bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide analysis of the U-box E3 ligases gene family in potato (Solanum tuberosum L.) and overexpress StPUB25 enhance drought tolerance in transgenic Arabidopsis
Authors: Liu Zhen , Wang Lei , Li Yuanming , Zhu Jinyong , Li Zhitao , Chen Limin , Li Hongyang , Shi Tianbin , Yao Panfeng , Bi Zhenzhen , Sun Chao , Bai Jiangping , Zhang Junlian , Liu Yuhui
Published: January 2024

Background

Plant U-box (PUB) E3 ubiquitin ligases have vital effects on various biological processes. Therefore, a comprehensive and systematic identification of the members of the U-box gene family in potato will help to understand the evolution and function of U-box E3 ubiquitin ligases in plants.

Results

This work identified altogether 74 PUBs in the potato (StPUBs) and examined their gene structures, chromosomal distributions, and conserved motifs. There were seventy-four StPUB genes on ten chromosomes with diverse densities. As revealed by phylogenetic analysis on PUBs within potato, Arabidopsis, tomato (Solanum lycopersicum), cabbage (Brassica oleracea), rice (Oryza sativa), and corn (Zea mays), were clustered into eight subclasses (C1-C8). According to synteny analysis, there were 40 orthologous StPUB genes to Arabidopsis, 58 to tomato, 28 to cabbage, 7 to rice, and 8 to corn. In addition, RNA-seq data downloaded from PGSC were utilized to reveal StPUBs’ abiotic stress responses and tissue-specific expression in the doubled-monoploid potato (DM). Inaddition, we performed RNA-seq on the ‘Atlantic’ (drought-sensitive cultivar, DS) and the ‘Qingshu NO.9’ (drought-tolerant cultivar, DT) in early flowering, full-blooming, along with flower-falling stages to detect genes that might be involved in response to drought stress. Finally, quantitative real-time PCR (qPCR) was carried out to analyze three candidate genes for their expression levels within 100 mM NaCl- and 10% PEG 6000 (w/v)-treated potato plantlets for a 24-h period. Furthermore, we analyzed the drought tolerance of StPUB25 transgenic plants and found that overexpression of StPUB25 significantly increased peroxidase (POD) activity, reduced ROS (reactive oxygen species) and MDA (malondialdehyde) accumulation compared with wild-type (WT) plants, and enhancing drought tolerance of the transgenic plants.

Conclusion

In this study, three candidate genes related to drought tolerance in potato were excavated, and the function of StPUB25 under drought stress was verified. These results should provide valuable information to understand the potato StPUB gene family and investigate the molecular mechanisms of StPUBs regulating potato drought tolerance.
Genomic dissection of additive and non-additive genetic effects and genomic prediction in an open-pollinated family test of Japanese larch
Authors: Dong Leiming , Xie Yunhui , Zhang Yalin , Wang Ruizhen , Sun Xiaomei
Published: January 2024

Genomic dissection of genetic effects on desirable traits and the subsequent use of genomic selection hold great promise for accelerating the rate of genetic improvement of forest tree species. In this study, a total of 661 offspring trees from 66 open-pollinated families of Japanese larch (Larix kaempferi (Lam.) Carrière) were sampled at a test site. The contributions of additive and non-additive effects (dominance, imprinting and epistasis) were evaluated for nine valuable traits related to growth, wood physical and chemical properties, and competitive ability using three pedigree-based and four Genomics-based Best Linear Unbiased Predictions (GBLUP) models and used to determine the genetic model. The predictive ability (PA) of two genomic prediction methods, GBLUP and Reproducing Kernel Hilbert Spaces (RKHS), was compared. The traits could be classified into two types based on different quantitative genetic architectures: for type I, including wood chemical properties and Pilodyn penetration, additive effect is the main source of variation (38.20-67.46%); for type II, including growth, competitive ability and acoustic velocity, epistasis plays a significant role (50.76-91.26%). Dominance and imprinting showed low to moderate contributions (< 36.26%). GBLUP was more suitable for traits of type I (PAs = 0.37–0.39 vs. 0.14–0.25), and RKHS was more suitable for traits of type II (PAs = 0.23–0.37 vs. 0.07–0.23). Non-additive effects make no meaningful contribution to the enhancement of PA of GBLUP method for all traits. These findings enhance our current understanding of the architecture of quantitative traits and lay the foundation for the development of genomic selection strategies in Japanese larch.
A de novo long-read genome assembly of the sacred datura plant (Datura wrightii) reveals a role of tandem gene duplications in the evolution of herbivore-defense response
Authors: Goldberg Jay K. , Olcerst Aaron , McKibben Michael , Hare J. Daniel , Barker Michael S. , Bronstein Judith L.
Published: January 2024

The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant–herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae: Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution of Datura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes.
Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae
Authors: Elameen Abdelhameed , Maduna Simo N. , Mageroy Melissa H. , van Eerde André , Knudsen Geir , Hagen Snorre B. , Eiken Hans Geir
Published: January 2024

Background

The order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit mothArgyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops.

Results

The mt genome ofA. conjugellacontains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon incox1is ATT. All 22 tRNAs had cloverleaf secondary structures, excepttrnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found thatA. conjugellahad the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae.

Conclusions

Our results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species.
Genome-wide identification and expression analysis of the glycosyl hydrolase family 1 genes in Medicago sativa revealed their potential roles in response to multiple abiotic stresses
Authors: Kong Haiming , Song Jiaxing , Ma Shihai , Yang Jing , Shao Zitong , Li Qian , Li Zhongxing , Xie Zhiguo , Yang Peizhi , Cao Yuman
Published: January 2024

Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs), are encoded by a large number of genes, which participate in the development and stress response of plants, particularly under biotic and abiotic stresses through the activation of phytohormones. However, there are few studies systematically analyzing stress or hormone-responsive BGLU genes in alfalfa. In this study, a total of 179 BGLU genes of the glycoside hydrolase family 1 were identified in the genome of alfalfa, and then were classified into five distinct clusters. Sequence alignments revealed several conserved and unique motifs among these MsBGLU proteins. Many cis-acting elements related to abiotic stresses and phytohormones were identified in the promoter of some MsBGLUs. Moreover, RNA-seq and RT-qPCR analyses showed that these MsBGLU genes exhibited distinct expression patterns in response to different abiotic stress and hormonal treatments. In summary, this study suggests that MsBGLU genes play crucial roles in response to various abiotic stresses and hormonal responses, and provides candidate genes for stress tolerance breeding in alfalfa.
Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing
Authors: Li Lanlan , Quan Jinqiang , Liu Hongyi , Yu Haibo , Chen Hongyan , Xia Changyou , Zhao Shengguo , Gao Caixia
Published: January 2024

Background

Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures.

Results

We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively.

Conclusions

In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.
Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype in EDNRB associated with two-end black coat color
Authors: Xu Zhong , Wu Junjing , Zhang Yu , Qiao Mu , Zhou Jiawei , Feng Yue , Li Zipeng , Sun Hua , Lin Ruiyi , Song Zhongxu , Zhao Haizhong , Li Lianghua , Chen Nanqi , Li Yujie , Oyelami Favour Oluwapelumi , Peng Xianwen , Mei Shuqi
Published: January 2024

Background

Jianli pig, a renowned indigenous breed in China, has the characteristics of a two-end black (TEB) coat color, excellent meat quality, strong adaptability and increased prolificacy. However, there is limited information available regarding the genetic diversity, population structure and genomic regions under selection of Jianli pig. On the other hand, the genetic mechanism of TEB coat color has remained largely unknown.

Results

In this study, the whole genome resequencing of 30 Jianli pigs within a context of 153 individuals representing 13 diverse breeds was performed. The population structure analysis revealed that Jianli pigs have close genetic relationships with the Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected heterozygosity, and runs of homozygosity) implied a relatively high level of genetic diversity and, a low inbreeding coefficient in Jianli compared with other pigs. We used Fst and XP-EHH to detect the selection signatures in Jianli pigs compared with Asian wild boar. A total of 451 candidate genes influencing meat quality (CREBBP, ADCY9, EEPD1 and HDAC9), reproduction (ESR1 and FANCA), and coat color (EDNRB, MITF and MC1R), were detected by gene annotation analysis. Finally, to fine-map the genomic region for the two-end black (TEB) coat color phenotype in Jianli pigs, we performed three signature selection methods between the TEB coat color and no-TEB coat color pig breeds. The current study, further confirmed that the EDNRB gene is a candidate gene for TEB color phenotype found in Chinese pigs, including Jinhua pigs, and the haplotype harboring 25 SNPs in the EDNRB gene may promote the formation of TEB coat color. Further ATAC-seq and luciferase reporter assays of these regions suggest that the 25-SNPs region was a strong candidate causative mutation that regulates the TEB coat color phenotype by altering enhancer function.

Conclusion

Our results advanced the understanding of the genetic mechanism behind artificial selection, and provided further resources for the protection and breeding improvement of Jianli pigs.
Differential responses of chili varieties grown under cadmium stress
Authors: Sana Sundas , Ramzan Musarrat , Ejaz Samina , Danish Subhan , Salmen Saleh H. , Ansari Mohammad Javed
Published: January 2024

Heavy metal cadmium (Cd) naturally occurs in soil and is a hazardous trace contaminant for humans, animals, and plants. The main sources of Cd pollution in soil include overuse of phosphatic fertilizers, manure, sewage sludge, and aerial deposition. That’s why an experiment was conducted to analyze the effect of Cd toxicity inCapsicum annuumL. by selecting its seven varieties: Hybrid, Desi, Sathra, G-916, BR-763, BG-912, and F1-9226. Cadmium was spiked in soil with four levels, i.e., (0, 3, 4, and 5 mg Cd kg− 1of soil) for a week for homogeneous dispersion of heavy metal. Chili seeds were sown in compost-filled loamy soil, and 25-day-old seedlings were transplanted into Cd-spiked soil. Cadmium increasing concentration in soil decreased chili growth characteristics, total soluble sugars, total proteins, and amino acids. On the other hand, the activities of antioxidant enzymes were increased with the increasing concentration of Cd in almost all the varieties. Treatment 5 mg Cd/kg application caused − 197.39%, -138.78%, -60.77%, -17.84%, -16.34%, -11.82% and − 10.37% decrease of carotenoids level in chili V2 (Desi) followed by V4 (G-916), V1 (Hy7brid), V7 (F1-9226), V6 (BG-912), V5 (BR-763) and V3 (Sathra) as compared to their controls. The maximum flavonoids among varieties were in V5 (BR-763), followed by V6 (BG-912), V7 (F1-9226), V3 (Sathra) and V1 (Hybrid). Flavonoids content was decreased with − 37.63% (Sathra), -34.78% (Hybrid), -33.85% (G-916), -31.96% (F1-9226), -31.44% (Desi), -30.58% (BR-763), -22.88% (BG-912) as compared to their control at 5 mg Cd/kg soil stress. The maximum decrease in POD, SOD, and CAT was − 31.81%, -25.98%, -16.39% in chili variety V7 (F1-9226) at 5 mg Cd/kg stress compared to its control. At the same time, maximum APX content decrease was − 82.91%, followed by -80.16%, -65.19%, -40.31%, -30.14%, -10.34% and − 6.45% in V4 (G-916), V2 (Desi), V3 (Sathra), V6 (BG-912), V1 (Hybrid), V7 (F1-9226) and V5 (BR-763) at 5 mg Cd/kg treatment as compared to control chili plants. The highest CAT was found in 5 chili varieties except Desi and G-916. Desi and G-916 varieties. V5 (BR-763) and V6 (BG-912) were susceptible, while V1 (Hybrid), V3 (Sathra), and V7 (F1-9226) were with intermediate growth attributes against Cd stress. Our results suggest that Desi and G-916 chili varieties are Cd tolerant and can be grown on a large scale to mitigate Cd stress naturally.
Reveal the kernel dehydration mechanisms in maize based on proteomic and metabolomic analysis
Authors: Zhang Hao , Gou Xiaonan , Ma Liangchuan , Zhang Xiaojun , Qu Jianzhou , Wang Xiaoyue , Huang Wenjie , Yan Shijuan , Zhang Xinghua , Xue Jiquan , Xu Shutu
Published: January 2024

Background

Kernel dehydration is an important factor for the mechanized harvest in maize. Kernel moisture content (KMC) and kernel dehydration rate (KDR) are important indicators for kernel dehydration. Although quantitative trait loci and genes related to KMC have been identified, where most of them only focus on the KMC at harvest, these are still far from sufficient to explain all genetic variations, and the relevant regulatory mechanisms are still unclear. In this study, we tried to reveal the key proteins and metabolites related to kernel dehydration in proteome and metabolome levels. Moreover, we preliminarily explored the relevant metabolic pathways that affect kernel dehydration combined proteome and metabolome. These results could accelerate the development of further mechanized maize technologies.

Results

In this study, three maize inbred lines (KB182, KB207, and KB020) with different KMC and KDR were subjected to proteomic analysis 35, 42, and 49 days after pollination (DAP). In total, 8,358 proteins were quantified, and 2,779 of them were differentially expressed proteins in different inbred lines or at different stages. By comparative analysis, K-means cluster, and weighted gene co-expression network analysis based on the proteome data, some important proteins were identified, which are involved in carbohydrate metabolism, stress and defense response, lipid metabolism, and seed development. Through metabolomics analysis of KB182 and KB020 kernels at 42 DAP, 18 significantly different metabolites, including glucose, fructose, proline, and glycerol, were identified.

Conclusions

In sum, we inferred that kernel dehydration could be regulated through carbohydrate metabolism, antioxidant systems, and late embryogenesis abundant protein and heat shock protein expression, all of which were considered as important regulatory factors during kernel dehydration process. These results shed light on kernel dehydration and provide new insights into developing cultivars with low moisture content.
Transcriptome analysis of axillary buds in low phosphorus stress and functional analysis of TaWRKY74s in wheat
Authors: Li Xue-zheng , Zhang Xiao-tong , Bie Xiao-min , Zhang Jing , Jiang Deng-ji , Tang Heng , Wang Fang
Published: January 2024

Background

Wheat is one of the main grain crops in the world, and the tiller number is a key factor affecting the yield of wheat. Phosphorus is an essential element for tiller development in wheat. However, due to decreasing phosphorus content in soil, there has been increasing use of phosphorus fertilizer, while imposing risk of soil and water pollution. Hence, it is important to identify low phosphorus tolerance genes and utilize them for stress resistance breeding in wheat.

Results

We subjected the wheat variety Kenong 199 (KN199) to low phosphorus stress and observed a reduced tiller number. Using transcriptome analysis, we identified 1651 upregulated genes and 827 downregulated of genes after low phosphorus stress. The differentially expressed genes were found to be enriched in the enzyme activity regulation related to phosphorus, hormone signal transduction, and ion transmembrane transport. Furthermore, the transcription factor analysis revealed that TaWRKY74s were important for low phosphorus tolerance. TaWRKY74s have three alleles: TaWRKY74-A, TaWRKY74-B, and TaWRKY74-D, and they all belong to the WRKY family with conserved WRKYGQK motifs. These proteins were found to be located in the nucleus, and they were expressed in axillary meristem, shoot apical meristem(SAM), young leaves, leaf primordium, and spikelet primordium. The evolutionary tree showed that TaWRKY74s were closely related to OsWRKY74s in rice. Moreover, TaWRKY74s-RNAi transgenic plants displayed significantly fewer tillers compared to wild-type plants under normal conditions. Additionally, the tiller numebr of the RNAi transgenic plants was also significantly lower than that of the wild-type plants under low-phosphorus stress, and increased the decrease amplitude. This suggestd that TaWRKY74s are related to phosphorus response and can affect the tiller number of wheat.

Conclusions

The results of this research showed that TaWRKY74s were key genes in wheat response to low phosphorus stress, which might regulate wheat tiller number through abscisic acid (ABA) and auxin signal transduction pathways. This research lays the foundation for further investigating the mechanism of TaWRKY74s in the low phosphorus environments and is significant for wheat stress resistance breeding.
Does preoperative multidisciplinary team assessment of high-risk patients improve the safety and outcomes of patients undergoing surgery?
Authors: Kuiper B. I. , Janssen L.M.J. , Versteeg K. S. , ten Tusscher B. L. , van der Spoel J. I. , Lubbers W. D. , Kazemier G. , Loer S. A. , Schober P. , van Halm V. P.
Published: January 2024

Background

International guidelines recommend preoperative multidisciplinary team (MDT) assessment for high-risk surgical patients. Preoperative MDT meetings can help to improve surgical care, but there is little evidence on whether they improve patient outcomes.

Methods

This paper aims to share our experience of MDT meetings for high-risk surgical patients to underline their added value to the current standard of care. An observational study of a retrospective cohort of preoperative high-risk MDT meetings of a tertiary referral hospital between January 2015 and December 2020. For 249 patients the outcomes preoperative data, MDT decisions, and patient outcomes were collected from electronic health records.

Main results

A total of 249 patients were discussed at high-risk MDT meetings. Most of the patients (97%) were assessed as having an American Society of Anesthesiology score ≥ 3, and 219 (88%) had a European Society of Cardiology and European Society of Anaesthesiology risk score of intermediate or high. After MDT assessment, 154 (62%) were directly approved for surgery, and 39 (16%) were considered ineligible for surgery. The remaining 56 (23%) patients underwent additional assessments before reconsideration at a high-risk MDT meeting. The main reason for patients being discussed at the high-risk MDT meeting was to assess the risk-benefit ratio of surgery. Ultimately, 184 (74%) patients underwent surgery. Of the operated patients, 122 (66%) did not have a major complication in the postoperative period, and 149 patients (81%) were alive after one year.

Conclusions

This cohort study shows the vulnerability and complexity of high-risk patients but also shows that the use of an MDT assessment contributes too improved peri- and postoperative treatment strategies in high-risk patients. Most patients underwent surgery after careful risk assessment and, if deemed necessary, preoperative and perioperative treatment optimization to reduce their risk.
Expectations of general practitioners on a practice based research network in Germany- a qualitative study within the Bavarian Research Practice Network (BayFoNet)
Authors: Sanftenberg Linda , Stofella Julia , Mayr Katharina , Nassehi Armin , Härdtlein Annette , Stark Stefanie , Kühlein Thomas , Kurotschka Peter Konstantin , Gágyor Ildikò , Eck Stefanie , Schneider Antonius , Bößenecker Melanie , Roos Marco , Dreischulte Tobias , Gensichen Jochen ,   for the BayFoNet study group, Baumgärtel Andrea , Endrich Isabell , Ermster Maike , Gehrmann Jan , Hapfelmeier Alexander , Hueber Susann , Klanke Merle , Kretzschmann Christian , Kurotschka Peter Konstantin , Linde Klaus , Lorenz Klara , Sanftenberg Linda , Schneider Antonius , Stark Stefanie , Uebel Til , Walter Fabian
Published: January 2024

Background

Despite general practitioners' (GPs') key role in Germany`s primary health care, clinical research in general practice is scarce. Clinical research is mainly conducted at inpatient facilities, although their results are rarely transferable. German GPs have no extra time or funding for research, as well as limited research training. To support clinical research in German primary health care, practice-based research networks (PBRNs) are developed. As they will be based on an active involvement of GPs, we need more information on GPs` participation-readiness. The aim of this study was to explore facilitators and barriers to participation in the Bavarian Research Practice Network (BayFoNet) from the GPs`perspective before clinical trials will be performed.

Methods

We have performed semi-structured qualitative interviews with a purposive sample of 20 Bavarian GPs in 2022 under the application of the consolidated framework for implementation research (CFIR). Transcriptions were analysed according to Kuckartz` qualitative content analysis. The five domains of the CFIR framework served as initial deductive codes.

Results

N = 14 interviewees already agreed to participate in BayFoNet, whereasn = 6 interviewees opted not to participate in BayFoNet at the time of data collection. Main facilitators to conduct clinical research within BayFoNet were the motivation to contribute to evidence strength and quality in general practice, professional development and training of practice staff, as well as networking. Barriers for an active participation were bad experiences with previous clinical studies and lack of resources.

Conclusions

PBRNS in Germany have to be promoted and the entire practice team has to be involved at an early stage of development. Professional training of general practice staff and a living network might enhance engagement. Participatory approaches could help to develop acceptable and feasible study designs. Furthermore, PBRNs should support patient recruitment and data collection in general practices and disseminate the results of their research projects regularly to maintain GPs` engagement.

Trial registration

DRKS00028805, NCT05667207.
Primary care physicians working in rural areas provide a broader scope of practice: a cross-sectional study
Authors: Kaneko Makoto , Higuchi Tomoya , Ohta Ryuichi
Published: January 2024

Background

Scope of practice (SoP) is an important factor for primary care physicians (PCPs). One of the strong determinants of SoP is rurality. Although Japan has several rural areas, the SoP in rural areas and the effect of rurality on SoP have not been investigated. This study aimed to describe SoP in Japanese primary care settings and examine the association between rurality and SoP.

Methods

This cross-sectional study included PCPs in Japan. The participants were randomly sampled from the mailing list of the Japan Primary Care Association. The Scope of Practice Inventory (SPI) and Scope of Practice for Primary Care (SP4PC) were used as indicators of SoP. The Rurality Index for Japan (RIJ) was used for rurality. This study compared the number of items of SPI (total score, inpatient care, urgent care and ambulatory care) and SP4PC experienced by > 80% of all PCPs in the most urban (RIJ:1–10) and rural areas (RIJ: 91–100). A multivariable linear regression analysis was also performed to examine the relationship between the RIJ and SPI/SP4PC.

Results

Of 1,000 potential participants, 299 physicians responded to the survey (response rate: 29.9%). PCPs in the most rural areas experienced a greater number of items in the inpatientl/urgent care domains of the SPI and SP4PC than those in the most urban areas. The RIJ was the only common factor for a broader SoP in both the SPI and SP4C models. The coefficients of SoP were 0.09 (95% confidence interval: 0.03–0.16) in the SPI model and 0.017 (0.005–0.03) in the SP4PC model.

Conclusion

Rurality was considerably associated with SoP. The findings of this study will be helpful in understanding the SoP on rural and urban areas.
The effect of an acute aspirin challenge on intestinal permeability in healthy adults with and without prophylactic probiotic consumption: a double-blind, placebo-controlled, randomized trial
Authors: Judkins Taylor C. , Solch-Ottaiano Rebecca J. , Ceretto-Clark Brendan , Nieves Carmelo , Colee James , Wang Yu , Tompkins Thomas A. , Caballero-Calero Sara E. , Langkamp-Henken Bobbi
Published: January 2024

Background

Healthy individuals may experience increases in intestinal permeability after chronic or acute use of non-steroidal anti-inflammatory drugs, which may be attenuated by probiotics. This study investigates the effects of an acute aspirin challenge on gastroduodenal barrier function with or without prophylactic probiotic consumption.

Methods

Twenty-nine generally healthy participants (26 ± 6 years) completed a 14-week randomized, double-blind, crossover trial. A probiotic containing 2 Lactobacilli strains or placebo was administered for 3 weeks, with a 4-week washout period between crossover phases. Daily and weekly questionnaires assessing gastrointestinal function were completed for 2 weeks before until 2 weeks after each intervention to assess gastrointestinal function. Gastroduodenal permeability was assessed by urinary excretion of orally administered sucrose after 1, 2, and 3 weeks of each intervention with a 1950 mg-aspirin challenge after 2 weeks of supplementation. Stool samples were collected weekly during supplementation for detection of species of interest.

Results

Gastroduodenal permeability increased with aspirin challenge (Week 1: 3.4 ± 0.6 μmol vs Week 2: 9.9 ± 1.0 μmol urinary sucrose; p < 0.05). There were no differences in the change in permeability after the aspirin challenge or gastrointestinal function between interventions.

Conclusion

The acute aspirin challenge significantly increased intestinal permeability similarly in both groups, and prophylactic probiotic consumption was unable to prevent the loss in this particular model.
Association of chronic hepatitis B infection with hepatic steatosis and injury in nonalcoholic fatty liver disease children
Authors: Wang Lu , Lu Chang , Zhang Yuncong , Liang Qingsheng , Zhang Jie
Published: January 2024

Background

The influence of chronic hepatitis B infection (CBI) on hepatic steatosis, necroinflammation, and fibrosis in nonalcoholic fatty liver disease (NAFLD) population was unclear. We aimed to investigate the effect of CBI on hepatic steatosis and assess the association between NAFLD co-existed CBI and hepatic injury in NAFLD pediatric population.

Methods

Consecutive hospitalized children with biopsy-proven NAFLD with or without CBI were included. Hepatic steatosis, necroinflammation and fibrosis were evaluated by NASH CRN system and/or METAVIR scoring system, appropriately. Using multivariate logistic analysis, we identified variables associated with hepatic steatosis and liver injury.

Results

Of 223 biopsy-proven NAFLD children, 161 were NAFLD without CBI, and 62 were NAFLD co-existed CBI. Grouped by mild, moderate and severe hepatic steatosis, there was an inverse association between CBI and the severity of hepatic steatosis [odd ratio (OR) 0.037, 95% confidence interval (CI) 0.014–0.098]. In addition, we explored the relationship between CBI and hepatic necroinflammation and fibrosis in NAFLD children. Hepatic necroinflammation and fibrosis, respectively, were divided into two groups according to severity. And CBI was positively associated with hepatic necroinflammation (OR 6.125, 95%CI 1.958–19.158). However, there was no statistically independent association between CBI and significant hepatic fibrosis.

Conclusions

CBI was inverse associated with the grade of steatosis and positively associated with severe hepatic necroinflammation, and does not appear to affect significant hepatic fibrosis in pediatric NAFLD children.
Reconstructing the COVID-19 incidence in India using airport screening data in Japan
Authors: Liu Shiqi , Anzai Asami , Nishiura Hiroshi
Published: January 2024

Background

A major epidemic of COVID-19 caused by the Delta variant (B.1.617.2) occurred in India from March to July 2021, resulting in 19 million documented cases. Given the limited healthcare and testing capacities, the actual number of infections is likely to have been greater than reported, and several modelling studies and excess mortality research indicate that this epidemic involved substantial morbidity and mortality.

Methods

To estimate the incidence during this epidemic, we used border entry screening data in Japan to estimate the daily incidence and cumulative incidence of COVID-19 infection in India. Analysing the results of mandatory testing among non-Japanese passengers entering Japan from India, we calculated the prevalence and then backcalculated the incidence in India from February 28 to July 3, 2021.

Results

The estimated number of infections ranged from 448 to 576 million people, indicating that 31.8% (95% confidence interval (CI): 26.1, 37.7) – 40.9% (95% CI: 33.5, 48.4) of the population in India had experienced COVID-19 infection from February 28 to July 3, 2021. In addition to obtaining cumulative incidence that was consistent with published estimates, we showed that the actual incidence of COVID-19 infection during the 2021 epidemic in India was approximately 30 times greater than that based on documented cases, giving a crude infection fatality risk of 0.47%. Adjusting for test-negative certificate before departure, the quality control of which was partly questionable, the cumulative incidence can potentially be up to 2.3–2.6 times greater than abovementioned estimates.

Conclusions

Our estimate of approximately 32–41% cumulative infection risk from February 28 to July 3, 2021 is roughly consistent with other published estimates, and they can potentially be greater, given an exit screening before departure. The present study results suggest the potential utility of border entry screening data to backcalculate the incidence in countries with limited surveillance capacity owing to a major surge in infections.
Exploring the biomarkers and potential therapeutic drugs for sepsis via integrated bioinformatic analysis
Authors: Liang Pingping , Wu Yongjian , Qu Siying , Younis Muhammad , Wang Wei , Wu Zhilong , Huang Xi
Published: January 2024

Background

Sepsis is a life-threatening condition caused by an excessive inflammatory response to an infection, associated with high mortality. However, the regulatory mechanism of sepsis remains unclear.

Results

In this study, bioinformatics analysis revealed the novel key biomarkers associated with sepsis and potential regulators. Three public datasets (GSE28750, GSE57065 and GSE95233) were employed to recognize the differentially expressed genes (DEGs). Taking the intersection of DEGs from these three datasets, GO and KEGG pathway enrichment analysis revealed 537 shared DEGs and their biological functions and pathways. These genes were mainly enriched in T cell activation, differentiation, lymphocyte differentiation, mononuclear cell differentiation, and regulation of T cell activation based on GO analysis. Further, pathway enrichment analysis revealed that these DEGs were significantly enriched in Th1, Th2 and Th17 cell differentiation. Additionally, five hub immune-related genes (CD3E, HLA-DRA, IL2RB, ITK and LAT) were identified from the protein–protein interaction network, and sepsis patients with higher expression of hub genes had a better prognosis. Besides, 14 drugs targeting these five hub related genes were revealed on the basis of the DrugBank database, which proved advantageous for treating immune-related diseases.

Conclusions

These results strengthen the new understanding of sepsis development and provide a fresh perspective into discriminating the candidate biomarkers for predicting sepsis as well as identifying new drugs for treating sepsis.
Bacterial contamination on clinical surfaces and oxygen device accessories in the emergency unit of a tertiary health facility in Ghana
Authors: Thompson Evans , Badu Akua Tutuwaa , Abban Emmanuella , Eyeson Evelyn Baawa , Afutu Leslie Larry , Amankwaah Bless , Buabeng Suzzana Dickson , Frimpong Abigail Agyen , Anning Alberta Serwah , Ghartey-Kwansah George
Published: January 2024

Background

Nosocomial infections have gradually become an emerging threat to the healthcare system over the past decades and have been attributed to poor decontamination of hospital articles and weak antibacterial stewardship policies. This study sought to investigate the effect of disinfection on the prevalence and resistance profile of bacterial contaminants on oxygen device accessories, and clinical surfaces at the emergency unit of a tertiary health facility in Ghana.

Methods

The study employed a cross-sectional study design to evaluate the occurrence of bacteria on surfaces in a tertiary hospital. Luminal swabs of the oxygen device accessories and swabs from clinical surfaces used by healthcare providers were collected for isolation and identification of bacteria. The identified bacteria isolates were then tested for their susceptibility to antibacterial agents. Data from this study were analyzed using Excel (Microsoft Office Suite), and GraphPad Prism 8 software programs.

Results

A quarter of the total 44 bacterial isolates obtained from both post-disinfected and pre-disinfected surfaces were Gram-positive, with the remaining isolates being Gram-negative. Pseudomonas aeruginosa was the most frequent bacteria species isolated (41%) followed by Citrobacter sp. (21%). P. aeruginosa, S. aureus, and S. pneumoniae were found to be highly resistant to Chloramphenicol (36%), and Sulfamethoxazole (100%); whereas Ciprofloxacin (91%) was the most effective antibacterial drug used.

Conclusion

The almost equal prevalence of multidrug-resistant bacteria from both post-disinfected and pre-disinfected surfaces of inanimate objects, and oxygen device accessories connote an ineffective disinfection process which may influence resistance in bacterial contaminants. This requires the overhaul of disinfection protocol and training of hospital staff, and rational use of antibacterial agents at the hospital to mitigating the burden of nosocomial infections.
The impact of spatial connectivity on NPIs effectiveness
Authors: Sabbatini Chiara E. , Pullano Giulia , Di Domenico Laura , Rubrichi Stefania , Bansal Shweta , Colizza Vittoria
Published: January 2024

Background

France implemented a combination of non-pharmaceutical interventions (NPIs) to manage the COVID-19 pandemic between September 2020 and June 2021. These included a lockdown in the fall 2020 – the second since the start of the pandemic – to counteract the second wave, followed by a long period of nighttime curfew, and by a third lockdown in the spring 2021 against the Alpha wave. Interventions have so far been evaluated in isolation, neglecting the spatial connectivity between regions through mobility that may impact NPI effectiveness.

Methods

Focusing on September 2020–June 2021, we developed a regionally-based epidemic metapopulation model informed by observed mobility fluxes from daily mobile phone data and fitted the model to regional hospital admissions. The model integrated data on vaccination and variants spread. Scenarios were designed to assess the impact of the Alpha variant, characterized by increased transmissibility and risk of hospitalization, of the vaccination campaign and alternative policy decisions.

Results

The spatial model better captured the heterogeneity observed in the regional dynamics, compared to models neglecting inter-regional mobility. The third lockdown was similarly effective to the second lockdown after discounting for immunity, Alpha, and seasonality (51% vs 52% median regional reduction in the reproductive number R0, respectively). The 6pm nighttime curfew with bars and restaurants closed, implemented in January 2021, substantially reduced COVID-19 transmission. It initially led to 49% median regional reduction of R0, decreasing to 43% reduction by March 2021. In absence of vaccination, implemented interventions would have been insufficient against the Alpha wave. Counterfactual scenarios proposing a sequence of lockdowns in a stop-and-go fashion would have reduced hospitalizations and restriction days for low enough thresholds triggering and lifting restrictions.

Conclusions

Spatial connectivity induced by mobility impacted the effectiveness of interventions especially in regions with higher mobility rates. Early evening curfew with gastronomy sector closed allowed authorities to delay the third wave. Stop-and-go lockdowns could have substantially lowered both healthcare and societal burdens if implemented early enough, compared to the observed application of lockdown-curfew-lockdown, but likely at the expense of several labor sectors. These findings contribute to characterize the effectiveness of implemented strategies and improve pandemic preparedness.
Severe pneumonia with co-infection of H5N1 and SARS-CoV-2: a case report
Authors: Jin Ke , Dai Zixing , Shi Ping , Li Yuwen , Zhu Chuanlong
Published: January 2024

Background

The H5N1 influenza virus is a cause of severe pneumonia. Co-infection of influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may lead to poor prognosis of patients during the COVID-19 epidemic. However, reports on patients co-infected with avian influenza virus and SARS-CoV-2 are scarce.

Case presentation

A 52-year-old woman presented with a fever, which has persisted for the past eight days, along with worsening shortness of breath and decreased blood pressure. Computed tomography (CT) revealed an air bronchogram, lung consolidation, and bilateral pleural effusion. The subsequent polymerase chain reaction (PCR) of the bronchoalveolar lavage fluid (BALF) revealed positivity for H5N1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Conclusion

The H5N1 influenza virus is a cause of severe pneumonia. The clinical presentation of the patient had a predomination of H5N1 influenza rather than COVID-19. A PCR analysis for the identification of the virus is necessary to reveal the pathogen causing the severe pneumonia. The patient exhibited an excellent prognosis upon the use of the appropriate antiviral medicine.
Treatment outcomes of retreated patients with isoniazid/rifampicin resistant pulmonary tuberculosis
Authors: Zhang Lijie , Han Xiqin , Ge Qiping , Shu Wei , Sun Yuxian , Gao Jingtao , Xie Shiheng , Wang Jingping , Gao Weiwei
Published: January 2024

Background

About 8% of TB cases worldwide are estimated to have rifampicin-susceptible, isoniazid-resistant tuberculosis (Hr-TB), ranging from 5 to 11% regions. However, Hr-TB has not received much attention while comparing to be given high priority to the management of rifampicin-resistant tuberculosis (RR-TB). This study aimed to compare the differences of treatment effects for Hr-TB and RR-TB, so as to intensify the treatment and management of Hr-TB.

Methods

A retrospective study was used to collect bacteriologically positive retreated patients with isoniazid/rifampicin resistant pulmonary tuberculosis, who were conducted at 29 tuberculosis control institutions in China from July 2009 to June 2021. We assessed effectiveness and safety of retreated patients with isoniazid/ rifampicin resistant pulmonary tuberculosis.

Results

A total of 147 with either positive smear or cultures were enrolled, and 80 cases were in Hr-TB group and 67 cases were in RR-TB group. There was no significant difference in terms of age, sex, body mass, type of retreatment and comorbid diabetes between the two groups (P > 0.05). The rate of number of lesions involving lung fields ≥ 3 in Hr-TB group 75.9% (60/79) was significantly higher than RR-TB group 56.7% (38/67) (χ2 = 6.077, P = 0.014). There was no statistically significant difference (P = 0.166) with regard to the treatment outcomes of the two groups, the cure rates were 54.7% (41/75) and 53.6% (30/56), respectively, and the failure rate in Hr-TB group 22.7% (17/75) was 10% higher than RR-TB group 10.7% (6/56). The rate of negative sputum smear at the end of the second month (65.7%) in the Hr-TB group was significantly lower than that in the RR-TB group (85.7%) (P = 0.025). There were no significant differences in the incidences of serious adverse reactions and chest X-ray changes between the two groups (P > 0.05). During the 5-year follow-up, recurrence in the Hr-TB group (7 cases, 14.9%) was no significantly lower than that in the RR-TB group (4 cases, 11.8%) (P = 0.754).

Conclusion

The treatment of retreated Hr-TB patients was difficult and could be statistically similar or considerably worse than RR-TB. It’s urgent to conduct further evaluation of the treatment status quo to guide the guideline development and clinical practice of Hr-TB patients.
Diarrheal diseases prevalence among children of Sudan and socio cultural risks related; systematic review and meta analysis
Authors: Badawi MM , SalahEldin MA , Idris AB , Idris EB , Mohamed SG
Published: January 2024

It is estimated that more than 4% of the causes of inpatient deaths in 2017 were due to diarrheal diseases. The current study is aimed to provide pooled prevalence of microorganisms causing diarrhea among Sudanese as well as determine any socio-cultural risk factors associated. A systematic review of the literature was conducted and regulated in accordance to PRISMA. After abstract and full text screening Twenty-one research articles were recruited to the study. Among witch eighteen research articles determined prevalence of causative microorganisms of Diarrhea; eight research articles determining prevalence of causative microorganisms of Diarrhea were conducted in Khartoum State, five in Gezira State, two in White Nile State, one in Kordofan State while two studies were conducted in several States. Moreover, majority of studies were concerned of prevalence among children while two studies were toward general population as well as mothers of children. The pooled prevalence of viral diarrhea in less than five years old children was 22.90% [15.37, 30.43] among more than 14 thousands’ participants, the pooled prevalence of parasitic diarrhea was 31.40% [19.53, 43.27] among participants from different age groups while the pooled prevalence of bacterial diarrhea was 36.20% [14.00, 58.40]. No associated risk factors were able to be synthesized from included studies.