bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes
Authors: Whittle Carrie A. , Kulkarni Arpita , Chung Nina , Extavour Cassandra G. 
Published: April 2021

Abstract
Background
For multicellular organisms, much remains unknown about the dynamics of synonymous codon and amino acid use in highly expressed genes, including whether their use varies with expression in different tissue types and sexes. Moreover, specific codons and amino acids may have translational functions in highly transcribed genes, that largely depend on their relationships to tRNA gene copies in the genome. However, these relationships and putative functions are poorly understood, particularly in multicellular systems.

Results
Here, we studied codon and amino acid use in highly expressed genes from reproductive and nervous system tissues (male and female gonad, somatic reproductive system, brain and ventral nerve cord, and male accessory glands) in the cricket Gryllus bimaculatus. We report an optimal codon, defined as the codon preferentially used in highly expressed genes, for each of the 18 amino acids with synonymous codons in this organism. The optimal codons were mostly shared among tissue types and both sexes. However, the frequency of optimal codons was highest in gonadal genes. Concordant with translational selection, a majority of the optimal codons had abundant matching tRNA gene copies in the genome, but sometimes obligately required wobble tRNAs. We suggest the latter may comprise a mechanism for slowing translation of abundant transcripts, particularly for cell-cycle genes. Non-optimal codons, defined as those least commonly used in highly transcribed genes, intriguingly often had abundant tRNAs, and had elevated use in a subset of genes with specialized functions (gametic and apoptosis genes), suggesting their use promotes the translational upregulation of particular mRNAs. In terms of amino acids, we found evidence suggesting that amino acid frequency, tRNA gene copy number, and amino acid biosynthetic costs (size/complexity) had all interdependently evolved in this insect model, potentially for translational optimization.

Conclusions
Collectively, the results suggest a model whereby codon use in highly expressed genes, including optimal, wobble, and non-optimal codons, and their tRNA abundances, as well as amino acid use, have been influenced by adaptation for various functional roles in translation within this cricket. The effects of expression in different tissue types and the two sexes are discussed.
Gene co-expression network analysis reveals key pathways and hub genes in Chinese cabbage (Brassica rapa L.) during vernalization
Authors: Dai Yun , Sun Xiao , Wang Chenggang , Li Fei , Zhang Shifan , Zhang Hui , Li Guoliang , Yuan Lingyun , Chen Guohu , Sun Rifei , Zhang Shujiang 
Published: April 2021

AbstractBackgroundVernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapaL.ssp. pekinensis), this process causes their commercial value to decline. Clarifying the mechanisms of vernalization is essential for its further application. We performed RNA sequencing of gradient-vernalization in order to explore the reasons for the different bolting process of two Chinese cabbage accessions during vernalization.ResultsThere was considerable variation in gene expression between different-bolting Chinese cabbage accessions during vernalization. Comparative transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were performed for different-bolting Chinese cabbage during different vernalization periods. The biological function analysis and hub gene annotation of highly relevant modules revealed that shoot system morphogenesis and polysaccharide and sugar metabolism caused early-bolting ‘XBJ’ to bolt and flower faster; chitin, ABA and ethylene-activated signaling pathways were enriched in late-bolting ‘JWW’; and leaf senescence and carbohydrate metabolism enrichment were found in the two Chinese cabbage-related modules, indicating that these pathways may be related to bolting and flowering. The high connectivity of hub genes regulated vernalization, includingMTHFR2,CPRD49,AAP8, endoglucanase 10,BXLs,GATLs, andWRKYs. Additionally, five genes related to flower development,BBX32(binds to theFTpromoter),SUS1(increasesFTexpression),TSF(the closest homologue ofFT),PAOandNAC029(plays a role in leaf senescence), were expressed in the two Chinese cabbage accessions.ConclusionThe present work provides a comprehensive overview of vernalization-related gene networks in two different-bolting Chinese cabbages during vernalization. In addition, the candidate pathways and hub genes related to vernalization identified here will serve as a reference for breeders in the regulation of Chinese cabbage production.
Mitogenomic phylogeny of Callithrix with special focus on human transferred taxa
Authors: Malukiewicz Joanna , Cartwright Reed A. , Curi Nelson H. A. , Dergam Jorge A. , Igayara Claudia S. , Moreira Silvia B. , Molina Camila V. , Nicola Patricia A. , Noll Angela , Passamani Marcello , Pereira Luiz C. M. , Pissinatti Alcides , Ruiz-Miranda Carlos R. , Silva Daniel L. , Stone Anne C. , Zinner Dietmar , Roos Christian 
Published: April 2021

AbstractBackgroundCallithrixmarmosets are a relatively young primate radiation, whose phylogeny is not yet fully resolved. These primates are naturally para- and allopatric, but three species with highly invasive potential have been introduced into the southeastern Brazilian Atlantic Forest by the pet trade. There, these species hybridize with each other and endangered, native congeners. We aimed here to reconstruct a robustCallithrixphylogeny and divergence time estimates, and identify the biogeographic origins of autochthonous and allochthonousCallithrixmitogenome lineages. We sequenced 49 mitogenomes from four species (C. aurita,C. geoffroyi,C. jacchus,C. penicillata) and anthropogenic hybrids (C. auritaxCallithrixsp.,C. penicillataxC. jacchus,Callithrixsp. xCallithrixsp.,C. penicillataxC. geoffroyi) via Sanger and whole genome sequencing. We combined these data with previously publishedCallithrixmitogenomes to analyze fiveCallithrixspecies in total.ResultsWe report the complete sequence and organization of theC. auritamitogenome. Phylogenetic analyses showed thatC. auritawas the first to diverge withinCallithrix3.54 million years ago (Ma), whileC. jacchusandC. penicillatalineages diverged most recently 0.5 Ma as sister clades. MtDNA clades ofC. aurita,C. geoffroyi, andC. penicillatashow intraspecific geographic structure, butC. penicillataclades appear polyphyletic. Hybrids, which were identified by phenotype, possessed mainlyC. penicillataorC. jacchusmtDNA haplotypes. The biogeographic origins of mtDNA haplotypes from hybrid and allochthonousCallithrixwere broadly distributed across naturalCallithrixranges. Our phylogenetic results also evidence introgression ofC. jacchusmtDNA intoC. aurita.ConclusionOur robustCallithrixmitogenome phylogeny showsC. auritalineages as basal andC. jacchuslineages among the most recent withinCallithrix. We provide the first evidence that parental mtDNA lineages of anthropogenic hybrid and allochthonous marmosets are broadly distributed inside and outside of the Atlantic Forest. We also show evidence of cryptic hybridization between allochthonousCallithrixand autochthonousC. aurita. Our results encouragingly show that further development of genomic resources will allow to more clearly elucidateCallithrixevolutionary relationships and understand the dynamics ofCallithrixanthropogenic introductions into the Brazilian Atlantic Forest.
Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions
Authors: Huang Shaojia , Zhou Wei , Tang Wei , Zhang Yong , Hu Yangbo , Chen Shiyun 
Published: April 2021

Abstract
Background
Hypoxic stress plays a critical role in the persistence of Mycobacterium tuberculosis (Mtb) infection, but the mechanisms underlying this adaptive response remain ill defined.

Material and methods
In this study, using M. marinum as a surrogate, we analyzed hypoxic responses at the transcriptional level by Cappable-seq and regular RNA-seq analyses.

Results
A total of 6808 transcriptional start sites (TSSs) were identified under normoxic and hypoxic conditions. Among these TSSs, 1112 were upregulated and 1265 were downregulated in response to hypoxic stress. Using SigE-recognized consensus sequence, we identified 59 SigE-dependent promoters and all were upregulated under hypoxic stress, suggesting an important role for SigE in this process. We also compared the performance of Cappable-seq and regular RNA-seq using the same RNA samples collected from normoxic and hypoxic conditions, and confirmed that Cappable-seq is a valuable approach for global transcriptional regulation analyses.

Conclusions
Our results provide insights and information for further characterization of responses to hypoxia in mycobacteria, and prove that Cappable-seq is a valuable approach for global transcriptional studies in mycobacteria.
Temporal dynamics of the plasma microbiome in recipients at early post-liver transplantation: a retrospective study
Authors: Okumura Toshihiko , Horiba Kazuhiro , Kamei Hideya , Takeuchi Suguru , Suzuki Takako , Torii Yuka , Kawada Jun-ichi , Takahashi Yoshiyuki , Ogura Yasuhiro , Ogi Tomoo , Ito Yoshinori 
Published: April 2021

Abstract
Background
Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection but poses a risk for severe infectious diseases. Immune modulation and antimicrobials affect the plasma microbiome. Thus, determining the impact of immunosuppression on the microbiome may be important to understand immunocompetence, elucidate the source of infection, and predict the risk of infection in LT recipients. We characterized the plasma microbiome of LT recipients at early post-LT and assessed the association between the microbiome and clinical events.

Results
In this study, 51 patients who received LT at Nagoya University Hospital from 2016 to 2018 were enrolled. Plasma samples were retrospectively collected at the following time points: 1) within a week after LT; 2) 4 ± 1 weeks after LT; 3) 8 ± 1 weeks after LT; and 4) within 2 days after a positive blood culture. A total of 111 plasma samples were analyzed using shotgun next-generation sequencing (NGS) with the PATHDET pipeline. Relative abundance of Anelloviridae, Nocardiaceae, Microbacteriaceae, and Enterobacteriaceae significantly changed during the postoperative period. Microbiome diversity was higher within a week after LT than that at 8 weeks after LT. Antimicrobials were significantly associated with the microbiome of LT recipients. In addition, the proportion of Enterobacteriaceae was significantly increased and the plasma microbiome diversity was significantly lower in patients with acute cellular rejection (ACR) than non-ACR patients. Sequencing reads of bacteria isolated from blood cultures were predominantly identified by NGS in 8 of 16 samples, and human herpesvirus 6 was detected as a causative pathogen in one recipient with severe clinical condition.

Conclusions
The metagenomic NGS technique has great potential in revealing the plasma microbiome and is useful as a comprehensive diagnostic procedure in clinical settings. Temporal dynamics of specific microorganisms may be used as indirect markers for the determination of immunocompetence and ACR in LT recipients.
Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease
Authors: Tateishi Yoshitaka , Ozeki Yuriko , Nishiyama Akihito , Miki Mari , Maekura Ryoji , Fukushima Yukari , Nakajima Chie , Suzuki Yasuhiko , Matsumoto Sohkichi 
Published: April 2021

AbstractBackgroundMycobacterium intracellulareis a representative etiological agent of emerging pulmonaryM. avium-intracellularecomplex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonaryM. avium-intracellularecomplex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially forM. avium; however, the genomic characteristics ofM. intracellulareremain to be elucidated.ResultsIn this study, we performed comparative genomic analysis of 55 M. intracellulareand related strains such asM. paraintracellulare(MP),M. indicus pranii(MIP) andM. yonogonense. Based on the average nucleotide identity, the clinicalM. intracellularestrains were phylogenetically grouped in two clusters: (1) the typicalM. intracellulare(TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g.,fadE3,fadE33), transporters (e.g.,mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains.M. intracellularewas shown to be pan-genomic at the species and subspecies levels. Themcegenes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies.ConclusionsOur data suggest that genomic diversity amongM. intracellulare,M. paraintracellulare,M. indicus praniiandM. yonogonenseremains at the subspecies or genovar levels and does not reach the species level. Genetic components such asmcegenes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis forM. intracellulareand related strains.
Ectopic pancreas appearing as a giant gastric cyst mimicking gastric lymphangioma: a case report and a brief review
Authors: Liu Xuemei , Wu Xinglong , Tuo Biguang , Wu Huichao 
Published: April 2021

Abstract
Background
Ectopic pancreas (EP) is defined as pancreatic tissue that lacks anatomical or vascular communication with the normal body of the pancreas. Despite improvements in diagnostic endoscopy and imaging studies, differentiating ectopic pancreatic tissue from gastric submucosal diseases remains a challenge.

Case presentation
Here, we present a case of a 44-year-old woman with severe epigastric pain. Initially, gastric lymphangioma was highly suspected due to a well-demarcated protruding mass with a large size that occurred in the submucosal layer of the gastric antrum and appeared as a cystic lesion. The final correct diagnosis of gastric EP was made during surgery.

Conclusion
Gastric EP with serous oligocystic adenoma appearing as a giant gastric cyst is extremely rare. The difficulty of making an accurate diagnosis and differential diagnosis is highlighted, which may provide additional clinical experience for the diagnosis of EP with serous oligocystic adenoma in the stomach.
Prognostic significance of MUC2, CDX2 and SOX2 in stage II colorectal cancer patients
Authors: Ribeirinho-Soares Sara , Pádua Diana , Amaral Ana Luísa , Valentini Elvia , Azevedo Daniela , Marques Cristiana , Barros Rita , Macedo Filipa , Mesquita Patrícia , Almeida Raquel 
Published: April 2021

Abstract
Background
Colorectal cancer (CRC) remains a serious health concern worldwide. Despite advances in diagnosis and treatment, about 15 to 30% of stage II CRC patients subjected to tumor resection with curative intent, develop disease relapse. Moreover, the therapeutic strategy adopted after surgery is not consensual for these patients. This supports the imperative need to find new prognostic and predictive biomarkers for stage II CRC.

Methods
For this purpose, we used a one-hospital series of 227 stage II CRC patient samples to assess the biomarker potential of the immunohistochemical expression of MUC2 mucin and CDX2 and SOX2 transcription factors. The Kaplan-Meier method was used to generate disease-free survival curves that were compared using the log-rank test, in order to determine prognosis of cases with different expression of these proteins, different mismatch repair (MMR) status and administration or not of adjuvant chemotherapy.

Results
In this stage II CRC series, none of the studied biomarkers showed prognostic value for patient outcome. However low expression of MUC2, in cases with high expression of CDX2, absence of SOX2 or MMR-proficiency, conferred a significantly worst prognosis. Moreover, cases with low expression of MUC2 showed a significantly clear benefit from treatment with adjuvant chemotherapy.

Conclusion
In conclusion, we observe that patients with stage II CRC with low expression of MUC2 in the tumor respond better when treated with adjuvant chemotherapy. This observation supports that MUC2 is involved in resistance to fluorouracil-based adjuvant chemotherapy and might be a promising future predictive biomarker in stage II CRC patients.
Designing and evaluation of E-health educational intervention on students’ physical activity: an application of Pender’s health promotion model
Authors: Sabooteh Sahar , Feizi Awat , Shekarchizadeh Parivash , Shahnazi Hossein , Mostafavi Firoozeh 
Published: April 2021

Abstract
Background
The present study was conducted to design and evaluate the software and web-based curriculum based on Pender Model in order to promote students’ physical activity.

Methods
This is a quasi-experimental study conducted on 225 eligible students who were randomly divided into two groups of web and software-based intervention and control. The sample size of the study was selected using stratified sampling method. The evaluation was done with pre-test and post-test and follow-up, which were performed immediately two and six months following the intervention. The data were analyzed employing statistical software SPSS using descriptive statistics, chi-square, one way ANOVA, and repeated measures ANOVA.

Results
The obtained results revealed that the level of physical activity after the intervention in the web and software groups significantly increased compared to the control group (p < 0.001). Moreover, the mean score of Pender model constructs, immediately two and six months after the intervention, was significantly different in the web and software groups (p < 0.001).

Conclusion
Our results indicated that, providing tailored message based on health promotion model’s constructs has a positive effect on promoting physical activity of students.

Trial registration
Name: Iranian Registry of Clinical Trials. Registration number: IRCT20181009041298N1. Registration date: 2018–12-02 [retrospectively registered].
Behavioral changes before lockdown and decreased retail and recreation mobility during lockdown contributed most to controlling COVID-19 in Western countries
Authors: Deforche Koen , Vercauteren Jurgen , Müller Viktor , Vandamme Anne-Mieke 
Published: April 2021

Abstract
Background
The COVID-19 pandemic has prompted a lockdown in many countries to control the exponential spread of the SARS-CoV-2 virus, hereby reducing the time-varying basic reproduction number (Rt) to below one. Governments are looking for evidence to balance the demand of their citizens to ease some of the restriction, against the fear of a new peak in infections. In this study, we wanted to quantify the relative contribution of mobility restrictions, and that of behavioral changes that occurred already before the lockdowns, on the reduction of transmission during lockdowns in Western countries in early 2020.

Methods
Incidence data of cases and deaths from the first wave of infections for 35 Western countries (32 European, plus Israel, USA and Canada) were analyzed using epidemiological compartment models in a Bayesian framework. Mobility data was used to estimate the timing of changes associated with a lockdown, and was correlated with estimated reductions of Rt.

Results
Across all countries, the initial median estimate for Rt was 3.6 (95% IQR 2.4–5.2), and it was reduced to 0.78 (95% IQR 0.58–1.01) during lockdown. 48% (18–65%) of the reduction occurred already in the week before lockdown, with lockdown itself causing the remaining drop in transmission. A lower Rt during lockdown was independently associated with an increased time spent at home (0.21 per 10% more time, p < 0.007), and decreased mobility related to retail and recreation (0.07 per 10% less mobility, p < 0.008).

Conclusions
In a Western population unaware of the risk, SARS-CoV-2 can be highly contagious with a reproduction number R0 > 5. Our results are consistent with evidence that recreational activities (including restaurant and bar visits) enable super-spreading events. Exiting from lockdown therefore requires continued physical distancing and tight control on this kind of activities.
Homebound by COVID19: the benefits and consequences of non-pharmaceutical intervention strategies
Authors: Oruc Buse Eylul , Baxter Arden , Keskinocak Pinar , Asplund John , Serban Nicoleta 
Published: April 2021

Abstract
Background
Recent research has been conducted by various countries and regions on the impact of non-pharmaceutical interventions (NPIs) on reducing the spread of COVID19. This study evaluates the tradeoffs between potential benefits (e.g., reduction in infection spread and deaths) of NPIs for COVID19 and being homebound (i.e., refraining from interactions outside of the household).

Methods
An agent-based simulation model, which captures the natural history of the disease at the individual level, and the infection spread via a contact network assuming heterogeneous population mixing in households, peer groups (workplaces, schools), and communities, is adapted to project the disease spread and estimate the number of homebound people and person-days under multiple scenarios, including combinations of shelter-in-place, voluntary quarantine, and school closure in Georgia from March 1 to September 1, 2020.

Results
Compared to no intervention, under voluntary quarantine, voluntary quarantine with school closure, and shelter-in-place with school closure scenarios 4.5, 23.1, and 200+ homebound adult-days were required to prevent one infection, with the maximum number of adults homebound on a given day in the range of 119 K–248 K, 465 K–499 K, 5388 K-5389 K, respectively. Compared to no intervention, school closure only reduced the percentage of the population infected by less than 16% while more than doubling the peak number of adults homebound.

Conclusions
Voluntary quarantine combined with school closure significantly reduced the number of infections and deaths with a considerably smaller number of homebound person-days compared to shelter-in-place.