bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic profiling of mitochondria-related transcriptome in tumorigenesis, prognosis, and tumor immune microenvironment of intrahepatic cholangiocarcinoma: a multi-center cohort study
Authors: Chen Bo , Lu Mengmeng , Chen Qiwen , Zou Enguang , Bo Zhiyuan , Li Jiacheng , Zhao Rui , Zhao Jungang , Yu Zhengping , Chen Gang , Wu Lijun 
Published: July 2024

BackgroundMitochondrial dysfunction has been shown to play a critical role in cancer biology. However, its involvement in intrahepatic cholangiocarcinoma (iCCA) remains significantly understudied.MethodsRNA sequencing data of 30 pairs of iCCA and paracancerous tissues were collected from the First Affiliated Hospital of Wenzhou Medical University (WMU). The WMU cohort (n = 30) was integrated with public TCGA (n = 30) and GSE107943 (n = 30) datasets to establish a multi-center iCCA cohort. We merged the TCGA and GSE107943 cohorts into an exploration cohort to develop a mitochondria signature for prognosis assessment, and utilized the WMU cohort for external validation. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Hallmarker analyses were used for functional interpretation of iCCA associated mitochondria-related genes (MRGs). In addition, unsupervised clustering was performed to identify mitochondria-based iCCA subtypes with the data of three institutions. Further investigations were conducted to examine the impact of mitochondrial dysfunction on drug responses, alteration of the tumor immune microenvironment, and immune responses.ResultsTwo hundred and sixty-three iCCA-related MRGs were identified to be related to fatty acid metabolism, oxidative phosphorylation, and apoptosis. Through univariate and multivariate Cox, and LASSO analyses, a mitochondria signature with five optimal MRGs was established to evaluate the prognosis of iCCA patients with the AUC values ranged from 0.785 to 0.928 in the exploration cohort. The signature also exhibited satisfactory performance in the WMU cohort with AUC values of 0.817–0.871, and was identified as an independent risk predictor in both cohorts. Additionally, we found that patients with higher mitochondria score with poor prognosis presented lower infiltration levels of CD4+ T-cell, NK cells, and monocytes, and demonstrated higher sensitivity to targeted therapies, including sorafenib. Furthermore, two distant mitochondria-based subtypes were determined, and subtype 2 was associated with shorter survival time and immunosuppressive tumor microenvironment. Finally, the differential protein expression of five key MRGs was verified by Immunohistochemistry.ConclusionWe found mitochondrial dysfunction modulates aberrant metabolism, oxidative stress, immune responses, apoptosis, and drug sensitivity in iCCA. A mitochondria signature and two mitochondria-based iCCA subtypes were identified for clinical risk stratification and immunophenotyping.
4th booster-dose SARS-CoV-2 heterologous and homologous vaccination in rheumatological patients
Authors: Gallardo-Nelson Maria Jose , Cruces Marcos , Gómez Yolanda M. , Fuenzalida Constanza , Silva Javiera , Aravena-Traipi Laura , Nuñez Eduardo , Gaete-Angel Aracelly , Rivas-Yañez Elizabeth , Kalergis Alexis M. , Soto-Rifo Ricardo , Valiente-Echeverria Fernando 
Published: July 2024

Objectiveto evaluate the immune response to the SARS-CoV-2 vaccines in adults with immune-mediated rheumatic diseases (IMRDs) in comparison to healthy individuals, observed 1-20 weeks following the fourth vaccine dose. Additionally, to evaluate the impact of immunosuppressive therapies, vaccination schedules, the time interval between vaccination and sample collection on the vaccine’s immune response.MethodsWe designed a longitudinal observational study conducted at the rheumatology department of Hospital de Copiapó. Neutralizing antibodies (Nabs) titers against the Wuhan and Omicron variant were analyzed between 1-20 weeks after administration of the fourth dose of the SARS-CoV-2 vaccine to 341 participants (218 IMRD patients and 123 healthy controls). 218 IMRD patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA), ankylosing spondylitis (AS), systemic lupus erythematosus (SLE), systemic vasculitis (VS) and systemic scleroderma (SS) were analyzed.ResultsPerforming a comparison between the variants, Wuhan vs Omicron, we noticed that there were significant differences (p&lt;0.05) in the level of the ID50, both for healthy controls and for patients with IMRDs. The humoral response of patients with IMRDs is significantly lower compared to healthy controls for the Omicron variant of SARS-CoV-2 (p = 0.0015). The humoral response of patients with IMRDs decreases significantly when the time interval between vaccination and sample collection is greater than 35 days. This difference was observed in the response, both for the Wuhan variant and for the Omicron variant.ConclusionThe IMRDs patients, the humoral response variation in the SARS-CoV-2 vaccine depends on doses and type of vaccine administered, the humoral response times and the treatment that these patients are receiving.
Efficacy of calcein as a chemical marker of Potamocorbula laevis
Authors: Gao Jin , Xie Xi , Liu Xiang-Feng , Bai Yong-An , Yang Miao , Teng Wei-Ming , Liu Hai-Jiao , Wang Qing-Zhi 
Published: July 2024

IntroductionCalcein was used to develop a shell marking method for Potamocorbula laevis.MethodsThe suitable conditions for marking were investigated, including marking concentration, immersion time, and water temperature. The impacts and feasibility of the marking method were assessed based on the survival rate of P. laevis, the success rate of fluorescence marking, marking quality, and alterations in activities of antioxidant enzymes in the digestive gland of the experimental bivalves. Two concentrations of calcein (20 and 50 mg/L) were used and the immersion time included 1 and 2 h, respectively. The experiment was performed in two rounds, with water temperatures of 12.84 ± 0.09 and 24.18 ± 0.04 °C, respectively.Results and discussionThe results indicated that calcein did not significantly impact the survival of P. laevis after 7 d of recovery. The catalase activity and malondialdehyde content in low temperature-marked P. laevis showed significant decreases, and the relative abundances of certain fatty acids also exhibited significant changes within 2 h post exposure to 20 mg/L of calcein. However, these indicators returned to normal levels within 7 d. The marking impact of calcein was proportional to the calcein concentration and immersion time. Higher temperature generated a negative impact on the marking effect of 20 mg/L of calcein, while no obvious impacts were observed for 50 mg/L of calcein. The marking success rates and the recapture rates of P. laevis for in situ tests in the two experimental groups were both 100% and 4.44 ± 1.29% after one month. Also, the recapture marking rates and the marking good rates of the recaptured individuals were both 100%. There were no significant differences between these parameters for 50 and 75 mg/L of calcein. Given the cost and safety of labeling, a strategy in terms of an immersion in 50 mg/L of calcein for 2 h could be considered as an effective in situ labeling scheme for P. laevis. In conclusion, calcein can be employed as a marking method for P. laevis. These findings could be potentially beneficial for development of in situ labeling technology, proliferation as well as release of shellfish in tidal flats and resource conservation.
Global citrus root microbiota unravels assembly cues and core members
Authors: Lombardo Monia F. , Zhang Yunzeng , Xu Jin , Trivedi Pankaj , Zhang Pengfan , Riera Nadia , Li Lei , Wang Yayu , Liu Xin , Fan Guangyi , Tang Jiliang , Coletta-Filho Helvécio D. , Cubero Jaime , Deng Xiaoling , Ancona Veronica , Lu Zhanjun , Zhong Balian , Roper M. Caroline , Capote Nieves , Catara Vittoria , Pietersen Gerhard , Al-Sadi Abdullah M. , Xu Xun , Wang Jian , Yang Huanming , Jin Tao , Cirvilleri Gabriella , Wang Nian 
Published: July 2024

IntroductionCitrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth.MethodsIn a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition.ResultsTen predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted.ConclusionOverall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health.
Effects of repetitive transcranial magnetic stimulation on lower extremity motor function and optimal parameters in stroke patients with different stages of stroke: a systematic evaluation and meta-analysis
Authors: Fan Shiyu , Yan Long , Zhang Junfeng , Qian Yulin , Wang Meng , Yang Lingqing , Yu Tao 
Published: July 2024

BackgroundRepetitive transcranial magnetic stimulation (rTMS), as an emerging non-invasive neuromodulation technique, is now widely employed in rehabilitation therapy. The purpose of this paper is to comprehensively summarize existing evidence regarding rTMS intervention for lower limb motor function in patients at different stages of stroke.MethodsA systematic search was conducted to identify randomized controlled trials (RCTs) assessing the efficacy of rTMS for treating lower limb motor dysfunction after stroke. Multiple databases, including China National Knowledge Infrastructure (CNKI), Wanfang Data Knowledge Service Platform, VIP Database, PubMed, Embase, Web of Science, and Cochrane Library, were searched. The search period extended from the inception of the libraries to June 2024. Literature information was extracted, and methodological quality was evaluated using the risk of bias assessment tool in the Cochrane Handbook. Meta-analysis was performed using Stata 17.0 software.ResultsOverall, 49 appropriate studies (including 3,558 stroke subjects) were found. Meta-analysis results demonstrated that rTMS effectively improved lower limb motor function across all stages of stroke. The intervention was particularly more effective in patients in the subacute stage than in the acute or chronic stages. Subgroup analysis revealed that, for acute-stage patients, low-frequency stimulation targeting the M1 or DLPFC brain regions on the unaffected side with 20–40 sessions significantly improved FMA-LE scores. In subacute-phase patients, low-frequency stimulation targeting the M1 brain regions on the unaffected side with 18 sessions significantly improved FMA-LE scores. The results demonstrated that HF-rTMS was more effective than LF-rTMS in improving walking speed, with the greatest efficacy observed at 20 sessions. While for enhancing gait balance in stroke patients, LF-rTMS with the best therapeutic effect was observed at a frequency of 20–40 treatments.ConclusionThis study demonstrates the efficacy of rTMS in improving lower limb motor function, balance, and walking speed in stroke patients at various stages. The findings provide a valuable reference for the development of optimized rTMS treatment plans in clinical practice.Systematic review registration: PROSPERO: CRD42023466094.
Development of an Aotearoa New Zealand adapted Mediterranean dietary pattern and Kai/food basket for the He Rourou Whai Painga randomised controlled trial
Authors: Worthington Anna , Liu Eva , Foster Meika , Wright Summer Rangimaarie , Lithander Fiona E. , Wall Clare , Roy Rajshri , Parry-Strong Amber , Krebs Jeremy , Braakhuis Andrea 
Published: July 2024

BackgroundFollowing a Mediterranean diet (MedDiet) is associated with a lower risk of cardiovascular disease. He Rourou Whai Painga is a dietary intervention trial with behaviour change support that seeks to determine whether a MedDiet pattern can provide equivalent benefits in Aotearoa New Zealand (NZ), a country where cardiovascular disease is a leading cause of death. To do this, the MedDiet needs to be adapted in an acceptable way for NZ, with consideration of the Māori (indigenous) population.MethodsThe MedDiet was defined using existing MedDiet scoring tools and adapted to the NZ context using local guidelines. The resulting NZ MedDiet pattern was used to develop a kai/food basket, including products from industry partners, for participants in He Rourou Whai Painga. Criteria set for the kai/food basket included providing up to 75% of energy requirements and falling within the Australia/NZ Acceptable Macronutrient Distribution Range to reduce risk of chronic disease. Māori researchers on the team provided support to ensure Mātauranga Māori (Māori knowledge and values) was upheld through this process.ResultsThe NZ MedDiet pattern criteria was similar to the identified MedDiet scoring tools, with differences in recommendations for dairy, red meat, alcohol and olive oil. The resulting kai/food baskets were estimated to provide on average 73.5% of energy requirements for households, with 36% from fat, 8.6% from saturated fat, 17% protein, and 42% carbohydrate. Forty-two industry partners, including 3 Māori businesses, agreed to provide 22 types of food products towards the total.ConclusionSmall, feasible changes to the MedDiet can be made to align with the NZ guidelines and food environment. However, this eating pattern still differs from what the population, particularly Māori, are currently consuming. Continued partnership with Māori and additional behavioural support is important to facilitate adherence to this dietary pattern within He Rourou Whai Painga.Trial registration: https://www.anzctr.org.au/Default.aspx, identifier ACTRN12622000906752 and https://www.isrctn.com/, identifier ISRCTN89011056.
Dexamethasone-sparing strategies in anthracycline and cyclophosphamide-based chemotherapy with a focus on 5-HT3 receptor antagonists: a network meta-analysis
Authors: Watanabe Daichi , Iihara Hirotoshi , Kobayashi Ryo , Fujii Hironori , Mori Ryutaro , Kumada Keisuke , Shimizu Masahito , Futamura Manabu , Suzuki Akio 
Published: July 2024

BackgroundThe effectiveness of a dexamethasone-sparing strategy in the treatment of breast cancer with anthracycline-cyclophosphamide therapy when combined with first-generation 5-HT3 receptor antagonists (RAs) and neurokinin-1 RAs is unclear. This is attributable to a lack of evidence from direct comparison of multiple doses of DEX to a single dose of DEX in combination with first-generation 5-HT3 RAs in anthracycline-cyclophosphamide therapy. Our goal was to clarify the impact of dexamethasone-sparing strategies that involve both first-generation 5-HT3 RAs and palonosetron when combined with neurokinin-1 RAs, using a network meta-analysis.Materials and methodsA literature search was conducted on PubMed/Medline for articles published up to July 4, 2023. We included randomized controlled trials which assessed the efficacy of antiemetic regimens which combined 5-HT3 RAs and dexamethasone, with or without neurokinin-1 RAs, for the initial dose in anthracycline-cyclophosphamide therapy for patients with breast cancer. The primary outcome was the proportion of patients achieving a complete response during the delayed phase (CR-DP).ResultsThe difference in the proportion of patients achieving CR-DP between multiple and single doses of dexamethasone was 0.1% (95%CI: -12.4 to 12.5) with palonosetron and neurokinin-1 RAs, compared to 5.3% (95%CI: -13.4 to 23.0) with a single dose of a first-generation 5-HT3 receptor antagonist. Additionally, the difference was 12.7% (95% CI: -2.8 to 28.2) when comparing palonosetron against first-generation 5-HT3 RAs in combination with a single dose of dexamethasone and neurokinin-1 RAs.ConclusionPalonosetron is recommended rather than a single dose of first-generation 5-HT3 RAs in dexamethasone-sparing strategies for anthracycline-cyclophosphamide therapy.
Congenital absence of the gallbladder in a child: a case report
Authors: Wei Xiao , You Liying , Liu Chun , Xu Xu 
Published: July 2024

BackgroundCongenital absence of the gallbladder (CAGB) is an exceedingly rare embryological anomaly of the biliary system, with a complex etiology involving the failure of gallbladder formation during embryogenesis. Clinical manifestations are diverse; most patients are asymptomatic, while some present with symptoms such as biliary colic. The complexity of its clinical presentation and radiological features renders diagnosis challenging.Case presentationFetal ultrasound at 22 weeks of gestation revealed an absent gallbladder. At 9 years and 11 months of age, the child exhibited significant weight gain and abnormalities. Abdominal ultrasound and magnetic resonance images demonstrated fatty liver and gallbladder agenesis. Liver function tests indicated mild abnormalities, with aspartate aminotransferase at 67 IU/L and alanine aminotransferase at 44 IU/L. Following 6 months of hepatoprotective and lipid-lowering therapy, a satisfactory treatment response was achieved, with normalization of liver function and improvement in fatty liver.ConclusionsCAGB may be associated with other congenital abnormalities, although isolated cases are uncommon. Clinically, it may manifest as nonspecific biliary, gastrointestinal, or urinary symptoms, mimicking various digestive disorders and leading to misdiagnosis. Genetic sequencing and in-depth embryological research may elucidate the etiology and enhance diagnostic accuracy.
Colquhounia root tablet improves diabetic kidney disease by regulating epithelial-mesenchymal transition via the PTEN/PI3K/AKT pathway
Authors: Ma Donghong , Zhang Jiao , Du Lu , Shi Jingjing , Liu Zhaoyan , Qin Jilin , Chen Xiaoxiao , Guo Minghao 
Published: July 2024

BackgroundDiabetic kidney disease (DKD) is a severe microvascular complication of diabetes mellitus that can lead to end-stage renal disease. Colquhounia root tablet (CRT) has shown therapeutic potential in treating DKD, but its efficacy and underlying mechanisms remain to be elucidated.MethodsA randomized controlled clinical trial was conducted on 61 DKD patients. The treatment group received CRT in addition to standard therapy, while the control group received standard therapy alone. Treatment efficacy and adverse events were evaluated after 3 months. Additionally, in vitro experiments using human renal tubular epithelial cells (HK-2) were performed to investigate the effect of CRT on high glucose (HG)-induced epithelial-mesenchymal transition (EMT) and the involvement of the PTEN/PI3K/AKT signaling pathway.ResultsCRT treatment significantly improved proteinuria and increased the effective treatment rate in DKD patients compared to the control group, with no significant difference in adverse events. Moreover, CRT reversed HG-induced EMT in HK-2 cells, as evidenced by the downregulation of α-SMA and upregulation of E-cadherin at both mRNA and protein levels. Mechanistically, CRT increased PTEN expression and inhibited the PI3K/AKT pathway, similar to the effects of the PI3K inhibitor LY29400. The combination of CRT and LY29400 further enhanced PTEN mRNA expression under HG conditions.ConclusionCRT effectively improves proteinuria in DKD patients and ameliorates HG-induced EMT in HK-2 cells. The underlying mechanism may involve the upregulation of PTEN and subsequent inhibition of the PI3K/AKT signaling pathway. These findings provide new insights into the therapeutic potential of CRT for DKD treatment.
Abundant resources compensate for the uneven distribution of ungulates in desert grassland
Authors: Gou Xiaowei , Tsunekawa Atsushi , Tsubo Mitsuru , Peng Fei , Cheng Yunxiang 
Published: July 2024

IntroductionStrategically managing livestock grazing in arid regions optimizes land use and reduces the damage caused by overgrazing. Controlled grazing preserves the grassland ecosystem and fosters sustainability despite resource limitations. However, uneven resource distribution can lead to diverse grazing patterns and land degradation, particularly in undulating terrains.MethodsIn this study, we developed a herbivore foraging algorithm based on a resource selection function model to analyze foraging distribution patterns, predict the probability of foraging, and identify the determinants of foraging probability in cattle. The study area was a complex desert landscape encompassing dunes and interdunes. Data on cattle movements and resource distribution were collected and analyzed to model and predict foraging behavior.ResultsOur findings revealed that cattle prefer areas with abundant vegetation in proximity to water sources and avoid higher elevations. However, abundant resource availability mitigated these impacts and enhanced the role of water points, particularly during late grazing periods. The analysis showed that available resources primarily determine foraging distribution patterns and lessen the effects of landforms and water distance on patch foraging.DiscussionThe results suggest that thoughtful water source placement and the subdivision of pastures into areas with varied terrain are crucial for sustainable grazing management. By strategically managing these factors, land degradation can be minimized, and the ecological balance of grassland ecosystems can be maintained. Further research is needed to refine the model and explore its applicability in other arid regions.