bluuebunny/crossref_metadata_2025_split huggingface dataset:
An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach
Authors: Hasan Zahid , Netherland Michael , Hasan Nur A. , Begum Nurjahan , Yasmin Mahmuda , Ahmed Sangita 
Published: July 2024

IntroductionThe dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility. MethodsMetagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods.Results and discussionIn the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.
A systematic literature review on contemporary and future trends in virtual machine scheduling techniques in cloud and multi-access computing
Authors: Rana Nadim , Jeribi Fathe , Khan Zeba , Alrawagfeh Wagdi , Ben Dhaou Imed , Haseebuddin Mohammad , Uddin Mueen 
Published: July 2024

IntroductionThe migration of business and scientific operations to the cloud and the surge in data from IoT devices have intensified the complexity of cloud resource scheduling. Ensuring efficient resource distribution in line with user-specified SLA and QoS demands novel scheduling solutions. This study scrutinizes contemporary Virtual Machine (VM) scheduling strategies, shedding light on the complexities and future prospects of VM design and aims to propel further research by highlighting existing obstacles and untapped potential in the ever-evolving realm of cloud and multi-access edge computing (MEC).MethodImplementing a Systematic Literature Review (SLR), this research dissects VM scheduling techniques. A meticulous selection process distilled 67 seminal studies from an initial corpus of 722, spanning from 2008 to 2022. This critical filtration has been pivotal for grasping the developmental trajectory and current tendencies in VM scheduling practices.ResultThe in-depth examination of 67 studies on VM scheduling has produced a taxonomic breakdown into three principal methodologies: traditional, heuristic, and meta-heuristic. The review underscores a marked shift toward heuristic and meta-heuristic methods, reflecting their growing significance in the advancement of VM scheduling.ConclusionAlthough VM scheduling has progressed markedly, the focus remains predominantly on metaheuristic and heuristic approaches. The analysis enlightens ongoing challenges and the direction of future developments, highlighting the necessity for persistent research and innovation in this sector.
PCSK9 inhibitors and inclisiran with or without statin therapy on incident muscle symptoms and creatine kinase: a systematic review and network meta-analysis
Authors: Li Wenshu , Sun Lichaoyue , Yan Sichao 
Published: July 2024

BackgroundAtherosclerotic cardiovascular disease (ASCVD), a leading cause of global fatalities, has inconsistent findings regarding the impact of muscle symptoms despite promising clinical trials involving PCSK9 inhibitors (PCSK9i) and siRNA as potential therapeutic options.MethodsThe databases EMBASE, PubMed, Web of Science, Cochrane, and ClinicalTrials.gov were thoroughly searched without any restrictions on language. Review Manager 5.3 software was utilized to calculate relative risks with 95% confidence intervals (CIs) for dichotomous data and mean differences or standardized mean differences with 95%CIs for continuous data. To evaluate publication bias, Egger's test was employed using Stata/SE software.ResultsThis analysis included 26 studies comprising 28 randomized controlled trials (RCTs) involving a total of 100,193 patients, and 4 different lipid-lowering therapy combinations. For events with creatine kinase &gt;3ULN, evolocumab and alirocumab demonstrated significant advantages compared to inclisiran. Evolocumab showed the best results in terms of both new muscle symptom events and creatine kinase &gt;3ULN.ConclusionsBased on this network meta-analysis (NMA) results, evolocumab has emerged as a promising treatment option for patients with hyperlipidemia and muscle disorders compared to other PCSK9 inhibitors and inclisiran.Systematic Review RegistrationPROSPERO [CRD42023459558].
The causal relationship between human brain morphometry and knee osteoarthritis: a two-sample Mendelian randomization study
Authors: Liu Yongming , Huang Chao , Xiong Yizhe , Wang Xiang , Shen Zhibi , Zhang Mingcai , Gao Ningyang , Wang Nan , Du Guoqing , Zhan Hongsheng 
Published: July 2024

BackgroundKnee Osteoarthritis (KOA) is a prevalent and debilitating condition affecting millions worldwide, yet its underlying etiology remains poorly understood. Recent advances in neuroimaging and genetic methodologies offer new avenues to explore the potential neuropsychological contributions to KOA. This study aims to investigate the causal relationships between brain-wide morphometric variations and KOA using a genetic epidemiology approach.MethodLeveraging data from 36,778 UK Biobank participants for human brain morphometry and 487,411 UK Biobank participants for KOA, this research employed a two-sample Mendelian Randomization (TSMR) approach to explore the causal effects of 83 brain-wide volumes on KOA. The primary method of analysis was the Inverse Variance Weighted (IVW) and Wald Ratio (WR) method, complemented by MR Egger and IVW methods for heterogeneity and pleiotropy assessments. A significance threshold of p &lt; 0.05 was set to determine causality. The analysis results were assessed for heterogeneity using the MR Egger and IVW methods. Brain-wide volumes with Q_pval &lt; 0.05 were considered indicative of heterogeneity. The MR Egger method was employed to evaluate the pleiotropy of the analysis results, with brain-wide volumes having a p-value &lt; 0.05 considered suggestive of pleiotropy.ResultsOur findings revealed significant causal associations between KOA and eight brain-wide volumes: Left parahippocampal volume, Right posterior cingulate volume, Left transverse temporal volume, Left caudal anterior cingulate volume, Right paracentral volume, Left paracentral volume, Right lateral orbitofrontal volume, and Left superior temporal volume. These associations remained robust after tests for heterogeneity and pleiotropy, underscoring their potential role in the pathogenesis of KOA.ConclusionThis study provides novel evidence of the causal relationships between specific brain morphometries and KOA, suggesting that neuroanatomical variations might contribute to the risk and development of KOA. These findings pave the way for further research into the neurobiological mechanisms underlying KOA and may eventually lead to the development of new intervention strategies targeting these neuropsychological pathways.
Dual roles of CD11b+CD33+HLA-DR-/lowCD14- myeloid-derived suppressor cells with a granulocytic morphology following allogeneic hematopoietic stem cell transplantation: from inflammation promoters to immune suppressors within 90 days
Authors: Ni Ming , Cui Jing , Yang Xin , Ding Yuntian , Zhao Peng , Hu Tianzhen , Zhan Yun , Kang Qian , Hu Xiuying , Zhao Jiangyuan , Xu Yao , Chen Lu , Liu Min , Zhao Mei , Zhang Fengqi , Huang Shisi , Li Ya , Yang Xueying , Zhang Luxin , Zhang Tianzhuo , Deng Bo , Yang Bing , Lu Deqin , Wang Jishi 
Published: July 2024

IntroductionGranulocytic myeloid-derived suppressor cells (G-MDSCs) show fast recovery following allogeneic hematopoietic stem cell transplantation (allo-HSCT) constituting the major part of peripheral blood in the early phase. Although G-MDSCs mediate immune suppression through multiple mechanisms, they may also promote inflammation under specific conditions. MethodsG-MDSCs were isolated from 82 patients following allo-HSCT within 90 days after allo-HSCT, and their interactions with autologous CD3+ T-cells were examined. T-cell proliferation was assessed by flow cytometry following CFSE staining, while differentiation and interferon-γ secretion were characterized using chemokine receptor profiling and ELISpot assays, respectively. NK cell cytotoxicity was evaluated through co-culture with K562 cells. An aGVHD xenogeneic model in humanized mice was employed to study the in vivo effects of human leukocytes. Furthermore, transcriptional alterations in G-MDSCs were analyzed via RNA sequencing to investigate functional transitions.ResultsG-MDSCs promoted inflammation in the early-stage, by facilitating cytokine secretion and proliferation of T cells, as well as their differentiation into pro-inflammatory T helper subsets. At day 28, patients with a higher number of G-MDSCs exhibited an increased risk of developing grades II-IV aGvHD. Besides, adoptive transfer of G-MDSCs from patients at day 28 into humanized mice exacerbated aGvHD. However, at day 90, G-MDSCs led to immunosuppression, characterized by upregulated expression of indoleamine 2,3-dioxygenase gene and interleukin-10 secretion, coupled with the inhibition of T cell proliferation. Furthermore, transcriptional analysis of G-MDSCs at day 28 and day 90 revealed that 1445 genes were differentially expressed. These genes were associated with various pathways, revealing the molecular signatures of early post-transplant differentiation in G-MDSCs. In addition, genes linked to the endoplasmic reticulum stress were upregulated in patients without aGvHD. The acquisition of immunosuppressive function by G-MDSCs may depend on the activation of CXCL2 and DERL1 genes. ConclusionOur findings revealed the alteration in the immune characteristics of G-MDSCs within the first 90 days post-allo-HSCT. Moreover, the quantity of G-MDSCs at day 28 may serve as a predictive indicator for the development of aGvHD.
A novel NKp80-based strategy for universal identification of normal, reactive and tumor/clonal natural killer-cells in blood
Authors: Morán-Plata F. Javier , Muñoz-García Noemí , González-González María , Pozo Julio , Carretero-Domínguez Sonia , Mateos Sheila , Barrena Susana , Belhassen-García Moncef , Lau Catarina , Teixeira Maria Dos Anjos , Santos Ana Helena , Yeguas Ana , Balanzategui Ana , García-Sancho Alejandro Martín , Orfao Alberto , Almeida Julia 
Published: July 2024

PurposeNatural killer (NK) cells are traditionally identified by flow cytometry using a combination of markers (CD16/CD56/CD3), because a specific NK-cell marker is still missing. Here we investigated the utility of CD314, CD335 and NKp80, compared to CD16/CD56/CD3, for more robust identification of NK-cells in human blood, for diagnostic purposes.MethodsA total of 156 peripheral blood (PB) samples collected from healthy donors (HD) and patients with diseases frequently associated with loss/downregulation of classical NK-cell markers were immunophenotyped following EuroFlow protocols, aimed at comparing the staining profile of total blood NK-cells for CD314, CD335 and NKp80, and the performance of distinct marker combinations for their accurate identification.ResultsNKp80 showed a superior performance (vs. CD314 and CD335) for the identification of NK-cells in HD blood. Besides, NKp80 improved the conventional CD16/CD56/CD3-based strategy to identify PB NK-cells in HD and reactive processes, particularly when combined with CD16 for further accurate NK-cell-subsetting. Although NKp80+CD16 improved the identification of clonal/tumor NK-cells, particularly among CD56- cases (53%), aberrant downregulation of NKp80 was observed in 25% of patients, in whom CD56 was useful as a complementary NK-cell marker. As NKp80 is also expressed on T-cells, we noted increased numbers of NKp80+ cytotoxic T-cells at the more advanced maturation stages, mostly in adults.ConclusionHere we propose a new robust approach for the identification of PB NK-cells, based on the combination of NKp80 plus CD16. However, in chronic lymphoproliferative disorders of NK-cells, addition of CD56 is recommended to identify clonal NK-cells, due to their frequent aberrant NKp80- phenotype.
Discrimination of different forms and oceanic regions of purpleback flying squid (Sthenoteuthis oualaniensis) based on stable isotopes and fatty acid composition
Authors: Zhu Kai , Xu Kaida , Zhu Wenbin 
Published: July 2024

IntroductionPelagic cephalopods play a key role in the Chinese food supply. The market value of seafood frequently fluctuates based on its geographical origin and species, making it imperative to trace the origin and distinguish forms to guarantee food quality and accurate information.MethodsIn this study, we used biochemical tracers, including stable isotope analysis and fatty acid composition profiling, to trace the origin of purpleback flying squid (Sthenoteuthis oualaniensis) from the Indian Ocean and South China Sea. We measured the δ13C and δ15N values and fatty acid (FA) contents in samples from different forms of S. oualaniensis obtained from these two oceanic regions. We analyzed the feeding and nutritional differences among these populations and conducted discriminant analysis.Results and discussionSignificant regional and form differences were observed in both isotopic values and FA profiles in the muscle tissues of S. oualaniensis. Forms with larger sizes exhibited higher δ13C and δ15N values, potentially resulting from different feeding preferences and geographical environments. The discriminant analysis revealed that isotopic composition could effectively distinguish individuals from different oceanic regions, whereas FA composition was more effective in distinguishing different forms within the same oceanic region. The combination of isotopes and FAs could accurately discriminate S. oualaniensis of different forms and from different oceanic regions, achieving a discrimination accuracy of 100%. This study provides a reference for tracing the origin of pelagic cephalopods with complex form structures.
Outcome after decompressive craniectomy in older adults after traumatic brain injury
Authors: Kapapa Thomas , Jesuthasan Stefanie , Schiller Franziska , Schiller Frederike , Woischneck Dieter , Gräve Stefanie , Barth Eberhard , Mayer Benjamin , Oehmichen Marcel , Pala Andrej 
Published: July 2024

ObjectiveGlobally, many societies are experiencing an increase in the number of older adults (&gt;65 years). However, there has been a widening gap between the chronological and biological age of older adults which trend to a more active and social participating part of the society. Concurrently, the incidence of traumatic brain injury (TBI) is increasing globally. The aim of this study was to investigate the outcome after TBI and decompressive craniectomy (DC) in older adults compared with younger patients.MethodsA retrospective, multi-centre, descriptive, observational study was conducted, including severe TBI patients who were treated with DC between 2005 and 2022. Outcome after discharge and 12 months was evaluated according to the Glasgow Outcome Scale (Sliding dichotomy based on three prognostic bands). Significance was established as p ≤ 0.05.ResultsA total of 223 patients were included. The majority (N = 158, 70.9%) survived TBI and DC at discharge. However, unfavourable outcome was predominant at discharge (88%) and after 12 months (67%). There was a difference in favour of younger patients (≤65 years) between the age groups at discharge (p = 0.006) and at 12 months (p &lt; 0.001). A subgroup analysis of the older patients (66 to ≤74 vs. ≥75 years) did not reveal any significant differences. After 12 months, 64% of the older patients had a fatal outcome. Only 10% of those &gt;65 years old had a good or very good outcome. 25% were depending on support in everyday activities. After 12 months, the age (OR 0.937, p = 0.007, CI 95%: 0.894–0.981; univariate) and performed cranioplasty (univariate and multivariate results) were influential factors for the dichotomized GOS. For unfavourable outcome after 12 months, the thresholds were calculated for age = 55.5 years (p &lt; 0.001), time between trauma and surgery = 8.25 h (p = 0.671) and Glasgow Coma Scale (GCS) = 4 (p = 0.429).ConclusionEven under the current modern conditions of neuro-critical care, with significant advances in intensive care and rehabilitation medicine, the majority of patients &gt;65 years of age following severe TBI and DC died or were dependent and usually required extensive support. This aspect should also be taken into account during decision making and counselling (inter-, intradisciplinary or with relatives) for a very mobile and active older section of society, together with the patient’s will.
Changes in the ocular surface microbiome of patients with coronavirus disease 2019 (COVID-19)
Authors: Lin Jia , Wang Jingrao , Feng Jiaoyang , Zhu Rui , Guo Yu , Dong Yueyan , Zhang Hong , Jin Xin 
Published: July 2024

PurposeTo elucidate the reasons behind the increased incidence of ocular disease in patients with coronavirus disease 2019 (COVID-19), this study delved deeper into the specific effects of COVID-19 on patients’ ocular surface microbiome (OSM) and investigated its relationship with the increased incidence of ocular disease.MethodsIn this study, conjunctival sac swabs were collected from 43 participants for 16S rRNA amplicon sequencing. The participants were categorized into three groups based on their COVID-19 status: the control group (C group) consisted of 15 participants who showed no evidence of COVID-19, the experimental group (E group) included 15 participants who tested positive for COVID-19, and the COVID-19 recovery period group (R group) comprised 13 participants.ResultsIn the comparison of alpha diversity, group E had a higher Shannon, Chao1 and Goods coverage index. When comparing beta diversity, groups E and R were more similar to each other. At the phylum level, although the OSM of the three groups was dominated by Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes, the compositional proportions were significantly different. At the genus level, the dominant species in the three OSM groups were significantly different, with Pseudomonas becoming the dominant genus in groups E and R compared to group C, and the abundance of Ralstonia decreasing significantly.ConclusionThis study provides additional evidence supporting the association between the OSM and COVID-19, which contributes to our understanding of the potential mechanisms underlying ocular symptoms and complications associated with COVID-19 in the future.
Pheromone cCF10 inhibits the antibiotic persistence of Enterococcus faecalis by modulating energy metabolism
Authors: Zhu Li , Yang Xiaobo , Fu Xinyue , Yang Panpan , Lin Xiaoli , Wang Feng , Shen Zhiqiang , Wang Jingfeng , Sun Feilong , Qiu Zhigang 
Published: July 2024

IntroductionBacterial resistance presents a major challenge to both the ecological environment and human well-being, with persistence playing a key role. Multiple studies were recently undertaken to examine the factors influencing the formation of persisters and the underlying process, with a primary focus on Gram-negative bacteria and Staphylococcus aureus (Gram-positive bacteria). Enterococcus faecalis (E. faecalis) is capable of causing a variety of infectious diseases, but there have been few studies of E. faecalis persisters. Previous studies have shown that the sex pheromone cCF10 secreted by E. faecalis induces conjugative plasmid transfer. However, whether the pheromone cCF10 regulates the persistence of E. faecalis has not been investigated.MethodsAs a result, we investigated the effect and potential molecular mechanism of pheromone cCF10 in regulating the formation of persisters in E. faecalis OG1RF using a persistent bacteria model.Results and discussionThe metabolically active E. faecalis OG1RF reached a persistence state and temporarily tolerated lethal antibiotic concentrations after 8  h of levofloxacin hydrochloride (20 mg/mL) exposure, exhibiting a persistence rate of 0.109 %. During the growth of E. faecalis OG1RF, biofilm formation was a critical factor contributing to antibiotic persistence, whereas 10 ng/mL cCF10 blocked persister cell formation. Notably, cCF10 mediated the antibiotic persistence of E. faecalis OG1RF via regulating metabolic activity rather than suppressing biofilm formation. The addition of cCF10 stimulated the Opp system and entered bacterial cells, inhibiting (p)ppGpp accumulation, thus maintaining the metabolically active state of bacteria and reducing persister cell generation. These findings offer valuable insights into the formation, as well as the control mechanism of E. faecalis persisters.