bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the relationship between plant species and physicochemical properties on rhizosphere and rhizoplane fungal communities in alpine wet meadows
Authors: Iqbal Awais , Maqsood Ur Rehman Muhammad , Usman Muhammad , Sajjad Wasim , Niu Jiahuan , Degen Abraham Allan , Rafiq Muhammad , Shang Zhanhuan 
Published: December 2023

Abstract
Background
Wet meadows, a type of wetland, are impacted by significant climate fluctuation and human activity, impacting soil microorganisms that play an essential role in ecosystem processes. Understanding the underlying ecological mechanisms and processes of wet meadows depends on the fungal communities associated with the plant roots. We used Illumina MiSeq profiling for amplicon sequencing to determine how environmental factors and elevation affect the fungal communities of the rhizosphere and rhizoplane related to three plant species, Cremanthodium ellisii, Cremanthodium lineare, and Caltha scaposa, in alpine wet meadows.

Results
The phyla Ascomycota and Basidiomycota dominated the rhizosphere (54.5% and 20.9%) and rhizoplane (51.6% and 36.4%), while the predominant fungal genera in the rhizosphere and rhizoplane were Unclassified fungi, Unclassified Ascomycota, Pseudeurotium, Tetracladium, Vishniacozyma, Rhodotorula, Cadophora, and Penicillium. Mantel test and network analysis revealed that the soil water content (SWC), soil organic carbon (SOC), and total nitrogen (TN) were the primary drivers of fungal communities. However, the influence of microbial biomass C (MBC), pH, microbial biomass N (MBN), and elevation varied. Stochastic assembly processes were dominant in both rhizosphere and rhizoplane fungal communities. FUNGuild functional prediction revealed site-specific variation in the trophic level and guild of plant-root-associated fungal communities. The rhizosphere contained 58.5% saprotrophs, 11.7% pathotrophs, and 12.6% symbiotrophs. In addition, 60.4% of the observed OTUs were arbuscular mycorrhizae, 13.2% were endophytes, 20.9% were ectomycorrhizae, and 1.09% were orchid mycorrhizae. The rhizoplane comprised 51.3% of OTUs linked with saprotrophs, 13.9% with pathotrophs, and 7.92% with symbiotrophs. Moreover, 36.1% of OTUs represented arbuscular mycorrhizae, 25.0% were endophytes, 30.6% were ectomycorrhizae, and 2.77% were ascribed to orchid mycorrhizae in the rhizoplane. The abundance of saprotrophs and pathotrophs in the rhizosphere was highest in C. ellisii at SI and SIII, while symbiotrophs were highest in C. lineare at SIII. Similar variations among the plant species and sites were observed in the fungal functional groups (guilds).

Conclusions
It was concluded that although root compartments significantly influenced the fungal communities in the rhizosphere and rhizoplane, environmental factors and plant types exhibited distinct effects. This study explains how physicochemical properties, plant species, and sites can alter the overall structure and functional repertoire of fungal communities in alpine wet meadows.

Graphical Abstract
TRPV1+ neurons alter Staphylococcus aureus skin infection outcomes by affecting macrophage polarization and neutrophil recruitment
Authors: Huang Changyu , Chen Yang , Cai Yuanqing , Ding Haiqi , Hong Jiaoying , You Shan , Lin Yiming , Hu Hongxin , Chen Yongfa , Hu Xueni , Chen Yanshu , Huang Ying , Zhang Chaofan , Lin Yunzhi , Huang Zida , Li Wenbo , Zhang Wenming , Fang Xinyu 
Published: December 2023

Abstract
Background
The interaction between the nervous system and the immune system can affect the outcome of a bacterial infection. Staphylococcus aureus skin infection is a common infectious disease, and elucidating the relationship between the nervous system and immune system may help to improve treatment strategies.

Results
In this study, we found that the local release of calcitonin gene-related peptide (CGRP) increased during S. aureus skin infection, and S. aureus could promote the release of CGRP from transient receptor potential cation channel subfamily V member 1 (TRPV1+) neurons in vitro. The existence of TRPV1+ neurons inhibited the recruitment of neutrophils to the infected region and regulated the polarization of macrophages toward M2 while inhibiting polarization toward M1. This reduces the level of inflammation in the infected area, which aggravates the local infection. Furthermore, this study demonstrates that TRPV1 may be a target for the treatment of S. aureus skin infections and that botulinum neurotoxin A (BoNT/A) and BIBN4096 may reverse the inhibited inflammatory effect of CGRP, making them potential therapeutics for the treatment of skin infection in S. aureus.

Conclusions
In S. aureus skin infection, TRPV1+ neurons inhibit neutrophil recruitment and regulate macrophage polarization by releasing CGRP. BoNT/A and BIBN4096 may be potential therapeutic agents for S. aureus skin infection.
Dissection of QTLs conferring drought tolerance in B. carinata derived B. juncea introgression lines
Authors: Limbalkar Omkar Maharudra , Vasisth Prashant , Singh Guman , Jain Priyanka , Sharma Mohit , Singh Rajendra , Dhanasekaran Gokulan , Kumar Manish , Meena Mohan Lal , Iquebal Mir Asif , Jaiswal Sarika , Rao Mahesh , Watts Anshul , Bhattacharya Ramcharan , Singh Kunwar Harendra , Kumar Dinesh , Singh Naveen 
Published: December 2023

AbstractBackgroundDrought is one of the important abiotic stresses that can significantly reduce crop yields. In India, about 24% ofBrassica juncea(Indian mustard) cultivation is taken up under rainfed conditions, leading to low yields due to moisture deficit stress. Hence, there is an urgent need to improve the productivity of mustard under drought conditions. In the present study, a set of 87B. carinata-derivedB. junceaintrogression lines (ILs) was developed with the goal of creating drought-tolerant genotypes.MethodThe experiment followed the augmented randomized complete block design with four blocks and three checks. ILs were evaluated for seed yield and its contributing traits under both rainfed and irrigated conditions in three different environments created by manipulating locations and years. To identify novel genes and alleles imparting drought tolerance, Quantitative Trait Loci (QTL) analysis was carried out. Genotyping-by-Sequencing (GBS) approach was used to construct the linkage map.ResultsThe linkage map consisted of 5,165 SNP markers distributed across 18 chromosomes and spanning a distance of 1,671.87 cM. On average, there was a 3.09 cM gap between adjoining markers. A total of 29 additive QTLs were identified for drought tolerance; among these, 17 (58.6% of total QTLs detected) were contributed byB. carinata(BC 4), suggesting a greater contribution ofB. carinatatowards improving drought tolerance in the ILs. Out of 17 QTLs, 11 (64.7%) were located on the B genome, indicating more introgression segments on the B genome ofB. juncea. Eight QTL hotspots, containing two or more QTLs, governing seed yield contributing traits, water use efficiency, and drought tolerance under moisture deficit stress conditions were identified. Seventeen candidate genes related to biotic and abiotic stresses, viz.,SOS2,SOS2 like,NPR1,FAE1-KCS,HOT5,DNAJA1,NIA1,BRI1,RF21, ycf2,WRKY33,PAL,SAMS2,orf147,MAPK3,WRR1 andSUS, were reported in the genomic regions of identified QTLs.ConclusionsThe significance ofB. carinatain improving drought tolerance and WUE by introducing genomic segments in Indian mustard is well demonstrated. The findings also provide valuable insights into the genetic basis of drought tolerance in mustard and pave the way for the development of drought-tolerant varieties.
LUM as a novel prognostic marker and its correlation with immune infiltration in gastric cancer: a study based on immunohistochemical analysis and bioinformatics
Authors: Xu Wu , Chen Shasha , Jiang Qiuju , He Jinlan , Zhang Feifei , Wang Zhuying , Ruan Caishun , Shi Bin 
Published: December 2023

AbstractBackgroundGastric cancer (GC) is considered the sixth highly prevailing malignant neoplasm and is ranked third in terms of cancer mortality rates. To enable an early and efficient diagnosis of GC, it is important to detect the fundamental processes involved in the oncogenesis and progression of gastric malignancy. The understanding of molecular signaling pathways can facilitate the development of more effective therapeutic strategies for GC patients.MethodsThe screening of genes that exhibited differential expression in early and advanced GC was performed utilizing the Gene Expression Omnibus databases (GSE3438). Based on this, the protein and protein interaction network was constructed to screen for hub genes. The resulting list of hub genes was evaluated with bioinformatic analysis and selected genes were validated the protein expression by immunohistochemistry (IHC). Finally, a competing endogenous RNA network of GC was constructed.ResultsThe three genes (ITGB1, LUM, and COL5A2) overexpressed in both early and advanced GC were identified for the first time. Their upregulation has been linked with worse overall survival (OS) time in patients with GC. Only LUM was identified as an independent risk factor for OS among GC patients by means of additional analysis. IHC results demonstrated that the expression of LUM protein was increased in GC tissue, and was positively associated with the pathological T stage. LUM expression can effectively differentiate tumorous tissue from normal tissue (area under the curve = 0.743). The area under 1-, 3-, and 5-year survival relative operating characteristics were greater than 0.6. Biological function enrichment analyses suggested that the genes related to LUM expression were involved in extracellular matrix development-related pathways and enriched in several cancer-related pathways. LUM affects the infiltration degree of cells linked to the immune system in the tumor microenvironment. In GC progression, the AC117386.2/hsa-miR-378c/LUM regulatory axis was also identified.ConclusionCollectively, a thorough bioinformatics analysis was carried out and an AC117386.2/hsa-miR-378c/LUM regulatory axis in the stomach adenocarcinoma dataset was detected. These findings should serve as a guide for future experimental investigations and warrant confirmation from larger studies.
Memory support training and lifestyle modifications to promote healthy aging in persons at risk for Alzheimer's disease: a digital application supported intervention (Brain Boosters)
Authors: Tomaszewski Farias S. , Fox J. , Dulaney H. , Chan M. , Namboodiri S. , Harvey D. J. , Weakley A. , Rahman S. , Luna C. , Beech B. F. , Campbell L. , Schmitter-Edgecombe M. 
Published: December 2023

Abstract
Background
Evidence-based interventions to protect against cognitive decline among older adults at risk for Alzheimer’s disease and related dementias (ADRD) are urgently needed. Rehabilitation approaches to support memory and behavioral/lifestyle interventions are recognized as promising strategies for preserving or improving cognitive health, although few previous interventions have combined both approaches. This paper describes the protocol of the Brain Boosters intervention, which synergistically combines training in compensatory and healthy lifestyle behaviors and supports implementation and tracking of new behaviors with a digital application.

Methods
The study utilizes a single-site, single-blinded, randomized controlled design to compare a structured lifestyle and compensatory aid intervention to an education-only self-guided intervention. We plan to enroll 225 community-dwelling adults (25% from underrepresented groups) aged 65 + who endorse subjective cognitive decline (SCD) and low baseline levels of healthy lifestyle behaviors. Both interventions will be administered in group format, consisting of 15 two-hour classes that occur weekly for ten weeks and taper to bi-monthly and monthly, for an intervention duration of 6 months. Participants in both interventions will receive education about a variety of memory support strategies and healthy lifestyle behaviors, focusing on physical and cognitive activity and stress management. The structured intervention will also receive support in adopting new behaviors and tracking set goals aided by the Electronic Memory and Management Aid (EMMA) digital application. Primary outcomes include global cognition (composite of memory, attention, and executive function tests) and everyday function (Everyday Cognition Questionnaire). Data will be collected at baseline and outcome visits, at approximately 6, 12, and 18 months. Qualitative interviews, self-report surveys (e.g., indicators of self-determination, health literacy) and EMMA data metrics will also be used to identify what components of the intervention are most effective and for whom they work.

Discussion
Successful project completion will provide valuable information about how individuals with SCD respond to a compensation and preventative lifestyle intervention assisted by a digital application, including an understanding of factors that may impact outcomes, treatment uptake, and adherence. The work will also inform development, scaling, and personalization of future interventions that can delay disability in individuals at risk for ADRD.

Trial Registration
ClinicalTrials.gov. (NCT05027789, posted 8/30/2021).
Development and validation of a new model for the early diagnosis of tuberculous meningitis in adults based on simple clinical and laboratory parameters
Authors: Liu Qiang , Cao Meiling , Shao Na , Qin Yixin , Liu Lu , Zhang Qing , Yang Xiao 
Published: December 2023

Abstract
Background
The differential diagnosis between tuberculous meningitis (TBM) and viral meningitis (VM) or bacterial meningitis (BM) remains challenging in clinical practice, particularly in resource-limited settings. This study aimed to establish a diagnostic model that can accurately and early distinguish TBM from both VM and BM in adults based on simple clinical and laboratory parameters.

Methods
Patients diagnosed with TBM or non-TBM (VM or BM) between January 2012 and October 2021 were retrospectively enrolled from the General Hospital (derivation cohort) and Branch Hospital (validation cohort) of Ningxia Medical University. Demographic characteristics, clinical symptoms, concomitant diseases, and cerebrospinal fluid (CSF) parameters were collated. Univariable logistic analysis was performed in the derivation cohort to identify significant variables (P < 0.05). A multivariable logistic regression model was constructed using these variables. We verified the performance including discrimination, calibration, and applicability of the model in both derivation and validation cohorts.

Results
A total of 222 patients (70 TBM and 152 non-TBM [75 BM and 77 VM]) and 100 patients (32 TBM and 68 non-TBM [31 BM and 37 VM]) were enrolled as derivation and validation cohorts, respectively. The multivariable logistic regression model showed that disturbance of consciousness for > 5 days, weight loss > 5% of the original weight within 6 months, CSF lymphocyte ratio > 50%, CSF glucose concentration < 2.2 mmol/L, and secondary cerebral infarction were independently correlated with the diagnosis of TBM (P < 0.05). The nomogram model showed excellent discrimination (area under the curve 0.959 vs. 0.962) and great calibration (P-value in the Hosmer–Lemeshow test 0.128 vs. 0.863) in both derivation and validation cohorts. Clinical decision curve analysis showed that the model had good applicability in clinical practice and may benefit the entire population.

Conclusions
This multivariable diagnostic model may help clinicians in the early discrimination of TBM from VM and BM in adults based on simple clinical and laboratory parameters.
Shared decision making in chronic kidney disease: a qualitative study of the impact of communication practices on treatment decisions for older patients
Authors: Dahm Maria R. , Raine Suzanne Eggins , Slade Diana , Chien Laura J. , Kennard Alice , Walters Giles , Spinks Tony , Talaulikar Girish 
Published: December 2023

Abstract
Background
Effective interpersonal communication is critical for shared decision-making (SDM). Previous SDM communication training in nephrology has lacked context-specific evidence from ethnographic analysis of SDM interactions with older patients considering treatment options of end stage kidney disease (ESKD). This study explores communication strategies in SDM discussions in nephrology, specifically focusing on older patients considering dialysis as kidney replacement therapy (KRT).

Methods
We conducted a qualitative study analysing naturally-occurring audio-recorded clinical interactions (n = 12) between Australian kidney doctors, patients aged 60+, and carers. Linguistic ethnography and qualitative socially-oriented functional approaches were used for analysis.

Results
Two types of communication strategies emerged: (1) Managing and advancing treatment decisions: involving active checking of knowledge, clear explanations of options, and local issue resolution. (2) Pulling back: Deferring or delaying decisions through mixed messaging. Specifically for non-English speaking patients, pulling back was further characterised by communication challenges deferring decision-making including ineffective issue management, and reliance on family as interpreters. Age was not an explicit topic of discussion among participants when it came to making decisions about KRT but was highly relevant to treatment decision-making. Doctors appeared reluctant to broach non-dialysis conservative management, even when it appears clinically appropriate. Conservative care, an alternative to KRT suitable for older patients with co-morbidities, was only explicitly discussed when prompted by patients or carers.

Conclusions
The findings highlight the impact of different communication strategies on SDM discussions in nephrology. This study calls for linguistic-informed contextualised communication training and provides foundational evidence for nephrology-specific communication skills training in SDM for KRT among older patients. There is urgent need for doctors to become confident and competent in discussing non-dialysis conservative management. Further international research should explore naturally-occurring SDM interactions in nephrology with other vulnerable groups to enhance evidence and training integration.
Do digital health interventions hold promise for stroke prevention and care in Black and Latinx populations in the United States? A scoping review
Authors: Rivera Bianca D. , Nurse Claire , Shah Vivek , Roldan Chastidy , Jumbo Adiebonye E. , Faysel Mohammad , Levine Steven R. , Kaufman David , Afable Aimee 
Published: December 2023

Abstract
Background
Black and Latinx populations are disproportionately affected by stroke and are likely to experience gaps in health care. Within fragmented care systems, remote digital solutions hold promise in reversing this pattern. However, there is a digital divide that follows historical disparities in health. Without deliberate attempts to address this digital divide, rapid advances in digital health will only perpetuate systemic biases. This study aimed to characterize the range of digital health interventions for stroke care, summarize their efficacy, and examine the inclusion of Black and Latinx populations in the evidence base.

Methods
We searched PubMed, the Web of Science, and EMBASE for publications between 2015 and 2021. Inclusion criteria include peer-reviewed systematic reviews or meta-analyses of experimental studies focusing on the impact of digital health interventions on stroke risk factors and outcomes in adults. Detailed information was extracted on intervention modality and functionality, clinical/behavioral outcome, study location, sample demographics, and intervention results.

Results
Thirty-eight systematic reviews met inclusion criteria and yielded 519 individual studies. We identified six functional categories and eight digital health modalities. Case management (63%) and health monitoring (50%) were the most common intervention functionalities. Mobile apps and web-based interventions were the two most commonly studied modalities. Evidence of efficacy was strongest for web-based, text-messaging, and phone-based approaches. Although mobile applications have been widely studied, the evidence on efficacy is mixed. Blood pressure and medication adherence were the most commonly studied outcomes. However, evidence on the efficacy of the various intervention modalities on these outcomes was variable. Among all individual studies, only 38.0% were conducted in the United States (n = 197). Of these U.S. studies, 54.8% adequately reported racial or ethnic group distribution. On average, samples were 27.0% Black, 17.1% Latinx, and 63.4% White.

Conclusion
While evidence of the efficacy of selected digital health interventions, particularly those designed to improve blood pressure management and medication adherence, show promise, evidence of how these interventions can be generalized to historically underrepresented groups is insufficient. Including these underrepresented populations in both digital health experimental and feasibility studies is critical to advancing digital health science and achieving health equity.
A population-based study of the trend in SARS-CoV-2 diagnostic modalities from the beginning of the pandemic to the Omicron surge in Kyoto City, Kyoto, Japan
Authors: Kyo Hiroki , Patel Shivani A. , Yamamoto Masaki , Matsumura Yasufumi , Ikeda Takeshi , Nagao Miki 
Published: December 2023

Abstract
Background
The coronavirus disease 2019 (COVID-19) presents critical diagnostic challenges for managing the pandemic. We investigated the 30-month changes in COVID-19 testing modalities and functional testing sites from the early period of the pandemic to the most recent Omicron surge in 2022 in Kyoto City, Japan.

Methods
This is a retrospective-observational study using a local anonymized population database that included patients' demographic and clinical information, testing methods and facilities from January 2020 to June 2022, a total of 30 months. We computed the distribution of symptomatic presentation, testing methods, and testing facilities among cases. Differences over time were tested using chi-square tests of independence.

Results
During the study period, 133,115 confirmed COVID-19 cases were reported, of which 90.9% were symptomatic. Although nucleic acid amplification testing occupied 68.9% of all testing, the ratio of lateral flow devices (LFDs) rapidly increased in 2022. As the pandemic continued, the testing capability was shifted from COVID-19 designated facilities to general practitioners, who became the leading testing providers (57.3% of 99,945 tests in 2022).

Conclusions
There was a dynamic shift in testing modality during the first 30 months of the pandemic in Kyoto City. General practitioners increased their role substantially as the use of LFDs spread dramatically in 2022. By comprehending and documenting the evolution of testing methods and testing locations, it is anticipated that this will contribute to the establishment of an even more efficient testing infrastructure for the next pandemic.