bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation and application of pseudo–long reads for metagenome assembly
Authors: Sim Mikang , Lee Jongin , Wy Suyeon , Park Nayoung , Lee Daehwan , Kwon Daehong , Kim Jaebum 
Published: May 2022

Abstract

Background
Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.

Results
In this study, we present a new method called PLR-GEN. It creates pseudo–long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo–long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo–long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes.

Conclusions
PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.
Chemical induction of leaf senescence and powdery mildew resistance involves ethylene-mediated chlorophyll degradation and ROS metabolism in cucumber
Authors: Zhang Dingyu , Wu Shengdong , Li Ning , Gao Jiong , Liu Shihui , Zhu Shuai , Li Zilin , Ren Guodong , Kuai Benke 
Published: May 2022

AbstractTimely initiation of leaf senescence is an integral part of plant development and, importantly, an adaptive strategy by which plants cope with various stresses, e.g. to limit the spread of pathogens. Powdery mildew is a major cucumber disease that promotes the initiation/progression of leaf senescence and reduces leaf photosynthesis, resulting in severe losses of yield and quality. However, how powdery mildew induces leaf senescence and how cucumber plants respond to enhance their resistance remain unclear. Here, with established agrochemical induction and pathogen inoculation systems, we demonstrate that both probenazole (PBZ) and powdery mildew activate ethylene (ET) biosynthesis and signal transduction, consequently promoting leaf senescence and enhancing plant resistance to powdery mildew through CsEIN3 to directly upregulate the expression of CsCCGs and CsRBOHs. Our analysis convincingly suggests that the regulation of leaf senescence and powdery mildew resistance is interconnected and mediated mainly by ET in cucumber.
Mechanism ofCsGPA1in regulating cold tolerance of cucumber
Authors: Yan Yan , Mintao Sun , Si Ma , Qian Feng , Yijia Wang , Qinghua Di , Mengdi Zhou , Chaoxing He , Yansu Li , Lihong Gao , Xianchang Yu 
Published: May 2022

AbstractG proteins function directly in cold tolerance of plants. However, the framework of the Gα subunit in regulating cold tolerance remains to be explored. Here, we used protein interaction techniques to elucidate cold-related pathways regulated by CsGPA1. Suppression of CsGPA1 decreased the cold tolerance of cucumber. Further protein interaction experiments showed that CsGPA1 interacted with Csa_4G663630.1 located in the cell membrane and nucleus and with CsCOR413PM2 located in the cell membrane. Csa_4G663630.1 was named CsCDL1 due to its 71% protein sequence similarity to AtCDL1, a positive brassinolide signal gene. Suppression of CsGPA1 decreased the expression of most of brassinolide-related genes (including CsCDL1) under cold stress. Principal component and linear regression analyses showed that expressions of CsGPA1 and brassinolide-related genes were positively correlated. Suppression of CsCOR413PM2 also decreased cold tolerance of cucumber. The expression and protein content of CsCOR413PM2 and CsGPA1 in CsGPA1-RNAi and CsCOR413PM2-RNAi lines were determined under cold tolerance. Only CsGPA1 silencing affected the expression and protein content of CsCOR413PM2 during cold stress. Moreover, suppression of CsGPA1 or CsCOR413PM2 decreased Ca 2+ influx at low temperature and then decreased the expression of CsICE–CsCBF. These results indicated that the CsGPA1–CsCOR413PM2–Ca2+ axis regulated the expression of CsICE–CsCBF during cold stress. In conclusion, Our results provide the first framework of CsGPA1 in regulating cold tolerance of cucumber, laying the foundation for further mechanistic studies of cold tolerance for Gα in cucumber.
Tea GOLDEN2-LIKE genes enhance catechin biosynthesis through activating R2R3-MYB transcription factor
Authors: Wang Lihuan , Tang Xiaofeng , Zhang Shiqiang , Xie Xiang , Li Mengfei , Liu Yongsheng , Wang Songhu 
Published: May 2022

Abstract
The biosynthesis of catechins, a major type of flavonoids accumulated in tea, is mediated by developmental cues and environmental stimuli. Light enhances but shading treatment reduces catechin accumulation in tea leaves. However, the transcription factors involved in light-mediated catechin biosynthesis remain to be identified. Two GOLDEN2 LIKE genes from tea plant (CsGLK1 and CsGLK2) were isolated and characterized in both tomato and tea plants. Transcripts of both CsGLK1 and CsGLK2 were affected by light intensity in tea plants. Overexpression of CsGLK1 and CsGLK2 promoted chloroplast development and carotenoid accumulation in tomato fruits. An integrated metabolomic and transcriptomic approach revealed that both catechin content and related biosynthetic genes were upregulated in CsGLK-overexpressing tomato leaves. Our further studies in tea plants indicated that CsGLKs directly regulate the transcription of CsMYB5b, a transcription factor involved in catechin biosynthesis. Suppression of CsGLKs in tea leaves led to the reduction of both CsMYB5b expression and catechin accumulation. Taken together, the results show that CsGLKs are involved in light-regulated catechin accumulation in tea plants by regulating expression of CsMYB5b and have great potential for enhancing the accumulation of both carotenoids and flavonoids in fruits of horticultural crops.
A systematic review and meta-analysis of vineyard techniques used to delay ripening
Authors: Previtali Pietro , Giorgini Filippo , Mullen Randall S , Dookozlian Nick K , Wilkinson Kerry L , Ford Christopher M 
Published: May 2022

AbstractSeveral vineyard techniques have been proposed to delay grape maturity in light of the advanced maturation driven by increasingly frequent water and heat stress events that are detrimental to grape quality. These studies differ in terms of their experimental conditions, and in the present work we have attempted to summarize previous observations in a quantitative, data-driven systematic review. A meta-analysis of quantitative data gathered across 43 relevant studies revealed the overall significance of the proposed treatments and evaluated the impact of different experimental conditions on the outcome of antitranspirants, delayed pruning and late source limitation. Antitranspirants were most effective when applied twice and closer to veraison, while di-1-p-menthene increased the ripening delay by about 1 °Brix compared to kaolin. Larger ripening delays were achieved with delayed pruning of low-yielding vines or by pruning at later stages of apical bud development. Late defoliation or shoot trimming delayed ripening in high-yielding vines and represent suitable solutions for late-harvested varieties, but became ineffective where the treatment decreased yield. This quantitative meta-analysis of 242 primary observations uncovers factors affecting the efficacy of vineyard practices to delay ripening, which should be carefully considered by grape growers attempting to achieve this outcome.
Growth and Mortality as Causes of Variation in Metabolic Scaling Among Taxa and Taxonomic Levels
Authors: Norin Tommy 
Published: May 2022

AbstractMetabolic rate (MR) usually changes (scales) out of proportion to body mass (BM) as MR = aBMb, where a is a normalisation constant and b is the scaling exponent that reflects how steep this change is. This scaling relationship is fundamental to biology, but over a century of research has provided little consensus on the value of b, and why it appears to vary among taxa and taxonomic levels. By analysing published data on fish and taking an individual-based approach to metabolic scaling, I show that variation in growth of fish under naturally restricted food availability can explain variation in within-individual (ontogenetic) b for standard (maintenance) metabolic rate (SMR) of brown trout (Salmo trutta), with the fastest growers having the steepest metabolic scaling (b ≈ 1). Moreover, I show that within-individual b can vary much more widely than previously assumed from work on different individuals or different species, from –1 to 1 for SMR among individual brown trout. The negative scaling of SMR for some individuals was caused by reductions in metabolic rate in a food limited environment, likely to maintain positive growth. This resulted in a mean within-individual b for SMR that was significantly lower than the across-individual (“static”) b, a difference that also existed for another species, cunner (Tautogolabrus adspersus). Interestingly, the wide variation in ontogenetic b for SMR among individual brown trout did not exist for maximum (active) metabolic rate (MMR) of the same fish, showing that these two key metabolic traits (SMR and MMR) can scale independently of one another. I also show that across-species (“evolutionary”) b for SMR of 134 fishes is significantly steeper (b approaching 1) than the mean ontogenetic b for the brown trout and cunner. Based on these interesting findings, I hypothesise that evolutionary and static metabolic scaling can be systematically different from ontogenetic scaling, and that the steeper evolutionary than ontogenetic scaling for fishes arises as a by-product of natural selection for fast-growing individuals with steep metabolic scaling (b ≈ 1) early in life, where size-selective mortality is high for fishes. I support this by showing that b for SMR tends to increase with natural mortality rates of fish larvae within taxa.
How can the rate of nontherapeutic thymectomy be reduced?
Authors: Wang Shuai , Ao Yongqiang , Jiang Jiahao , Lin Miao , Chen Gang , Liu Junzhen , Zhao Shihai , Gao Jian , Zhang Yi , Ding Jianyong , Tan Lijie 
Published: May 2022

Abstract

OBJECTIVES
The aim of this study was to determine the prevalence of nontherapeutic thymectomy and define a clinical standard to reduce it.

METHODS
From 2016 to 2020, consecutive patients who underwent thymectomy were retrospectively reviewed. Univariable and multivariable analyses were used to identify the correlation factors of nontherapeutic thymectomy. A receiver operating characteristic curve was analysed to assess the cut-off threshold of factors correlated with nontherapeutic thymectomy.

RESULTS
A total of 1039 patients were included in this study. Overall, 78.4% (n = 814) of thymectomies were therapeutic and 21.6% (n = 225) were nontherapeutic. Thymoma (57.9%, n = 602) was the most common diagnosis in therapeutic thymectomy. Among those of nontherapeutic thymectomy, thymic cysts (11.9%, n = 124) were the most common lesion. Compared with therapeutic thymectomy, patients with nontherapeutic thymectomy were more likely to be younger (median age 50.1 vs 55.6 years, P &lt; 0.001) with a smaller precontrast and postcontrast computed tomography (CT) value (P &lt; 0.001, P &lt; 0.001), as well as ΔCT value [10.7 vs 23.5 Hounsfield units (HU), P &lt; 0.001]. Multivariable analysis indicated that only age and ΔCT value were significantly different between therapeutic and nontherapeutic thymectomy groups. Receiver operating characteristic curve analysis showed that cut-off values of age and ΔCT value were 44 years and 6 HU, respectively. Patients with age ≤44 years and a ΔCT value ≤6 HU had a 95% probability of nontherapeutic thymectomy.

CONCLUSIONS
Surgeons should be cautious to perform thymectomy for patients with age ≤44 years and ΔCT value ≤6 HU. This simple clinical standard is helpful to reduce the rate of nontherapeutic thymectomy.
Early postoperative pain after subxiphoid uniportal thoracoscopic major lung resection: a prospective, single- blinded, randomized controlled trial
Authors: Chen Zhigang , Jiang Lei , Zheng Hua , Zhang Wentian , Lv Xin , Abdellateef Amr 
Published: May 2022

Abstract

OBJECTIVES
Preoperative selection bias led to the inability to generalize the proposed benefit of subxiphoid uniportal video-assisted thoracoscopic surgery (SVATS) as having less postoperative pain than uniportal intercostal VATS. So, we conducted this prospective, single-blinded, randomized controlled trial to investigate the hypothesis that SVATS may have less early postoperative pain than UVATS in patients who undergo major lung resection for early-stage lung cancer.

METHODSA total of
262 patients were randomly allocated between 2 groups (each with 131 patients), the first being the UVATS group and the second being the SVATS group. The values indicated on the numerical rating scale (NRS) of pain were collected at 24 h and 48 h during rest and during coughing. In addition, different perioperative variables were analysed and compared between the 2 groups.

RESULTS
Multiple linear regression analysis showed that the type of surgical approach was a significant predictor of the postoperative NRS values. The postoperative NRS pain values were significantly lower in the SVATS group after 24 h during rest and coughing and after 48 h during coughing. Postoperatively, patients in the SVATS group got out of bed significantly earlier [16.37 (2.54) vs 18.05 (3.29) h, p &lt; 0.001]. The SVATS group showed a significantly higher rate of intraoperative arrhythmia [20 (15.3%) vs 3 (2.3%) patients, p = 0.03].

CONCLUSIONS
SVATS major pulmonary resection in early-stage lung cancer is associated with less early postoperative pain than the UVATS approach. Operating on patients with cardiac problems using the SVATS approach is still a limiting factor for randomization due to the potential compression on the heart with resulting arrhythmia.

Clinical trial registration
The trial was registered under clinical trials.gov Identifier: NCT03331588. https://clinicaltrials.gov/ct2/show/NCT03331588.
Development and implementation of a prescription opioid registry across diverse health systems
Authors: Ray G Thomas , Altschuler Andrea , Karmali Ruchir , Binswanger Ingrid , Glanz Jason M , Clarke Christina L , Ahmedani Brian , Andrade Susan E , Boscarino Joseph A , Clark Robin E , Haller Irina V , Hechter Rulin , Roblin Douglas W , Sanchez Katherine , Yarborough Bobbi Jo , Bailey Steffani R , McCarty Dennis , Stephens Kari A , Rosa Carmen L , Rubinstein Andrea L , Campbell Cynthia I 
Published: May 2022

Abstract

Objective
Develop and implement a prescription opioid registry in 10 diverse health systems across the US and describe trends in prescribed opioids between 2012 and 2018.

Materials and Methods
Using electronic health record and claims data, we identified patients who had an outpatient fill for any prescription opioid, and/or an opioid use disorder diagnosis, between January 1, 2012 and December 31, 2018. The registry contains distributed files of prescription opioids, benzodiazepines and other select medications, opioid antagonists, clinical diagnoses, procedures, health services utilization, and health plan membership. Rates of outpatient opioid fills over the study period, standardized to health system demographic distributions, are described by age, gender, and race/ethnicity among members without cancer.

Results
The registry includes 6 249 710 patients and over 40 million outpatient opioid fills. For the combined registry population, opioid fills declined from a high of 0.718 per member-year in 2013 to 0.478 in 2018, and morphine milligram equivalents (MMEs) per fill declined from 985 MMEs per fill in 2012 to 758 MMEs in 2018. MMEs per member declined from 692 MMEs per member in 2012 to 362 MMEs per member in 2018.

Conclusion
This study established a population-based opioid registry across 10 diverse health systems that can be used to address questions related to opioid use. Initial analyses showed large reductions in overall opioid use per member among the combined health systems. The registry will be used in future studies to answer a broad range of other critical public health issues relating to prescription opioid use.
Impact of explainable artificial intelligence assistance on clinical decision-making of novice dental clinicians
Authors: Glick Aaron , Clayton Mackenzie , Angelov Nikola , Chang Jennifer 
Published: May 2022

Abstract

Objective
Despite artificial intelligence (AI) being used increasingly in healthcare, implementation challenges exist leading to potential biases during the clinical decision process of the practitioner. The interaction of AI with novice clinicians was investigated through an identification task, an important component of diagnosis, in dental radiography. The study evaluated the performance, efficiency, and confidence level of dental students on radiographic identification of furcation involvement (FI), with and without AI assistance.

Materials and Methods
Twenty-two third- and 19 fourth-year dental students (DS3 and DS4, respectively) completed remotely administered surveys to identify FI lesions on a series of dental radiographs. The control group received radiographs without AI assistance while the test group received the same radiographs and AI-labeled radiographs. Data were appropriately analyzed using the Chi-square, Fischer’s exact, analysis of variance, or Kruskal–Wallis tests.

Results
Performance between groups with and without AI assistance was not statistically significant except for 1 question where tendency was to err with AI-generated answer (P &lt; .05). The efficiency of task completion and confidence levels was not statistically significant between groups. However, both groups with and without AI assistance believed the use of AI would improve the clinical decision-making.

Discussion
Dental students detecting FI in radiographs with AI assistance had a tendency towards over-reliance on AI.

Conclusion
AI input impacts clinical decision-making, which might be particularly exaggerated in novice clinicians. As it is integrated into routine clinical practice, caution must be taken to prevent overreliance on AI-generated information.
Maternal undernutrition during periconceptional period affects whole-genome ovine muscle methylation in adult offspring
Authors: Capra Emanuele , Toschi Paola , Del Corvo Marcello , Lazzari Barbara , Stella Alessandra , Williams John Lewis , Loi Pasqualino , Ajmone Marsan Paolo 
Published: May 2022

Abstract
Experimental and epidemiological studies suggest that maternal nutritional status during early pregnancy, including the period around the time of conception, may induce long-lasting epigenetic changes in the offspring. However, this remains largely unexplored in livestock. Therefore, the objective of this study was to evaluate if modification of the maternal diet of sheep (CTR: control; UND: 50% undernutrition) during the periconceptional period (42 d in total: −14/+28 from mating), would impact CpG methylation in muscle tissue (Longissimus dorsi) of adult offspring (11.5 mo old). Reduced representation bisulfite sequencing identified 262 (Edge-R, FDR &lt; 0.05) and 686 (logistic regression, FDR &lt; 0.001) differentially methylated regions (DMRs) between the UND and CTR groups. Gene ontology analysis identified genes related to development, functions of the muscular system, and steroid hormone receptor activity within the DMRs. The data reported here show that nutritional stress during early pregnancy leads to epigenetic modifications in the muscle of the resulting offspring, with possible implications for cardiac dysfunction, muscle physiology, and meat production.
Insulin resistance increases as days on feed advance in feedlot Bos indicus beef cattle offered a high-concentrate finishing diet
Authors: de Sousa Osvaldo A , Cappellozza Bruno I , Fonseca Vitor G L , Cooke Reinaldo F 
Published: May 2022

Abstract
This experiment evaluated the effects of advancing days on feed (DOF) on insulin resistance (IR) of finishing Bos indicus bulls offered a high-concentrate diet. On day 0, 100 Bos indicus Nellore bulls were housed in 12 feedlot pens (8 or 9 bulls/pen) for a 108-d feeding period, in a manner that all pens had an equivalent BW at the beginning of the finishing period. Bulls received the same diets throughout the 108-d feeding period. Diets were corn-based (38% starch) and were offered in amounts to ensure ad libitum intake. Individual shrunk BW was obtained on days 0 and 108 after 16 h of feed and water withdrawal, whereas unshrunk BW was recorded on days 19 and 60 for average daily gain (ADG) calculation. From days 0 to 108, feed intake and feed efficiency (FE) were calculated from each pen. Blood samples were collected on days 0, 60, and 108 to assess serum concentrations of haptoglobin, cortisol, glucose, and non-esterified fatty acids (NEFA), and insulin. Glucose, NEFA, and insulin concentrations were used to determine revised quantitative insulin sensitivity check index (RQUICKI), so that lower RQUICKI values indicate a greater IR of the herd. Pen was used as the experimental unit. Overall, DMI increased as DOF also increased (R2 = 0.71), being greater from days 19 to 60 and 60 to 108 vs. 0 to 19 (P &lt; 0.0001), but did not differ between days 19 to 60 and 60 to 108 (P = 0.79). Conversely, ADG and FE linearly decreased as DOF increased from days 0 to 108 (P &lt; 0.0001; R2 = 0.68 and 0.79, respectively). Log-transformed RQUICKI decreased as DOF increased up to 108 (P &lt; 0.0001; r = −0.61). Similarly, serum concentrations of haptoglobin and cortisol increased as RQUICKI increased (P &lt; 0.0001; r = 0.43 and 0.67, respectively). In summary, insulin resistance, per RQUICKI, increased and performance reduced in feedlot bulls with the advance of days on feed. Moreover, inflammatory markers were also positively associated with insulin resistance, suggesting that inflammation might be involved with the incidence of insulin resistance.
Agency Independence, Campaign Contributions, and Favoritism in US Federal Government Contracting
Authors: Fazekas Mihály , Ferrali Romain , Wachs Johannes 
Published: May 2022

AbstractThe impacts of money in US politics have long been debated. Building on principal-agent models, we test whether and to what degree companies’ political donations lead to their favored treatment in federal procurement. We expect the impact of donations on favoritism to vary by the strength of control by political principals over their bureaucratic agents. We compile a comprehensive dataset of published federal contracts and registered campaign contributions for 2004–15. We develop risk indices capturing tendering practices and outcomes likely characterized by favoritism. Using fixed effects regressions, matching, and regression discontinuity analyses, we find confirming evidence for our theory. A large increase in donations from $10,000 to $5m (in USD) increases favoritism risks by about 1/4th standard deviation (SD). These effects are largely partisan, with firms donating to the party that holds the presidency showing higher risk. Donations influence favoritism risks most in less independent agencies: the same donation increases the risk of favoritism by an additional 1/3rd SD in agencies least insulated from politics. Exploiting sign-off thresholds, we demonstrate that donating contractors are subject to less scrutiny by political appointees.