bluuebunny/crossref_metadata_2025_split huggingface dataset:
Randomized multicenter trial of sirolimus vs prednisone as initial therapy for standard-risk acute GVHD: the BMT CTN 1501 trial
Authors: Pidala Joseph , Hamadani Mehdi , Dawson Peter , Martens Michael , Alousi Amin M. , Jagasia Madan , Efebera Yvonne A. , Chhabra Saurabh , Pusic Iskra , Holtan Shernan G. , Ferrara James L. M. , Levine John E. , Mielcarek Marco , Anasetti Claudio , Antin Joseph H. , Bolaños-Meade Javier , Howard Alan , Logan Brent R. , Leifer Eric S. , Pritchard Theresa S. , Horowitz Mary M. , MacMillan Margaret L. 
Published: November 2019

Abstract
Clinical- and biomarker-based tools may identify a lower-risk acute graft-versus-host disease (GVHD) population amenable to novel, reduced-intensity treatments. Previous data suggest sirolimus may rival standard of care prednisone. We conducted a National Heart, Lung, and Blood Institute/National Cancer Institute-funded Blood and Marrow Transplant Clinical Trials Network multicenter, open-label, randomized phase 2 trial to estimate the difference in day 28 complete response (CR)/partial response (PR) rates for sirolimus vs prednisone as initial treatment of patients with standard risk (SR) acute GVHD as defined by the Minnesota (MN) GVHD Risk Score and Ann Arbor (AA1/2) biomarker status. A total of 127 MN-SR patients were randomized (1:1), and 122 were AA1/2 (sirolimus, n = 58; prednisone, n = 64). Others were AA3 (n = 4), or AA status missing (n = 1). The day 28 CR/PR rates were similar for sirolimus 64.8% (90% confidence interval [CI], 54.1%-75.5%) vs 73% (90% CI, 63.8%-82.2%) for prednisone. The day 28 rate of CR/PR with prednisone ≤0.25 mg/kg/day was significantly higher for sirolimus than prednisone (66.7% vs 31.7%; P &lt; .001). No differences were detected in steroid-refractory acute GVHD, disease-free survival, relapse, nonrelapse mortality, or overall survival. Sirolimus was associated with reduced steroid exposure and hyperglycemia, reduced grade 2 to 3 infections, improvement in immune suppression discontinuation and patient-reported quality of life, and increased risk for thrombotic microangiopathy. For patients with clinical- and biomarker-based SR acute GVHD, sirolimus demonstrates similar overall initial treatment efficacy as prednisone. In addition, sirolimus therapy spares steroid exposure and allied toxicity, does not compromise long-term survival outcomes, and is associated with improved patient-reported quality of life. This trial was registered at www.clinicaltrials.gov as #NCT02806947.
Recombinant human milk fat globule-EGF factor VIII (rhMFG-E8) as a therapy for sepsis after acute exposure to alcohol
Authors: Chaung Wayne W. , Brenner Max , Yen Hao-Ting , Ochani Mahendar L. , Jacob Asha , Wang Ping 
Published: November 2019

Abstract
Background
Alcohol intake predisposes to infections and sepsis. Alcohol and sepsis inhibit the expression of milk fat globule epidermal growth factor-factor VIII (MFG-E8), a glycoprotein essential for optimal efferocytosis, resulting in the release of proinflammatory molecules and increased sepsis severity. We previously reported that recombinant mouse (rm) MFG-E8 attenuates sepsis-induced organ injury in rats with acute alcohol intoxication. In order to develop a therapy that can be safely used in humans, we have produced recombinant human (rh) MFG-E8 and evaluated its efficacy to ameliorate sepsis after acute exposure to alcohol.

Methods
We induced acute alcohol intoxication with a bolus injection of alcohol (1.75 g/kg BW) followed by an intravenous infusion of 300 mg/kg/h alcohol for 10 h. Sepsis was then induced by cecal ligation and puncture (CLP). At -10, 0, and 10 h relative to CLP, rats received MFG-E8 or vehicle (albumin) intravenously. Animals were euthanized at 20 h after CLP for blood and tissue collection. Additional groups of animals were used for a survival study.

Results
Compared to vehicle, rhMFG-E8 treatment ameliorated blood levels of proinflammatory cytokines (% improvement: TNF-α 49.8%, IL-6 34.7%) and endotoxin (61.7%), as well as of transaminases (AST 36.2%, ALT 40.1%) and lactate (18.4%). Rats treated with rhMFG-E8 also had a significant histological attenuation of the acute lung injury, as well as a reduction in the number of apoptotic cells in the thymus (43.4%) and cleaved caspase 3 (38.7%) in the spleen. In addition, rhMFG-E8 improved the 10-day sepsis survival rate from 45 to 80%

Conclusion
rhMFG-E8 significantly ameliorated sepsis in rats with acute alcohol exposure, demonstrating rhMFG-E8’s potential to be developed as an effective therapy for sepsis in alcohol abusers.
Comparison of blood lipid profile/thyroid function markers between unipolar and bipolar depressed patients and in depressed patients with anhedonia or suicidal thoughts
Authors: Su Meilei , Li Enze , Tang Chong , Zhao Yongzhi , Liu Ruqing , Gao Keming 
Published: November 2019

Abstract
Background
This study aimed to investigate the differences in the serum levels of glucose, lipid, and thyroid function markers between unipolar and bipolar depressed patients, as well as the effect of anhedonia and suicidal thoughts on the levels of these biochemical parameters.

Methods
A total of 287 unmedicated depressed patients from January 2016 to December 2017 were included in this study, including 92 bipolar depressions and 195 unipolar depressions. Anhedonia was determined using the item 32 of Symptom Checklist (SCL-90). Suicide ideation was assessed by item 15 of SCL-90.

Results
The bipolar group had significantly lower lipid levels (including triglycerides, cholesterol, low-density lipoprotein cholesterol [LDL], very low-density lipoprotein cholesterol [VLDL]) and insulin resistance index but higher levels of prolactin, low triiodothyronine (T3) and free T3 (FT3) as well as higher incidence of anhedonia as compared with the unipolar group. Depressed patients with anhedonia had significantly higher LDL level than those without anhedonia. Depressed patients with suicidal thoughts had cholesterol and high-density lipoprotein cholesterol (HDL) level. The above-mentioned differences were confirmed by logistic regression analysis. Receiver operating characteristic curve (ROC) analysis showed that the area under the ROC curve (AUC) ranged from 0.546 to 0.685.

Conclusion
Triglycerides, cholesterol, LDL, VLDL T3, FT3 levels were significantly different between unipolar and bipolar depressed patients, which might have the potential to be the markers for differential diagnosis. Patients with anhedonia had lower LDL level, while patients with suicidal thoughts had higher levels of cholesterol and HDL as compared with the corresponding control groups.
Functional connectivity studies in migraine: what have we learned?
Authors:   European Headache Federation School of Advanced Studies (EHF-SAS), Skorobogatykh Kirill , van Hoogstraten Willem Sebastiaan , Degan Diana , Prischepa Anastasia , Savitskaya Anastasya , Ileen Biondo Michela , Bentivegna Enrico , Skiba Iaroslav , D’Acunto Laura , Ferri Livia , Sacco Simona , Hansen Jakob Møller , Amin Faisal Mohammad 
Published: November 2019

Abstract
Background
Resting-state functional connectivity (FC) MRI has widely been used to understand migraine pathophysiology and to identify an imaging marker of the disorder. Here, we review what we have learned from FC studies.

Methods
We performed a literature search on the PubMed website for original articles reporting data obtained from conventional resting-state FC recording in migraine patients compared with healthy controls or during and outside of migraine attacks in the same patients.

Results
We found 219 articles and included 28 in this review after screening for inclusion and exclusion criteria. Twenty-five studies compared migraine patients with healthy controls, whereas three studies investigated migraine patients during and outside of attacks. In the studies of interictal migraine more alterations of more than 20 FC networks (including amygdala, caudate nucleus, central executive, cerebellum, cuneus, dorsal attention network, default mode, executive control, fronto-parietal, hypothalamus, insula, neostriatum, nucleus accumbens, occipital lobe, periaqueductal grey, prefrontal cortex, salience, somatosensory cortex I, thalamus and visual) were reported. We found a poor level of reproducibility and no migraine specific pattern across these studies.

Conclusion
Based on the findings in the present review, it seems very difficult to extract knowledge of migraine pathophysiology or to identify a biomarker of migraine. There is an unmet need of guidelines for resting-state FC studies in migraine, which promote the use of homogenous terminology, public availability of protocol and the a priori hypothesis in line with for instance randomized clinical trial guidelines.
Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging
Authors: Qin Hong 
Published: November 2019

Abstract
Background
Cellular aging is best studied in the budding yeast Saccharomyces cerevisiae. As an example of a pleiotropic trait, yeast lifespan is influenced by hundreds of interconnected genes. However, no quantitative methods are currently available to infer system-level changes in gene networks during cellular aging.

Results
We propose a parsimonious mathematical model of cellular aging based on stochastic gene interaction networks. This network model is made of only non-aging components: the strength of gene interactions declines with a constant mortality rate. Death of a cell occurs in the model when an essential node loses all of its interactions with other nodes, and is equivalent to the deletion of an essential gene. Stochasticity of gene interactions is modeled using a binomial distribution. We show that the exponential increase of mortality rate over time can emerge from this gene network model during the early stages of aging.We developed a maximal likelihood approach to estimate three lifespan-influencing network parameters from experimental lifespans: t0, the initial virtual age of the network system; n, the average lifespan-influencing interactions per essential node; and R, the initial mortality rate. We applied this model to yeast mutants with known effects on replicative lifespans. We found that deletion of SIR2, FOB1, and HXK2 considerably altered the initial virtual age but not the average lifespan-influencing interactions per essential node, suggesting that these mutations mainly influence the reliability of gene interactions but not the overall configurations of gene networks.We applied this model to investigate replicative lifespans of yeast natural isolates. We estimated that the average number of lifespan-influencing interactions per essential node is 7.0 (6.1–8) and the average estimated initial virtual age is 45.4 (30.6–74) cell divisions in these isolates. We also found that t0 could potentially mediate the observed Strehler-Mildvan correlation in yeast natural isolates.

Conclusions
Our theoretical model provides a parsimonious interpretation of experimental lifespan data from the perspective of gene networks. We hope that our work will stimulate more interest in developing network models to study aging as a pleiotropic trait.
Molecular cloning and characterization of a grapevine (Vitis vinifera L.) serotonin N-acetyltransferase (VvSNAT2) gene involved in plant defense
Authors: Yu Yihe , Bian Lu , Jiao Zeling , Yu Keke , Wan Yutong , Zhang Guohai , Guo Dalong 
Published: November 2019

AbstractBackgroundMelatonin is a ubiquitous molecule and exists across kingdoms. Studies on melatonin in plants have mainly focused on its physiological influence on growth and development, and on its biosynthesis. A number of studies have been conducted on the melatonin content and exogenous melatonin treatment of grapevine (Vitis viniferaL.). However, key genes or enzymes of the melatonin biosynthetic pathway remain unclear.ResultsIn this study, we cloned and identified the gene encoding serotoninN-acetyltransferase (SNAT) in grapevine (VvSNAT2).The VvSNAT2 protein was identified from a collection of 30 members of the grapevine GCN5-relatedN-acetyltransferase (GNAT) superfamily. Phylogenetic and protein sublocalization analyses showed that the candidate geneVvGNAT16isVvSNAT2. Characterization of VvSNAT2 showed that its enzymatic activity is highest at a pH of 8.8 and a temperature of 45 °C. Analysis of enzyme kinetics showed the values ofKmandVmaxof VvSNAT2 using serotonin were 392.5 μM and 836 pmol/min/mg protein, respectively. The expression of VvSNAT2 was induced by melatonin treatment and pathogen inoculation. Overexpression ofVvSNAT2in Arabidopsis resulted in greater accumulation of melatonin and chlorophyll and enhanced resistance to powdery mildew in the transgenic plants compared with the wild type (WT). Additionally, our data showed that the marker genes in the salicylic acid (SA) signaling pathway were expressed to higher levels in the transgenic plants compared with the WT.ConclusionsTheVvSNAT2gene was cloned and identified in grapevine for the first time. Our results indicate thatVvSNAT2overexpression activates the SA and JA signaling pathways; however, the SA pathway plays a central role inVvSNAT2-mediated plant defense.
Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa
Authors: Guerra Fernando P. , Suren Haktan , Holliday Jason , Richards James H. , Fiehn Oliver , Famula Randi , Stanton Brian J. , Shuren Richard , Sykes Robert , Davis Mark F. , Neale David B. 
Published: November 2019

AbstractBackgroundPopulus trichocarpais an important forest tree species for the generation of lignocellulosic ethanol. Understanding the genomic basis of biomass production and chemical composition of wood is fundamental in supporting genetic improvement programs. Considerable variation has been observed in this species for complex traits related to growth, phenology, ecophysiology and wood chemistry. Those traits are influenced by both polygenic control and environmental effects, and their genome architecture and regulation are only partially understood. Genome wide association studies (GWAS) represent an approach to advance that aim using thousands of single nucleotide polymorphisms (SNPs). Genotyping using exome capture methodologies represent an efficient approach to identify specific functional regions of genomes underlying phenotypic variation.ResultsWe identified 813 K SNPs, which were utilized for genotyping 461P. trichocarpaclones, representing 101 provenances collected from Oregon and Washington, and established in California. A GWAS performed on 20 traits, considering single SNP-marker tests identified a variable number of significant SNPs (p-value < 6.1479E-8) in association with diameter, height, leaf carbon and nitrogen contents, and δ15N. The number of significant SNPs ranged from 2 to 220 per trait. Additionally, multiple-marker analyses by sliding-windows tests detected between 6 and 192 significant windows for the analyzed traits. The significant SNPs resided within genes that encode proteins belonging to different functional classes as such protein synthesis, energy/metabolism and DNA/RNA metabolism, among others.ConclusionsSNP-markers within genes associated with traits of importance for biomass production were detected. They contribute to characterize the genomic architecture ofP. trichocarpabiomass required to support the development and application of marker breeding technologies.
Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul
Authors: Kahraman Kadriye , Lucas Stuart James 
Published: November 2019

Abstract
Background
Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar ‘Tombul’ with multiple annotation tools.

Results
Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales.

Conclusion
In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.
The ABA-induced soybean ERF transcription factor gene GmERF75 plays a role in enhancing osmotic stress tolerance in Arabidopsis and soybean
Authors: Zhao Meng-Jie , Yin Li-Juan , Liu Ying , Ma Jian , Zheng Jia-Cheng , Lan Jin-Hao , Fu Jin-Dong , Chen Ming , Xu Zhao-Shi , Ma You-Zhi 
Published: November 2019

Abstract
Background
Ethylene-responsive factors (ERFs) play important roles in plant growth and development and the response to adverse environmental factors, including abiotic and biotic stresses.

Results
In the present study, we identified 160 soybean ERF genes distributed across 20 chromosomes that could be clustered into eight groups based on phylogenetic relationships. A highly ABA-responsive ERF gene, GmERF75, belonging to Group VII was further characterized. Subcellular localization analysis showed that the GmERF75 protein is localized in the nucleus, and qRT-PCR results showed that GmERF75 is responsive to multiple abiotic stresses and exogenous hormones. GmERF75-overexpressing Arabidopsis lines showed higher chlorophyll content compared to WT and mutants under osmotic stress. Two independent Arabidopsis mutations of AtERF71, a gene homologous to GmERF75, displayed shorter hypocotyls, and overexpression of GmERF75 in these mutants could rescue the short hypocotyl phenotypes. Overexpressing GmERF75 in soybean hairy roots improved root growth under exogenous ABA and salt stress.

Conclusions
These results suggested that GmERF75 is an important plant transcription factor that plays a critical role in enhancing osmotic tolerance in both Arabidopsis and soybean.
The influences of morphine or ketamine pre-treatment on hemodynamic, acid-base status, biochemical markers of brain damage and early survival in rats after asphyxial cardiac arrest
Authors: Kuklin Vladimir , Akhatov Nurlan , Kondratiev Timofei , Konkayev Aidos , Baigenzhin Abai , Konkayeva Maiya , Karibekov Temirlan , Barlow Nicholas , Tveita Torkjel , Dahl Vegard 
Published: November 2019

Abstract
Background
In different models of hypoxia, blockade of opioid or N-methyl-D-aspartate (NMDA) receptors shows cardio- and neuroprotective effects with a consequent increase in animal survival. The aim of the study was to investigate effects of pre-treatment with Morphine or Ketamine on hemodynamic, acid-base status, early survival, and biochemical markers of brain damage in a rat model of asphyxial cardiac arrest (ACA).

Methods
Under anaesthesia with Thiopental Sodium 60 mg/kg, i.p., Wistar rats (n = 42) were tracheostomized and catheters were inserted in a femoral vein and artery. After randomization, the rats were pre-treated with: Morphine 5 mg/kg i.v. (n = 14); Ketamine 40 mg/kg i.v. (n = 14); or equal volume of i.v. NaCl 0.9% as a Control (n = 14). ACA was induced by corking of the tracheal tube for 8 min, and defined as a mean arterial pressure (MAP) < 20 mmHg. Resuscitation was started at 5 min after cardiac arrest (CA). Invasive MAP was recorded during experiments. Arterial pH and blood gases were sampled at baseline (BL) and 10 min after CA. At the end of experiments, all surviving rats were euthanised, brain and blood samples for measurement of Neuron Specific Enolase (NSE), s100 calcium binding protein B (s100B) and Caspase-3 (CS-3) were retrieved.

Results
At BL no differences between groups were found in hemodynamic or acid-base status. After 3 min of asphyxia, all animals had cardiac arrest (CA). Return of spontaneous circulation (MAP > 60 mmHg) was achieved in all animals within 3 min after CA. At the end of the experiment, the Ketamine pre-treated group had increased survival (13 of 14; 93%) compared to the Control (7 of 14; 50%) and Morphine (10 of 14; 72%) groups (p = 0.035). Biochemical analysis of plasma concentration of NSE and s100B as well as an analysis of CS-3 levels in the brain tissue did not reveal any differences between the study groups.

Conclusion
In rats after ACA, pre-treatment with Morphine or Ketamine did not have any significant influence on hemodynamic and biochemical markers of brain damage. However, significantly better pH level and increased early survival were found in the Ketamine pre-treated group.
Elevated blood pressure level based on 2017 ACC/AHA guideline in relation to stroke risk in rural areas of Liaoning province
Authors: Xie Yanxia , Ma Mingfeng , Li Zhao , Guo Xiaofan , Sun Guozhe , Sun Zhaoqing , Zheng Jia , Sun Yingxian , Zheng Liqiang 
Published: November 2019

Abstract
Background
The new ACC/AHA hypertension guideline lower the definition of hypertension from 140/90 mmHg to 130/80 mmHg and eliminate the category of prehypertension thus increasing the prevalence of hypertension. A purpose of this study is to explore the applicability of the new guidelines in rural China.

Methods
In total, 3229 participants aged ≥35 years and free of stroke at baseline were followed for up to 4.8 years during 2012 to 2017 in a rural community-based prospective cohort study of Xifeng County. The hazard ratio (HR) and 95% Confidence interval (CI) of different blood pressure (BP) levels for risk of incident stroke were analyzed by multivariable Cox proportional hazard models.

Results
During the follow-up, 81 new strokes occurred among the 3229 participants. Compared with normal BP (Systolic BP (SBP)<120 mmHg and Diastolic BP (DBP)<80 mmHg), stage 2 hypertension (SBP ≥ 140 mmHg or DBP ≥ 90 mmHg) had approximately 2.1 greater risks for stroke (HR: 2.10, 95% CI: 1.13 to 3.91, P = 0.020). However, there was no significant association between elevated (SBP:120-129 mmHg and DBP<80 mmHg), stage1 hypertension (SBP:130-139 mmHg or DBP:80-89 mmHg) and stroke incidence (HR: 0.93, 95% CI: 0.33 to 2.61, P = 0.888; HR: 0.96, 95% CI: 0.46 to 2.02, P = 0.920, respectively). An increase of the SBP by 1-SD increases the risk for stroke by 56% (HR: 1.56, 95%CI: 1.29 to 1.88, P < 0.001). An increase of the SBP by 20 mmHg increases the risk for stroke by 51% (HR: 1.51, 95%CI: 1.27 to 1.80, P < 0.001).

Conclusions
Compared with normal BP, the stage 2 hypertension based on 2017 ACC/AHA guideline significantly increases the risk of stroke incidence, but this association was not observed between elevated, stage1 hypertension and stroke incidence in Chinese rural adults.