bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatic transcriptome perturbations in dairy cows fed different forage resources
Authors: Gao S. T. , Ma Lu , Zhang Y. D. , Wang J. Q. , Loor J. J. , Bu D. P. 
Published: January 2021

Abstract
Background
Forage plays critical roles in milk performance of dairy. However, domestic high-quality forage such as alfalfa hay is far from being sufficient in China. Thus, more than 1 million tons of alfalfa hay were imported in China annually in recent years. At the same time, more than 10 million tons of corn stover are generated annually in China. Thus, taking full advantage of corn stover to meet the demand of forage and reduce dependence on imported alfalfa hay has been a strategic policy for the Chinese dairy industry. Changes in liver metabolism under different forage resources are not well known. Thus, the objective of the present study was to investigate the effect of different forage resources on liver metabolism using RNAseq and bioinformatics analyses.

Results
The results of this study showed that the cows fed a diet with corn stover (CS) as the main forage had lower milk yield, DMI, milk protein content and yield, milk fat yield, and lactose yield than cows fed a mixed forage (MF) diet (P <  0.01). KEGG analysis for differently expressed genes (DEG) in liver (81 up-regulated and 423 down-DEG, Padj ≤0.05) showed that pathways associated with glycan biosynthesis and metabolism and amino acid metabolism was inhibited by the CS diet. In addition, results from DAVID and ClueGO indicated that biological processes related to cell-cell adhesion, multicellular organism growth, and amino acid and protein metabolism also were downregulated by feeding CS. Co-expression network analysis indicated that FAM210A, SLC26A6, FBXW5, EIF6, ZSCAN10, FPGS, and ARMCX2 played critical roles in the network. Bioinformatics analysis showed that genes within the co-expression network were enriched to “pyruvate metabolic process”, “complement activation, classical pathway”, and “retrograde transport, endosome to Golgi”.

Conclusions
Results of the present study indicated that feeding a low-quality forage diet inhibits important biological functions of the liver at least in part due to a reduction in DMI. In addition, the results of the present study provide an insight into the metabolic response in the liver to different-quality forage resources. As such, the data can help develop favorable strategies to improve the utilization of corn stover in China.
Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria
Authors: Duru Ilhan Cem , Ylinen Anne , Belanov Sergei , Pulido Alan Avila , Paulin Lars , Auvinen Petri 
Published: January 2021

Abstract
Background
Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C.

Results
We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures.

Conclusions
The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.
A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs
Authors: Flossmann Gabriele , Wurmser Christine , Pausch Hubert , Tenghe Amabel , Dodenhoff Jörg , Dahinten Günther , Götz Kay-Uwe , Russ Ingolf , Fries Ruedi 
Published: January 2021

Abstract
Background
Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means for identifying chromosomal regions harboring deleterious DNA-variants causing such phenotypes. We performed a GWAS to unravel the causes of incidental cases of atypically small vulvae in German Landrace gilts.

Results
A case-control GWAS involving Illumina porcine SNP60 BeadChip-called genotypes of 17 gilts with atypically small vulvae and 1818 control animals (fertile German Landrace sows) identified a significantly associated region on the X-chromosome (P = 8.81 × 10− 43). Inspection of whole-genome sequencing data in the critical area allowed us to pinpoint a likely causal variant in the form of a nonsense mutation of bone morphogenetic protein-15 (BMP15; Sscrofa11.1_X:g.44618787C>T, BMP15:p.R212X). The mutant allele occurs at a frequency of 6.2% in the German Landrace breeding population. Homozygous gilts exhibit underdeveloped, most likely not functional ovaries and are not fertile. Male carriers do not seem to manifest defects. Heterozygous sows produce 0.41±0.02 (P=4.5 × 10-83) piglets more than wildtype animals. However, the mutant allele’s positive effect on litter size accompanies a negative impact on lean meat growth.

Conclusion
Our results provide an example for the power of GWAS in identifying the genetic causes of a fuzzy phenotype and add to the list of natural deleterious BMP15 mutations that affect fertility in a dosage-dependent manner, the first time in a poly-ovulatory species. We advise eradicating the mutant allele from the German Landrace breeding population since the adverse effects on the lean meat growth outweigh the larger litter size in heterozygous sows.
Leptospira in river and soil in a highly endemic area of Ecuador
Authors: Miller Erin , Barragan Veronica , Chiriboga Jorge , Weddell Chad , Luna Ligia , Jiménez Dulce J. , Aleman John , Mihaljevic Joseph R. , Olivas Sonora , Marks Jane , Izurieta Ricardo , Nieto Nathan , Keim Paul , Trueba Gabriel , Caporaso J. Gregory , Pearson Talima 
Published: January 2021

Abstract
Background
Leptospira are shed into the environment via urine of infected animals. Rivers are thought to be an important risk factor for transmission to humans, though much is unknown about the types of environment or characteristics that favor survival. To address this, we screened for Leptospira DNA in two rivers in rural Ecuador where Leptospirosis is endemic.

Results
We collected 112 longitudinal samples and recorded pH, temperature, river depth, precipitation, and dissolved oxygen. We also performed a series of three experiments designed to provide insight into Leptospira presence in the soil. In the first soil experiment, we characterized prevalence and co-occurrence of Leptospira with other bacterial taxa in the soil at dispersed sites along the rivers (n = 64). In the second soil experiment, we collected 24 river samples and 48 soil samples at three points along eight transects to compare the likelihood of finding Leptospira in the river and on the shore at different distances from the river. In a third experiment, we tested whether Leptospira presence is associated with soil moisture by collecting 25 soil samples from two different sites.
In our river experiment, we found pathogenic Leptospira in only 4 (3.7%) of samples. In contrast, pathogenic Leptospira species were found in 22% of shore soil at dispersed sites, 16.7% of soil samples (compared to 4.2% of river samples) in the transects, and 40% of soil samples to test for associations with soil moisture.

Conclusions
Our data are limited to two sites in a highly endemic area, but the scarcity of Leptospira DNA in the river is not consistent with the widespread contention of the importance of river water for leptospirosis transmission. While Leptospira may be shed directly into the river, onto the shores, or washed into the river from more remote sites, massive dilution and limited persistence in rivers may reduce the environmental load and therefore, the epidemiological significance of such sources. It is also possible that transmission may occur more frequently on shores where people are liable to be barefoot. Molecular studies that further explore the role of rivers and water bodies in the epidemiology of leptospirosis are needed.
Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea
Authors: Li Jingling , Tang Jianmin , Zeng Siyuan , Han Fang , Yuan Jing , Yu Jie 
Published: January 2021

Abstract
Background
Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca ‘Greizy’, Pilea peperomioides and Pilea serpyllacea ‘Globosa’) and performed comprehensive comparative analysis.

Results
The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.

Conclusion
Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.
Comparative genomic analysis of Polypodiaceae chloroplasts reveals fine structural features and dynamic insertion sequences
Authors: Liu Shanshan , Wang Zhen , Su Yingjuan , Wang Ting 
Published: January 2021

Abstract
Background
Comparative chloroplast genomics could shed light on the major evolutionary events that established plastomic diversity among closely related species. The Polypodiaceae family is one of the most species-rich and underexplored groups of extant ferns. It is generally recognized that the plastomes of Polypodiaceae are highly notable in terms of their organizational stability. Hence, no research has yet been conducted on genomic structural variation in the Polypodiaceae.

Results
The complete plastome sequences of Neolepisorus fortunei, Neolepisorus ovatus, and Phymatosorus cuspidatus were determined based on next-generation sequencing. Together with published plastomes, a comparative analysis of the fine structure of Polypodiaceae plastomes was carried out. The results indicated that the plastomes of Polypodiaceae are not as conservative as previously assumed. The size of the plastomes varies greatly in the Polypodiaceae, and the large insertion fragments present in the genome could be the main factor affecting the genome length. The plastome of Selliguea yakushimensis exhibits prominent features including not only a large-scale IR expansion exceeding several kb but also a unique inversion. Furthermore, gene contents, SSRs, dispersed repeats, and mutational hotspot regions were identified in the plastomes of the Polypodiaceae. Although dispersed repeats are not abundant in the plastomes of Polypodiaceae, we found that the large insertions that occur in different species are mobile and are always adjacent to repeated hotspot regions.

Conclusions
Our results reveal that the plastomes of Polypodiaceae are dynamic molecules, rather than constituting static genomes as previously thought. The dispersed repeats flanking insertion sequences contribute to the repair mechanism induced by double-strand breaks and are probably a major driver of structural evolution in the plastomes of Polypodiaceae.
Identification of plant leaf phosphorus content at different growth stages based on hyperspectral reflectance
Authors: Siedliska Anna , Baranowski Piotr , Pastuszka-Woźniak Joanna , Zubik Monika , Krzyszczak Jaromir 
Published: January 2021

AbstractBackgroundModern agriculture strives to sustainably manage fertilizer for both economic and environmental reasons. The monitoring of any nutritional (phosphorus, nitrogen, potassium) deficiency in growing plants is a challenge for precision farming technology. A study was carried out on three species of popular crops, celery (Apium graveolensL., cv. Neon), sugar beet (Beta vulgarisL., cv. Tapir) and strawberry (Fragaria × ananassaDuchesne, cv. Honeoye), fertilized with four different doses of phosphorus (P) to deliver data for non-invasive detection of P content.ResultsData obtained via biochemical analysis of the chlorophyll and carotenoid contents in plant material showed that the strongest effect of P availability for plants was in the diverse total chlorophyll content in sugar beet and celery compared to that in strawberry, in which P affects a variety of carotenoid contents in leaves. The measurements performed using hyperspectral imaging, obtained in several different stages of plant development, were applied in a supervised classification experiment. A machine learning algorithm (Backpropagation Neural Network, Random Forest, Naive Bayes and Support Vector Machine) was developed to classify plants from four variants of P fertilization. The lowest prediction accuracy was obtained for the earliest measured stage of plant development. Statistical analyses showed correlations between leaf biochemical constituents, phosphorus fertilization and the mass of the leaf/roots of the plants.ConclusionsObtained results demonstrate that hyperspectral imaging combined with artificial intelligence methods has potential for non-invasive detection of non-homogenous phosphorus fertilization on crop levels.
Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel Orange
Authors: Zhang Haipeng , Chen Jiajing , Peng Zhaoxin , Shi Meiyan , Liu Xiao , Wen Huan , Jiang Youwu , Cheng Yunjiang , Xu Juan , Zhang Hongyan 
Published: January 2021

Abstract
Background
Carotenoids and flavonoids are important secondary metabolites in plants, which exert multiple bioactivities and benefits to human health. Although the genes that encode carotenogenesis and flavonoid biosynthetic enzymes are well characterized, the transcriptional regulatory mechanisms that are related to the pathway genes remain to be investigated. In this study, ‘Cara cara’ navel orange (CNO) fruit at four development stages were used to identify the key genes and TFs for carotenoids and flavonoids accumulation.

Results
In this study, CNO was used to investigate the profiles of carotenoids and flavonoids by a combination of metabolomic and transcriptomic analyses. The important stage for the accumulation of the major carotenoid, lycopene was found to be at 120 days after florescence (DAF). The transcripts of five carotenogenesis genes were highly correlated with lycopene contents, and 16, 40, 48, 24 and 18 transcription factors (TFs) were predicted to potentially bind 1-deoxy-D-xylulose-5-phosphate synthase (DXS1), deoxyxylulose 5-phosphate reductoisomerase (DXR), geranylgeranyl diphosphate synthase (GGPPS2), phytoene synthase (PSY1) and lycopene β-cyclase (LCYB) promoters, respectively. Narirutin was the most abundant flavonoid in the flesh at the early stages, 60 DAF was the most important stage for the accumulation of flavonoids, and 17, 22, 14, 25, 24 and 16 TFs could potentially bind phenylalanine ammonia-lyase (PAL-1 and PAL-4), 4-Coumarate-CoA ligase (4CL-2 and 4CL-5), chalcone synthase (CHS-1) and chalcone isomerase (CHI) promoters, respectively. Furthermore, both sets of 15 candidate TFs might regulate at least three key genes and contribute to carotenoids/flavonoids accumulation in CNO fruit. Finally, a hierarchical model for the regulatory network among the pathway genes and TFs was proposed.

Conclusions
Collectively, our results suggest that DXS1, DXR, GGPPS2, PSY1 and LCYB genes were the most important genes for carotenoids accumulation, while PAL-1, PAL-4, 4CL-2, 4CL-5, CHS-1 and CHI for flavonoids biosynthesis. A total of 24 TFs were postulated as co-regulators in both pathways directly, which might play important roles in carotenoids and flavonoids accumulation in CNO fruit.
The analgesic efficacy of ultrasound-guided transversus abdominis plane (TAP) block combined with oral multimodal analgesia in comparison with oral multimodal analgesia after caesarean delivery: a randomized controlled trial
Authors: Yu Yang , Gao Shenshan , Yuen Vivian Man-ying , Choi Siu-Wai , Xu Xuebing 
Published: January 2021

Abstract
Background
The transversus abdominis plane (TAP) block is used increasingly in parturients after caesarean delivery. This is a randomized controlled trial to evaluate the effectiveness of bilateral single-shot of TAP blocks in patients who received multimodal oral analgesia for postoperative pain relief.

Methods
Parturients who were scheduled for elective caesarean delivery under spinal anaesthesia were recruited and randomized to receive bilateral single-shot of TAP blocks or placebo in addition to multimodal oral analgesia which consisted of regular tramadol, celecoxib and paracetamol, with oral oxycodone used as a rescue for breakthrough pain. Only parturients in the TAP group would receive the TAP blocks with an injection of 15 ml (0.25%) ropivacaine on each side under aseptic techniques. All the parturients were evaluated for pain or related complications in the first 24 h after surgery. The primary outcome is the percentage of parturients who required oxycodone as a rescue analgesia.

Results
Eighty and 79 parturients were allocated to the TAP and placebo group respectively. Nine out of 79 (11.4%) parturients in the TAP group and 15 out of 73 (20.5%) parturients in the placebo group required oxycodone for breakthrough pain, P = 0.122.

Conclusions
Bilateral single-shot of TAP blocks confer little additional benefit when a multimodal oral analgesic regimen is used for pain control after caesarean section under spinal anaesthesia.

Trial registration
Clinical Trial Registry of China (http://www.chictr.org.cn) identifier: ChiCTR-INR-16010130, retrospectively registered on Dec 12, 2016.
The comparison of efficacy and complications of coblation and radiofrequency thermocoagulation for V2/V3 idiopathic trigeminal neuralgia: a retrospective cohort study of 292 cases
Authors: Wang Chenhui , Dou Zhi , Yan Mengwei , Tang Yuanzhang , Zhao Rui , Han Yujie , Ni Jiaxiang 
Published: January 2021

Abstract
Background
Coblation is a novel technique in respect of treating idiopathic trigeminal neuralgia. We aimed to identify the efficacy and complications between radiofrequency thermocoagulation (RFT) and coblation for V2/V3 idiopathic trigeminal neuralgia (ITN) and investigate the risk factors associated with postoperative facial numbness.
Methods: We retrospectively reviewed our cohort of 292 patients who had undergone RFT or coblation for V2/V3 ITN. The characteristics of the baseline were collected before surgery. Pain scores, the degree of facial numbness and other complications were evaluated at discharge and 1 month, 3 months, 6 months and 12 months after surgery.

Results
Postoperative pain intensity was apparently alleviated in both groups. The initial and 12-months remission rates were 94.0 and 75.3% in coblation group compared with 96.9 and 78.4% in RFT group (P = 0.462, P = 0.585). The degree of postoperative facial numbness tended to be more severe in RFT group at discharge, 1 month, 6 months and 12 months (P = 0.006, P = 0.026, P = 0.004, P = 0.003). Factors significantly associated with more severe facial numbness were procedure of RFT (OR = 0.46, 95%CI: 0.28–0.76, P = 0.002), history of previous RFT at the affected side (OR = 2.33, 95%CI: 1.21–4.48, P = 0.011), and ITN with concomitant continuous pain (OR = 0.36, 95%CI: 0.18–0.71, P = 0.004).

Conclusion
Coblation could reduce the degree of postoperative facial numbness for ITN, and the efficacy was no less effective than RFT. History of previous RFT at the affected side, procedure of RFT, ITN with concomitant continuous pain was identified as significant factors of the development of postoperative facial numbness.
Composition and risk assessment of perioperative patient safety incidents reported by anesthesiologists from 2009 to 2019: a single‐center retrospective cohort study
Authors: Zhang Xue , Ma Shuang , Sun Xueqin , Zhang Yuelun , Chen Weiyun , Chang Qing , Pan Hui , Zhang Xiuhua , Shen Le , Huang Yuguang 
Published: January 2021

Abstract
Background
Patient safety incident (PSI) reporting has been an important means of improving patient safety and enhancing organizational quality control. Reports of anesthesia-related incidents are of great value for analysis to improve perioperative patient safety. However, the utilization of incident data is far from sufficient, especially in developing countries such as China.

Methods
All PSIs reported by anesthesiologists in a Chinese academic hospital between September 2009 and August 2019 were collected from the incident reporting system. We reviewed the freeform text reports, supplemented with information from the patient medical record system. Composition analysis and risk assessment were performed.

Results
In total, 847 PSIs were voluntarily reported by anesthesiologists during the study period among 452,974 anesthetic procedures, with a reported incidence of 0.17%. Patients with a worse ASA physical status were more likely to be involved in a PSI. The most common type of incident was related to the airway (N = 208, 27%), followed by the heart, brain and vascular system (N = 99, 13%) and pharmacological incidents (N = 79, 10%). Those preventable incidents with extreme or high risk were identified through risk assessment to serve as a reference for the implementation of more standard operating procedures by the department.

Conclusions
This study describes the characteristics of 847 PSIs voluntarily reported by anesthesiologists within eleven years in a Chinese academic hospital. Airway incidents constitute the majority of incidents reported by anesthesiologists. Underreporting is common in China, and the importance of summarizing and utilizing anesthesia incident data should be scrutinized.