bluuebunny/crossref_metadata_2025_split huggingface dataset:
SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions
Authors: Dantas Carlos Willian Dias , da Costa Neto Sebastião Rodrigues , Alves Sandy Ingrid Aguiar , da Costa Pinheiro Kenny , De Los Santos Edian Franklin Franco , Ramos Rommel Thiago Jucá 
Published: June 2024

Abstract
Background
Tandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisatellites, and microsatellites, being the last two of specific interest because they can identify polymorphisms between organisms due to their instability. Currently, most mining tools focus on Simple Sequence Repeats (SSR) mining, and only a few can identify SSRs in the coding regions.

Results
We developed a microsatellite mining software called SATIN (Micro and Mini SATellite IdentificatioN tool) based on a new sliding window algorithm written in C and Python. It represents a new approach to SSR mining by addressing the limitations of existing tools, particularly in coding region SSR mining. SATIN is available at https://github.com/labgm/SATIN.git. It was shown to be the second fastest for perfect and compound SSR mining. It can identify SSRs from coding regions plus SSRs with motif sizes bigger than 6. Besides the SSR mining, SATIN can also analyze SSRs polymorphism on coding-regions from pre-determined groups, and identify SSRs differentially abundant among them on a per-gene basis. To validate, we analyzed SSRs from two groups of Escherichia coli (K12 and O157) and compared the results with 5 known SSRs from coding regions. SATIN identified all 5 SSRs from 237 genes with at least one SSR on it.

Conclusions
The SATIN is a novel microsatellite search software that utilizes an innovative sliding window technique based on a numerical list for repeat region search to identify perfect, and composite SSRs while generating comprehensible and analyzable outputs. It is a tool capable of using files in fasta or GenBank format as input for microsatellite mining, also being able to identify SSRs present in coding regions for GenBank files. In conclusion, we expect SATIN to help identify potential SSRs to be used as genetic markers.
Susceptibility gene identification and risk evaluation model construction by transcriptome-wide association analysis for salt sensitivity of blood pressure
Authors: Qi Han , Xie Yun-Yi , Yang Xiao-Jun , Xia Juan , Liu Kuo , Zhang Feng-Xu , Peng Wen-Juan , Wen Fu-Yuan , Li Bing-Xiao , Zhang Bo-Wen , Yao Xin-Yue , Li Bo-Ya , Meng Hong-Dao , Shi Zu-Min , Wang Yang , Zhang Ling 
Published: June 2024

AbstractBackgroundSalt sensitivity of blood pressure (SSBP) is an intermediate phenotype of hypertension and is a predictor of long-term cardiovascular events and death. However, the genetic structures of SSBP are uncertain, and it is difficult to precisely diagnose SSBP in population. So, we aimed to identify genes related to susceptibility to the SSBP, construct a risk evaluation model, and explore the potential functions of these genes.Methods and resultsA genome-wide association study of the systemic epidemiology of salt sensitivity (EpiSS) cohort was performed to obtain summary statistics for SSBP. Then, we conducted a transcriptome-wide association study (TWAS) of 12 tissues using FUSION software to predict the genes associated with SSBP and verified the genes with an mRNA microarray. The potential roles of the genes were explored. Risk evaluation models of SSBP were constructed based on the serial P value thresholds of polygenetic risk scores (PRSs), polygenic transcriptome risk scores (PTRSs) and their combinations of the identified genes and genetic variants from the TWAS. The TWAS revealed that 2605 genes were significantly associated with SSBP. Among these genes, 69 were differentially expressed according to the microarray analysis. The functional analysis showed that the genes identified in the TWAS were enriched in metabolic process pathways. The PRSs were correlated with PTRSs in the heart atrial appendage, adrenal gland, EBV-transformed lymphocytes, pituitary, artery coronary, artery tibial and whole blood. Multiple logistic regression models revealed that a PRS ofP < 0.05 had the best predictive ability compared with other PRSs and PTRSs. The combinations of PRSs and PTRSs did not significantly increase the prediction accuracy of SSBP in the training and validation datasets.ConclusionsSeveral known and novel susceptibility genes for SSBP were identified via multitissue TWAS analysis. The risk evaluation model constructed with the PRS of susceptibility genes showed better diagnostic performance than the transcript levels, which could be applied to screen for SSBP high-risk individuals.
Intestinal parasitic infections in children from marginalised Roma communities: prevalence and risk factors
Authors: Štrkolcová Gabriela , Fiľakovská Bobáková Daniela , Kaduková Michaela , Schreiberová Andrea , Klein Daniel , Halán Miloš , Urbančíková Ingrid 
Published: June 2024

AbstractBackgroundIntestinal parasitic infections remain a significant global health issue, particularly affecting poor and marginalised populations. These infections significantly contribute to children’s diseases, malnutrition, poor school performance, cognitive disorders, and future economic losses. This study aimed to explore and compare the occurrence of intestinal parasites in early childhood among the group of infants from the Slovak majority population and from marginalised Roma communities (MRCs). Furthermore, it aimed to explore the health complaints of children with and without intestinal parasitic infection in the past month and assess the effect of various risk factors on the occurrence of intestinal parasitic infection in infants from MRCs.MethodsWe obtained cross-sectional data from mothers and stool samples of their children aged 13–21 months using the first wave of the longitudinal RomaREACH study. A total of 181 stools from infants were analysed: 105 infants from the Slovak majority population and 76 from MRCs.ResultsInfants from MRCs are significantly more often infected byAscaris lumbricoides,Trichuris trichiuraandGiardia duodenalisthan their better-off peers from the majority population. Infection rates are 30% in infants from MRCs vs. 0% in the majority population (p < 0.001). Single and mixed infections were observed in children from MRCs. Infants with intestinal parasitic infections suffer significantly more often from various health complaints, particularly cough, stomach ache, irritability, and diarrhoea. Within MRCs, the risk of parasitic infections in infants is significantly increased by risk factors such as the absence of flushing toilets in households (OR = 4.17,p < 0.05) and contact with un-dewormed animals (OR = 3.61,p < 0.05). Together with the absence of running water in the household, these three factors combined increase the risk more than ten times (p < 0.01).ConclusionMaintaining hygienic standards in conditions of socioeconomic deprivation in MRCs without running water and sewage in the presence of un-dewormed animals is problematic. These living conditions contribute to the higher prevalence of parasitic infections in children from MRCs, causing various health complaints and thus threatening their health and healthy development.
Characteristics of chronic enteropathy associated with SLCO2A1 gene (CEAS) in children, a unique type of monogenic very early-onset inflammatory bowel disease
Authors: Lim Jin Gyu , Ko Jae Sung , Ko Jung Min , Kim Hyun Young , Kim Man Jin , Seong Moon Woo , Choi Young Hun , Kang Gyeong Hoon , Koh Jaemoon , Moon Jin Soo 
Published: June 2024

Abstract
Background
Chronic enteropathy associated with SLCO2A1 gene (CEAS) is a unique type of inflammatory bowel disease. CEAS is monogenic disease and is thought to develop from childhood, but studies on pediatric CEAS are scarce. We analyzed characteristics of pediatric CEAS.

Methods
Eleven patients diagnosed with CEAS at Seoul National University Children’s Hospital were identified and analyzed. Clinical data of patients were collected. Sanger sequencing of SLCO2A1 was performed on all patients.

Results
Patients were diagnosed at a median age of 16.0 years (IQR 11.0 ~ 20.0), and the median age at symptoms onset was only 4.0 years (IQR 2.5 ~ 6.0). Growth delay was observed at the time of diagnosis. Patients showed multiple ulcers or strictures in the small intestine, while the esophagus and colon were unaffected in any patients. Almost half of the patients underwent small intestine resection. The major laboratory features of pediatric CEAS include iron deficiency anemia (IDA), hypoalbuminemia, and near-normal levels of C-reactive protein (CRP). Two novel mutations of SLCO2A1 were identified. The most prevalent symptoms were abdominal pain and pale face. None of the immunomodulatory drugs showed a significant effect on CEAS.

Conclusions
Pediatric CEAS typically develop from very young age, suggesting it as one type of monogenic very early onset inflammatory bowel disease. CEAS can cause growth delay in children but there is no effective treatment currently. We recommend screening for SLCO2A1 mutations to pediatric patients with chronic IDA from a young age and small intestine ulcers without elevation of CRP levels.
Effectiveness of spaced repetition for clinical problem solving amongst undergraduate medical students studying paediatrics in Pakistan
Authors: Durrani Shazia F. , Yousuf Naveed , Ali Rahila , Musharraf Fatima Fakhir , Hameed Ammara , Raza Hussain Ahmed 
Published: June 2024

Abstract
Background
Studies using spaced repetition for teaching and learning in undergraduate clinical rotations such as paediatrics are limited, even more so in the South Asian region. Therefore, this study aimed to identify the effectiveness of utilizing spaced repetition compared to traditional learning methods among undergraduate medical students during their paediatric rotation at a medical university in Pakistan.

Methods
Bahria University Medical and Dental College (BUMDC) conducted quasii-experimental research in Karachi. Four topics were identified from the Year 5 Pediatrics curriculum to be used in the study, using which the study content was developed along with 50 multiple choice questions (MCQs) for assessment. All BUMDC Year 5 medical students rotating in Pediatrics were included and randomly allocated to the control or intervention group. In the control group, they provided the students with traditional study methods consisting of books and lectures to learn topics. In the intervention group, we created an Anki flashcard deck of the same topics to enable learning via spaced repetition. The researchers conducted a pretest and post test assessment of the 50 MCQs in both groups at the beginning and after the four-week study interval. The data were analysed using SPSS 19.

Results
A total of 115 BUMDC medical students agreed to participate in the study; 70 (59.1%) were in the intervention group, and 45 (41.7%) were in the control group. The pretest mean score of the control group was 27.96 ± 3.70, and the posttest mean score was 27.22 ± 5.02, with no statistically significant difference at the 95% confidence level. The mean score of the pretest for the intervention group was 27.93 ± 4.53, and that of the posttest was 30.8 ± 4.56, with a statistically significant difference at the 95% confidence level. The intervention showed a significant effect size of 0.8.

Conclusion
The use of spaced repetitions resulted in significantly greater scores for medical students studying paediatrics than for those using more traditional methods of learning, compromising medical books and lectures. Considering that medical students need to retain a vast amount of information, using spaced repetition through flashcards can be a more effective learning tool that is more cost-efficient and time-efficient than traditional learning methods.
Treating sleep-disordered breathing of idiopathic pulmonary fibrosis patients with CPAP and nocturnal oxygen treatment. A pilot study
Authors: Bordas-Martinez Jaume , Salord Neus , Vicens-Zygmunt Vanesa , Carmezim João , Pérez Sandra , Prado Eliseo , Calvo María , Blavia Rosana , Bermudo Guadalupe , Santos Salud , Monasterio Carmen , Molina-Molina María 
Published: June 2024

Abstract
Introduction
Sleep-disordered breathing (SDB) is a major comorbidity in idiopathic pulmonary fibrosis (IPF) and is associated with a poor outcome. There is a lack of knowledge regarding the impact of SDB treatment on IPF. We assessed at one year: (1) the effect of CPAP and/or nocturnal oxygen therapy on IPF regarding lung function, blood mediators, and quality of life; (2) adherence to SDB treatment and SDB changes.

Methodology
This is a prospective study of consecutive newly diagnosed IPF patients initiating anti-fibrotic treatment. Lung function, polysomnography, blood tests and quality of life questionnaires were performed at inclusion and after one year. Patients were classified as obstructive sleep apnoea (OSA), central sleep apnoea (CSA), and sleep-sustained hypoxemia (SSH). SDB therapy (CPAP and/or nocturnal oxygen therapy) was initiated if needed.

Results
Fifty patients were enrolled (36% had OSA, 22% CSA, and 12% SSH). CPAP was started in 54% of patients and nocturnal oxygen therapy in 16%. At one-year, polysomnography found improved parameters, though 17% of patients had to add nocturnal oxygen therapy or CPAP, while 33% presented SDB onset at this second polysomnography. CPAP compliance at one year was 6.74 h/night (SD 0.74). After one year, matrix metalloproteinase-1 decreased in OSA and CSA (p = 0.029; p = 0.027), C-reactive protein in OSA (p = 0.045), and surfactant protein D in CSA group (p = 0.074). There was no significant change in lung function.

Conclusions
Treatment of SBD with CPAP and NOT can be well tolerated with a high compliance. IPF patients may exhibit SDB progression and require periodic re-assessment. Further studies to evaluate the impact of SDB treatment on lung function and serological mediators are needed.
Non-invasive diagnosis of esophageal cancer by a simplified circulating cell-free DNA methylation assay targeting OTOP2 and KCNA3: a double-blinded, multicenter, prospective study
Authors: Bian Yan , Gao Ye , Lin Han , Sun Chang , Wang Wei , Sun Siyu , Li Xiuling , Feng Zhijie , Ren Jianlin , Chen Hezhong , Lu Chaojing , Xu Jinfang , Zhou Jun , Wan Kangkang , Xin Lei , Li Zhaoshen , Wang Luowei 
Published: June 2024

Abstract
Background
Esophageal cancer (EC) is a highly lethal disease lacking early detection approaches. We previously identified that OTOP2 and KCNA3 were specifically hypermethylated in circulating cell-free DNA from patients with EC. We then developed a blood-based methylation assay targeting OTOP2 and KCNA3 (named “IEsohunter”) for esophageal cancer noninvasive detection. This double-blinded, multicenter, prospective study aimed to comprehensively evaluate its clinical diagnostic performance.

Methods
Participants with EC, high-grade intraepithelial neoplasia (HGIN), other malignancies, benign gastrointestinal lesions, or no abnormalities were prospectively enrolled from 5 tertiary referral centers across China. Peripheral blood samples were collected, followed by plasma cell-free DNA methylation analysis using the IEsohunter test based on multiplex quantitative polymerase chain reaction adopting an algorithm-free interpretation strategy. The primary outcome was the diagnostic accuracy of IEsohunter test for EC.

Results
We prospectively enrolled 1116 participants, including 334 patients with EC, 71 with HGIN, and 711 controls. The areas under the receiver operating characteristic curves of the IEsohunter test for detecting EC and HGIN were 0.903 (95% CI 0.880–0.927) and 0.727 (95% CI 0.653–0.801), respectively. IEsohunter test showed sensitivities of 78.5% (95% CI 69.1–85.6), 87.3% (95% CI 79.4–92.4), 92.5% (95% CI 85.9–96.2), and 96.9% (95% CI 84.3–99.8) for stage I-IV EC, respectively, with an overall sensitivity of 87.4% (95% CI 83.4–90.6) and specificity of 93.3% (95% CI 91.2–94.9) for EC detection. The IEsohunter test status turned negative (100.0%, 47/47) after surgical resection of EC.

Conclusions
The IEsohunter test showed high diagnostic accuracy for EC detection, indicating that it could potentially serve as a tool for noninvasive early detection and surveillance of EC.
The G Protein Estrogen Receptor (GPER) is involved in the resistance to the CDK4/6 inhibitor palbociclib in breast cancer
Authors: Talia Marianna , Cirillo Francesca , Scordamaglia Domenica , Di Dio Marika , Zicarelli Azzurra , De Rosis Salvatore , Miglietta Anna Maria , Capalbo Carlo , De Francesco Ernestina Marianna , Belfiore Antonino , Grande Fedora , Rizzuti Bruno , Occhiuzzi Maria Antonietta , Fortino Giancarlo , Guzzo Antonella , Greco Gianluigi , Maggiolini Marcello , Lappano Rosamaria 
Published: June 2024

Abstract
Background
The cyclin D1-cyclin dependent kinases (CDK)4/6 inhibitor palbociclib in combination with endocrine therapy shows remarkable efficacy in the management of estrogen receptor (ER)-positive and HER2-negative advanced breast cancer (BC). Nevertheless, resistance to palbociclib frequently arises, highlighting the need to identify new targets toward more comprehensive therapeutic strategies in BC patients.

Methods
BC cell lines resistant to palbociclib were generated and used as a model system. Gene silencing techniques and overexpression experiments, real-time PCR, immunoblotting and chromatin immunoprecipitation studies as well as cell viability, colony and 3D spheroid formation assays served to evaluate the involvement of the G protein-coupled estrogen receptor (GPER) in the resistance to palbociclib in BC cells. Molecular docking simulations were also performed to investigate the potential interaction of palbociclib with GPER. Furthermore, BC cells co-cultured with cancer-associated fibroblasts (CAFs) isolated from mammary carcinoma, were used to investigate whether GPER signaling may contribute to functional cell interactions within the tumor microenvironment toward palbociclib resistance. Finally, by bioinformatics analyses and k-means clustering on clinical and expression data of large cohorts of BC patients, the clinical significance of novel mediators of palbociclib resistance was explored.

Results
Dissecting the molecular events that characterize ER-positive BC cells resistant to palbociclib, the down-regulation of ERα along with the up-regulation of GPER were found. To evaluate the molecular events involved in the up-regulation of GPER, we determined that the epidermal growth factor receptor (EGFR) interacts with the promoter region of GPER and stimulates its expression toward BC cells resistance to palbociclib treatment. Adding further cues to these data, we ascertained that palbociclib does induce pro-inflammatory transcriptional events via GPER signaling in CAFs. Of note, by performing co-culture assays we demonstrated that GPER contributes to the reduced sensitivity to palbociclib also facilitating the functional interaction between BC cells and main components of the tumor microenvironment named CAFs.

Conclusions
Overall, our results provide novel insights on the molecular events through which GPER may contribute to palbociclib resistance in BC cells. Additional investigations are warranted in order to assess whether targeting the GPER-mediated interactions between BC cells and CAFs may be useful in more comprehensive therapeutic approaches of BC resistant to palbociclib.
A radiomics-boosted deep-learning for risk assessment of synchronous peritoneal metastasis in colorectal cancer
Authors: Zhang Ding , Zheng BingShu , Xu LiuWei , Wu YiCong , Shen Chen , Bao ShanLei , Tan ZhongHua , Sun ChunFeng 
Published: June 2024

Abstract
Objectives
Synchronous colorectal cancer peritoneal metastasis (CRPM) has a poor prognosis. This study aimed to create a radiomics-boosted deep learning model by PET/CT image for risk assessment of synchronous CRPM.

Methods
A total of 220 colorectal cancer (CRC) cases were enrolled in this study. We mapped the feature maps (Radiomic feature maps (RFMs)) of radiomic features across CT and PET image patches by a 2D sliding kernel. Based on ResNet50, a radiomics-boosted deep learning model was trained using PET/CT image patches and RFMs. Besides that, we explored whether the peritumoral region contributes to the assessment of CRPM. In this study, the performance of each model was evaluated by the area under the curves (AUC).

Results
The AUCs of the radiomics-boosted deep learning model in the training, internal, external, and all validation datasets were 0.926 (95% confidence interval (CI): 0.874–0.978), 0.897 (95% CI: 0.801–0.994), 0.885 (95% CI: 0.795–0.975), and 0.889 (95% CI: 0.823–0.954), respectively. This model exhibited consistency in the calibration curve, the Delong test and IDI identified it as the most predictive model.

Conclusions
The radiomics-boosted deep learning model showed superior estimated performance in preoperative prediction of synchronous CRPM from pre-treatment PET/CT, offering potential assistance in the development of more personalized treatment methods and follow-up plans.

Critical relevance statement
The onset of synchronous colorectal CRPM is insidious, and using a radiomics-boosted deep learning model to assess the risk of CRPM before treatment can help make personalized clinical treatment decisions or choose more sensitive follow-up plans.

Key Points

Prognosis for patients with CRPM is bleak, and early detection poses challenges.

The synergy between radiomics and deep learning proves advantageous in evaluating CRPM.

The radiomics-boosted deep-learning model proves valuable in tailoring treatment approaches for CRC patients.

Graphical Abstract