bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections
Authors: PALLEN M. J. 
Published: February 2014

SUMMARYThe term ‘shotgun metagenomics’ is applied to the direct sequencing of DNA extracted from a sample without culture or target-specific amplification or capture. In diagnostic metagenomics, this approach is applied to clinical samples in the hope of detecting and characterizing pathogens. Here, I provide a conceptual overview, before reviewing several recent promising proof-of-principle applications of metagenomics in virus discovery, analysis of outbreaks and detection of pathogens in contemporary and historical samples. I also evaluate future prospects for diagnostic metagenomics in the light of relentless improvements in sequencing technologies.
Kinematic modeling and control for human-robot cooperation considering different interaction roles
Authors: Adorno B. V. , Bó A. P. L. , Fraisse P. 
Published: February 2014

SUMMARYThis paper presents a novel approach for the description of physical human-robot interaction (pHRI) tasks that involve two-arm coordination, and where tasks are described by the relative pose between the human hand and the robot hand. We develop a unified kinematic model that takes into account the human-robot system from a holistic point of view, and we also propose a kinematic control strategy for pHRI that comprises different levels of shared autonomy. Since the kinematic model takes into account the complete human-robot interaction system and the kinematic control law is closed loop at the interaction level, the kinematic constraints of the task are enforced during its execution. Experiments are performed in order to validate the proposed approach, including a particular case where the robot controls the human arm by means of functional electrical stimulation (FES), which may potentially provide useful solutions for the interaction between assistant robots and impaired individuals (e.g., quadriplegics and hemiplegics).
Sorbitol non-fermenting shiga toxin-producingEscherichia coliin cattle on smallholdings
Authors: ISLAM M. Z. , CHRISTENSEN J. P. , BISWAS P. K. 
Published: February 2014

SUMMARYWe investigated faecal samples collected from the rectum of 518 cattle on 371 randomly selected smallholdings in Bangladesh for the presence of sorbitol non-fermenting (SN-F) shiga toxin-producingEscherichia coli(STEC). The SN-F isolates were tested for the presence ofrfbO157,stx1, stx2, eaeandhlyAgenes by polymerase chain reaction (PCR). Seven SN-F isolates lacking these genes were profiled by pulsed-field gel electrophoresis (PFGE) to verify their clonality. SN-FE. coliwas identified in 44 [8·5%, 95% confidence interval (CI) 6·4–11·2] samples; of these, 28 (5·4%, 95% CI 3·8–7·7) had shiga toxin-producing strains, although only two carried therfbO157 gene. Thirteen isolates carried thehlyAgene while 18 harboured theeaegene. Based on PFGE, six pulsotypes were observed among the seven isolates that had no virulence genes. To the best of our knowledge this is the first report on shiga toxin-producingE. colifrom direct rectal faecal samples of cattle on smallholdings.
A Systematic Review of Noncommunicable Health Issues in Mass Gatherings
Authors: Alquthami Ahmed H. , Pines Jesse M. 
Published: February 2014

AbstractIntroductionThe review was conducted to evaluate if the field of mass-gathering medicine has evolved in addressing: (1) the lack of uniform standard measures; (2) the effectiveness of and needs for various interventions during a mass gathering; and (3) the various types of noncommunicable health issues (trauma and medical complaints) encountered and their severity during a gathering.MethodsA systematic review of papers published from 2003 through 2012 was conducted using databases of MEDLINE, Ovid, CINHAL, EBSCOHost, National Library of Medicine (NLM), Agency for Healthcare Research and Quality (AHRQ), Elsevier, Scopus, and Proquest databases. Of 37,762 articles, 17 articles were included in this review, covering 18 mass-gathering events; 14 were multiple-day events.ResultsAcross all events, the patient presentation rate (PPR) ranged from 0.13 to 20.8 patients per 1,000 attendees and the transfer to hospital rate (TTHR) ranged from 0.01 to 10.2 ambulance transports per 1,000 attendees. In four out of the seven studies, having on-site providers was associated with a lower rate of ambulance transports. The highest frequencies of noncommunicable presentations were headaches, abdominal complaints, and abrasions/lacerations. Most presentations were minor. Emergent cases requiring hospitalization (such as acute myocardial infarction) were rare.ConclusionsThe rate of noncommunicable health issues varies across events and very serious emergencies are rare.AlquthamiAH, PinesJM. A systematic review of noncommunicable health issues in mass gatherings. Prehosp Disaster Med. 2014;29(2):1-9.
Orientation Precision of Electron Backscatter Diffraction Measurements Near Grain Boundaries
Authors: Wright Stuart I. , Nowell Matthew M. , de Kloe René , Chan Lisa 
Published: February 2014

AbstractElectron backscatter diffraction (EBSD) has become a common technique for measuring crystallographic orientations at spatial resolutions on the order of tens of nanometers and at angular resolutions <0.1°. In a recent search of EBSD papers using Google Scholar™, 60% were found to address some aspect of deformation. Generally, deformation manifests itself in EBSD measurements by small local misorientations. An increase in the local misorientation is often observed near grain boundaries in deformed microstructures. This may be indicative of dislocation pile-up at the boundaries but could also be due to a loss of orientation precision in the EBSD measurements. When the electron beam is positioned at or near a grain boundary, the diffraction volume contains the crystal lattices from the two grains separated by the boundary. Thus, the resulting pattern will contain contributions from both lattices. Such mixed patterns can pose some challenge to the EBSD pattern band detection and indexing algorithms. Through analysis of experimental local misorientation data and simulated pattern mixing, this work shows that some of the rise in local misorientation is an artifact due to the mixed patterns at the boundary but that the rise due to physical phenomena is also observed.
The Coase theorem: coherent, logical, and not disproved
Authors: ALLEN DOUGLAS W. 
Published: February 2014

Abstract:There exists a long line of challengers to the ‘Coase Theorem’. All of these rest on fundamental misconceptions of property rights, transaction costs, and their interaction. Here I examine two attacks that have gone unchallenged: one by Halpin, the other by Usher. I argue that both, in failing to either use or understand an adequate definition of transaction costs, fail to deliver a fatal blow to Coase's famous idea.
A ‘hidden’ 18O-enriched reservoir in the sub-arc mantle
Authors: Liu Chuan-Zhou , Wu Fu-Yuan , Chung Sun-Lin , Li Qiu-Li , Sun Wei-Dong , Ji Wei-Qiang 
Published: February 2014

AbstractPlate subduction continuously transports crustal materials with high-δ18O values down to the mantle wedge, where mantle peridotites are expected to achieve the high-δ18O features. Elevated δ18O values relative to the upper mantle value have been reported for magmas from some subduction zones. However, peridotites with δ18O values significantly higher than the well-defined upper mantle values have never been observed from modern subduction zones. Here we present in-situ oxygen isotope data of olivine crystals in Sailipu mantle xenoliths from South Tibet, which have been subjected to a long history of Tethyan subduction before the India-Asia collision. Our data identify for the first time a metasomatized mantle that, interpreted as the sub-arc lithospheric mantle, shows anomalously enriched oxygen isotopes (δ18O = +8.03 ± 0.28 ‰). Such a high-δ18O mantle commonly does not contribute significantly to typical island arc basalts. However, partial melting or contamination of such a high-δ18O mantle is feasible to account for the high-δ18O signatures in arc basalts.
A Case for the Implementation of Cognitive-Communication Screenings in Acute Stroke
Authors: Hinckley Jacqueline J. 
Published: February 2014

PurposeThe purpose of this article was to illustrate the importance of the implementation of cognitive-communication screenings in acute stroke and to discuss the need for further research on whether and how these screenings are implemented. Cognitive-communication screenings after stroke are the subject of existing practice guidelines and are supported by accumulated evidence.MethodThe author uses anautoethnographic narrative—a tool founded in phenomenology—to provide an in-depth description of the experiences of a family in which one member experienced right-hemispheric stroke. She uses systematic introspection to produce a narrative using literary techniques.ResultsThe narrative illustrates the experiences of one family when one of their members has a right-hemisphere stroke, and cognitive-communication impairments are never formally identified by professionals involved in the patient's care.ConclusionsThe narrative is linked to the published literature and the importance of identifying and managing cognitive-communication impairments after stroke. A model of implementation science is presented as one way to consider the challenges clinicians face when attempting to implement evidence-based practices. The model and examples from other fields show avenues for further research.
An Enhanced Protocol for Constraint-Induced Aphasia Therapy II: A Case Series
Authors: Johnson Margaret L. , Taub Edward , Harper Leslie H. , Wade Jamie T. , Bowman Mary H. , Bishop-McKay Staci , Haddad Michelle M. , Mark Victor W. , Uswatte Gitendra 
Published: February 2014

Purpose
The initial version of Constraint-Induced Aphasia Therapy (CIAT I) consisted of a single exercise. This study sought to evaluate the feasibility for future trials of an expanded and restructured protocol designed to increase the efficacy of CIAT I.

Method

The subjects were 4 native English speakers with chronic stroke who exhibited characteristics of moderate Broca's aphasia. Treatment was carried out for 3.5 hr/day for 15 consecutive weekdays. It consisted of 3 components: (a) intensive training by a behavioral method termed
shaping
using a number of expressive language exercises in addition to the single original language card game, (b) strong discouragement of attempts to use gesture or other nonverbal means of communication, and (c) a transfer package of behavioral techniques to promote transfer of treatment gains from the laboratory to real-life situations.

Results

Participation in speech in the life situation improved significantly after treatment. The effect sizes (i.e.,
d
′) in this domain were ≥ 2.2;
d
′ values ≥ 0.8 are considered large. Improvement in language ability on a laboratory test, the Western Aphasia Battery—Revised (Kertesz, 2006), did not achieve statistical significance, although the effect size was large—that is, 1.3 (13.1 points).

Conclusion
These pilot results suggest in preliminary fashion that CIAT II may produce significant improvements in everyday speech.

Supplemental Material

https://doi.org/10.23641/asha.6170207
Speech event analysis of seventeenth-century military protocol in Hamlet, 1.1
Authors: Lanteigne Betty 
Published: February 2014

The opening scene of Hamlet portrays two military-related speech events — changing of the guard and unknown persons approaching a sentry. This article utilizes insights from military history, Shakespearean playhouse practice, and military protocol pragmatics to analyze these speech events. Diachronic pragmatics investigation reveals military protocol for changing of the guard portrayed by Shakespeare has continued to be followed from the late 1500s to the present time.
Identifying early seventeenth-century military protocol for guard duty at night and analyzing the function of the opening scene in Shakespearean theater, the article compares use of direct and indirect speech acts, including use of conventional and institutional ellipses, in the 1603 Quarto and 1623 First Folio. Pragmatic stylistic analysis shows the Folio version violates military protocol through use of more indirect speech acts, including expressives, unusual in these two military speech events, more effectively portraying underlying tension through the sentries’ sense of an inward, personally disturbing threat than the Quarto’s presentation of straightforward military protocol regarding unknown persons approaching sentries on duty.
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing
Authors: López-Domingo Francisco J. , Florido Javier P. , Rueda Antonio , Dopazo Joaquín , Santoyo-Lopez Javier 
Published: February 2014

Motivation: Targeted enrichment sequencing by next-generation sequencing is a common approach to interrogate specific loci or the whole exome in the human genome. The efficiency and the lack of bias in the enrichment process need to be assessed as a quality control step before performing downstream analysis of the sequence data. Tools that can report on the sensitivity, specificity, uniformity and other enrichment-specific features are needed.
Results: We have implemented the next-generation sequencing data Capture Assessment Tool (ngsCAT), a tool that takes the information of the mapped reads and the coordinates of the targeted regions as input files, and generates a report with metrics and figures that allows the evaluation of the efficiency of the enrichment process. The tool can also take as input the information of two samples allowing the comparison of two different experiments.
Availability and implementation: Documentation and downloads for ngsCAT can be found at http://www.bioinfomgp.org/ngscat.
Contact: support@bioinfomgp.org
Supplementary information: Supplementary Data is available at Bioinformatics online.
LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser
Authors: Lee Chih , Huang Chun-Hsi 
Published: February 2014

Abstract
Summary: LASAGNA-Search 2.0 is an integrated webtool for transcription factor (TF) binding site search and visualization. The tool is based on the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm. It eliminates manual TF model collection and promoter sequence retrieval. Search results can be visualized locally or in the University of California Santa Cruz Genome Browser. Gene regulatory network inference based on the search results offers another way of visualization. A list of TFs and target genes is all a user needs to start using the tool. LASAGNA-Search 2.0 currently offers 1792 TF models and supports 15 species for automatic promoter retrieval and visualization in the University of California Santa Cruz Genome Browser. It is a user-friendly tool designed for non-bioinformaticians and is suitable for research and teaching. We describe important changes made since the initial release.
Availability and implementation: LASAGNA-Search 2.0 is freely available without registration at http://biogrid.engr.uconn.edu/lasagna_search/ .
Contact: chihlee@engr.uconn.edu or huang@engr.uconn.edu
Measuring the transition to homogeneity with photometric redshift surveys
Authors: Alonso D. , Bueno Belloso A. , Sánchez F. J. , García-Bellido J. , Sánchez E. 
Published: February 2014

Abstract
We study the possibility of detecting the transition to homogeneity using photometric redshift catalogues. Our method is based on measuring the fractality of the projected galaxy distribution, using angular distances, and relies only on observable quantities. It thus provides a way to test the cosmological principle in a model-independent unbiased way. We have tested our method on different synthetic inhomogeneous catalogues and shown that it is capable of discriminating some fractal models with relatively large fractal dimensions, in spite of the loss of information due to the radial projection. We have also studied the influence of the redshift bin width, photometric redshift errors, bias, non-linear clustering, and surveyed area on the angular homogeneity index H2(θ) in a Λ cold dark matter cosmology. The level to which an upcoming galaxy survey will be able to constrain the transition to homogeneity will depend mainly on the total surveyed area and the compactness of the surveyed region. In particular, a Dark Energy Survey (DES)-like survey should be able to easily discriminate certain fractal models with fractal dimensions as large as D2 = 2.95. We believe that this method will have relevant applications for upcoming large photometric redshift surveys, such as DES or the Large Synoptic Survey Telescope.
Pasta‐to‐Water Ratio, Hotplate Surface Temperature, and Beaker Material Affect Pasta Cooking Time and Cooked Quality
Authors: de la Peña Elena , Wiesenborn Dennis P. , Manthey Frank A. 
Published: February 2014

ABSTRACTThree experiments were conducted to determine the influence of hotplate surface temperature (250, 300, 350, and 400°C), pasta‐to‐water ratio, and beaker material (glass versus stainless steel) on the final quality of cooked spaghetti. In all the experiments, 13, 20, 27, 33, and 48 g of pasta were cooked and its final quality measured as cooking loss, cooked weight, and cooked firmness. Cooking time was greater when cooked at 250 than 400°C, with 48 than 13 g of pasta, and with a glass than with a stainless steel vessel. Cooking loss, cooked weight, and cooked firmness were greater when cooked at 400 than 250°C, with 13 than 48 g of pasta, and with a stainless steel than with a glass vessel. Evidence of the effects of hotplate surface temperature, pasta‐to‐water ratio, and beaker material on pasta cooking time and cooked quality suggests that these parameters should be addressed in AACC International Approved Method 66‐50.01.
Root Cause Analysis of Ambulatory Adverse Drug Events That Present to the Emergency Department
Authors: Gertler Sarah A. , Coralic Zlatan , López Andrea , Stein John C. , Sarkar Urmimala 
Published: February 2014

Background
Adverse drug events (ADEs) among patients self-administering medications in home/community settings are a common cause of emergency department (ED) visits, but the causes of these ambulatory ADEs remain unclear. Root cause analysis, rarely applied in outpatient settings, may reveal the underlying factors that contribute to adverse events.

Study Objectives
To elicit patient and provider perspectives on ambulatory ADEs and apply root cause analysis methodology to identify cross-cutting themes among these events.

Methods
Emergency department clinical pharmacists screened, identified, and enrolled a convenience sample of adult patients 18 years or older who presented to a single, urban, academic ED with symptoms or diagnoses consistent with suspected ADEs. Semistructured phone interviews were conducted with the patients and their providers. We conducted a qualitative analysis. We applied a prespecified version of the injury prevention framework (deductive coding), identifying themes relating to the agent (drug), host (patient), and environment (social and health systems). These themes were used to construct a root cause analysis for each ADE.

Results
From 18 interviews overall, we identified the following themes within the injury prevention framework. Agent factors included high-risk drugs, narrow therapeutic indices, and uncommon severe effects. Host factors included patient capacity or understanding of how to use medications, awareness of side effects, mistrust of the medical system, patients with multiple comorbidities, difficult risk-benefit assessments, and high health-care users. Environmental factors included lack of social support, and health systems issues included access to care, encompassing medication availability, access to specialists, and a lack of continuity and communication among prescribing physicians. Root cause analysis revealed multiple underlying factors relating to agent, host, and environment for each event.

Conclusion
Patient and physician perspectives can inform a root cause analysis of ambulatory ADEs. Such methodology may be applied to understand the factors that contribute to ambulatory ADEs and serve as the formative work for future interventions improving home/community medication use.
Rapid Learning of Adverse Medical Event Disclosure and Apology
Authors: Raemer Daniel B. , Locke Steven , Walzer Toni Beth , Gardner Roxane , Baer Lee , Simon Robert 
Published: February 2014

Introduction
Despite published recommended best practices for full disclosure and apology to patients and families after adverse medical events, actual practice can be inadequate. The use of “cognitive aids” to help practitioners manage complex critical events has been successful in a variety of fields and healthcare. We wished to extend this concept to disclosure and apology events. The aim of this study was to test if a brief opportunity to review a best practice guideline for disclosure and apology would improve communication performance.

Methods
Thirty pairs of experienced obstetricians and labor nurses participated in a 3-part exercise with mixed-realism simulation. The first part used a standardized actor patient to meet the obstetrical team. The second part used a high-fidelity simulation leading to an adverse medical event (retained sponge), and the third part used standardized actors, patient, and husband, who systematically move through stages of grief response. The participants were randomized into 2 groups, one was provided with a cognitive aid in the form of a best practice guideline for disclosure and apology and the other was only given time to plan. Four blinded raters working in pairs scored subjects on a 7-point scale using a previously developed assessment instrument modified for this study.

Results
Pooled ratings of the disclosure and apology discussion for the intervention group (n = 167, mean = 4.9, SD = 0.92) were higher than those from the control group (n = 167, mean = 4.3, SD = 1.21) (P < 0.0001). One specific element was rated higher for the intervention group than the control group; posture toward the patient (n = 27, mean = 5.1, SD = 0.82 versus n = 28, mean = 4.3, SD = 1.33) (P = 0.020). The elements of dealing with anger, dealing with depression, dealing with denial, bargaining, and acceptance were not different.

Conclusions
Experienced practitioners performed better in a simulated disclosure and apology conversation after reviewing a cognitive aid in the form of a best practice guideline than a control group that was only given time to prepare.