bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leaf:wood allometry and functional traits together explain substantial growth rate variation in rainforest trees
Authors: Gray E F , Wright I J , Falster D S , Eller A S D , Lehmann C E R , Bradford M G , Cernusak L A 
Published: April 2019

Abstract
Plant growth rates drive ecosystem productivity and are a central element of plant ecological strategies. For seedlings grown under controlled conditions, a large literature has firmly identified the functional traits that drive interspecific variation in growth rate. For adult plants, the corresponding knowledge is surprisingly poorly understood. Until recently it was widely assumed that the key trait drivers would be the same (e.g. specific leaf area, or SLA), but an increasing number of papers has demonstrated this not to be the case, or not generally so. New theory has provided a prospective basis for understanding these discrepancies. Here we quantified relationships between stem diameter growth rates and functional traits of adult woody plants for 41 species in an Australian tropical rainforest. From various cost-benefit considerations, core predictions included that: (i) photosynthetic rate would be positively related to growth rate; (ii) SLA would be unrelated to growth rate (unlike in seedlings where it is positively related to growth); (iii) wood density would be negatively related to growth rate; and (iv) leaf mass:sapwood mass ratio (LM:SM) in branches (analogous to a benefit:cost ratio) would be positively related to growth rate. All our predictions found support, particularly those for LM:SM and wood density; photosynthetic rate was more weakly related to stem diameter growth rates. Specific leaf area was convincingly correlated to growth rate, in fact negatively. Together, SLA, wood density and LM:SM accounted for 52 % of variation in growth rate among these 41 species, with each trait contributing roughly similar explanatory power. That low SLA species can achieve faster growth rates than high SLA species was an unexpected result but, as it turns out, not without precedent, and easily understood via cost-benefit theory that considers whole-plant allocation to different tissue types. Branch-scale leaf:sapwood ratio holds promise as an easily measurable variable that may help to understand growth rate variation. Using cost-benefit approaches teamed with combinations of leaf, wood and allometric variables may provide a path towards a more complete understanding of growth rates under field conditions.
Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data
Authors: Magi Alberto , Bolognini Davide , Bartalucci Niccoló , Mingrino Alessandra , Semeraro Roberto , Giovannini Luna , Bonifacio Stefania , Parrini Daniela , Pelo Elisabetta , Mannelli Francesco , Guglielmelli Paola , Maria Vannucchi Alessandro 
Published: April 2019

Abstract

Motivation
The past few years have seen the emergence of nanopore-based sequencing technologies which interrogate single molecule of DNA and generate reads sequentially.

Results
In this paper, we demonstrate that, thanks to the sequentiality of the nanopore process, the data generated in the first tens of minutes of a typical MinION/GridION run can be exploited to resolve the alterations of a human genome at a karyotype level with a resolution in the order of tens of Mb, while the data produced in the first 6–12 h allow to obtain a resolution comparable to currently available array-based technologies, and thanks to a novel probabilistic approach are capable to predict the allelic fraction of genomic alteration with high accuracy. To exploit the unique characteristics of nanopore sequencing data we developed a novel software tool, Nano-GLADIATOR, that is capable to perform copy number variants/alterations detection and allelic fraction prediction during the sequencing run (‘On-line’ mode) and after experiment completion (‘Off-line’ mode). We tested Nano-GLADIATOR on publicly available (‘Off-line’ mode) and on novel whole genome sequencing dataset generated with MinION device (‘On-line’ mode) showing that our tool is capable to perform real-time copy number alterations detection obtaining good results with respect to other state-of-the-art tools.

Availability and implementation
Nano-GLADIATOR is freely available at https://sourceforge.net/projects/nanogladiator/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Marked Increases in Resting-State MEG Gamma-Band Activity in Combat-Related Mild Traumatic Brain Injury
Authors: Huang Ming-Xiong , Huang Charles W , Harrington Deborah L , Nichols Sharon , Robb-Swan Ashley , Angeles-Quinto Annemarie , Le Lu , Rimmele Carl , Drake Angela , Song Tao , Huang Jeffrey W , Clifford Royce , Ji Zhengwei , Cheng Chung-Kuan , Lerman Imanuel , Yurgil Kate A , Lee Roland R , Baker Dewleen G 
Published: April 2019

Abstract
Combat-related mild traumatic brain injury (mTBI) is a leading cause of sustained impairments in military service members and veterans. Recent animal studies show that GABA-ergic parvalbumin-positive interneurons are susceptible to brain injury, with damage causing abnormal increases in spontaneous gamma-band (30–80 Hz) activity. We investigated spontaneous gamma activity in individuals with mTBI using high-resolution resting-state magnetoencephalography source imaging. Participants included 25 symptomatic individuals with chronic combat-related blast mTBI and 35 healthy controls with similar combat experiences. Compared with controls, gamma activity was markedly elevated in mTBI participants throughout frontal, parietal, temporal, and occipital cortices, whereas gamma activity was reduced in ventromedial prefrontal cortex. Across groups, greater gamma activity correlated with poorer performances on tests of executive functioning and visuospatial processing. Many neurocognitive associations, however, were partly driven by the higher incidence of mTBI participants with both higher gamma activity and poorer cognition, suggesting that expansive upregulation of gamma has negative repercussions for cognition particularly in mTBI. This is the first human study to demonstrate abnormal resting-state gamma activity in mTBI. These novel findings suggest the possibility that abnormal gamma activities may be a proxy for GABA-ergic interneuron dysfunction and a promising neuroimaging marker of insidious mild head injuries.
Diabetes Mellitus Among Pulmonary Tuberculosis Patients From 4 Tuberculosis-endemic Countries: The TANDEM Study
Authors: Ugarte-Gil Cesar , Alisjahbana Bachti , Ronacher Katharina , Riza Anca Lelia , Koesoemadinata Raspati C , Malherbe Stephanus T , Cioboata Ramona , Llontop Juan Carlos , Kleynhans Leanie , Lopez Sonia , Santoso Prayudi , Marius Ciontea , Villaizan Katerine , Ruslami Rovina , Walzl Gerhard , Panduru Nicolae Mircea , Dockrell Hazel M , Hill Philip C , Mc Allister Susan , Pearson Fiona , Moore David A J , Critchley Julia A , van Crevel Reinout 
Published: April 2019

Abstract

Background
Diabetes mellitus (DM) increases active tuberculosis (TB) risk and worsens TB outcomes, jeopardizing TB control especially in TB-endemic countries with rising DM prevalence rates. We assessed DM status and clinical correlates in TB patients across settings in Indonesia, Peru, Romania, and South Africa.

Methods
Age-adjusted DM prevalence was estimated using laboratory glycated hemoglobin (HbA1c) or fasting plasma glucose in TB patients. Detailed and standardized sociodemographic, anthropometric, and clinical measurements were made. Characteristics of TB patients with or without DM were compared using multilevel mixed-effect regression models with robust standard errors.

Results
Of 2185 TB patients (median age 36.6 years, 61.2% male, 3.8% human immunodeficiency virus–infected), 12.5% (267/2128) had DM, one third of whom were newly diagnosed. Age-standardized DM prevalence ranged from 10.9% (South Africa) to 19.7% (Indonesia). Median HbA1c in TB–DM patients ranged from 7.4% (Romania) to 11.3% (Indonesia). Compared to those without DM, TB–DM patients were older and had a higher body mass index (BMI) (P value &lt; .05). Compared to those with newly diagnosed DM, TB patients with diagnosed DM had higher BMI and HbA1c, less severe TB, and more frequent comorbidities, DM complications, and hypertension (P value &lt; .05).

Conclusions
We show that DM prevalence and clinical characteristics of TB–DM vary across settings. Diabetes is primarily known but untreated, hyperglycemia is often severe, and many patients with TB–DM have significant cardiovascular disease risk and severe TB. This underlines the need to improve strategies for better clinical management of combined TB and DM.
Preemptive Tecovirimat Use in an Active Duty Service Member Who Presented With Acute Myeloid Leukemia After Smallpox Vaccination
Authors: Lindholm David A , Fisher Raymond D , Montgomery Jay R , Davidson Whitni , Yu Patricia A , Yu Yon C , Burgado Jillybeth , Wilkins Kimberly , Petersen Brett W , Okulicz Jason F 
Published: April 2019

Abstract
Smallpox vaccine is contraindicated in immunosuppression due to increased risk for adverse reactions (eg, progressive vaccinia). We describe the first-ever use of tecovirimat as a preemptive vaccinia virus treatment strategy during induction chemotherapy in an active duty service member who presented with acute leukemia and inadvertent autoinoculation after smallpox vaccination.
Gender and socioeconomic inequalities in the implementation of the Basque programme for multimorbid patients
Authors: Soto-Gordoa Myriam , Arrospide Arantzazu , Millán Eduardo , Calvo Montserrat , Igartua Juan Ignacio , Esnaola Santiago , Ganzarain Jaione , Mar Javier 
Published: April 2019

Abstract

Background
The aim of our study was to increase awareness of the relevance of the implemented programmes to inequity of access and inequality of health by analyzing the impact of a patient-centred strategy for multimorbid patients.

Methods
This retrospective study compared the 2014 multimorbid patient group (intervention group) with its 2012 analogue (control group), before the Department of Health of the Basque Country launched the strategy for managing disease chronicity. Inequalities in healthcare access were represented by differences in the inclusion of patients in the programme and in contacts with primary care (PC) services by gender and socioeconomic status (measured by deprivation index by census track). Likewise, differences in hospital care represented inequalities in health outcomes. Generalized linear models were used to analyze relationships among variables. A propensity score by a genetic matching approach was used to minimize possible selection bias.

Results
At baseline, women had less probability of being eligible for the programme. No clear patterns were seen in resource consumption in PC. The probability of hospitalization was higher for men and increased according to socioeconomic status. The implementation of the programme yielded more contacts with PC services in all groups and a reduction in hospitalizations, especially among men and the most socioeconomically deprived patients.

Conclusion
The patient-centred, integrated-care intervention launched by the Department of Health of the Basque Country might have reduced some gender and socioeconomic inequalities in health outcomes, as it avoided more hospitalizations in subgroups that presented with more episodes of decompensation in the reference year.
Oral anticoagulants usage in Japanese patients aged 18–74 years with non-valvular atrial fibrillation: a retrospective analysis based on insurance claims data
Authors: Ohshima Ayako , Koyama Toshihiro , Ogawa Aiko , Zamami Yoshito , Tanaka Hiroyoshi Y , Kitamura Yoshihisa , Sendo Toshiaki , Hinotsu Shiro , Miller Michael W , Kano Mitsunobu R 
Published: April 2019

Abstract

Background
Oral anticoagulants use has increased rapidly, internationally. Here we look at risks and benefits, based on Japanese data, of therapy with low risk non-valvular atrial fibrillation patients.

Objectives
Using a health insurance claims data set we assessed: (i) oral anticoagulants usage in Japan, and (ii) efficacy and safety of dabigatran compared with warfarin, in Japanese patients with non-valvular atrial fibrillation, aged 18–74 years.

Methods
We identified 4380 non-valvular atrial fibrillation patients treated with anticoagulants between 1 January 2005, and 28 February 2014, and estimated the adjusted hazard ratio for stroke or systemic embolism, and any hemorrhagic event (Cox proportional hazards regression model with stabilized inverse probability treatment weighting).

Results
The data included 101 989 anticoagulant prescriptions for 4380 patients, of which direct oral anticoagulants increased to 40.0% of the total by the end of the study. After applying exclusion criteria, 1536 new non-valvular atrial fibrillation patients were identified, including 1071 treated with warfarin and 465 with dabigatran. Mean ages were 56.11 ± 9.70 years for warfarin, and 55.80 ± 9.65 years for dabigatran. The adjusted hazard ratio (95% confidence interval), comparing dabigatran with warfarin, was 0.48 (0.25–0.91) for stroke or systemic embolism, and 0.91 (0.60–1.39) for any hemorrhage including intracranial and gastrointestinal.

Conclusions
Number of patients prescribed direct oral anticoagulants steadily increased, and incidence of all-cause bleeding related to dabigatran was similar to warfarin, in our study population of younger non-valvular atrial fibrillation patients. Dabigatran, compared with warfarin, generally reduced risk of all-cause stroke and systemic embolism.
TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer
Authors: Carazo Fernando , Campuzano Lucía , Cendoya Xabier , Planes Francisco J , Rubio Angel 
Published: April 2019

Abstract

Background
Aberrant alternative splicing plays a key role in cancer development. In recent years, alternative splicing has been used as a prognosis biomarker, a therapy response biomarker, and even as a therapeutic target. Next-generation RNA sequencing has an unprecedented potential to measure the transcriptome. However, due to the complexity of dealing with isoforms, the scientific community has not sufficiently exploited this valuable resource in precision medicine.

Findings
We present TranscriptAchilles, the first large-scale tool to predict transcript biomarkers associated with gene essentiality in cancer. This application integrates 412 loss-of-function RNA interference screens of &gt;17,000 genes, together with their corresponding whole-transcriptome expression profiling. Using this tool, we have studied which are the cancer subtypes for which alternative splicing plays a significant role to state gene essentiality. In addition, we include a case study of renal cell carcinoma that shows the biological soundness of the results. The databases, the source code, and a guide to build the platform within a Docker container are available at GitLab. The application is also available online.

Conclusions
TranscriptAchilles provides a user-friendly web interface to identify transcript or gene biomarkers of gene essentiality, which could be used as a starting point for a drug development project. This approach opens a wide range of translational applications in cancer.
A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome
Authors: Jiang Justin B , Quattrini Andrea M , Francis Warren R , Ryan Joseph F , Rodríguez Estefanía , McFadden Catherine S 
Published: April 2019

Abstract

Background
More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral “forests,” which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri.

Findings
We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256–448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.

Conclusions
The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.
Risk Factors Associated with the Development of Transaminitis in Oxandrolone-Treated Adult Burn Patients
Authors: Kiracofe Brittany , Zavala Sarah , Gayed Rita M , Foster Charles J , Jones Kendrea M , Oltrogge Pape Kate , Hill David M , Reger Melissa , Porter Kyle , Murphy Claire V 
Published: April 2019

Abstract
Oxandrolone has proven benefits in thermal burn injury and has become a standard of care. Transaminitis is the most frequent side effect of oxandrolone use, although no risk factors have been identified that increase the risk of transaminitis. The objective was to evaluate the frequency of transaminitis while on oxandrolone and to identify risk factors leading to an increased risk of transaminitis in adult burn patients. This multicenter retrospective risk factor analysis compared two patient groups with and without occurrence of transaminitis, which was detected by an aspartate aminotransferase (AST) or alanine aminotransferase (ALT) >100 mg/dL. Secondary outcomes included percentage increase from baseline for AST/ALT, length of stay, and mortality. After univariable analysis, a multivariable logistic regression analysis was performed to detect possible risk factors leading to transaminitis. A total of 309 patients were included, with transaminitis occurring in 128 patients (41.4%) after 13 (interquartile range [IQR] 8–23) days on oxandrolone. After multivariable analysis, age (odds ratio [OR] 0.91; 95% confidence interval [CI] 0.84–0.99 for a 5-year increase in age), intravenous vasopressor use (OR 1.85; 95% CI 1.05–3.27), and amiodarone use (OR 2.51; 95% CI 1.09–5.77) were independent predictors of transaminitis, controlling for TBSA%. Transaminitis was not significantly associated with length of stay or mortality after adjusting for age and TBSA%. We conclude that patients who are younger and have concurrent amiodarone or vasopressor use have the highest risk of developing oxandrolone induced transaminitis and should be monitored closely.
Cold Tolerance of the Tribolium castaneum (Coleoptera: Tenebrionidae), Under Different Thermal Regimes: Impact of Cold Acclimation
Authors: Izadi H , Mohammadzadeh M , Mehrabian M 
Published: April 2019

Abstract
The red flour beetle, Tribolium castaneum (Herbst), is a serious pest of stored product worldwide. Cold tolerance or cold hardiness is an important ecophysiological trait related directly to survival, fitness, and distribution of insects. In this study, the effects of four thermal regimes, i.e., control (C), cold acclimation (CA), rapid cold hardening (RCH), and fluctuating-acclimation (FA), were examined for their effects on cold tolerance, supercooling point (SCP), lower lethal temperature (LLT), and chill-coma recovery time (CCRT) of the red flour beetle. In addition, changes in cryoprotectant (trehalose, sorbitol, and myo-inositol) levels were investigated under each thermal treatment. The results documented a substantial enhancement in the SCP, cold hardiness, and cryoprotectant levels of the adults of T. castaneum under CA regimes. The lowest SCP, highest trehalose and myo-inositol contents, and, subsequently, the greatest survival rate were observed in cold-acclimated beetles. In addition, coordination between cryoprotectant level, SCP, and cold tolerance of the pest was observed. The highest and lowest CCRT were observed at control and CA, respectively. In RCH regime with the highest impact, LLT reached the lowest level of −22°C. As most of the mortality of T. castaneum occurred at a temperature above the SCP, so this pest could be considered as a chill-susceptible insect.
Residual Negative Pressure in Vacuum Blood-Collection Tube and Hemolysis in Pediatric Blood Specimens
Authors: Hu Jing , Zhang Qiao-Xin , Xiao Tong-Tong , Pan Mei-Chen , Cai Ying-Mu 
Published: April 2019

ABSTRACT

Objective
To determine a method to reduce specimen hemolysis rates in pediatric blood specimens.

Methods
A total of 290 blood specimens from pediatric patients were classiﬁed into the capped group or uncapped group. The hemolysis index and levels of lactate dehydrogenase (LDH) were measured using an automated biochemical analyzer. Also, we performed a paired test to measure the concentration of free hemoglobin in specimens from 25 randomly selected healthy adult volunteers, using a direct spectrophotometric technique.

Results
The hemolytic rate of capped specimens was 2-fold higher than that of uncapped specimens. We found significant differences for LDH. Also, there was a significant difference in the concentration of free hemoglobin in the random-volunteers test.

Conclusions
Eliminating the residual negative pressure of vacuum blood-collection tubes was effective at reducing the macrohemolysis and/or microhemolysis rate.