bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood Pressure Variability Is Associated With White Matter Lesion Growth in Intracranial Atherosclerosis
Authors: Kim Bum Joon , Kwon Sun U , Park Jong-Moo , Hwang Yang-Ha , Heo Sung Hyuk , Rha Joung-Ho , Lee Jun , Park Man-Seok , Kim Joon-Tae , Song Hee-Jung , Park Jong-Ho , Yu Sungwook , Lee Soo Joo , Park Tai Hwan , Cha Jae-Kwan , Kwon Hyung-Min , Kim Eung-Gyu , Lee Seung-Hoon , Lee Ji Sung , Lee Juneyoung , Kang Dong-Wha 
Published: April 2019

Abstract

BACKGROUND
High blood pressure variability (BPV) is associated with recurrent stroke. We investigated the association between BPV, new ischemic lesions (NILs), and white matter lesion (WML) growth in patients with ischemic stroke due to intracranial atherosclerosis (ICAS).

METHODS
This study was performed as a post-hoc analysis of the STABLE-ICAS trial, which enrolled subacute ischemic stroke patients with symptomatic ICAS (&gt;50% stenosis) and hypertension. BPV was measured at the office (visit by visit) and at home (day by day). Patients were divided into 3 groups (tertiles) according to their home BPV. WML growth and the occurrence of NILs were compared among the 3 groups. Multivariable analyses were performed to identify the independent risk factors of WML growth and NILs.

RESULTS
Of the 111 enrolled patients, 69 patients (67.6%) demonstrated WML growth and 15 patients (13.7%) had NILs. Patients with higher BPV demonstrated a more WML growth (50% vs. 61.8% vs. 83.8; P = 0.02, by tertiles) and more NILs (5.4% vs. 5.4% vs. 29.7%; P = 0.002, by tertiles). In multivariable analyses, old age [odds ratio (OR) = 1.052 (95% confidence interval (CI) = 1.005–1.101); P = 0.03] and home BPV [OR = 1.149 (95% CI = 1.013–1.304); P = 0.02] were independently associated with WML growth. Low mean diastolic blood pressure [OR = 0.913 (95% CI = 0.874–0.984); P = 0.02] and high home BPV [OR = 1.287 (95% CI = 1.086–1.526); P = 0.004] were independently associated with NILs at follow-up.

CONCLUSIONS
High BPV is associated with WML growth and NIL in ischemic stroke patients with symptomatic ICAS. BPV monitoring at home may be helpful.
Efficient multivariate analysis algorithms for longitudinal genome-wide association studies
Authors: Ning Chao , Wang Dan , Zhou Lei , Wei Julong , Liu Yuanxin , Kang Huimin , Zhang Shengli , Zhou Xiang , Xu Shizhong , Liu Jian-Feng 
Published: April 2019

AbstractMotivationCurrent dynamic phenotyping system introduces time as an extra dimension to genome-wide association studies (GWAS), which helps to explore the mechanism of dynamical genetic control for complex longitudinal traits. However, existing methods for longitudinal GWAS either ignore the covariance among observations of different time points or encounter computational efficiency issues.ResultsWe herein developed efficient genome-wide multivariate association algorithms for longitudinal data. In contrast to existing univariate linear mixed model analyses, the proposed method has improved statistic power for association detection and computational speed. In addition, the new method can analyze unbalanced longitudinal data with thousands of individuals and more than ten thousand records within a few hours. The corresponding time for balanced longitudinal data is just a few minutes.Availability and implementationA software package to implement the efficient algorithm named GMA (https://github.com/chaoning/GMA) is available freely for interested users in relevant fields.Supplementary informationSupplementary data are available at Bioinformatics online.
FP2VEC: a new molecular featurizer for learning molecular properties
Authors: Jeon Woosung , Kim Dongsup 
Published: April 2019

Abstract

Motivation
One of the most successful methods for predicting the properties of chemical compounds is the quantitative structure–activity relationship (QSAR) methods. The prediction accuracy of QSAR models has recently been greatly improved by employing deep learning technology. Especially, newly developed molecular featurizers based on graph convolution operations on molecular graphs significantly outperform the conventional extended connectivity fingerprints (ECFP) feature in both classification and regression tasks, indicating that it is critical to develop more effective new featurizers to fully realize the power of deep learning techniques. Motivated by the fact that there is a clear analogy between chemical compounds and natural languages, this work develops a new molecular featurizer, FP2VEC, which represents a chemical compound as a set of trainable embedding vectors.

Results
To implement and test our new featurizer, we build a QSAR model using a simple convolutional neural network (CNN) architecture that has been successfully used for natural language processing tasks such as sentence classification task. By testing our new method on several benchmark datasets, we demonstrate that the combination of FP2VEC and CNN model can achieve competitive results in many QSAR tasks, especially in classification tasks. We also demonstrate that the FP2VEC model is especially effective for multitask learning.

Availability and implementation
FP2VEC is available from https://github.com/wsjeon92/FP2VEC.

Supplementary information
Supplementary data are available at Bioinformatics online.
Degraded or Just Dusty? Examining Ecological Change in Arid Lands
Authors: Silcock Jennifer L , Fensham Rod J 
Published: April 2019

AbstractThe ecological history of rangelands is often presented as a tale of devastation, where fragile drylands are irreversibly degraded through inappropriate land use. However, there is confusion about how to recognize and measure degradation, especially in low-productivity environments characterized by extreme natural variability and where abrupt and comprehensive management upheavals preclude benchmarks. These issues have important consequences for rangeland management programs, which are typically founded on presumptions of substantial and ongoing degradation from former “natural” states. We explore complementary approaches to critically assess degradation: the historical record, long-term grazing exclosures, surveys for potentially rare and sensitive plant species, and assessment of water-remote areas in relation to rare plant occurrence. Employing these approaches in inland Australia, we show that prevailing paradigms have become entrenched despite being inconsistent with empirical evidence. Our methodology can be applied to drylands with abrupt changes in management and contentious ecological narratives.
Immunometabolism orchestrates training of innate immunity in atherosclerosis
Authors: van Tuijl Julia , Joosten Leo A B , Netea Mihai G , Bekkering Siroon , Riksen Niels P 
Published: April 2019

Abstract
Atherosclerosis is characterized by a persistent, low-grade inflammation of the arterial wall. Monocytes and monocyte-derived macrophages play a pivotal role in the various stages of atherosclerosis. In the past few years, metabolic reprogramming has been identified as an important controller of myeloid cell activation status. In addition, metabolic and epigenetic reprogramming are key regulatory mechanisms of trained immunity, which denotes the non-specific innate immune memory that can develop after brief stimulation of monocytes with microbial or non-microbial stimuli. In this review, we build the case that metabolic reprogramming of monocytes and macrophages, and trained immunity in particular, contribute to the pathophysiology of atherosclerosis. We discuss the specific metabolic adaptations, including changes in glycolysis, oxidative phosphorylation, and cholesterol metabolism, that have been reported in atherogenic milieus in vitro and in vivo. In addition, we will focus on the role of these metabolic pathways in the development of trained immunity.
Comparison between lymph node station- and zone-based classification for the future revision of node descriptors proposed by the International Association for the Study of Lung Cancer in surgically resected patients with non-small-cell lung cancer
Authors: Yun Jae Kwang , Lee Geun Dong , Choi Sehoon , Kim Hyeong Ryul , Kim Yong-Hee , Kim Dong Kwan , Park Seung-Il 
Published: April 2019

AbstractOBJECTIVESThe International Association for the Study of Lung Cancer (IASLC) proposed further subdivisions of pathological N1 (pN1) and pN2 by including the location and the number of involved lymph node (LN) stations. We adopted the subdivided N descriptors and reclassified them according to the involved LN zones or LN stations, and compared the discrimination abilities of the 2 classifications.METHODSA retrospective analysis was carried out on patients who underwent complete resection with systematic LN dissection for non-small cell lung cancer diagnosed as pathological stages I–III between 2006 and 2015. N classification was grouped into 6 categories: no LN involvement, single-station N1, multiple-station N1, single-station N2 without N1, single-station N2 with N1 and multiple-station N2. LN zones were defined by grouping the LN stations: peripheral or hilar for N1 nodes, and upper mediastinal, lower mediastinal, aortopulmonary and subcarinal for N2 nodes.RESULTSA total of 3971 patients (2451 men, median age: 63 years) were analysed. Median follow-up was 59 months. A multivariable analysis showed that the subdivided N descriptors based on LN station and zone were both independent prognostic factors in terms of both overall survival and freedom from recurrence. Whether multiple LN involvements were confined within a single LN zone was a significant prognostic factor in the multiple-station N2 group. A zone-based classification showed similar discrimination ability to the station-based classification.CONCLUSIONSBoth LN station- and zone-based classifications showed favourable prognostic discrimination abilities. The new N classifications could be considered for future revisions of tumour, node and metastasis (TNM) staging system for lung cancer.
Microbiome characterization of poultry products based on the poultry part and production label
Authors: Lee Sang In , Choi Jungmin , Daeschel Devin Z , Park Si Hong 
Published: April 2019

ABSTRACT
Poultry is one of the most consumed meats worldwide and there are many different types of poultry products available on the market for consumers. Many poultry producers provide a variety of labeled meats based on rearing system such as organic, free-range and antibiotic-free. However, these labels often can be misleading by implying organic products are better in safety and quality compared to poultry products without additional labels. In this study, the microbiological profiles of commercial poultry products were characterized via a next generation sequencing. A variety of poultry products including whole carcass, leg, breast and thigh were purchased from local markets and subdivided by labels indicating organic, non-antibiotic, free range and no-label. According to the microbiome analysis based on the 16S rRNA gene, similar level of species richness were observed in comparison by labels, however, different parts and producers exhibited significant differences. Also, microbial similarities among groups were measured and most samples showed relatively close clustering based on the poultry part and the producer. The results emphasize potential contamination routes and the importance of the control strategy during the pre-harvest step of poultry products. The results also envision potential opportunities to improve current production procedure being utilized by industries.
Physiological and comparative genomic analysis of new isolated yeasts Spathaspora sp. JA1 and Meyerozyma caribbica JA9 reveal insights into xylitol production
Authors: Trichez Débora , Steindorff Andrei S , Soares Carlos E V F , Formighieri Eduardo F , Almeida João R M 
Published: April 2019

ABSTRACT
Xylitol is a five-carbon polyol of economic interest that can be produced by microbial xylose reduction from renewable resources. The current study sought to investigate the potential of two yeast strains, isolated from Brazilian Cerrado biome, in the production of xylitol as well as the genomic characteristics that may impact this process. Xylose conversion capacity by the new isolates Spathaspora sp. JA1 and Meyerozyma caribbica JA9 was evaluated and compared with control strains on xylose and sugarcane biomass hydrolysate. Among the evaluated strains, Spathaspora sp. JA1 was the strongest xylitol producer, reaching product yield and productivity as high as 0.74 g/g and 0.20 g/(L.h) on xylose, and 0.58 g/g and 0.44 g/(L.h) on non-detoxified hydrolysate. Genome sequences of Spathaspora sp. JA1 and M. caribbica JA9 were obtained and annotated. Comparative genomic analysis revealed that the predicted xylose metabolic pathway is conserved among the xylitol-producing yeasts Spathaspora sp. JA1, M. caribbica JA9 and Meyerozyma guilliermondii, but not in Spathaspora passalidarum, an efficient ethanol-producing yeast. Xylitol-producing yeasts showed strictly NADPH-dependent xylose reductase and NAD+-dependent xylitol-dehydrogenase activities. This imbalance of cofactors favors the high xylitol yield shown by Spathaspora sp. JA1, which is similar to the most efficient xylitol producers described so far.
Overexpression of endogenous stress-tolerance related genes in Saccharomyces cerevisiae improved strain robustness and production of heterologous cellobiohydrolase
Authors: Lamour Jarryd , Wan Chun , Zhang Mingming , Zhao Xinqing , Den Haan Riaan 
Published: April 2019

ABSTRACT
To enable Saccharomyces cerevisiae to produce renewable fuels from lignocellulose in a consolidated bioprocess, a heterologous cellulase system must be engineered into this yeast. In addition, inherently low secretion titers and sensitivity to adverse environmental conditions must be overcome. Here, two native S. cerevisiae genes related to yeast stress tolerance, YHB1 and SET5, were overexpressed under transcriptional control of the constitutive PGK1 promoter and their effects on heterologous secretion of Talaromyces emersonii cel7A cellobiohydrolase was investigated. Transformants showed increased secreted enzyme activity that ranged from 22% to 55% higher compared to the parental strains and this did not lead to deleterious growth effects. The recombinant strains overexpressing either YHB1 or SET5 also demonstrated multi-tolerant characteristics desirable in bioethanol production, i.e. improved tolerance to osmotic and heat stress. Quantitative reverse transcriptase PCR analysis in these strains showed decreased transcription of secretion pathway genes. However, decreased unfolded protein response was also observed, suggesting novel mechanisms for enhancing enzyme production through stress modulation. Overexpression of YHB1 in an unrelated diploid strain also enhanced stress tolerance and improved ethanol productivity in medium containing acetic acid. To our knowledge, this is the first demonstration that improved heterologous secretion and environmental stress tolerance could be engineered into yeast simultaneously.
A Criterion for Splitting of a Projective Module in Terms of Its Generic Sections
Authors: Kanti Das Mrinal 
Published: April 2019

Abstract
Let $R$ be a smooth affine domain of dimension $d\geq 3$ over $\overline{{\mathbb{F}}}_p$ with $p\neq 2$. Let $P$ be a projective $R$-module of rank $d-1$ with trivial determinant. We prove that $P$ splits off a free summand of rank 1 if and only if $P$ surjects onto a complete intersection ideal of height $d-1$.
Effects of 3-nitrooxypropanol on enteric methane production, rumen fermentation, and feeding behavior in beef cattle fed a high-forage or high-grain diet1
Authors: Kim Seon-Ho , Lee Chanhee , Pechtl Heather A , Hettick Jade M , Campler Magnus R , Pairis-Garcia Monique D , Beauchemin Karen A , Celi Pietro , Duval Stephane M 
Published: April 2019

AbstractThe objective of the study was to determine whether feeding a diet supplemented with 3-nitrooxypropanol (3-NOP) affects feeding behavior altering intake and rumen fermentation. Two experiments were conducted with 9 rumen-cannulated beef steers in a replicated 3 × 3 Latin square design where animals received a high-forage or high-grain diet. Treatments were 1) a basal diet (CON), the CON diet supplemented with 3-NOP (dNOP; 100 mg/kg in dietary DM or 1 g/d), or the CON diet with 3-NOP (1 g/d) infused into the rumen (infNOP). Each experimental period consisted of 14-d diet adaptation and 7-d sample collection. A 7-d washout period was provided between experiment periods. All data were analyzed as a Latin square design using Mixed Procedure of SAS. In Exp. 1 (high-forage diet), methane yield (measured by the Greenfeed system) was lowered by 18% (18.6 vs. 22.7 g/kg DMI; P < 0.01) by dNOP compared with CON. Rumen fermentation was altered similarly by both NOP treatments compared with CON where dNOP and infNOP increased (P < 0.01) rumen pH at 3 h and decreased (P < 0.01) proportion of acetate in total VFA. However, DMI, feed consumption rate (0 to 3, 3 to 6, 6 to 12, and 12 to 24 h after feeding), particle size distribution of orts, and feeding behavior (videotaped for individual animals over 48 h) were not affected by dNOP and infNOP compared with CON. In Exp. 2 (high-grain diet), methane production was not affected by dNOP or infNOP compared with CON. Dry matter intake, feed consumption rate, particle size distribution of orts, and feeding behavior were not altered by dNOP and infNOP compared with CON. However, both dNOP and infNOP affected rumen fermentation where total VFA decreased (P = 0.04) and acetate proportion in total VFA tended to decrease (P = 0.07) compared with CON. In conclusion, dietary supplementation of 3-NOP did not affect feeding behavior of beef steers fed a high-forage or high-grain diet. However, rumen fermentation was similarly changed when 3-NOP was provided in the diet or directly infused in the rumen. Thus, observed changes in rumen fermentation with 3-NOP were not due to changes in feeding behavior indicating no effects on the organoleptic property of the diets. In addition, according to small or no changes in DMI in both experiments and relatively small changes in rumen fermentation in Exp. 2, a greater dosage level of 3-NOP than 100 mg/kg (dietary DM) may need further examination of its effects on feeding behavior of beef cattle.
Supplementation with eicosapentaenoic and docosahexaenoic acids in late gestation in ewes changes adipose tissue gene expression in the ewe and growth and plasma concentration of ghrelin in the offspring1
Authors: Nickles Kirsten R , Hamer Lauren , Coleman Danielle N , Relling Alejandro E 
Published: April 2019

AbstractOmega-3 long chain fatty acids have a positive impact on production. When consumed during late gestation, it might have fetal programming effects on the fetus, which will have lifelong impacts on development and production. The objectives of the present study were to evaluate the effect of increasing doses of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in the diet of ewes in the last third of gestation on their body weight (BW), subcutaneous adipose tissue relative mRNA abundance of genes associated with adipose tissue metabolism, and growth performance and plasma metabolites and hormones of their offspring during the finishing phase. Ewes (n = 72) were blocked by BW and allotted to pens (8 per treatment) with 3 ewes per pen. Ewes were supplemented with an EPA and DHA source (Strata G113) at concentrations of 0, 1, or 2% of dry matter intake during the last 50 d of gestation. At lambing, all ewes were penned together and offered the same diet. After weaning at 60 d of age, lambs were blocked by BW and sex and fed for 56 d. All lambs were fed the same pellet diet (61.09% ground corn, 24.08% soy hulls, 11.09% soybean meal, 1.48% Ca salt of palm oil, and 2.26% mixed mineral vitamin), and were weighed every 14 d until the end of the trial. Blood samples were collected on the weight sampling days. Dry matter intake and refusals were weighed daily. Data were analyzed as a randomized complete block design with repeated measurements (SAS 9.4). Polynomial contrast (linear-L and quadratic-Q) was used for mean separation. There were no differences in ewe body condition score, milk production, milk fat, or milk protein, but there was a trend for increased (L, P = 0.06) lactose concentration, and also differences in DGAT1 (L, P = 0.04), Δ5-desaturase (Q, P = 0.06) and Δ6-desaturase (Q, P = 0.07), PPARα (Q, P = 0.03), ELOVL2 and 5 (Q, P &lt; 0.07), FABP4 (Q, P = 0.04), FATP1 (Q, P = 0.06), leptin (Q, P = 0.02), and resistin (L, P = 0.05). Feeding pregnant ewes an increased amount of EPA and DHA in late gestation increased final BW (L, P = 0.01), ADG (L, P = 0.04; Q, P = 0.01), DMI (Q, P ≤ 0.01), plasma glucose concentration (L, P = 0.04), and trended to decrease ghrelin concentrations (L, P = 0.07) in offspring during the finishing period. Dam supplementation did not affect G:F, nor plasma NEFA concentration (P ≥ 0.53) of lambs. Therefore, increasing supplementation of EPA and DHA in pregnant ewes has an impact on offspring performance, increasing DMI, ADG, and BW.
Contact Chemosensory Genes Identified in Leg Transcriptome of Apis cerana cerana (Hymenoptera: Apidae)
Authors: Du Yali , Xu Kai , Ma Weihua , Su Wenting , Tai Miaomiao , Zhao Huiting , Jiang Yusuo , Li Xianchun 
Published: April 2019

Abstract
Correct gustatory recognition and selection of foods both within and outside the hive by honey bee workers are fundamental to the maintenance of colonies. The tarsal chemosensilla located on the legs of workers are sensitive to nonvolatile compounds and proposed to be involved in gustatory detection. However, little is known about the molecular mechanisms underlying the gustatory recognition of foods in honey bees. In the present study, RNA-seq was performed with RNA samples extracted from the legs of 1-, 10-, and 20-d-old workers of Apis cerana cerana Fabricius, a dominant indigenous crop pollinator with a keen perception ability for phytochemicals. A total of 124 candidate chemosensory proteins (CSPs), including 15 odorant-binding proteins (OBPs), 5 CSPs, 7 gustatory receptors (GRs), 2 sensory neuron membrane proteins (SNMPs), and 95 odorant receptors (ORs), were identified from the assembled leg transcriptome. In silico analysis of expression showed that 36 of them were differentially expressed among the three different ages of A. c. cerana workers. Overall, the genes encoding OBPs and CSPs had great but extremely variable FPKM values and thus were highly expressed in the legs of workers, whereas the genes encoding ORs, GRs, and SNMPs (except SNMP2) were expressed at low levels. Tissue-specific expression patterns indicated that two upregulated genes, AcerOBP15 and AcerCSP3, were predominately expressed in the legs of 20-d-old foragers, suggesting they may play an essential role in gustatory recognition and selection of plant nectars and pollens. This study lays a foundation for further research on the feeding preferences of honey bees.
A New Hoccleve Literary Manuscript: The Trilingual Miscellany in London, British Library, MS Harley 219
Authors: Schieberle Misty 
Published: April 2019

Abstract
This essay identifies a hand which copies and corrects much of the literary manuscript, London, British Library, MS Harley 219, as that of Thomas Hoccleve. Texts in Hoccleve’s handwriting include selections from Odo of Cheriton’s Fables and the Gesta Romanorum (a source for the Series), all of a unique copy of Christine de Pizan’s Epistre Othea, and a glossary of French terms translated into Latin and English. Additionally, Hoccleve’s handwriting can be found in corrections to a French Secretum Secretorum (a source for The Regiment of Princes) that is otherwise copied in another hand. This essay offers preliminary observations on the literary implications of these identifications and attempts to situate these texts within Hoccleve’s career as a clerk and poet.