bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins
Authors: Souza Leonardo R. , Colonna Juan G. , Comodaro Joseana M. , Naveca Felipe G. 
Published: February 2022

Abstract
Background
Dengue is a common vector-borne disease in tropical countries caused by the Dengue virus. This virus may trigger a disease with several symptoms like fever, headache, nausea, vomiting, and muscle pain. Indeed, dengue illness may also present more severe and life-threatening conditions like hemorrhagic fever and dengue shock syndrome. The causes that lead hosts to develop severe infections are multifactorial and not fully understood. However, it is hypothesized that different viral genome signatures may partially contribute to the disease outcome. Therefore, it is plausible to suggest that deeper DENV genetic information analysis may bring new clues about genetic markers linked to severe illness.

Method
Pattern recognition in very long protein sequences is a challenge. To overcome this difficulty, we map protein chains onto matrix data structures that reveal patterns and allow us to classify dengue proteins associated with severe illness outcomes in human hosts. Our analysis uses co-occurrence of amino acids to build the matrices and Random Forests to classify them. We then interpret the classification model using SHAP Values to identify which amino acid co-occurrences increase the likelihood of severe outcomes.

Results
We trained ten binary classifiers, one for each dengue virus protein sequence. We assessed the classifier performance through five metrics: PR-AUC, ROC-AUC, F1-score, Precision and Recall. The highest score on all metrics corresponds to the protein E with a 95% confidence interval. We also compared the means of the classification metrics using the Tukey HSD statistical test. In four of five metrics, protein E was statistically different from proteins M, NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5, showing that E markers has a greater chance to be associated with severe dengue. Furthermore, the amino acid co-occurrence matrix highlight pairs of amino acids within Domain 1 of E protein that may be associated with the classification result.

Conclusion
We show the co-occurrence patterns of amino acids present in the protein sequences that most correlate with severe dengue. This evidence, used by the classification model and verified by statistical tests, mainly associates the E protein with the severe outcome of dengue in human hosts. In addition, we present information suggesting that patterns associated with such severe cases can be found mostly in Domain 1, inside protein E. Altogether, our results may aid in developing new treatments and being the target of debate on new theories regarding the infection caused by dengue in human hosts.
csdR, an R package for differential co-expression analysis
Authors: Pettersen Jakob P. , Almaas Eivind 
Published: February 2022

Abstract
Background
Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networks by comparing gene co-expressions from two different conditions. Each of the gene pairs is assigned conserved (C), specific (S) and differentiated (D) scores based on the co-expression of the gene pair between the two conditions. The result of the procedure is a network where the nodes are genes and the links are the gene pairs with the highest C-, S-, and D-scores. However, the existing CSD-implementations suffer from poor computational performance, difficult user procedures and lack of documentation.

Results
We created the R-package aimed at reaching good performance together with ease of use, sufficient documentation, and with the ability to play well with other tools for data analysis. was benchmarked on a realistic dataset with 20,645 genes. After verifying that the chosen number of iterations gave sufficient robustness, we tested the performance against the two existing CSD implementations. was superior in performance to one of the implementations, whereas the other did not run. Our implementation can utilize multiple processing cores. However, we were unable to achieve more than $$\sim$$
∼
2.7 parallel speedup with saturation reached at about 10 cores.

Conclusion
The results suggest that is a useful tool for differential co-expression analysis and is able to generate robust results within a workday on datasets of realistic sizes when run on a workstation or compute server.
Mitochondria in tumour progression: a network of mtDNA variants in different types of cancer
Authors: Cavalcante Giovanna C. , Ribeiro-dos-Santos Ândrea , de Araújo Gilderlanio S. 
Published: February 2022

Abstract
Background
Mitochondrial participation in tumorigenesis and metastasis has been studied for many years, but several aspects of this mechanism remain unclear, such as the association of mitochondrial DNA (mtDNA) with different cancers. Here, based on two independent datasets, we modelled an mtDNA mutation-cancer network by systematic integrative analysis including 37 cancer types to identify the mitochondrial variants found in common among them.

Results
Our network showed mtDNA associations between gastric cancer and other cancer types, particularly kidney, liver, and prostate cancers, which is suggestive of a potential role of such variants in the metastatic processes among these cancer types. A graph-based interactive web tool was made available at www2.lghm.ufpa.br/mtdna. We also highlighted that most shared variants were in the MT-ND4, MT-ND5 and D-loop, and that some of these variants were nonsynonymous, indicating a special importance of these variants and regions regarding cancer progression, involving genomic and epigenomic alterations.

Conclusions
This study reinforces the importance of studying mtDNA in cancer and offers new perspectives on the potential involvement of different mitochondrial variants in cancer development and metastasis.
Identification of quantitative trait loci (QTLs) and candidate genes of seed Iron and zinc content in soybean [Glycine max (L.) Merr.]
Authors: Wang Huan , Jia Jia , Cai Zhandong , Duan Mingming , Jiang Ze , Xia Qiuju , Ma Qibin , Lian Tengxiang , Nian Hai 
Published: February 2022

Abstract
Background
Deciphering the hereditary mechanism of seed iron (Fe) and zinc (Zn) content in soybean is important and sustainable to address the “hidden hunger” that presently affects approximately 2 billion people worldwide. Therefore, in order to detect genomic regions related to soybean seed Fe and Zn content, a recombinant inbred line (RIL) population with 248 lines was assessed in four environments to detect Quantitative Trait Loci (QTLs) related to soybean seed Fe and Zn content.

Result
Wide variation was found in seed Fe and Zn content in four environments, and genotype, environment, and genotype × environment interactions had significant influences on both the seed Fe and Zn content. A positive correlation was observed between seed Fe content and seed Zn content, and broad-sense heritability (H2) of seed Fe and Zn content were 0.73 and 0.75, respectively. In this study, five QTLs for seed Fe content were detected with 4.57 - 32.71% of phenotypic variation explained (PVE) and logarithm of odds (LOD) scores ranging from 3.60 to 33.79. Five QTLs controlling the seed Zn content were detected, and they individually explained 3.35 to 26.48% of the phenotypic variation, with LOD scores ranging from 3.64 to 20.4. Meanwhile, 409,541 high-quality single-nucleotide variants (SNVs) and 85,102 InDels (except intergenic regions) between two bi-parental lines were identified by whole genome resequencing. A total of 12 candidate genes were reported in one major QTL for seed Fe content and two major QTLs for seed Zn content, with the help of RNA-Seq analysis, gene ontology (GO) enrichment, gene annotation, and bi-parental whole genome sequencing (WGS) data.

Conclusions
Limited studies were performed about microelement of soybean, so these results may play an important role in the biofortification of Fe and Zn and accelerate the development of marker-assisted selection (MAS) for breeding soybeans fortified with iron and zinc.
Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes
Authors: Niu Yingfeng , Gao Chengwen , Liu Jin 
Published: February 2022

Abstract
Background
Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. However, very few studies have been conducted on the Mangifera mitochondrial genome. This study reports and compares the newly sequenced mitochondrial genomes of three Mangifera species.

Results
Mangifera mitochondrial genomes showed partial similarities in the overall size, genomic structure, and gene content. Specifically, the genomes are circular and contain about 63–69 predicted functional genes, including five ribosomal RNA (rRNA) genes and 24–27 transfer RNA (tRNA) genes. The GC contents of the Mangifera mitochondrial genomes are similar, ranging from 44.42–44.66%. Leucine (Leu) and serine (Ser) are the most frequently used, while tryptophan (Trp) and cysteine (Cys) are the least used amino acids among the protein-coding genes in Mangifera mitochondrial genomes. We also identified 7–10 large chloroplast genomic fragments in the mitochondrial genome, ranging from 1407 to 6142 bp. Additionally, four intact mitochondrial tRNAs genes (tRNA-Cys, tRNA-Trp, tRNA-Pro, and tRNA-Met) and intergenic spacer regions were identified. Phylogenetic analysis based on the common protein-coding genes of most branches provided a high support value.

Conclusions
We sequenced and compared the mitochondrial genomes of three Mangifera species. The results showed that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome were identified. This study provides valuable information for evolutionary and molecular studies of Mangifera and a basis for further studies on genomic breeding of mango.
The impact of chitosan on the early metabolomic response of wheat to infection by Fusarium graminearum
Authors: Deshaies Myriam , Lamari Nadia , Ng Carl K. Y. , Ward Patrick , Doohan Fiona M. 
Published: February 2022

AbstractBackgroundChitosan has shown potential for the control of Fusarium head blight (FHB) disease caused byFusarium graminearum.The objective of this study was to compare the effect of chitosan hydrochloride applied pre- or post-fungal inoculation on FHB and to better understand its’ mode of action via an untargeted metabolomics study.ResultsChitosan inhibited fungal growthin vitroand, when sprayed on the susceptible wheat cultivar Remus 24 hours pre-inoculation withF. graminearum,it significantly reduced the number of infected spikelets at 7, 14 and 21 days post-inoculation. Chitosan pre-treatment also increased the average grain weight per head, the number of grains per head and the 1000-grain weight compared to the controls sprayed with water. No significant impact of chitosan on grain yield was observed when the plants were sprayed 24 hours post-inoculation withF. graminearum,even if it did result in a reduced number of infected spikelets at every time point. An untargeted metabolomic study using UHPLC-QTOF-MS on wheat spikes revealed that spraying the spikes with both chitosan andF. graminearumactivated known FHB resistance pathways (e.g. jasmonic acid). Additionally, more metabolites were up- or down-regulated when both chitosan andF. graminearumspores were sprayed on the spikes (117), as compared with chitosan (51) orF. graminearumon their own (32). This included a terpene, a terpenoid and a liminoid previously associated with FHB resistance.ConclusionsIn this study we showed that chitosan hydrochloride inhibited the spore germination and hyphal development ofF. graminearum in vitro, triggered wheat resistance against infection byF. graminearumwhen used as a pre-inoculant, and highlighted metabolites and pathways commonly and differentially affected by chitosan, the pathogen and both agents. This study provides insights into how chitosan might provide protection or stimulate wheat resistance to infection byF. graminearum. It also unveiled new putatively identified metabolites that had not been listed in previous FHB or chitosan-related metabolomic studies.
An insight to rhizosphere bacterial community composition and structure of consecutive winter-initiated sugarcane ratoon crop in Southern China
Authors: Khan Abdullah , Jiang Hongtao , Bu Junyao , Adnan Muhammad , Gillani Syeda Wajeeha , Zhang Muqing 
Published: February 2022

Abstract
Background
Ratooning in sugarcane is a crucial strategy for ensuring the long-term sustainability of the sugarcane industry. Knowledge gap relating to the interaction between rhizosphere microbiome and ratooning crop, particularly the impact of different sugarcane cultivars on the rhizosphere microbiome in consecutive ratooning, requires additional research. The response of two different sugarcane cultivars, viz ZZ-1 and ZZ-13, were evaluated in consecutive ratooning towards the rhizosphere microbial community and cane morphological characters.

Results
Significant changes in the rhizosphere microbiome were observed in the second ratooning over the years. Several important genera were observed in high abundance during the second ratooning, including Burkholderia, Sphingomonas, Bradyzhizobium, and Acidothermus. Cultivar ZZ-13 caused more alterations in the rhizosphere microbiome than ZZ-1, resulting in a more favorable rhizosphere environment for sugarcane growth. The genotypes also varied in terms of nutrients and enzyme activity over the years. There were significant differences between the genotypes and year for number of stalks and yield was significant for genotypes, years and genotype × year.

Conclusion
This finding will help to understand thorough interactions between rhizosphere microorganisms and ratoon sugarcane and lay the foundation for promoting and maximizing yield as far as possible. In the future, this work can serve as guidance in sugarcane husbandry, mainly in Guangxi, China.
The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species
Authors: Moghaddam Mahtab , Ohta Atsushi , Shimizu Motoki , Terauchi Ryohei , Kazempour-Osaloo Shahrokh 
Published: February 2022

Abstract
Background
Plastome (Plastid genome) sequences provide valuable markers for surveying evolutionary relationships and population genetics of plant species. Papilionoideae (papilionoids) has different nucleotide and structural variations in plastomes, which makes it an ideal model for genome evolution studies. Therefore, by sequencing the complete chloroplast genome of Onobrychis gaubae in this study, the characteristics and evolutionary patterns of plastome variations in IR-loss clade were compared.

Results
In the present study, the complete plastid genome of O. gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes. The O. gaubae plastid genome was 122,688 bp in length and included a large single-copy (LSC) region of 81,486 bp, a small single-copy (SSC) region of 13,805 bp and one copy of the inverted repeat (IRb) of 29,100 bp. The genome encoded 110 genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes and possessed 83 simple sequence repeats (SSRs) and 50 repeated structures with the highest proportion in the LSC. Comparative analysis of the chloroplast genomes across IRLC revealed three hotspot genes (ycf1, ycf2, clpP) which could be used as DNA barcode regions. Moreover, seven hypervariable regions [trnL(UAA)-trnT(UGU), trnT(GGU)-trnE(UUC), ycf1, ycf2, ycf4, accD and clpP] were identified within Onobrychis, which could be used to distinguish the Onobrychis species. Phylogenetic analyses revealed that O. gaubae is closely related to Hedysarum. The complete O. gaubae genome is a valuable resource for investigating evolution of Onobrychis species and can be used to identify related species.

Conclusions
Our results reveal that the plastomes of the IRLC are dynamic molecules and show multiple gene losses and inversions. The identified hypervariable regions could be used as molecular markers for resolving phylogenetic relationships and species identification and also provide new insights into plastome evolution across IRLC.
Comparison between dexmedetomidine and propofol on outcomes after coronary artery bypass graft surgery: a retrospective study
Authors: Hu Jie , Lv Bingfeng , West Raha , Chen Xingpeng , Yan Yali , Pac Soo Chen , Ma Daqing 
Published: February 2022

Abstract
Background
Dexmedetomidine (DEX) has a pharmacological profile that should allow rapid recovery and prevent undesirable outcomes such as pulmonary complications.

Methods
This large retrospective study compared the beneficial effects of perioperative infusion of DEX with propofol on the postoperative outcome after coronary artery bypass graft surgery. We reviewed patients’ medical notes at Luoyang Central Hospital from 1st January 2012 to 31st December 2019. All continuous variables, if normally distributed, were presented as mean ± SD; Otherwise, the non-normally distributed data and categorical data were presented as median (25-75 IQR) or number (percentage). The Mann-Whitney U test and Chi-square test were used to evaluate the difference of variables between the DEX and propofol groups. Multivariate logistic regression analysis was performed on the main related and differential factors in the perioperative period.

Results
A total of 1388 patients were included in the study; of those, 557 patients received propofol infusion, and 831 patients received dexmedetomidine. DEX significantly reduced postoperative pulmonary complications compared with propofol, 7.82% vs 13.29%; P < 0.01, respectively. When compared with propofol, DEX significantly shortened the duration of mechanical lung ventilation, 18 (13,25) hours vs 21 (16,37) hours; P < 0.001, the length of stay in the intensive care unit, 51 (42,90) vs 59 (46,94.5) hours; P = 0.001 and hospital stay, 20 (17,24) vs 22 (17,28) days; P < 0.001, respectively. The incidences of postoperative wound dehiscence and infection were significantly reduced with DEX compared with propofol groups, 2.53% vs 6.64%; P < 0.001, respectively. Interestingly, patients receiving DEX had significantly shorter surgical time compared to propofol; 275 (240,310) vs 280 (250,320) minutes respectively (P = 0.005) and less estimated blood loss (P = 0.001).

Conclusion
Perioperative infusion of dexmedetomidine improved the desirable outcomes in patients who had coronary artery bypass graft surgery compared with propofol.
Gastric polyps: a 10-year analysis of 18,496 upper endoscopies
Authors: Yacoub Haythem , Bibani Norsaf , Sabbah Mériam , Bellil Nawel , Ouakaa Asma , Trad Dorra , Gargouri Dalila 
Published: February 2022

Abstract
Background/aims
Gastric polyps (GPs) are usually asymptomatic lesions of the upper gastrointestinal tract observed in 1–3% of esophagogastroduodenoscopies (EGD). Most GPs are benign. The aim of this study was to precise the frequency of different types of gastric polyps in our population, and to analyze their possible association with other factors.

Materials and methods
A total of 18,496 consecutive patients undergoing EGD over a 10-year period (between 2007 and 2018) in a tertiary hospital were retrospectively reviewed. Eighty-six patients diagnosed with gastric polyps were analysed. Demographics, medical history of the patients, and indication for gastroscopy were collected. Morphological, histological characteristics of polyps, and therapeutic management data were also collected.

Results
GPs were found in 86 out of 18,496 (0.46%) reviewed EGD, corresponding to a total of 141 polyps. There were 64 female (74.4%) and 22 male patients (25.6%) with a sex ratio (M/F) of 0.34. The average age was 58.1 years. One hundred and forty one polyps were included, and histopathology was obtained on 127 GPs. The most common location was the fundus (59.6%) and 48.9% were smaller than 5 mm. The polyp was unique in 75.6% of cases. According to Paris classification, 80% of the polyps were sessile (Is). Hyperplastic polyps were the most common (55.9%), followed by sporadic fundic gland polyps observed in 23 patients (18.1%), 7 (5.5%) were adenomas and 4 (3.1%) were neuroendocrine tumors type 1. The following factors were associated with hyperplastic polyps: anemia (p = 0.022), single polyp (p = 0.025) and size ≥ 5 mm (p = 0.048). Comparing hyperplastic polyps’ biopsies to resected polyps, no difference was found in the evolutionary profile of the 2 groups. A size less than 10 mm (p = 0.013) was associated with fundic gland polyps. Sixty polyps (47.2%) were treated by cold forceps, 19 (15%) treated by a mucosal resection and 15 (11.8%) with diathermic snare. Five procedural bleeding incidents were observed (3.9%). Only the use of anticoagulant treatment was associated with a high bleeding risk (p = 0.005). The comparative histological study between specimens of biopsied GPs and endoscopic polypectomy led to an overall agreement of 95.3%.

Conclusion
In our study, the GPs frequency was 0.36%. Hyperplastic polyps and fundic gland are the most common in our country. The high frequency of Helicobacter pylori infection in our patients and in our area may explain the high frequency of HP.
Maintaining work life under threat of symptoms: a grounded theory study of work life experiences in persons with Irritable Bowel Syndrome
Authors: Frändemark Åsa , Törnblom Hans , Simrén Magnus , Jakobsson Sofie 
Published: February 2022

Abstract
Background
Irritable Bowel Syndrome (IBS) is a highly prevalent functional gastrointestinal disorder. Earlier studies have shown that IBS can limit the ability to perform at work and lead to absenteeism. However, few studies focus on work life experiences based on patients’ narratives. The purpose of this study was to construct a theory for how persons with IBS maintain their work life.

Methods
A qualitative study was performed using constructivist grounded theory. Semi-structured interviews with 15 women and 8 men with IBS (26–64 years of age) were conducted. Fourteen participants worked full-time, six worked part-time and three were on sick leave. The interviews were transcribed verbatim and coded line-by-line, incident-by-incident and thereafter focused coding was done. From the data and codes, categories were generated. Finally, a core category was constructed explaining the process of maintaining work life when living with IBS.

Results
Balancing work life while being under threat of symptoms constituted of four categories, being prepared, restricting impact, reconciling and adjusting. Persons with IBS restricted the impact of IBS on work by using strategies and upholding daily routines and strived to being prepared by exerting control over work life. These ongoing processes served to limit the influence of IBS on work by symptoms being less intense, perceived as less frequent, or not as bothersome. Reconciling IBS with work life was understood as a successful outcome from being prepared and restricting impact but was also influenced by the individual’s outlook on life. Adjusting to other people at work interfered with the strategies of being prepared, restricting impact, and reconciling, leaving persons with IBS more susceptible to symptoms.

Conclusions
This study deepens the understanding of the work situation for persons with IBS. Health care professionals can use the results of this study in the dialogue with the patient discussing work ability and sick leave. The results imply that although balancing work life under threat of symptoms can be a struggle, there are strategies that persons with IBS and employers together can initiate and use to reduce impact on work on several different levels.