bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic dissection of stem WSC accumulation and remobilization in wheat (Triticum aestivum L.) under terminal drought stress
Authors: Li Mengfei , Liu Yuan , Ma Jingfu , Zhang Peipei , Wang Caixiang , Su Junji , Yang Delong 
Published: April 2020

Abstract
Background
The accumulation and remobilization of stem water soluble carbohydrates (WSC) are determinant physiological traits highly influencing yield potential in wheat against drought stress. However, knowledge gains of the genetic control are still limited. A hexaploid wheat population of 120 recombinant inbred lines were developed to identify quantitative trait loci (QTLs) and to dissect the genetic basis underlying eight traits related to stem WSC under drought stress (DS) and well-watered (WW) conditions across three environments.

Results
Analysis of variance (ANOVA) revealed larger environmental and genotypic effects on stem WSC-related traits, indicating moderate heritabilities of 0.51–0.72. A total of 95 additive and 88 pairs of epistatic QTLs were identified with significant additive and epistatic effects, as well as QTL× water environmental interaction (QEI) effects. Most of additive QTLs and additive QEIs associated with drought-stressed environments functioned genetic effects promoting pre-anthesis WSC levels and stem WSC remobilization to developing grains. Compared to other genetic components, both genetic effects were performed exclusive contributions to phenotypic variations in stem WSC-related traits. Nineteen QTL clusters were identified on chromosomes 1B, 2A, 2B, 2D, 3B, 4B, 5A, 6A, 6B and 7A, suggestive of the genetic linkage or pleiotropy. Thirteen additive QTLs were detectable repeatedly across two of the three water environments, indicating features of stable expressions. Some loci were consistent with those reported early and were further discussed.

Conclusion
Stem WSC-related traits were inherited predominantly by additive and QEI effects with a moderate heritability. QTL cluster regions were suggestive of tight linkage or pleiotropy in the inheritance of these traits. Some stable and common loci, as well as closely linked molecular markers, had great potential in marker-assisted selection to improve stem WSC-related traits in wheat, especially under drought-stressed environments.
Transcriptomic analysis of flower induction for long-day pitaya by supplementary lighting in short-day winter season
Authors: Xiong Rui , Liu Chengli , Xu Min , Wei Shuang-shuang , Huang Jia-quan , Tang Hua 
Published: April 2020

Abstract
Background
Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April in Hainan, China. To harvest pitayas with high economic value in the winter season, it is necessary to provide supplementary lighting at night to induce flowering. To further explore the molecular regulating mechanisms of flower induction in pitaya plants exposed to supplementary lighting, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya plants subjected to light induction.

Results
We assembled 68,113 unigenes in total, comprising 29,782 unigenes with functional annotations in the NR database, 20,716 annotations in SwissProt, 18,088 annotations in KOG, and 11,059 annotations in KEGG. Comparisons between different samples revealed different numbers of significantly differentially expressed genes (DEGs). A number of DEGs involved in energy metabolism-related processes and plant hormone signaling were detected. Moreover, we identified many CONSTANS-LIKE, FLOWERING LOCUS T, and other DEGs involved in the direct regulation of flowering including CDF and TCP, which function as typical transcription factor genes in the flowering process. At the transcriptomic level, we verified 13 DEGs with different functions in the time-course response to light-induced flowering by quantitative reverse-transcription PCR analysis.

Conclusions
The identified DEGs may include some key genes controlling the pitaya floral-induction network, the flower induction and development is very complicated, and it involves photoperiod perception and different phytohormone signaling. These findings will increase our understanding to the molecular mechanism of floral regulation of long-day pitaya plants in short-day winter season induced by supplementary lighting.
The influence of balanced complex chromosomal rearrangements on preimplantation embryonic development potential and molecular karyotype
Authors: Li Gang , Shi Weiyi , Niu Wenbin , Xu Jiawei , Guo Yihong , Su Yingchun , Sun Yingpu 
Published: April 2020

Abstract
Background
Balanced complex chromosome rearrangements (BCCR) are balanced chromosomal structural aberrations that involve two or more chromosomes and at least three breakpoints. It is very rare in the population. The objective is to explore the difference of influence of three types of BCCR on early embryonic development and molecular karyotype.

Results
Twelve couples were recruited including four couples of three-way rearrangements carriers (group A), three couples of double two-way translocations carriers (group B) and five couples of exceptional CCR carriers (group C). A total of 243 oocytes were retrievedin the seventeen preimplantation genetic testing (PGT) cycles, and 207 of these were available for fertilization. After intracytoplasmic sperm injection, 181oocytes normally fertilized. The rates of embryos forming on day3 in three groups were 87.88, 97.78 and77.14%, which was significantly different (P = 0.01). Compared with group B, the rate of embryo formation was statistically significantly lower in group C (P = 0.01). Furthermore, the rates of high-quality blastocysts in three group were 14.71, 48.15 and 62.96%, respectively, which was significantly different (P = 0.00). Compared with group B andC, the rate of high-quality blastocysts in group A was statistically significantly lower (P = 0.00;P = 0.00).
Comprehensive chromosome analysis was performed on 83 embryos, including 75 trophectodermcellsand 8 blastomeres. Except 7 embryos failed to amplify, 9.01%embryos were diagnosed as euploidy, and 90.91% were diagnosed as abnormal. As for group A, the euploid embryo rate was 10.71%and the abnormal embryo rate was 89.29%. In group B,the euploid embryo rate was 3.85%, the abnormal embryo rate was 96.15%. The euploid embryo rate was 13.04%, the abnormal embryo rate was 86.96% in group C. There were no significant differences among the three groups (P = 0.55).

Conclusions
The lowest rate of high quality blastocysts has been for three-way rearrangements and the lowest rate of euploidy has been for double two-way translocations, although no significant difference. Different types of BCCR maybe have little effect on the embryonic molecular karyotype. The difference of influence of BCCR on early embryonic developmentandmolecular karyotypeshould be further studied.
Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations
Authors: Chu Duan , Wei Lai 
Published: April 2020

Abstract
Background
Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate. Intuitively, one may hypothesize that those synonymous mutations which increase the tAI values are favored by natural selection.

Results
We use the maize (Zea mays) genome to test our assumption. The first supporting evidence is that the tAI-increasing synonymous mutations have higher fixed-to-polymorphic ratios than the tAI-decreasing ones. Next, the DAF (derived allele frequency) or MAF (minor allele frequency) of the former is significantly higher than the latter. Moreover, similar results are obtained when we investigate CAI (codon adaptation index) instead of tAI.

Conclusion
The synonymous mutations in the maize genome are not strictly neutral. The tAI-increasing mutations are positively selected while those tAI-decreasing ones undergo purifying selection. This selection force might be weak but should not be automatically ignored.
Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
Authors: Schwarzkopf Enrique J. , Motamayor Juan C. , Cornejo Omar E. 
Published: April 2020

Abstract
Background
Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the frequency of beneficial mutations in a population. To understand the role of recombination generating and maintaining haplotypic variation in a population, we can construct fine-scale recombination maps. Such maps have been used to study a variety of model organisms and proven to be informative of how selection and demographics shape species-wide variation. Here we present a fine-scale recombination map for ten populations of Theobroma cacao – a non-model, long-lived, woody crop. We use this map to elucidate the dynamics of recombination rates in distinct populations of the same species, one of which is domesticated.

Results
Mean recombination rates in range between 2.5 and 8.6 cM/Mb for most populations of T. cacao with the exception of the domesticated Criollo (525 cM/Mb) and Guianna, a more recently established population (46.5 cM/Mb). We found little overlap in the location of hotspots of recombination across populations. We also found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. We find mutations in FIGL-1, a protein shown to downregulate cross-over frequency in Arabidopsis, statistically associated to higher recombination rates in domesticated Criollo.

Conclusions
We generated fine-scale recombination maps for ten populations of Theobroma cacao and used them to understand what processes are associated with population-level variation in this species. Our results provide support to the hypothesis of increased recombination rates in domesticated plants (Criollo population). We propose a testable mechanistic hypothesis for the change in recombination rate in domesticated populations in the form of mutations to a previously identified recombination-suppressing protein. Finally, we establish a number of possible correlates of recombination hotspots that help explain general patterns of recombination in this species.
Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus
Authors: Li Mengdi , Wang Ruihua , Wu Xiaoming , Wang Jianbo 
Published: April 2020

Abstract
Background
Allopolyploidy is widespread in angiosperms, and they can coordinate two or more different genomes through genetic and epigenetic modifications to exhibit stronger vigor and adaptability. To explore the changes in homologous gene expression patterns in the natural allotetraploid Brassica napus (AnAnCnCn) relative to its two diploid progenitors, B. rapa (ArAr) and B. oleracea (CoCo), after approximately 7500 years of domestication, the global gene pair expression patterns in four major tissues (stems, leaves, flowers and siliques) of these three species were analyzed using an RNA sequencing approach.

Results
The results showed that the ‘transcriptomic shock’ phenomenon was alleviated in natural B. napus after approximately 7500 years of natural domestication, and most differentially expressed genes (DEGs) in B. napus were downregulated relative to those in its two diploid progenitors. The KEGG analysis indicated that three pathways related to photosynthesis were enriched in both comparison groups (AnAnCnCn vs ArAr and AnAnCnCn vs CoCo), and these pathways were all downregulated in four tissues of B. napus. In addition, homoeolog expression bias and expression level dominance (ELD) in B. napus were thoroughly studied through analysis of expression levels of 27,609 B. rapa-B. oleracea orthologous gene pairs. The overwhelming majority of gene pairs (an average of 86.7%) in B. napus maintained their expression pattern in two diploid progenitors, and approximately 78.1% of the gene pairs showed expression bias with a preference toward the A subgenome. Overall, an average of 48, 29.7 and 22.3% homologous gene pairs exhibited additive expression, ELD and transgressive expression in B. napus, respectively. The ELD bias varies from tissue to tissue; specifically, more gene pairs in stems and siliques showed ELD-A, whereas the opposite was observed in leaves and flowers. More transgressive upregulation, rather than downregulation, was observed in gene pairs of B. napus.

Conclusions
In general, these results may provide a comprehensive understanding of the changes in homologous gene expression patterns in natural B. napus after approximately 7500 years of evolution and domestication and may enhance our understanding of allopolyploidy.
Human CD8+CD28− T suppressor cells expanded by common gamma chain (γc) cytokines retain steady allospecific suppressive capacity in vivo
Authors: Liu Guihuan , Yu Yuming , Feng Fu , Zhu Ping , Zhang Hua , Zhang Danni , Feng Xiaoqiang , Zhang Zedan , Liu Yanjun 
Published: April 2020

AbstractBackgroundCD8+CD28−T suppressor (Ts) cells play critical role in transplant tolerance. Our previous study has generated CD8+CD28−Ts cells in vitro which exert robust allospecific suppressive capacity in vitro.ResultsCD8+CD28−Ts cells were expanded by stimulating human CD8+T cells with allogeneic antigen presenting cells in the presence of the common gamma chain cytokines IL-2, IL-7 and IL-15 in vitro, and were further verified in vitro through day 7 to 11 for their persistency of the allospecific suppressive capacity. When CD8+CD28−Ts cells were adoptively transferred into NOG mice, their capacity to inhibit CD4+T cell proliferation in allospecific manner remained potent on 11 days after their injection. The mechanisms for expansion of CD8+CD28−Ts cells by the common gamma chain cytokines were investigated. These included promoting CD8+CD28−T cells proliferation, converting CD8+CD28+T cells to CD8+CD28−T cells and decreasing CD8+CD28−T cell death. Furthermore, the expanded CD8+CD28−Ts cells showed upregulation of the co-inhibitory molecule Tim-3 and down-regulation of the cytotoxic molecule granzyme B.ConclusionsIn summary, these results demonstrated that the in vitro-expanded human CD8+CD28−T cells retained potent allospecific suppressive capacity in vivo and depicted multiple mechanisms for the expansion of Ts cells, which might promote further bench to clinic research.
Low phosphatase activity of LiaS and strong LiaR-DNA affinity explain the unusual LiaS to LiaR in vivo stoichiometry
Authors: Jani Shailee , Sterzenbach Karen , Adatrao Vijaya , Tajbakhsh Ghazal , Mascher Thorsten , Golemi-Kotra Dasantila 
Published: April 2020

Abstract
Background
LiaRS mediates Bacillus subtilis response to cell envelope perturbations. A third protein, LiaF, has an inhibitory role over LiaRS in the absence of stimulus. Together, LiaF and LiaRS form a three-component system characterized by an unusual stoichiometry, a 4:1 ratio between LiaS and LiaR, the significance of which in the signal transduction mechanism of LiaRS is not entirely understood.

Results
We measured, for the first time, the kinetics of the phosphorylation-dependent processes of LiaRS, the DNA-binding affinity of LiaR, and characterized the effect of phosphorylation on LiaR oligomerization state. Our study reveals that LiaS is less proficient as a phosphatase. Consequently, unspecific phosphorylation of LiaR by acetyl phosphate may be significant in vivo. This drawback is exacerbated by the strong interaction between LiaR and its own promoter, as it can drive LiaRS into losing grip over its own control in the absence of stimuli. These intrinsic, seemingly ‘disadvantageous”, attributes of LiaRS are likely overcome by the higher concentration of LiaS over LiaR in vivo, and a pro-phosphatase role of LiaF.

Conclusions
Overall, our study shows that despite the conservative nature of two-component systems, they are, ultimately, tailored to meet specific cell needs by modulating the dynamics of interactions among their components and the kinetics of phosphorylation-mediated processes.
The neutrophil/lymphocyte ratio as a predictor of successful conversion surgery for stage IV gastric cancer: a retrospective study
Authors: Nakamura Naohiko , Kinami Shinichi , Tomita Yasuto , Miyata Takashi , Fujita Hideto , Takamura Hiroyuki , Ueda Nobuhiko , Kosaka Takeo 
Published: April 2020

AbstractBackgroundConversion surgery (CS) following a response to chemotherapy occasionally leads to prolonged survival in patients with stage IV gastric cancer (GC). This study aimed to evaluate the predictive value of the neutrophil/lymphocyte ratio (NLR) for the success of CS in patients with stage IV GC.MethodsWe retrospectively analyzed data of 50 patients with stage IV GC who received systemic chemotherapy between January 2009 and December 2017 at the Kanazawa Medical University Hospital. The successful CS group included the patients who underwent R0 or R1 resection with CS, and the failed CS group included the patients who did not undergo CS after chemotherapy or those who, despite undergoing CS, had to additionally undergo R2 resection. Clinicopathological characteristics were examined in both groups. Univariate and multivariate analyses were performed to identify pretherapeutic parameters that were independently associated with the achievement of successful CS.ResultsThe number of patients in the successful and failed CS groups were 12 and 38, respectively. On univariate analysis, gender (P = 0.01), NLR (P = 0.003), albumin levels (P = 0.004), and absence of peritoneal metastasis (P = 0.004) were found to be significantly correlated with a successful CS. On multivariate analysis, NLR < 4 and absence of peritoneal metastasis were independently correlated with a successful CS (P = 0.02 andP = 0.002, respectively). In patients without peritoneal metastasis, successful CS rates in patients with NLR < 4 were significantly higher than those in patients with NLR ≥ 4 (61.1% vs. 10.0%,P = 0.005).ConclusionsThe NLR was a significant independent predictor of the achievement of successful CS in stage IV GC patients, especially among the patients without peritoneal metastasis. Patients with a low NLR could have higher possibility of achieving successful CS.
Workplace violence against hospital healthcare workers in China: a national WeChat-based survey
Authors: Tian Yusheng , Yue Yuchen , Wang Jianjian , Luo Ting , Li Yamin , Zhou Jiansong 
Published: April 2020

Abstract
Background
Workplace violence (WPV) is a serious issue for healthcare workers and leads to many negative consequences. Several studies have reported on the prevalence of WPV in China, which ranges from 42.2 to 83.3%. However, little information is available regarding the correlates of WPV among healthcare workers and the differences across the different levels of hospitals in China. This study aimed to explore the correlates of WPV and career satisfaction among healthcare workers in China.

Methods
A self-designed WeChat-based questionnaire was used that included demographic and occupational factors. The Chinese version of the Workplace Violence Scale was used to measure WPV. Career satisfaction was assessed using two questions about career choices. Descriptive analyses, chi-square tests and multivariate logistic regressions were used.

Results
A total of 3706 participants (2750 nurses and 956 doctors) responded to the survey. Among the 3684 valid questionnaires, 2078 (56.4%) reported at least one type of WPV in the last year. Multivariate logistic regressions revealed that male sex, shift work, bachelor’s degree education, a senior professional title, working more than 50 h per week and working in secondary-level hospitals were risk factors associated with WPV. Healthcare workers who had experienced higher levels of WPV were less likely to be satisfied with their careers.

Conclusions
WPV remains a special concern for the Chinese healthcare system. Interventions to reduce WPV should be implemented by health authorities to create a zero-violence practice environment.
Barriers and facilitators to retaining a cohort of street-based cisgender female sex workers recruited in Baltimore, Maryland, USA: results from the SAPPHIRE study
Authors: Silberzahn Bradley E. , Morris Miles B. , Riegger Katelyn E. , White Rebecca Hamilton , Tomko Catherine A. , Park Ju Nyeong , Footer Katherine H.A. , Huettner Steven S. , Sherman Susan G. 
Published: April 2020

Abstract
Background
Despite experiencing HIV/STIs, violence, and other morbidities at higher rates than the general public, street-based female sex workers are often absent from public health research and surveillance due to the difficulty and high costs associated with engagement and retention. The current study builds on existing literature by examining barriers and facilitators of retaining a street-based cohort of cisgender female sex workers recruited in a mobile setting in Baltimore, Maryland who participated in the SAPPHIRE study. Participants completed interviews and sexual health testing at baseline, 3-, 6-, 9-, and 12-months.

Methods
Retention strategies are described and discussed in light of their benefits and challenges. Strategies included collecting several forms of participant contact information, maintaining an extensive field presence by data collectors, conducting social media outreach and public record searches, and providing cash and non-cash incentives. We also calculated raw and adjusted retention proportions at each follow-up period. Lastly, baseline sample characteristics were compared by number of completed visits across demographic, structural vulnerabilities, work environment, and substance use variables using F-tests and Pearson’s chi-square tests.

Results
Although there were drawbacks to each retention strategy, each method was useful in tandem in achieving a successful follow-up rate. While direct forms of contact such as phone calls, social media outreach, and email were useful for retaining more stable participants, less stable participants required extensive field-based efforts such as home and site visits that increase the likelihood of random encounters. Overall, adjusted retention exceeded 70% for the duration of the 12-month study. Participants who were younger, recently experienced homelessness, and injected drugs daily were less likely to have completed all or most follow-up visits.

Conclusion
Retention of street-based female sex workers required the simultaneous use of diverse retention strategies that were tailored to participant characteristics. With familiarity of the dynamic nature of the study population characteristics, resources can be appropriately allocated to strategies most likely to result in successful retention.