bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of environmental single-stranded DNA phages revealed by PCR amplification of the partial major capsid protein
Authors: Hopkins Max , Kailasan Shweta , Cohen Allison , Roux Simon , Tucker Kimberly Pause , Shevenell Amelia , Agbandje-McKenna Mavis , Breitbart Mya 
Published: April 2014

Abstract
The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles.
Habitat stress initiates changes in composition, CO2 gas exchange and C-allocation as life traits in biological soil crusts
Authors: Colesie Claudia , Allan Green T G , Haferkamp Ilka , Büdel Burkhard 
Published: April 2014

Abstract
Biological soil crusts (BSC) are the dominant functional vegetation unit in some of the harshest habitats in the world. We assessed BSC response to stress through changes in biotic composition, CO2 gas exchange and carbon allocation in three lichen-dominated BSC from habitats with different stress levels, two more extreme sites in Antarctica and one moderate site in Germany. Maximal net photosynthesis (NP) was identical, whereas the water content to achieve maximal NP was substantially lower in the Antarctic sites, this apparently being achieved by changes in biomass allocation. Optimal NP temperatures reflected local climate. The Antarctic BSC allocated fixed carbon (tracked using 14CO2) mostly to the alcohol soluble pool (low-molecular weight sugars, sugar alcohols), which has an important role in desiccation and freezing resistance and antioxidant protection. In contrast, BSC at the moderate site showed greater carbon allocation into the polysaccharide pool, indicating a tendency towards growth. The results indicate that the BSC of the more stressed Antarctic sites emphasise survival rather than growth. Changes in BSC are adaptive and at multiple levels and we identify benefits and risks attached to changing life traits, as well as describing the ecophysiological mechanisms that underlie them.
Global link between deformation and volcanic eruption quantified by satellite imagery
Authors: Biggs J. , Ebmeier S. K. , Aspinall W. P. , Lu Z. , Pritchard M. E. , Sparks R. S. J. , Mather T. A. 
Published: April 2014

AbstractA key challenge for volcanological science and hazard management is that few of the world’s volcanoes are effectively monitored. Satellite imagery covers volcanoes globally throughout their eruptive cycles, independent of ground-based monitoring, providing a multidecadal archive suitable for probabilistic analysis linking deformation with eruption. Here we show that, of the 198 volcanoes systematically observed for the past 18 years, 54 deformed, of which 25 also erupted. For assessing eruption potential, this high proportion of deforming volcanoes that also erupted (46%), together with the proportion of non-deforming volcanoes that did not erupt (94%), jointly represent indicators with ‘strong’ evidential worth. Using a larger catalogue of 540 volcanoes observed for 3 years, we demonstrate how this eruption–deformation relationship is influenced by tectonic, petrological and volcanic factors. Satellite technology is rapidly evolving and routine monitoring of the deformation status of all volcanoes from space is anticipated, meaning probabilistic approaches will increasingly inform hazard decisions and strategic development.
Porphyrin–phospholipid liposomes permeabilized by near-infrared light
Authors: Carter Kevin A. , Shao Shuai , Hoopes Matthew I. , Luo Dandan , Ahsan Bilal , Grigoryants Vladimir M. , Song Wentao , Huang Haoyuan , Zhang Guojian , Pandey Ravindra K. , Geng Jumin , Pfeifer Blaine A. , Scholes Charles P. , Ortega Joaquin , Karttunen Mikko , Lovell Jonathan F. 
Published: April 2014

AbstractThe delivery of therapeutic compounds to target tissues is a central challenge in treating disease. Externally controlled drug release systems hold potential to selectively enhance localized delivery. Here we describe liposomes doped with porphyrin–phospholipid that are permeabilized directly by near-infrared light. Molecular dynamics simulations identified a novel light-absorbing monomer esterified from clinically approved components predicted and experimentally demonstrated to give rise to a more stable porphyrin bilayer. Light-induced membrane permeabilization is enabled with liposomal inclusion of 10 molar % porphyrin–phospholipid and occurs in the absence of bulk or nanoscale heating. Liposomes reseal following laser exposure and permeability is modulated by varying porphyrin–phospholipid doping, irradiation intensity or irradiation duration. Porphyrin–phospholipid liposomes demonstrate spatial control of release of entrapped gentamicin and temporal control of release of entrapped fluorophores following intratumoral injection. Following systemic administration, laser irradiation enhances deposition of actively loaded doxorubicin in mouse xenografts, enabling an effective single-treatment antitumour therapy.
Hearing Loss Prevention Education Using Adopt-a-Band: Changes in Self-Reported Earplug Use in Two High School Marching Bands
Authors: Auchter Melissa , Le Prell Colleen G. 
Published: April 2014

Purpose
Hearing loss prevention has always been an important issue for audiologists. The importance of hearing loss prevention education for young musicians is now recognized by the National Association for Music Education as well as the National Association of Schools of Music. Adopt-a-Band is a commercial program designed to foster hearing loss prevention behavior in young musicians.

Method
This study assessed changes in earplug use, measured using self-report surveys, after Adopt-a-Band training. Participants were members of 2 high school marching bands who viewed an informational DVD and reviewed fact sheets. Flat-attenuation earplugs were distributed, and training was provided. In addition, study participants engaged in discussion of hearing loss with a doctor of audiology student.

Results
Before training, 23% of participants reported they had previously used hearing protection. Immediately after training, 94% of participants reported they planned to use hearing protection at least occasionally. In a final end-of-season survey, earplug use had reliably increased; 62% of participants reported they used earplugs at least occasionally.

Conclusions
Earplug use increased, but self-reported behavioral change was not as robust as predicted from self-reported participant intentions. Participant comments regarding factors that influenced their earplug use decisions suggest opportunities to improve training.
A Review of 30 Speech Assessments in 19 Languages Other Than English
Authors: McLeod Sharynne , Verdon Sarah 
Published: April 2014

Purpose
In this study, the authors aimed to evaluate instruments designed to assess children's speech production in languages other than English.

Method
Ninety-eight speech assessments in languages other than English were identified: 62 were commercially published, 17 published within journal articles, and 19 informal assessments. A review was undertaken of 30 commercially published assessments that could be obtained.

Results
The 30 instruments assessed 19 languages: Cantonese, Danish, Finnish, German, Greek, Japanese, Korean, Maltese-English, Norwegian, Pakistani-heritage languages (Mirpuri, Punjabi, Urdu), Portuguese, Putonghua (Mandarin), Romanian, Slovenian, Spanish, Swedish, and Turkish. The majority (70.0%) assessed speech sound production in monolingual speakers, 20.0% assessed one language of bilingual speakers, and 10.0% assessed both languages of bilingual speakers. All used single-word picture elicitation. Approximately half (53.3%) were norm-referenced, and the number of children in the normative samples ranged between 145 and 2,568. The remaining assessments were criterion-referenced (50.0%) (one fitted both categories). The assessments with English manuals met many of the psychometric criteria for operationalization; however, only 2 provided sensitivity and specificity data.

Conclusions
Despite the varying countries of origin, there were many similarities between speech assessments in languages other than English. Few were designed for use with multilingual children, so validation is required for use in English-speaking contexts.
Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis
Authors: Lee Eunjee , de Ridder Jeroen , Kool Jaap , Wessels Lodewyk F. A. , Bussemaker Harmen J. 
Published: April 2014

Significance
Each individual tumor harbors a unique combination of genetic lesions, which together are responsible for the aberrant behavior of its cells. Cancer-causing viruses have been used in mice to systematically sample this genetic diversity. Corresponding changes in global gene expression can be monitored using high-throughput technology. In this study, we present a computational strategy that integrates information at the genetic and molecular level to construct a genome-wide signature that captures the effect of an individual genetic lesion on the gene regulatory network of the cell. We show how these signatures can be exploited to gain insight into the processes and regulatory pathways perturbed by each lesion and suggest drugs that can counteract its effect.
Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin
Authors: Rognoni Lorenz , Möst Tobias , Žoldák Gabriel , Rief Matthias 
Published: April 2014

Significance
Biological processes in the cell are highly dynamic and complex, and their correct interplay is ensured by a multitude of regulatory mechanisms. Among these, proline isomerization acts as a molecular switch that toggles two protein conformations, and thus functions, over time. In mechanosensing, mechanical stress is transduced into chemical signals. The molecular mechanisms underlying this regulation are crucial for understanding cell behavior and development. However, only a few experimental techniques are capable of studying force at the molecular level. In this paper, we use single-molecule mechanical experiments to investigate how the force-sensing region of the cytoskeletal cross-linker filamin is modulated by a proline switch.
Trimmomatic: a flexible trimmer for Illumina sequence data
Authors: Bolger Anthony M. , Lohse Marc , Usadel Bjoern 
Published: April 2014

Abstract
Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data.
Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic
Contact: usadel@bio1.rwth-aachen.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
Authors: Li Yi , Xie Xiaohui 
Published: April 2014

AbstractMotivation: Next-generation sequencing (NGS) has revolutionized the study of cancer genomes. However, the reads obtained from NGS of tumor samples often consist of a mixture of normal and tumor cells, which themselves can be of multiple clonal types. A prominent problem in the analysis of cancer genome sequencing data is deconvolving the mixture to identify the reads associated with tumor cells or a particular subclone of tumor cells. Solving the problem is, however, challenging because of the so-called ‘identifiability problem’, where different combinations of tumor purity and ploidy often explain the sequencing data equally well.Results: We propose a new model to resolve the identifiability problem by integrating two types of sequencing information—somatic copy number alterations and loss of heterozygosity—within a unified probabilistic framework. We derive algorithms to solve our model, and implement them in a software package called PyLOH. We benchmark the performance of PyLOH using both simulated data and 12 breast cancer sequencing datasets and show that PyLOH outperforms existing methods in disambiguating the identifiability problem and estimating tumor purity.Availability and implementation: The PyLOH package is written in Python and is publicly available at https://github.com/uci-cbcl/PyLOH .Contact: xhx@ics.uci.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Heparin-Binding Protein: A Diagnostic Biomarker of Urinary Tract Infection in Adults
Authors: Kjölvmark Charlott , Påhlman Lisa I. , Åkesson Per , Linder Adam 
Published: April 2014

Abstract
Background.  Urinary tract infections (UTIs) are associated with significant morbidity and high frequency of antibiotic prescription. Diagnosing UTI is often difficult, particularly in the critically ill patient and in patients with unspecific and mild symptoms. The standard rapid tests have limited value, and there is a need for more reliable diagnostic tools. Heparin-binding protein (HBP) is released from neutrophils and has previously been studied as a diagnostic and predictive biomarker in different bacterial infections.
Methods.  This prospective survey enrolled adult patients at 2 primary care units and 2 hospital emergency departments, to investigate in urine HBP as a biomarker of UTI. In addition, urine levels of interleukin-6, white blood cells, and nitrite were analyzed and compared with HBP. Based on symptoms of UTI and microbiological findings, patients were classified into different groups, UTI (cystitis and pyelonephritis) and no UTI.
Results.  Three hundred ninety patients were evaluated. The prevalence of UTI in the study group was 45.4%. The sensitivity and specificity for HBP in urine as a marker for UTI were 89.2% and 89.8%, respectively. The positive and negative predictive values were 90.2% and 88.8%, respectively. Heparin-binding protein was the best diagnostic marker for UTI, with an area-under-curve value of 0.94 (95% confidence interval, 0.93–0.96). Heparin-binding protein was significantly better in distinguishing cystitis from pyelonephritis, compared with the other markers.
Conclusions.  An elevated level of HBP in the urine is associated with UTI and may be a useful diagnostic marker in adult patients with a suspected UTI.
New Onset of Kaposi Sarcoma in a Human Immunodeficiency Virus-1-Infected Homosexual Man, Despite Early Antiretroviral Treatment, Sustained Viral Suppression, and Immune Restoration
Authors: von Braun Amrei , Braun Dominique L. , Kamarachev Jivko , Günthard Huldrych F. 
Published: April 2014

Abstract
This is a rare case of new onset Kaposi sarcoma in a man infected with human immunodeficiency virus (HIV) and receiving antiretroviral treatment since primary HIV infection, with normal CD4+ cell count and suppressed viral load. The presentation questions the general understanding of Kaposi sarcoma as an acquired immune deficiency syndrome-defining disease occurring predominantly in severely immunocompromised patients infected with HIV.
Empiric Vancomycin Use in Febrile Neutropenic Oncology Patients
Authors: Libuit Jessica , Whitman Andrew , Wolfe Rebecca , Washington Casey S. 
Published: April 2014

Abstract
Vancomycin is commonly added as empiric therapy for febrile neutropenia. A retrospective chart review was conducted at a large community teaching institution to evaluate vancomycin use in oncology patients. The results revealed that a majority of empiric vancomycin therapy was inappropriate, raising concern for antibiotic resistance and prompting opportunities for improvement.
ID Learning Unit: Understanding and Interpreting Testing for Clostridium difficile
Authors: Solomon Daniel A. , Milner Danny A. 
Published: April 2014

Abstract
Understanding and interpreting the molecular tests for Clostridium difficile is challenging because there are several different types of assays and most laboratories combine multiple tests in order to assess for presence of disease. This learning unit demonstrates the basic principles of each test along with its strengths and weaknesses, and illustrates how the tests are used in clinical practice.
Multigene Engineering of Triacylglycerol Metabolism Boosts Seed Oil Content in Arabidopsis
Authors: van Erp Harrie , Kelly Amélie A. , Menard Guillaume , Eastmond Peter J. 
Published: April 2014

Abstract
Increasing the yield of oilseed crops is an important objective for biotechnologists. A number of individual genes involved in triacylglycerol metabolism have previously been reported to enhance the oil content of seeds when their expression is altered. However, it has yet to be established whether specific combinations of these genes can be used to achieve an additive effect and whether this leads to enhanced yield. Using Arabidopsis (Arabidopsis thaliana) as an experimental system, we show that seed-specific overexpression of WRINKLED1 (a transcriptional regulator of glycolysis and fatty acid synthesis) and DIACYLGLYCEROL ACYLTRANSFERASE1 (a triacylglycerol biosynthetic enzyme) combined with suppression of the triacylglycerol lipase SUGAR-DEPENDENT1 results in a higher percentage seed oil content and greater seed mass than manipulation of each gene individually. Analysis of total seed yield per plant suggests that, despite a reduction in seed number, the total yield of oil is also increased.
Who is more likely to become business angels?
Authors: Li Yaokuang , Ling Li , Wu Juan , Li Peng 
Published: April 2014

Purpose– The paper is aimed to obtain a clear understanding of influence factors that can increase the possibility to be business angels (BA).Design/methodology/approach– This study develops the 3A model in the Chinese context to design questionnaire, and 334 questionnaires are obtained via focus group sample and targeted snowball approach, and the multinomial logit analysis is used to test a serious of hypotheses.Findings– The paper confirmed that the entrepreneurial experience and wealth are determinants of investment for potential BA, and the wealth have both directly and indirectly positive influence on investment activity through risk preference, namely that richer people prefer risk which impel them to invest as BA.Research limitations/implications– There are two limitations in the paper: first, the macro environment in China has not been taken into consideration in the model; second, the source of the sample focuses on the developed cities in the middle and eastern of China, only reflect the characteristic of angels in these areas, which may somewhat diverges from the reality.Practical implications– The paper would contribute to form the policy which could promote the development of angel investment in China.Originality/value– This paper conducts a preliminary exploration of the factors that have impact on Chinese BA' investment activity based on current research.
A US-China comparative study of cloud computing adoption behavior
Authors: Ratten Vanessa 
Published: April 2014

Purpose– The purpose of this paper is to examine the effects of privacy concerns and consumer innovativeness towards consumer's adoption of a technological innovation in the form of cloud computing technology.Design/methodology/approach– A cross-cultural comparison between consumers in the USA and China is made through a study of consumers intending to adopt cloud computing services. A review of the technology innovation adoption literature forms the basis of the research propositions, which are based on the extant literature and focused on the innovative adoption behaviour of consumers. A comparative approach is taken to analyse the differences between US and Chinese consumers intending to adopt cloud computing services.Findings– Findings suggest that there are more similarities than differences between US and Chinese consumers adopting cloud computing services. The survey suggests that the performance expectancy, perceived usefulness and perceived ease of use can help predict intention to adopt cloud computing services in both the USA and China, but consumer innovativeness is a better indicator in the USA than in China for consumers adopting technological innovations.Practical implications– This paper is important for cloud service technology marketers by indicating how social influencers can influence consumer's usage of cloud computing by affecting their social network of friends and family. In addition, insight into how consumers adopt cloud computing by focusing on privacy concerns of personal information being shared can help future technology innovations enter the marketplace at a faster rate.Originality/value– This paper fills the gap in the current technology marketing and innovation literature on how consumers adopt technological innovations and highlights the importance of increasing the perceptions of performance expectation of service innovations.