination. The prevalence of IMDs in hospitalized patients is high and underestimated in the medical record and may have significant implications for patient care.
ABCs of Hospitalized Patients: A Simple Before-After Study of a Communication Tool to Improve Quality of Inpatient Care
Authors: Afsar-manesh Nasim , Perkins Colby E. , Breger Kevin S. , Zadunayski Michelle M. 
Published: June 2015

Objectives
Within the past several years, innovative communication tools have been established as viable quality improvement mechanisms in health care. Meanwhile, the economic and societal burdens of hospital-acquired conditions (HACs) continue to rise. Various interventions have been attempted to reduce HACs. This study evaluated the effectiveness of a communication tool in reducing risk factors for HACs.

Methods
A communication tool aimed at reducing HAC risk factors was developed by an interdisciplinary team of physicians and nurses and tested in a simple before-after quality improvement study. It included 8 components: ambulation/fall risk, blood glucose greater than 200 mg/dL, central venous catheters, deep venous thrombosis prophylaxis, erosions of the skin/dermal ulcers, Foley/urinary catheters, got communication, and heart monitor/telemetry. This communication tool facilitated multidisciplinary communication. The nurses completed it nightly, and the physicians reviewed the communication tool each morning and, when appropriate, addressed components of care that were out of compliance with best practices.

Results
The use of the ABCs of Hospitalized Patients Communication Tool led to daily improvements with reduction in the percentage of patients with blood glucose greater than 200 mg/dL from 43.3% to 35.1%, reduction in the use of central venous catheters from 8.2% to 1.0% of patients, increase in the use of chemical deep venous thrombosis prophylaxis from 45.4% of patients to 56.7%, reduction in the use of urinary catheters from 27.6% to 13.2%, and decrease in use of telemetry from 67.5% to 55.1%. All of the results have P < 0.05. These improvements were sustained over time.

Conclusions
Implementation of a multidisciplinary communication tool serves as a simple, resource-conscious, and customizable instrument to reduce the risk factors for developing HACs. This communication tool can be easily disseminated and used by other institutions.
The past, present, and future (?) of crime-related forensic accounting methodology
Authors: Louwers Timothy J. 
Published: June 2015

Purpose
– The purpose of this paper is to explore the origins of crime-related forensic accounting methodology in the USA.

Design/methodology/approach
– The author describes how these early methods have evolved through the use of technology.

Findings
– The author also discusses the next generation of crime-related forensic accounting tools and techniques which, although in limited use today, will grow to widespread use in the near future.

Originality/value
– This viewpoint is a summary of a presentation made at the 3rd National Forensic Accounting Teaching and Research Symposium held at the Queensland University of Technology on February 10, 2014.
An empirical investigation of fraud risk assessment and knowledge requirement on fraud related problem representation in Nigeria
Authors: Popoola Oluwatoyin Muse Johnson , Che-Ahmad Ayoib B , Samsudin Rose Shamsiah 
Published: June 2015

Purpose– The paper aims to investigate Task Performance Fraud Risk Assessment (TPFRA) and Knowledge Requirement (KR) of the forensic accountant and auditor on Fraud-Related Problem Representation (FRPR) in the Nigerian public sector.Design/methodology/approach– The study used cross-sectional design and 400 survey questionnaires. The respondents are real professional people (auditors and forensic accountants in the Nigerian public sector) as true representatives to enhance the generalization of the outcomes. A total of 36 indicator items was measured on five-point Likert scale from 1 (strongly disagree) to 5 (strongly agree). Partial Least Square – Structural Equation Modelling 2.0 3M and IBM SPSS Statistics 20.0 were used as the primary statistical analysis tool for the study.Findings– The results of the present study confirm the positive relationship between KR on TPFRA, positive relationship of KR on FRPR and positive relationship of FRPR and TPFRA. Specifically, the results revealed that FRPR positively mediates the relationship between TPFRA and KR (forensic accountant and auditor) in the areas of fraud prevention, detection and response.Research limitations/implications– The first limitation deals with fraud and corrupt practices in a developing country, Nigeria. Examining the mediating influence of FRPR on KR and TPFRA in the public sector could be considered as sensitive and raise the issue of bias. The second limitation is the adoption of cross-sectional design in which data are collected at one point in time. Researchers are encouraged to use a longitudinal design to explore interactions between KR, FRPR and TPFRA.Practical implications– This empirical study has revealed the value of KR (forensic accountant and auditor) as a significant capability requirement in the workplace. In addition, it shows the importance of FRPR as an important mental state in decision-making or judgment and also the significance of FRPR as an important mediating variable on KR and TPFRA.Originality/value– No nation is immune to fraud, and loss due to fraud in the public sector is enormous and costly; the result of this research will improve the KR of auditors and forensic accountants in the areas of fraud detection, prevention and response. It will also contribute to the regulatory, legal and institutional frameworks in accounting and auditing systems in Nigeria and portend an increase in demand for forensic accountants.
Factors which may bias judges’ decisions to exclude accounting expert witnesses testimony
Authors: Domino Madeline Ann , Stradiot Matthew , Webinger Mariah 
Published: June 2015

Purpose
– This paper aims to investigate factors which may influence or bias judges’ decisions to exclude or admit the testimony of accounting expert witnesses, under the US judicial guidelines commonly known as the Daubert/Kuhmo standards. Accounting experts are increasingly providing expert testimony as a part of financial litigation support services.

Design/methodology/approach
– Judges’ decisions, in which opposing council evoked a Daubert/Kuhmo challenge to the testimony provided by 130 professional accountants serving as expert witnesses, were analyzed. The period of study was 2010 through 2014. Based on prior research, three variables believed to potentially influence or bias judges to systematically exclude expert testimony were examined: gender, complexity and familiarity.

Findings
– The results of binary logistic regression show that none of the variables has a significant relationship to the accounting expert witnesses’ probability of surviving a challenge to Daubert/Kuhmo standards. Findings suggest that judges are objective in evaluating the testimony provided by accounting experts under Daubert/Kuhmo guidelines and that they may be immune to biases based solely on gender, complexity and familiarity.

Originality/value
– These results will be of interest to judges, lawyers and forensic accountants acting as expert witnesses.