Miracle-dz/UniFAR-FTUs huggingface dataset:
Data‐driven spatial b value estimation with applications to California seismicity: To b or not to b

In this paper we present a penalized likelihood‐based method for spatial estimation of Gutenberg‐Richter's b value. Our method incorporates a nonarbitrary partitioning scheme based on Voronoi tessellation, which allows for the optimal partitioning of space using a minimum number of free parameters. By random placement of an increasing number of Voronoi nodes, we are able to explore the whole solution space in terms of model complexity. We obtain an overall likelihood for each model by estimating the b values in all Voronoi regions and calculating its joint likelihood using Aki's formula. Accounting for the number of free parameters, we then calculate the Bayesian Information Criterion for all random realizations. We investigate the ensemble of the best performing models and demonstrate the robustness and validity of our method through extensive synthetic tests. We apply our method to the seismicity of California using two different time spans of the Advanced National Seismic System catalog (1984–2014 and 2004–2014). The results show that for the last decade, the b value variation in the well‐instrumented parts of mainland California is limited to the range of (0.94 ± 0.04–1.15 ± 0.06). Apart from the Geysers region, the observed variation can be explained by network‐related discrepancies in the magnitude estimations. Our results suggest that previously reported spatial b value variations obtained using classical fixed radius or nearest neighbor methods are likely to have been overestimated, mainly due to subjective parameter choices. We envision that the likelihood‐based model selection criteria used in this study can be a useful tool for generating improved earthquake forecasting models.
Gut Phageome—An Insight into the Role and Impact of Gut Microbiome and Their Correlation with Mammal Health and Diseases

The gut microbiota, including bacteria, archaea, fungi, and viruses, compose a diverse mammalian gut environment and are highly associated with host health. Bacteriophages, the viruses that infect bacteria, are the primary members of the gastrointestinal virome, known as the phageome. However, our knowledge regarding the gut phageome remains poorly understood. In this review, the critical role of the gut phageome and its correlation with mammalian health were summarized. First, an overall profile of phages across the gastrointestinal tract and their dynamic roles in shaping the surrounding microorganisms was elucidated. Further, the impacts of the gut phageome on gastrointestinal fitness and the bacterial community were highlighted, together with the influence of diets on the gut phageome composition. Additionally, new reports on the role of the gut phageome in the association of mammalian health and diseases were reviewed. Finally, a comprehensive update regarding the advanced phage benchwork and contributions of phage-based therapy to prevent/treat mammalian diseases was provided. This study provides insights into the role and impact of the gut phagenome in gut environments closely related to mammal health and diseases. The findings provoke the potential applications of phage-based diagnosis and therapy in clinical and agricultural fields. Future research is needed to uncover the underlying mechanism of phage–bacterial interactions in gut environments and explore the maintenance of mammalian health via phage-regulated gut microbiota.
VALORACIÓN DE ÁREAS FAUNÍSTICAS EN EL AIGUABARREIG DEL SEGRE, CINCA Y EBRO*

A study that values the present faunistic communities in Aiguabarreig (Confluence of Segre, Cinca, and Ebro rivers)is presented from a geographic point of view, considering its spatial distribution, and the relations whichare established between the different natural envi- ronments that form this wet territory. Through the creation of faunistic areas supported in the handling of SIG and the interpretation of field data, a division of the zone of study based on the potential habitats has been obtained to come to its valuation from an ecological nature crite- ria.
Tumor Vaccines: Unleashing the Power of the Immune System to Fight Cancer

This comprehensive review delves into the rapidly evolving arena of cancer vaccines. Initially, we examine the intricate constitution of the tumor microenvironment (TME), a dynamic factor that significantly influences tumor heterogeneity. Current research trends focusing on harnessing the TME for effective tumor vaccine treatments are also discussed. We then provide a detailed overview of the current state of research concerning tumor immunity and the mechanisms of tumor vaccines, describing the complex immunological processes involved. Furthermore, we conduct an exhaustive analysis of the contemporary research landscape of tumor vaccines, with a particular focus on peptide vaccines, DNA/RNA-based vaccines, viral-vector-based vaccines, dendritic-cell-based vaccines, and whole-cell-based vaccines. We analyze and summarize these categories of tumor vaccines, highlighting their individual advantages, limitations, and the factors influencing their effectiveness. In our survey of each category, we summarize commonly used tumor vaccines, aiming to provide readers with a more comprehensive understanding of the current state of tumor vaccine research. We then delve into an innovative strategy combining cancer vaccines with other therapies. By studying the effects of combining tumor vaccines with immune checkpoint inhibitors, radiotherapy, chemotherapy, targeted therapy, and oncolytic virotherapy, we establish that this approach can enhance overall treatment efficacy and offset the limitations of single-treatment approaches, offering patients more effective treatment options. Following this, we undertake a meticulous analysis of the entire process of personalized cancer vaccines, elucidating the intricate process from design, through research and production, to clinical application, thus helping readers gain a thorough understanding of its complexities. In conclusion, our exploration of tumor vaccines in this review aims to highlight their promising potential in cancer treatment. As research in this field continues to evolve, it undeniably holds immense promise for improving cancer patient outcomes.
Evaluating global warming potentials as historical temperature proxies: An application of ACC2 inverse calculation

Global Warming Potentials (GWPs) are evaluated as proxies of the historical temperature by applying them to convert historical CH4 and N2O emissions to equivalent CO2 emissions. Our GWP analysis is based on the historical Earth system evolution obtained from the inverse calculation for the Aggregated Carbon Cycle, Atmospheric Cycle, and Climate Model (ACC2). Indices higher than the Kyoto GWPs are required to reproduce the historical temperature. The GWP for N2O, in particular, does not approximate the historical temperature with any time horizon because the GWP definition and calculations assume a background system different from the ACC2 inversion results. In addition, indices have to be progressively updated upon the acquisition of new measurements and/or the change in our understanding on the Earth system processes.
Ecology, planning, and management of urban forests: international perspectives.

Preface. - Part One: Perspectives and Approaches in Urban Forestry: Introduction: The Growth of Cities and Urban Forestry. - Towards a Landscape Ecology of Cities: Beyond Buildings, Trees, and Urban Forests. - Principles for Guiding Eco-City Development. - A Multiple-Indicators Approach for Monitoring Urban Sustainable Development. - Assessment and Valuation of the Ecosystem Services Provided by Urban Forests. - Benefits of Urban Green Space for Improving Urban Climate. - Applying Ecosystem Management to Urban Forestry. - Approaches to Urban Forestry in the United Kingdom. - Opportunities and Alternatives for Enhancing Urban Forests in Compact Cities in Developing Countries. - Urban Ecology Studies in China with an Emphasis on Shanghai. - Using the Urban-Rural Gradient Approach to Determine the Effects of Land Use on Forest Remnants. - A Philosophical Basis for Restoring Ecologically Functioning Urban Forests: Current Methods and Results. - Part Two: Planning, Managing and Restoring Urban Forests: Strategic Planning for Urban Woodlands in North West England. - Landscape Corridors in Shanghai and their Importance in Urban Forest Planning. - Management of Urban Forests in the U.S.A. - The Urban Forest of Nanjing City: Key Characteristics and Management Assessment. - Urban Forest Structure in Hefei, China. - Forests and Forestry in Hesse (Federal Republic of Germany): Meeting the Challenge of Multipurpose Forestry. - Experiences in the Management of Urban Recreational Forests in Germany. - Modeling the Social Benefits of Urban Parks for Users. - Potential Leaf Area Index Analyses for the Urban Forest in Toronto, Canada. - Spatial and Temporal Change in the Distribution of Urban Vegetation in Beijing. - Long-Term Observations of Secondary Forests Growing on Hard Coal Mining Spoils in the Industrial Ruhr Region of Germany. - Selection of Pollution Tolerant Trees for Restoration of Degraded Forests and Evaluation of the Experimental Restoration Practices at the Ulsan Industrial Complex, Korea. - Restoration Planning in the Seoul Metropolitan Area, Korea. - the Construction of Near-Natural Forests in the Urban Areas of Shanghai. - Part Three: Synthesis and Directions for Future Research, Planning, and Implementation: The Future of Urban Forestry: Comparing National and International Needs and Perspectives. - Appendix: Recommendations for Urban Forestry and Planning in Shanghai. - Index.
The Costs of Urban Sprawl - Infrastructure and Transportation

This is one of three companion papers taken from a study that assesses the comparative costs of urban redevelopment with the costs of greenfield development. This paper shows that substantial costs could be saved in infrastructure and transport if urban redevelopment became the focus. The second paper GEN 83: The Costs of Urban Sprawl - Predicting Transport Greenhouse Gases from Urban Form Parameters assesses how these different urban typologies perform with respect to greenhouse gases. The third paper GEN 85: The Costs of Urban Sprawl - Physical Activity Links to Healthcare Costs and Productivity discusses the health costs and productivity losses that can be linked to human inactivity in suburban living. The savings in transport and infrastructure for 1000 dwellings are in the order of $86 million up-front for infrastructure and $250 million for annualised transportation costs over 50 years.
Minimizing post-harvest losses against coleoptera species: A review

This review focuses on the principal coleopteran beetles that cause post-harvest losses and the use of only botanical pesticides to control them. Food loss prevention during postharvest storage is critical for economic reasons. Integrated pest management, which includes the use of chemical (contact/residual) insecticides and fumigants, is now a generally recognised pest control technique, including postharvest infestation treatment. Because of the residue problem and health concerns to consumers, the use of synthetic chemical pesticides is either prohibited or restricted. Given the foregoing, there is a demand for plants that can serve as viable replacements to presently employed insecticides since they contain a large number of bioactive chemicals. According to the literature, the plant might be used to develop novel pesticides. As a result, insecticidal chemicals originating from plants have a lot of promise. The current state of botanical insecticides as grain protectants, as well as their method of action, are the subjects of this research.
Purification of linearized template plasmid DNA decreases double-stranded RNA formation during IVT reaction

After the COVID-19 pandemic, messenger RNA (mRNA) has revolutionized traditional vaccine manufacturing. With the increasing number of RNA-based therapeutics, valuable new scientific insights into these molecules have emerged. One fascinating area of study is the formation of double-stranded RNA (dsRNA) during in vitro transcription (IVT) which is considered a significant impurity, as it has been identified as a major trigger in the cellular immune response pathway. Therefore, there is a growing importance placed to develop and optimize purification processes for the removal of this by-product. Traditionally, efforts have primarily focused on mRNA purification after IVT through chromatographic separations, with anion exchange and reverse phase chromatography emerging as effective tools for this purpose. However, to the best of our knowledge, the influence and significance of the quality of the linearized plasmid have not been thoroughly investigated. Plasmids production involves the growth of bacterial cultures, bacterial harvesting and lysis, and multiple filtration steps for plasmid DNA purification. The inherent complexity of these molecules, along with the multitude of purification steps involved in their processing, including the subsequent linearization and the less-developed purification techniques for linearized plasmids, often result in inconsistent batches with limited control over by-products such as dsRNA. This study aims to demonstrate how the purification process employed for linearized plasmids can impact the formation of dsRNA. Several techniques for the purification of linearized plasmids based on both, resin filtration and chromatographic separations, have been studied. As a result of that, we have optimized a chromatographic method for purifying linearized plasmids using monolithic columns with C4 chemistry (butyl chains located in the surface of the particles), which has proven successful for mRNAs of various sizes. This chromatographic separation facilitates the generation of homogeneous linearized plasmids, leading to mRNA batches with lower levels of dsRNA during subsequent IVT processes. This finding reveals that dsRNA formation is influenced not only by RNA polymerase and IVT conditions but also by the quality of the linearized template. The results suggest that plasmid impurities may contribute to the production of dsRNA by providing additional templates that can be transcribed into sequences that anneal with the mRNA molecules. This highlights the importance of considering the quality of plasmid purification in relation to dsRNA generation during transcription. Further investigation is needed to fully understand the mechanisms and implications of plasmid-derived dsRNA. This discovery could shift the focus in mRNA vaccine production, placing more emphasis on the purification of linearized plasmids and potentially saving, in some instances, a purification step for mRNA following IVT.
Single cell and bulk transcriptome analysis identified oxidative stress response-related features of Hepatocellular Carcinoma

Background: Hepatocellular Carcinoma (HCC) is a common lethal digestive system tumor. The oxidative stress mechanism is crucial in the HCC genesis and progression. Methods: Our study analyzed single-cell and bulk sequencing data to compare the microenvironment of non-tumor liver tissues and HCC tissues. Through these analyses, we aimed to investigate the effect of oxidative stress on cells in the HCC microenvironment and identify critical oxidative stress response-related genes that impact the survival of HCC patients. Results: Our results showed increased oxidative stress in HCC tissue compared to non-tumor tissue. Immune cells in the HCC microenvironment exhibited higher oxidative detoxification capacity, and oxidative stress-induced cell death of dendritic cells was attenuated. HCC cells demonstrated enhanced communication with immune cells through the MIF pathway in a highly oxidative hepatoma microenvironment. Meanwhile, using machine learning and Cox regression screening, we identified PRDX1 as a predictor of early occurrence and prognosis in patients with HCC. The expression level of PRDX1 in HCC was related to dysregulated ribosome biogenesis and positively correlated with the expression of immunological checkpoints (PDCD1LG2, CTLA4, TIGIT, LAIR1). High PRDX1 expression in HCC patients correlated with better sensitivity to immunotherapy agents such as sorafenib, IGF-1R inhibitor, and JAK inhibitor. Conclusion: In conclusion, our study unveiled variations in oxidative stress levels between non-tumor liver and HCC tissues. And we identified oxidative stress gene markers associated with hepatocarcinogenesis development, offering novel insights into the oxidative stress response mechanism in HCC.
CGAAL: Distributed On-The-Fly ATL Model Checker with Heuristics

We present CGAAL, our efficient on-the-fly model checker for alternating-time temporal logic (ATL) on concurrent game structures (CGS). We present how our tool encodes ATL as extended dependency graphs with negation edges and employs the distributed on-the-fly algorithm by Dalsgaard et al. Our tool offers multiple novel search strategies for the algorithm, including DHS which is inspired by PageRank and uses the in-degree of configurations as a heuristic, IHS which estimates instability of assignment values, and LPS which estimates the distance to a state satisfying the constituent property using linear programming. CGS are input using our modelling language LCGS, where composition and synchronisation are easily described. We prove the correctness of our encoding, and our experiments show that our tool CGAAL is often one to three orders of magnitude faster than the popular tool PRISM-games on case studies from PRISM's documentation and among case studies we have developed. In our evaluation, we also compare and evaluate our search strategies, and find that our custom search strategies are often significantly faster than the usual breadth-first and depth-first search strategies.
Determinación del perfil de los estudiantes universitarios con base a variables académicas y tecnológicas

Se presenta un estudio sobre las actividades educativas que realizan estudiantes universitarios a traves del smartphone y la eventual relacion de variables tecnologicas y academicas con el promedio de calificacion. A partir de los resultados se logro clasificar las actividades, comprobar la posesion y frecuencia de uso. Ademas, se compararon grupos de estudiantes con base a variables de uso educativo y posesion de tecnologia. Finalmente, se reflexiona sobre el potencial del smartphone como herramienta pedagogica.
Simulation of steady-state ground water and spring flow in the upper Floridan aquifer of coastal Citrus and Hernando Counties, Florida

A digital ground-water flow model was developed to approximate steadystate, predevelopment flow conditions in the Upper Floridan aquifer of coastal west-central Florida. The aquifer is the major source of public water supply and natural spring flow in the area. The aquifer was simulated as a one-layer system with constant vertical recharge and discharge rates. A head-dependent drain function was used to simulate spring flow. Model calibration consisted of adjustments of aquifer transmiss ivit ies and recharge-discharge rates until the average absolute error per grid block was less than 3 feet and computed spring discharge was within 10 percent of measured or estimated discharges. Calibration transmissivities ranged from 8,640 feet squared per day in the northern part of the area to nearly 13,000,000 feet squared per day near large springs. Calibration inflows were about 2,700 cubic feet per second. Of this, about 2,567 cubic feet per second discharges as natural spring flow and 137 cubic feet per second discharges as upward leakage along the coast. A sensitivity analysis indicated that the model was most sensitive to changes in transmissivity and least sensitive to changes in upward leakage. The model was used to demonstrate aquifer response to large manmade stresses. Withdrawing 116 cubic feet per second from hypo the tical regional well fields resulted in potentiometric-surface drawdowns ranging from 0.1 to 1.7 feet and a drawdown of generally less than 0.2 foot along the coast. Total spring flow decreased about 5 percent, and the change to individual spring discharge varied from 0.1 to 8.0 percent of predevelopment discharge. Withdrawing 62 cubic feet per second from each of the 4-square-mile spring nodes resulted in six of the seven springs to the south of Chassahowitzka River contributing 50 percent of their flow to pumpage and three contributed 100 percent of their flow to pumpage. Springs located north of Chassahowitzka River contributed as much as 18 percent of their flow to pumpage.
Impact of rooting depth and soil hydraulic properties on the transpiration peak of an evergreen forest in northern Thailand in the late dry season

[1] Previous research showed that transpiration in an evergreen broad-leaved forest in northern Thailand (18°48′N, 98°54′E) peaked at the end of the dry season. However, rooting depth limitations on soil water use were not investigated. This study examined the impact of rooting depth and soil hydraulic properties on transpiration using a newly developed soil plant air continuum model. The soil texture at the site was classified as silty sand from the measured relationship between the volumetric soil water content and soil water potential at 0.1-m depths. To effectively simulate heat pulse velocity variation corresponding to dry season transpiration and annual discharge, a rooting depth of 4–5 m was needed, assuming a silty sand soil texture under unsaturated conditions. This value is less than the reported maximum rooting depth of trees and is considered reasonable. A penetration test showed that soil became harder at depths of 4–5 m. The model results suggest that a shallower rooting depth is sufficient to maintain the late dry season transpiration peak if other soil textures with lower hydraulic conductivity are assumed. By contrast, the late dry season transpiration peak could not be maintained under unsaturated conditions if a sandy soil texture with high hydraulic conductivity was assumed, even with a rooting depth of 12 m.
Dishevelled Segment Polarity Protein 3: A Novel Prognosis-related Marker in Pan-driver-gene-negative Lung Adenocarcinoma

Purpose: In this study, we aimed to investigate the potential prognostic molecular marker in patients with “pan-driver-gene-negative” lung adenocarcinoma (PDGN-LUAD). LUAD patients who were negative for mutations in EGFR, KRAS, BRAF, HER2, MET, ALK, RET and ROS1 were identified as PDGN-LUAD. Methods: In the screening phase, we profiled the mRNA expression levels in 52 paired PDGN-LUAD tumor tissues and adjacent normal tissues using a genome-wide microarray, and the results revealed that the expression level of dishevelled segment polarity protein 3 (DVL3) was higher in PDGN-LUAD tumor tissues than in normal lung tissues. Then, we enrolled 626 PDGN-LUAD patients from three independent hospital centers and divided them into a training cohort, an internal validation cohort and two external validation cohorts. In the training cohort, tissue microarrays (TMAs) were used to confirm the protein expression level of DVL3. Statistical methods were applied to explore the prognostic role of DVL3. Results: The results indicated that the level of DVL3 could be used to classify patients with PDGN-LUAD in the training cohort into a high-risk group (high expression level of DVL3) and a low-risk group (low expression level of DVL3). In the training cohort, high-risk patients had shorter overall survival (OS) times (hazard ratio [HR] 2.27; 95% CI, 1.57-2.97; p<0.001) than low-risk patients. In the validation phase, the performance of DVL3 as a prognostic marker was successfully validated in the internal and external cohorts. Conclusions: In conclusion, DVL3 is an important prognostic indicator for PDGN-LUAD and may provide new insights into the treatment of PDGN-LUAD.