bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq
Authors: Feng Xiu , Jia Yintao , Zhu Ren , Chen Kang , Chen Yifeng 
Published: June 2019

AbstractThe lakes on the Qinghai-Tibet Plateau (QTP) are the largest and highest lake group in the world. Gymnocypris selincuoensis is the only cyprinid fish living in lake Selincuo, the largest lake on QTP. However, its genetic resource is still blank, limiting studies on molecular and genetic analysis. In this study, the transcriptome of G. selincuoensis was first generated by using PacBio Iso-Seq and Illumina RNA-seq. A full-length (FL) transcriptome with 75,435 transcripts was obtained by Iso-Seq with N50 length of 3,870 bp. Among all transcripts, 75,016 were annotated to public databases, 64,710 contain complete open reading frames and 2,811 were long non-coding RNAs. Based on all- vs.-all BLAST, 2,069 alternative splicing events were detected, and 80% of them were validated by reverse transcription polymerase chain reaction (RT-PCR). Tissue gene expression atlas showed that the number of detected expressed transcripts ranged from 37,397 in brain to 19,914 in muscle, with 10,488 transcripts detected in all seven tissues. Comparative genomic analysis with other cyprinid fishes identified 77 orthologous genes with potential positive selection (Ka/Ks > 0.3). A total of 56,696 perfect simple sequence repeats were identified from FL transcripts. Our results provide valuable genetic resources for further studies on adaptive evolution, gene expression and population genetics in G. selincuoensis and other congeneric fishes.
Efficacy and safety of alirocumab and evolocumab: a systematic review and meta-analysis of randomized controlled trials
Authors: Guedeney Paul , Giustino Gennaro , Sorrentino Sabato , Claessen Bimmer E , Camaj Anton , Kalkman Deborah N , Vogel Birgit , Sartori Samantha , De Rosa Salvatore , Baber Usman , Indolfi Ciro , Montalescot Gilles , Dangas George D , Rosenson Robert S , Pocock Stuart J , Mehran Roxana 
Published: June 2019

Abstract

Aims
The effect of low-density lipoprotein cholesterol-lowering therapy with alirocumab or evolocumab on individual clinical efficacy and safety endpoints remains unclear. We aimed to evaluate the efficacy and safety of alirocumab and evolocumab in patients with dyslipidaemia or atherosclerotic cardiovascular disease.

Methods and results
We performed a review of randomized controlled trials (RCTs) comparing treatment with alirocumab or evolocumab vs. placebo or other lipid-lowering therapies up to March 2018. Primary efficacy endpoints were all-cause death, cardiovascular death, myocardial infarction (MI), and stroke. We estimated risk ratios (RR) and 95% confidence intervals (CI) using random effect models. We included 39 RCTs comprising 66 478 patients of whom 35 896 were treated with proprotein convertase subtilisin–kexin type 9 (PCSK9) inhibitors (14 639 with alirocumab and 21 257 with evolocumab) and 30 582 with controls. Mean weighted follow-up time across trials was 2.3 years with an exposure time of 150 617 patient-years. Overall, the effects of PCSK9 inhibition on all-cause death and cardiovascular death were not statistically significant (P = 0.15 and P = 0.34, respectively). Proprotein convertase subtilisin–kexin type 9 inhibitors were associated with lower risk of MI (1.49 vs. 1.93 per 100 patient-year; RR 0.80, 95% CI 0.74–0.86; I 2 = 0%; P &lt; 0.0001), ischaemic stroke (0.44 vs. 0.58 per 100 patient-year; RR 0.78, 95% CI 0.67–0.89; I 2 = 0%; P = 0.0005), and coronary revascularization (2.16 vs. 2.64 per 100 patient-year; RR 0.83, 95% CI 0.78–0.89; I 2 = 0%; P &lt; 0.0001), compared with the control group. Use of these PCSK9 inhibitors was not associated with increased risk of neurocognitive adverse events (P = 0.91), liver enzymes elevations (P = 0.34), rhabdomyolysis (P = 0.58), or new-onset diabetes mellitus (P = 0.97).

Conclusion
Proprotein convertase subtilisin–kexin type 9 inhibition with alirocumab or evolocumab was associated with lower risk of MI, stroke, and coronary revascularization, with favourable safety profile.
Effects of synbiotics on the gut microbiota, blood and rearing parameters of chickens
Authors: Śliżewska Katarzyna , Markowiak Paulina , Żbikowski Artur , Szeleszczuk Piotr 
Published: June 2019

ABSTRACT
The aim of the study was to assess the safety of three newly developed synbiotic preparations in feeding chickens. The study was carried out on 84 Specific Pathogen Free chickens, between 1st and 21st day of their life. Animals were divided into four groups fed ad libitum: three with an addition of synbiotics A, B or C and a control group (feed with no additives). Synbiotics contained Lactobacillus, Saccharomyces cerevisiae and inulin (prebiotic). Rearing parameters were determined taking into account undesirable clinical and sectional symptoms, daily mortality and body weight of birds. In addition, chicken blood parameters were determined based on haematological, biochemical and serological tests. Samples of the intestinal content and of the excreta constituted a material for research aimed at determination of the dominant chicken gut microbiota. On the basis of the conducted investigation, it was found that synbiotics met the basic requirements for this type of formulas regarding the safety of use and had a positive effect on the health of chickens. Therefore, further research is being carried out on the application of these formulas in large-scale production. The next step of the research will be the comparison of effects of synbiotics with commercial probiotics.
Within-Patch Structures Influence Small Mammal Abundance in Managed Forests of Northern California, USA
Authors: Gray Steven M , Roloff Gary J , Dennhardt Andrew J , Dotters Brian P , Engstrom Thomas T 
Published: June 2019

AbstractWe evaluated how forest type, vegetation structure in trapping webs, and proximate forest types influenced localized (~6.35 hectares) abundances for commonly captured small mammals in northern California, USA. We trapped from May to August of 2011–13 in 69 forest patches that represented: (1) clearcuts (3–5 years postharvest), (2) 10–20 year-old conifer plantations, (3) rotation-aged conifer stands, and (4) Watercourse and Lake Protection Zones. We captured 11 species; four in sufficient numbers for regression modeling. Our average abundance estimates for the study were 4.57 (standard error [SE] = 0.43), 0.32 (SE = 0.11), 0.90 (SE = 0.30), and 0.25 (SE = 0.09) individuals per web location (~0.75 hectares) for Peromyscus spp., Neotoma spp., California ground squirrels, and Allen’s chipmunks. We found that web-level ground cover (shrubs and grass), downed wood, and types of forests containing our trapping webs best described small mammal abundances, whereas proximate forest types were not important. Our results indicated that retaining localized structures in the form of understory shrub cover and downed wood positively influences small mammal abundance in intensively managed forests of northern California.
The Role of Gene Conversion between Transposable Elements in Rewiring Regulatory Networks
Authors: Fawcett Jeffrey A , Innan Hideki 
Published: June 2019

AbstractNature has found many ways to utilize transposable elements (TEs) throughout evolution. Many molecular and cellular processes depend on DNA-binding proteins recognizing hundreds or thousands of similar DNA motifs dispersed throughout the genome that are often provided by TEs. It has been suggested that TEs play an important role in the evolution of such systems, in particular, the rewiring of gene regulatory networks. One mechanism that can further enhance the rewiring of regulatory networks is nonallelic gene conversion between copies of TEs. Here, we will first review evidence for nonallelic gene conversion in TEs. Then, we will illustrate the benefits nonallelic gene conversion provides in rewiring regulatory networks. For instance, nonallelic gene conversion between TE copies offers an alternative mechanism to spread beneficial mutations that improve the network, it allows multiple mutations to be combined and transferred together, and it allows natural selection to work efficiently in spreading beneficial mutations and removing disadvantageous mutations. Future studies examining the role of nonallelic gene conversion in the evolution of TEs should help us to better understand how TEs have contributed to evolution.
Audiometric Age-Related Hearing Loss and Cognition in the Hispanic Community Health Study
Authors: Golub Justin S , Brickman Adam M , Ciarleglio Adam J , Schupf Nicole , Luchsinger José A 
Published: June 2019

Abstract

Background
Age-related hearing loss (HL), a common and treatable condition, has been associated with other age-related conditions. Late life cognitive impairment is a major public health concern that is rarely treatable. Studies examining the relationship between HL and cognition have been limited by non-Hispanic cohorts, small samples, or limited confounding control. We overcome these limitations in a large Hispanic cohort.

Methods
This was a multisite cross-sectional study of 5,277 subjects at least 50 years old (Hispanic Community Health Study, HCHS). The main exposure was audiometric HL. The main outcome measure was neurocognitive performance ascertained by the Digit Symbol Substitution Test (DSST), Word Frequency Test, Spanish-English Verbal Learning Test (SEVLT), and Six-Item Screener.

Results
The mean age was 58.4 years (SD = 6.2). A 20-dB (equivalent to a one-category worsening) increase in HL was associated with a −1.53 (95% CI, −2.11, −0.94) raw score point difference in the DSST, adjusting for demographics, hearing aid use, and cardiovascular disease. Similarly, a 20-dB increase in HL was associated with a −0.86 (−1.23, −0.49) point difference on the Word Frequency Test, −0.76 (−1.04, −0.47) on the SEVLT 3 trials, −0.45 (−0.60, −0.29) on the SELVT recall, and −0.07 (−0.12, −0.02) on the Six-Item Screener.

Conclusions
In the largest study of formal, audiometric HL and cognition to date, HL was independently associated with worse performance in a range of neurocognitive measures. Because HL is common and potentially treatable, it should be investigated as a modifiable risk factor for neurocognitive decline and dementia.
GenPipes: an open-source framework for distributed and scalable genomic analyses
Authors: Bourgey Mathieu , Dali Rola , Eveleigh Robert , Chen Kuang Chung , Letourneau Louis , Fillon Joel , Michaud Marc , Caron Maxime , Sandoval Johanna , Lefebvre Francois , Leveque Gary , Mercier Eloi , Bujold David , Marquis Pascale , Van Patrick Tran , Anderson de Lima Morais David , Tremblay Julien , Shao Xiaojian , Henrion Edouard , Gonzalez Emmanuel , Quirion Pierre-Olivier , Caron Bryan , Bourque Guillaume 
Published: June 2019

Abstract

Background
With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing.

Findings
Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences long-read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has already been configured on several servers, and a Docker image is also available to facilitate additional installations.

Conclusions
GenPipes offers genomics researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
Genetic approaches to the treatment of inherited neuromuscular diseases
Authors: Ravi Bhavya , Antonellis Anthony , Sumner Charlotte J , Lieberman Andrew P 
Published: June 2019

Abstract
Inherited neuromuscular diseases are a heterogeneous group of developmental and degenerative disorders that affect motor unit function. Major challenges toward developing therapies for these diseases include heterogeneity with respect to clinical severity, age of onset and the primary cell type that is affected (e.g. motor neurons, skeletal muscle and Schwann cells). Here, we review recent progress toward the establishment of genetic therapies to treat inherited neuromuscular disorders that affect both children and adults with a focus on spinal muscular atrophy, Charcot–Marie–Tooth disease and spinal and bulbar muscular atrophy. We discuss clinical features, causative mutations and emerging approaches that are undergoing testing in preclinical models and in patients or that have received recent approval for clinical use. Many of these efforts employ antisense oligonucleotides to alter pre-mRNA splicing or diminish target gene expression and use viral vectors to replace expression of mutant genes. Finally, we discuss remaining challenges for optimizing the delivery and effectiveness of these approaches. In sum, therapeutic strategies for neuromuscular diseases have shown encouraging results, raising hope that recent strides will translate into significant clinical benefits for patients with these disorders.
Fostering the growth of student start-ups from university accelerators: an entrepreneurial ecosystem perspective
Authors: Breznitz Shiri M , Zhang Qiantao 
Published: June 2019

AbstractDespite their significance, firms created by students have been the subject of little research. Adopting the entrepreneurial ecosystem framework, this paper examines the growth of student start-ups, especially those that participate in university accelerators. Focused on the University of Toronto, this paper contributes to an understanding of how university accelerators can better support the entrepreneurial efforts of students. It is clear that firms that participate in accelerators with a screening process have a stronger performance in both employment and product growth. Moreover, a habitual entrepreneur director or a more intensive accelerator program is found to have more positive effects on product growth at firms than on employment growth.
Reflection on modern methods: when worlds collide—prediction, machine learning and causal inference
Authors: Blakely Tony , Lynch John , Simons Koen , Bentley Rebecca , Rose Sherri 
Published: June 2019

AbstractCausal inference requires theory and prior knowledge to structure analyses, and is not usually thought of as an arena for the application of prediction modelling. However, contemporary causal inference methods, premised on counterfactual or potential outcomes approaches, often include processing steps before the final estimation step. The purposes of this paper are: (i) to overview the recent emergence of prediction underpinning steps in contemporary causal inference methods as a useful perspective on contemporary causal inference methods, and (ii) explore the role of machine learning (as one approach to ‘best prediction’) in causal inference. Causal inference methods covered include propensity scores, inverse probability of treatment weights (IPTWs), G computation and targeted maximum likelihood estimation (TMLE). Machine learning has been used more for propensity scores and TMLE, and there is potential for increased use in G computation and estimation of IPTWs.
Minimal Generators of Hall Algebras of 1-cyclic Perfect Complexes
Authors: Zhang Haicheng 
Published: June 2019

AbstractLet $A$ be the path algebra of a Dynkin quiver over a finite field, and let $C_1(\mathscr{P})$ be the category of 1-cyclic complexes of projective $A$-modules. In the present paper, we give a PBW-basis and a minimal set of generators for the Hall algebra ${\mathcal{H}}\,(C_1(\mathscr{P}))$ of $C_1(\mathscr{P})$. Using this PBW-basis, we firstly prove the degenerate Hall algebra of $C_1(\mathscr{P})$ is the universal enveloping algebra of the Lie algebra spanned by all indecomposable objects. Secondly, we calculate the relations among the generators in ${\mathcal{H}}\,(C_1(\mathscr{P}))$, and obtain quantum Serre relations in a quotient of certain twisted version of ${\mathcal{H}}\,(C_1(\mathscr{P}))$. Moreover, we establish relations between the degenerate Hall algebra, twisted Hall algebra of $A$ and those of $C_1(\mathscr{P})$, respectively.
Effects of dietary exogenous fibrolytic enzymes on ruminal fermentation characteristics of beef steers fed high- and low-quality growing diets1
Authors: Kondratovich Lucas B , Sarturi Jhones O , Hoffmann Carly A , Ballou Michael A , Trojan Sara J , Campanili Pedro R B 
Published: June 2019

AbstractThe effects of dietary pretreatment with fibrolytic enzyme-based cocktail were evaluated in 2 studies: (1) in vitro true digestibility; and (2) intake, digestibility, feeding behavior, and ruminal fermentation of beef steers fed growing diets. For the in vitro assessment, the ruminal inoculum was collected from 2 steers (BW = 543 ± 45 kg; 4-h after feeding; growing diets) and enzymes included or not (Trichoderma reesei fermentation extract; 0.75 µL/g of substrate DM). Within in vitro batches (n = 4), 12 substrates were incubated and in vitro true nutrient digestibility was evaluated. For study 2, 5 ruminally cannulated beef steers (BW = 520 ± 30 kg) were used in a 5 × 4 unbalanced Latin square using a 2 × 2 factorial arrangement of treatments: (a) diet quality (high = HQ; and low = LQ) and (b) enzyme inclusion (0 or 0.75 mL/kg of diet DM). Steers were fed ad libitum during four 21-d periods consisting of 14-d of adaptation and 7-d of collections. An enzyme × substrate was observed (P < 0.01), in which DM, OM, and NDF disappearance of sorghum grain increased with enzymes addition. Addition of enzymes increased (P < 0.01) ADF digestibility for all substrates. No diet quality × enzyme (P ≥ 0.18) was observed for intake variables in study 2. Enzyme-fed steers increased (P ≤ 0.05) intake of DM, digestible DM, NDF, and ADF compared with steers not fed fibrolytic enzymes. Addition of enzyme did not affect (P ≥ 0.28) apparent total tract digestibility of beef steers. Steers fed HQ diets consumed more (P ≤ 0.04) DM, digestible DM and OM, and less (P ≤ 0.03) total and digestible fiber than steers fed LQ diets. Ruminal pH average decreased (P = 0.01) for steers fed HQ or enzyme-fed diets compared with other treatments. A tendency (P = 0.06) toward improved total VFA was observed on enzyme-fed steers with HQ diets, but not for LQ diets. The molar proportion of ruminal propionate increased (P = 0.01) when steers were fed enzyme. Steers fed HQ diets had greater (P < 0.01) propionate and valerate molar proportions, lower (P < 0.01) acetate and acetate:propionate ratio than steers fed LQ diets. In vitro methane and total gas production were not affected (P ≥ 0.50) by dietary treatments. Fibrolytic enzymes positively affected digestion of multiple roughage sources commonly fed to cattle and might have additional benefit when used on unprocessed sorghum grain. Fibrolytic enzymes in beef cattle growing diets stimulated intake and generated positive impacts on ruminal fermentation.
Surrounding Vegetation, Climatic Elements, and Predators Affect the Spatial Dynamics of Bemisia tabaci (Hemiptera: Aleyrodidae) in Commercial Melon Fields
Authors: Felicio Thiago Nunes Pinto , Costa Thiago Leandro , Sarmento Renato Almeida , Ramos Rodrigo Soares , Pereira Poliana Silvestre , da Silva Ricardo Siqueira , Picanço Marcelo Coutinho 
Published: June 2019

Abstract
Studying the spatial dynamics of pests allows the determination of abiotic and biotic factors affecting time and locations of pest attack to the crops. Such abiotic and biotic factors mainly include 1) climatic elements, 2) natural enemies, 3) phenological stage of plants, and 4) surrounding vegetation. Melon (Cucumis melo L. [Cucurbitales: Cucurbitaceae]) is among the most consumed fruit in the world, and the whitefly Bemisia tabaci (Gennadius) is among the main pests of this crop. This work aimed to determine the effects of surrounding vegetation, natural enemies, climatic elements, and stages of plants on the spatial dynamics of B. tabaci in commercial melon fields. Adult whitefly densities were monitored on four melon fields in a tropical climate region. Sampling location in crops was georeferenced. Experimental data were submitted to geostatistical analysis. The highest densities of B. tabaci occurred during hot periods experiencing lower rainfall, and when the surrounding area presented crops hosting B. tabaci, especially other melon farms. The density ratio of the predators (i.e., spiders and Geocoris sp.) were dependent on pest density. The pattern of field colonization by B. tabaci varies according to its density. Therefore, the surrounding vegetation, air temperature, and predators influence the spatial distribution of B. tabaci in melon fields. These results provide important information to melon farmers, assisting them to improve the management of B. tabaci in the field.
Adverse Outcomes Associated With Potentially Inappropriate Antibiotic Use in Heart Failure Admissions
Authors: Frisbee Jason , Heidel R Eric , Rasnake Mark S 
Published: June 2019

Abstract

Background
Acute decompensated heart failure (ADHF) can be confused with other conditions that cause dyspnea. Patients with ADHF are often simultaneously treated for community-acquired pneumonia (CAP), even when evidence for infection is lacking. We hypothesized that the fluid and sodium content of potentially unnecessary intravenous antibiotic (IVAB) therapy could worsen outcomes of ADHF patients.

Methods
We reviewed 144 ADHF patients at low risk of pneumonia based on diagnostic findings and clinical documentation. The primary end point was length of stay. Secondary outcomes were mortality, readmission rates, amount of diuretic received, and fluid volume and quantity of sodium administered as part of IVAB therapy.

Results
Of the 144 admissions reviewed, 88 did not and 56 did receive IVAB. IVAB-treated patients received an average of 1.7 L of additional fluid (230 mL/d) and 9311 mg of additional sodium (1381 mg/d) as a result of IVAB therapy. Length of stay was longer in the IVAB arm (6.6 days) compared with the no-IVAB arm (3.0 days; P &lt; .001). Patients required more furosemide in the IVAB arm (930 mg) compared with the no-IVAB arm (320 mg; P &lt; .001). Patients who received IVAB were also 2.51 times more likely to be readmitted compared with patients who did not receive IVAB (P = .04).

Conclusions
ADHF patients who received IVAB without evidence of infection had longer lengths of stay, required more diuretics, and were more likely to be readmitted compared with ADHF patients not exposed to IVAB. ADHF patients are a promising target of antibiotic stewardship interventions.