Miracle-dz/UniFAR-FTUs huggingface dataset:
Global Mapping and Visualization Analysis of One Health Knowledge in the COVID-19 Context

Globally, the COVID-19 pandemic had a significant impact on the health, social, and economic systems, triggering lasting damage and exposing the complexity of the problem beyond just being a health emergency. This crisis has highlighted the need for a comprehensive and collaborative strategy to successfully counter infectious diseases and other global challenges. With the COVID-19 pandemic pushing One Health to the forefront of global health and sustainable development agendas, this concept has emerged as a potential approach for addressing these challenges. In the context of COVID-19, this study investigates global knowledge about One Health by examining its state, significant contributions, and future directions. It seeks to offer an integrated framework of insights guiding the development of well-informed decisions. A comprehensive search using the Scopus database was conducted, employing specific terms related to One Health and COVID-19. VOSviewer 1.6. 19 software was used to generate network visualization maps. Countries’ research output was adjusted based on their gross domestic product (GDP) and population size. The study identified a total of 527 publications. The United States led with 134 documents (25.4%), but India topped the adjusted ranking. One Health journal stood as the most common outlet for disseminating knowledge (49 documents; 9.3%), while Centers for Disease Control and Prevention (CDC), the United States emerged as the most prolific institution (13 documents; 2.5%). Key topics were related to the virus transmission mechanisms, climate change impacts, antimicrobial resistance, ecosystem health, preparedness, collaboration, community engagement, and developing of efficient surveillance systems. The study emphasizes how critical it is to capitalize on the present momentum of COVID-19 to advance One Health concepts. Integrating social and environmental sciences, and a variety of professions for better interaction and collaboration is crucial. Additionally, increased funding for developing countries, and legislative empowerment are vital to advance One Health and boost disease prevention.
Agricultura migratoria conductor del cambio de uso del suelo de ecosistemas alto-andinos de Colombia

The migratory agriculture (MA) as a direct driver in the dynamics of land use (LU) and land use change (LUC) in the Colombian Andean is evaluated by the spatial and temporal analysis of patterns of change Of cover crops during the periods 1989-1999 and 1999-2008; Where it was identified that the processes of deforestation and fragmentation have been generated by direct causes related to the dominant land uses (monkey potato crop, extensive pastureland) about coverage of natural origin (dense high Andean forest, low Paramo and natural wetland). The LU that presented the largest transformed area were: fragmented forest, pasture cover, potato cultivation, and extensive pasture (79%), low Paramo (78%) and dense Alto Andean forest (80,9%). These LU/LUCs had a direct relationship with spatial factors (elevation, slope, soil fertility, temperature and precipitation), which influenced the dynamics of change or permanence. It was also identified that driving forces such as: public development policies, intensive agriculture, infrastructure improvement, peasant organization, institutional support and armed conflict have streamlined the processes of modification and conversion in the territory mainly those associated with traditional and migratory agriculture; The latter becoming the direct driver of LUC in high Andean ecosystems.
Culex pipiens and Culex restuans larval interactions shape the bacterial communities in container aquatic habitats

Abstract Container aquatic habitats host a community of aquatic insects, primarily mosquito larvae that browse on container surface microbial biofilm and filter-feed on microorganisms in the water column. We examined how the bacterial communities in these habitats respond to feeding by larvae of two container-dwelling mosquito species, Culex pipiens and Cx. restuans. We also investigated how the microbiota of these larvae is impacted by intra- and interspecific interactions. Microbial diversity and richness were significantly higher in water samples when mosquito larvae were present, and in Cx. restuans compared to Cx. pipiens larvae. Microbial communities of water samples clustered based on the presence or absence of mosquito larvae and were distinct from those of mosquito larvae. Culex pipiens and Cx. restuans larvae harbored distinct microbial communities when reared under intraspecific conditions and similar microbial communities when reared under interspecific conditions. These findings demonstrate that mosquito larvae play a major role in structuring the microbial communities in container habitats and that intra- and interspecific interactions in mosquito larvae may shape their microbiota. This has important ecological and public health implications since larvae of the two mosquito species are major occupants of container habitats while the adults are vectors of West Nile virus.
Low resting metabolic rate and increased hunger due to β-MSH and β-endorphin deletion in a canine model

Mutations that perturb leptin-melanocortin signaling are known to cause hyperphagia and obesity, but energy expenditure has not been well studied outside rodents. We report on a common canine mutation in pro-opiomelanocortin (POMC), which prevents production of β–melanocyte-stimulating hormone (β-MSH) and β-endorphin but not α-MSH; humans, similar to dogs, produce α-MSH and β-MSH from the POMC propeptide, but rodents produce only α-MSH. We show that energy expenditure is markedly lower in affected dogs, which also have increased motivational salience in response to a food cue, indicating increased wanting or hunger. There was no difference in satiety at a modified ad libitum meal or in their hedonic response to food, nor disruption of adrenocorticotropic hormone (ACTH) or thyroid axes. In vitro, we show that β-MSH signals comparably to α-MSH at melanocortin receptors. These data implicate β-MSH and β-endorphin as important in determining hunger and moderating energy expenditure and suggest that this role is independent of the presence of α-MSH.
Advances in cancer mechanobiology: Metastasis, mechanics, and materials

Within the tumor microenvironment (TME), tumor cells are exposed to numerous mechanical forces, both internally and externally, which contribute to the metastatic cascade. From the initial growth of the tumor to traveling through the vasculature and to the eventual colonization of distant organs, tumor cells are continuously interacting with their surroundings through physical contact and mechanical force application. The mechanical forces found in the TME can be simplified into three main categories: (i) shear stress, (ii) tension and strain, and (iii) solid stress and compression. Each force type can independently impact tumor growth and progression. Here, we review recent bioengineering strategies, which have been employed to establish the connection between mechanical forces and tumor progression. While many cancers are explored in this review, we place great emphasis on cancers that are understudied in their response to mechanical forces, such as ovarian and colorectal cancers. We discuss the major steps of metastatic transformation and present novel, recent advances in model systems used to study how mechanical forces impact the study of the metastatic cascade. We end by summarizing systems that incorporate multiple forces to expand the complexity of our understanding of how tumor cells sense and respond to mechanical forces in their environment. Future studies would also benefit from the inclusion of time or the aspect of mechanical memory to further enhance this field. While the knowledge of mechanical forces and tumor metastasis grows, developing novel materials and in vitro systems are essential to providing new insight into predicting, treating, and preventing cancer progression and metastasis.
San Luis Dam Case History: Seepage and Slope Stability Analyses and Lessons Learned

Rapid drawdown is an important condition controlling the design of the upstream slope in embankment dams and levees. This paper presents the upstream slope failure at San Luis Dam as a case study for performing effective stress drawdown stability analyses. In effective stress analyses, stress-dependent drained shear strengths were used for the fine-grained core and slopewash materials. The seepage-induced pore-water pressures were estimated in the slopewash and fine-grained core by first calibrating the saturated and unsaturated hydraulic parameters with piezometers installed after the slide. The shear-induced pore-water pressures due to the changes in total stress were estimated from Skempton’s A coefficient. The stability analysis methodology incorporates stress-dependent drained shear strength envelopes and shear-induced pore-water pressures to determine the factor of safety (FS). The FS determined at various reservoir levels and slopewash shear strengths are used to provide recommendations for calibrating unsaturated soil properties, integrating seepage-induced and shear-induced pore-water pressures in stability analyses, and use of commercial software for drawdown stability analyses.
World Journal of Stem Cells

Blood vessels constitute a closed pipe system distributed throughout the body, transporting blood from the heart to other organs and delivering metabolic waste products back to the lungs and kidneys. Changes in blood vessels are related to many disorders like stroke, myocardial infarction, aneurysm, and diabetes, which are important causes of death worldwide. Translational research for new approaches to disease modeling and effective treatment is needed due to the huge socio-economic burden on healthcare systems. Although mice or rats have been widely used, applying data from animal studies to human-specific vascular physiology and pathology is difficult. The rise of induced pluripotent stem cells (iPSCs) provides a reliable in vitro resource for disease modeling, regenerative medicine, and drug discovery because they carry all human genetic information and have the ability to directionally differentiate into any type of human cells. This review summarizes the latest progress from the establishment of iPSCs, the strategies for differentiating iPSCs into vascular cells, and the in vivo trans-plantation of these vascular derivatives. It also introduces the application of these technologies in disease modeling, drug screening, and regenerative medicine. Additionally, the application of high-tech tools, such as omics analysis and high-throughput sequencing, in this field is reviewed.
Novos métodos em Ecologia de Estradas : correção da heterogeneidade espacial na análise de agregação de atropelamentos de fauna e definição da suficiência amostral

Roadkills is considered by several authors as the main direct cause of death of animals in nature. However, the interventions needed to mitigate this negative effect of the highways are usually onerous and therefore it is necessary to have reliability in proposing sites for them. The roadkill aggregation analyzes used in Road Ecology do not correct the effect of first order density heterogeneity by generating spatial autocorrelation between events greater than the actual is. The first chapter of this dissertation presents a method of correction, called Windowned Method, which weighs the results obtained in a radius of analysis by an observation window with less heterogeneity than the total area of study. The proposed method presented lower hotspot classification error rates and was less influenced by the heterogeneity of event distribution when compared to two other methods used in Road Ecology. This dissertation also addressed the deficiency of a sample adequacy analysis for Road Ecology studies. In the second chapter of this dissertation it was verified that there is a positive relationship between the hotspot classification accuracy and the sample size. By means of Bootstrap resampling simulations and extrapolations using Quantile Regression, this relation was used to construct a Precision Curve with which it is possible to identify the desired sample size to reach a degree of precision determined by the researcher. With this method the sampling sufficiency can be determined by the accumulation of record allowing diverse collection protocols, it permits researchers to vary both the speed of carcasses search as the frequency of collections campaigns, according to their convenience.
Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization

Abstract Antimicrobial peptides (AMPs), short peptides with diverse functions, effectively target and combat various organisms. The widespread misuse of chemical antibiotics has led to increasing microbial resistance. Due to their low drug resistance and toxicity, AMPs are considered promising substitutes for traditional antibiotics. While existing deep learning technology enhances AMP generation, it also presents certain challenges. Firstly, AMP generation overlooks the complex interdependencies among amino acids. Secondly, current models fail to integrate crucial tasks like screening, attribute prediction and iterative optimization. Consequently, we develop a integrated deep learning framework, Diff-AMP, that automates AMP generation, identification, attribute prediction and iterative optimization. We innovatively integrate kinetic diffusion and attention mechanisms into the reinforcement learning framework for efficient AMP generation. Additionally, our prediction module incorporates pre-training and transfer learning strategies for precise AMP identification and screening. We employ a convolutional neural network for multi-attribute prediction and a reinforcement learning-based iterative optimization strategy to produce diverse AMPs. This framework automates molecule generation, screening, attribute prediction and optimization, thereby advancing AMP research. We have also deployed Diff-AMP on a web server, with code, data and server details available in the Data Availability section.
Evaluating the Relationship between Interannual Variations in the Antarctic Ozone Hole and Southern Hemisphere Surface Climate in Chemistry–Climate Models

Studies have recently reported statistically significant relationships between observed year-to-year spring Antarctic ozone variability and the Southern Hemisphere annular mode and surface temperatures in spring–summer. This study investigates whether current chemistry–climate models (CCMs) can capture these relationships, in particular, the connection between November total column ozone (TCO) and Australian summer surface temperatures, where years with anomalously high TCO over the Antarctic polar cap tend to be followed by warmer summers. The interannual ozone–temperature teleconnection is examined over the historical period in the observations and simulations from the Whole Atmosphere Community Climate Model (WACCM) and nine other models participating in the Chemistry–Climate Model Initiative (CCMI). There is a systematic difference between the WACCM experiments forced with prescribed observed sea surface temperatures (SSTs) and those with an interactive ocean. Strong correlations between TCO and Australian temperatures are only obtained for the uncoupled experiment, suggesting that the SSTs could be important for driving both variations in Australian temperatures and the ozone hole, with no causal link between the two. Other CCMI models also tend to capture this relationship with more fidelity when driven by observed SSTs, although additional research and targeted modeling experiments are required to determine causality and further explore the role of model biases and observational uncertainty. The results indicate that CCMs can reproduce the relationship between spring ozone and summer Australian climate reported in observational studies, suggesting that incorporating ozone variability could improve seasonal predictions; however, more work is required to understand the difference between the coupled and uncoupled simulations.
Interviews With Lay Caregivers About Their Experiences Supporting Patients Throughout Kidney Transplantation.

Introduction: Lay caregivers provide essential support to patients throughout the kidney transplant process, pretransplant through discharge. Sparse data exists about kidney transplant caregiver experience and facilitators of caregiver engagement. The aim of this study was to explore and describe lay caregivers' accounts of supporting a patient before and early after kidney transplantation. Methods: Caregivers of recent kidney transplant recipients were individually interviewed about their experiences, coping strategies, and perspectives of center-specific support approaches for patients and caregivers in a single transplant center. Results: Inductive content analysis of transcribed interviews with 23 caregivers revealed 6 domain areas: visit preparation, initial evaluation, caregiver role discussion, exposure to support resources, transplant preparedness, and coping styles. Caregivers used and appreciated information offered by the transplant center, including materials directed to the patient. They recommended repeating information, online access, and adding video to complement print resources. They valued and requested information directed to them, both within passive materials and communication with providers. Social network interactions were helpful for practical, emotional, and informational support. Support group reminders and connection pathways to peers were suggested for both patients and caregivers. Conclusion: Findings highlight steps that can be taken by transplant centers and may stimulate caregiver engagement. Featuring caregiver-focused information and communication more prominently may support caregivers to improve patient progress in navigating kidney transplantation.
ABCG2 polymorphisms and susceptibility to ARV‐associated hepatotoxicity

Abstract Background The ABCG2 421C/A polymorphism contributes significantly to the distribution and absorption of antiretroviral (ARV) regimens and is associated with the undesirable side effects of efavirenz. Methods To investigate this, we examined ABCG2 34G/A (rs2231137) and 421C/A (rs2231142) genetic variations in 149 HIV‐infected patients (116 without hepatotoxicity, 33 with ARV‐induced hepatotoxicity) and 151 healthy controls through the PCR‐restriction fragment length polymorphism (PCR‐RFLP) technique. Results and Discussion The ABCG2 34GA genotype and 34A allele indicated a risk for antiretroviral therapy‐associated hepatotoxicity development (p = 0.09, OR = 1.58, 95% CI: 0.93–2.69; p = 0.06, OR = 1.50, 95% CI: 0.98–2.30). The haplotype GA was associated with hepatotoxicity (p = 0.042, OR = 2.37, 95% CI: 1.04–5.43; p = 0.042, OR = 2.49, 95% CI: 1.04–5.96). Moreover, when comparing HIV patients with hepatotoxicity to healthy controls, the haplotype GA had an association with an elevated risk for the development of hepatotoxicity (p = 0.041, OR = 1.73, 95% CI: 1.02–2.93). Additionally, the association of the ABCG2 34GA genotype with the progression of HIV (p = 0.02, OR = 1.97, 95% CI: 1.07–3.63) indicated a risk for advanced HIV infection. Furthermore, the ABCG2 421AA genotype was linked to tobacco users and featured as a risk factor for the progression of HIV disease (p = 0.03, OR = 11.07, 95% CI: 1.09–270.89). Conclusion The haplotype GA may enhance the risk of hepatotoxicity development and its severity. Individuals with the ABCG2 34A allele may also be at risk for the development of hepatotoxicity. Additionally, individuals with an advanced stage of HIV and the ABCG2 34GA genotype may be at risk for disease progression.
Two‐Branch Break‐up Systems by a Single Mantle Plume: Insights from Numerical Modeling

Thermomechanical modeling of plume‐induced continental break‐up reveals that the initial location of a mantle anomaly relative to a lithosphere inhomogeneity has a major impact on the geometry and timing of a rift‐to‐spreading system. Models with a warmer Moho temperature are more likely to result in “plume‐centered” mode, where the rift and subsequent spreading axis grow directly above the plume. Models with weak far‐field forcing are inclined to develop a “structural‐inherited” mode, with lithosphere deformation localized at the lateral lithospheric boundary. Models of a third group cultivate two break‐up branches (both “plume‐centered” and “structural inherited”) that form consecutively with a few million years delay. With our experimental setup, this break‐up mode is sensitive to relatively small lateral variations of the initial anomaly position. We argue that one single mantle anomaly can be responsible for nonsimultaneous initiation and development of two rift‐to‐spreading systems in a lithosphere with a lateral strength contrast.
Termite mounds as bio-indicators of groundwater: Prospects and constraints

Reliance on modern sophisticated equipment for making 'discoveries' has limited the human power of observing subtle clues in the environment that are capable of saving cost and labour that come with researching new resources and methods to improve life for all. Due to the growing scarcity of potable water, especially in African and Asian countries, newer, cheaper and reliable methods of investigating groundwater resources are becoming critical. One such potentially promising method is mapping the distribution of termite mounds in the environment. Termite mounds are conspicuous landscape features in tropical and sub-tropical regions of the world. Built from surrounding soils by several species of termite, the properties of mound soil are relatively different from the surrounding soil in most cases, indicating improved hydraulic properties. In this paper, the aim is to review the possibility of employing termite mounds as prospecting tools for groundwater search from three spatial scales of observation. From assessing the smallest to the highest scale of observation, it can be concluded that termite mounds' prospect as surface indicators of groundwater is apparent. Review findings indicate increased surface water infiltration, presence of riparian tree vegetation and other trees with tap-root system around termite mounds, linear assemblage of termite mounds along aquiferous dykes and seep-lines as well as the dependence of termites on water but avoidance of places with risk of inundation. Whether they indicate permanent groundwater reserves in all cases or whether all species depend largely on water for their metabolism is a subject for further research.
Rapid generation of high-quality structure figures for publication with PyMOL-PUB

Abstract Motivation The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands. Therefore, providing interfaces based on established software instead of manual editing becomes a significant necessity. Results We developed PyMOL-PUB, based on the original design of PyMOL, to effectively create publication-quality figures from molecular structure data. It provides functions including structural alignment methods, functional coloring schemes, conformation adjustments, and layout plotting strategies. These functions allow users to easily generate high-quality figures, demonstrate structural differences, illustrate inter-molecular interactions, and predict performances of biomacromolecules. Availability and implementation Our tool is publicly available at https://github.com/BGI-SynBio/PyMOL-PUB.