bluuebunny/crossref_metadata_2025_split huggingface dataset:
Standardized Methods for Enhanced Quality and Comparability of Tuberculous Meningitis Studies
Authors: Marais Ben J. , Heemskerk Anna D. , Marais Suzaan S. , van Crevel Reinout , Rohlwink Ursula , Caws Maxine , Meintjes Graeme , Misra Usha K. , Mai Nguyen T. H. , Ruslami Rovina , Seddon James A. , Solomons Regan , van Toorn Ronald , Figaji Anthony , McIlleron Helen , Aarnoutse Robert , Schoeman Johan F. , Wilkinson Robert J. , Thwaites Guy E. ,   for the Tuberculous Meningitis International Research Consortium
Published: November 2016

Abstract
Tuberculous meningitis (TBM) remains a major cause of death and disability in tuberculosis-endemic areas, especially in young children and immunocompromised adults. Research aimed at improving outcomes is hampered by poor standardization, which limits study comparison and the generalizability of results. We propose standardized methods for the conduct of TBM clinical research that were drafted at an international tuberculous meningitis research meeting organized by the Oxford University Clinical Research Unit in Vietnam. We propose a core dataset including demographic and clinical information to be collected at study enrollment, important aspects related to patient management and monitoring, and standardized reporting of patient outcomes. The criteria proposed for the conduct of observational and intervention TBM studies should improve the quality of future research outputs, can facilitate multicenter studies and meta-analyses of pooled data, and could provide the foundation for a global TBM data repository.
$\vee$ -Systems, Holonomy Lie Algebras, and Logarithmic Vector Fields
Authors: Feigin Misha V , Veselov Alexander P 
Published: November 2016

AbstractIt is shown that the description of certain class of representations of the holonomy Lie algebra $\mathfrak g_{\Delta}$ associated with hyperplane arrangement $\Delta$ is essentially equivalent to the classification of $\vee$-systems associated with $\Delta.$ The flat sections of the corresponding $\vee$-connection can be interpreted as vector fields, which are both logarithmic and gradient. We conjecture that the hyperplane arrangement of any $\vee$-system is free in Saito's sense and show this for all known $\vee$-systems and for a special class of $\vee$-systems called harmonic, which includes all Coxeter systems. In the irreducible Coxeter case the potentials of the corresponding gradient vector fields turn out to be Saito flat coordinates, or their one-parameter deformations. We give formulas for these deformations as well as for the potentials of the classical families of harmonic $\vee$-systems.
Proof of Concept of an Endoscopic Sutureless Valve Sizer
Authors: Vola Marco , Maureira Juan Pablo , Ruggieri Vito Giovanni , Fuzellier Jean-François , Campisi Salvatore , Favre Jean-Pierre , Gerbay Antoine , Folliguet Thierry A. 
Published: November 2016

Objective In this paper, we present an endoscopic expandable sizer conceived to allow thoracoscopic aortic valve replacement with a sutureless prosthesis using a dynamic sizing of the aortic annulus. Methods Ten aortic torsos were prepared using a five-trocar thoracoscopic setting. Once the aortotomy was performed and the aortic valve leaflets removed, the technical feasibility of the endoscopic sizing (introduction into the trocar, expansion into the aortic annulus, determination of the valve size, and retraction) with the device was assessed. In case of successful thoracoscopic sizing, endoscopic implantation of a sutureless valve (five LivaNova Perceval prosthesis and five Medtronic 3f Enable bioprosthesis) was performed. Before ascending aorta closure, we assessed the appropriate sealing of the bioprosthesis in the native annulus with camera visualization and a nerve hook inspection. Results All the 10 endoscopic sizings were technically feasible. The scheduled aortic sutureless valve implantations were successfully performed. In all cases, fitting and placement of the sutureless bio-prosthesis in the flaccid heart was satisfactory, with no paraprosthetic leakage detectable by the nerve hook. Conclusions The use of the endoscopic expandable sizer is technically possible. In this early-stage test in the flaccid heart, selection of the valve size was satisfactory during thoracoscopic sutureless aortic bioprosthesis implantation. Further laboratory evaluation with fluid dynamics (aortic root pressurization) will be performed before a clinical study is started.
Reconstruction Outcomes Following Lateral Skull Base Resection
Authors: Thompson Nicholas J. , Roche Joseph P. , Schularick Nathan M. , Chang Kristi E. , Hansen Marlan R. 
Published: November 2016

Objective:
Compare reconstruction outcomes for various lateral skull base closure techniques.

Study Design:
Retrospective medical records review.

Setting:
University-based tertiary referral center.

Patients:
Patients who underwent resections of tumors involving the lateral skull base requiring reconstruction beyond primary closure.

Intervention(s):
Reconstructive techniques, from rotational flaps to free tissue transfer.

Main Outcome Measure(s):
Outcome data including wound complications, cerebrospinal fluid (CSF) leakage, and need for surgical revision were tabulated.

Results:
Eighty-six patients underwent lateral skull base tumor resection and reconstruction. Procedures were primarily lateral temporal bone resections but also included subtotal temporal bone, total temporal bone, and infratemporal fossa resections. Cutaneous malignancy was the most common resection indication (83%) and the temporalis rotational flap was the most commonly employed reconstructive option (30%). When free tissue transfer techniques were used, the radial forearm, anterolateral thigh, and latissimus dorsi were the most frequent donor sites. Patients with T2 disease were more likely to undergo temporalis flaps, whereas patients with T4 disease were more likely to undergo free flap reconstruction. Major complications were uncommon (∼8%), the most frequent being stroke (∼3%). The postoperative wound complication rate was approximately 45%. The majority involved minor dehiscences and were managed conservatively. Patients with T4 disease were more likely to have wound complications (p < 0.05). Radial forearm free flaps were less likely to have wound complications when compared with other reconstruction techniques (p < 0.05).

Conclusions:
Many factors go into planning lateral skull base reconstruction. Free flaps were more often used for T4 disease. Radial forearm free flaps tended to have lower wound complication rates when compared with other techniques.
Improving prognosis for patients with hepatocellular carcinoma in Ireland 1994–2008
Authors: Gaynor Caroline , Iqbal Masood , Comber Harry , Deady Sandra , McCormick P Aiden 
Published: November 2016

Objectives
The incidence of hepatocellular carcinoma (HCC) is increasing in low-prevalence countries such as the USA, UK and Ireland. Over the past two decades, diagnostic techniques have improved and new treatments have been introduced. The aim of this study was to determine whether there has been an impact on hepatoma mortality in Ireland.

Methods
Anonymized cancer registration data from the National Cancer Registry of Ireland were used to investigate patient characteristics and trends in treatment and survival for Irish patients diagnosed with histologically confirmed HCC between 1994 and 2008. Analyses were carried out according to sex, age, stage of disease treatment received and period of incidence.

Results
The incidence of HCC in Ireland increased steadily from 1994 to 2008. The median overall survival was 580 days for the entire cohort, with 1, 2, 3 and 5-year survivals of 56, 46, 39 and 36%, respectively. One-year cause-specific survival improved from 38% during 1994–1998, to 51% during 1999–2002 and to 66% during 2003–2007. Five-year cause-specific survival also improved over time from 19 to 34 to 38%, respectively. Surgery was associated with 1, 2, 3 and 5-year survivals of 92, 82, 78 and 78%, respectively.

Conclusion
This is the first population-based report of incidence, treatment patterns and outcomes of HCC in Ireland. Prognosis improved over time in this biopsy-proven cohort of patients with HCC. This improvement in survival seemed to be largely because of the effect of surgical interventions.
A clinician’s guide to the cost and health benefits of hepatitis C cure assessed from the individual patient perspective
Authors: McEwan Phil , Selvapatt Nowlan , Brown Ashley , Thursz Mark , Bennett Hayley , Webster Samantha , Kalsekar Anupama , Yuan Yong , Brenner Michael , Gordon Jason 
Published: November 2016

Background and aims
The hepatitis C virus (HCV) remains a considerable public health challenge. Novel direct-acting antiviral (DAA) regimens offer high cure rates and the promise of reduced HCV incidence and prevalence following the up-scaling of treatment. This has focused attention towards affordability. This study aimed to estimate the economic value of cure to evaluate the treatment costs justifiable from the patient perspective.

Patients and methods
A published, validated HCV model was utilized to contrast clinical and cost outcomes for patients aged 30–70 years, stratified by METAVIR F0–F4, for (i) no treatment and (ii) successful treatment [i.e. sustained virologic response (SVR)] ignoring the cost of treatment. Regression equations were fitted and used to determine the financial expenditure justifiable to achieve a cost-neutral or a cost-effective [£20 000 per quality-adjusted life-year (QALY)] cure. Model inputs were derived from UK literature; costs and utilities were discounted at 3.5% over a lifetime horizon.

Results
To achieve cost-neutrality, the maximum discounted expenditure justifiable for SVR was £3774–43 607 across ages and fibrosis stages. Spending between £19 745 (70 years, F0) and £188 420 (30 years, F4) on SVR is expected to be cost-effective at £20 000/QALY willingness-to-pay threshold.

Conclusion
Heterogeneity across HCV patients is considerable, which can obscure the relevance of conventional cohort-based economic models evaluated at the mean, particularly when considering the value of treatment at the individual patient level. By quantifying the full exposition of HCV cost-savings and health benefits realizable following HCV cure, this study provides insight into the economic value of successful treatment from the patient perspective.
Effects of Helicobacter pylori eradication on insulin resistance and metabolic parameters: a systematic review and meta-analysis
Authors: Upala Sikarin , Sanguankeo Anawin , Saleem Sheikh A. , Jaruvongvanich Veeravich 
Published: November 2016

Introduction
Previous studies have shown a close relationship between Helicobacter pylori (H. pylori), insulin resistance, and altered metabolic parameters. However, the effects of H. pylori eradication on these conditions remain controversial. We carried out a systematic review and meta-analysis to evaluate the effects of H. pylori eradication on insulin resistance and metabolic parameters.

Methods
We searched CENTRAL, MEDLINE, and EMBASE databases from their inception to July 2016. Insulin resistance (HOMA-IR), body weight (BW), BMI, waist circumference, triglycerides (TG), high-density and low-density lipoprotein-cholesterol (HDL-C and LDL-C), and fasting blood glucose (FBG) were compared between patients with and without H. pylori eradication using a random-effects model. We reported pooled mean differences (MD) and 95% confidence intervals (CI) for the change in outcomes.

Results
Data from five studies showed no difference in HOMA-IR after H. pylori eradication (pooled MD=−0.52, 95% CI: −1.47 to 0.42). Eradication significantly increased BMI (MD=0.36, 95% CI: 0.11–0.60) and BW (MD=1.1, 95% CI: 0.8–1.5), but had no significant effects on TG, LDL-C, HDL-C, or FBG.

Conclusion

H. pylori eradication does not improve insulin resistance, TG, HDL-C, LDL-C, or FBG, but may increase BW and BMI. Further studies are needed to clarify the effect of H. pylori eradication on metabolism.
Adapting an Evidence-Based Intervention to Address Targeted Therapy–Related Fatigue in Chronic Myeloid Leukemia Patients
Authors: Poort Hanneke , Meade Cathy D. , Knoop Hans , Gielissen Marieke F.M. , Pinilla-Ibarz Javier , Jacobsen Paul B. 
Published: November 2016

Background:
Fatigue is one of the most important quality of life issues experienced by patients being treated with oral targeted therapy for chronic myeloid leukemia (CML). However, no intervention exists that specifically addresses strategies to reduce targeted therapy–related fatigue.

Objective:
This study adapted an evidence-based clinic-delivered intervention (EBI) “cognitive behavior therapy for post-cancer fatigue” for use in CML patients. The existing EBI was based on 6 established perpetuating factors of fatigue (ie, sleep, activity, helpful thinking, coping with cancer, social support, and fear of disease recurrence). Study aims were to gauge reactions to (1) existing content and (2) a new Internet-assisted intervention delivery format.

Methods:
Guided by the ADAPT-ITT framework, we used a series of systematic steps and adaptation methodologies, including semistructured interviews with CML patients and providers and feedback from topical experts.

Results:
Patients were receptive to existing content topics and an Internet-assisted delivery format was acceptable. A key theme reflected the need for a new customized psychoeducational module about CML as a disease and its treatment. Both providers and patients held positive views about the potential of the adapted EBI to improve fatigue.

Conclusions:
Findings offered essential guidance for the adaptation and reinforced the utility of the adapted intervention.

Implications for Practice:
Adapting existing EBIs for new audiences contributes to advancing findings of evidence-based research, ultimately providing nurses and other healthcare providers with important referral options to interventions that may provide useful strategies to improve quality of life and reduce targeted therapy–related fatigue.
An Event-Level Analysis of Condom Use During Anal Intercourse Among Self-Reported Human Immunodeficiency Virus–Negative Gay and Bisexual Men in a Treatment as Prevention Environment
Authors: Lachowsky Nathan John , Tanner Zach , Cui Zishan , Sereda Paul , Rich Asheligh , Jollimore Jody , Montaner Julio SG , Hogg Robert S , Moore David M , Roth Eric A 
Published: November 2016

Background
We sought to identify factors associated with condom use during anal intercourse among self-identified human immunodeficiency virus–negative gay, bisexual, and other men who have sex with men (GBM) in Vancouver, Canada following “treatment as prevention” (TasP) scale-up in 2010.

Methods
Sexually active GBM were recruited using respondent-driven sampling from 2012 to 2014. We analyzed participants' most recent sexual encounter with up to their last 5 sexual partners within the past 6 months. In addition to individual- and event-level explanatory factors, we assessed potential associations with TasP awareness, TasP-related prevention practice (viral load sorting), and TasP-related attitudes (human immunodeficiency virus treatment optimism). Accounting for clustering at the respondent-driven sampling chain-level and participant-level, factors associated with event-level condom use versus nonuse were determined using a multivariable generalized linear mixed model built using backward selection and AIC minimization.

Results
Of 513 participants, 436 GBM (85%) reported a total of 1196 anal sex events with 56% condom use. The proportion of condom-protected sexual events decreased monthly over the study period (odds ratio [OR], 0.95 per month, 95% confidence interval [CI], 0.92–0.98). The TasP practices and attitudes were significantly associated with lower odds of condom use at the univariate level, but were no longer significant at multivariate level. In the multivariable model, event-level partner methamphetamine use (adjusted OR [aOR], 0.18; 95% CI, 0.06–0.58), frequency of recent anal intercourse with that partner (aOR, 0.97 per act; 95% CI, 0.95–0.98) and time since first sex with that partner (aOR, 0.97 per 6 months; 95% CI, 0.95–0.99) were associated with lower odds of condom use, whereas event-level participant alcohol use (aOR, 1.41; 95% CI, 1.01–1.98) and no planned future sex with that partner (aOR, 1.56; 95% CI, 1.08–2.27) were associated with greater odds of condom use. Event-level receptive-only (aOR, 2.10; 95% CI, 1.38–3.20) or insertive-only (aOR, 2.53; 95% CI, 1.64–3.90) sexual positions were associated with greater odds of condom use compared with reporting both positions.

Conclusions
The TasP-related factors were not the most salient predictors of GBM's condom use. Health promotion must consider associations between condomless anal sex and substance use and relational factors.
RBC Distribution Width: Biomarker for Red Cell Dysfunction and Critical Illness Outcome?*
Authors: Said Ahmed S. , Spinella Philip C. , Hartman Mary E. , Steffen Katherine M. , Jackups Ronald , Holubkov Richard , Wallendorf Mike , Doctor Allan 
Published: November 2016

Objectives:
RBC distribution width is reported to be an independent predictor of outcome in adults with a variety of conditions. We sought to determine if RBC distribution width is associated with morbidity or mortality in critically ill children.

Design:
Retrospective observational study.

Setting:
Tertiary PICU.

Patients:
All admissions to St. Louis Children’s Hospital PICU between January 1, 2005, and December 31, 2012.

Interventions:
We collected demographics, laboratory values, hospitalization characteristics, and outcomes. We calculated the relative change in RBC distribution width from admission RBC distribution width to the highest RBC distribution width during the first 7 days of hospitalization. Our primary outcome was ICU mortality or use of extracorporeal membrane oxygenation as a composite. Secondary outcomes were ICU- and ventilator-free days.

Measurements and Main Results:
We identified 3,913 eligible subjects with an estimated mortality (by Pediatric Index of Mortality 2) of 2.94% ± 9.25% and an actual ICU mortality of 2.91%. For the study cohort, admission RBC distribution width was 14.12% ± 1.89% and relative change in RBC distribution width was 2.63% ± 6.23%. On univariate analysis, both admission RBC distribution width and relative change in RBC distribution width correlated with mortality or the use of extracorporeal membrane oxygenation (odds ratio, 1.19 [95% CI, 1.12–1.27] and odds ratio, 1.06 [95% CI, 1.04–1.08], respectively; p < 0.001). After adjusting for confounding variables, including severity of illness, both admission RBC distribution width (odds ratio, 1.13; 95% CI, 1.03–1.24) and relative change in RBC distribution width (odds ratio, 1.04; 95% CI, 1.01–1.07) remained independently associated with ICU mortality or the use of extracorporeal membrane oxygenation. Admission RBC distribution width and relative change in RBC distribution width both weakly correlated with fewer ICU- (r
2 = 0.038) and ventilator-free days (r
2 = 0.05) (p < 0.001).

Conclusions:
Independent of illness severity in critically ill children, admission RBC distribution width is associated with ICU mortality and morbidity. These data suggest that RBC distribution width may be a biomarker for RBC injury that is of sufficient magnitude to influence critical illness outcome, possibly via oxygen delivery impairment.
Establishing wonder oil, Solanesol, as a novel inhibitor for Focal Adhesive Kinase by in silico strategies
Authors: Daneial Betty , Das Devashish , Jacob Paul V. J. , Guruprasad R. 
Published: November 2016

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been implicated in a series of cellular processes, including cell migration and survival. Inhibiting the activity of FAK for cancer therapy is currently under investigation. Hence, FAK and its inhibitors has been the subject of intensive research. To understand the structural factors affecting inhibitory potency, kinetic analysis, molecular docking and molecular dynamics simulation were studied in this project. Though, Solanesol was found have inhibitory activities towards FAK, noin silicotests were ever done on the same.Due to high flexibility of Solanesol (Rotatable bonds = 25), it is difficult to analyze using normal docking protocols. This paper introduces a novel method to dock and analyze molecules with high flexibility based on weighed contact based scoring method. This method uses blind docking technique, which was developed for protein peptide docking method, to generate conformations which were used to calculate contact based weights of residues. This method reveals the possible binding site for the small molecule. An exhaustive docking search on the acquired area reveals the docked confirmation of the compound. The final docked conformation was subjected to molecular dynamics to understand of binding stability. This study is in a good agreement with experimental results which shows Solanesol binds at ATP binding site and inhibit the phosphorylation of Focal Adhesion Kinase.
Unified Framework for Representing and Ranking
Authors: Wang Jim Jing-Yan , Bensmail Halima 
Published: November 2016

AbstractIn the database retrieval and nearest neighbor classification tasks, the two basic problems are to represent the query and database objects, and to learn the ranking scores of the database objects to the query. Many studies have been conducted for the representation learning and the ranking score learning problems, however, they are always learned independently from each other. In this paper, we argue that there are some inner relationships between the representation and ranking of database objects, and try to investigate their relationships by learning them in a unified way. To this end, we proposed theUnified framework forRepresentation andRanking (UR2) of objects for the database retrieval and nearest neighbor classification tasks. The learning of representation parameter and the ranking scores are modeled within one single unified objective function. The objective function is optimized alternately with regarding to representation parameter and the ranking scores. Based on the optimization results; iterative algorithms are developed to learn the representation parameter and the ranking scores on a unified way. Moreover, with two different formulas of representation (feature selection and subspace learning), we give two versions of UR2. The proposed algorithms are tested on two challenging tasks - MRI image based brain tumor retrieval and nearest neighbor classification based protein identification. The experiments show the advantage of the proposed unified framework over the state-of-the-art independent representation and ranking methods.