bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the gut microbiome in a porcine model of thoracic spinal cord injury
Authors: Doelman Adam , Tigchelaar Seth , McConeghy Brian , Sinha Sunita , Keung Martin S. , Manouchehri Neda , Webster Megan , Fisk Shera , Morrison Charlotte , Streijger Femke , Nislow Corey , Kwon Brian K. 
Published: October 2021

Abstract
Background
The gut microbiome is a diverse network of bacteria which inhabit our digestive tract and is crucial for efficient cellular metabolism, nutrient absorption, and immune system development. Spinal cord injury (SCI) disrupts autonomic function below the level of injury and can alter the composition of the gut microbiome. Studies in rodent models have shown that SCI-induced bacterial imbalances in the gut can exacerbate the spinal cord damage and impair recovery. In this study we, for the first time, characterized the composition of the gut microbiome in a Yucatan minipig SCI model. We compared the relative abundance of the most dominant bacterial phyla in control samples to those collected from animals who underwent a contusion-compression SCI at the 2nd or 10th Thoracic level.

Results
We identify specific bacterial fluctuations that are unique to SCI animals, which were not found in uninjured animals given the same dietary regimen or antibiotic administration. Further, we identified a specific time-frame, “SCI-acute stage”, during which many of these bacterial fluctuations occur before returning to “baseline” levels.

Conclusion
This work presents a dynamic view of the microbiome changes that accompany SCI, establishes a resource for future studies and to understand the changes that occur to gut microbiota after spinal cord injury and may point to a potential therapeutic target for future treatment.
Identification of defense related gene families and their response against powdery and downy mildew infections in Vitis vinifera
Authors: Goyal Neetu , Bhatia Garima , Garewal Naina , Upadhyay Anuradha , Singh Kashmir 
Published: October 2021

Abstract
Background
Grapevine (Vitis vinifera) productivity has been severely affected by various bacterial, viral and fungal diseases worldwide. When a plant is infected with the pathogen, various defense mechanisms are subsequently activated in plants at various molecular levels. Thus, for substantiating the disease control in an eco-friendly way, it is essential to understand the molecular mechanisms governing pathogen resistance in grapes.

Results
In our study, we performed genome-wide identification of various defensive genes expressed during powdery mildew (PM) and downy mildew (DM) infections in grapevine. Consequently, we identified 6, 21, 2, 5, 3 and 48 genes of Enhanced Disease Susceptibility 1 (EDS1), Non-Race-specific Disease Resistance (NDR1), Phytoalexin deficient 4 (PAD4), Nonexpressor of PR Gene (NPR), Required for Mla-specified resistance (RAR) and Pathogenesis Related (PR), respectively, in the grapevine genome. The phylogenetic study revealed that V. vinifera defensive genes are evolutionarily related to Arabidopsis thaliana. Differential expression analysis resulted in identification of 2, 4, 7, 2, 4, 1 and 7 differentially expressed Nucleotide-binding leucine rich repeat receptor (NLR), EDS1, NDR1, PAD4, NPR, RAR1 and PR respectively against PM infections and 28, 2, 5, 4, 1 and 19 differentially expressed NLR, EDS1, NDR1, NPR, RAR1 and PR respectively against DM infections in V. vinifera. The co-expression study showed the occurrence of closely correlated defensive genes that were expressed during PM and DM stress conditions.

Conclusion
The PM and DM responsive defensive genes found in this study can be characterized in future for impelling studies relaying fungal and oomycete resistance in plants, and the functionally validated genes would then be available for conducting in-planta transgenic gene expression studies for grapes.
Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.)
Authors: Fan Yu , Lai Dili , Yang Hao , Xue Guoxing , He Ailing , Chen Long , Feng Liang , Ruan Jingjun , Xiang Dabing , Yan Jun , Cheng Jianping 
Published: October 2021

Abstract
Background
Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied.

Results
In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions.

Conclusions
In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.
Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus
Authors: Wang Panpan , Mao Yong , Su Yongquan , Wang Jun 
Published: October 2021

Abstract
Background
Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data.

Results
Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification.

Conclusions
This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.
SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels
Authors: Di Pasquale Adriano , Radomski Nicolas , Mangone Iolanda , Calistri Paolo , Lorusso Alessio , Cammà Cesare 
Published: October 2021

Abstract
Background
Faced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model.

Results
GENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. ‘UK variant’) are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model.

Conclusions
The genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.
Phenotypic variation of floral organs in flowering crabapples and its taxonomic significance
Authors: Zhou Ting , Ning Kun , Zhang Wangxiang , Chen Hong , Lu Xiaoqing , Zhang Donglin , El-Kassaby Yousry A. , Bian Jian 
Published: October 2021

Abstract
Background
In angiosperms, phenotypic variation of floral organs is often considered as the traditional basis for the evolutionary relationship of different taxonomic groups above the species level. However, little is known about that at or below the species level. Here, we experimentally tested the phenotypic variation of Malus floral organs using combined methods of intraspecific uniformity test, interspecific distinctness analysis, principal component analysis, Pearson correlation analysis, and Q-type cluster analysis. The ancestor-inclined distribution characteristic analysis of Malus species and cultivars floral attributes was also carried out, so as to explore its taxonomic significance.

Results
15/44 phenotypic traits (e.g., flower shape, flower type, flower diameter, ...) were highly consistent, distinguishable, and independent and could be used as the basis for Malus germplasm taxonomy. The studied 142 taxa were divided into two groups (A, B) and five sub-groups (A1, A2, B1, B2, B3), with significantly variable floral phenotypic attributes between groups and within sub-groups. Malus natural species were relatively clustered in the same section (series) while homologous cultivars showed evidence of ancestor-inclined distribution characteristics. However, no significant correlation between the evolutionary order of sections (Sect. Docyniopsis → Sect. Chloromeles → Sect. Sorbomalus → Sect. Eumalus) and group/sub-groups (B3 → B2 → B1 → A).

Conclusions
Phenotypic variation of floral organs could better explore the genetic relationship between Malus taxa. The findings improved our cognition of floral phenotypic variation taxonomic significance under the species level.
Disseminated intravascular coagulation following air embolism during orthotropic liver transplantation: is this just a coincidence?
Authors: Arstikyte Karolina , Vitkute Gintare , Traskaite-Juskeviciene Vilma , Macas Andrius 
Published: October 2021

Abstract
Background
During orthotopic liver transplantation, venous air embolism may occur due to iatrogenic injury of the inferior vena cava. However, venous air embolism followed by coagulopathy is a rare event. In this case report, we discuss a possible connection between venous air embolism and disseminated intravascular coagulation.

Case presentation
A 37-year-old male patient with chronic hepatitis B- and C-induced liver cirrhosis was admitted for orthotopic liver transplantation. During the dissection phase of the surgery, arterial blood pressure, heart rate, saturation and end-tidal carbon dioxide levels suddenly decreased, indicating the occurrence of venous air embolism. After stabilizing the patient’s condition, various coagulation issues started developing. Venous air embolism-induced coagulopathy was handled by administering transfusions of various blood products. However, the patient’s condition continued to deteriorate leading to a complete asystole.

Conclusions
This is a rare case of venous air embolism-induced disseminated intravascular coagulation. The real connection remains unclear as disseminated intravascular coagulation for end-stage liver disease patients can be induced by various causes during different stages of liver transplantation. Certainly, both venous air embolism and coagulopathy were significant and led to an unfavorable outcome. Further studies are needed to better understand the possible mechanisms and correlation between these two life-threatening complications.
Predictors for participation in DNA self-sampling of childhood cancer survivors in Switzerland
Authors: Waespe Nicolas , Strebel Sven , Marino Denis , Mattiello Veneranda , Muet Fanny , Nava Tiago , Schindera Christina , Belle Fabien N. , Mader Luzius , Spoerri Adrian , Kuehni Claudia E. , Ansari Marc 
Published: October 2021

AbstractBackgroundResearch on germline genetic variants relies on enough eligible participants which is difficult to achieve for rare diseases such as childhood cancer. With self-collection kits, participants can contribute genetic samples conveniently from their home. Demographic and clinical factors were identified previously that influenced participation in mailed self-collection. People with pre-existing heritable diagnoses might participate differently in germline DNA collection which might render sampling biased in this group. In this nationwide cross-sectional study, we analysed predictive factors of participation in DNA self-collection including heritable diagnoses.MethodsWe identified childhood cancer survivors from the Swiss Childhood Cancer Registry for invitation to germline DNA self-sampling in September 2019. Participants received saliva sampling kits by postal mail at their home, were asked to fill them, sign an informed consent, and send them back by mail. Two reminders were sent to non-participants by mail. We compared demographic, clinical, and treatment information of participants with non-participants using univariable and multivariable logistic regression models.ResultsWe invited 928 childhood cancer survivors in Switzerland with a median age of 26.5 years (interquartile range 19-37), of which 463 (50%) participated. After the initial send out of the sampling kit, 291 (63%) had participated, while reminder letters led to 172 additional participants (37%). Foreign nationality (odds ratio [OR] 0.5; 95%-confidence interval [CI] 0.4-0.7), survivors aged 30-39 years at study versus other age groups (OR 0.5; CI 0.4-0.8), and survivors with a known cancer predisposition syndrome (OR 0.5; CI 0.3-1.0) were less likely to participate in germline DNA collection. Survivors with a second primary neoplasm (OR 1.9; CI 1.0-3.8) or those living in a French or Italian speaking region (OR 1.3; CI 1.0-1.8) tended to participate more.ConclusionsWe showed that half of childhood cancer survivors participated in germline DNA self-sampling relying completely on mailing of sample kits. Written reminders increased the response by about one third. More targeted recruitment strategies may be advocated for people of foreign nationality, aged 30-39 years, and those with cancer predisposition syndromes. Perceptions of genetic research and potential barriers to participation of survivors need to be better understood.Trial registrationBiobank:https://directory.bbmri-eric.eu/#/collection/bbmri-eric:ID:CH_HopitauxUniversitairesGeneve:collection:CH_BaHOP Research project: Clinicaltrials.gov:NCT04702321.
Factors affecting statin uptake among people living with HIV: primary care provider perspectives
Authors: Ober Allison J. , Takada Sae , Zajdman Deborah , Todd Ivy , Horwich Tamara , Anderson Abraelle , Wali Soma , Ladapo Joseph A. 
Published: October 2021

Abstract
Background
Cardiovascular disease (CVD) is a major cause of morbidity and mortality among people living with HIV (PLWH), but statin therapy, safe and effective for PLWH, is under-prescribed. This study examined clinic leadership and provider perceptions of factors associated with statin prescribing for PLWH receiving care in eight community health clinics across Los Angeles, California.

Methods
We conducted semi-structured telephone interviews with clinic leadership and providers across community health clinics participating in a larger study (INSPIRE) aimed at improving statin prescribing through education and feedback. Clinics included federally qualified health centers (N = 5), community clinics (N = 1) and county-run ambulatory care clinics (N = 2). Leadership and providers enrolled in INSPIRE (N = 39) were invited to participate in an interview. We used the Consolidated Framework for Implementation Research (CFIR) to structure our interview guide and analysis. We used standard qualitative content analysis methods to identify themes within CFIR categories; we also assessed current CVD risk assessment and statin-prescribing practices.

Results
Participants were clinic leaders (n = 6), primary care physicians with and without an HIV specialization (N = 6, N = 6, respectively), infectious diseases specialists (N = 12), nurse practitioners, physician assistants and registered nurses (N = 7). Ninety-five percent of providers from INSPIRE participated in an interview. We found that CVD risk assessment for PLWH is standard practice but that there is variation in risk assessment practices and that providers are unsure whether or how to adjust the risk threshold to account for HIV. Time, clinic and patient priorities impede ability to conduct CVD risk assessment with PLWH.

Conclusions
Providers desire more data and standard practice guidance on prescribing statins for PLWH, including estimates of the effect of HIV on CVD, how to adjust the CVD risk threshold to account for HIV, which statins are best for people on antiretroviral therapy and on shared decision-making around prescribing statins to PLWH. While CVD risk assessment and statin prescribing fits within the mission and workflow of primary care, clinics may need to emphasize CVD risk assessment and statins as priorities in order to improve uptake.
Nutrition assessment and geriatric associated conditions among free living elderly people in Birjand, East of Iran: a cross-sectional study
Authors: Hoseinzadeh-Chahkandak Fatemeh , Rahimlou Mehran , Salmani Fatemeh , Ansarifar Elham , Moodi Mitra , Sharifi Farshad , Zeinali Tayebeh 
Published: October 2021

Abstract
Background
Few data are available on the nutritional status of Iranian geriatric population. The present study aimed to determine the nutritional status of older adults’ population in Birjand, East of Iran.

Methods
The community-based cohort study was performed on older adults population (60 years and older) living in urban and rural areas of Birjand. The mini nutritional assessment (MNA) questionnaire was used to assess nutritional status. Anthropometric and biochemical evaluation were also performed for all of the participants.

Results
A total of 1417 geriatric person were enrolled in this study, which, most of them were female (51.9 %). According to MNA tool, most of the participants (73.3 %) had normal nutrition (MNA score ≥ 24). Malnourished (MNA score < 17) and at high risk of malnutrition (MNA score: 17- 23.5) were constituted 0.9 % and 25.8 % of the participants, respectively. Marital status, occupation, period of education and family member were associated with nutritional status. Multiple logistic regression showed that with increase of body mass index (BMI) (OR = 0.96), education years (OR = 0.95), hemoglobin (OR = 0.86) and lymphocyte (OR = 0.98), the odds of malnutrition decreased, but with increase of age the odds (1.03) of malnutrition is also elevated.

Conclusions
MNA could successfully forecast the risk of malnutrition and malnourished people. Sociodemographic factors are associated with the nutritional status.