Miracle-dz/UniFAR-FTUs huggingface dataset:
Revealing the association between vitamin D metabolic pathway gene variants and lung cancer risk: a systematic review and meta-analysis

Lung cancer is a crucial global issue, with more than one million deaths annually. While smoking is considered the main etiology of the disease, several genetic variants are associated with it. Alterations in vitamin D pathway genes have also been studied in regards to lung cancer, but the findings have been inconclusive. We here present a systematic review and meta-analysis of seven genes in this pathway: CYP2R1, CYP27B1, CYP24A1, CYP3A4, CYP3A5, GC, and VDR. Four databases (PubMed, Scopus, Cochrane Library, and Web of Science (WOS) databases) were searched. From these, 16 eligible case–control studies comprising 6,206 lung cancer cases and 7,272 health controls were obtained. These studies were subjected to comprehensive data extraction and quality scoring, and the pooled odds ratio with a 95% confidence interval was calculated to estimate the effect of each variant along with heterogeneity analysis and a risk of bias assessment. Our meta-analysis revealed an association between CYP3A4 (rs2740574) and lung cancer in the allelic, heterozygous, and dominant models. In addition, both VDR (Fok1: rs2228570) and VDR (Cdx-2: rs11568820) displayed a protective role in lung cancer development in the heterozygous and dominant models. Furthermore, VDR (Taq1: rs731236) showed a decreased risk of lung cancer in the allelic, homozygous, and recessive models. Similarly, VDR (BsmI: rs1544410) had a positive effect on lung cancer risk when subjected to allelic and recessive models. Our meta-analysis revealed the lack of association of CYP2R1 (rs10741657), CYP27B1 (rs3782130), CYP27B1 (rs10877012), CYP24A1 (rs6068816), CYP24A1 (rs4809960), CYP3A5 (rs776746), GC (rs7041), GC (rs4588), and VDR (ApaI: rs7975232) with lung cancer. Our work revealed that CYP3A4 (rs2740574) can represent an independent risk factor for lung cancer. This conclusion can aid better personalized medicine for lung cancer management, while further assessment for genetic variants of CYP3A4, CYP27B1, CYP24A1, GC, and VDR is still required to address more robust evidence.
Histone Acetylation Enhancing Host Melanization in Response to Parasitism by an Endoparasitoid Wasp

Simple Summary Endoparasitic wasps are nature’s pest controllers, targeting various harmful insects. They lay their eggs inside these pests and release special substances (like viruses or venoms) that change the way the pest’s immune system works. However, we are still uncovering exactly how these changes happen. Our research looks into how certain wasps, which do not use these viruses, can still affect their host’s immune system. We studied this using a specific wasp–beetle pair as an example. We found that these wasps can control a crucial part of the beetle’s immune response through a process that modifies the beetle’s genetic material, specifically by adjusting certain markers on the genes that are important for immunity. This discovery sheds light on the sophisticated ways wasps can suppress the immune systems of their hosts, making them more effective at controlling pest populations. Abstract Endoparasitoids are insects that develop within other insects, employing unique strategies to enhance their offspring’s survival. They inject polydnavirus and/or venom into their hosts along with eggs, effectively suppressing the host’s immune system. Polydnavirus from Braconidae and Ichneumonidae wasps can integrate into the host’s genome to express viral genes using the host’s transcription systems. However, the ability of parasitoids without polydnavirus to manipulate host gene expression remains unclear. Lysine acetylation (LysAc), a post-translational modification critical for gene regulation, is hypothesized to be used by endoparasitoids lacking polydnavirus. We utilized the Chalcidoidea wasp Tetrastichus brontispae, which lacks polydnavirus, as an idiobiont endoparasitoid model to test this hypothesis, with pupae of the nipa palm hispid beetle Octodonta nipae as the host. Parasitism by T. brontispae resulted in the reduced expression of histone deacetylase Rpd3 and elevated levels of LysAc modification at histones H3.3K9 and H3.3K14 through proteomics and LysAc modification omics. The knockdown of Rpd3 increased the expression level of OnPPAF1 and OnPPO involved in the phenoloxidase cascade, leading to melanization in the host body whereby it resembled a mummified parasitized pupa and ultimately causing pupa death. This study enhances our understanding of how endoparasitoids employ histone acetylation to regulate immunity-related genes, offering valuable insights into their survival strategies.
CHANGES IN TEMPERATURE EXTREMES IN BOSNIA AND HERZEGOVINA: A FIXED THRESHOLDS-BASED INDEX ANALYSIS

The paper analyzes trends in the extreme temperature indices based on fixed thresholds in Bosnia and Herzegovina during the 1961–2016. Based on data from 12 meteorological stations, trends in both warm and cold temperature indices were determined using the nonparametric Mann-Kendall test and the nonparametric Sen’s slope estimator. The observed tendencies in indices based on fixed thresholds were as expected in a warming world – warm temperature indices (summer days, tropical days and tropical nights) displayed the significant positive trends, whereas cold temperature indices (icing days and frost days) showed the downward tendencies. The annual occurrence of summer days and tropical days increased on average for 5.3 and 4.8 days per decade, respectively, whereas icing days and frost days displayed downward trends in the range of -1.7 and -3.6 days per decade, respectively. The obtained results indicate that the climate system warming was more a result of very pronounced positive trends in the warm temperature indices than the downward tendency of cold ones. The most prominent changes were observed in Banja Luka, Bugojno and Zenica regions. Both trends, positive in warm indices and negative in cold ones, become more pronounced in the 1990s and particularly since the beginning of the 21 st century. Further research should focus on the assessment of the observed trends impacts on natural and socio-economic systems.
Unveiling the driving role of pH on community stability and function during lignocellulose degradation in paddy soil

Introduction Crop straw, a major by-product of agricultural production, is pivotal in maintaining soil health and preserving the ecological environment. While straw incorporation is widely recognized as a sustainable practice, the incomplete decomposition of crop residues poses challenges to plant growth, increasing the risk of pests and diseases. This necessitates a comprehensive investigation. Methods The current study employs a 28-day pot experiment to simulate the degradation of rice straw in paddy soils. The impacts of bioaugmentation and biostimulation on lignocellulose degradation are systematically evaluated. Results Results indicate a high lignocellulose degradation ability in paddy soil, with over 80% straw weight loss within 28 days. Bioaugmentation with a lignocellulolytic microbial consortium enhances straw degradation during the initial stage (0–14 days). In contrast, biostimulation with readily available nutrients leads to soil acidification, hindering straw degradation and reducing microbial diversity. Furthermore, pH emerges as a critical factor influencing microbial community stability and function during lignocellulose degradation. Microbial co-occurrence network analysis reveals that microorganisms occupy ecological niches associated with different cellulose components. Notably, Module M2, comprising Proteobacteria, Firmicutes, Gemmatimonadota, Actinobacteriota, Bacteroidota, Myxococcota, Halobacterota, and Acidobacteriota, positively correlates with pH and weight loss. Discussion This study significantly advances our understanding of microbial mechanisms in soil decomposition, emphasizing the pivotal role of pH in community stability and function in paddy soil. These findings can inform future strategies for managing rice straw while safeguarding soil ecosystem health.
Zooarchaeology of Cinnamon Bay, St. John, U.S. Virgin Islands: Pre-Columbian Overexploitation of Animal Resources

The zooarchaeological remains from a stratigraphic sequence excavated from the ceremonial site of Cinnamon Bay, St. John, U.S. Virgin Islands, were studied. The samples were recovered using a fine-gauge (1/16 in) screen. During the course of this study, 443 minimum numbers of individuals and 99 species of vertebrates and invertebrates were identified. The fauna was analyzed by estimating the trophic level of reef, inshore, and pelagic zooarchaeological components from three strata representing the Monserrate (ca. A.D. 950), Santa Elena (ca. A.D. 570), and Chican (ca. A.D. 460) ceramic periods. The trophic level model shows an initial increase in the trophic level of taxa from the reef between the Monserrate and Santa Elena periods. This initial increase corresponds to the exponential growth of midden density. Relative to the earlier faunal assemblages, midden density and the mean trophic level of reef resources declines during the Chican period. Greater reliance on pelagic species from the deeper waters offshore and the increased use of mollusks from inshore habitats is also seen. The data show that at low levels of cultural complexity humans can alter their environments. This is particularly true of island biota where biological reservoirs are small.
Schulisches Wohlbefinden am Übergang in die Sekundarstufe. Vertiefende Analysen zu bildungsbenachteiligten Schüler:innen

Schulisches Wohlbefinden dient als kognitive und emotionale Ressource, um schulische Anforderungen erfolgreich bewältigen zu können, und rückt seit geraumer Zeit immer mehr in den Fokus. Am Übergang von der Primar- in die Sekundarstufe müssen sich Schüler:innen an die neue Lernumwelt anpassen und ihre sozialen Beziehungen zu Lehrkräften und Gleichaltrigen neu gestalten. Dies gelingt jedoch nicht allen Schüler:innen gleichermaßen. In der vorzustellenden Studie wurde basierend auf Daten des Nationalen Bildungspanels (NEPS, Startkohorte Kindergarten) die Entwicklung des schulischen Wohlbefindens am Übergang in die Sekundarstufe (4. auf 5. Klasse) analysiert. Zusätzlich wurde untersucht, ob verschiedene Benachteiligungsmerkmale (z. B. Strukturmerkmal Bildungshintergrund, Prozessmerkmal elterliche Unterstützung) einen Effekt auf den Ausgangswert und die Veränderung des schulischen Wohlbefindens aufweisen. Ergebnisse latenter Wachstumskurvenmodelle (N = 2737) zeigten im Mittel eine Zunahme des schulischen Wohlbefindens am Übergang. Zusätzlich konnte ein positiver Effekt der elterlichen Bildungsaspiration und des Bildungshintergrunds auf den Ausgangswert des schulischen Wohlbefindens beobachtet werden. Allerdings liefern die Befunde keine Hinweise auf systematische Unterschiede zwischen bildungsbenachteiligten und nicht benachteiligten Kindern.
Estimations of the Geothermal Energy Potential in The Mount Anak Krakatau Region Based on Derivative Analysis and 3D Model of Gravitational Satellite Data

Geothermal energy is a source of renewable energy that has the potential to be produced, considering that Indonesia is in the ring of fire, where there are many volcanoes, one of which is Mount Anak Krakatau. Even though direct exploration is not permitted, at least information on the geothermal system on the mountain can still be obtained using satellite data. Therefore, this study aims to analyze the geothermal energy potential of Mount Anak Krakatau using gravity satellite data with a total of 320 data consisting of gravity disturbance, geoid, and Digital Elevation Model. The data processing describes a 3D model that is correlated with the First Horizontal Derivative (FHD) and Second Vertical Derivative (SVD) analysis. Based on the results of the residual anomaly map analysis, the low anomaly has a value of -1.85–(-0.89) mGal which is suspected to be associated with magma pockets, and the high anomaly ranges from 0.04–2.13 mGal which is suspected to be associated with the caldera of Mount Anak Krakatau. Based on the results of the FHD and SVD graphical analysis, there are 18 faults that control the geothermal system. Based on the results of 3D modeling trending from west-east it can be seen that there is a clay cap layer with a value density 2.32–2.37 gr/cc at depths of 0–550 m and reservoir layers with density values of 2.23–2.29 gr/cc at depths of 500–1100 m. This geothermal research using the gravity method can be developed and become a reference for future research to calculate the potential for electrification in a research area.
Can Brain Volume-Driven Characteristic Features Predict the Response of Alzheimer’s Patients to Repetitive Transcranial Magnetic Stimulation? A Pilot Study

This study is a post-hoc examination of baseline MRI data from a clinical trial investigating the efficacy of repetitive transcranial magnetic stimulation (rTMS) as a treatment for patients with mild–moderate Alzheimer’s disease (AD). Herein, we investigated whether the analysis of baseline MRI data could predict the response of patients to rTMS treatment. Whole-brain T1-weighted MRI scans of 75 participants collected at baseline were analyzed. The analyses were run on the gray matter (GM) and white matter (WM) of the left and right dorsolateral prefrontal cortex (DLPFC), as that was the rTMS application site. The primary outcome measure was the Alzheimer’s disease assessment scale—cognitive subscale (ADAS-Cog). The response to treatment was determined based on ADAS-Cog scores and secondary outcome measures. The analysis of covariance showed that responders to active treatment had a significantly lower baseline GM volume in the right DLPFC and a higher GM asymmetry index in the DLPFC region compared to those in non-responders. Logistic regression with a repeated five-fold cross-validated analysis using the MRI-driven features of the initial 75 participants provided a mean accuracy of 0.69 and an area under the receiver operating characteristic curve of 0.74 for separating responders and non-responders. The results suggest that GM volume or asymmetry in the target area of active rTMS treatment (DLPFC region in this study) may be a weak predictor of rTMS treatment efficacy. These results need more data to draw more robust conclusions.
Review of Recent Research Directions and Practical Implementation of Low-Frequency Algorithmic Trading

Financial trading has undergone substantial technological evolution, with automation taking center stage, leading to approximately 80% of US market trades being executed by computer systems, predominantly by large financial institutions. The rise of algorithmic trading, poised to engage smaller entities, international markets, and individual traders, drives this article’s exploration of research in this field. Providing a comprehensive overview, it outlines the evolution of trading practices and defines algorithmic trading as a computer-powered tool aiding investment decisions. The article details the steps involved in algorithmic trading, covering opportunity identification, quantitative research, implementation, testing phases, and continuous monitoring. It also examines prevalent programming languages and open-source platforms facilitating algorithm development. Focusing on trading frequencies across financial instruments, it delves into high-frequency trading as a subset, alongside methodologies like technical and fundamental analysis, time series analysis, option trading strategies, and machine learning techniques used in algorithm creation. Categorized by trading frequencies, analytical approaches, involved financial instruments, and analysis objectives, the reviewed papers contribute insights into algorithmic trading’s diverse landscape and methodologies, offering valuable perspectives for industry participants and researchers alike.
Alternative splicing of pre-mRNA modulates the immune response in Holstein cattle naturally infected with Mycobacterium avium subsp. paratuberculosis

Little is known about the role of alternative splicing (AS) in regulating gene expression in Mycobacteria-infected individuals in distinct stages of infection. Pre-mRNA AS consists of the removal of introns and the assembly of exons contained in eukaryotic genes. AS events can influence transcript stability or structure with important physiological consequences. Using RNA-Seq data from peripheral blood (PB) and ileocecal valve (ICV) samples collected from Holstein cattle with focal and diffuse paratuberculosis (PTB)-associated histopathological lesions in gut tissues and without lesions (controls), we detected differential AS profiles between the infected and control groups. Four of the identified AS events were experimentally validated by reverse transcription-digital droplet PCR (RT-ddPCR). AS events in several genes correlated with changes in gene expression. In the ICV of animals with diffuse lesions, for instance, alternatively spliced genes correlated with changes in the expression of genes involved in endocytosis, antigen processing and presentation, complement activation, and several inflammatory and autoimmune diseases in humans. Taken together, our results identified common mechanisms of AS involvement in the pathogenesis of PTB and human diseases and shed light on novel diagnostic and therapeutic interventions to control these diseases.
Genomic Insights into Moderately Thermophilic Methanotrophs of the Genus Methylocaldum

Considering the increasing interest in understanding the biotic component of methane removal from our atmosphere, it becomes essential to study the physiological characteristics and genomic potential of methanotroph isolates, especially their traits allowing them to adapt to elevated growth temperatures. The genetic signatures of Methylocaldum species have been detected in many terrestrial and aquatic ecosystems. A small set of representatives of this genus has been isolated and maintained in culture. The genus is commonly described as moderately thermophilic, with the growth optimum reaching 50 °C for some strains. Here, we present a comparative analysis of genomes of three Methylocaldum strains—two terrestrial M. szegediense strains (O-12 and Norfolk) and one marine strain, Methylocaldum marinum (S8). The examination of the core genome inventory of this genus uncovers significant redundancy in primary metabolic pathways, including the machinery for methane oxidation (numerous copies of pmo genes) and methanol oxidation (duplications of mxaF, xoxF1-5 genes), three pathways for one-carbon (C1) assimilation, and two methods of carbon storage (glycogen and polyhydroxyalkanoates). We also investigate the genetics of melanin production pathways as a key feature of the genus.
Distributed agency in HRI—an exploratory study of a narrative robot design

We explore an alternative approach to the design of robots that deviates from the common envisionment of having one unified agent. What if robots are depicted as an agentic ensemble where agency is distributed over different components? In the project presented here, we investigate the potential contributions of this approach to creating entertaining and joyful human-robot interaction (HRI), which also remains comprehensible to human observers. We built a service robot—which takes care of plants as a Plant-Watering Robot (PWR)—that appears as a small ship controlled by a robotic captain accompanied by kinetic elements. The goal of this narrative design, which utilizes a distributed agency approach, is to make the robot entertaining to watch and foster its acceptance. We discuss the robot’s design rationale and present observations from an exploratory study in two contrastive settings, on a university campus and in a care home for people with dementia, using a qualitative video-based approach for analysis. Our observations indicate that such a design has potential regarding the attraction, acceptance, and joyfulness it can evoke. We discuss aspects of this design approach regarding the field of elderly care, limitations of our study, and identify potential fields of use and further scopes for studies.
Comparison of 3DVar and EnSRF Data Assimilation Using Radar Observations for the Analysis and Prediction of an MCS

Using radar observations, the performances of the ensemble square root filter (EnSRF) and an indirect three-dimensional variational (3DVar) data assimilation method were compared for a mesoscale convective system (MCS) that occurred in the Front Range of the Rocky Mountains, Colorado (USA). The results showed that the root mean square innovations (RMSIs) of EnSRF were lower than 3DVar for radar reflectivity and radial velocity and that the spread of EnSRF was generally consistent with its RMSIs. EnSRF substantially improved the analysis of the MCS compared with an experiment without radar data assimilation, and it produced a slight but noticeable improvement over 3DVar in terms of both coverage and intensity. Forecast results initiated from the final analysis revealed that EnSRF generally produced the best prediction of the MCS, with improved quantitative reflectivity and precipitation forecast skills. EnSRF also demonstrated better performance than 3DVar in the prediction of neighborhood probability for reflectivity at thresholds of 20 and 35 dBZ, which better matched the observed radar reflectivity in terms of both shape and extension. Additionally, the humidity, temperature, and wind fields were also improved by EnSRF; the largest error reduction was found in the water vapor field near the surface and at upper levels.
Comprehensive Co-Inhibitory Receptor (Co-IR) Expression on T Cells and Soluble Proteins in Rheumatoid Arthritis

Co-inhibitory receptors (Co-IRs) are essential in controlling the progression of immunopathology in rheumatoid arthritis (RA) by limiting T cell activation. The objective of this investigation was to determine the phenotypic expression of Co-IR T cells and to assess the levels of serum soluble PD-1, PDL-2, and TIM3 in Taiwanese RA patients. Methods: Co-IRs T cells were immunophenotyped employing multicolor flow cytometry, and ELISA was utilized for measuring soluble PD-1, PDL-2, and TIM3. Correlations have been detected across the percentage of T cells expressing Co-IRs (MFI) and different indicators in the blood, including ESR, high-sensitivity CRP (hsCRP), 28 joint disease activity scores (DAS28), and soluble PD-1/PDL-2/TIM3. Results: In RA patients, we recognized elevated levels of PD-1 (CD279), CTLA-4, and TIGIT in CD4+ T cells; TIGIT, HLA-DR, TIM3, and LAG3 in CD8+ T cells; and CD8+CD279+TIM3+, CD8+HLA-DR+CD38+ T cells. The following tests were revealed to be correlated with hsCRP: CD4/CD279 MFI, CD4/CD279%, CD4/TIM3%, CD8/TIM3%, CD8/TIM3 MFI, CD8/LAG3%, and CD8+HLA-DR+CD38+%. CD8/LAG3 and CD8/TIM3 MFIs are linked to ESR. DAS28-ESR and DAS28-CRP exhibited relationships with CD4/CD127 MFI, CD8/CD279%, and CD8/CD127 MFI, respectively. CD4+CD279+TIM3+% was correlated with DAS28-ESR (p = 0.0084, N = 46), DAS28-CRP (p = 0.007, N = 47), and hsCRP (p = 0.002, N = 56), respectively. In the serum of patients with RA, levels of soluble PD-1, PDL-2, and Tim3 were extremely elevated. CD4+ TIM3+% (p = 0.0089, N = 46) and CD8+ TIM3+% (p = 0.0305, N = 46) were correlated with sTIM3 levels; sPD1 levels were correlated with CD4+CD279+% (p < 0.0001, N = 31) and CD3+CD279+% (p = 0.0084, N = 30). Conclusions: Co-IR expressions on CD4+ and CD8+ T cells, as well as soluble PD-1, PDL-2, and TIM3 levels, could function as indicators of disease activity and potentially play crucial roles in the pathogenesis of RA.