bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools
Authors:   Econogene Consortium, Ciani Elena ,   Sheephapmap Consortium, Mastrangelo Salvatore , Da Silva Anne , Marroni Fabio , Ferenčaković Maja , Ajmone-Marsan Paolo , Baird Hayley , Barbato Mario , Colli Licia , Delvento Chiara , Dovenski Toni , Gorjanc Gregor , Hall Stephen J. G. , Hoda Anila , Li Meng-Hua , Marković Božidarka , McEwan John , Moradi Mohammad H. , Ruiz-Larrañaga Otsanda , Ružić-Muslić Dragana , Šalamon Dragica , Simčič Mojca , Stepanek Ondrej , Curik Ino , Cubric-Curik Vlatka , Lenstra Johannes A. 
Published: May 2020

AbstractBackgroundIn the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation.ResultsWe collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed$$f_{4}$$f4profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.ConclusionsOur results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.
The TERB1-TERB2-MAJIN complex of mouse meiotic telomeres dates back to the common ancestor of metazoans
Authors: da Cruz Irene , Brochier-Armanet Céline , Benavente Ricardo 
Published: May 2020

Abstract
Background
Meiosis is essential for sexual reproduction and generates genetically diverse haploid gametes from a diploid germ cell. Reduction of ploidy depends on active chromosome movements during early meiotic prophase I. Chromosome movements require telomere attachment to the nuclear envelope. This attachment is mediated by telomere adaptor proteins. Telomere adaptor proteins have to date been identified in fission yeast and mice. In the mouse, they form a complex composed of the meiotic proteins TERB1, TERB2, and MAJIN. No sequence similarity was observed between these three mouse proteins and the adaptor proteins of fission yeast, raising the question of the evolutionary history and significance of this specific protein complex.

Result
Here, we show the TERB1, TERB2, and MAJIN proteins are found throughout the Metazoa and even in early-branching non-bilateral phyla such as Cnidaria, Placozoa and Porifera. Metazoan TERB1, TERB2, and MAJIN showed comparable domain architecture across all clades. Furthermore, the protein domains involved in the formation of the complex as well as those involved for the interaction with the telomere shelterin protein and the LINC complexes revealed high sequence similarity. Finally, gene expression in the cnidarian Hydra vulgaris provided evidence that the TERB1-TERB2-MAJIN complex is selectively expressed in the germ line.

Conclusion
Our results indicate that the TERB1-TERB2-MAJIN complex has an ancient origin in metazoans, suggesting conservation of meiotic functions.
Dynamic distribution of gut microbiota in meat rabbits at different growth stages and relationship with average daily gain (ADG)
Authors: Fang Shaoming , Chen Xuan , Pan Jiahua , Chen Qiaohui , Zhou Liwen , Wang Chongchong , Xiao Tianfang , Gan Qian Fu 
Published: May 2020

AbstractBackgroundThe mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown.ResultsIn this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the familyRuminococcaceaeandBacteroidales_S24-7_groupwere positively associated with ADG. Conversely,Eubacterium_coprostanoligenes_group,Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome.ConclusionsOur findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.
Growth inhibition and metabolomic analysis of Xanthomonas oryzae pv. oryzae treated with resveratrol
Authors: Luo Huai-Zhi , Guan Ying , Yang Rui , Qian Guo-Liang , Yang Xian-Hui , Wang Jun-Song , Jia Ai-Qun 
Published: May 2020

AbstractBackgroundXanthomonas oryzaepv.oryzae(Xoo) can cause destructive bacterial blight in rice. As an antibacterial, resveratrol may inhibitXoogrowth. This study focused on the potential structural-activity relationship of resveratrol and its derivatives againstXoogrowth, and1H-NMR-based metabolomic analysis was applied to investigate the global metabolite changes inXooafter resveratrol treatment.ResultsResveratrol showed the strongest inhibitory effects onXoogrowth compared with its derivatives, which lacked double bonds (compounds4–6) or hydroxyls were substituted with methoxyls (compounds7–9). The IC50of resveratrol againstXoogrowth was 11.67 ± 0.58 μg/mL. Results indicated that the double bond of resveratrol contributed to its inhibitory effects onXoogrowth, and hydroxyls were vital for this inhibition. Interestingly, resveratrol also significantly inhibitedXooflagellum growth. Based on1H-NMR global metabolic analysis, a total of 30Xoometabolites were identified, the changes in the metabolic profile indicated that resveratrol could cause oxidative stress as well as disturb energy, purine, amino acid, and NAD+metabolism inXoo, resulting in the observed inhibitory effects on growth.ConclusionsThis study showed that the double bond of resveratrol contributed to its inhibitory effects onXoogrowth, and hydroxyls were also the important active groups. Resveratrol could cause oxidative stress ofXoocells, and disturb the metabolism of energy, purine, amino acid and NAD +, thus inhibitXoogrowth.
In vitro synergistic potentials of novel antibacterial combination therapies against Salmonella enterica serovar Typhimurium
Authors: Hossain Md. Akil , Park Hae-Chul , Lee Kwang-Jick , Park Sung-Won , Park Seung-Chun , Kang JeongWoo 
Published: May 2020

Abstract
Background
The antibiotics generally used in farm animals are rapidly losing their effectiveness all over the world as bacteria develop antibiotic resistance. Like some other pathogenic bacteria multidrug-resistant strains of Salmonella enterica serovar Typhimurium (S. Typhimurium) are also frequently found in animals and humans which poses a major public health concern. New strategies are needed to block the development of resistance and to prolong the life of traditional antibiotics. Thus, this study aimed to increase the efficacy of existing antibiotics against S. Typhimurium by combining them with opportunistic phenolic compounds gallic acid (GA), epicatechin, epicatechin gallate, epigallocatechin and hamamelitannin. Fractional inhibitory concentration indexes (FICI) of phenolic compound-antibiotic combinations against S. Typhimurium were determined. Based on the FICI and clinical importance, 1 combination (GA and ceftiofur) was selected for evaluating its effects on the virulence factors of this bacterium. Viability of Rattus norvegicus (IEC-6) cell in presence of this antibacterial combination was evaluated.

Results
Minimum inhibitory concentrations (MICs) of GA, epigallocatechin and hamamelitannin found against different strains of S. Typhimurium were 256, (512–1024), and (512–1024) μg/mL, respectively. Synergistic antibacterial effect was obtained from the combination of erythromycin-epicatechin gallate (FICI: 0.50) against S. Typhimurium. Moreover, additive effects (FICI: 0.502–0.750) were obtained from 16 combinations against this bacterium. The time-kill assay and ultrastructural morphology showed that GA-ceftiofur combination more efficiently inhibited the growth of S. Typhimurium compared to individual antimicrobials. Biofilm viability, and swimming and swarming motilities of S. Typhimurium in presence of GA-ceftiofur combination were more competently inhibited than individual antimicrobials. Viabilities of IEC-6 cells were more significantly enhanced by GA-ceftiofur combinations than these antibacterials alone.

Conclusions
This study suggests that GA-ceftiofur combination can be potential medication to treat S. Typhimurium-associated diarrhea and prevent S. Typhimurium-associated blood-stream infections (e.g.: fever) in farm animals, and ultimately its transmission from animal to human. Further in vivo study to confirm these effects and safety profiles in farm animal should be undertaken for establishing these combinations as medications.
Exogenous melatonin alleviates PEG-induced short-term water deficiency in maize by increasing hydraulic conductance
Authors: Qiao Yujie , Ren Jianhong , Yin Lina , Liu Yijian , Deng Xiping , Liu Peng , Wang Shiwen 
Published: May 2020

Abstract
Background
Water deficiency is likely to become more frequent and intense as a result of global climate change, which may severely impact agricultural production in the world. The positive effects of melatonin (MEL) on alleviation drought or osmotic stress-induced water deficiency in plants has been well reported. However, the underlying mechanism of MEL on the detailed process of plant water uptake and transport under water deficiency condition remains largely unknown.

Results
Application of 1 μM MEL led to enhanced tolerance to water deficiency stress in maize seedlings, as evidenced by maintaining the higher photosynthetic parameters, leaf water status and plant transpiration rate. The relatively higher whole-plant hydraulic conductance (Kplant) and root hydraulic conductance (Lpr) in MEL-treated seedlings suggest that exogenous MEL alleviated water deficiency stress by promoting root water absorption. HgCl2 (aquaporin inhibitor) treatment inhibit the transpiration rate in MEL-treated plants greater than those of MEL-untreated; after recovery by dithiothreitol (DTT, anti-inhibitor), the transpiration rate in MEL-treated plants increased much higher than those of untreated plants. Moreover, under water deficiency, the transcription level of aquaporin genes was up-regulated by MEL application, and the H2O2 was less accumulated in MEL-treated root.

Conclusions
Exogenous MEL promoted aquaporin activity, which contributed to the maintaining of Lpr and Kplant under short-term water deficiency. The increased water uptake and transport lead to improved water status and thus increased tolerance to PEG-induced short-term water deficiency in maize seedlings.
Outcomes of tranexamic acid administration in military trauma patients with intracranial hemorrhage: a cohort study
Authors: Walker Patrick F. , Bozzay Joseph D. , Johnston Luke R. , Elster Eric A. , Rodriguez Carlos J. , Bradley Matthew J. 
Published: May 2020

Abstract
Background
Tranexamic acid (TXA) may be a useful adjunct for military patients with severe traumatic brain injury (TBI). These patients are often treated in austere settings without immediate access to neurosurgical intervention. The purpose of this study was to evaluate any association between TXA use and progression of intracranial hemorrhage (ICH), neurologic outcomes, and venous thromboembolism (VTE) in TBI.

Methods
This was a retrospective cohort study of military casualties from October 2010 to December 2015 who were transferred to a military treatment facility (MTF) in the United States. Data collected included: demographics, types of injuries, initial and interval head computerized tomography (CT) scans, Glasgow Coma Scores (GCS), and six-month Glasgow Outcome Scores (GOS). Results were stratified based on TXA administration, progression of ICH, and VTE.

Results
Of the 687 active duty service members reviewed, 71 patients had ICH (10.3%). Most casualties were injured in a blast (80.3%), with 36 patients (50.7%) sustaining a penetrating TBI. Mean ISS was 28.2 ± 12.3. Nine patients (12.7%) received a massive transfusion within 24 h of injury, and TXA was administered to 14 (19.7%) casualties. Patients that received TXA had lower initial reported GCS (9.2 ± 4.4 vs. 12.5 ± 3.4, p = 0.003), similar discharge GCS (13.3 ± 4.0 vs. 13.8 ± 3.2, p = 0.58), and a larger improvement between initial and discharge GCS (3.7 ± 3.9 vs. 1.3 ± 3.1, p = 0.02). However, there was no difference in mortality (7.1% vs. 7.0%, p = 1.00), progression of ICH (45.5% vs. 14.7%, p = 0.09), frequency of cranial decompression (50.0% vs. 42.1%, p = 0.76), or mean GOS (3.5 ± 0.9 vs. 3.8 ± 1.0, p = 0.13). Patients administered TXA had a higher rate of VTE (35.7% vs. 7.0%, p = 0.01). On multivariate analysis, however, TXA was not independently associated with VTE.

Conclusions
Patients that received TXA were associated with an improvement in GCS but not in progression of ICH or GOS. TXA was not independently associated with VTE, although this may be related to a paucity of patients receiving TXA. Decisions about TXA administration in military casualties with ICH should be considered in the context of the availability of neurosurgical intervention as well as severity of extracranial injuries and need for massive transfusion.
Application of the matched nested case-control design to the secondary analysis of trial data
Authors: Partlett Christopher , Hall Nigel J. , Leaf Alison , Juszczak Edmund , Linsell Louise 
Published: May 2020

Abstract
Background
A nested case-control study is an efficient design that can be embedded within an existing cohort study or randomised trial. It has a number of advantages compared to the conventional case-control design, and has the potential to answer important research questions using untapped prospectively collected data.

Methods
We demonstrate the utility of the matched nested case-control design by applying it to a secondary analysis of the Abnormal Doppler Enteral Prescription Trial. We investigated the role of milk feed type and changes in milk feed type in the development of necrotising enterocolitis in a group of 398 high risk growth-restricted preterm infants.

Results
Using matching, we were able to generate a comparable sample of controls selected from the same population as the cases. In contrast to the standard case-control design, exposure status was ascertained prior to the outcome event occurring and the comparison between the cases and matched controls could be made at the point at which the event occurred. This enabled us to reliably investigate the temporal relationship between feed type and necrotising enterocolitis.

Conclusions
A matched nested case-control study can be used to identify credible associations in a secondary analysis of clinical trial data where the exposure of interest was not randomised, and has several advantages over a standard case-control design. This method offers the potential to make reliable inferences in scenarios where it would be unethical or impractical to perform a randomised clinical trial.
Targeted imaging of orthotopic prostate cancer by using clinical transformable photoacoustic molecular probe
Authors: Qiu Chen , Bai Yuanyuan , Yin Tinghui , Miao Xiaoyan , Gao Rongkang , Zhou Huichao , Ren Jie , Song Liang , Liu Chengbo , Zheng Hairong , Zheng Rongqin 
Published: May 2020

Abstract
Background
To obtain high-yield histological samples by targeted prostate cancer (PCa) biopsy is the current trend compared with transrectal ultrasound (TRUS)-guided systematic histological biopsy, which is regarded as the gold standard for prostate cancer (PCa) diagnosis. In this paper, we present a targeted PCa imaging strategy using a real-time molecular photoacoustic imaging system integrated with a handheld US probe (PAI/US) and synthesized an integrin αvβ3 targeted probe based on ICG (cRGD–ICG).

Methods
To prepare cRGD–ICG, ICG-NHS was linked to cRGD through carboxyl-co-reaction. In vitro PA imaging ability of cRGD–ICG was tested. Orthotopic PCa-bearing rats were used as animal models. After injected with either cRGD–ICG or non-targeted probe, rats were implemented with PA imaging to confirm the specific accumulation of cRGD–ICG at tumor region. Moreover, pathological frozen slices were made to observe distribution of the probe in prostate tissue ex vivo.

Results
A small molecular PAI probe was synthesized and exhibited excellent targeted imaging ability in vitro. In vivo photoacoustic imaging was carried out after intravenous injection of cRGD-ICG in orthotopic PCa-bearing rats under the facilitation of the PAI/US system. Maximum molecular photoacoustic signals were observed in the tumor area in vivo after the probe injection, which showed 3.8-fold higher signal enhancement than that in the control group (P < 0.05). Significantly higher cRGD-ICG accumulation was observed under confocal microscopy in the tumor region than in normal prostate tissue.

Conclusions
All our results showed that the comprehensive strategy provided a high-yield and reliable method for PCa diagnosis and targeted prostate biopsy, with great clinical translation potential.
Disease-free survival as a surrogate endpoint for overall survival in adjuvant trials of pancreatic cancer: a meta-analysis of 20 randomized controlled trials
Authors: Nie Run-Cong , Zou Xue-Bin , Yuan Shu-Qiang , Chen Ying-Bo , Chen Shi , Chen Yong-Ming , Chen Guo-Ming , Chen Xiao-Jiang , Luo Tian-Qi , Li Shu-Man , Duan Jin-Ling , Wang Yun , Li Yuan-Fang 
Published: May 2020

Abstract
Background
We aimed to assess whether disease-free survival (DFS) could serve as a reliable surrogate endpoint for overall survival (OS) in adjuvant trials of pancreatic cancer.

Methods
We systematically reviewed adjuvant randomized trials for non-metastatic pancreatic cancer after curative resection that reported a hazard ratio (HR) for DFS and OS. We assessed the correlation between treatment effect (HR) on DFS and OS, weighted by sample size or precision of hazard ratio estimate, assuming fixed and random effects, and calculated the surrogate threshold effect (STE). We also performed sensitivity analyses and a leave-one-out cross validation approach to evaluate the robustness of our findings.

Results
After screening 450 relevant articles, we identified a total of 20 qualifying trails comprising 5170 patients for quantitative analysis. We noted a strong correlation between the treatment effects for DFS and OS, with coefficient of determination of 0.82 in the random effect model, 0.82 in the fixed effect model, and 0.80 in the sample size weighting; the robustness of this finding was further verified by the leave-one-out cross-validation approach. Sensitivity analyses with restriction to phase 3 trials, large trials, trials with mature follow-up periods, and trials with adjuvant therapy versus adjuvant therapy strengthened the correlation (0.75 to 0.88) between DFS and OS. The STE was 0.96 for DFS.

Conclusions
Therefore, DFS could be regarded as a surrogate endpoint for OS in adjuvant trials of pancreatic cancer. In future similar adjuvant trials, a hazard ratio for DFS of 0.96 or less would predict a treatment impact on OS.
Sickness absence and disability pension in relation to first childbirth and in nulliparous women according to occupational groups: a cohort study of 492,504 women in Sweden
Authors: Björkenstam Charlotte , László Krisztina D. , Orellana Cecilia , Lidwall Ulrik , Lindfors Petra , Voss Margaretha , Svedberg Pia , Alexanderson Kristina 
Published: May 2020

Abstract
Background
Childbirth has been suggested to increase sickness absence (SA) and disability pension (DP). This may vary by occupation; however, knowledge in this field remains limited. We explored SA and DP in the years before and after childbirth among women in four occupational groups and those without occupation.

Methods
We studied nulliparous women aged 18–39 years, living in Sweden on December 31, 2004 (n = 492,504). Women were categorized into five skill-level based occupational groups and three childbirth groups; no childbirths within 3 years (B0), first childbirth in 2005 with no childbirth within 3 years (B1), and first childbirth in 2005 with at least one more birth within 3 years (B1+). We compared crude and standardized annual mean SA (in spells> 14 days) and DP net days in the 3 years before and 3 years after first childbirth date.

Results
Women in the highest skill level occupations and managers, had less mean SA/DP days during most study years than women in the lowest skill level occupations group. In B1 and B1+, absolute differences in mean SA/DP, particularly in SA, among occupational groups were highest during the year before childbirth. DP was most common in B0, regardless of group and year.

Conclusions
We found that women’s mean SA/DP days before and after first childbirth was higher with decreasing skill-level of the occupational group and these differences were most pronounced in the year before childbirth. DP was most common among women not giving birth, regardless of occupational group.