bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Conserved Metal Binding Motif in the Bacillus subtilis Competence Protein ComFA Enhances Transformation
Authors: Chilton Scott S. , Falbel Tanya G. , Hromada Susan , Burton Briana M. 
Published: May 2017

ABSTRACT

Genetic competence is a process in which cells are able to take up DNA from their environment, resulting in horizontal gene transfer, a major mechanism for generating diversity in bacteria. Many bacteria carry homologs of the central DNA uptake machinery that has been well characterized in
Bacillus subtilis
. It has been postulated that the
B. subtilis
competence helicase ComFA belongs to the DEAD box family of helicases/translocases. Here, we made a series of mutants to analyze conserved amino acid motifs in several regions of
B. subtilis
ComFA. First, we confirmed that ComFA activity requires amino acid residues conserved among the DEAD box helicases, and second, we show that a zinc finger-like motif consisting of four cysteines is required for efficient transformation. Each cysteine in the motif is important, and mutation of at least two of the cysteines dramatically reduces transformation efficiency. Further, combining multiple cysteine mutations with the helicase mutations shows an additive phenotype. Our results suggest that the helicase and metal binding functions are two distinct activities important for ComFA function during transformation.

IMPORTANCE
ComFA is a highly conserved protein that has a role in DNA uptake during natural competence, a mechanism for horizontal gene transfer observed in many bacteria. Investigation of the details of the DNA uptake mechanism is important for understanding the ways in which bacteria gain new traits from their environment, such as drug resistance. To dissect the role of ComFA in the DNA uptake machinery, we introduced point mutations into several motifs in the protein sequence. We demonstrate that several amino acid motifs conserved among ComFA proteins are important for efficient transformation. This report is the first to demonstrate the functional requirement of an amino-terminal cysteine motif in ComFA.
A Screen for
rfaH
Suppressors Reveals a Key Role for a Connector Region of Termination Factor Rho
Authors: Hu Kuang , Artsimovitch Irina 
Published: May 2017

ABSTRACT

RfaH activates horizontally acquired operons that encode lipopolysaccharide core components, pili, toxins, and capsules. Unlike its paralog NusG, which potentiates Rho-mediated silencing, RfaH strongly inhibits Rho. RfaH is recruited to its target operons via a network of contacts with an elongating RNA polymerase (RNAP) and a specific DNA element called
ops
to modify RNAP into a pause- and NusG-resistant state.
rfaH
null mutations confer hypersensitivity to antibiotics and detergents, altered susceptibility to bacteriophages, and defects in virulence. Here, we carried out a selection for suppressors that restore the ability of a Δ
rfaH
mutant
Escherichia coli
strain to grow in the presence of sodium dodecyl sulfate. We isolated
rho
,
rpoC
, and
hns
suppressor mutants with changes in regions previously shown to be important for their function. In addition, we identified mutants with changes in an unstructured region that connects the primary RNA-binding and helicase domains of Rho. The connector mutants display strong defects
in vivo
, consistent with their ability to compensate for the loss of RfaH, and act synergistically with bicyclomycin (BCM), which has been recently shown to inhibit Rho transformation into a translocation-competent state. We hypothesize that the flexible connector permits the reorientation of Rho domains and serves as a target for factors that control the motor function of Rho allosterically. Our results, together with the existing data, support a model in which the connector segment plays a hitherto overlooked role in the regulation of Rho-dependent termination.

IMPORTANCE
The transcription termination factor Rho silences foreign DNA, reduces antisense transcription, mediates surveillance of mRNA quality, and maintains genome integrity by resolving transcription-replication collisions and deleterious R loops. Upon binding to RNA, Rho undergoes a rate-limiting transition from an open “lock washer” state to a closed ring capable of processive translocation on, and eventually the release of, the nascent transcript. Recent studies revealed that Rho ligands, including its cofactor NusG and inhibitor bicyclomycin, control the ring dynamics allosterically. In this work, we used a genetic selection for suppressors of RfaH, a potent inhibitor of Rho, to isolate a new class of mutations in a flexible region that connects the primary RNA-binding and ATPase/translocase domains of Rho. We propose that the connector is essential for the modulation of Rho activity by different RNA sequences and accessory proteins.
Predictors of clinical recovery from concussion: a systematic review
Authors: Iverson Grant L , Gardner Andrew J , Terry Douglas P , Ponsford Jennie L , Sills Allen K , Broshek Donna K , Solomon Gary S 
Published: May 2017

ObjectiveA systematic review of factors that might be associated with, or influence, clinical recovery from sport-related concussion. Clinical recovery was defined functionally as a return to normal activities, including school and sports, following injury.DesignSystematic review.Data sourcesPubMed, PsycINFO, MEDLINE, CINAHL, Cochrane Library, EMBASE, SPORTDiscus, Scopus and Web of Science.Eligibility criteria for selecting studiesStudies published by June of 2016 that addressed clinical recovery from concussion.ResultsA total of 7617 articles were identified using the search strategy, and 101 articles were included. There are major methodological differences across the studies. Many different clinical outcomes were measured, such as symptoms, cognition, balance, return to school and return to sports, although symptom outcomes were the most frequently measured. The most consistent predictor of slower recovery from concussion is the severity of a person’s acute and subacute symptoms. The development of subacute problems with headaches or depression is likely a risk factor for persistent symptoms lasting greater than a month. Those with a preinjury history of mental health problems appear to be at greater risk for having persistent symptoms. Those with attention deficit hyperactivity disorder (ADHD) or learning disabilities do not appear to be at substantially greater risk. There is some evidence that the teenage years, particularly high school, might be the most vulnerable time period for having persistent symptoms—with greater risk for girls than boys.ConclusionThe literature on clinical recovery from sport-related concussion has grown dramatically, is mostly mixed, but some factors have emerged as being related to outcome.
Activation of ganglion cells and axon bundles using epiretinal electrical stimulation
Authors: Grosberg Lauren E. , Ganesan Karthik , Goetz Georges A. , Madugula Sasidhar S. , Bhaskhar Nandita , Fan Victoria , Li Peter , Hottowy Pawel , Dabrowski Wladyslaw , Sher Alexander , Litke Alan M. , Mitra Subhasish , Chichilnisky E. J. 
Published: May 2017

Epiretinal prostheses for treating blindness activate axon bundles, causing large, arc-shaped visual percepts that limit the quality of artificial vision. Improving the function of epiretinal prostheses therefore requires understanding and avoiding axon bundle activation. This study introduces a method to detect axon bundle activation on the basis of its electrical signature and uses the method to test whether epiretinal stimulation can directly elicit spikes in individual retinal ganglion cells without activating nearby axon bundles. Combined electrical stimulation and recording from isolated primate retina were performed using a custom multielectrode system (512 electrodes, 10-μm diameter, 60-μm pitch). Axon bundle signals were identified by their bidirectional propagation, speed, and increasing amplitude as a function of stimulation current. The threshold for bundle activation varied across electrodes and retinas, and was in the same range as the threshold for activating retinal ganglion cells near their somas. In the peripheral retina, 45% of electrodes that activated individual ganglion cells (17% of all electrodes) did so without activating bundles. This permitted selective activation of 21% of recorded ganglion cells (7% of expected ganglion cells) over the array. In one recording in the central retina, 75% of electrodes that activated individual ganglion cells (16% of all electrodes) did so without activating bundles. The ability to selectively activate a subset of retinal ganglion cells without axon bundles suggests a possible novel architecture for future epiretinal prostheses. NEW & NOTEWORTHY Large-scale multielectrode recording and stimulation were used to test how selectively retinal ganglion cells can be electrically activated without activating axon bundles. A novel method was developed to identify axon activation on the basis of its unique electrical signature and was used to find that a subset of ganglion cells can be activated at single-cell, single-spike resolution without producing bundle activity in peripheral and central retina. These findings have implications for the development of advanced retinal prostheses.
Development of a Cancer Risk Prediction Tool for Use in the UK Primary Care and Community Settings
Authors: Lophatananon Artitaya , Usher-Smith Juliet , Campbell Jackie , Warcaba Joanne , Silarova Barbora , Waters Erika A. , Colditz Graham A. , Muir Kenneth R. 
Published: May 2017

AbstractSeveral multivariable risk prediction models have been developed to asses an individual's risk of developing specific cancers. Such models can be used in a variety of settings for prevention, screening, and guiding investigations and treatments. Models aimed at predicting future disease risk that contains lifestyle factors may be of particular use for targeting health promotion activities at an individual level. This type of cancer risk prediction is not yet available in the UK. We have adopted the approach used by the well-established U.S.-derived "YourCancerRisk" model for use in the UK population, which allow users to quantify their individual risk of developing individual cancers relative to the population average risk. The UK version of “YourCancerRisk" computes 10-year cancer risk estimates for 11 cancers utilizing UK figures for prevalence of risk factors and cancer incidence. Because the prevalence of risk factors and the incidence rates for cancer are different between the U.S. and the UK population, this UK model provides more accurate estimates of risks for a UK population. Using an example of breast cancer and data from UK Biobank cohort, we demonstrate that the individual risk factor estimates are similar for the U.S. and UK populations. Assessment of the performance and validation of the multivariate model predictions based on a binary score confirm the model's applicability. The model can be used to estimate absolute and relative cancer risk for use in Primary Care and community settings and is being used in the community to guide lifestyle change. Cancer Prev Res; 10(7); 421–30. ©2017 AACR.
Procedimentos ômicos aplicados em qualidade e segurança de pescado
Authors: Monteiro Maria Lúcia Guerra , Mársico Eliane Teixeira , Conte Junior Carlos Adam 
Published: May 2017

Os procedimentos ômicos são uma nova tecnologia que utiliza a genômica, proteômica e metabolômica para avaliar metabólitos dos alimentos. A demanda mundial de pescado tem aumentado progressivamente devido à elevada qualidade de proteínas, minerais e ácidos graxos poli-insaturados, especialmente ômega-3. Todavia, a cadeia produtiva aquícola apresenta limitações como falta de padronização, ausência de conhecimento e transferência de tecnologia para as indústrias. Além disso, torna-se difícil garantir um monitoramento efetivo do pescado em decorrência das limitações dos parâmetros de qualidade atuais e dos métodos analíticos estabelecidos pela legislação nacional. O presente trabalho analisa os fatores limitantes relacionados aos parâmetros químicos, bem como os avanços recentes nos procedimentos analíticos, para determinação da qualidade do pescado. Levando-se em consideração a melhoria no controle de qualidade dessa matriz, os parâmetros de bases voláteis totais (BVT), trimetilamina (TMA), amônia, pH e aminas biogênicas deveriam ser revisados e estabelecidos por categorias de pescado e/ou por tipo de produto à base de pescado. Em contrapartida, parâmetros relacionados à concentração de carbonilas, ácidos graxos livres (AGLs), índice de peróxidos (IP) e malonaldeído (MDA) poderiam ser inseridos na legislação nacional. Simultaneamente, as autoridades oficiais devem levar em consideração metodologias analíticas que apresentem efetividade, praticidade, baixo custo e rapidez, facilitando e aprimorando o controle de qualidade de produtos de pescado e garantindo a saúde dos consumidores. Além disso, técnicas analíticas para identificação das espécies de peixes devem ser incluídas na legislação brasileira visando evitar substituições ilegais e impactos negativos aos consumidores.
Support Vector Algorithms for Optimizing the Partial Area under the ROC Curve
Authors: Narasimhan Harikrishna , Agarwal Shivani 
Published: May 2017

The area under the ROC curve (AUC) is a widely used performance measure in machine learning. Increasingly, however, in several applications, ranging from ranking to biometric screening to medicine, performance is measured not in terms of the full area under the ROC curve but in terms of the partial area under the ROC curve between two false-positive rates. In this letter, we develop support vector algorithms for directly optimizing the partial AUC between any two false-positive rates. Our methods are based on minimizing a suitable proxy or surrogate objective for the partial AUC error. In the case of the full AUC, one can readily construct and optimize convex surrogates by expressing the performance measure as a summation of pairwise terms. The partial AUC, on the other hand, does not admit such a simple decomposable structure, making it more challenging to design and optimize (tight) convex surrogates for this measure. Our approach builds on the structural SVM framework of Joachims ( 2005 ) to design convex surrogates for partial AUC and solves the resulting optimization problem using a cutting plane solver. Unlike the full AUC, where the combinatorial optimization needed in each iteration of the cutting plane solver can be decomposed and solved efficiently, the corresponding problem for the partial AUC is harder to decompose. One of our main contributions is a polynomial time algorithm for solving the combinatorial optimization problem associated with partial AUC. We also develop an approach for optimizing a tighter nonconvex hinge loss–based surrogate for the partial AUC using difference-of-convex programming. Our experiments on a variety of real-world and benchmark tasks confirm the efficacy of the proposed methods.
A new species of the genus Discoelius Latreille, 1809 (Hymenoptera: Vespidae: Eumeninae) from India
Authors: PANNURE ARATI , BELAVADI VASUKI V. , CARPENTER JAMES M. 
Published: May 2017

Discoelius vasukii Pannure & Carpenter, sp. nov. is described and illustrated from Tamil Nadu, India. Discoelius Latreille, 1809 is a small genus of solitary wasp with ten species and one subspecies described, of which D. aurantiacus Nguyen, D. emeishanensus Zhou & Li, D. esakii Yasumatsu, D. longinodus Yamane, D. nigriclypeus Zhou & Li, D. turneri (Meade-Waldo), D. wangi Yamane and D. zonalis (Panzer) are recorded from Oriental Region (Zhou et al. 2013; Nguyen 2016). Only a single species, D. turneri described from Shillong (Meghalaya) (Meade-Waldo, 1910) and later recorded from Sikkim (Giordani Soika 1960) has been previously known from India. In this study, we describe a new species of Discoelius from India based on a single female specimen collected at Valparai (Tamil Nadu), India.
Further Evaluation of Probabilistic Convective Precipitation Forecasts Using the QPF–PoP Neighborhood Relationship
Authors: Kochasic Michael C. , Gallus William A. , Schaffer Christopher J. 
Published: May 2017

Abstract
A neighborhood postprocessing approach that relates quantitative precipitation forecasts (QPF) to probability of precipitation (PoP) forecasts applied to a single model run was found by Schaffer et al. to be as good as traditional ensemble-based approaches using 10 members in 30-h forecasts of convective precipitation. The present study evaluates if PoP forecasts derived from additional variations of the approach can improve PoP forecasts further compared with previous methods. Ensemble forecasts from the Center for Analysis and Prediction of Storms (CAPS) are used for neighborhood tests comparing a single model run and a traditional ensemble. In the first test, PoP forecasts for different combinations of training and testing datasets using a single model member with 4-km grid spacing are compared against those obtained with a 10-member traditional ensemble. Overall, forecasts for the neighborhood approach with just one member are only slightly less accurate to those using a more traditional neighborhood approach with the ensemble. PoP forecasts improve when using older data for training and newer data for testing. Assessments of the sensitivity of the neighborhood PoPs suggest that thinning of the horizontal grid at fine grid spacing is an effective way of maintaining the accuracy of PoP forecasts while reducing computational expenses. In an additional test, the diurnal variation of the forecast is examined on a day-by-day basis, showing good agreement between the two approaches for all but a few cases during 2008.
E-Cigarette Advice to Patients From Physicians and Dentists in the United States
Authors: Drouin Olivier , McMillen Robert C. , Klein Jonathan D. , Winickoff Jonathan P. 
Published: May 2017

Purpose: To report on adults’ recall of discussion by physicians and dentists about e-cigarettes. Design: A nationally representative cross-sectional survey (Internet and random digit dialing) in the United States. Participants: Adults who ever used e-cigarettes. Measures: Participant-reported discussion about the potential benefits and harms of e-cigarettes with their doctor, dentist, or child’s doctor in the past 12 months. Analysis: Fisher exact test for the analysis between benefits and harms for each type of provider and for rates of advice between provider types. Results: Among the 3030 adults who completed the survey, 523 (17.2%) had ever used e-cigarettes. Of those who had seen their doctor, dentist, or child’s doctor in the last year, 7.3%, 1.7%, and 10.1%, respectively, reported discussing potential harms of e-cigarettes. Conversely, 5.8%, 1.7%, and 9.3% of patients who had seen their doctor, dentist, or child’s doctor in the last year reported that the clinician discussed the potential benefits of e-cigarettes. Each clinician type was as likely to discuss harms as benefits. Rates of advice were similar between doctors and child’s doctors but lower for dentists. Rates were comparable when the analysis was limited to current e-cigarette users, participants with children, or those who reported using both e-cigarettes and combusted tobacco. Conclusions: Few physicians and dentists discuss either the harms or benefits of e-cigarettes with their patients. These data suggest an opportunity to educate, train, and provide resources for physicians and dentists about e-cigarettes and their use.
A Review of the Efficacy and Safety of Genvoya® (Elvitegravir, Cobicistat, Emtricitabine, and Tenofovir Alafenamide) in the Management of HIV-1 Infection
Authors: Angione Sara A. , Cherian Sibyl M. , Özdener Ayşe Elif 
Published: May 2017

Introduction: This review evaluates the efficacy and safety of Genvoya® (elvitegravir, cobicistat, emtricitabine, and tenofovir alafenamide [EVG/c/TAF/FTC]), a single-tablet regimen used for the management of HIV-1 infection. Phase II and III randomized clinical trials evaluate the efficacy and safety of EVG/c/TAF/FTC and tenofovir disoproxil fumerate (TDF)–containing arms; renal impairment, bone mineral density, metabolic effects, and other adverse events are topics explored within this review. Methods: A MEDLINE with full text and PubMed literature search was conducted for the past 5 years, up to April 2016. Results: Virologic suppression was similar between the EVG/c/TAF/FTC and TDF-containing groups (<50 copies/mL) at week 48. The bone mineral density in the hip and spine showed a significant reduction in the TDF-containing groups. The glomerular filtration rate increased in patients in the EVG/c/TAF/FTC arm and there were significant differences in total proteinuria, albuminuria, and tubular proteinuria in patients switching to EVG/c/TAF/FTC. The most common adverse events were diarrhea, nausea, and headache. Discussion: The coformulated Genvoya regimen is well tolerated and effective in treatment-naive and virologically suppressed patients. Data seem to suggest it may also be effective and safe in patients with mild to moderate renal impairment. The lower-dosed single-tablet regimen has significantly reduced bone and renal side effects.
Omeprazole-Domperidone Fixed Dose Combination vs Omeprazole Monotherapy: A Phase 4, Open-Label, Comparative, Parallel Randomized Controlled Study in Mild to Moderate Gastroesophageal Reflux Disease
Authors: Marakhouski KY , Karaseva GA , Ulasivich DN , Marakhouski Y Kh 
Published: May 2017

Aim: To compare the efficacy and safety of omeprazole-domperidone combination vs omeprazole monotherapy in gastroesophageal reflux disease (GERD). Methods: In a comparative, randomized controlled, phase 4 study, outpatients with GERD were randomly allocated to either group 1 (omeprazole 20 mg + domperidone 30 mg) or group 2 (omeprazole 20 mg) in an equal ratio; 2 capsules daily in the morning were administered for 8 weeks. Results: Sixty patients were enrolled. Esophagitis reversal was observed in 92% patients in group 1 vs 65.2% in group 2. Approximately, 83.3% patients in group 1 vs 43.3% patients in group 2 demonstrated full cupping of reflux symptoms at 8 weeks. Combined therapy resulted in significantly longer period of heartburn-free days (23 vs 12 days on omeprazole). There were no safety concerns. Conclusions: Omeprazole-domperidone combination was more effective than omeprazole alone in providing complete cupping of reflux symptoms and healing of esophagitis in patients with GERD. Both the treatments were well tolerated with few reports of adverse events. Trial registration: This trial is registered with http://clinicaltrials.gov , number NCT02140073.
Managing Customers and Information for Improved Performance
Authors: Foreman Susan 
Published: May 2017

Customer Relationship Management (CRM) is a buzz word in marketing. Each year more and more is spent on software-based systems for managing customer relationships. Yet there is growing evidence that many of these systems do not add value and that many may in fact harm customer relationships. Susan Foreman reviews this evidence as well as providing useful pointers to how CRM can be implemented successfully in organisations.