Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction differences and implications of acute kidney injury with and without urine output criteria in adult critically ill patients

ABSTRACT Background Due to the convenience of serum creatinine (SCr) monitoring and the relative complexity of urine output (UO) monitoring, most studies have predicted acute kidney injury (AKI) only based on SCr criteria. This study aimed to compare the differences between SCr alone and combined UO criteria in predicting AKI. Methods We applied machine learning methods to evaluate the performance of 13 prediction models composed of different feature categories on 16 risk assessment tasks (half used only SCr criteria, half used both SCr and UO criteria). The area under receiver operator characteristic curve (AUROC), the area under precision recall curve (AUPRC) and calibration were used to assess the prediction performance. Results In the first week after ICU admission, the prevalence of any AKI was 29% under SCr criteria alone and increased to 60% when the UO criteria was combined. Adding UO to SCr criteria can significantly identify more AKI patients. The predictive importance of feature types with and without UO was different. Using only laboratory data maintained similar predictive performance to the full feature model under only SCr criteria [e.g. for AKI within the 48-h time window after 1 day of ICU admission, AUROC (95% confidence interval) 0.83 (0.82, 0.84) vs 0.84 (0.83, 0.85)], but it was not sufficient when the UO was added [corresponding AUROC (95% confidence interval) 0.75 (0.74, 0.76) vs 0.84 (0.83, 0.85)]. Conclusions This study found that SCr and UO measures should not be regarded as equivalent criteria for AKI staging, and emphasizes the importance and necessity of UO criteria in AKI risk assessment.
Acute adaptation of central and peripheral motor unit features to exercise‐induced fatigue differs with concentric and eccentric loading

What is the central question of this study? Conflicting evidence exists on motor unit (MU) firing rate in response to exercise‐induced fatigue, possibly due to the contraction modality used: Do MU properties adapt similarly following concentric and eccentric loading? What is the main finding and its importance? MU firing rate increased following eccentric loading only despite a decline in absolute force. Force steadiness deteriorated following both loading methods. Central and peripheral MU features are altered in a contraction type‐dependant manner, which is an important consideration for training interventions.
High expression of serine protease 2 (PRSS2) associated with invasion, metastasis, and proliferation in gastric cancer

Background: Accumulating evidence indicates that the occurrence and development of tumors are related to the activation of oncogenes and the inactivation of tumor suppressor genes caused by epigenetic mechanisms. However, the function of serine protease 2 (PRSS2) in gastric cancer (GC) is still unknown. Our study aimed to find a regulation network involved in GC. Methods: The mRNA data (GSE158662 and GSE194261) of GC and normal tissues were downloaded from the Gene Expression Omnibus (GEO) dataset. Differential expression analysis was performed using R software, and Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted by using Xiantao software. Besides, we used Quantitative Real-time PCR (qPCR) to verify our conclusions. After gene knockdown, cell migration and CCK-8 experiment were carried out to detect the effect of gene on cell proliferation and invasion. Results: Totally, 412 differentially expressed genes (DEGs) were identified from GSE158662 and 94 DEGs were identified from GSE196261. Km-plot database results indicated that PRSS2 exhibited high diagnosis worth for GC. Gene functional annotation enrichment analysis revealed that these hub mRNAs were mainly taken part in the process of tumorigenesis and development. Besides, vitro experiments showed that down-regulation of PRSS2 gene reduced the proliferation and invasion ability of GC cells. Conclusions: Our results indicated that PRSS2 may play vital roles in the carcinogenesis and progression of GC and can be potential biomarkers for patients with GC.
Effects of Mexican Ganoderma lucidum extracts on liver, kidney, and the gut microbiota of Wistar rats: A repeated dose oral toxicity study

Well-characterized and standardized extracts of a Mexican genotype of Ganoderma lucidum (Gl), a medicinal mushroom, cultivated on oak sawdust (Gl-1) or oak sawdust plus acetylsalicylic acid (Gl-2, ASA), have been shown to exert antioxidant, hypocholesterolemic, anti-inflammatory, prebiotic, and anticancer properties. However, toxicity analyses still need to be carried out. Different doses of these Gl-1 or Gl-2 extracts were administered to Wistar rats for 14 days in a repeated dose oral toxicity study. We assessed the external clinical signs, biochemical parameters, liver and kidney tissues, injury and inflammation biomarkers, gene expression, inflammatory responses, proinflammatory mediators, and gut microbiota. Gl extracts had no significant adverse, toxic or harmful effects on male and female rats compared to the control groups. No injury or dysfunction were recorded in the kidney or liver, as there were no significant abnormal variations in organ weight, tissue histopathology, serum biochemical parameters (C-reactive protein, creatinine, urea, glucose, ALT and AST transaminases, TC, LDL-c, TG, HDL-c), urinary parameters (creatinine, urea nitrogen, albumin, the albumin-to-creatinine ratio, glucose), injury and inflammatory biomarkers (KIM-1/TIM-1, TLR4, and NF-кB protein expression; IL-1β, TNF-α and IL-6 gene expression), or the expression of genes linked to cholesterol metabolism (HMG-CoA, Srebp2, Ldlr). Gl-1 and Gl-2 extracts showed prebiotic effects on the gut microbiota of male and female Wistar rats. Bacterial diversity and relative bacterial abundance (BRA) increased, positively modulating the Firmicutes/Bacteroidetes ratio. The ASA (10 mM) added to the substrate used for mushroom cultivation changed properties and effects of the Gl-2 extract on Wistar rats. The no-observed-adverse-effect-level (NOAEL) was 1000 mg/kg body weight/day of Gl-1 or Gl-2 extracts. Clinical trials are recommended for further exploring the potential therapeutic applications of studied extracts.
Measurement of lactate in pleural fluid rapidly identify infection and guide therapy

Abstract Background Measurements of pleural fluid biomarkers for rapid identification of complicated parapneumonic effusion (CPPE) are crucial for optimal management. Previous studies for biomarker evaluation were however based on pleura culture, not modern DNA technique. Lactate has not been thoroughly studied earlier as a potential biomarker in this regard. Objectives To evaluate whether the routine biomarkers pH, glucose, lactate dehydrogenase (LDH) measured in pleural fluid in a microbiological well characterised cohort could differentiate simple parapneumonic effusion (SPPE) from CPPE and if pleural fluid lactate could be of additional use in this discrimination. Methods Pleural fluid prospectively collected from adult patients (n = 112) with PPE admitted to the Departments of Infectious Diseases (DIDs) at four Stockholm County hospitals were characterised microbiologically with bacterial culture and 16S rDNA sequencing, and biochemically with pH, glucose, LDH and lactate. Results Forty and seventy two patients were categorised as SPPE/CPPE. The median values between SPPE/CPPE differed significantly for all biomarkers with varying overlap. Receiver operating characteristics (ROC) curves showed the area under the curve (AUC) for pH 0.905 (CI 0.847–0.963), glucose 0.861 (CI 0.79–0.932), LDH 0.917 (CI 0.860–0.974) and lactate 0.927 (CI 0.877–0.977), corresponding to best cut-off levels and sensitivity/specificity for pH of 7.255, 0.819/0.9, glucose 5.35 mmol/L, 0.847/0.775, LDH 9.8 µcat/L, 0.905/0.825 and lactate 4.9 mmol/L, 0.875/0.85. Conclusions To distinguish between SPPE/CPPE, pH and LDH performed well, but optimal cut-off values differed from earlier established recommendations. Pleura lactate had the largest AUC of the investigated biomarkers and may be used in the analyses of PPE-staging.
The management of women of childbearing age with rheumatoid arthritis: an expert report

ABSTRACT Introduction The introduction of biologic therapies and a treat-to-target approach has transformed the management of rheumatoid arthritis (RA), which has led to improved outcomes for women with RA who wish to become pregnant. However, guidelines for the management of reproductive health in female patients with RA are still lacking. Areas covered A task force (Women of Childbearing Age [WoCBA]-Rheumatoid Arthritis in Japan) comprising 10 experts in the fields of rheumatology, obstetrics and orthopedic surgery developed 10 clinical questions (CQ) related to the management of WoCBA with RA. For each CQ, a systematic literature review was conducted to identify relevant evidence. Based on this evidence, a set of recommendations for each CQ were drafted and evaluated using the modified Delphi method. This article describes the agreed recommendations along with the supporting evidence. Expert opinion There are many ongoing challenges associated with the provision of reproductive healthcare in WoCBA with RA. It is hoped that the consensus-based recommendations provided here can be implemented in clinical practice in order to increase collaboration between rheumatologists and obstetricians/gynecologists and to improve reproductive health outcomes for WoCBA with RA.
An overview of the digital occlusion technologies: Intraoral scanners, jaw tracking systems, and computerized occlusal analysis devices.

OBJECTIVES Within the development of digital technologies, dental professionals aim to integrate virtual diagnostic articulated casts obtained by using intraoral scanners (IOSs), the mandibular motion of the patient recorded by using an optical jaw tracking system, and the information provided by computerized occlusal analysis systems. This article describes the various digital technologies available for obtaining the digital occlusion of a patient and outlines its challenges and limitations. OVERVIEW The factors that influence the accuracy of the maxillomandibular relationship of diagnostic casts obtained by using IOSs are reviewed, as well as the occurrence of occlusal collisions or mesh interpenetrations. Different jaw tracking systems with varying digital technologies including ultrasonic systems, photometric devices, and artificial intelligence algorithms are reviewed. Computerized occlusal analysis systems for detecting occlusal contacts in a time sequential manner with the pressure distribution on the occlusal surfaces are reviewed. CONCLUSIONS Digital technologies provide powerful diagnostic and design tools for prosthodontic care. However, the accuracy of these digital technologies for acquiring and analyzing the static and dynamic occlusion need to be further analyzed. CLINICAL SIGNIFICANCE Efficiently implementing digital technologies into dental practice requires an understanding of the limitations and state of current development of the digital acquisition methods for digitizing the static and dynamic occlusion of a patient by using IOSs, digital jaw trackers, and computerized occlusal analysis devices.
Predicting the body core temperature of recreational athletes at the end of a 10 km self‐paced run under environmental heat stress

What is the central question of this study? The aim was to identify the factors predicting the body core temperature of athletes at the end of a 10 km self‐paced run in a hot environment. What is the main finding and its importance? Hyperthermia in athletes subjected to self‐paced running depends on several factors, highlighting the integrated control of core temperature during exercise under environmental heat stress. Five of the seven variables that significantly predicted core temperature are not invasive and, therefore, practical for use outside the laboratory environment: heart rate, sweat rate, wet‐bulb globe temperature, running speed and maximal oxygen consumption.
Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

Abstract The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.
Whole-Genome Sequencing and Comparative Genomics Analysis of a Newly Emerged Multidrug-Resistant Klebsiella pneumoniae Isolate of ST967

Whole-genome sequencing and population genetics analysis of K. pneumoniae are scarce from LMICs, and none has been reported for Armenia. Multilevel comparative analysis revealed that ARM01 (an isolate belonging to a newly emerged K. pneumoniae ST967 lineage) was genetically similar to two isolates recovered from Qatar. ABSTRACT Klebsiella pneumoniae is a common cause of hospital- and community-acquired infections globally, yet its population structure remains unknown for many regions, particularly in low- and middle-income countries (LMICs). Here, we report for the first-time whole-genome sequencing (WGS) of a multidrug-resistant K. pneumoniae isolate, ARM01, recovered from a patient in Armenia. Antibiotic susceptibility testing revealed that ARM01 was resistant to ampicillin, amoxicillin-clavulanic acid, ceftazidime, cefepime, norfloxacin, levofloxacin, and chloramphenicol. Genome sequencing analysis revealed that ARM01 belonged to sequence type 967 (ST967), capsule type K18, and antigen type O1. ARM01 carried 13 antimicrobial resistance (AMR) genes, including blaSHV-27, dfrA12, tet(A), sul1, sul2, catII.2, mphA, qnrS1, aadA2, aph3-Ia, strA, and strB and the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-15, but only one known virulence factor gene, yagZ/ecpA, and one plasmid replicon, IncFIB(K)(pCAV1099-114), were detected. The plasmid profile, AMR genes, virulence factors, accessory gene profile, and evolutionary analyses of ARM01 showed high similarity to isolates recovered from Qatar (SRR11267909 and SRR11267906). The date of the most recent common ancestor (MRCA) of ARM01 was estimated to be around 2017 (95% confidence interval [CI], 2017 to 2018). Although in this study, we report the comparative genomics analysis of only one isolate, it emphasizes the importance of genomic surveillance for emerging pathogens, urging the need for implementation of more effective infection prevention and control practices. IMPORTANCE Whole-genome sequencing and population genetics analysis of K. pneumoniae are scarce from LMICs, and none has been reported for Armenia. Multilevel comparative analysis revealed that ARM01 (an isolate belonging to a newly emerged K. pneumoniae ST967 lineage) was genetically similar to two isolates recovered from Qatar. ARM01 was resistant to a wide range of antibiotics, reflecting the unregulated usage of antibiotics (in most LMICs, antibiotic use is typically unregulated.) Understanding the genetic makeup of these newly emerging lineages will aid in optimizing antibiotic use for patient treatment and contribute to the worldwide efforts of pathogen and AMR surveillance and implementation of more effective infection prevention and control strategies.
Cyclical phases and processes of self-regulated learning

Self-regulated learning (SRL) is a self-directive, proactive process of self-generated behaviors, thoughts and actions planned and enacted to attain a learning goal (Boekaerts et. al. 2000; Zimmerman & Schunk 2001). The acquisition of expertise and mastery performance requires high levels of self-regulation. SRL skills can be taught and learned. A variety of methods have been used to promote and assess SRL. They include self-reported questionnaires, think aloud protocols, and microanalytic methods (structured, contextbound interviews to capture thinking and actions of one’s performance during each phase of SRL) (Schunk & Zimmerman 2012). SRL has important implications for learners’ development, fostering learning effectiveness and efficiency while focusing on the critical, lifelong skill of ‘learning to learn’. Self-regulation interventions can enhance the acquisition and control of learning strategies that can be particularly effective in improving the performance of low achieving students yet also enhancing even further the academic achievements of high performing students. In the concept map of this feature article, we depict the three cyclical, recursive phases of the self-regulation model (Schunk & Zimmerman 2012):
Protein Kinase CK2 Modulates the Calcium Sensitivity of Type 3 Small-conductance Calcium-activated Potassium Channels in Colonic Platelet-derived Growth Factor Receptor Alpha-positive Cells From Streptozotocin-induced Diabetic Mice

Background/Aims The gastrointestinal symptom of diabetes mellitus, chronic constipation, seriously affects patients’ life. Whereas, the mechanism of chronic constipation is still ambiguous, resulting in a lack of effective therapies for this symptom. As a part of the smooth muscle cells, interstitial cells of Cajal, and platelet-derived growth factor receptor alpha-positive (PDGFRα+) cells syncytium (SIP syncytium), PDGFRα+ cells play an important role in regulating colonic motility. According to our previous study, in PDGFRα+ cells in colons of diabetic mice, the function of the P2Y1 purinergic receptor/type 3 small-conductance calcium-activated potassium (SK3) channel signaling pathway is strengthened, which may lead to colonic dysmotility. The purpose of this study is to investigate the changes in SK3 channel properties of PDGFRα+ cells in diabetic mice. Methods Whole-cell patch clamp, Western blotting, superoxide dismutase activity measurement, and malondialdehyde measurement were main methods in the present study. Results The present study revealed that when dialysed with low calcium ion (Ca2+) solution, the SK3 current density was significantly decreased in PDGFRα+ cells from diabetic mice. However, the SK3 current density in PDGFRα+ cells was enhanced from diabetic mice when dialysed with high Ca2+ solution. Moreover, hydrogen peroxide-treatment mimicked this phenomenon in SK3 transgenic HEK293 cells. The subunit of SK3 channels, protein kinase CK2, was up-regulated in colonic muscle layers and hydrogen peroxide-treated HEK293 cells. Additionally, protein phosphatase 2A, the subunit of SK3 channels, was not changed in streptozotocin-treated mouse colons or hydrogen peroxide-treated HEK293 cells. Conclusion The diabetic oxidative stress-induced upregulation of CK2 contributed to modulating SK3 channel sensitivity to Ca2+ in colonic PDGFRα+ cells, which may result in colonic dysmotility in diabetic mice.
Total Transit Time and Probiotic Persistence in Healthy Adults: A Pilot Study

Background/Aims Motility, stool characteristics, and microbiota composition are expected to modulate probiotics’ passage through the gut but their effects on persistence after intake cessation remain uncharacterized. This pilot, open-label study aims at characterizing probiotic fecal detection parameters (onset, persistence, and duration) and their relationship with whole gut transit time (WGTT). Correlations with fecal microbiota composition are also explored. Methods Thirty healthy adults (30.4 ± 13.3 years) received a probiotic (30 × 109 CFU/capsule/day, 2 weeks; containing Lactobacillus helveticus R0052, Lacticaseibacillus paracasei HA-108, Bifidobacterium breve HA-129, Bifidobacterium longum R0175, and Streptococcus thermophilus HA-110). Probiotic intake was flanked by 4-week washout periods, with 18 stool collections throughout the study. WGTT was measured using 80% recovery of radio-opaque markers. Results Tested strains were detected in feces ~1-2 days after first intake and persistence after intake cessation was not significantly different for R0052, HA-108, and HA-129 (~3-6 days). We identified 3 WGTT subgroups within this population (named Fast, Intermediate, and Slow), which could be classified by machine learning with high accuracy based on differentially abundant taxa. On average, R0175 persisted significantly longer in the intermediate WGTT subgroup (~8.5 days), which was mainly due to 6 of the 13 Intermediate participants for whom R0175 persisted ≥ 15 days. Machine learning classified these 13 participants according to their WGTT cluster (≥ 15 days or < 5 days) with high accuracy, highlighting differentially abundant taxa potentially associated with R0175 persistence. Conclusion These results support the notion that host-specific parameters such as WGTT and microbiota composition should be considered when designing studies involving probiotics, especially for the optimization of washout duration in crossover studies but also for the definition of enrollment criteria or supplementation regimen in specific populations.