bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the chloroplast genome and phylogenetic evolution of Bidens pilosa
Authors: Zhang Danchun , Tu Jiajun , Ding Xiaoxia , Guan Wan , Gong Lu , Qiu Xiaohui , Huang Zhihai , Su He 
Published: March 2023

AbstractChloroplast genomes for 3Bidensplants endemic to China (Bidens bipinnataLinn.,Bidens pilosaLinn., andBidens albavar.radiata) have been sequenced, assembled and annotated in this study to distinguish their molecular characterization and phylogenetic relationships. The chloroplast genomes are in typical quadripartite structure with two inverted repeat regions separating a large single copy region and a small single copy region, and ranged from 151,599 to 154,478 bp in length. Similar number of SSRs and long repeats were found inBidens, wherein mononucleotide repeats (A/T), forward and palindromic repeats were the most in abundance. Gene loss ofclpPandpsbD, IR expansion and contraction were detected in theseBidensplants. It seems thatndhE,ndhF,ndhG, andrpl32from theBidensplants were under positive selection while the majority of chloroplast genes were under purifying selection. Phylogenetic analysis revealed that 3Bidensplants clustered together and further formed molophyletic clade with otherBidensspecies, indicatingBidensplants might be under radiation adaptive selection to the changing environment world-widely. Moreover, mutation hotspot analysis and in silico PCR analysis indicated that inter-genic regions ofndhD-ccsA,ndhI-ndhG, ndhF-rpl32, trnL_UAG-rpl32, ndhE-psaC, matK-rps16, rps2-atpI, cemA-petA,petN-psbMwere candidate markers of molecular identification forBidensplants. This study may provide useful information for genetic diversity analysis and molecular identification forBidensspecies.
Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis
Authors: Corona Ramirez Andrea , Bregnard Danaé , Junier Thomas , Cailleau Guillaume , Dorador Cristina , Bindschedler Saskia , Junier Pilar 
Published: March 2023

AbstractAt particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.
Mechanisms of salinity tolerance and their possible application in the breeding of vegetables
Authors: Shams Mostafakamal , Khadivi Ali 
Published: March 2023

AbstractBackgroundIn dry and semi-arid areas, salinity is the most serious hazard to agriculture, which can affect plant growth and development adversely. Over-accumulation of Na+in plant organs can cause an osmotic effect and an imbalance in nutrient uptake. However, its harmful impact can vary depending on genotype, period of exposure to stress, plant development stage, and concentration and content of salt. To overcome the unfavorable effect of salinity, plants have developed two kinds of tolerance strategies based on either minimizing the entrance of salts by the roots or administering their concentration and diffusion.ResultsHaving sufficient knowledge of Na+accumulation mechanisms and an understanding of the function of genes involved in transport activity will present a new option to enhance the salinity tolerance of vegetables related to food security in arid regions. Considerable improvements in tolerance mechanisms can be employed for breeding vegetables with boosted yield performance under salt stress. A conventional breeding method demands exhaustive research work in crops, while new techniques of molecular breeding, such as cutting-edge molecular tools and CRISPR technology are now available in economically important vegetables and give a fair chance for the development of genetically modified organisms.ConclusionsTherefore, this review highlights the molecular mechanisms of salinity tolerance, various molecular methods of breeding, and many sources of genetic variation for inducing tolerance to salinity stress.
Vitamin D3 supplementation as an adjunct in the management of childhood infectious diarrhea: a systematic review
Authors: Uwaezuoke Samuel N , Odimegwu Chioma L , Mbanefo Ngozi R , Eneh Chizoma I , Arodiwe Ijeoma O , Muoneke Uzoamaka V , Ogbuka Francis N , Ndiokwelu Chibuzo O , Akwue Anthony T 
Published: March 2023

Abstract
Background
Some studies have reported the possible role of vitamin D3 in ameliorating disease outcomes in childhood infectious diarrhea. However, findings about its effectiveness and the association of serum vitamin D levels with diarrhea risk appear inconsistent. We aimed to determine the efficacy of oral vitamin D3 as an adjunct in managing childhood infectious diarrhea and the relationship between vitamin D status and the disease.

Methods
We searched the PubMed and Google Scholar electronic databases for relevant articles without limiting their year of publication. We selected primary studies that met the review’s inclusion criteria, screened their titles and abstracts, and removed duplicates. We extracted data items from selected studies using a structured data-extraction form. We conducted a quality assessment of randomized controlled trials (RCTs) and non-randomized studies with the Cochrane collaboration tool and the Newcastle Ottawa Scale, respectively. We assessed the strength of the relationship between serum vitamin D levels and diarrhea using the correlation model. We estimated the I2 and tau2 values to assess between-study heterogeneity.

Results
Nine full-text articles were selected, consisting of one RCT, three cross-sectional studies, two cohort studies, two longitudinal/prospective studies, and one case-control study. A total of 5,545 participants were evaluated in the nine studies. Six non-randomized studies provided weak evidence of the relationship between vitamin D levels and diarrhea risk as there was no correlation between the two variables. The only RCT failed to demonstrate any beneficial role of vitamin D3 in reducing the risk of recurrent diarrhea. The calculated I2 and tau2 values of 86.5% and 0.03, respectively suggested a high between-study heterogeneity which precluded a meta-analysis of study results.

Conclusion
Oral vitamin D3 may not be an effective adjunct in managing childhood infectious diarrhea. Additionally, the relationship between vitamin D status and infectious diarrhea appears weak. We recommend more adequately-powered RCTs to determine the effectiveness of vitamin D3 as an adjunct therapy in infectious diarrhea.
A case of acute tubulointerstitial nephritis following administration of the Oxford-AstraZeneca COVID-19 vaccine: a case report
Authors: Williams Samuel B. M. , Holwill Stephen D. J. , Clissold Rhian L. , Bingham Coralie 
Published: March 2023

Abstract
Background
More than 4 billion doses of the Coronavirus disease (COVID-19) vaccine have been administered worldwide but the relationship between the different vaccines and the development of renal disease is unknown. We present a case of tubulointerstitial nephritis following administration of the Oxford-AstraZeneca COVID-19 vaccine.

Case presentation
A previously fit and well 51-year-old female presented on 27th May 2021 with a one-month history of weight loss, fatigue, nausea, and a metallic taste. She had an acute kidney injury with a creatinine of 484 umol/L. She was on no regular medications and denied taking any over-the-counter or alternative medicines. She had received her first dose of the Oxford-AstraZeneca vaccine on 23rd March 2021 and her second dose on 20th May 2021. A renal biopsy was performed the following day. The 19 glomeruli appeared normal to light microscopy but the tubulointerstitial compartment contained a dense inflammatory infiltrate including many eosinophils. There was widespread acute tubular injury with tubulitis, but no established or longstanding atrophy. A diagnosis was made of an acute tubulointerstitial nephritis. She was commenced on oral prednisolone and her renal function improved. She did not require renal replacement therapy at any time.

Conclusions
To our knowledge, this was the first described case of acute tubulointerstitial nephritis following administration of the Oxford-AstraZeneca COVID-19 vaccine, although a number of cases have emerged more recently. In our case the patient was very fit and well, had no previous past medical history and had not taken any recent prescribed, over-the-counter or alternative medications. The absence of these provoking factors in our case makes the vaccine the most likely explanation for the development of tubulointerstitial nephritis although the pathophysiology behind this remains unknown. Given the unprecedented number of vaccinations being delivered around the world, nephrologists should be aware of this possible link although more research into the topic is required.
Hypertrophic olivary degeneration associated with bilateral vocal cord adductor dystonia
Authors: Lycett Mitchell , Cui Cathy Kexin , Dragicevich Dijana , Harris Roger , Ng Karl 
Published: March 2023

Abstract
Background
Hypertrophic olivary degeneration (HOD) is a rare condition caused by lesions within the dentato-rubro-olivary pathway, resulting in ocular nystagmus and palatal myoclonus (oculopalatal tremor) but not usually dystonia. Dystonia is an uncommon association, and we present the first reported association of hypertrophic olivary degeneration with bilateral vocal cord dystonia.

Case presentation
A 33 year old male presented initially with acute hydrocephalus on the background of previous ventriculoperitoneal (VP) shunting for previously treated medulloblastoma. After revision of the VP shunt, the patient developed progressive hiccups and stridor leading to respiratory failure requiring intubation. Ocular pendular nystagmus and palatal myoclonus at 3 Hz was observed. Flexible nasendoscopy (FNE) demonstrated bilateral tonic adduction of the vocal folds with 3 Hz coarse supraglottic, pharyngeal and palatal rhythmic myoclonus. MRI imaging demonstrated T2 hyperintensity within the bilateral inferior olivary nuclei consistent with stage 3 radiological HOD.

Conclusions
Dystonia is a rarely reported phenomenon in HOD but is not unexpected with the inferior olivary nucleus implicated in dystonic disorders. We report the association of HOD with bilateral vocal cord adductor dystonia, a potentially life threatening condition.
Integrated analyzes identify CCT3 as a modulator to shape immunosuppressive tumor microenvironment in lung adenocarcinoma
Authors: Huang Junfeng , Hu Bingqi , Yang Ying , Liu Huanhuan , Fan Xingyu , Zhou Jing , Chen Liwen 
Published: March 2023

Abstract
Background
Chaperonin-containing tailless complex polypeptide 1 (TCP1) subunit 3 (CCT3) has tumor-promoting effects in lung adenocarcinoma (LUAD). This study aims to investigate the molecular mechanisms of CCT3 in LUAD oncogenesis.

Methods
The UALCAN databases, Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) data were used to analyze CCT3 expression in LUAD. Both the Wilcoxon rank-sum test and the regression model were used to investigate the connection between clinicopathologic characteristics of LUAD patients and CCT3 expression. The prognostic value of CCT3 was determined by Cox regression models, the Kaplan-Meier method and Nomogram prediction. Next, we identified the most related genes with CCT3 via GeneMANIA and String databases, and the association between CCT3 and infiltrated immune cells using single-sample Gene Set Enrichment Analysis (ssGSEA). CCT3-related pathway enrichment analysis was investigated by GSEA. Finally, CCT3 roles in cell proliferation and apoptosis of LUAD A549 cells was verified by siRNA (small interfering RNA) mediated CCT3 knockdown.

Results
CCT3 was upregulated in LUAD both in mRNA and protein levels. CCT3 overexpression was associated with clinicopathological characteristics including sex, smoking, T- and N-categories, pathological staging, and a poor prognosis of LUAD patients. GeneMANIA and String databases found a set of CCT3-related genes that are connected to the assembly and stability of proteins involved in proteostasis of cytoskeletal filaments, DNA repair and protein methylation. Furthermore, CCT3 was found to be positively correlated with the infiltrating Th2 cells (r = 0.442, p < 0.01) while negatively correlated with mast cells (r = -0.49, p < 0.01) and immature dendritic cells (iDCs, r = -0.401, p < 0.001) according to ssGSEA analyzes. The pathway analysis based on GSEA method showed that the cell cycle pathway, the protein export pathway, the proteasome pathway and the ribosome pathway are enriched in CCT3 high group, whereas the JAK/STAT pathway, B cell receptor pathway, T cell receptor pathway and toll like receptor pathway were enriched in CCT3 low group. Finally, CCT3 knockdown substantially inhibited proliferation while promoted apoptosis of A549 cells.

Conclusion
Integrated analyzes identify CCT3 as a modulator to shape immunosuppressive tumor microenvironment in LUAD and therefore, a prognostic factor for LUAD.
A nomogram based on platelet-to-lymphocyte ratio for predicting pathological complete response of breast cancer after neoadjuvant chemotherapy
Authors: Ma Rulan , Wei Wanzhen , Ye Haixia , Dang Chengxue , Li Kang , Yuan Dawei 
Published: March 2023

Abstract
Objective
To investigate the role of platelet-to-lymphocyte ratio (PLR) in complete pathological response (pCR) of breast cancer (BC) patients after neoadjuvant chemotherapy (NAC), as well as to establish and validate a nomogram for predicting pCR.

Methods
BC patients diagnosed and treated in the First Affiliated Hospital of Xi’an Jiaotong University from January 2019 to June 2022 were included. The correlation between pCR and clinicopathological characteristics was analyzed by Chi-square test. Logistic regression analysis was performed to evaluate the factors that might affect pCR. Based on the results of regression analysis, a nomogram for predicting pCR was established and validated.

Results
A total of 112 BC patients were included in this study. 50.89% of the patients acquired pCR after NAC. Chi-square test showed that PLR was significantly correlated with pCR (X2 = 18.878, P < 0.001). And the PLR before NAC in pCR group was lower than that in Non-pCR group (t = 3.290, P = 0.001). Logistic regression analysis suggested that white blood cell (WBC) [odds ratio (OR): 0.19, 95% confidence interval (CI): 0.04–0.85, P = 0.030)], platelet (PLT) (OR: 0.19, 95%CI: 0.04–0.85, P = 0.030), PLR (OR: 0.18, 95%CI: 0.04–0.90, P = 0.036) and tumor grade (OR: 9.24, 95%CI: 1.89–45.07, P = 0.006) were independent predictors of pCR after NAC. A nomogram prediction model based on WBC, PLR, PLR and tumor grade showed a good predictive ability.

Conclusion
PLR, PLT, WBC and tumor grade were independent predictors of pCR in BC patients after NAC. The nomogram based on the above positive factors showed a good predictive ability.
Clinical characteristics and prognostic characterization of endometrial carcinoma: a comparative analysis of molecular typing protocols
Authors: Yang Zihui , Yang Xi , Liu Xinyu , Ma Ke , Meng Yi-Ting , Yin Hong-Fang , Wen Jia , Yang Jiang-Hui , Zhen Zeng , Feng Zong-Hao , Liao Qin-Ping 
Published: March 2023

Abstract
Background
Endometrial carcinoma (EC) is one of the most common gynecological malignancies in China and globally, accounting for the fourth-prevalent cancer in women. Although numerous studies have confirmed prognostic value of The Cancer Genome Atlas (TCGA) molecular subgroups, it is unclear how they are combined with histological features. The main objective of this study was to compare ProMisE and TCGA classification for the rapid and accurate prediction of prognosis within EC patients, together with the provision of a revised strategy for individualized diagnosis and treatment of patients.

Methods
Within this study, 70 patients with EC from Beijing Tsinghua Changgeng Hospital (affiliated to Tsinghua University) were retrospectively examined between July 2015 and December 2021. Samples were processed for determination of clinical markers, together with ProMisE and TCGA classification.

Results
Comparative analysis across four TCGA types (POLE, Low-CN, High-CN, and MSI-H) and age, was statistically significant (χ²= 7.000, p = 0.029). There was no significant difference observed among the four TCGA types and FIGO stage, vascular invasion and depth of invasion, or lymph node metastasis and tumor area. There was no significant association between the expression of Vimentin, Ki-67, PTEN, MSH2, PAX-8, β-catenin, CD10, ER, PR, P16, MLH1, and PMS2 with the four TCGA types. In addition, p63 expression (χ²= 11.09, p = 0.029) and p53 expression (χ²= 11.585, p = 0.005) were statistically significant. Numerous models demonstrated that patients with POLE mutations and low-CN had higher progression free survival (PFS) and overall survival (OS), whereas those with high-CN had lowest values. The log-rank test revealed that the survival rate of PR-positive and ER-positive patients was significantly higher (p < 0.001).

Conclusion
Overall, these results can be of additional benefit for clinical applications, in comparison to the ProMisE classification method. In addition, PR, ER, vascular infiltration, hyperlipidemia and atherosclerosis were found to be the key factors affecting EC prognosis.
Spinal muscular atrophy and anorexia nervosa: a case report
Authors: Yeung Siu Tsin Au , Alford Colleen , You Daniel 
Published: March 2023

Abstract
Background
Spinal muscular atrophy (SMA) is an autosomal recessive condition affecting lower motor neurons causing progressive muscle atrophy. Anorexia nervosa (AN) is a psychiatric disorder characterised by intense fear of weight gain, restriction of energy intake, and preoccupation with body weight and shape. Low weight, gastrointestinal dysmotility, and respiratory infections are common in SMA but may mask AN. No paediatric cases of AN in SMA have been reported to date.

Case presentation
A 14-year-old female with SMA2 presented with 12 months of declining body weight to a nadir of 24.8 kg (BMI 11). This was initially attributed to medical complications including pneumonia and gastroenteritis, and chronic gut dysmotility associated with SMA. Despite almost 2 years of dietetic input and nutritional supplementation due to the weight plateauing from age 11, no significant restoration or gain was achieved. The Eating Disorder Examination-Questionnaire (EDE-Q) indicated a possible eating disorder and psychiatric evaluation confirmed AN.
Initial management prioritised close medical monitoring and outpatient weight restoration on an oral meal plan. Skin fold anthropometric measurement was conducted to determine a minimum healthy weight. Individual psychological therapy and family sessions were undertaken. The patient developed major depression and a brief relapse with weight loss to 28 kg. Since then, the patient has maintained a weight of around 35 kg with stable mood.

Conclusions
Low body weight, feeding issues, gastrointestinal dysmotility, and respiratory infections are common in SMA and diagnostic overshadowing can lead to delayed recognition of anorexia nervosa. Change to growth trajectory and prolonged weight loss should prompt consideration of comorbid psychiatric issues. Screening measures such as the EDE-Q and DASS may be helpful in this population. Close liaison between the neurogenetics and psychiatry teams is helpful. Skin fold anthropometry can assist in identifying a minimum healthy weight range.
Experiences of microdosing psychedelics in an attempt to support wellbeing and mental health
Authors: Ryan Rebecca S. , Copello Alex , Fox Andrew P. 
Published: March 2023

Abstract
Background
Microdosing psychedelic drugs is a growing phenomenon, but little is known about the experiences surrounding this. Research broadly suggests that people may use psychedelics in an attempt to self-medicate for mental health and wellbeing. However, the precise details, rationale and meaning of such attempts remains unclear, and would benefit from clarification, using tailored experiential methods. This research therefore aimed to explore the way that users make sense of microdosing psychedelics, with a particular focus on the experience of any perceived mental health or wellbeing changes.

Method
Participants were recruited via websites and online forums. An internet text-based, semi-structured interview was conducted anonymously with 13 participants regarding their experiences of microdosing psychedelic drugs. Interpretive Phenomenological Analysis was used to analyse the transcripts.

Results
Three superordinate themes were identified through the interviews: 1) Seeking a solution: Agency and rationale; 2) Microdosers as scientists; 3) Catalysing desirable and beneficial effects.

Conclusions
All participants approached microdosing methodically and with purpose. Participants reported that they had experienced beneficial effects of microdosing on their mental health, alongside cognitive, physical and social changes. By microdosing, participants reported that they had supported their own mental health and wellbeing, with microdosing described as a catalyst to achieving their aims in this area. This study provided additional knowledge and understanding of the experience, rationale and personal meaning of the microdosing phenomenon which can be used to inform future investigations in the areas of psychedelic use and mental health.