Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of GGT5 as a Novel Prognostic Biomarker for Gastric Cancer and its Correlation With Immune Cell Infiltration

Gastric cancer (GC) is a common malignant tumor of the digestive system. Recent studies revealed that high gamma-glutamyl-transferase 5 (GGT5) expression was associated with a poor prognosis of gastric cancer patients. In the present study, we aimed to confirm the expression and prognostic value of GGT5 and its correlation with immune cell infiltration in gastric cancer. First, we compared the differential expression of GGT5 between gastric cancer tissues and normal gastric mucosa in the cancer genome atlas (TCGA) and GEO NCBI databases using the most widely available data. Then, the Kaplan-Meier method, Cox regression, and univariate logistic regression were applied to explore the relationships between GGT5 and clinical characteristics. We also investigated the correlation of GGT5 with immune cell infiltration, immune-related genes, and immune checkpoint genes. Finally, we estimated enrichment of gene ontologies categories and relevant signaling pathways using GO annotations, KEGG, and GSEA pathway data. The results showed that GGT5 was upregulated in gastric cancer tissues compared to normal tissues. High GGT5 expression was significantly associated with T stage, histological type, and histologic grade (p < 0.05). Moreover, gastric cancer patients with high GGT5 expression showed worse 10-years overall survival (p = 0.008) and progression-free intervals (p = 0.006) than those with low GGT5 expression. Multivariate analysis suggested that high expression of GGT5 was an independent risk factor related to the worse overall survival of gastric cancer patients. A nomogram model for predicting the overall survival of GC was constructed and computationally validated. GGT5 expression was positively correlated with the infiltration of natural killer cells, macrophages, and dendritic cells but negatively correlated with Th17 infiltration. Additionally, we found that GGT5 was positively co-expressed with immune-related genes and immune checkpoint genes. Functional analysis revealed that differentially expressed genes relative to GGT5 were mainly involved in the biological processes of immune and inflammatory responses. In conclusion, GGT5 may serve as a promising prognostic biomarker and a potential immunological therapeutic target for GC, since it is associated with immune cell infiltration in the tumor microenvironment.
Transcriptional Regulation of Pine Male and Female Cone Initiation and Development: Key Players Identified Through Comparative Transcriptomics

With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of reproductive structures (cones) in monoecious conifers remains limited. Genes with inferred roles in conifer reproduction have mostly been identified through homology and phylogenetic reconstruction with their angiosperm counterparts. We used RNA-sequencing to generate transcriptomes of the early morphological stages of cone development in the conifer species Pinus densiflora and used these to gain a deeper insight into the transcriptional changes during male and female cone development. Paired-end Illumina sequencing was used to generate transcriptomes from non-reproductive tissue and male and female cones at four time points with a total of 382.82 Gbp of data generated. After assembly and stringent filtering, a total of 37,164 transcripts were retrieved, of which a third were functionally annotated using the Mercator plant pipeline. Differentially expressed gene (DEG) analysis resulted in the identification of 172,092 DEGs in the nine tissue types. This, alongside GO gene enrichment analyses, pinpointed transcripts putatively involved in conifer reproductive structure development, including co-orthologs of several angiosperm flowering genes and several that have not been previously reported in conifers. This study provides a comprehensive transcriptome resource for male and early female cone development in the gymnosperm species Pinus densiflora. Characterisation of this resource has allowed the identification of potential key players and thus provides valuable insights into the molecular regulation of reproductive structure development in monoecious conifers.
Experimental Warming Has Not Affected the Changes in Soil Organic Carbon During the Growing Season in an Alpine Meadow Ecosystem on the Qinghai–Tibet Plateau

The effects of climate warming and season on soil organic carbon (SOC) have received widespread attention, but how climate warming affects the seasonal changes of SOC remains unclear. Here, we established a gradient warming experiment to investigate plant attributes and soil physicochemical and microbial properties that were potentially associated with changes in SOC at the beginning (May) and end (August) of the growing season in an alpine meadow ecosystem on the Qinghai–Tibet Plateau. The SOC of August was lower than that of May, and the storage of SOC in August decreased by an average of 18.53 million grams of carbon per hectare. Warming not only failed to alter the content of SOC regardless of the season but also did not affect the change in SOC during the growing season. Among all the variables measured, microbial biomass carbon was highly coupled to the change in SOC. These findings indicate that alpine meadow soil is a source of carbon during the growing season, but climate warming has no significant impact on it. This study highlights that in the regulation of carbon source or pool in alpine meadow ecosystem, more attention should be paid to changes in SOC during the growing season, rather than climate warming.
Refining Mitochondrial Intron Classification With ERPIN: Identification Based on Conservation of Sequence Plus Secondary Structure Motifs

Mitochondrial genomes—in particular those of fungi—often encode genes with a large number of Group I and Group II introns that are conserved at both the sequence and the RNA structure level. They provide a rich resource for the investigation of intron and gene structure, self- and protein-guided splicing mechanisms, and intron evolution. Yet, the degree of sequence conservation of introns is limited, and the primary sequence differs considerably among the distinct intron sub-groups. It makes intron identification, classification, structural modeling, and the inference of gene models a most challenging and error-prone task—frequently passed on to an “expert” for manual intervention. To reduce the need for manual curation of intron structures and mitochondrial gene models, computational methods using ERPIN sequence profiles were initially developed in 2007. Here we present a refinement of search models and alignments using the now abundant publicly available fungal mtDNA sequences. In addition, we have tested in how far members of the originally proposed sub-groups are clearly distinguished and validated by our computational approach. We confirm clearly distinct mitochondrial Group I sub-groups IA1, IA3, IB3, IC1, IC2, and ID. Yet, IB1, IB2, and IB4 ERPIN models are overlapping substantially in predictions, and are therefore combined and reported as IB. We have further explored the conversion of our ERPIN profiles into covariance models (CM). Current limitations and prospects of the CM approach will be discussed.
Associations Between Severity of Depression, Lifestyle Patterns, and Personal Factors Related to Health Behavior: Secondary Data Analysis From a Randomized Controlled Trial

Background Depression is a prevalent condition that has a significant impact on psychosocial functioning and quality of life. The onset and persistence of depression have been linked to a variety of biological and psychosocial variables. Many of these variables are associated with specific lifestyle characteristics, such as physical activity, diet, and sleep patterns. Some psychosocial determinants have an impact on people’ health-related behavior change. These include personal factors such as sense of coherence, patient activation, health literacy, self-efficacy, and procrastination. This study aims to analyze the association between the severity of depression, lifestyle patterns, and personal factors related to health behavior. It also aims to analyze whether personal factors moderate the relationship between lifestyles and depression. Methods This study is a secondary data analysis (SDA) of baseline data collected at the start of a randomized controlled trial (RCT). A sample of 226 patients with subclinical, mild, or moderate depression from primary healthcare centers in two sites in Spain (Zaragoza and Mallorca) was used, and descriptive, bivariate, multivariate, and moderation analyses were performed. Depression was the primary outcome, measured by Beck II Self-Applied Depression Inventory. Lifestyle variables such as physical exercise, adherence to Mediterranean diet and sleep quality, social support, and personal factors such as self-efficacy, patient activation in their own health, sense of coherence, health literacy, and procrastination were considered secondary outcomes. Results Low sense of coherence (β = −0.172; p < 0.001), poor sleep quality (β = 0.179; p = 0.008), low patient activation (β = −0.119; p = 0.019), and sedentarism (more minutes seated per day; β = 0.003; p = 0.025) are predictors of having more depressive symptoms. Moderation analyses were not significant. Discussion Lifestyle and personal factors are related to depressive symptomatology. Our findings reveal that sense of coherence, patient’s activation level, sedentarism, and sleep quality are associated with depression. Further research is needed regarding adherence to Mediterranean diet, minutes walking per week and the interrelationship between lifestyles, personal factors, and depression.
Eye and Head Movement Recordings Using Smartphones for Telemedicine Applications: Measurements of Accuracy and Precision

Objective Smartphones have shown promise in the assessment of neuro-ophthalmologic and vestibular disorders. We have shown that the head impulse test results recorded using our application are comparable with measurements from clinical video-oculography (VOG) goggles. The smartphone uses ARKit's capability to acquire eye and head movement positions without the need of performing a calibration as in most eye-tracking devices. Here, we measure the accuracy and precision of the eye and head position recorded using our application. Methods We enrolled healthy volunteers and asked them to direct their eyes, their heads, or both to targets on a wall at known eccentricities while recording their head and eye movements with our smartphone application. We measured the accuracy as the error between the eye or head movement measurement and the location of each target and the precision as the standard deviation of the eye or head position for each of the target positions. Results The accuracy of head recordings (15% error) was overall better than the accuracy of eye recordings (23% error). We also found that the accuracy for horizontal eye movements (17% error) was better than for vertical (27% error). Precision was also better for head movement (0.8 degrees) recordings than eye movement recordings (1.3 degrees) and variability tended to increase with eccentricity. Conclusion Our results provide basic metrics evaluating the utility of smartphone applications in the quantitative assessment of head and eye movements. While the new method may not replace the more accurate dedicated VOG devices, they provide a more accessible quantitative option. It may be advisable to include a calibration recording together with any planned clinical test to improve the accuracy.
Dwarfs on the Shoulders of Giants: Bayesian Analysis With Informative Priors in Elite Sports Research and Decision Making

While sample sizes in elite sports are necessarily small, so are the effects that may be relevant. This conundrum is complicated by an understandable reluctance of athletes to comply with extensive study requirements. In Bayesian analyses, pre-existing knowledge (e.g., from sub-elite trials) can be formally included to supplement scarce data. Moreover, some design specifics for small sample research extend to the extreme case of a single subject. This provides the basis for actionable feedback (e.g., about individual responses) thereby incentivising participation. As a proof-of-concept, we conducted a replicated cross-over trial on the effect of cold-water immersion (CWI) on sprint performance recovery in soccer players. Times for 30 m linear sprint and the initial 5 m section, respectively, were measured by light gates before and 24 h after induction of fatigue. Data were analysed by Bayesian and by standard frequentist methods. Informative priors are based on a published metaanalysis. Seven players completed the trial. Sprint performance was 4.156 ± 0.193 s for 30 m linear sprint and 0.978 ± 0.064 s for the initial 5 m section. CWI improved recovery of sprint time for the initial 5 m section (difference to control: −0.060 ± 0.060 s, p = 0.004) but not for the full 30 m sprint (0.002 ± 0.115 s, p = 0.959), with general agreement between Bayesian and frequentist interval estimates. On the individual level, relevant differences between analytical approaches were present for most players. Changes in the two performance measures are correlated (p = 0.009) with a fairly good reproducibility of individual response patterns. Bayesian analyses with informative priors may be a practicable and meaningful option particularly for very small samples and when the analytical aim is decision making (use / don't use in the specific setting) rather than generalizable inference.
Predicting Sit-to-Stand Adaptations due to Muscle Strength Deficits and Assistance Trajectories to Complement Them

Sit-to-stand (STS) transition is one of the most bio-mechanically challenging task necessary for performing activities of daily life. With muscle strength being the most dominant, many co-occurring factors influence how individuals perform STS. This study investigates the STS changes and STS failure caused by strength deficits using the trajectories generated employing an open-loop single shooting optimization framework and musculoskeletal models. The strength deficits were introduced by simultaneously scaling the maximum isometric strength of muscles in steps of 20%. The optimization framework could generate successful STS transitions for models with up to 60% strength deficits. The joint angle kinematics, muscle activation patterns, and the ground reaction forces from the 0% strength deficit model’s STS transition match those observed experimentally for a healthy adult in literature. Comparison of different strength deficit STS trajectories shows that the vasti muscle saturation leads to reduced activation of the antagonistic hamstring muscle, and consequently, the gluteus maximus muscle saturation. Subsequently, the observation of reduced hamstring activation and the motion tracking results are used to suggest the vasti muscle weakness to be responsible for STS failure. Finally, the successful STS trajectory of the externally assisted 80% strength deficit model is presented to demonstrate the optimization framework’s capability to synthesize assisted STS transition. The trajectory features utilization of external assistance as and when needed to complement strength deficits for successful STS transition. Our results will help plan intervention and design novel STS assistance devices.
Do Higher Education and Financial Institutions Improve Health in China? A New Perspective

The importance of human wellbeing is documented in the literature of development economics because of its intensifying impacts on economic growth and productivity of labor in the long-run. To the best of the authors' knowledge, no empirical study has examined the symmetric association between China's financial institutional development, education, and health outcomes. Thus, our study aims to fill this vacuum by employing an autoregressive distributed lag (ARDL) approach to explore the impact of financial institutional development and education on life expectancy and infant mortality rate from 1990 to 2020. The empirical analysis reveals that financial institutional development and education report a significant increase in life expectancy and meaningful reduction in mortality rate in the long-run. Based on these findings, the study may deliver intuitive policy implications regarding improvement in health conditions that are imperative for promoting economic growth in the long-run.
Modified FCI (Fédération Cynologique Internationale) Scoring of the Coxofemoral Joint in Labrador Retrievers Without and With Hip Dysplasia

The objective is to propose a modified FCI scoring protocol of the canine hip joint via: (1) providing morphometric criteria of each score; (2) quantifying the extent of lateral and dorsal acetabular femoral head (AFH) coverage; (3) evaluating the steepness of cranial acetabular edge (acetabular index angle) and inclination angle (IA) in normal and dysplastic coxofemoral joints of Labrador Retrievers. The long-term goal is to achieve a selective breeding protocol using parental phenotypically healthy coxofemoral joints based on the standard extended-leg VD radiograph to help reduce the prevalence of CHD among offspring. Investigated populations were classified into normal (grade A) and dysplastic coxofemoral joints (grades B to E) based on the morphometric criteria previously established by the conventional FCI scoring system. Center-edge (CE) angle, Norberg angle (NA), indices of dorsal AFH coverage width and area, acetabular index angle, and inclination angle were determined for each group. Variables were compared between groups using ANOVA. Spearman correlation coefficient was used to determine the linear relationship between selected variables. Overall, all radiographic measurements differed significantly (P < 0.0001) among the five tested groups using ANOVA test. Dorsal AFH coverage area index was the only measure that differed significantly (P ≤ 0.007) between every two consecutive groups using Tukey's test. Significant correlations were identified between the Norberg and CE angles (rs = 0.95, P < 0.0001), the width and area of dorsal AFH coverage (rs = 0.96, P < 0.0001), and the radiographic techniques utilized to assess lateral vs. dorsal AFH coverage (rs ≥ 0.80, P < 0.0001). Evaluation of CE-angle, dorsal AFH coverage area index and acetabular index angle is recommended during selective breeding to include parents with radiographically healthy joints and reduce the incidence of hip dysplasia among offspring. Dogs with CE-angle <27°, dorsal AFH coverage area index <53%, and/or acetabular index angle >9° may be consistent with hip dysplasia and are recommended to be excluded from potential breeding groups. Re-evaluation of coxofemoral joints with borderline values located between near-normal and mildly dysplastic coxofemoral joints is strongly recommended to be performed after 6 months.
Under Voltages Load Shedding Based on Catastrophe Theory Method for Surabaya Electrical Distribution Systems

Voltage stability problem has received much attention of distribution companies because of the serious consequences on distribution systems. This problem is associated with a rapid voltage drop because of heavy system load, which might result in system collapse. One of the actions to prevent this serious consequence is Under Voltage Load Shedding (UVLS). In this paper, Catastrophe theory is used to determine the ranking of system buses based on voltage stability index. Basuki Rahmat feeder and Kaliasin feeder of Surabaya Utara electrical distribution system are used to implement the proposed method, and the results are compared with Loss Sensitivity method to determine the best locations for load shedding. For a simple radial distribution system like Kaliasin feeder, the Loss Sensitivity and Catastrophe theory result in the same bus ranks. However, for a complex one like Basuki rahmat feeder, Loss Sensitivity and Catastrophe theory result in different best locations for load shedding. Then, the same amount of loads are shed for the different best locations, and the results show that the application of Catastrophe theory method for load shedding result in a better voltage profile than the Loss Sensitivity method.
Eichhornia crassipes (Mart.) Solms: A Comprehensive Review of Its Chemical Composition, Traditional Use, and Value-Added Products

Eichhornia crassipes (Mart.) Solms, commonly known as water hyacinth, is one of the world’s most invasive aquatic plants of the Pontederiaceae family occurring in tropical and subtropical regions of the world. Although, E. crassipes causes significant ecological and socioeconomic issues such as a high loss in water resources, it has multipurpose applications since it is famous for many industrial applications such as bioenergy, biofertilizer production, wastewater treatment (absorption of heavy metals), and animal feed. Furthermore, E. crassipes is rich in diverse bioactive secondary metabolites including sterols, alkaloids, phenolics, flavonoids, tannins, and saponins. These secondary metabolites are well known for a wide array of therapeutic properties. The findings of this review suggest that extracts and some isolated compounds from E. crassipes possess some pharmacological activities including anticancer, antioxidant, anti-inflammatory, antimicrobial, skin whitening, neuroprotective, and hepatoprotective activities, among other biological activities such as allelopathic, larvicidal, and insecticidal activities. The present review comprehensively summarizes the chemical composition of E. crassipes, reported to date, along with its traditional uses and pharmacological and biological activities.