bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymeric nanofiber coating with tunable combinatorial antibiotic delivery prevents biofilm-associated infection in vivo
Authors: Ashbaugh Alyssa G. , Jiang Xuesong , Zheng Jesse , Tsai Andrew S. , Kim Woo-Shin , Thompson John M. , Miller Robert J. , Shahbazian Jonathan H. , Wang Yu , Dillen Carly A. , Ordonez Alvaro A. , Chang Yong S. , Jain Sanjay K. , Jones Lynne C. , Sterling Robert S. , Mao Hai-Quan , Miller Lloyd S. 
Published: October 2016

Significance
Biofilm infections are a major complication associated with implantable medical devices and prostheses, which are exceedingly difficult to treat. To date, there has been no effective clinical solution that combines antibacterial efficiency with excellent osseointegration. Here, a nanofiber-based conformal coating capable of controlled and independent local delivery of two or more combinatorial antibiotics was developed to provide optimal antimicrobial activity for the prevention of biofilm-associated infections. In a preclinical animal model of orthopedic-implant infection, this technology demonstrated complete bacterial clearance from the implant and surrounding bone/joint tissue while promoting osseointegration. This tunable nanofiber composite coating could be highly effective in preventing medical device infections in patients.
Optogenetic activation of dopamine neurons in the ventral tegmental area induces reanimation from general anesthesia
Authors: Taylor Norman E. , Van Dort Christa J. , Kenny Jonathan D. , Pei JunZhu , Guidera Jennifer A. , Vlasov Ksenia Y. , Lee Justin T. , Boyden Edward S. , Brown Emery N. , Solt Ken 
Published: October 2016

Significance
Although dopamine is known to promote wakefulness, the specific dopamine circuits in the brain that regulate arousal are not clear. Here we report that selective optogenetic stimulation of ventral tegmental area (VTA) dopamine neurons in mice produces a powerful arousal response sufficient to restore conscious behaviors, including the righting reflex, during continuous, steady-state general anesthesia. Although previous studies found that VTA dopamine neurons do not appear to play a central role in regulating sleep–wake transitions, our findings demonstrate that selective stimulation of these neurons is sufficient to induce the transition from an unconscious, anesthetized state to an awake state. These results suggest that VTA DA neurons play a critical role in promoting wakefulness.
Acid activation mechanism of the influenza A M2 proton channel
Authors: Liang Ruibin , Swanson Jessica M. J. , Madsen Jesper J. , Hong Mei , DeGrado William F. , Voth Gregory A. 
Published: October 2016

Significance
The influenza A M2 channel (AM2) transports protons into the influenza virus upon acid activation. It is an important pharmacological target as well as a prototypical case to study proton conduction through biological channels. The current work provides the most complete computational characterization to date of the physical basis for the acid activation mechanism of the AM2 proton channel. Our results show that lowering the pH value gradually opens the Trp41 gate and decreases the deprotonation barrier of the His37 tetrad, leading to channel activation. Our result also demonstrates that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain.
Serum stimulation of CCR7 chemotaxis due to coagulation factor XIIa-dependent production of high-molecular-weight kininogen domain 5
Authors: Ponda Manish P. , Breslow Jan L. 
Published: October 2016

Significance
We describe a mechanism of regulating immune cell chemotaxis. We identified in serum a peptide derived from domain 5 of high-molecular-weight kininogen produced by coagulation factor XIIa cleavage that accelerates C-C chemokine receptor 7-mediated chemotaxis. Thus, we present a paradigm in which a humoral peptide functions as a chemotactic cofactor that links inflammation to immunity.
Highly sensitive, direct and real-time detection of silver nanowires by using a quartz crystal microbalance
Authors: Jang Kuewhan , Park Chanho , You Juneseok , Choi Jaeyeong , Park Hyunjun , Park Jinsung , Lee Howon , Choi Chang-Hwan , Na Sungsoo 
Published: October 2016

Abstract
For several decades, silver nanomaterials (AgNMs) have been used in various research areas and commercial products. Among the many AgNMs, silver nanowires (AgNWs) are one of the mostly widely used nanomaterials due to their high electrical and thermal conductivity. However, recent studies have investigated the toxicity of AgNWs. For this reason, it is necessary to develop a successful detection method of AgNWs for protecting human health. In this study, label-free, highly sensitive, direct, and real-time detection of AgNWs is performed for the first time. The detection mechanism is based on the resonance frequency shift upon the mass change from the hybridization between the probe DNA on the electrode and the linker DNA attached on AgNWs. The frequency shift is measured by using a quartz crystal microbalance. We are able to detect 1 ng ml−1 of AgNWs in deionized water in real-time. Moreover, our detection method can selectively detect AgNWs among other types of one-dimensional nanomaterials and can also be applied to detection in drinking water.
The Political Economy of Fertilizer Subsidy Programs in Africa: Evidence from Zambia
Authors: Mason Nicole M. , Jayne Thomas S. , van de Walle Nicolas 
Published: October 2016

AbstractFertilizer subsidy programs have re‐emerged as popular policy tools in sub‐Saharan Africa. Despite a burgeoning body of literature on program impacts, the political economy of the programs remains poorly understood. In particular, there is a dearth of empirical evidence to support or refute the conventional wisdoms that governments systematically target subsidized inputs to certain areas based on past voting patterns and that fertilizer subsidies win votes. This article discusses the theoretical links between government targeting of subsidized fertilizer and voter behavior, then uses panel data from Zambia to empirically test these conventional wisdoms. Results suggest that Zambia's Movement for Multi‐Party Democracy governments targeted more subsidized fertilizer to households in areas where it had strong support in the previous presidential election. However, contrary to conventional wisdom, marginal changes in the scale or coverage of the fertilizer subsidy program had no statistically significant effect on the share or number of votes won by incumbent presidents.
JADOPPT: java based AutoDock preparing and processing tool
Authors: García-Pérez Carlos , Peláez Rafael , Therón Roberto , Luis López-Pérez José 
Published: October 2016

Abstract

Motivation
AutoDock is a very popular software package for docking and virtual screening. However, currently it is hard work to visualize more than one result from the virtual screening at a time. To overcome this limitation we have designed JADOPPT, a tool for automatically preparing and processing multiple ligand-protein docked poses obtained from AutoDock. It allows the simultaneous visual assessment and comparison of multiple poses through clustering methods. Moreover, it permits the representation of reference ligands with known binding modes, binding site residues, highly scoring regions for the ligand, and the calculated binding energy of the best ranked results.

Availability and Implementation
JADOPPT, supplementary material (Case Studies 1 and 2) and video tutorials are available at http://visualanalytics.land/cgarcia/JADOPPT.html

Supplementary information
Supplementary data are available at Bioinformatics online.
Big Data Smart Socket (BDSS): a system that abstracts data transfer habits from end users
Authors: Watts Nicholas A , Feltus Frank A 
Published: October 2016

Abstract

Motivation
The ability to centralize and store data for long periods on an end user’s computational resources is increasingly difficult for many scientific disciplines. For example, genomics data is increasingly large and distributed, and the data needs to be moved into workflow execution sites ranging from lab workstations to the cloud. However, the typical user is not always informed on emerging network technology or the most efficient methods to move and share data. Thus, the user defaults to using inefficient methods for transfer across the commercial internet.

Results
To accelerate large data transfer, we created a tool called the Big Data Smart Socket (BDSS) that abstracts data transfer methodology from the user. The user provides BDSS with a manifest of datasets stored in a remote storage repository. BDSS then queries a metadata repository for curated data transfer mechanisms and optimal path to move each of the files in the manifest to the site of workflow execution. BDSS functions as a standalone tool or can be directly integrated into a computational workflow such as provided by the Galaxy Project. To demonstrate applicability, we use BDSS within a biological context, although it is applicable to any scientific domain.

Availability and Implementation
BDSS is available under version 2 of the GNU General Public License at https://github.com/feltus/BDSS.
Prevalence and Transmission of Beta and Gamma Human Papillomavirus in Heterosexual Couples
Authors: Moscicki Anna-Barbara , Ma Yifei , Gheit Tarik , McKay-Chopin Sandrine , Farhat Sepideh , Widdice Lea E. , Tommasino Massimo 
Published: October 2016

Abstract

Background
Beta (β) and gamma (γ) human papillomavirus (HPV) are commonly found on the skin. Few of the β types are associated with nonmelanoma skin cancer. Little is known about transmission patterns of these HPV, specifically in the anogenital (AG) areas. The primary objective of this study was to examine the AG concordance and transmission of β and γHPV types between heterosexual couples.

Methods
Archival samples from a previously published study examining concordance of alpha HPV types between couples were tested for β and γHPV. Hand, mouth, and genital samples were obtained 5 times over a 6-week period.

Results
Of the 21 couples examined, β and γHPV were detected in AG sites in 67% and 30% of men, respectively, and 41% and 25% of women. Positive concordance for β and γHPV was 27% and 20%, respectively, which was greater than the observed concordance between noncouples (10% for βHPV and 4% for γHPV). Transmission rate of βHPV between AG areas was 15.9 (95% confidence interval [CI], 3.3–46.5) per 100 person months for men-to-women at risk and for γHPV was 6.6 (95% CI, .2–36.7). Risks for women-to-men were similar.

Conclusions
Beta and γHPV are common in the AG area, and data suggest that they can be sexually transmitted.
Autochthonous Transmission of Trypanosoma Cruzi in Southern California
Authors: Hernandez Salvador , Flores Carmen A. , Viana Gracia M. , Sanchez Daniel R. , Traina Mahmoud I. , Meymandi Sheba K. 
Published: October 2016

Abstract
Trypanosoma cruzi usually infects humans via triatomine insects in Latin America. Vector-borne transmission in the United States is exceedingly rare. We describe (1) the first case of probable autochthonous transmission reported in California in more than 30 years and (2) the first ever reported case in the greater Los Angeles area.
Infants With Technology Dependence
Authors: Bowles Jennifer D. , Jnah Amy J. , Newberry Desi M. , Hubbard Carol A. , Roberston Tracey 
Published: October 2016

Background:
The incidence of premature infants with complex medical needs, dependent upon medical technology at discharge, is on the rise in the United States.

Purpose:
Preparing the family for the hospital-to-home transition can be challenging due to the complex medical and emotional needs of the vulnerable infant and the volume of subspecialty services and equipment required.

Methods/Search Strategy:
Relevant articles from PubMed, Google Scholar, CINAHL

Findings/Results:
There is an increasing incidence of technology dependent infants discharged from neonatal intensive care units in the United States. Transition from hospital to home requires lengthy preparation, multidisciplinary-open communication, and family centered care.

Implications for Practice:
Early assimilation of the parents into the ongoing care of their infant, the provision of comprehendible parental education by neonatal nurses and other members of the healthcare team, the provision of adequate rooming-in experiences prior to discharge, and the collaborative coordination of outpatient community services are crucial elements of the discharge process. Neonatal nurses possess population-specific education, training, commitment, and expertise that make them the ideal experts to implement and evaluate a discharge planning framework, in collaboration with the medical team and the family.

Implications for Research:
Methods to prevent readmission and ensure successful discharge from hospital to home is indicated. Standardization of a discharge process of infants of technology dependence combining medical team, family, outpatient coordinators, and primary care providers.
Moderate-vigorous recreational physical activity and breast cancer risk, stratified by menopause status: a systematic review and meta-analysis
Authors: Neilson Heather K. , Farris Megan S. , Stone Chelsea R. , Vaska Marcus M. , Brenner Darren R. , Friedenreich Christine M. 
Published: October 2016

Abstract

Objective:
Physical inactivity increases postmenopausal and possibly premenopausal breast cancer risk, although different biologic mechanisms are proposed. Our primary objective was to estimate breast cancer risk associated with high versus low levels of moderate-vigorous recreational activity, separately for premenopausal and postmenopausal women.

Methods:
We conducted a systematic review of literature published to July 2015. Included reports were cohort or case-control studies relating moderate-vigorous recreational physical activity (metabolic equivalent ≥3.0) to breast cancer incidence, exclusively (≥90%) in premenopausal or postmenopausal women. We appraised study quality and performed meta-analyses using random effects modeling. Subgroup meta-analyses were based on tumor subtype, race, body mass index, parity, hormone therapy use, family history of cancer, and statistical adjustment for body fatness. Dose-response relations were examined.

Results:
Pooled relative risks (RRs, 95% CI) for women with higher versus lower levels of moderate-vigorous recreational activity were RR = 0.80 (0.74-0.87) and RR = 0.79 (0.74-0.84) for premenopausal (43 studies) and postmenopausal (58 studies) breast cancer, respectively, with high heterogeneity. Inverse associations were weaker among postmenopausal cohort studies (RR = 0.90 [0.85-0.95]) and studies that statistically adjusted for nonrecreational (eg, occupational, household) activity (RR = 0.91 [0.77-1.06] premenopausal, RR = 0.96 [0.86-1.08] postmenopausal). Risk estimates with versus without body fatness adjustment did not vary by menopause status, although other subgroup effects were menopause-dependent. Among studies of overweight/obese women, there was an inverse association with postmenopausal but not premenopausal breast cancer (RR = 0.88 [0.82-0.95] and RR = 0.99 [0.98-1.00], respectively). Dose-response curves were generally nonlinear.

Conclusions:
Although risk estimates may be similar for premenopausal and postmenopausal breast cancer, subgroup effects may be menopause-dependent.
In-hospital complications of bilateral salpingo-oophorectomy at benign hysterectomy: a population-based cohort study
Authors: Lai Jerry Cheng-Yen , Chen Hung-Hui , Chu Kuei-Hui , Wang Kung-Liahng , Huang Nicole , Hu Hsiao-Yun , Chou Yiing-Jenq 
Published: October 2016

Abstract

Objective:
The study compared the in-hospital complications and related outcomes between women who underwent bilateral salpingo-oophorectomy at hysterectomy for benign diseases and those who had hysterectomy only.

Methods:
We conducted a population-based, retrospective cohort study using data from Taiwan's National Health Insurance program. Women who underwent concurrent bilateral salpingo-oophorectomy at hysterectomy for benign indications (n = 34,509) were compared with those who had hysterectomy only (n = 176,305). Separate models were estimated to account for the effect of baseline comorbid condition, age, and hysterectomy approach on the relationship between bilateral salpingo-oophorectomy and study outcomes. A secondary analysis was also performed to evaluate the association of inpatient readmission within 30 days and complications among women who underwent bilateral salpingo-oophorectomy.

Results:
The addition of a bilateral salpingo-oophorectomy to hysterectomy was associated with a lower risk of surgical complications, a longer length of hospital stay, and an increased risk of inpatient readmission within 30 days. Among women who underwent bilateral salpingo-oophorectomy, women with complications were also more likely to require inpatient readmission within 30 days than those without complications. Our data also suggested that bilateral salpingo-oophorectomy was not associated with an overall risk of medical complications, with the exception of urethral obstruction. The relationships remained even after adjustments by age, surgical indications, hysterectomy approach, and health-related risk factors, such as baseline comorbid condition and status of any prior catastrophic illness.

Conclusions:
Bilateral salpingo-oophorectomy at hysterectomy for benign conditions is not associated with an increased risk of in-hospital complications.
Evaluation of Migraine Surgery Outcomes through Social Media
Authors: Egan Katie G. , Israel Jacqueline S. , Ghasemzadeh Rezvaneh , Afifi Ahmed M. 
Published: October 2016

Background:
Social media have been used to study many aspects of health and human behavior. Although social media present a unique opportunity to obtain unsolicited patient-reported outcomes, its use has been limited in plastic and reconstructive surgical procedures, including migraine nerve surgery. The goal of this study was to utilize the most popular social media site, Facebook, to evaluate patients’ experience with migraine surgery.

Methods:
Six months of data regarding nerve surgery, nerve stimulators, and radiofrequency nerve ablation were collected from posts and comments written by members of 2 Facebook groups. Outcomes were classified by degree of resolution of symptoms.

Results:
A total of 639 posts related to migraine surgery. Of 304 posts commenting on postoperative success of nerve surgery, 16% reported elimination of headaches and 65% significant improvement (81% with complete or significant improvement), 5% partial improvement, 11% no change, and 3% worsening symptoms. Nerve surgery had a higher success rate than nerve stimulators and radiofrequency ablation. Nerve surgery was recommended by 90% of users.

Conclusions:
The 81% rate of complete or significant improvement of symptoms in this study is close to the 79% to 84% shown in current literature. Similar to the findings of a recent systematic review, surgery is more efficacious compared with nerve stimulators and ablation. This study adds to evidence favoring migraine surgery by removing evaluator bias and demonstrates that surgical outcomes and satisfaction data may be obtained from social media.
Does Exercise Ventilatory Inefficiency Predict Poor Outcome in Heart Failure Patients With COPD?
Authors: Alencar Maria Clara , Arbex Flavio F. , Souza Aline , Mazzuco Adriana , Sperandio Priscila A. , Rocha Alcides , Hirai Daniel M. , Mancuso Frederico , Berton Danilo C. , Borghi-Silva Audrey , Almeida Dirceu , O'Donnel Denis E. , Neder J. Alberto 
Published: October 2016

PURPOSE:
To investigate whether the opposite effects of heart failure (HF) and chronic obstructive pulmonary disease (COPD) on exercise ventilatory inefficiency (minute ventilation [

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E]-carbon dioxide output [

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co
2] relationship) would negatively impact its prognostic relevance.

METHODS:
After treatment optimization and an incremental cardiopulmonary exercise test, 30 male patients with HF-COPD (forced expiratory volume in 1 second [FEV1] = 57% ± 17% predicted, ejection fraction = 35% ± 6%) were prospectively followed up during 412 ± 261 days for major cardiac events.

RESULTS:
Fourteen patients (46%) had a negative outcome. Patients who had an event had lower echocardiographically determined right ventricular fractional area change (RVFAC), greater ventilatory inefficiency (higher

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E/

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co
2 nadir), and lower end-tidal CO2 (PETCO2) (all P < .05). Multivariate Cox models revealed that

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E/

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co
2 nadir >36, ΔPETCO2(PEAK-REST)≥2 mm Hg, and PETCO2PEAK≤33 mm Hg added prognostic value to RVFAC≤45%. Kaplan-Meyer analyses showed that although 18% of patients with RVFAC>45% had a major cardiac event after 1 year, no patient with RVFAC>45% and

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E/

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co
2 nadir ≤36 (or PETCO2PEAK>33 mm Hg) had a negative event. Conversely, although 69% of patients with RVFAC≤45% had a major cardiac event after 1 year, all patients with RVFAC≤45% and ΔPETCO2(PEAK-REST)≥2 mm Hg had a negative event.

CONCLUSION:
Ventilatory inefficiency remains a powerful prognostic marker in HF despite the presence of mechanical ventilatory constraints induced by COPD. If these preliminary findings are confirmed in larger studies, optimal thresholds for outcome prediction are likely greater than those traditionally recommended for HF patients without COPD.