bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensing of cell stress by human γδ TCR-dependent recognition of annexin A2
Authors: Marlin Romain , Pappalardo Angela , Kaminski Hannah , Willcox Carrie R. , Pitard Vincent , Netzer Sonia , Khairallah Camille , Lomenech Anne-Marie , Harly Christelle , Bonneville Marc , Moreau Jean-François , Scotet Emmanuel , Willcox Benjamin E. , Faustin Benjamin , Déchanet-Merville Julie 
Published: March 2017

Significance
Human γδ T lymphocytes have innate-like and adaptive-like functions and can circulate in blood or reside in tissues. They are activated by specific antigens recognized by their T-cell receptor and recognize infected and transformed cells, suggesting that cellular stress is involved in specific antigen expression. However, molecular characterization of stress-induced antigens remains elusive, hampering our understanding of the role of γδ T cells in cancer and infections. In the present study we identify annexin A2 as such stress-induced antigen known as a phospholipid-binding protein involved in tumorigenesis, redox potential regulation, and wound healing. Stress-mediated membrane exposure of annexin A2 could thus constitute a danger signal for γδ T cells to recognize various cell dysregulations and protect the host against cancer and infections.
Diverse regulation of mammary epithelial growth and branching morphogenesis through noncanonical Wnt signaling
Authors: Kessenbrock Kai , Smith Prestina , Steenbeek Sander Christiaan , Pervolarakis Nicholas , Kumar Raj , Minami Yasuhiro , Goga Andrei , Hinck Lindsay , Werb Zena 
Published: March 2017

Significance
The extracellular signals that regulate cell growth and tissue rearrangements during organogenesis are still poorly understood. One large family of secreted signaling molecules, called wingless-type MMTV integration site family member (WNTs), governs many of these processes by controlling cell–cell interactions. Here, we show that two closely related members of the WNT superfamily influence the development of the mammary gland by signaling through different tyrosine kinase receptors. WNT5A enhances the growth of mammary stem/progenitor cells while restricting the process of branching morphogenesis. In contrast, WNT5B represses mammary stem/progenitor cell proliferation through a different receptor. Together, the distinct actions of these highly homologous extracellular cues regulate the developmental processes that supply cells and shape tissues during periods of rapid growth.
Earning their Stripes: The Potential of Tiger Trout and Other Salmonids as Biological Controls of Forage Fishes in a Western Reservoir
Authors: Winters Lisa K. , Budy Phaedra , Thiede Gary P. 
Published: March 2017

Abstract
Maintaining a balance between predator and prey populations can be an ongoing challenge for fisheries managers, especially in managing artificial ecosystems such as reservoirs. In a high-elevation Utah reservoir, the unintentional introduction of the Utah Chub Gila atraria and its subsequent population expansion prompted managers to experimentally shift from exclusively stocking Rainbow Trout Oncorhynchus mykiss to also stocking tiger trout (female Brown Trout Salmo trutta × male Brook Trout Salvelinus fontinalis) and Bonneville Cutthroat Trout O. clarkii utah (hereafter, Cutthroat Trout) as potential biological control agents. We measured a combination of diet, growth, temperature, and abundance and used bioenergetic simulations to quantify predator demand versus prey supply. Utah Chub were the predominant prey type for tiger trout, contributing up to 80% of the diet depending on the season. Utah Chub represented up to 70% of the total diet consumed by Cutthroat Trout. Although Utah Chub dominated the fish biomass in the reservoir, we still estimated abundances of 238,000 tiger trout, 214,000 Cutthroat Trout, and 55,000 Rainbow Trout. Consequently, when expanded to the population level of each predator, tiger trout and Cutthroat Trout consumed large quantities of Utah Chub on an annual basis: tiger trout consumed 508,000 kg (2,660 g/predator) of the standing prey population, and Cutthroat Trout consumed an estimated 322,000 kg (1,820 g/predator). The estimated combined consumption by Cutthroat Trout and tiger trout exceeded the estimate of Utah Chub annual production. As such, our results suggest that the high rates of piscivory exhibited by Cutthroat Trout and tiger trout in artificial lentic ecosystems are likely sufficient to effectively reduce the overall abundance of forage fishes and to prevent forage fishes from dominating fish assemblages. Collectively, this research provides the first documented findings on tiger trout ecology and performance, which will aid managers in designing and implementing the best stocking strategy to optimize sport fish performance, control undesirable forage fish, and enhance and maintain angler satisfaction.
Received April 1, 2016; accepted November 8, 2016 Published online March 8, 2017
Salient Needs for Conservation of Atlantic Salmon
Authors: Gibson Robert John 
Published: March 2017

Abstract
A short review is presented on the major factors contributing to recent precipitous declines in populations of wild Atlantic Salmon Salmo salar, with the approach of describing the major needs for stabilizing or enhancing factors to conserve and reverse the decline of salmon populations and incidentally of other salmonid species. Some aspects of physiology and required habitat characteristics through the life history of Atlantic Salmon are reviewed that determine responses to degradation of habitats. Anthropogenic developments, including obstructions to migration and degradation of freshwater habitats, are major reasons for declines in the resource. Thus, habitat is a primary factor to be considered in conservation and restoration. Socioeconomic considerations may override ecological and public interest concerns, and examples are given from Canada, where environmental regulations have been relaxed in favor of economic interests. Public education and awareness and advocacy in order for political “will” for better conservation of the resource are required to slow, and eventually stop, the decline in Atlantic Salmon populations.
Innovation after Brexit
Authors: Kingston William 
Published: March 2017

Abstract
Brexit is intended to return autonomy for law-making to the UK Parliament, and this opportunity could be used to improve intellectual property laws. These were originally drafted to support innovation, but like other laws of property they were captured by interests. The result is that their original function has been far surpassed in economic importance by their use for moving corporate profits to and through tax havens for tax evasion and avoidance. Although an opportunity to improve information protection laws may indeed result, Britain has never been a leader in drafting these, compared with Germany and the United States. Also, to the extent that better laws could refocus investment on technological innovation, and away from financial innovation, it could be expected that they would be opposed by interests with a major stronghold in the City of London. Reference is made to specific proposals for change already advanced in Prometheus, to which is added a new suggestion about how more generous overhead payments from public funding of innovation could help to stimulate more firms to bid for this. Also, a proposal is made for a means of rectifying a series of legal decisions which have had the effect of denying firms the ability to benefit from new ideas offered by outsiders.
poRe GUIs for parallel and real-time processing of MinION sequence data
Authors: Stewart Robert D , Watson Mick 
Published: March 2017

Abstract

Motivation
Oxford Nanopore’s MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. The nature of the MinION output requires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs.

Results
We have developed two GUIs for the R package poRe that allow parallel and real-time processing of MinION datasets. Both GUIs are capable of extracting sequence- and meta- data from large MinION datasets via a friendly point-and-click interface using commodity hardware.

Availability and Implementation
The GUIs are packaged within poRe which is available on SourceForge: https://sourceforge.net/projects/rpore/files/.
Documentation is available on GitHub: https://github.com/mw55309/poRe_docs.
The effects of 50 Hz magnetic field exposure on DNA damage and cellular functions in various neurogenic cells
Authors: Su Liling , Yimaer Aziguli , Wei Xiaoxia , Xu Zhengping , Chen Guangdi 
Published: March 2017

AbstractEpidemiological studies have indicated a possible association between extremely low–frequency magnetic field (ELF-MF) exposure and the risk of nervous system diseases. However, laboratory studies have not provided consistent results for clarifying this association, despite many years of studies. In this study, we have systematically investigated the effects of 50 Hz MF exposure on DNA damage and cellular functions in both neurogenic tumor cell lines (U251, A172, SH-SY5Y) and primary cultured neurogenic cells from rats (astrocytes, microglia, cortical neurons). The results showed that exposure to a 50 Hz MF at 2.0 mT for up to 24 h did not influence γH2AX foci formation (an early marker of DNA double-strand breaks) in any of six different neurogenic cells. Exposure to a 50 Hz MF did not affect cell cycle progression, cell proliferation or cell viability in neurogenic tumor U251, A172 or SH-SY5Y cells. Furthermore, the MF exposure for 24 h did not significantly affect the secretion of cytokines (TNF-α, IL-6 or IL-1β) in astrocytes or microglia, or the phagocytic activity of microglia. In addition, MF exposure for 1 h per day did not significantly influence expression levels of microtubule-associated protein tau, microtubule-associated protein 2, postsynaptic density 95 or gephyrin in cortical neurons, indicating an absence of effects of MF exposure on the development of cortical neurons. In conclusion, our data suggest that exposure to a 50 Hz MF at 2.0 mT did not elicit DNA damage effects or abnormal cellular functions in the neurogenic cells studied.
Acute care in glioblastoma: the burden and the consequences
Authors: Wasilewski Andrea , Serventi Jennifer , Kamalyan Lily , Wychowski Thomas , Mohile Nimish 
Published: March 2017

Abstract

Background
The utilization of inpatient medical services by patients with glioblastoma (GBM) is not well studied. We sought to describe causes, frequency, and outcomes of acute care visits in GBM.

Methods
We conducted a retrospective study of 158 GBM patients at the University of Rochester over 5 years. Electronic medical records were reviewed to identify all local and outside acute care visits. Acute care visits were defined as any encounter resulting in an emergency department visit or inpatient admission.

Results
Seventy-one percent (112/158) of GBM patients had 235 acute care visits corresponding to 163 hospitalizations (69%) and 72 emergency department visits (31%). Sixty-three percent of patients had multiple visits. Admission diagnoses were seizure (33%), neurosurgical procedure (15%), infection (12%), focal neurologic symptoms (9%), and venous thromboembolism (VTE, 9%). Forty-six patients had 1 or more visits for seizures. Median time to first acute care visit was 65.6 days and 22% of patients had an acute care visit within 30 days of diagnosis. Median length of stay was 5 days. Thirty-five percent of admitted patients were discharged home; 62% required a higher level of care than prior to admission (23% were discharged home with services, 17% to a nursing facility, 16% to hospice, 6% to acute rehab) and 3% died. Thirty-eight percent of patients had ACV within 30 days of death. Median survival was 14 months for patients who had acute care visits and 22.2 months for patients who did not.

Conclusion
The majority of GBM patients utilize acute care, most commonly for seizures. The high number of emergency department visits, short length of stay, and many patients discharged home suggest that some acute care visits may be avoidable.
EFFICACY OF INTRAVITREAL INJECTION OF BEVACIZUMAB IN VITRECTOMY FOR PATIENTS WITH PROLIFERATIVE VITREORETINOPATHY RETINAL DETACHMENT
Authors: Zhao Xin-Yu , Xia Song , Wang Er-Qian , Chen You-Xin 
Published: March 2017

Purpose:
To evaluate the effect of intravitreal injection of bevacizumab in vitrectomy for patients with proliferative vitreoretinopathy (PVR)-related retinal detachment.

Methods:
The PubMed, Embase, and the Cochrane Central Register of Controlled Trials were searched from their earliest entries through October, 2016, to identify the studies that had evaluated the effects of intravitreal injection of bevacizumab in vitrectomy for eyes with PVR-related retinal detachment. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines were followed. The relevant data were analyzed using Stata 12.0 software. The weighted mean difference, relative risk, and their 95% confidence intervals were used to assess the strength of the association.

Results:
The authors' search yielded 133 records from which 3 studies that have examined the effects of intravitreal injection of bevacizumab (120 eyes with PVR-related retinal detachment) were included for review and analysis. Their meta-analyses showed that neither the best-corrected visual acuity nor retinal redetachment rate showed any clinically or statistically important difference between the nonbevacizumab and bevacizumab groups (P > 0.05). In addition, bevacizumab did not influence the interval between vitrectomy and retinal redetachment (P > 0.05).

Conclusion:
Based on the available evidence, intravitreal injection of bevacizumab in vitrectomy for patients with PVR-related retinal detachment did not decrease retinal redetachment rate or improve visual acuity. Better-designed studies with larger simple sizes and longer follow-up periods are required to reach valid conclusions regarding benefits and harms. Moreover, evaluation of anti–vascular endothelial growth factor therapy on surgical outcomes in eyes with milder subtypes of PVR or no PVR, but deemed at high risk of PVR, may be worthy of future consideration.
QUANTITATIVE ANALYSIS OF STRUCTURAL ALTERATIONS IN THE CHOROID OF PATIENTS WITH ACTIVE BEHÇET UVEITIS
Authors: Onal Sumru , Uludag Gunay , Oray Merih , Mengi Emre , Herbort Carl P. , Akman Mehmet , Metin Mustafa M. , Koc Akbay Aylin , Tugal-Tutkun Ilknur 
Published: March 2017

Purpose:
To quantitatively analyze in vivo morphology of subfoveal choroid during an acute attack of Behçet uveitis.

Methods:
In this prospective study, 28 patients with Behçet uveitis of ≤4-year duration, and 28 control subjects underwent enhanced depth imaging optical coherence tomography. A novel custom software was used to calculate choroidal stroma-to-choroidal vessel lumen ratio. Subfoveal choroidal thickness was measured at fovea and 750 μm nasal, temporal, superior, and inferior to fovea. Patients underwent fluorescein angiography and indocyanine green angiography. Receiver operating characteristic curve and area under the curve were computed for central foveal thickness. The eye with a higher Behçet disease ocular attack score 24 was studied. The main outcome measures were choroidal stroma-to-choroidal vessel lumen ratio and choroidal thickness.

Results:
The mean total Behçet disease ocular attack score 24, fluorescein angiography, and indocyanine green angiography scores were 7.42 ± 4.10, 17.42 ± 6.03, and 0.66 ± 0.73, respectively. Choroidal stroma-to-choroidal vessel lumen ratio was significantly higher in patients (0.413 ± 0.056 vs. 0.351 ± 0.063, P = 0.003). There were no significant differences in subfoveal choroidal thickness between patients and control subjects. Choroidal stroma-to-choroidal vessel lumen ratio correlated with retinal vascular staining and leakage score of fluorescein angiography (r = 0.300, P = 0.036). Central foveal thickness was significantly increased in patients (352.750 ± 107.134 μm vs. 263.500 ± 20.819 μm, P < 0.001). Central foveal thickness showed significant correlations with logarithm of minimum angle of resolution vision, Behçet disease ocular attack score 24, total fluorescein angiography score, retinal vascular staining and/or leakage and capillary leakage scores of fluorescein angiography, and total indocyanine green angiography score. At 275 μm cutoff, diagnostic sensitivity and specificity of central foveal thickness for acute Behçet uveitis were 89% and 72%, respectively (area under the curve = 0.902; 95% CI = 0.826–0.978, P < 0.001).

Conclusion:
There was choroidal stromal expansion which was not associated with thickening of the choroid. Central foveal thickness may be used as a noninvasive measure to assess inflammatory activity in early Behçet uveitis.
Brief Report: Long-Term (96-Week) Efficacy and Safety After Switching From Tenofovir Disoproxil Fumarate to Tenofovir Alafenamide in HIV-Infected, Virologically Suppressed Adults
Authors: Raffi François , Orkin Chloe , Clarke Amanda , Slama Laurence , Gallant Joel , Daar Eric , Henry Keith , Santana-Bagur Jorge , Stein David K. , Bellos Nicholaos , Scarsella Anthony , Yan Mingjin , Abram Michael E. , Cheng Andrew , Rhee Martin S. 
Published: March 2017

Abstract:
In a double-blind, phase 3 trial, 663 HIV-infected, virologically suppressed adults were randomized to switch to tenofovir alafenamide (TAF; n = 333) vs. remain on tenofovir disoproxil fumarate (TDF; n = 330), each coformulated with emtricitabine (FTC), while continuing their third agent (boosted protease inhibitor or unboosted third agent). At week 96, 88.6% on FTC/TAF and 89.1% on FTC/TDF had HIV-1 RNA <50 copies per milliliter [adjusted difference −0.5% (95% confidence interval: −5.3 to 4.4%)]. Proteinuria, albuminuria, proximal renal tubular function, and bone mineral density improved after switching to TAF- from TDF-containing regimens. These longer-term data support FTC/TAF as a safe, well-tolerated, and durable nucleotide reverse transcriptase inhibitor backbone.
Transcranial Direct Current Stimulation in Substance Use Disorders
Authors: Lupi Matteo , Martinotti Giovanni , Santacroce Rita , Cinosi Eduardo , Carlucci Maria , Marini Stefano , Acciavatti Tiziano , di Giannantonio Massimo 
Published: March 2017

Introduction
New treatment options such as noninvasive brain stimulation have been recently explored in the field of substance use disorders (SUDs), including transcranial direct current stimulation (tDCS).

Objectives
In light of this, we have performed a review of the scientific literature to assess efficacy and technical and methodological issues resulting from applying tDCS to the field of SUDs.

Methods
Our analysis highlighted the following selection criteria: clinical studies on tDCS and SUDs (alcohol, caffeine, cannabis, cocaine, heroin, methamphetamine, and nicotine). Study selection, data analysis, and reporting were conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Exclusion criteria were as follows: clinical studies about tDCS among behavioral addiction; review and didactic articles; physiopathological studies; and case reports.

Results
Eighteen scientific papers were selected out of 48 articles. Among these, 16 studied the efficacy of tDCS applied to the dorsolateral prefrontal cortex, and 8 suggested the efficacy of tDCS in reducing substance craving.

Conclusions
In light of these data, it is premature to conclude that tDCS over the dorsolateral prefrontal cortex is a very efficient technique in reducing craving. Small sample size, different stimulation protocols, and study duration were the main limitations. However, the efficacy of tDCS in treating SUDs requires further investigation.
Exact sequence variants should replace operational taxonomic units in marker gene data analysis
Authors: Callahan Benjamin J , McMurdie Paul J , Holmes Susan P 
Published: March 2017

AbstractRecent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently that sequence variants (SVs) can be resolved exactly, down to the level of single-nucleotide differences over the sequenced gene region. The benefits of finer taxonomic resolution are immediately apparent, and arguments for SV methods have focused on their improved resolution. Less obvious, but we believe more important, are the broad benefits deriving from the status of SVs asconsistent labelswithintrinsic biological meaningidentifiedindependently from a reference database. Here we discuss how those features grant SVs the combined advantages of closed-reference OTUs — including computational costs that scale linearly with study size, simple merging between independently processed datasets, and forward prediction — and of de novo OTUs — including accurate diversity measurement and applicability to communities lacking deep coverage in reference databases. We argue that the improvements in reusability, reproducibility and comprehensiveness are sufficiently great that SVs should replace OTUs as the standard unit of marker gene analysis and reporting.
On the genetic and environmental reasons why intelligence correlates with criminal victimization
Authors: Boutwell Brian B. , Connolly Eric J. , Barbaro Nicole , Shackelford Todd K. , Petkovsek Melissa , Beaver Kevin M. 
Published: March 2017

AbstractResearchers have expended considerable effort to understand the causes and correlates of criminal victimization. More recently, scholars have focused on identifying individual-level traits that increase the odds of victimization. Generally absent from this line of research, however, is examining the extent to which previously unmeasured genetic and environmental influences contribute to the covariation between victimization and individual-level risk factors. The current study aims to replicate and extend prior research by examining the contribution of genetic and environmental influences on the association between intelligence and victimization by analyzing twin and sibling data from two nationally representative samples of American youth. Quantitative genetic analyses indicate that common additive genetic factors, as well as non-shared environmental factors, explained the phenotypic association between intelligence and victimization. Finally, our results revealed that after correcting for possible familial confounding, the effect of intelligence on victimization experiences remained statistically significant. The findings of the current study replicate and extend prior research on the phenotypic association between indicators of general intelligence and the experience of victimization.
Alzheimer related genes show accelerated evolution
Authors: Nitsche Anne , Reiche Kristin , Ueberham Uwe , Arnold Christian , Hackermüller Jörg , Horn Friedemann , Stadler Peter F. , Arendt Thomas 
Published: March 2017

AbstractAlzheimer's disease (AD) is a neurodegenerative disorder of unknown cause with complex genetic and environmental traits. Here, we show that gene structures of loci, that show AD-associated changes in their expression, evolve faster than the genome at large. This phylogenetic trait of AD suggests a critical pathogenetic role of recent adaptive evolution of human brain and might have far reaching consequences with respect to the appropriateness of model systems and the development of disease-modifying strategies.