bluuebunny/crossref_metadata_2025_split huggingface dataset:
The bleeding phenotype in people with nonsevere hemophilia
Authors: Kloosterman Fabienne R. , Zwagemaker Anne-Fleur , Bagot Catherine N. , Beckers Erik A. M. , Castaman Giancarlo , Cnossen Marjon H. , Collins Peter W. , Hay Charles , Hof Michel , Laros-van Gorkom Britta , Leebeek Frank W. G. , Male Christoph , Meijer Karina , Pabinger Ingrid , Shapiro Susan , Coppens Michiel , Fijnvandraat Karin , Gouw, Samantha C. 
Published: May 2022

Abstract
Detailed information on the onset, frequency, and severity of bleeding in nonsevere hemophilia is limited. We aimed to assess the bleeding phenotype of persons with nonsevere hemophilia and to analyze the association between baseline factor VIII/IX (FVIII/IX) levels and the joint bleeding rate. In the DYNAMO (Dynamic Interplay Between Bleeding Phenotype and Baseline Factor Level in Moderate and Mild Hemophilia A and B) study, an international multicenter cohort, we included males with nonsevere hemophilia (FVIII/IX, 0.02-0.35 IU/mL) aged 12 to 55 years. Information on age at first treated (joint) bleed, annual bleeding rates (ABRs), and annual joint bleeding rates (AJBRs) was collected from the medical files. The association between baseline FVIII/IX levels and the joint bleeding rate was assessed by using a frailty model for recurrent events. In total, 304 persons (70 with moderate hemophilia and 234 with mild hemophilia) were included. The median age was 38 years (interquartile range [IQR], 25-49 years), and the median baseline FVIII/IX level was 0.12 IU/mL (IQR, 0.05-0.21 IU/mL). In total, 245 (81%) persons had experienced at least 1 bleed, and 156 (51%) had experienced at least 1 joint bleed. The median age at first bleed and first joint bleed was 8 and 10 years, respectively. The median ABR and AJBR was 0.2 (IQR, 0.1-0.5) and 0.0 (IQR, 0.0-0.2). From baseline FVIII/IX levels 0.02 to 0.05 IU/mL to &gt;0.25 IU/mL, the median ABR decreased from 0.6 (IQR, 0.2-1.4) to 0.1 (IQR, 0.0-0.2) and the AJBR from 0.2 (IQR, 0.0-0.4) to 0.0 (IQR, 0.0-0.0). Baseline FVIII/IX was inversely associated with the joint bleeding rate (P &lt; .001). Low bleeding rates were observed in persons with nonsevere hemophilia. However, one-half of all adolescents and adults had experienced a joint bleed.
HGGA: hierarchical guided genome assembler
Authors: Walve Riku , Salmela Leena 
Published: May 2022

AbstractBackgroundDe novogenome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is needed to resolve the complete structure of the genome. Most of the previous work uses the additional data to order and orient contigs.ResultsHere we introduce a framework to guide genome assembly with additional data. Our approach is based on clustering the reads, such that each read in each cluster originates from nearby positions in the genome according to the additional data. These sets are then assembled independently and the resulting contigs are further assembled in a hierarchical manner. We implemented our approach for genetic linkage maps in a tool called HGGA.ConclusionsOur experiments on simulated and real Pacific Biosciences long reads and genetic linkage maps show that HGGA produces a more contiguous assembly with less contigs and from 1.2 to 9.8 times higher NGA50 or N50 than a plain assembly of the reads and 1.03 to 6.5 times higher NGA50 or N50 than a previous approach integrating genetic linkage maps with contig assembly. Furthermore, also the correctness of the assembly remains similar or improves as compared to an assembly using only the read data.
Identification of novel key regulatory lncRNAs in gastric adenocarcinoma
Authors: Razavi Houri , Katanforosh Ali 
Published: May 2022

Abstract
Background
Stomach adenocarcinoma (STAD) is one of the most common and deadly cancers worldwide. Recent evidence has demonstrated that dysregulation of long noncoding RNAs (lncRNA) is associated with different hallmarks of cancer. lncRNAs also were suggested as novel promising biomarkers for cancer diagnosis and prognosis. Despite these previous investigations, the expression pattern, diagnostic role, and hallmark association of lncRNAs in STAD remain unclear.

Results
In this study, The STAD lncRNA-mRNA network was constructed based on RNAs that differentially expressed among tumor and normal samples and had a strong expression correlation with others. The high degree nodes of the network were associated with overall survival. In addition, we found that the hubs’ regulatory roles have previously been confirmed in different types of cancers by literature. For example, the HCG22 hub inhibited cell proliferation and invasion and induced apoptosis in oral squamous cell carcinoma (OSCC) cells. The levels of PCNA, Vimentin, and Bcl2 were decreased and E-cadherin and Bax expression was elevated in OSCC cells after HCG22 overexpression. Additionally, HCG22 overexpression inhibited the Akt, mTOR, and Wnt/β-catenin pathways.
Then lncRNAs were mapped to their related GO terms and cancer hallmarks. Based on these mappings, we predict the hallmarks that might be associated with each lncRNA. Finally, the literature review confirmed our prediction.
Among the 20 lncRNAs of the STAD network, 11 lncRNAs (LINC02560, SOX21-AS1, C5orf66-AS1, HCG22, PGM5-AS1, NALT1, ENSG00000241224.2, TINCR, MIR205HG, HNF4A-AS1, ENSG00000262756) demonstrated expression correlation with overall survival (OS). Based on expression analysis, survival analysis, hallmark associations, and literature review, LINC02560, SOX21-AS1, C5orf66-AS1, HCG22, PGM5-AS1, NALT1, ENSG00000241224.2, TINCR, MIR205HG, HNF4A-AS1 plays a regulatory role in STAD. For example, our prediction of association between C5orf66-AS1 expression dysregulation and “sustaining proliferative signal” and “Activating invasion and metastasis” has been confirmed in STAD, OSCC and cervical cancer. Finally, we developed a lncRNA signature with SOX21-AS1 and LINC02560, which classified patients into high and low-risk subgroups with significantly different survival outcomes. The mortality rate of the high-risk patients was significantly higher compared to the low-risk patients (28/1% vs 60.13).

Conclusion
These findings help in designing more precise and detailed experimental studies to find STAD biomarkers and therapeutic targets.
Genomic features of the polyphagous cotton leafworm Spodoptera littoralis
Authors: Wu Chao , Zhang Lei , Liu Bo , Gao Bojia , Huang Cong , Zhang Ji , Jin Minghui , Wang Hanyue , Peng Yan , Rice Annabel , Hegazi Esmat , Wilson Kenneth , Xu Pengjun , Xiao Yutao 
Published: May 2022

AbstractBackgroundThe cotton leafworm,Spodoptera littoralis, is a highly polyphagous pest of many cultivated plants and crops in Africa and Europe. The genome of this pest will help us to further understand the molecular mechanisms of polyphagy.ResultsHerein, the high-quality genome ofS. littoraliswas obtained by Pacific Bioscience (PacBio) sequencing. The assembled genome size ofS. littoralisis 436.55 Mb with a scaffold N50 of 6.09 Mb, consisting of 17,207 annotated protein-coding genes. Phylogenetic analysis shows thatS. littoralisand its sibling speciesS. lituradiverged about 5.44 million years ago. Expanded gene families were mainly involved in metabolic detoxification and tolerance to toxic xenobiotics based on GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis. Comparative genomics analysis showed that gene families involved in detoxification and chemosensation were significantly expanded inS. littoralis, representing genetic characteristics related to polyphagy and an extensive host range.ConclusionsWe assembled and annotated the reference genome ofS. littoralis, and revealed that this pest has the genetic features of strong detoxification capacity, consistent with it being a significant risk to a wide range of host crops. These data resources will provide support for risk assessment and early warning monitoring of major polyphagous agricultural pests.
Association between high immune activity and worse prognosis in uveal melanoma and low-grade glioma in TCGA transcriptomic data
Authors: Matsuo Hitoshi , Kamatani Takashi , Hamba Yu , Boroevich Keith A. , Tsunoda Tatsuhiko 
Published: May 2022

Abstract
Background
Immune status in the tumor microenvironment is an important determinant of cancer progression and patient prognosis. Although a higher immune activity is often associated with a better prognosis, this trend is not absolute and differs across cancer types. We aimed to give insights into why some cancers do not show better survival despite higher immunity by assessing the relationship between different biological factors, including cytotoxicity, and patient prognosis in various cancer types using RNA-seq data collected by The Cancer Genome Atlas.

Results
Results showed that a higher immune activity was associated with worse overall survival in patients with uveal melanoma and low-grade glioma, which are cancers of immune-privileged sites. In these cancers, epithelial or endothelial mesenchymal transition and inflammatory state as well as immune activation had a notable negative correlation with patient survival. Further analysis using additional single-cell data of uveal melanoma and glioma revealed that epithelial or endothelial mesenchymal transition was mainly induced in retinal pigment cells or endothelial cells that comprise the blood-retinal and blood-brain barriers, which are unique structures of the eye and central nervous system, respectively. Inflammation was mainly promoted by macrophages, and their infiltration increased significantly in response to immune activation. Furthermore, we found the expression of inflammatory chemokines, particularly CCL5, was strongly correlated with immune activity and associated with poor survival, particularly in these cancers, suggesting that these inflammatory mediators are potential molecular targets for therapeutics.

Conclusions
In uveal melanoma and low-grade glioma, inflammation from macrophages and epithelial or endothelial mesenchymal transition are particularly associated with a poor prognosis. This implies that they loosen the structures of the blood barrier and impair homeostasis and further recruit immune cells, which could result in a feedback loop of additional inflammatory effects leading to runaway conditions.
Small RNA sequencing and bioinformatics analysis of RAW264.7-derived exosomes after Mycobacterium Bovis Bacillus Calmette-Guérin infection
Authors: Zhan Xuehua , Yuan Wenqi , Zhou Yueyong , Ma Rong , Ge Zhaohui 
Published: May 2022

Abstract
Background
The mechanisms through which Mycobacterium tuberculosis evades immune surveillance during tuberculosis (TB) infection remain complex. Previous studies have found that Mycobacteria can manipulate the miRNAs of host cells to promote their survival during host-pathogen interactions, and most of these effects occur at the cellular miRNA level. We attempted to investigate the possible related mechanisms at the exosomal miRNA level.

Results
High-throughput sequencing revealed that Bacillus Calmette-Guérin (BCG) infection could alter the composition of the macrophage exosome content, and the expression levels of miRNAs in exosomes derived from the cell culture media of macrophages showed significant differences between the BCG-infected and non-infected groups. Compared with the non-infected group, 20 exosomal miRNAs were up-regulated and 7 exosomal miRNAs were down-regulated in the infection group (p < 0.05), of which mmu-miR-27b-3p, mmu-miR-93-5p, mmu-miR-25-3p, mmu-miR-1198-5p, mmu-let-7c-5p and let-7a-5p were significantly up-regulated. A bioinformatic analysis indicated that these differentially expressed exosomal miRNAs were involved in multiple biological processes and pathways. The target genes of top six miRNAs in up-regulated groups were positively correlated with the regulation of apoptosis.

Conclusions
The expression profile of miRNA in exosomes derived from macrophage were altered after Mycobacterium Bovis Bacillus Calmette-Guérin infection, and the differentially expressed miRNAs were involved in multiple biological processes and signalling pathways. The top six up-regulated miRNAs and their targeted genes were predominantly correlated with the regulation of apoptosis.
Comparative transcriptomic analysis of the super hybrid rice Chaoyouqianhao under salt stress
Authors: Xia-Yu Guo , Meng Zhang , Ming-Dong Zhu , Ji-Rui Long , Zhong-Wei Wei , Jian-Wu Li , Bin Zhou , Zhi-Yong Ai , Hua-Feng Deng 
Published: May 2022

AbstractBackgroundSoil salinization is a threat to food security. China is rich in saline land resources for potential and current utilization. The cultivation and promotion of salt-tolerant rice varieties can greatly improve the utilization of this saline land. The super hybrid rice Chaoyouqianhao (CY1000) is one of the most salt-tolerant rice varieties and is widely used, but the molecular mechanism underlying its salt tolerance is not clear.ResultsIn this study, the characteristics of CY1000 and its parents were evaluated in the field and laboratory. The results showed that aboveground parts of CY1000 were barely influenced by salt stress, while the roots were less affected than those of its parents. A comparative transcriptomic strategy was used to analyze the differences in the response to salt stress among the male and female parents of CY1000 at the seedling stage and the model indica rice 93–11. We found that the salt tolerance of CY1000 was mainly inherited from its male parent R900, and its female parent GX24S showed hardly any salt tolerance. To adapt to salt stress, CY1000 and R900 upregulated the expression of genes associated with soluble component synthesis and cell wall synthesis and other related genes and downregulated the expression of most genes related to growth material acquisition and consumption. In CY1000 and R900, the expression of genes encoding some novel key proteins in the ubiquitination pathway was significantly upregulated. After treatment with MG-132, the salt tolerance of CY1000 and R900 was significantly decreased and was almost the same as that of the wild type after salt stress treatment, indicating that ubiquitination played an important role in the salt tolerance mechanism of CY1000. At the same time, we found that some transcription factors were also involved in the salt stress response, with some transcription factors responding only in hybrid CY1000, suggesting that salt tolerance heterosis might be regulated by transcription factors in rice.ConclusionOur results revealed that the ubiquitination pathway is important for salt tolerance in rice, and several novel candidate genes were identified to reveal a novel salt tolerance regulation network. Additionally, our work will help clarify the mechanism of heterosis in rice. Further exploration of the molecular mechanism underlying the salt tolerance of CY1000 can provide a theoretical basis for breeding new salt-tolerant rice varieties.
Is there an association between inflammatory markers and lower physical performance in older adults?
Authors: Manrique-Espinoza Betty , Palazuelos-González Rosa , Pando-Robles Victoria , Rosas-Carrasco Oscar , Salinas-Rodríguez Aarón 
Published: May 2022

Abstract
Background
Maintenance of physical performance is essential for achievement of healthy aging. A few studies have explored the association between inflammatory markers and physical performance in older adults with inconclusive results. Our aim was to analyze the association of tumor necrosis factor-alpha (TNF-α), Interleukin-10 (IL-10), and C-reactive protein (CRP) with physical performance in a sample of older adults in rural settings of Mexico.

Methods
Our study comprised 307 community-dwelling older men and women who participated in the third wave of the Rural Frailty Study. We assessed the physical performance with the Short Physical Performance Battery (SPPB) and classified older adults as low performance if SPPB scored ≤8. Inflammatory markers were ascertained using serum by immunodetection methods. Logistic regression models were used to estimate the associations between inflammatory markers and physical performance.

Results
In comparison with the normal physical performance group, low physical performance individuals mainly were female (P <  0.01), older (P <  0.01), more illiterate (P = 0.02), more hypertensive (P < 0.01), fewer smokers (P = 0.02), and had higher CRP levels (P < 0.01). The logistic model results showed a significant association between the 3rd tertile of CRP and low physical performance (OR = 2.23; P = 0.03). IL-10 and TNF-α levels did not show a significant association.

Conclusions
The results of this study were mixed, with a significant association of physical performance with higher CRP levels but nonsignificant with IL-10 and TNF-α. Further studies with improved designs are needed by incorporating a broader set of inflammatory markers.
Antimicrobial resistance among GLASS pathogens in Morocco: an epidemiological scoping review
Authors: Nejjari Chakib , El Achhab Youness , Benaouda Amina , Abdelfattah Chakib 
Published: May 2022

Abstract
Background
Monitoring of antimicrobial resistance (AMR) is of great importance due to the frequency of strains becoming increasingly resistant to antibiotics. This review, using a public health focused approach, which aims to understand and describe the current status of AMR in Morocco in relation to WHO priority pathogens and treatment guidelines.

Methods
PubMed, ScienceDirect and Google Scholar Databases and grey literature are searched published articles on antimicrobial drug resistance data for GLASS priority pathogens isolated from Morocco between January 2011 and December 2021. Articles are screened using strict inclusion/exclusion criteria. AMR data is extracted with medians and IQR of resistance rates.

Results
Forty-nine articles are included in the final analysis. The most reported bacterium is Escherichia coli with median resistance rates of 90.9%, 64.0%, and 56.0%, for amoxicillin, amoxicillin-clavulanic acid, and co-trimoxazole, respectively. Colistin had the lowest median resistance with 0.1%. A median resistance of 63.0% is calculated for amoxicillin-clavulanic acid in Klebsiella pneumonia. Imipenem resistance with a median of 74.5% is reported for Acinetobacter baumannii. AMR data for Streptococcus pneumonie does not exceed 50.0% as a median.

Conclusions
Whilst resistance rates are high for most of GLASS pathogens, there are deficient data to draw vigorous conclusions about the current status AMR in Morocco. The recently join to the GLASS system surveillance will begin to address this data gap.
SARS-CoV-2 vaccine effectiveness against infection, symptomatic and severe COVID-19: a systematic review and meta-analysis
Authors: Ssentongo Paddy , Ssentongo Anna E. , Voleti Navya , Groff Destin , Sun Ashley , Ba Djibril M. , Nunez Jonathan , Parent Leslie J. , Chinchilli Vernon M. , Paules Catharine I. 
Published: May 2022

AbstractBackgroundThe temporal evolution of SARS-CoV-2 vaccine efficacy and effectiveness (VE) against infection, symptomatic, and severe COVID-19 is incompletely defined. The temporal evolution of VE could be dependent on age, vaccine types, variants of the virus, and geographic region. We aimed to conduct a systematic review and meta-analysis of the duration of VE against SARS-CoV-2 infection, symptomatic COVID-19 and severe COVID-19.MethodsMEDLINE, Scopus, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, the World Health Organization Global Literature on Coronavirus Disease, and CoronaCentral databases were searched and studies were selected. Independent reviewers selected randomized controlled trials and cohort studies with the outcome of interest. Independent reviewers extracted data, and assessed the risk of bias. Meta-analysis was performed with the DerSimonian-Laird random-effects model with Hartung-Knapp-Sidik-Jonkman variance correction. The GRADE (Grading of Recommendations, Assessment, Development and Evaluation) approach was used to assess certainty (quality) of the evidence. Primary outcomes included VE as a function of time against SARS-CoV-2 infection, symptomatic and severe COVID-19.ResultsEighteen studies were included representing nearly 7 million individuals. VE against all SARS-CoV-2 infections declined from 83% in the first month after completion of the original vaccination series to 22% at 5 months or longer. Similarly, VE against symptomatic COVID-19 declined from 94% in the first month after vaccination to 64% by the fourth month. VE against severe COVID-19 for all ages was high overall, with the level being 90% (95% CI, 87–92%) at five months or longer after being fully vaccinated. VE against severe COVID-19 was lower in individuals ≥ 65 years and those who received Ad26.COV2.S.ConclusionsVE against SARS-CoV-2 infection and symptomatic COVID-19 waned over time but protection remained high against severe COVID-19. These data can be used to inform public health decisions around the need for booster vaccination.
Comparison of the cardiovascular system, clinical condition, and laboratory results in COVID-19 patients with and without vitamin D insufficiency
Authors: Kazemi Erfan , Mansoursamaei Ali , Rohani-Rasaf Marzieh , Sheibani Hossein 
Published: May 2022

AbstractBackgroundSerum vitamin D levels may have a protective role against severe coronavirus disease 2019 (COVID-19). Studies have shown that deficiency in vitamin D may be a significant risk factor for poor outcomes. This study aims to compare the outcome and clinical condition of patients diagnosed with COVID-19 infection considering serum vitamin D levels.MethodsIn this cross-sectional study, 202 COVID-19 patients without known cardiovascular disease (reduced ejection fraction, uncontrolled arrhythmia, pericardial effusion, cardiac block, valvular disease, or hypertension) were included. Patients were divided into three groups of insufficient (< 30 ng/mL), normal (30 to 50 ng/mL), and high (> 50 ng/mL) serum vitamin D levels. Clinical outcome was defined as severe if invasive respiratory intervention and ICU admission was required.ResultsThe patients were divided into three groups based on their vitamin D level: 127 cases in the insufficient vitamin D group, 53 cases in the normal vitamin D group, and 22 cases in the high vitamin D group. The mean age of the population study was 56 years. Thirty-four patients had severe clinical outcomes. The distribution of this group was as follows: 21 patients in the insufficient vitamin D group (16.5%), eight patients in the normal vitamin D group (15.1%), and five patients in the high vitamin D group (22.7%); P = 0.74. No significant differences were found between the groups in terms of mortality rate (P = 0.46). Moreover, the mean of leukocytes (mean ± SD = 6873.5 ± 4236.2), ESR (mean ± SD = 38.42 ± 26.7), and CPK-MB (mean ± SD = 63 ± 140.7) were higher in the insufficient vitamin D group, but it was not statistically significant (P > 0.05).ConclusionThe finding of the present study showed that vitamin D could not make a significant difference in cardiovascular systems, laboratory results, and severity of the disease in COVID-19 patients.