bluuebunny/crossref_metadata_2025_split huggingface dataset:
AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes
Authors: Vuong Hue , Che Anney , Ravichandran Sarangan , Luke Brian T. , Collins Jack R. , Mudunuri Uma S. 
Published: April 2015

Abstract
Summary: As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants.
Availability and implementation: AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov.
Contact: Hue.Vuong@fnlcr.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Multiple mutations and increased RNA expression in tetracycline-resistant Streptococcus pneumoniae as determined by genome-wide DNA and mRNA sequencing
Authors: Lupien Andréanne , Gingras Hélène , Bergeron Michel G. , Leprohon Philippe , Ouellette Marc 
Published: April 2015

Abstract

Objectives
The objective of this study was to characterize chromosomal mutations associated with resistance to tetracycline in Streptococcus pneumoniae.

Methods
Chronological appearance of mutations in two S. pneumoniae R6 mutants (R6M1TC-5 and R6M2TC-4) selected for resistance to tetracycline was determined by next-generation sequencing. A role for the mutations identified was confirmed by reconstructing resistance to tetracycline in a S. pneumoniae R6 WT background. RNA sequencing was performed on R6M1TC-5 and R6M2TC-4 and the relative expression of genes was reported according to R6. Differentially expressed genes were classified according to their ontology.

Results
WGS of R6M1TC-5 and R6M2TC-4 revealed mutations in the gene rpsJ coding for the ribosomal protein S10 and in the promoter region and coding sequences of the ABC genes patA and patB. These cells were cross-resistant to ciprofloxacin. Resistance reconstruction confirmed a role in resistance for the mutations in rpsJ and patA. Overexpression of the ABC transporter PatA/PatB or mutations in the coding sequence of patA contributed to resistance to tetracycline, ciprofloxacin and ethidium bromide, and was associated with a decreased accumulation of [3H]tetracycline. Comparative transcriptome profiling of the resistant mutants further revealed that, in addition to the overexpression of patA and patB, several genes of the thiamine biosynthesis and salvage pathway were increased in the two mutants, but also in clinical isolates resistant to tetracycline. This overexpression most likely contributes to the tetracycline resistance phenotype.

Conclusions
The combination of genomic and transcriptomic analysis coupled to functional studies has allowed the discovery of novel tetracycline resistance mutations in S. pneumoniae.
Total quality management performance in multinational companies
Authors: Jiménez-Jiménez Daniel , Martinez-Costa Micaela , Martínez-Lorente Angel R. , Rabeh Hammady Ahmed Dine 
Published: April 2015

Purpose– Multinational corporations face a more intense competence and a higher number of changes in the different countries they operate. In this regard, organizational learning and quality management are key elements that could help them to survive in the market. Convinced by the numerous benefits and competitive potential of total quality management (TQM) programmes, corporations have promoted its implementation. The purpose of this paper is to analyse the interaction between these programmes and organizational learning, more precisely with exploitation and exploration capabilities, in order to understand the way in which quality management programmes could help to develop learning in the companies.Design/methodology/approach– Structural equation modelling was used to test the proposed model. The sample comprised 111 medium-sized Spanish companies, with four different responses each. Constructs are measured with Likert scales previously tested in the literature.Findings– The results show that TQM is positively and strongly related to both exploitation and exploration and that the relationship between TQM and exploitation is higher. Concerning the effects of exploitation and exploration on firm performance; results of the analysis show that only exploration capability positively affects organizational performance. It is also confirmed a positive effect of a TQM system in performance.Originality/value– This research covers a gap in the literature regarding the relationship between organizational learning and TQM, particularly with the concepts of exploitation and exploration in the context of multinational companies.
Evaluation of the presence of reduced nicotinamide adenine dinucleotide phosphate in bacterial metabolites used as immunostimulators and its role in nitric oxide induction
Authors: Singh Namrata , Bhattacharyya Debasish 
Published: April 2015

ABSTRACTBacterial metabolites that act as immunostimulators have aroused interest because of their therapeutic potential in several immune disorders. These metabolites are complex, heterogeneous, and comprise numerous immune‐boosting biomolecules. To better understand their immune stimulatory properties, characterization of their components is essential. An ether extract of metabolites from nine bacterial species was analyzed for the presence of reduced nicotinamide adenine dinucleotide phosphate (NADPH) or other fluorophores. This metabolite in combination with bile lipids is a licensed immune stimulatory drug. Excitation of the extract at 340 nm resulted in fluorescence with an emission maximum of around 410 nm, which is fairly specific for NADH and NADPH. Reverse‐phase‐HPLC and electro‐spray ionization‐mass analysis confirmed the presence of NADPH in the bacterial metabolites. Quantification by glutathione reductase assay indicated 11.90 ± 0.01 µM of NADPH in the metabolites. Further characterization of the individual bacterial extracts of the metabolite confirmed the presence of NADPH. Subsequently, studies were performed to evaluate the role/s of NADPH in immune‐stimulatory drugs. NADPH is known to be involved in production of nitric oxide (NO), which has versatile roles in the immune system. The biological function of NADPH in NO induction by RAW 264.7 (mouse macrophage) cells was evaluated and it was found that bacterial NADPH has a significant role in inducing NO and that NADPH from individual bacterial extracts is capable of inducing NO. Investigation on the stability and biological potency of NADPH in bacterial metabolites is important because of NADPH's wide therapeutic applications, most of which are associated with its role in NO induction.
Penetration Depth of Projectiles Fired from a Replica of Colt Navy of 1851 in 20% Gelatin Blocks Correlated with Fatal Injuries Assessed in an Autopsy of a 78‐Year‐Old Man
Authors: Smędra‐Kaźmirska Anna , Barzdo Maciej , Jurczyk Agnieszka P. , Berent Jarosław 
Published: April 2015

AbstractPursuant to the Polish Weapons and Ammunitions Law, muzzle‐loading black powder weapons, manufactured before 1885, or their replicas, as well as suitable projectiles, can be possessed legally without registration and special licenses. The aim of the study was to assess the penetration depth of projectiles fired from a black powder weapon, replica of Colt Navy of 1851, in 20% gelatin blocks and to compare the obtained results with the actual injuries found on autopsy of a 78‐year‐old man who had committed suicide. In the experiments, we used the black powder weapon and ammunitions, as well as gelatin blocks serving as a soft tissue model. We ascertained that solid spherical projectiles fired from black powder weapons cause extensive injuries, especially in the initial segment of the wound canal. Additionally, based on the presence and location of the wad in the wound canal, the distance from which the shot was fired can be determined.
The Relationship Between the Surface Morphology and Chemical Composition of Gunshot Residue Particles
Authors: Kara Ilker , Lisesivdin Sefer Bora , Kasap Mehmet , Er Elif , Uzek Ugur 
Published: April 2015

AbstractIn this study, chemical composition and morphology of gunshot residue (GSR) of 9 × 19 mm Parabellum‐type MKE (Turkey)‐brand ammunition were analyzed by scanning electron microscope and energy dispersive X‐ray spectrometer. GSR samples were collected by “swab” technique from the shooter's right hand immediately after shooting. According to general principles of thermodynamics, it is likely that the structures will have a more regular (homogeneous) spherical form to minimize their surface area due to very high temperatures and pressures that occur during explosion. Studied samples were collected under the same conditions with the same original ammunition, from the same firearm and a single shooter. This is because many other variables may affect size, structure, and composition in addition to the concentrations of elements of the structure. Results indicated that the chemical compositions are effective in the formation of GSR morphological structures.
Gluten‐Free Snacks Using Plantain–Chickpea and Maize Blend: Chemical Composition, Starch Digestibility, and Predicted Glycemic Index
Authors: Flores‐Silva Pamela C. , Rodriguez‐Ambriz Sandra L. , Bello‐Pérez Luis A. 
Published: April 2015

AbstractAn increase in celiac consumers has caused an increasing interest to develop good quality gluten‐free food products with high nutritional value. Snack foods are consumed worldwide and have become a normal part of the eating habits of the celiac population making them a target to improve their nutritive value. Extrusion and deep‐frying of unripe plantain, chickpea, and maize flours blends produced gluten‐free snacks with high dietary fiber contents (13.7–18.2 g/100 g) and low predicted glycemic index (28 to 35). The gluten‐free snacks presented lower fat content (12.7 to 13.6 g/100 g) than those reported in similar commercial snacks. The snack with the highest unripe plantain flour showed higher slowly digestible starch (11.6 and 13.4 g/100 g) than its counterpart with the highest chickpea flour level (6 g/100 g). The overall acceptability of the gluten‐free snacks was similar to that chili‐flavored commercial snack. It was possible to develop gluten‐free snacks with high dietary fiber content and low predicted glycemic index with the blend of the 3 flours, and these gluten‐free snacks may also be useful as an alternative to reduce excess weight and obesity problems in the general population and celiac community.
Intrinsic Connectivity Networks in post‐traumatic stress disorder during sub‐ and supraliminal processing of threat‐related stimuli
Authors: Rabellino D. , Tursich M. , Frewen P. A. , Daniels J. K. , Densmore M. , Théberge J. , Lanius R. A. 
Published: April 2015

AbstractObjectiveTo investigate the functional connectivity of large‐scale intrinsic connectivity networks (ICNs) in post‐traumatic stress disorder (PTSD) during subliminal and supraliminal presentation of threat‐related stimuli.MethodGroup independent component analysis was utilized to study functional connectivity within the ICNs most correlated with the Default‐mode Network (DMN), Salience Network (SN), and Central Executive Network (CEN) in PTSD participants (n = 26) as compared to healthy controls (n = 20) during sub‐ and supraliminal processing of threat‐related stimuli.ResultsComparing patients with PTSD with healthy participants, prefrontal and anterior cingulate cortex involved in top‐down regulation showed increased integration during subliminal threat processing within the CEN and SN and during supraliminal threat processing within the DMN. The right amygdala showed increased connectivity with the DMN during subliminal processing in PTSD as compared to controls. Brain regions associated with self‐awareness and consciousness exhibited decreased connectivity during subliminal threat processing in PTSD as compared to controls: the claustrum within the SN and the precuneus within the DMN.ConclusionKey nodes of the ICNs showed altered functional connectivity in PTSD as compared to controls, and differential results characterized sub‐ and supraliminal processing of threat‐related stimuli. These findings enhance our understanding of ICNs underlying PTSD at different levels of conscious threat perception.
Associations between chronic non‐cancer pain and medication assisted treatment outcomes for opiate addiction
Authors: Stevenson Erin , Cole Jennifer 
Published: April 2015

Background and ObjectivesAn increased percentage of individuals entering opioid addiction treatment programs also report the presence of chronic non‐cancer pain (CNCP). This study examined associations between the presence of CNCP and 6‐month medication assisted addiction treatment (MAT) outcomes.MethodsThe sample included 585 individuals at opiate treatment programs who completed a structured intake interview and a 6‐month follow‐up telephone interview between March 2007 and December 2010. Of the sample, 115 individuals reported CNCP at intake and 6‐month follow‐up. Bivariate analyses compared individuals with CNCP (n = 115) and without CNCP (n = 470) at MAT intake.ResultsA greater percentage of individuals with CNCP were older, were retired or disabled, and had experienced depression or anxiety before intake compared to individuals without CNCP. Results of binomial logistic regression models found that having CNCP was associated with increased odds of depression/anxiety at follow‐up, but had no association with employment or substance use.Conclusions and Scientific SignificanceThe correlations between CNCP and co‐occurring depression/anxiety among MAT clients indicate an area of special concern for providers. A full biopsychosocial, including a focus on history of chronic physical pain, might be beneficial to help highlight potential co‐morbidities and to encourage closer monitoring of the intertwining relationships between addiction, CNCP, and depression/anxiety. (Am J Addict 2015;24:138–143)
Self‐reported physical activity in smoking pre‐cessation is not a protective factor against relapse for all
Authors: Bernard Paquito , Ninot Gregory , Quantin Xavier 
Published: April 2015

BackgroundIn recent years, the relationship between physical activity (PA) and smoking cessation has been increasingly studied. However, very few studies have investigated the possible protective role of PA on smoking relapse on the long term.ObjectivesThis study evaluated the impact of self‐reported PA in precessation on smoking relapse. Other variables evaluated included measures of dependence, socio‐demographic factors and smoking‐related variables. Several possible interactions between PA and well identified factors influencing smoking relapse rate were also explored.MethodsAfter the initial consultation, 345 smokers were consecutively recruited in a smoking‐cessation unit. Smoking abstinence was collected regularly during consultation or by phone calls. PA was measured with the International Physical Activity Questionnaire short form. Cox proportional hazard model was performed to determine factors associated with smoking relapse.ResultsAmong the initial sample, 227 adults were included in the survival analysis. After adjustment for potential cofounders, PA was not associated with smoking relapse. Self‐efficacy level, absence of professional activity, previous attempts to quit and alcohol use disorders were associated with relapse. Secondary analysis showed a statistically significant effect of an interaction term for PA and antidepressant use on reducing smoking relapse (HR = .81, 95% CI: .66–.99).Conclusion and Scientific SignificancePrevious quit attempts and professional activity were positive predictors of smoking abstinence, with alcohol use disorder a negative predictor. PA was not found to be a significant predictor of smoking relapse, with only a positive interaction term seen for persons on antidepressant treatment. (Am J Addict 2015;24:153–159)
Impact of marijuana use on self‐rated cognition in young adult men and women
Authors: Conroy Deirdre A. , Kurth Megan E. , Brower Kirk J. , Strong David R. , Stein Michael D. 
Published: April 2015

Background and ObjectivesMarijuana (MJ) is a widely used substance that has been shown to impair cognition in laboratory settings. There is a growing number of medical MJ dispensaries and state policies permitting the use of MJ in the United States. This study is a naturalistic study that explores the association of same day MJ use on self‐rated cognition in young adult men and women.MethodsForty‐eight (n = 48) young adults (22 F; mean age = 22.3) participated. After a baseline assessment, participants made daily phone calls to study staff over the next 3 weeks. Cumulative minutes of MJ use in the last 24‐hours were assessed. Demographic information collected and self‐ratings of cognitive impairment were assessed using six questions about areas of difficulty thinking each day.ResultsThere was a significant relationship between greater number of minutes of MJ use and higher levels of self‐rated cognitive difficulties (b = .004; SE = .001; p < .006). There was no main effect of gender (b = 1.0; SE = .81; p < .22). Planned evaluation of the interaction between gender and minutes of MJ use was not significant statistically, suggesting a similar relationship between minutes of MJ use and cognitive difficulties among women compared to men (p < .54).Conclusions and Scientific SignificanceThere is an association between current and heavy MJ use and self‐perceived cognitive ability in both males and females. These findings reveal important information regarding one consequence of MJ use that has real‐world meaning to young adult smokers. (Am J Addict 2015;24:160–165)
Prescription medication misuse among opioid dependent patients seeking inpatient detoxification
Authors: Wilens Timothy , Zulauf Courtney , Ryland Denece , Carrellas Nicholas , Catalina‐Wellington Isela 
Published: April 2015

Background and ObjectivesOpioid related morbidity and mortality is heightened in context to the concomitant use of psychotropic medications. The aim of this project was to examine the extent to which opioid dependent patients seeking detoxification are using and misusing specific psychotropic agents.MethodsAs part of a quality assurance/improvement project, we systematically assessed prospectively consecutive admissions to a public detoxification program using a self‐report questionnaire to query for specific psychotropic medication use. Patients were asked about having a current prescription, appropriate use, and/or medical misuse (higher doses, using without prescription) of amphetamine salts, clonazepam, clonidine, gabapentin, and pregabalin.ResultsWe had data on 196 admissions including 162 patients with opioid dependency. Patients receiving detoxification from opioids compared to alcohol had statistically significant higher rates of medication misuse (30% vs. 0%, respectively; χ2 = 12.8, p < .0003). Of opioid dependent patients receiving prescription medication, 28% reported using higher amounts of each medication than prescribed. Of opioid patients, 10% self‐reported misusing clonidine, 22% gabapentin, 7% pregabalin, 25% clonazepam, 11% amphetamine salts, and 36% any of these medications.Discussion and ConclusionsDespite the “nonaddictive nature” of some medications (eg, gabapentin, clonidine), high rates of medication misuse in opioid dependent patients admitted for detoxification was found and appeared similar to rates of misuse among controlled substances such as clonazepam and amphetamine salts. These data suggest that opioid dependent patients should be queried for the appropriate use of prescribed medications and that practitioners need to monitor for medication misuse in opioid dependent patients. (Am J Addict 2015;24:173–177)
Haemostatic profile of reconstituted blood in a proposed 1:1:1 ratio of packed red blood cells, platelet concentrate and four different plasma preparations
Authors: Ponschab M. , Schöchl H. , Gabriel C. , Süssner S. , Cadamuro J. , Haschke‐Becher E. , Gratz J. , Zipperle J. , Redl H. , Schlimp C. J. 
Published: April 2015

SummaryThe concept of haemostatic resuscitation implies early and high‐volume plasma transfusion. We investigated the haemostatic profile of reconstituted whole blood prepared in a 1:1:1 ratio of blood, platelets and plasma. This consisted of packed red blood cells, platelet concentrate and four different plasma variants: fresh frozen; solvent‐detergent; lyophilised quarantine; and lyophilised methylene blue‐inactivated plasma. Haematocrit, platelet count, endogenous thrombin potential and coagulation factor activity were significantly lower in reconstituted blood compared with citrated whole blood (p < 0.01). Except for lyophilised methylene blue‐inactivated plasma, no substantial differences between plasma variants in coagulation factor activity, endogenous thrombin potential and standard coagulation tests were observed. After reconstitution, haematocrit and platelet counts were slightly above recommended transfusion triggers, most thromboelastometry (ROTEM®) parameters were within the normal range and fibrinogen concentrations were between 1.57 g.l−1 and 1.91 g.l−1. Reconstitution of whole blood in a 1:1:1 ratio resulted in significant dilution of haematocrit and platelet count, but values remained above limits recommended by transfusion guidelines. Fibrinogen concentrations of reconstituted whole blood were also significantly reduced, and these were below the threshold value for supplementation recommended by recent guidelines.
Use of hormonal therapy is associated with reduced nerve fiber density in deep infiltrating, rectovaginal endometriosis
Authors: Tarjanne Satu , Ng Cecilia H.M. , Manconi Frank , Arola Johanna , Mentula Maarit , Maneck Bharvi , Fraser Ian S. , Heikinheimo Oskari 
Published: April 2015

AbstractObjectiveTo study the density of nerve fibers in cases of deep infiltrating endometriosis (DIE) of the rectovaginal septum in relation to various clinical factors.DesignA research laboratory‐based study.SettingA tertiary center together with a research laboratory.MethodsArchived DIE tissue samples from 45 women operated upon for rectovaginal septum DIE were re‐examined histologically, and by immunohistochemistry.Main outcome measuresThe effect of progestogens or combined oral contraceptives on the density of nerve fibers, and the expression of nerve growth factor (NGF) and its high‐affinity receptor (tyrosine kinase receptor A, Trk‐A).ResultsThe use of hormonal therapy was associated with reduced densities of sympathetic, parasympathetic and sensory nerve fibers in DIE lesions. Density of total nerve fibers (with pan‐neuronal marker PGP9.5) was significantly lower (p < 0.05) in lesions collected from hormone‐treated women (8.6/mm², 4.2–20.8/mm²; median density, from 25th to 75th quartiles) compared with that in lesions from untreated women (24.9/mm², 11.2–34.9/mm²). DIE lesions stained strongly for NGF and its receptor Trk‐A. Expression of NGF, but not of Trk‐A, was significantly reduced during use of hormonal therapy.ConclusionsUse of hormonal therapy was associated with significantly reduced nerve fiber density in DIE lesions. This may be an important mechanism of action of hormonal therapy for controlling DIE pain symptoms. The expression of estrogen‐regulated NGF and its receptor was only partially suppressed during the use of hormonal therapy, suggesting that local estrogen action is often maintained during conventional hormonal therapy in cases of DIE.