bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multidrug resistant invasive non-typhoidal Salmonella ST313 isolated in Brazil features unique pathogenic mechanisms
Authors: Martins Isabela Mancini , Seribelli Amanda Aparecida , Ribeiro Tamara R. Machado , Silva Patrick , Lustri Bruna Cardinali , Hernandes Rodrigo T. , Falcão Juliana Pfrimer , Moreira Cristiano Gallina 
Published: April 2023

Abstract
Invasive non-typhoidal Salmonella (iNTS) from the clonal type ST313 (S. Typhimurium ST313) is the major cause of invasive salmonellosis disease in Africa. Recently in Brazil, iNTS ST313 strains have been isolated from different sources, but there is a lack of understanding the mechanisms behind how these gut bacteria are able to break the gut barrier and reach the patient’s bloodstream. Herein, we compared 13 S. Typhimurium ST313 strains genomes isolated from human-blood cultures investigating aspects of virulence and resistance mechanisms. RNAseq analyses were also performed between the clinical blood isolate and SL1344 prototype, which belongs to ST19 and it was originally isolated from human feces. That analysis reveals here 15-upregulated genes related to pathogenesis in S. Typhimurium ST313 compared to SL1344 (ST19) such as sopD2, sifB, pipB, amongst others. We have also compared these clinical with non-clinical isolates from Brazil, a total of 22 genomes were studied by single nucleotide polymorphism (SNPs). The epidemiological analysis of 22 genomes of S. Typhimurium ST313 strains grouped them into three distinct clusters (A, B and C) by SNP analysis, where cluster A comprised five, the group B six, and the group C 11. The 13 clinical blood isolates were all resistant to streptomycin, 92. 3% strains were resistant to ampicillin and 15.39% strains were resistant to kanamycin. The resistance genes acrA, acrB, mdtK, emrB, emrR, mdsA and mdsB related to the production of efflux pumps were detected in all (100%) strains studied, similar to pathogenic traits investigated. In conclusion, we evidenced the S. Typhimurium ST313 strains isolated in Brazil are different of the African strains ST313. The elevated frequencies of virulence genes such as sseJ, sopD2 and pipB are a major concern in these Brazilian isolates, showing a higher pathogenic potential.
S100PBP is regulated by mutated KRAS and plays a tumour suppressor role in pancreatic cancer
Authors: Srivast Kirtiman , Lines Kate , Jach Daria , Crnogorac-Jurcevic Tatjana 
Published: April 2023

Abstract
We have previously shown that expression of S100PBP, an S100P binding partner, gradually decreases during progression of pancreatic ductal adenocarcinomas (PDAC). Here, we show that loss of S100PBP leads to oncogenic transformation of pancreatic cells; after deregulation of S100PBP expression, both in silico and in vitro analyses highlighted alterations of genes known to modulate cytoskeleton, cell motility and survival. Overexpression of S100P reduced S100PBP expression, while co-immunoprecipitation indicated the interaction of S100P with S100PBP-p53-ubiquitin protein complex, likely causing S100PBP degradation. The doxycycline-induced KrasG12D activation resulted in decreased S100PBP levels, while low-dose treatment with HDAC inhibitor MS-275 rescued its expression in both human and mouse PDAC cell lines. This indicates KrasG12D as an upstream epigenetic regulator of S100PBP. Finally, analysis of TCGA PanCancer Atlas PDAC datasets demonstrated poor prognosis in patients with high S100P and low S100PBP expression, suggesting that S100PBP is a novel tumour suppressor gene with potential clinical utility.
Differences of prevalence and risk factors of diabetic retinopathy among rural and urban residents in South China
Authors: Xiao Baixiang , Duan Fang , Gu Xuejun , Zuo Jiahao , Chan Ving Fai , Virgili Gianni , Zhou Xiaojun , Price-Sanchez Carlos , Jin Ling , Liu Yuanping , Wang Yanfang , Zhong Yichun , Liao Qinghua , Fu Haoxiang , He Yun , Li Dongfeng , Xu Ping , Li Jia , Huang Wenyong , Congdon Nathan 
Published: April 2023

Abstract
Objective To determine the prevalence of diabetic retinopathy (DR) and associated risk factors among rural and urban people living with diabetes mellitus (PwDM ) in southern China.Methods This cross-sectional study informed all the 3,646 PwDM aged > = 18 years in 2019. All were registered at primary health centers in Qujiang district. A questionnaire was administered to collect information on demographic, socioeconomic, medical and lifestyle factors. Blood glucose, lipids and indices of renal function were measured. Presence of DR was determined by trained graders based on fundus photographs using criteria of the United Kingdom National Health Service (NHS) Diabetic Eye Screening (DES) Programme. Multiple logistic regression analyses were used to assess potential risk factors for presence of DR.Results The mean age of the 2,677 participants (73.4%) was 63.4 years (SD 10.1 years), 1,503 (56.2%) were female, 1,749 (65.3%) were rural residents, 1,654 (71.0%) participants had HbA1c > = 6.5%, 1,773 (66.3%) had uncontrolled high blood pressure, and the median duration of DM was < 5 years. Although half (52.0%) of these participants had brief (< 5 years) exposure to DM, 831 (31.3%, 95% CI: 29.3–32.8%) had DR, among whom 412 (49.6%) had sight threatening DR. Men (33.1%), had a significantly higher prevalence of any DR than women (29.4%, p < 0.05). There were no significant differences in DR prevalence at any level between rural and urban residents. In multivariate regression models, risk factors for any DR were HbA1C > 6.5% (OR = 1.58 p < 0.01), using insulin and hypoglycemic drugs (OR = 1.76, p < 0.01), longer duration of DM and higher systolic blood pressure (OR = 1.01 for each mmHg, p < 0.01).Conclusion Although half of participants had DM for < 5 years, the high prevalence of DR, poorly controlled blood glucose and uncontrolled hypertension highlight the need for better management of non-communicable diseases in rural China.
Accurate long-read sequencing identified GBA variants as a major genetic risk factor in the Luxembourg Parkinson’s study
Authors: Krüger Rejko , Pachchek Sinthuja , Landoulsi Zied , Pavelka Lukas , Schulte Claudia , Buena-Atienza Elena , Gross Caspar , Hauser Ann-Kathrin , Bobbili Dheeraj , Casadei Nicolas , May Patrick 
Published: April 2023

Abstract
Heterozygous variants in the glucocerebrosidase GBAgene are an increasingly recognized risk factor for Parkinson’s disease (PD). Due to the pseudogene GBAP1 that shares 96% sequence homology with the GBAcoding region, accurate variant calling by array-based or short-read sequencing methods remains a major challenge in understanding the genetic landscape of GBA-related PD. We established a novel long-read sequencing technology for assessing the full length of the GBA gene. We used subsequent regression models for genotype-phenotype analyses. We sequenced 752 patients with parkinsonism and 806 healthy controls of the Luxembourg Parkinson’s study. All GBAvariants identified showed a 100% true positive rate by Sanger validation. We found 12% of unrelated PD patients carrying GBA variants. Three novel variants of unknown significance (VUS) were identified. Using a structure-based approach, we defined a potential risk prediction method for VUS. This study describes the full landscape of GBA-related parkinsonism in Luxembourg, showing a high prevalence of GBA variants as the major genetic risk for PD. Our approach provides an important advancement for highly accurate GBA variant calling, which is essential for providing access to emerging causative therapies for GBA carriers.
Genome-wide identification of Cell Wall Associated Kinases -Like (WAKL) family in maize (Zea mays L.) and its Gibberellin mediated transcriptional regulation during kernel early development
Authors: Hu Kun , Dai Qiao , Ajayo Babatope , Wang Hao , Hu Yufeng , Li Yangping , Huang Huanhuan , Liu Hanmei , Liu Yinghong , Wang Yayun , Gao Lei , Xie Ying 
Published: April 2023

Abstract
Background The wall associated kinase (WAK) and WAK-like kinase (WAKL) form a kinase family which is reported to be involved in cell expansion and development. However, genome-wide analysis of WAK/WAKLs in maize was barely performed and their molecular regulations remain unclear.Results 58 maize WAKL genes were identified and classified into 3 phylogenetic groups and structure prediction indicated functions of WAKLs are conserved. Cis-acting elements revealed that ZmWAKL genes may be transcriptionally regulated by Gibberellins (GA). Expression and co-expression analyses indicated that ZmWAKL38, ZmWAKL42 and ZmWAKL52 were highly expressed in maize kernels and respectively exhibited a high correlation with GA up-regulated kernel preferentially expressed transcription factors, TF5 (Zm00001d027802), TF6 (Zm00001d006551), and TF8 (Zm00001d036768). qPCR shew that ZmWAKL38, ZmWAKL42, ZmWAKL52, TF5, TF6 and TF8 increased their expression after GA treated. Furthermore, the transcriptional activity of ZmWAKL52 promoter shew the most dramatic enhance activated by TF8 and ZmWAKL52 were located in plasma membrane. ZmWAKL38 and ZmWAKL42 were positively regulated by TF5 and TF6 respectively.Conclusion Our study preliminarily identifies three ZmWAKL genes which are preferentially expressed in maize kernel and transcriptionally regulated by GA-mediated TFs. In summary, our research provides a better understanding of ZmWAKL genes, facilitates maize breeding and offers acknowledge for future functional studies.
Pituitary Macroadenomas in Childhood and Adolescence: A Clinical Analysis of 7 Patients
Authors: aguilar-riera cristina , Clemente María , Gonzalez-Llorens Núria , Mogas Eduard , Campos-Martorell Ariadna , Fàbregas Anna , Biagetti Betina , Vázquez Elida , Yeste Diego 
Published: April 2023

Abstract
BACKGROUND

Pituitary adenomas (PPAs) are uncommon in childhood and adolescence, accounting for 2-6% of all intracranial neoplasms. Delayed puberty, growth retardation, galactorrhea and weight gain are common features at presentation in pediatric patients. Functional tumors constitute a vast majority (90%) of PPAs, with the most frequent being prolactinomas.

CASE PRESENTATION

A retrospective review of the clinical features and outcomes of 7 pediatric patients with pituitary macroadenomas was conducted. We included PPAs in patients under 18 years at diagnosis with diameters larger than 10mm by magnetic resonance (MRI).
Six patients were males (85%), with age at diagnosis ranging from 8 to 15 (median 14+/2.8SDS). The primary symptoms that led to medical attention were growth retardation, gigantism and secondary amenorrhea. The visual field was reduced in three cases (42%). Suprasellar extension was present in 3 subjects, and one had a giant adenoma. Adenomas were clinically functioning in 6 patients (85%) (three prolactinomas, two somatropinomas, one secreting FSH and one no-producer). The prolactinomas responded to treatment with cabergoline. For the rest, one required transsphenoidal surgery and the other three both surgery and radiotherapy. All patients undergoing radiotherapy had secondary panhypopituitarism. In relation to the genetic studies, two patients presented a pathogenic mutation of the AIP gene and one of the MEN1.

DISCUSION AND CONCLUSION

Pediatric pituitary macroadenomas are a distinct entity, mostly found in males and with a predominance of functional tumors leading to detrimental effects on growth and puberty in addition to neuro-ophthalmological manifestations. It is important to perform genetic studies in patients with macroadenomas appearing under the age of 30 years as genetic and syndromic associations are more frequent in this age group.
Ki 67 Cut-off Level &amp; mPEPI Score: Any Predictive Role for Neoadjuvant ‘Chemotherapy’ Efficacy in Locally Advanced HER2 Negative Luminal-like Breast Cancer?
Authors: Dogan Mutlu , Karacin Cengiz , Kaman Omur , Bulut Zarife Melda , Kiziltan Gamze , Oksuzoglu Berna , Dogan Lutfi 
Published: April 2023

Abstract
Purpose:Role of neoadjuvant chemotherapy(NAC) & modified preoperative endocrine prognostic index (mPEPI) score after NAC is unclear in locally advanced HER2(-) breast cancer(LA-HnLBC).We evaluated prognostic & predictive factors for NAC in LA-HnLBC retrospectively. Methods:All had doxorubicin+/-taxane as NAC.They were grouped as pCR/non-pCR & categorized for PR/ki67/ki67 decline/mPEPI score. Ki67 cut-offs were as 20 & median values in our study. Results:142 LA-HnLBC pCR( n:26) & non-pCR(n:116) patients were included.Median age was 53 years. pCR rate was 18.3%. Median ER/PR/ki67 were as 90/40/40 %. Median ki67 was 40 for basal & postoperative. pCR group had more T2(73%), grade 3(69%) & non-pCR had more T3(21%), grade 2(46%) tumors (p=0.03,p=0.03). pCR group had lower mPEPI score (3.5 vs 5,p=0.05). 5y-DFS was 69% (93.8% vs 63.4%, p=0.012). 5y-OS was 77% (100% vs 72%, p=0.018). In univariate analysis, high basal/postoperative ki67 levels, ki67 decline & mPEPI score were significant poor prognostic factors for DFS (p=0.01, p< 0.001, p=0.017, p<0.001) & OS (p=0.006, p=0.003, p=0.05, p=0.001) in non-pCR goup. Prognostic cut-offs were as 40 for basal ki67 (DFS & OS), 20 for postoperative ki67 (DFS), 4 for mPEPI (DFS) & 30 for ki67 decline (OS). Conclusion: Favorable prognostic factors were defined as lower basal ki67 level (<40%) & higher ki67 decline (ki67 <30%) for OS; lower basal ki67 (<40%), po ki 67 (<20%) & mPEPI score (<4) for DFS after NAC in LA HnLBC. Different prognostic cut-offs for basal & postoperative ki 67 is striking. mPEPI score may also have prognostic significance after NAC, T in LA-HnLBC pts.
Axial compression performance of concrete filled double skin (SHS outer and SHS inner) steel tubular columns confined by CFRP
Authors: Wang Caisen , Liang Jiongfeng , Li Wei , He Chunfeng 
Published: April 2023

Abstract
This paper focuses on the axial compression performance of 15 concrete filled double skin tubes CFDST columns by the different CFRP reinforcement schemes. The design of this test used an outer square steel tube with a square steel tube inside and concrete poured at the sandwich and the inner steel tube kept in hollow. Firstly, the damage mechanisms of the specimens were observed and analysed. Secondly, the mechanical properties of the specimens were further analysed from the data of load displacement, peak load and ultimate displacement. The data analysis was mainly used to compare the different axial compressive properties of CFDST columns wrapped with CFRP sheet and those without CFRP sheet. Finally, by referring to the previous model on CFRP-CFST, a modification was made and a computational model of a CFRP-confined CFDST column was developed, which was found to be in good agreement with the experimental results by comparison.
Source variation in nutrient profile and the effects of Black soldier fly (Hermetia illucens) larva meal at graded levels in diet on performance, carcass traits, serum biochemical profile and cellular immune response in broiler chicken
Authors: Raju M.V.L.N. , Rao S.V. Rama , Paul S.S. , Prakash Bhukya , Reddy M.R. , Kannan A. , Shanmugam M. , Kumar P. Santosh Phani 
Published: April 2023

Abstract
Four samples of Black soldier fly (Hermetia illucens) larva meal (BSFLM), procured from 3 different sources, were analysed for nutrient profile. One of those, a partially-defatted BSFLM, was evaluated in male broiler chicken diet at 0, 2.5 and 5.0% (expt. 1), and at 0, 5.0, 7.5 and 10.0% levels (expt. 2). Each of the experimental diets was fed to 12 replicates of 6 chickens each in expt. 1 (n=216) and 15 replicates of 25 chickens each in expt. 2 (n=1500). The nutrient profile varied greatly amongst the BSFLM samples (crude protein: 49.8 to 59.6%, crude fat: 12.0 to 38.4%, lysine: 2.4-4.7%, methionine: 2.3-4.6%, lauric acid: 15.2-62.4%). Body weight gain (BWG) and feed intake (FI) of broilers increased linearly in the groups fed BSFLM upto 5.0% during 0-3 weeks of age (expt. 1) and was similar during the remaining period, whereas the feed conversion ratio (FCR) linearly increased during 3 to 5 weeks. At higher levels of BSFLM (≥7.5% in diet) (expt. 2), significantly depressed BWG and FI, and increased FCR were observed. Dressing yield, breast weight and abdominal fat content linearly increased with BSFLM level in diet (expt. 2), while other organ weights, serum biochemical profile and PHA-P response were unaffected (expt. 1). It is concluded that the nutrient profile of BSFLM varied with the source and it could be used upto 5% in the diet of broiler chickens with beneficial effects on growth during the early life.
Registry-derived stage (RD-Stage) for capturing cancer stage at diagnosis for endometrial cancer: development and validation of business rules and capacity to report at a national level.
Authors: Evans Sue M , Ivanova Kris , Rome Robert M , Cossio Danica , Pilgrim Charles , Zalcberg John , Antill Yoland , Blake Louis , Du Guesclin Alexandra , Garrett Andrea , Giffard Dalisay , Golobic Nikkitia , Moir Diana , Parikh Sumit , Parisi Andrea , Sanday Karen , Shadbolt Clair , Smith Mirka , Marvelde Luc Te , Williams Karen 
Published: April 2023

Abstract
Background
Registry-derived stage (RD-Stage) provides a mechanism to capture cancer stage at diagnosis from routinely captured data available to population-based cancer registries (PBCRs). In 2021, a project was undertaken to develop business rules to capture RD-Stage for endometrial cancer, understand current capacity to capture this information at a national level, and assess how it compares with stage recorded in clinical notes at diagnosis by clinicians.
Methodology
Business rules for deriving RD-stage (Endometrial carcinoma) were developed using AJCC Cancer Staging Manual 8th edition and endorsed by a tumour-specific Expert Working group comprising cancer specialists responsible for delivering cancer care and PBCR epidemiologists and medical coders. Baseline completeness of data fields required to calculate RD-Stage, and an overall proportion of cases for whom an RD stage could be assigned was assessed across each Australian jurisdiction. A validation study was undertaken in one jurisdiction to compare RD-Stage (Endometrial cancer) calculated by the Victorian Cancer Registry (VCR) with clinical stage recorded in cases diagnosed in 2018-2020 in the National Gynae-Oncology Registry (NGOR).
Results
The level of completeness of data to enable RD-Stage (Endometrial carcinoma) to be calculated across jurisdictions ranged from 0 to 89%. Three jurisdictions captured degree of spread of cancer only (instead of TNM data) and therefore captured no data which would enable RD-Stage to be calculated.
The RD-Stage (Endometrial carcinoma) validation study found that RD-Stage could not be derived for 64/485 (13%) cases in the VCR and was not captured for 44/485 (9%) cases in NGOR. There was concordance at stage level (I, II, III, IV) in 393/410 (96%) of cases (95.8%, Kendall’s coefficient=0.95).
Conclusion
A lack of consistency in data captured by, and data sources reporting to, PBCRs meant that it was not possible to provide an accurate national baseline of endometrial carcinoma stage at diagnosis. In a sample of Victorian cases, there was very good concordance between RD-Stage (Endometrial carcinoma) and that recorded by clinicians in medical records and captured by NGOR. However, for 10% of cases RD-Stage could not be calculated because data was not available. RD-Stage provides a useful tool to be used for population epidemiological purposes.
GBDT_KgluSite: An improved computational prediction model for lysine glutarylation sites based on Feature Fusion and GBDT classifier
Authors: Liu Xin , Zhu Bao , Dai XiaWei , Xu ZhiAo , Li Rui , Qian Yuting , Lu YaPing , Zhang Wenqing , Liu Yong , Zheng Junnian 
Published: April 2023

Abstract
Background Lysine glutarylation(Kglu) is one of the most important Post-translational modifications(PTMs), which plays significant roles in various cellular functions, including metabolism, mitochondrial processes, and translation. Therefore, accurate identification of Kglu site is important for elucidating protein molecular function. Due to the time-consuming and expensive limitations of traditional biological experiment, computational-based Kglu site prediction research are gaining more and more attention.Results In this study, we proposed a new model named GBDT_KgluSite to identify Kglu and non-Kglu sequences based on the gradient-boosting decision tree (GBDT). Here, sequence-based features, physicochemical property-based features, structural-based features, and evolutionary-derived features were used to characterize proteins. The imbalance between positive and negative samples was addressed using the NearMiss-3 approach, and extraneous data was eliminated using the Elastic Net. The experimental results show that GBDT_KgluSite has good robustness and generalization ability, with accuracy and AUC values of 93.73%, and 98.14% on five-fold cross-validation as well as 90.11%, and 96.75% on the independent test dataset, respectively.Conclusion GBDT_KgluSite is an effectively computational method for identifying Kglu sites in protein sequences. It has good stability and generalization ability and could be useful for the identification of new Kglu sites in Mus musculus protein. The code and dataset of GBDT_KgluSite is available at https://github.com/flyinsky6/GBDT_KgluSite.
Cervical Vertebral Maturation: An Objective Staging System
Authors: Alhamady Ahlam M. , Ishaq Ramy Abdul Rahman , Alhammadi Maged Sultan , Al-mashraqi Abeer A. , Alhashimi Najah 
Published: April 2023

Abstract
Background The aim of this study was to evaluate an objective method for Cervical Vertebral Maturation (CVM) staging.Methods An initial sample of 647 Lateral Cephalometric Radiographs (LCR) were staged according to the CVM Baccetti et. al. by 4 examiners. The final sample (n = 394) included LCR on which the staging of the 4 investigators matched. The objective staging was performed by a single operator. The sample was divided according to the maturational stages into pre-pubertal, pubertal and post-pubertal groups. Measurements were performed on the Cervical Vertebrae (C2, C3 and C4). The angle between posterior and superior borders for C3 and C4 was the SWIA. Concavity Depth (CD) for C2, C3 and C4, and Body Shape (BS) (ratio of width to height of C3 and C4). Measurements of the 3 groups were compared.Results Mean values of SWIA and BS and median values of CD within maturational stage showed significant differences. Similar results were revealed for the comparisons between the values at different stages (P < 0.001).Conclusions A standardized, objective staging system using linear and angular measurements and ratios was applied for the determination of CVM.