bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disulfiram (DSF) acts as a copper ionophore to induce copper‐dependent oxidative stress and mediate anti‐tumor efficacy in inflammatory breast cancer
Authors: Allensworth Jennifer L. , Evans Myron K. , Bertucci François , Aldrich Amy J. , Festa Richard A. , Finetti Pascal , Ueno Naoto T. , Safi Rachid , McDonnell Donald P. , Thiele Dennis J. , Van Laere Steven , Devi Gayathri R. 
Published: February 2015

Cancer cells often have increased levels of reactive oxygen species (ROS); however, acquisition of redox adaptive mechanisms allows for evasion of ROS‐mediated death. Inflammatory breast cancer (IBC) is a distinct, advanced BC subtype characterized by high rates of residual disease and recurrence despite advances in multimodality treatment. Using a cellular model of IBC, we identified an oxidative stress response (OSR) signature in surviving IBC cells after administration of an acute dose of an ROS inducer. Metagene analysis of patient samples revealed significantly higher OSR scores in IBC tumor samples compared to normal or non‐IBC tissues, which may contribute to the poor response of IBC tumors to common treatment strategies, which often rely heavily on ROS induction. To combat this adaptation, we utilized a potent redox modulator, the FDA‐approved small molecule Disulfiram (DSF), alone and in combination with copper. DSF forms a complex with copper (DSF‐Cu) increasing intracellular copper concentration both in vitro and in vivo, bypassing the need for membrane transporters. DSF‐Cu antagonized NFκB signaling, aldehyde dehydrogenase activity and antioxidant levels, inducing oxidative stress‐mediated apoptosis in multiple IBC cellular models. In vivo, DSF‐Cu significantly inhibited tumor growth without significant toxicity, causing apoptosis only in tumor cells. These results indicate that IBC tumors are highly redox adapted, which may render them resistant to ROS‐inducing therapies. DSF, through redox modulation, may be a useful approach to enhance chemo‐ and/or radio‐sensitivity for advanced BC subtypes where therapeutic resistance is an impediment to durable responses to current standard of care.
Protection Against Cold in Prehospital Care: Wet Clothing Removal or Addition of a Vapor Barrier
Authors: Henriksson Otto , Lundgren Peter J. , Kuklane Kalev , Holmér Ingvar , Giesbrecht Gordon G. , Naredi Peter , Bjornstig Ulf 
Published: February 2015

Objective The purpose of this study was to evaluate the effect of wet clothing removal or the addition of a vapor barrier in shivering subjects exposed to a cold environment with only limited insulation available. Methods Volunteer subjects (n = 8) wearing wet clothing were positioned on a spineboard in a climatic chamber (–18.5°C) and subjected to an initial 20 minutes of cooling followed by 30 minutes of 4 different insulation interventions in a crossover design: 1) 1 woolen blanket; 2) vapor barrier plus 1 woolen blanket; 3) wet clothing removal plus 1 woolen blanket; or 4) 2 woolen blankets. Metabolic rate, core body temperature, skin temperature, and heart rate were continuously monitored, and cold discomfort was evaluated at 5-minute intervals. Results Wet clothing removal or the addition of a vapor barrier significantly reduced metabolic rate (mean difference ± SE; 14 ± 4.7 W/m2) and increased skin temperature rewarming (1.0° ± 0.2°C). Increasing the insulation rendered a similar effect. There were, however, no significant differences in core body temperature or heart rate among any of the conditions. Cold discomfort (median; interquartile range) was significantly lower with the addition of a vapor barrier (4; 2–4.75) and with 2 woolen blankets (3.5; 1.5–4) compared with 1 woolen blanket alone (5; 3.25–6). Conclusions In protracted rescue scenarios in cold environments with only limited insulation available, wet clothing removal or the use of a vapor barrier is advocated to limit the need for shivering thermogenesis and improve the patient’s condition on admission to the emergency department.
Presence of L-Canavanine in Hedysarum alpinum Seeds and Its Potential Role in the Death of Chris McCandless
Authors: Krakauer Jon , Long Ying , Kolbert Andrew , Thanedar Shri , Southard Jonathan 
Published: February 2015

Objective For the past 2 decades there has been vigorous disagreement over the purported toxicity of Hedysarum alpinum seeds, and whether the consumption of such seeds was a factor in the 1992 death of Chris McCandless, the subject of the book Into the Wild. Our objective was to confirm or disprove the presence of L-canavanine (a nonprotein amino acid known to induce systemic lupuslike symptoms in humans) in H alpinum seeds. Methods Liquid chromatography–tandem mass spectrometry analysis of H alpinum seeds was performed. Results Our analysis confirmed the presence of L-canavanine in H alpinum seeds and demonstrated that it is a significant component of the seeds, with a concentration of 1.2% (weight/weight), roughly half of that found in Canavalia ensiformis. Conclusions The data led us to conclude it is highly likely that the consumption of H alpinum seeds contributed to the death of Chris McCandless.
Gastropods from upper Pliensbachian–Toarcian (Lower Jurassic) sediments of Causses Basin, southern France and their recovery after the early Toarcian anoxic event
Authors: GATTO ROBERTO , MONARI STEFANO , NEIGE PASCAL , PINARD JEAN-DANIEL , WEIS ROBERT 
Published: February 2015

AbstractA gastropod fauna has been studied from upper Pliensbachian – upper Toarcian deposits of two sections of the Causses Basin (southern France) in order to investigate the mode of recovery after the early Toarcian anoxic event. The fauna consists of 15 species, one of which is new (Bathrotomaria kronzwilmesorumsp. nov.). Their stratigraphical distribution shows two peaks of diversity – in the Bifrons Zone (Bifrons Subzone) and in the Aalensis Zone (Mactra Subzone) – which reflect brief times during which the oxygen content and bottom consistency favoured the settlement of a relatively diversified fauna. In the Variabilis–Pseudoradiosa zones, gastropods are only represented by two species. This probably indicates more severe and unstable environmental conditions, only allowing the survival of gastropod taxa with wide adaptive capacities. The very low species diversity and the discontinuous and slow faunal recovery were probably determined by physiographic factors. The Causses area was a small basin confined by exposed lands and open towards the central part of western Tethys. Gastropods described here occur exclusively in the Toarcian – early Aalenian communities of the European epicontinental seas, whereas species from the central region of western Tethys are absent. Geographic isolation and marginal location of the Causses Basin restricted faunal exchange with the western European epicontinental seas, preventing fast recovery after the anoxic event. Gastropods of the central region of the western Tethys were probably unable to settle and colonize that area due to the strongly different environment.
Conjugate-like immunogens produced as protein capsular matrix vaccines
Authors: Thanawastien Ann , Cartee Robert T. , Griffin Thomas J. , Killeen Kevin P. , Mekalanos John J. 
Published: February 2015

Significance
Conjugate vaccines have dramatically reduced the incidence of disease in infants and young children caused by encapsulated bacterial pathogens. These vaccines, however, are difficult and expensive to manufacture, deterring their widespread use. We present an alternative technology for the production of conjugate-like vaccines whereby capsular antigens are entrapped in a cross-linked protein matrix. The versatility and ease of protein capsular matrix vaccine production compared with conjugates will likely render the manufacture of these vaccines simpler and more cost effective than conjugate vaccines. This in turn would improve the availability of such vaccines to the developing world, which has shown a limited capacity to afford the cost of conventional conjugate vaccines.
Assessment of Finfish Aquaculture Effect on Newfoundland Epibenthic Communities through Video Monitoring
Authors: Hamoutene Dounia , Salvo Flora , Bungay Terrence , Mabrouk Gehan , Couturier Cyr , Ratsimandresy Andry , Dufour Suzanne C 
Published: February 2015

Abstract
In Newfoundland fjords, evaluating changes to benthic communities resulting from finfish aquaculture is difficult because the depth (&gt;30 m) and presence of patches of hard substrates at production sites hinder grab sampling. In this study, we used video surveys to characterize benthic assemblages at sites with no aquaculture, with varying amounts of finfish production, and undergoing fallowing periods. Video analyses revealed a patchy distribution of benthic organisms (identifiable at a high taxonomic level), characterized by low natural abundances and richness. Benthic communities at aquaculture sites showed evidence of organic matter enrichment through the presence of Beggiatoa sp. or opportunistic polychaete-dominated assemblages (or both), bare stations, flocculent matter, and lower abundances and richness near aquaculture cages. Maps of sites in production showed that the area of aquaculture impact was influenced by bathymetry, located underneath cages and in some instances up to 145 m away from net-pens, and often directed away from the coastline. However, correlations of abundances and richness with distance from cage were weak, and stations close to cages were not always statistically different from stations further away or at the nonproduction site. At the fallow site, a large percentage (∼70%) of stations was barren, suggesting potentially hypoxic or anoxic conditions and warranting further investigations of fallow periods. Our analysis confirms that video-based assessments can detect major aquaculture-related changes in benthic communities but cannot, at present, identify lower levels of disturbance.
Apparent Phosphorus Availabilities of Selected Traditional and Alternative Feedstuffs for Channel Catfish
Authors: Li Menghe H , Robinson Edwin H , Lucas Penelope M 
Published: February 2015

Abstract
A digestibility trial with Channel Catfish Ictalurus punctatus was conducted to determine apparent availability coefficients (AACs) of phosphorus for selected common feedstuffs: soybean meal, cottonseed meal, wheat middlings, corn gluten feed (CGF), and corn distillers dried grains with solubles (DDGS). A 32% protein diet containing mostly chemically defined ingredients was used as a reference diet. Test diets were formulated to contain 70% of the reference diet mix and 30% of the test ingredient. Chromic oxide was used at 0.75% of the diet as a marker. Fifteen Channel Catfish of a mean weight of 316 g/fish (SD, 5) were placed into 110-L flow-through aquaria. Water temperature and dissolved oxygen were maintained at approximately 30°C and ≥ 5 mg/L, respectively. Each diet had three replicated tanks. Apparent availability coefficients of phosphorus were 36, 22, 20, 75, and 77% for soybean meal, cottonseed meal, wheat middlings, CGF, and DDGS, respectively. Corn by-products CGF and DDGS had considerably greater phosphorus AACs than soybean meal, cottonseed meal, and wheat middlings, likely because the wet milling and fermentation processes that result in these by-products degrade the phytate form of phosphorus making it more available to the fish. It appears that phosphorus AACs of these ingredients for Channel Catfish are generally correlated to their nonphytate phosphorus levels. Phosphorus AACs obtained from the present study can be used in formulating commercial Channel Catfish feeds to optimize available phosphorus levels.
CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions
Authors: Desouki Abdelmoneim Amer , Jarre Florian , Gelius-Dietrich Gabriel , Lercher Martin J. 
Published: February 2015

Abstract
Motivation: Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are routinely used to predict metabolic phenotypes, e.g. growth rates, ATP yield or the fitness of gene knockouts. One frequent difficulty of constraint-based solutions is the inclusion of thermodynamically infeasible loops (or internal cycles), which add nonbiological fluxes to the predictions.
Results: We propose a simple postprocessing of constraint-based solutions, which removes internal cycles from any given flux distribution v(0) without disturbing other fluxes not involved in the loops. This new algorithm, termed CycleFreeFlux, works by minimizing the sum of absolute fluxes ||v||1 while (i) conserving the exchange fluxes and (ii) using the fluxes of the original solution to bound the new flux distribution. This strategy reduces internal fluxes until at least one reaction of every possible internal cycle is inactive, a necessary and sufficient condition for the thermodynamic feasibility of a flux distribution. If alternative representations of the input flux distribution in terms of elementary flux modes exist that differ in their inclusion of internal cycles, then CycleFreeFlux is biased towards solutions that maintain the direction given by v(0) and towards solutions with lower total flux ||v||1. Our method requires only one additional linear optimization, making it computationally very efficient compared to alternative strategies.
Availability and implementation: We provide freely available R implementations for the enumeration of thermodynamically infeasible cycles as well as for cycle-free FBA solutions, flux variability calculations and random sampling of solution spaces.
Contact: lercher@cs.uni-duesseldorf.de
Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs
Authors: Musacchia Francesco , Basu Swaraj , Petrosino Giuseppe , Salvemini Marco , Sanges Remo 
Published: February 2015

Abstract
Summary: The eukaryotic transcriptome is composed of thousands of coding and long non-coding RNAs (lncRNAs). However, we lack a software platform to identify both RNA classes in a given transcriptome. Here we introduce Annocript, a pipeline that combines the annotation of protein coding transcripts with the prediction of putative lncRNAs in whole transcriptomes. It downloads and indexes the needed databases, runs the analysis and produces human readable and standard outputs together with summary statistics of the whole analysis.
Availability and implementation: Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at https://github.com/frankMusacchia/Annocript.
Contact: remo.sanges@szn.it
tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks
Authors: Gerstl Matthias P. , Jungreuthmayer Christian , Zanghellini Jürgen 
Published: February 2015

AbstractSummary: Elementary flux modes (EFMs) are important structural tools for the analysis of metabolic networks. It is known that many topologically feasible EFMs are biologically irrelevant. Therefore, tools are needed to find the relevant ones. We present thermodynamic tEFM analysis (tEFMA) which uses the cellular metabolome to avoid the enumeration of thermodynamically infeasible EFMs. Specifically, given a metabolic network and a not necessarily complete metabolome, tEFMA efficiently returns the full set of thermodynamically feasible EFMs consistent with the metabolome. Compared with standard approaches, tEFMA strongly reduces the memory consumption and the overall runtime. Thus tEFMA provides a new way to analyze unbiasedly hitherto inaccessible large-scale metabolic networks.Availability and implementation: https://github.com/mpgerstl/tEFMAContact: christian.jungreuthmayer@boku.ac.at or juergen.zanghellini@boku.ac.atSupplementary information: Supplementary data are available at Bioinformatics online.
Unified representation of genetic variants
Authors: Tan Adrian , Abecasis Gonçalo R. , Kang Hyun Min 
Published: February 2015

Abstract
Summary: A genetic variant can be represented in the Variant Call Format (VCF) in multiple different ways. Inconsistent representation of variants between variant callers and analyses will magnify discrepancies between them and complicate variant filtering and duplicate removal. We present a software tool vt normalize that normalizes representation of genetic variants in the VCF. We formally define variant normalization as the consistent representation of genetic variants in an unambiguous and concise way and derive a simple general algorithm to enforce it. We demonstrate the inconsistent representation of variants across existing sequence analysis tools and show that our tool facilitates integration of diverse variant types and call sets.
Availability and implementation: The source code is available for download at http://github.com/atks/vt. More detailed documentation is available at http://genome.sph.umich.edu/wiki/Variant_Normalization.
Contact: hmkang@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Age-dependent trends in postoperative mortality and preoperative comorbidity in isolated coronary artery bypass surgery: a nationwide study
Authors: Thorsteinsson Kristinn , Fonager Kirsten , Mérie Charlotte , Gislason Gunnar , Køber Lars , Torp-Pedersen Christian , Mortensen Rikke N. , Andreasen Jan J. 
Published: February 2015

Abstract

OBJECTIVES
An increasing number of octogenarians are being subjected to coronary artery bypass grafting (CABG). The purpose of this study was to examine age-dependent trends in postoperative mortality and preoperative comorbidity over time following CABG.

METHODS
All patients who underwent isolated CABG surgery between January 1996 and December 2012 in Denmark were included. Patients were identified through nationwide administrative registers. Age was categorized into five different groups and time into three periods to see if mortality and preoperative comorbidity had changed over time. Predictors of 30-day mortality were analysed in a multivariable Cox proportional-hazard models and survival at 1 and 5 years was estimated by Kaplan–Meier curves.

RESULTS
A total of 38 830 patients were included; the median age was 65.4 ± 9.5 years, increasing over time to 66.6 ± 9.5 years. Males comprised 80%. The number of octogenarians was 1488 (4%). The median survival was 14.7 years (60–69 years), 10.7 years (70–74 years), 8.9 years (75–79 years) and 7.2 years (≥80 years). The 30-day mortality rate was 3%, increasing with age (1% in patients &lt;60 years, 8% in octogenarians). The long-term mortality rate at 1 and 5 years was 2 and 7% (age &lt;60 years) and 14 and 36% (age &gt;80 years), respectively. The proportion of patients &gt;75 years increased from 10 to 20% during the study period as well as the proportion of patients undergoing urgent or emergency surgery. The burden of comorbidities increased over time, e.g. congestive heart failure 13–17%, diabetes 12–21%, stroke 9–11%, in all age groups. Age and emergency surgery were the main predictors of 30-day mortality: age &gt;80 years [hazard ratio (HR): 5.75, 95% confidence interval (CI): 4.41–7.50], emergency surgery (HR: 5.23, 95% CI: 4.38–6.25).

CONCLUSION
Patients are getting older at the time of surgery and have a heavier burden of comorbidities than before. The proportion of patients undergoing urgent or emergency surgery increased with age and over time. Despite this, the 30-day mortality decreased over time and long-term survival increased, except in octogenarians where it was stable. Octogenarians had substantially higher 30-day mortality compared with younger patients but surgery can be performed with acceptable risks and good long-term outcomes.
Radiation drag effects in black hole outflows from super-critical accretion disks via special relativistic radiation magnetohydrodynamics simulations
Authors: Takahashi Hiroyuki R. , Ohsuga Ken 
Published: February 2015

Abstract
By performing 2.5-dimensional special relativistic radiation magnetohydrodynamics simulations, we study super-critical accretion disks and the outflows launched via the radiation force. We find that the outflow is accelerated by the radiation flux force, but the radiation drag force prevents the outflow velocity from increasing. The outflow velocity saturates around 30%–40% of the light speed around the rotation axis, since then the flux force balances with the drag force. Our simulations show that the outflow velocity is kept nearly constant in the region of $\skew4\dot{M}_{\rm BH}\sim 10^{2-3}L_{\rm Edd}/c^{\,2}$, where $\skew4\dot{M}_{\rm BH}$ is the mass accretion rate, LEdd is the Eddington luminosity, and c is the light speed. Such a faster outflow is surrounded by a slower outflow of ∼ 0.1c. This velocity is also determined by the balance between the radiation flux force and the radiation drag. The radiation drag works to collimate the slower outflow in cooperation with the Lorentz force, although the faster outflow is mainly collimated by the Lorentz force. The kinetic energy is carried by the slower outflow rather than by the faster outflow. The total kinetic luminosity of the outflow as well as the photon luminosity is ∼ LEdd, almost independent of the mass accretion rate.
Growth of Indonesian Infants Compared With World Health Organization Growth Standards
Authors: Dwipoerwantoro Pramita G. , Mansyur Muchtaruddin , Oswari Hanifah , Makrides Maria , Cleghorn Geoffrey , Firmansyah Agus 
Published: February 2015

ABSTRACTObjectives:The ability of the World Health Organization (WHO) growth standards to represent the growth of South East Asian infants has been questioned. The aim of this study was to provide contemporary data on the growth of Indonesian breast‐fed and formula‐fed infants, compared with the WHO growth standards.Methods:A prospective cohort study of 160 normal healthy infants was undertaken in a suburban area of South Jakarta, Indonesia. Infants from 2 to 6 weeks of age were recruited, and they consumed exclusively either breast milk or infant formula for at least 6 months, with follow‐up until 12 months of age.Results:Overall, the infants in the present study were lighter (weight‐for‐age), were shorter (length‐for‐age), and had smaller head circumferences (head circumference‐for‐age) than the average WHO Growth Reference Study population but were of similar proportion (weight‐for‐length). Compared with the WHO Growth Reference Study, the z scores for weight‐for‐age, length‐for‐age, and head circumference‐for‐age in the Indonesian children fell from birth to 6 weeks of age and then increased until 3 months of age in both the breast‐fed and the formula‐fed infants. At 6 weeks of age, the weight‐for‐age z scores fell below −2 standard deviations for 16 (20.5%) breast‐fed and 40 (51.3%) formula‐fed infants, and the length‐for‐age z scores fell below −2 standard deviations for 31 (39.7%) breast‐fed and 41 (52.6%) formula‐fed infants.Conclusion:The WHO growth standards do not reflect the growth of the present cohort of Indonesian infants and may overestimate the levels of underweight and stunted children.