bluuebunny/crossref_metadata_2025_split huggingface dataset:
Should Immediate Autologous Breast Reconstruction Be Considered in Women Who Require Postmastectomy Radiation Therapy? A Prospective Analysis of Outcomes
Authors: Billig Jessica , Jagsi Reshma , Qi Ji , Hamill Jennifer B. , Kim Hyungjin M. , Pusic Andrea L. , Buchel Edward , Wilkins Edwin G. , Momoh Adeyiza O. 
Published: February 2017

Background:
In women who require postmastectomy radiation therapy, immediate autologous breast reconstruction is often discouraged. The authors prospectively evaluated postoperative morbidity and satisfaction reported by women undergoing delayed or immediate autologous breast reconstruction in the setting of postmastectomy radiation therapy.

Methods:
Patients enrolled in the Mastectomy Reconstruction Outcomes Consortium study, who received postmastectomy radiotherapy and underwent immediate or delayed free abdominally based autologous breast reconstruction, were identified. Postoperative complications at 1 and 2 years after reconstruction were assessed. Patient-reported outcomes were evaluated using the BREAST-Q questionnaire preoperatively and at 1 and 2 years postoperatively. Bivariate analyses and mixed-effects regression models were used to compare outcomes.

Results:
A total of 175 patients met the authors’ inclusion criteria. Immediate reconstructions were performed in 108 patients and delayed reconstructions in 67 patients; 93.5 percent of immediate reconstructions were performed at a single center. Overall complication rates were similar based on reconstructive timing (25.9 percent immediate and 26.9 percent delayed at 1 year; p = 0.54). Patients with delayed reconstruction reported significantly lower prereconstruction scores (p < 0.0001) for Satisfaction with Breasts and Psychosocial and Sexual Well-being than did patients with immediate reconstruction. At 1 and 2 years postoperatively, both groups reported comparable levels of satisfaction in assessed BREAST-Q domains.

Conclusions:
From this prospective cohort, immediate autologous breast reconstruction in the setting of postmastectomy radiation therapy appears to be a safe option that may be considered in select patients and centers. Breast aesthetics and quality of life, evaluated from the patient’s perspective, were not compromised by flap exposure to radiation therapy.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Brief Report: Longitudinal Opioid Use Among HIV-Infected Patients, 2000 to 2014
Authors: Brunet Laurence , Napravnik Sonia , Heine Amy D. , Leone Peter A. , Eron Joseph J. 
Published: February 2017

Abstract:
Longitudinal opioid prescription use is unknown among HIV-infected patients. Group-based trajectory modeling followed by multinomial logistic regression was used to identify distinct trajectories and their association with baseline characteristics among 1239 HIV-infected UNC CFAR HIV Clinical Cohort participants, 2000–2014. Three trajectories were identified: (1) 72% never/sporadic opioid use (referent group), (2) 11% episodic use (associated with female sex, depression, drug-related diagnoses, antiretroviral therapy use, and undetectable HIV RNA), and (3) 16% chronic use (associated with older age, female sex, and mental health diagnoses). Overall, opioid prescription decreased substantially with longer time in HIV care among both episodic and chronic users.
Detection and Alterations of Acetylcarnitine in Human Skeletal Muscles by 1H MRS at 7 T
Authors: Klepochová Radka , Valkovič Ladislav , Gajdošík Martin , Hochwartner Thomas , Tschan Harald , Krebs Michael , Trattnig Siegfried , Krššák Martin 
Published: February 2017

Objectives
The aims of this study were to detect the acetylcarnitine resonance line at 2.13 ppm in the human vastus lateralis and soleus muscles, assess T1 and T2 relaxation times, and investigate the diurnal and exercise-related changes in absolute concentration noninvasively, using proton magnetic resonance spectroscopy at 7 T.

Materials and Methods
All measurements were performed on a 7 T whole-body Magnetom MR system with a 28-channel knee coil. Five healthy, moderately trained volunteers participated in the assessment of the detectability, repeatability, and relaxation times of acetylcarnitine. For the evaluation of the effect of training status, another 5 healthy, normally active volunteers were examined. In addition, normally active volunteers underwent a day-long protocol to estimate diurnal changes and response to the exercise.

Results
Using a long echo time of 350 milliseconds, we were able to detect the acetylcarnitine resonance line at 2.13 ppm in both muscle groups without significant lipid contamination. The T1 of acetylcarnitine in the vastus lateralis muscle was found to be 1807.2 ± 513.1 milliseconds and T2 was found to be 129.9 ± 44.9 milliseconds. Concentrations of acetylcarnitine from the vastus lateralis muscle in moderately trained volunteers were higher than concentrations from normally active volunteers. Acetylcarnitine concentrations changed during the day, tending to be higher in the morning after an overnight fast than after lunch. After 10 minutes of high-intensity exercise, the concentration significantly increased, and 15 minutes after cessation of exercise, a decrease could be observed.

Conclusions
Our results demonstrate an effective detection of acetylcarnitine using a long TE of 350 milliseconds at 7 T in the vastus lateralis and soleus muscles with high repeatability and reliability on a 7 T scanner. Our data emphasize the need for strict standardization, physical activity, and dietary conditions for the measurement of the acetylcarnitine.
Benefits of Dexmedetomidine in Management of Post-ECT Agitation
Authors: Narang Puneet , Ianovich Francesca , Sarai Simrat Kaur , Lippmann Steven 
Published: February 2017

Abstract
Electroconvulsive therapy (ECT) is an intervention for patients with a variety of psychiatric conditions. Occasionally, people exhibit dangerous degrees of agitation after this treatment, and some do not respond well to conventional pharmacotherapies. Dexmedetomidine is a central α-2 agonist that can induce significantly calmative effects in persons with post-ECT agitation. The indication for it is in calming individuals with acute and/or recurrent posttreatment agitation. Dexmedetomidine is safe and effective when infused just before, or postictally, at ECT sessions.
A Sign of Disparity: Racial/Ethnic Composition of Treatment Centers is an Independent Risk Factor in SPRINT Trial
Authors: Matlock Matthew , Dang Na Le , Brown David , Joshua Swamidass S. 
Published: February 2017

AbstractThe racial composition of treatment centers in the SPRINT trial is an independent risk factor for myocardial infarction (MI) and stroke. Independent of individual race or ethnicity, patients face a 39% increase in relative risk of MI or stroke when associated to treatment centers with a high proportion of African Americans. The magnitude of this effect is comparable to smoking. This suggests the strong influence of social determinants on health outcomes among hypertensive patients.
SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks
Authors: Dalle Pezze Piero , Le Novère Nicolas 
Published: February 2017

AbstractBackground:The rapid growth of the number of mathematical models in Systems Biology fostered the development of many tools to simulate and analyse them. The reliability and precision of these tasks often depend on multiple repetitions and they can be optimised if executed as pipelines. In addition, new formal analyses can be performed on these repeat sequences, revealing important insights about the accuracy of model predictions.Results:Here we introduce SBpipe, an open source software tool for automating repetitive tasks in model building and simulation. Using basic configuration files, SBpipe builds a sequence of repeated model simulations or parameter estimations, performs analyses from this generated sequence, and finally generates a LaTeX/PDF report. The parameter estimation pipeline offers analyses of parameter profile likelihood and parameter correlation using samples from the computed estimates. Specific pipelines for scanning of one or two model parameters at the same time are also provided. Pipelines can run on multicore computers, Sun Grid Engine (SGE), or Load Sharing Facility (LSF) clusters, speeding up the processes of model building and simulation. SBpipe can execute models implemented in Copasi, Python or coded in any other programming language using Python as a wrapper module. Future support for other software simulators can be dynamically added without affecting the current implementation.Conclusions:SBpipe allows users to automatically repeat the tasks of model simulation and parameter estimation, and extract robustness information from these repeat sequences in a solid and consistent manner, facilitating model development and analysis. The source code and documentation of this project are freely available at the web site:https://pdp10.github.io/sbpipe/.
Modeling Epidemics in Seed Systems to Guide Management Strategies: The Case of Sweetpotato in Northern Uganda
Authors: Andersen K. F. , Buddenhagen C. E. , Rachkara P. , Gibson R. , Kalule S. , Phillips D. , Garrett K. A. 
Published: February 2017

AbstractSeed systems are critical for deployment of improved varieties, but also serve as major conduits for the spread of seed-borne pathogens. We evaluated the structure of an informal sweetpotato seed system for its vulnerability to the spread of epidemics, and its utility for disseminating improved varieties. During the 2014 growing season, vine sellers were surveyed weekly in the Gulu Region of Northern Uganda. Our analysis draws on tools from network theory to evaluate the potential for epidemic spread in this region. Using empirical seed transaction data and estimated spatial spread, we constructed a network of seed and pathogen movement. We modeled the introduction of a pathogen, and evaluated the influence of both epidemic starting point and quarantine treatments on epidemic progress. Quarantine of 30 out of 99 villages reduced epidemic progress by up to 66%, when compared to the control (no quarantine), over 20 time steps. The starting position in the network was critical for epidemic progress and final epidemic outcomes, and influenced the percent control conferred by quarantine treatments. Considering equal likelihood of any node being an introduction point for a new epidemic, villages of particular utility for disease monitoring were identified. Sensitivity analysis identified important parameters and priorities for future data collection. The efficacy of node degree, closeness, and eigenvector centrality was similar for selecting quarantine locations, while betweenness had more limited utility. This analysis framework can be applied to provide recommendations for a wide variety of seed systems.
A memory of recent oxygen experience switches pheromone valence inC. elegans
Authors: Fenk Lorenz A. , de Bono Mario 
Published: February 2017

ABSTRACTAnimals adjust their behavioral priorities according to momentary needs and prior experience. We show thatC. eleganschanges how it processes sensory information according to the oxygen environment it experienced recently.C.elegansacclimated to 7% O2are aroused by CO2and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2levels. A sustained change in the activity of O2sensing neurons reprograms the properties of their post-synaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggestC. elegansstores a memory of recent O2experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.
Enzymatic production of single molecule FISH and RNA capture probes
Authors: Gaspar Imre , Wippich Frank , Ephrussi Anne 
Published: February 2017

AbstractArrays of singly-labelled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single molecule microscopy analysis and high efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that 1) all steps of the oligonucleotide labelling – including conjugation, enzymatic synthesis and product purification – can be performed in a standard biology laboratory, 2) the process yields >90 %, often >95 % labeled product with minimal carry-over of impurities and 3) the oligonucleotides can be labeled with different dyes or biotin, allowing single molecule FISH or RNA affinity purification to be performed.Graphical abstract
Inhibition of histone deacetylase 1 or 2 reduces microglia activation through a gene expression independent mechanism
Authors: Durham Benjamin S. , Grigg Ronald , Wood Ian C. 
Published: February 2017

AbstractHistone deacetylase (HDAC) inhibitors prevent neural cell death inin vivomodels of cerebral ischaemia, brain injury and neurodegenerative disease. One mechanism by which HDAC inhibitors may do this is by suppressing the excessive inflammatory response of chronically activated microglia. However, the molecular mechanisms underlying this anti-inflammatory effect and the specific HDAC responsible are not fully understood. Recent data fromin vivorodent studies has shown that inhibition of class I HDACs suppresses neuroinflammation and is neuroprotective. In our study we have identified that selective HDAC inhibition with inhibitors apicidin, MS-275 or MI-192, or specific knockdown of HDAC1 or 2 using siRNA, suppresses the expression of cytokines interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) in BV2 murine microglia activated with lipopolysaccharide (LPS). Furthermore, we found that in the absence of HDAC1, HDAC2 is upregulated and these increased levels are compensatory, suggesting these two HDACs have redundancy in regulating the inflammatory response of microglia. Investigating the possible underlying anti-inflammatory mechanisms suggests an increase in protein expression is not important. Taken together, this study supports the idea that inhibitors selective towards HDAC1 or HDAC2, may be therapeutically useful for targeting neuroinflammation in brain injuries and neurodegenerative disease.Significance StatementThe number of patients suffering a stroke or a neurodegenerative disease, such as Alzheimer’s is increasing These conditions are severely debilitating and are leading causes of mortality, with neural cell death and loss of brain tissue being a major feature. A number of mechanisms contribute to neuronal death, including inflammation in the brain, but we still lack clinical therapies to inhibit this. The work presented here provides further insight into potential molecular therapeutic targets called histone deacetylases (HDACs), which are thought to contribute to neural cell death by promoting inflammation. We show that down regulation of HDAC1 and 2 is sufficient to reduce this inflammatory response. Our findings have clinical relevance because they identify HDAC1 and 2 as promising targets for therapy.
Contextual diversity of the human cell-essential proteome
Authors: Bertomeu Thierry , Coulombe-Huntington Jasmin , Chatr-Aryamontri Andrew , Bourdages Karine , Xia Yu , Tyers Mike 
Published: February 2017

AbstractEssential genes define central biological functions required for cell growth, proliferation and survival, but the nature of gene essentiality across human cell types is not well understood. We assessed essential gene function in a Cas9-inducible human B-cell lymphoma cell line using an extended knockout (EKO) library of 278,754 sgRNAs that targeted 19,084 RefSeq genes, 20,852 alternatively-spliced exons and 3,872 hypothetical genes. A new statistical analysis tool called RANKS identified 2,280 essential genes, 234 of which had not been reported previously. Essential genes exhibited a bimodal distribution across 10 cell lines screened in different studies, consistent with a continuous variation in essentiality as a function of cell type. Genes essential in more lines were associated with more severe fitness defects and encoded the evolutionarily conserved structural cores of protein complexes. Genes essential in fewer lines tended to form context-specific modules and encode subunits at the periphery of essential complexes. The essentiality of individual protein residues across the proteome correlated with evolutionary conservation, structural burial, modular domains, and protein interaction interfaces. Many alternatively-spliced exons in essential genes were dispensable and tended to encode disordered regions. We also detected a significant fitness defect for 44 newly evolved hypothetical reading frames. These results illuminate the nature and evolution of essential gene functions in human cells.
Sparse synaptic connectivity is required for decorrelation and pattern separation in feedforward networks
Authors: Cayco-Gajic N. Alex , Clopath Claudia , Silver R. Angus 
Published: February 2017

AbstractPattern separation is a fundamental function of the brain. Divergent feedforward networks separate overlapping activity patterns by mapping them onto larger numbers of neurons, aiding learning in downstream circuits. However, the relationship between the synaptic connectivity within these circuits and their ability to separate patterns is poorly understood. To investigate this we built simplified and biologically detailed models of the cerebellar input layer and systematically varied the spatial correlation of their inputs and their synaptic connectivity. Performance was quantified by the learning speed of a classifier trained on either the mossy fiber input or granule cell output patterns. Our results establish that the extent of synaptic connectivity governs the pattern separation performance of feedforward networks by counteracting the beneficial effects of expanding coding space and threshold-mediated decorrelation. The sparse synaptic connectivity in the cerebellar input layer provides an optimal solution to this trade-off, enabling efficient pattern separation and faster learning.
Prospects for genomic selection in cassava breeding
Authors: Wolfe Marnin D. , Carpio Dunia Pino Del , Alabi Olumide , Egesi Chiedozie , Ezenwaka Lydia C. , Ikeogu Ugochukwu N. , Kawuki Robert S. , Kayondo Ismail S. , Kulakow Peter , Lozano Roberto , Rabbi Ismail Y. , Williams Esuma , Ozimati Alfred A. , Jannink Jean-Luc 
Published: February 2017

ABSTRACTCassava (Manihot esculentaCrantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) reduces selection cycle times by the prediction of breeding value for selection of unevaluated lines based on genome-wide marker data. GS has been implemented at three breeding programs in sub-Saharan Africa. Initial studies provided promising estimates of predictive abilities in single populations using standard prediction models and scenarios. In the present study we expand on previous analyses by assessing the accuracy of seven prediction models for seven traits in three prediction scenarios: (1) cross-validation within each population, (2) cross-population prediction and (3) cross-generation prediction. We also evaluated the impact of increasing training population size by phenotyping progenies selected either at random or using a genetic algorithm. Cross-validation results were mostly consistent across breeding programs, with non-additive models like RKHS predicting an average of 10% more accurately. Accuracy was generally associated with heritability. Cross-population prediction accuracy was generally low (mean 0.18 across traits and models) but prediction of cassava mosaic disease severity increased up to 57% in one Nigerian population, when combining data from another related population. Accuracy across-generation was poorer than within (cross-validation) as expected, but indicated that accuracy should be sufficient for rapid-cycling GS on several traits. Selection of prediction model made some difference across generations, but increasing training population (TP) size was more important. In some cases, using a genetic algorithm, selecting one third of progeny could achieve accuracy equivalent to phenotyping all progeny. Based on the datasets analyzed in this study, it was apparent that the size of a training population (TP) has a significant impact on prediction accuracy for most traits. We are still in the early stages of GS in this crop, but results are promising, at least for some traits. The TPs need to continue to grow and quality phenotyping is more critical than ever. General guidelines for successful GS are emerging. Phenotyping can be done on fewer individuals, cleverly selected, making for trials that are more focused on the quality of the data collected.Abbreviations(GS)Genomic selection(GBS)genotype-by-sequencing(IITA)International Institute of Tropical Agriculture(NRCRI)National Root Crops Research Institute(NaCRRI)National Crops Resources Research Institute(GEBVs)genomic estimated breeding values(TP)training population(RTWT)fresh root weight(RTNO)root number(SHTWT)fresh shoot weight(HI)harvest index(DM)dry matter(CMD)content cassava mosaic disease(MCMDS)mean CMD severity(VIGOR)early vigor
Chemical reaction, radiation and slip effects on MHD mixed convection stagnation-point flow in a porous medium with convective boundary condition
Authors: Sivasankaran S. , Niranjan H. , Bhuvaneswari M. 
Published: February 2017

Purpose
The purpose of this paper is to investigate the Newtonian heating and slip effect on mixed convective flow near a stagnation point in a porous medium with thermal radiation in the presence of magnetohydrodynamic (MHD), heat generation/absorption and chemical reaction.

Design/methodology/approach
The governing nonlinear coupled equations are converted into ordinary differential equations by similarity transformation. These equations are solved numerically using a Runge–Kutta–Fehlberg method with shooting technique and analytically using the homotopy analysis method (HAM).

Findings
The effects of different parameters on the fluid flow and heat transfer are investigated. It is found that the velocity and temperature profiles increase on an increase in the Biot number. The velocity and concentration profiles increase on decreasing the chemical reaction parameter.

Practical implications
This paper is helpful to the engineers and scientists in the field of thermal and manufacturing engineering.

Originality/value
The two-dimensional boundary layer flow over a vertical plate with slip and convective boundary conditions near the stagnation-point is analysed in the presence of magnetic field, radiation and heat generation/absorption. This paper is helpful to the engineers and scientists in the field of thermal and manufacturing engineering.