Miracle-dz/UniFAR-FTUs huggingface dataset:
Commercial exploitation and conservation status of high value medicinal plants across the borderline of India and Nepal in Pithoragarh

Across the borderline of Nepal and India in the Jhulaghat region of Pithoragarh District (Uttaranchal), a total of 16 medicinal plants were documented during the present survey, which are in trade for commercial purpose. Most of these medicinal plants are being collected from the Baitedi District of Nepal and then supplied to the India via Jhulaghat and Dharchula. Reetha ( Sapindus mukorosii ) was traded commercially in highest quantity (about 4,000 qt1s) during 2001-2002. Six species of rare and endangered categories were also collected from Baitadi District for sale to India, inspite of the total ban on their collection for commercial purpose. Based on the survey and findings, various conservation and management steps have been discussed to protect the medicinal plants and also for future course of action.
SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells

Abstract RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures minimal background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5′ and 3′-terminal regions of authentic SARS-CoV-2 RNAs in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.
Small- and large-scale model tests on the buckling property of slender pile

ABSTRACT Slender piles embedded in soft ground or liquefied soil may buckle under vertical load. In this paper, both small- and large-scale model tests are conducted to investigate the buckling mechanisms of a slender pile and the lateral earth pressure acting on the pile. To observe the buckling of a slender pile, the strain-controlled loading method is adopted to apply a vertical load. When the two ends of a slender pile are hinged, the buckling mechanisms of small- and large-scale model tests are same. It should be noted that this applies only to a system with a small ratio of pile bending stiffness to soil bending stiffness. An applied vertical load increases with an increasing pile head settlement until it reaches the critical buckling load. By further increasing the pile head settlement, the measured load approaches the critical buckling load. In the large-scale model test, the measured lateral earth pressure (i.e., active and passive) acting on the slender pile varies linearly with the lateral pile displacement when the measured range is 3–5 m beneath the ground. A critical buckling calculation method has been adopted to compare with the conventional “m” method. The two-sided earth pressure calculation method can achieve more approximate results with the model test.
Suspended sediment sources in British rivers

Sedimentation problems have traditionally been viewed as being of limited importance in Britain. As a result there is no national sediment monitoring programme and relatively little is known about the suspended sediment loads of British rivers. The recent growth of awareness of the wider environmental significance of fine sediment and its important role in the sediment-associated transfer of nutrients and contaminants and in degrading aquatic ecosystems has emphasized the need for sediment control and management programmes. The design of such programmes requires an improved knowledge and understanding of the suspended sediment budgets of British catchments. In addition to information on sediment loads and sediment yields, there is a need for information on sediment source. Such information is difficult to obtain using traditional techniques, but source fingerprinting procedures offer an effective and reliable means of assembling such data. The authors and their co-workers have undertaken a number of source tracing investigations in British catchments and the findings from 48 catchments are synthesized in this contribution. The results are reviewed and their implications for the sediment budgets of British catchments and for the design and implementation of effective sediment management programmes are discussed.
The relationship between HIV‐1 neuroinflammation, neurocognitive impairment and encephalitis pathology: A systematic review of studies investigating post‐mortem brain tissue

Abstract The activities of HIV‐1 in the central nervous system (CNS) are responsible for a dysregulated neuroinflammatory response and the subsequent development of HIV‐associated neurocognitive disorders (HAND). The use of post‐mortem human brain tissue is pivotal for studying the neuroimmune mechanisms of CNS HIV infection. To date, numerous studies have investigated HIV‐1‐induced neuroinflammation in post‐mortem brain tissue. However, from the commonly investigated studies in this line of research, it is not clear which neuroinflammatory markers are consistently associated with HIV neurocognitive impairment (NCI) and neuropathology (i.e., HIV‐encephalitis, HIVE). Therefore, we conducted a systematic review of the association between neuroinflammation and NCI/HIVE from studies investigating post‐mortem brain tissue. Our aim was to synthesise the published data to date to provide commentary on the most noteworthy markers that are associated with NCI/HIVE. PubMed, Scopus, and Web of Science databases were searched using a search protocol designed specifically for this study. Sixty‐one studies were included that investigated the levels of inflammatory markers based on their gene and protein expression in association with NCI/HIVE. The findings revealed that the (1) transcript expressions of IL‐1β and TNF‐α were consistently associated with NCI/HIVE, whereas CCL2 and IL‐6 were commonly not associated with NCI/HIVE, (2) protein expressions of CD14, CD16, CD68, Iba‐1, IL‐1β and TNF‐α were consistently associated with NCI/HIVE, while CD45, GFAP, HLA‐DR, IL‐1 and IL‐6 were commonly not associated with NCI/HIVE, and (3) gene and protein expressions of CNS IL‐1β and TNF‐α were consistently associated with NCI/HIVE, while IL‐6 was consistently not associated with NCI/HIVE. These markers highlight the commonly investigated markers in this line of research and elucidates the neuroinflammatory mechanisms in the HIV‐1 brain that are involved in the pathophysiology of NCI/HIVE. These markers and related pathways should be investigated for the development of improved diagnostics, prognostics, and therapeutics of HAND.
One-year mortality rates after standardized management for emergency laparotomy: results from the Swedish SMASH study

Abstract Background Patients who require an emergency laparotomy suffer from high mortality and morbidity rates. Studies have shown that the standardization of perioperative management reduces complications in the short term. The aim of the present study was to report long-term mortality rates for the SMASH (Standardized perioperative Management of patients operated with acute Abdominal Surgery in a High-risk and emergency setting) study, as well as short- and long-term outcomes for different age groups within the SMASH study. Methods A prospective intervention study was introduced in 2018, with the aim of investigating the introduction of a standardized protocol for emergency laparotomy. For 42 months, intervention patients were managed according to the protocol and outcomes were then compared with those of historical controls. Results A total of 1344 unique patients were included (681 in the intervention group and 663 in the control group). The 90-day mortality rate was 14.1 per cent in the intervention group and 20.8 per cent in the control group (P = 0.002) and the 1-year mortality rate in adjusted analyses was 19.7 and 27.8 per cent respectively (P =< 0.001). An age-related subgroup analysis showed that the oldest patients (76 years and older, 260 in the intervention group and 240 in the control group) had a 1-year mortality rate of 29.6 and 43.8 per cent respectively (P = 0.004) and a mean duration of hospital stay of 9.9 and 11.6 days respectively (P = 0.027). Among older adults (61–75 years), the mean duration of hospital stay was 11.7 days in the intervention group compared with 15.1 days in the control group (P = 0.009) and the mean duration of ICU care was reduced to 4.49 days compared with 7.29 days (P = 0.046). Conclusion The standardized protocol associated with an emergency laparotomy appears to be beneficial, even in the long term. For elderly patients, it appears to reduce mortality rates and the durations of hospital stay and ICU care.
Intercropping maize and Caucasian clover to reduce environmental impact of maize silage production.

Maize (Zea mays L.) silage has become an increasingly important forage crop in high output dairy farming systems in Europe and North America because of its high energy density, relatively uniform nutritive value, and efficiency of production. But due to lack of surface residue and organic matter inputs and high nitrogen (N) fertilizer inputs, maize silage production is one of the most demanding cropping systems imposed on our soil and water resources. We investigated intercropping maize with the persistent rhizomatous legume, Caucasian clover (Trifolium ambiguum M. Bieb.), as a means to provide continuous living groundcover to minimize nitrate leaching, nutrient runoff and soil erosion. Maize was sown into existing stands of Caucasian clover that had been suppressed to reduce competition, and into areas with no clover. Total nitrate-N leached was reduced by 74% relative to the control monocrop maize under intercropped maize silage. On loess soils with 8 to 15% slope, during simulated, short, heavy rainstorms, Caucasian clover intercrop reduced water runoff by 50%, soil loss by 77%, and P and N losses by 80% relative to monocrop maize. Intercropping maize with Caucasian clover can eliminate N-fertilizer inputs and greatly reduce negative environmental impacts associated with maize silage production.
Excited State Vibrational Dynamics Reveals a Photocycle That Enhances the Photostability of the TagRFP-T Fluorescent Protein

High photostability is a desirable property of fluorescent proteins (FPs) for imaging, yet its molecular basis is poorly understood. We performed ultrafast spectroscopy on TagRFP and its 9-fold more photostable variant TagRFP-T (TagRFP S158T) to characterize their initial photoreactions. We find significant differences in their electronic and vibrational dynamics, including faster excited-state proton transfer and transient changes in the frequency of the v520 mode in the excited electronic state of TagRFP-T. The frequency of v520, which is sensitive to chromophore planarity, downshifts within 0.58 ps and recovers within 0.87 ps. This vibrational mode modulates the distance from the chromophore phenoxy to the side chain of residue N143, which we suggest can trigger cis/trans photoisomerization. In TagRFP, the dynamics of v520 is missing, and this FP therefore lacks an important channel for chromophore isomerization. These dynamics are likely to be a key mechanism differentiating the photostability of the two FPs.
Various methods of 3D and Bio-printing

Summary There is growing need for synthetic tissue replacement materials designed in a way that mimic complex structure of tissues and organs. Among various methods for fabrication of implants (scaffolds), 3D printing is very powerful technique because it enables creation of scaffolds with complex internal structures and high resolution, based on medical data sets. This method allows fabrication of scaffolds with desired macro- and micro-porosity and fully interconnected pore network. Rapid development of 3D printing technologies has enabled various applications from the creation of anatomical training models for complex surgical procedures to the printing of tissue engineering constructs. The aim of current investigations was to develop compatible printers and materials (bioinks) to obtain biomimetic scaffolds, which allow printing of living cells without significant loss of cell viability. The advanced level of such printing assumes “in situ” printing, i.e. printing cells and biomaterials directly onto or in a patient that will reduce recovery time.
COVID-19 pandemic and its impact on medical interns’ mental health of public and private hospitals in Guadalajara

ABSTRACT Introduction Burnout syndrome is a global burden characterized by exhaustion, work detachment, and a sense of ineffectiveness. It affects millions of individuals worldwide, with a particularly high prevalence among medical students. Factors such as demanding education, exposure to suffering, and the COVID-19 pandemic have contributed to elevated stress levels. Addressing this issue is crucial due to its impact on well-being and health-care quality. Materials and methods This cross-sectional survey study assessed fear of COVID-19 and burnout levels among medical student interns in hospitals in Guadalajara, Jalisco. The study used validated scales and collected data from September 2021 to September 2022. A snowball sampling method was employed and a minimum sample size of 198 participants was calculated. Results This study included 311 medical students (62.1% female and 37.9% male with a mean age of 23.51 ± 2.21 years). The majority were in their second semester of internship (60.5%) and from public hospitals (89.1%). Most students believed that the COVID-19 pandemic affected the quality of their internship (82.6%). Female students had higher personal burnout scores, while male students had higher work-related burnout scores. The mean score for fear of COVID-19 was 13.71 ± 6.28, with higher scores among women (p = 0.004) and those from public hospitals (p = 0.009). A positive weak correlation was found between COVID-19 scores and burnout subscales. Conclusion Our study emphasizes the significant impact of various factors on burnout levels among medical students and health-care professionals during the COVID-19 pandemic. Prolonged exposure to COVID-19 patients, reduced staffing, and increased workload contributed to burnout, affecting well-being and quality of care. Targeted interventions and resilience-building strategies are needed to mitigate burnout and promote well-being in health-care settings.
Why Think? Just Do: The Dawn of a New Era in Australia and Implications for Australian LIS Research

Work undertaken by the Australian Library and Information Association (ALIA) Research Committee for the Australian Research Council’s (ARC) Excellence in Research (ERA) initiative revealed a commitment by Australian library and information studies (LIS) academics to undertake serious research for the profession in Australia, a necessity in order to survive in the current Australian research and university policy climate. Yet on a world scale, LIS research being undertaken by research academics and students in the Australian LIS context is not extensive. The paper describes the current context of research activity in Australian universities and outlines the ALIA ERA experience, the final outcome of which was, in the eyes of many, unfavourable to Australian LIS research community. It concludes by addressing the question: Is there room for optimism?
Prediction of the risk of 3-year chronic kidney disease among elderly people: a community-based cohort study

Abstract Objective We conducted a community-based cohort study to predict the 3-year occurrence of chronic kidney disease (CKD) among population aged ≥60 years. Method Participants were selected from two communities through randomized cluster sampling in Jiading District of Shanghai, China. The two communities were randomly divided into a development cohort (n = 12012) and a validation cohort (n = 6248) with a 3-year follow-up. Logistic regression analysis was used to determine the independent predictors. A nomogram was established to predict the occurrence of CKD within 3 years. The area under the curve (AUC), the calibration curve and decision curve analysis (DCA) curve were used to evaluate the model. Result At baseline, participants in development cohort and validation cohort were with the mean age of 68.24 ± 5.87 and 67.68 ± 5.26 years old, respectively. During 3 years, 1516 (12.6%) and 544 (8.9%) new cases developed CKD in the development and validation cohorts, respectively. Nine variables (age, systolic blood pressure, body mass index, exercise, previous hypertension, triglycerides, fasting plasma glucose, glycated hemoglobin and serum creatinine) were included in the prediction model. The AUC value was 0.742 [95% confidence interval (CI), 0.728–0.756] in the development cohort and 0.881(95%CI, 0.867–0.895) in the validation cohort, respectively. The calibration curves and DCA curves demonstrate an effective predictive model. Conclusion Our nomogram model is a simple, reasonable and reliable tool for predicting the risk of 3-year CKD in community-dwelling elderly people, which is helpful for timely intervention and reducing the incidence of CKD.
Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human

Abstract Ribosomal frameshifting refers to the process that ribosomes slip into +1 or −1 reading frame, thus produce chimeric trans-frame proteins. In viruses and bacteria, programmed ribosomal frameshifting can produce essential trans-frame proteins for viral replication or regulation of other biological processes. In humans, however, functional trans-frame protein derived from ribosomal frameshifting is scarcely documented. Combining multiple assays, we show that short codon repeats could act as cis-acting elements that stimulate ribosomal frameshifting in humans, abbreviated as CRFS hereafter. Using proteomic analyses, we identified many putative CRFS events from 32 normal human tissues supported by trans-frame peptides positioned at codon repeats. Finally, we show a CRFS-derived trans-frame protein (HDAC1-FS) functions by antagonizing the activities of HDAC1, thus affecting cell migration and apoptosis. These data suggest a novel type of translational recoding associated with codon repeats, which may expand the coding capacity of mRNA and diversify the regulation in human.
Synthèse de coupes minimales fonctionnelles en coupes minimales composant

Résumé La construction de la safety pour un système complexe est une tâche qu’il est préférable de commencer lors des étapes initiales de définition de ce système. L’impact d’une correction d’erreur sur les coûts et les délais est en effet d’autant plus grand que cette erreur est détectée plus tard. Par ailleurs, les pratiques courantes du métier sont fondées sur des tâches manuelles, fortement sujettes à erreur, qui peuvent effectivement induire des surcoûts de certification. Ceci explique l’apparition, à partir des années 1990, des techniques de « construction de la safety à base de modèles » (Model-Based Safety Assessment). La démarche proposée dans le présent article s’inscrit dans le cadre de ces techniques. L’objectif est de décrire sur un exemple réel une méthode d’évaluation de performances de safety, applicable aux étapes amont (« early validation ») du développement de ce système. L’architecture n’étant, à ce stade, pas figée, la méthode permet d’effectuer des comparaisons entre variantes du point de vue des performances de safety, et au final de choisir l’option la plus intéressante de ce point de vue. La méthode est supportée par le logiciel SYNTHECOUPE développé par Thales.
Muscle parameters in fragility fracture risk prediction in older adults: A scoping review.

Half of osteoporotic fractures occur in patients with normal/osteopenic bone density or at intermediate or low estimated risk. Muscle measures have been shown to contribute to fracture risk independently of bone mineral density. The objectives were to review the measurements of muscle health (muscle mass/quantity/quality, strength and function) and their association with incident fragility fractures and to summarize their use in clinical practice. This scoping review follows the PRISMA-ScR guidelines for reporting. Our search strategy covered the three overreaching concepts of 'fragility fractures', 'muscle health assessment' and 'risk'. We retrieved 14 745 references from Medline Ovid SP, EMBASE, Web of Science Core Collection and Google Scholar. We included original and prospective studies on community-dwelling adults aged over 50 years that analysed an association between at least one muscle parameter and incident fragility fractures. We systematically extracted 17 items from each study, including methodology, general characteristics and results. Data were summarized in tables and graphically presented in adjusted forest plots. Sixty-seven articles fulfilled the inclusion criteria. In total, we studied 60 muscle parameters or indexes and 322 fracture risk ratios over 2.8 million person-years (MPY). The median (interquartile range) sample size was 1642 (921-5756), age 69.2 (63.5-73.6) years, follow-up 10.0 (4.4-12.0) years and number of incident fragility fractures 166 (88-277). A lower muscle mass was positively/not/negatively associated with incident fragility fracture in 28 (2.0), 64 (2.5) and 10 (0.2 MPY) analyses. A lower muscle strength was positively/not/negatively associated with fractures in 53 (1.3), 57 (1.7 MPY) and 0 analyses. A lower muscle function was positively/not/negatively associated in 63 (1.9), 45 (1.0 MPY) and 0 analyses. An in-depth analysis shows how each single muscle parameter was associated with each fragility fractures subtype. This review summarizes markers of muscle health and their association with fragility fractures. Measures of muscle strength and function appeared to perform better for fracture risk prediction. Of these, hand grip strength and gait speed are likely to be the most practical measures for inclusion in clinical practice, as in the evaluation of sarcopenia or in further fracture risk assessment scores. Measures of muscle mass did not appear to predict fragility fractures and might benefit from further research, on D3-creatine dilution test, lean mass indexes and artificial intelligence methods.