Miracle-dz/UniFAR-FTUs huggingface dataset:
Hip joint contact pressure and force: a scoping review of in vivo and cadaver studies

Aims Research on hip biomechanics has analyzed femoroacetabular contact pressures and forces in distinct hip conditions, with different procedures, and used diverse loading and testing conditions. The aim of this scoping review was to identify and summarize the available evidence in the literature for hip contact pressures and force in cadaver and in vivo studies, and how joint loading, labral status, and femoral and acetabular morphology can affect these biomechanical parameters. Methods We used the PRISMA extension for scoping reviews for this literature search in three databases. After screening, 16 studies were included for the final analysis. Results The studies assessed different hip conditions like labrum status, the biomechanical effect of the cam, femoral version, acetabular coverage, and the effect of rim trimming. The testing and loading conditions were also quite diverse, and this disparity limits direct comparisons between the different researches. With normal anatomy the mean contact pressures ranged from 1.54 to 4.4 MPa, and the average peak contact pressures ranged from 2 to 9.3 MPa. Labral tear or resection showed an increase in contact pressures that diminished after repair or reconstruction of the labrum. Complete cam resection also decreased the contact pressure, and acetabular rim resection of 6 mm increased the contact pressure at the acetabular base. Conclusion To date there is no standardized methodology to access hip contact biomechanics in hip arthroscopy, or with the preservation of the periarticular soft-tissues. A tendency towards improved biomechanics (lower contact pressures) was seen with labral repair and reconstruction techniques as well as with cam correction. Cite this article: Bone Joint Res 2023;12(12):712–721.
Identification of Immune-Related Genes as Biomarkers for Uremia

Purpose Uremia, which is characterized by immunodeficiency, is associated with the deterioration of kidney function. Immune-related genes (IRGs) are crucial for uremia progression. Methods The co-expression network was constructed to identify key modular genes associated with uremia. IRGs were intersected with differentially expressed genes (DEGs) between uremia and control groups and key modular genes to obtain differentially expressed IRGs (DEIRGs). DEIRGs were subjected to functional enrichment analysis. The protein-protein interaction (PPI) network was constructed. The candidate genes were identified using the cytoHubba tool. The biomarkers were identified using various machine learning algorithms. The diagnostic value of the biomarkers was evaluated using receiver operating characteristic (ROC) analysis. The immune infiltration analysis was implemented. The biological pathways of biomarkers were identified using gene set enrichment analysis and ingenuity pathway analysis. The mRNA expression of biomarkers was validated using blood samples of patients with uremia and healthy subjects with quantitative real-time polymerase chain reaction (qRT-PCR). Results In total, four biomarkers (PDCD1, NGF, PDGFRB, and ZAP70) were identified by machine learning methods. ROC analysis demonstrated that the area under the curve values of individual biomarkers were > 0.9, indicating good diagnostic power. The nomogram model of biomarkers exhibited good predictive power. The proportions of six immune cells significantly varied between the uremia and control groups. ZAP70 expression was positively correlated with the proportions of resting natural killer (NK) cells, naïve B cells, and regulatory T cells. Functional enrichment analysis revealed that the biomarkers were mainly associated with translational function and neuroactive ligand-receptor interaction. ZAP70 regulated NK cell signaling. The PDCD1 and NGF expression levels determined using qRT-PCR were consistent with those determined using bioinformatics analysis. Conclusion PDCD1, NGF, PDGFRB, and ZAP70 were identified as biomarkers for uremia, providing a theoretical foundation for uremia diagnosis.
Quantification of Debris Potential and the Evolution of a Regional Culvert Blockage Model

During flood events, materials that exist on the floodplain are mobilised by overland flow and by stream flow and transported downstream. Such materials are sourced from many parts of the floodplain, and consist of floating, non-floating and urban matter. As this material is mobilised and transported downstream, it can be trapped at waterway structures. When this occurs, it causes a blockage of the structure and a subsequent modification of the hydraulic capacity of that structure. This paper builds upon previous investigations and asks the question: What mechanisms exist within a particular catchment that trigger the mobilisation and transportation of debris? This paper explores the factors behind debris availability, mobilisation and transportation, and draws relationships between characteristics of the catchment such as slope, land use, area etc, and recorded debris load, as evidenced by structure blockage patterns. This paper documents the development of a Regional Culvert Blockage Model based on the relationships found between features of a catchment and debris load/structure interaction. This paper also proposes an extrapolation of the Regional Culvert Blockage Model to a National Model and quantifies the additional work required to do so.
Integrative approaches based on genomic techniques in the functional studies on enhancers

Abstract With the development of sequencing technology and the dramatic drop in sequencing cost, the functions of noncoding genes are being characterized in a wide variety of fields (e.g. biomedicine). Enhancers are noncoding DNA elements with vital transcription regulation functions. Tens of thousands of enhancers have been identified in the human genome; however, the location, function, target genes and regulatory mechanisms of most enhancers have not been elucidated thus far. As high-throughput sequencing techniques have leapt forwards, omics approaches have been extensively employed in enhancer research. Multidimensional genomic data integration enables the full exploration of the data and provides novel perspectives for screening, identification and characterization of the function and regulatory mechanisms of unknown enhancers. However, multidimensional genomic data are still difficult to integrate genome wide due to complex varieties, massive amounts, high rarity, etc. To facilitate the appropriate methods for studying enhancers with high efficacy, we delineate the principles, data processing modes and progress of various omics approaches to study enhancers and summarize the applications of traditional machine learning and deep learning in multi-omics integration in the enhancer field. In addition, the challenges encountered during the integration of multiple omics data are addressed. Overall, this review provides a comprehensive foundation for enhancer analysis.
Circulating immune signatures across clinical stages of chronic pancreatitis: a pilot study

Objective This pilot study seeks to identify serum immune signatures across clinical stages of patients with chronic pancreatitis (CP). Methods We performed a cross-sectional analysis of prospectively collected serum samples from the PROspective Evaluation of Chronic Pancreatitis for EpidEmiologic and Translation StuDies-study. CP subjects were categorised into three clinical stages based on the presence/absence of metabolic complications: (1) CP with no diabetes and exocrine pancreatic dysfunction (EPD), (2) CP with either diabetes or EPD, and (3) CP with diabetes and EPD. Blinded samples were analysed using an 80-plex Luminex assay of cytokines/chemokines/adhesion molecules. Group and pairwise comparisons were performed to characterise immune signatures across CP subgroups. Results A total of 135 CP subjects (evenly distributed between clinical stages) and 50 controls were studied. Interleukin-6 (IL-6), interleukin-8 (IL-8), and soluble intercellular adhesion molecule 1 (sICAM-1) were significantly elevated in CP subjects compared to controls. The levels of IL-6 and IL-8 increased with advancing disease stages, with the highest levels observed in CP with diabetes and EPD (clinical stage 3). Furthermore, hepatocyte growth factor and macrophage-derived chemokine were significantly increased in clinical stage 3 compared to controls. Conclusion Our study reveals a progressive elevation in pro-inflammatory cytokines and chemokines with advancing clinical stages of CP. These findings indicate potential targets for the development of disease-modifying interventions.
Bayesian analysis of the multivariate dependence of three transitional water ecosystem classifications

The Water Framework Directive (WFD) recognizes benthic macroinvertebrates as a good biological quality element for transitional waters as they are the most exposed to natural variability patterns characteristic of these ecosystems, due to their life cycles and space-use behavior. Here, we address the ecological status classification issue for three lagoons in Apulia, using benthic macroinvertebrates and three proposed multimetric indices (namely M-AMBI, BITS and ISS), likely to respond differently to different sources of stress and natural variability. Lagoon classification is based on discretization by standard classification boundaries with only partial consideration of the natural variability of ecosystem properties and possible inaccuracies of the classification procedures. In order to investigate the possible contrasting behavior of the three classifications, we propose Bayesian hierarchical models in which the multimetric indices and their discrete counterparts are jointly modeled as function of abiotic covariates, external anthropogenic pressures indicators and spatio-temporal effects.
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations

Abstract Environmental perturbations are encountered by microorganisms regularly and will require metabolic adaptations to ensure an organism can survive in the newly presenting conditions. In order to study the mechanisms of metabolic adaptation in such conditions, various experimental and computational approaches have been used. Genome-scale metabolic models (GEMs) are one of the most powerful approaches to study metabolism, providing a platform to study the systems level adaptations of an organism to different environments which could otherwise be infeasible experimentally. In this review, we are describing the application of GEMs in understanding how microbes reprogram their metabolic system as a result of environmental variation. In particular, we provide the details of metabolic model reconstruction approaches, various algorithms and tools for model simulation, consequences of genetic perturbations, integration of ‘-omics’ datasets for creating context-specific models and their application in studying metabolic adaptation due to the change in environmental conditions.
Environmental surveillance of fungi and susceptibility to antifungal agents in tertiary care hospitals

ABSTRACT This study aimed to evaluate the epidemiology of fungi in environment of tertiary care hospitals and their susceptibility patterns to seven antifungal agents for controlling and preventing fungal infections in patients. Environmental samplings on the surfaces of different parts of hospitals were collected from four university-affiliated teaching hospitals in Iran. Routine and molecular procedures identified isolated fungi, and antifungal susceptibility tests were performed in vitro. Of the 400 samples, 152 presented positive culture results, and 193 fungal species were isolated. Mold fungi accounted for 59.1% (115 species) of isolates. Most isolated fungal species in descending order were 22 Aspergillus flavus (11.4%), 21 Candida albicans (10.9%), 17 Mucor species (8.8%), 16 Penicillium species (8.3%), 16 Candida famata (8.3%), 15 Alternaria species (7.8%), 13 Fusarium species (6.7%), 11 Candida parapsilosis (5.7%), and 10 Aspergillus niger sensu stricto (5.2%). The isolated Aspergillus species revealed relatively low susceptibility to itraconazole and posaconazole with MIC90 values of 8 µg/mL. The MIC90 values of amphotericin and luliconazole in Candida species were 0.5 and 0.064 µg/mL, respectively. In this study, different species of filamentous and yeast fungi with varying susceptibility to antifungal agents were reported from the environment of the studied hospitals. IMPORTANCE Saprophytic fungi can cause nosocomial infections in high-risk patients. These infections are related to high mortality and cost. In the current study, different species of filamentous fungi and yeast were isolated from the environment of the studied hospitals. Some species were resistant to antifungal drugs. We suggest that the future work concentrates on the relationship between the level/quantification of saprophytic contamination in the environment of hospitals and fungal infections in patients. Saprophytic fungi can cause nosocomial infections in high-risk patients. These infections are related to high mortality and cost. In the current study, different species of filamentous fungi and yeast were isolated from the environment of the studied hospitals. Some species were resistant to antifungal drugs. We suggest that the future work concentrates on the relationship between the level/quantification of saprophytic contamination in the environment of hospitals and fungal infections in patients.
Physical activity on prescription in Swedish primary care: a survey on use, views, and implementation determinants amongst general practitioners

Abstract Introduction Swedish Physical Activity on Prescription (PAP) has been shown to increase physical activity levels, which is known to lead to positive health effects. PAP is being implemented in Swedish healthcare to various extents. However, there is a lack of knowledge about how Swedish general practitioners (GPs) work with PAP and what hinders and facilitates wider implementation. Aims This study aimed to survey GPs’ use and views of PAP, identify barriers and facilitators for implementing PAP, and explore associations to gender, practice location, and experience. Methods The study was framed by the Normalization Process Theory. A survey was sent to 463 GPs at 69 different healthcare centres in Region Västra Götaland. Data were analysed using multiple logistic and linear regressions. Results A total of 143 GPs completed the survey (response rate 31%). Views on PAP were generally positive amongst respondents, but only 27% reported using PAP regularly. The most prominent reported barriers were insufficient training and resources. Positive views and willingness to collaborate in using PAP were identified as facilitators. Responding GPs in Gothenburg used PAP more often (OR 6.4; 95% CI 2.7–14.8) and were significantly more positive to the method than GPs in other areas of the region. GPs with more than 10 years of practice used PAP more often (OR 2.5; 95% CI 1.1–6.0) than less experienced GPs. Few of the investigated variables were associated with gender. Conclusions The positive views amongst responding GPs are helpful, but more education, training and resources are needed for successful implementation of PAP in Swedish primary health care.
Outer membrane vesicles mediating horizontal transfer of the epidemic blaOXA-232 carbapenemase gene among Enterobacterales

ABSTRACT OXA-232 is one of the most common OXA-48-like carbapenemase derivatives and is widely disseminated in nosocomial settings across countries. The blaOXA-232 gene is located on a 6-kb non-conjugative ColKP3-type plasmid, while the dissemination of blaOXA-232 into different Enterobacterales species and the polyclonal dissemination of OXA-232-producing K. pneumoniae revealed the horizontal transfer of blaOXA-232. However, it’s still unclear how this non-conjugative ColKP3 plasmid could facilitate the mobilization of blaOXA-232. Here, we observed the in vivo intraspecies transfer of blaOXA-232 during a nosocomial outbreak of OXA-232-producing K. pneumoniae. We demonstrated the presence of ColKP3 OXA-232 plasmid in the outer membrane vesicles (OMVs) derived from clinical isolates, and OMVs could facilitate the horizontal transfer of blaOXA-232 among Enterobacterales. In contrast, for the most prevalent carbapenemase genes, including blaKPC-2 and blaNDM-1, though the presence of carbapenemase genes and plasmid backbones in the vesicular lumen was observed, OMVs couldn’t promote effective transformation, probably due to the low copy number of plasmids in clinical isolates and the low number of plasmids loaded into vesicles. Conjugation assay revealed that the epidemic IncX3 NDM-1 and IncFII(pHN7A8)/IncR KPC-2 plasmids were conjugative and could be horizontally transferred via independent conjugation or with the help of a co-existent conjugative plasmid. For the large-size and low-copy number conjugative plasmids carrying carbapenemase genes, OMVs-mediated gene exchange may only serve as an alternative pathway for horizontal transfer. In conclusion, diverse mobilization strategies were employed by plasmids harbouring carbapenemase genes, and plasmids display a proper choice of mobility pathway due to their individual properties.
GYPSUM DEPOSITS IN THE FRASASSI CAVES, CENTRAL ITALY

The Frasassi Caves are hypogenic caves in central Italy, where H2S-rich groundwater flows in the lowest cave level. Near the water table, the H2S is converted to sulfuric acid by biotic and abiotic processes, which have enhanced cave development. The sulfate generally deposits above the water table as a replacement gypsum crust coating limestone walls or as large gypsum crystals. Although the oxidation of sulfide also occurs below the water table, sulfate saturation is not achieved, therefore, sulfate does not precipitate below the water table. In the upper dry levels of the cave, three main types of ancient gypsum deposits occurs: (1) replacement crusts, similar to the presently forming deposits of the active zone, (2) microcrystalline large and thick floor deposits, and (3) euhedral crystals inside mud. The study of the depositional setting and the analysis of sulfur isotopes in the gypsum and groundwater clearly demonstrate that all the sampled gypsum in the cave formed by H2S oxidation above the water table. Some fraction of small sulfur isotopic differences between H2S in the water and gypsum can be explained by isotopic fractionation during abiotic and/or biotic oxidation of H2S.
Hellebrigenin induces oral cancer cell apoptosis by modulating MAPK signalling and XIAP expression

Abstract Oral squamous cell carcinoma (OSCC), which accounts for 90% of all oral cancers, has become a public health crisis worldwide. despite advances in therapeutic interventions, the prognosis remains poor for advanced‐stage OSCC. In this study, we investigate the anticancer activity and the mode of action of hellebrigenin in human OSCC. The findings demonstrated that hellebrigenin exerted cytotoxic effects in OSCC cells through cell cycle arrest at the G2/M phase and downregulation of cell cycle‐related proteins (cyclins A2, B1 and D3, Cdc2, CDK4 and CDK6). Moreover, hellebrigenin caused activation of PARP and caspase 3, 8 and 9, followed by downregulation of antiapoptotic proteins (Bcl‐2 and Bcl‐xL) and upregulation of pro‐apoptotic proteins (Bax and Bak). The hellebrigenin treatment also increased Fas, DR5, DcR2 and DcR3 expressions in oral cancer cells, indicating the compound causes oral cancer cell apoptosis through both intrinsic and extrinsic pathways. Regarding upstream signalling, hellebrigenin was found to reduce the phosphorylation of ERK, p38, and JNK, indicating that hellebrigenin triggers caspase‐mediated apoptosis by downregulating MAPK signalling pathway. Finally, the human apoptosis array findings revealed that hellebrigenin specifically suppressed the expression of XIAP to execute its pro‐apoptotic activities. Taken together, the study suggests that hellebrigenin can act as a potent anticancer compound in human OSCC.
Distance education: a system view

Chapter 5 – Technologies and Means In this Chapter the technologies presented more in detail are discussed. The characteristics of the different technologies and communication means are presented, as well as how they are implemented in Distance Education. Also, the most suitable communication means according to the course or program being employed are presented, and how they can be combined in order to attain the utmost efficiency.
Geochemical Vertical Transportation along Soil Profiles in Baiyinnuoer Pb-Zn Deposit Areas,Mongolia,China

Geochemical soil survey is of great significance to find the geochemical soil anomalies related to ore deposits.Baiyinnuoer lead-zinc deposit in Inner Mongolia is one typical Skarn deposit in North China and detailed geological mining survey had been done in this area to prospect ore-bodies.In this study,3typical vertical soil profiles had been sampled to study the geochemical vertical transportation modes and then to further explore new ideas for mineral resource prospecting.Soil profile 6was collected upon one Pb-Zn ore-body.Profile 3and Profile 8were 1km and 4.5km away from Profile 6,respectively.Along Profile 6and Profile 3,soil magnetic susceptibility values decrease significantly with the depth of the soil samples increasing.The distribution patterns of all the 9geochemical elements along Profile 6display a similar trend which shows the concentrations are lower in both topsoil layer and half-weathered rock layer,but higher in residual subsoil layer,showing as"C-shape",which are quite different from those patterns for profile 3and profile 8,since the element concentration values do fluctuate violently without a similar trend as shown in Profile 6.The research approach and results of this paper could be useful references for evaluating mineral resources in covered areas from the surface geochemical soil surveys and it also could provide new avenues for detecting the geochemical mechanisms for vertical transportation.
From seismic to bed: surface–subsurface correlations within the turbiditic Cellino Formation (central Italy)

The area east of the Gran Sasso Chain in central Italy has been explored in detail because it holds a hydrocarbon field (Cellino Field), located in the Lower Pliocene foredeep turbidites of the Cellino Formation. Correlation has been made between the hydrocarbon-bearing sedimentary bodies and the same stratigraphic intervals cropping out only few kilometres to the west. The area, thus, offers a rare example where comparison can be made between lithofacies – observed in the field, electrofacies – displayed by the electric logs of the wells, and seismofacies – revealed by seismic survey. This surface–subsurface integrated study of the Cellino Formation has revealed the presence of different turbiditic facies associations, their related electrical expressions and the possibility of a seismostratigraphic subdivision of the unit. These correlations exemplify the different resolution of these three complementary methods of investigation.