Miracle-dz/UniFAR-FTUs huggingface dataset:
Contrasting Responses of Rhizosphere Bacteria, Fungi and Arbuscular Mycorrhizal Fungi Along an Elevational Gradient in a Temperate Montane Forest of China

Elevational gradients strongly affect microbial biodiversity in bulk soil through altering plant and soil properties, but the effects on rhizosphere microbial patterns remain unclear, especially at large spatial scales. We therefore designed an elevational gradient experiment to examine rhizosphere microbial (bacteria, fungi and arbuscular mycorrhizal fungi) diversity and composition using Illumina sequencing of the 16S rRNA and ITS genes for comparison to plant and soil properties. Our results showed that bacterial and fungal alpha diversity was significantly higher at mid-elevation, while AMF alpha diversity decreased monotonically. The beta diversities of the three groups were significantly affected by elevational gradients, but the effect on bacterial beta diversity was larger than on fungal and AMF beta diversity. Proteobacteria, the dominant phyla of bacteria, was significantly higher at the mid-elevation, while Acidobacteria and Actinobacteria significantly decreased as elevation increased. The main fungal taxa, Basidiomycota, significantly decreased with elevation, and Ascomycota significantly increased with elevation. Glomeromycota, the dominant AMF phyla, responded insignificantly to the elevational gradients. The responses of bacterial and fungal alpha diversity were mostly associated with tree diversity and organic carbon, whereas AMF alpha diversity mainly depended on litter N and P. Changes in bacterial community composition along the elevational gradient were explained primarily by litter N and P, and litter P was the main driver of fungal and AMF community composition. Overall, our results suggest that plant litter, particularly litter N and P, were the main source of external carbon input and drove the observed differences in rhizosphere microbial diversity and community composition. Our results highlight the importance of litter nutrition in structuring rhizosphere microbial communities in mountain ecosystems.
Direct and indirect effects of parental involvement, deviant peer affiliation, and school connectedness on prosocial behaviors in U.S. Latino/a youth

Parental involvement has been associated with increased adolescent prosocial behaviors, but we know little about the peer and school-level explanatory mechanisms behind these associations. The current study aimed to examine the intervening roles of deviant peer affiliation and school connectedness in links between parental involvement and prosocial behaviors among U.S. Latino/a adolescents. Participants included 306 U.S. Latino/a adolescents (Mage = 15.50 years, SD = .42 years, 46% girls, 81.0% U.S. Mexican) from communities in the Northern Great Plains, who reported on parental involvement, deviant peer affiliation, school connectedness, and prosocial behaviors. Path analyses showed that parental involvement was directly and indirectly related to prosocial behaviors via both deviant peer affiliation and school connectedness. Parental involvement was related to lesser deviant peer affiliation, which was in turn related to greater school connectedness, which was further related to higher prosocial behaviors. The discussion focuses on the importance of studying the interplay of parent, peer, and school factors in understanding prosocial behaviors among U.S. Latino/a youth.
Fabrication of Indomethacin-Loaded Polyvinyl Alcohol Filaments through Hot-Melt Extrusion

The main objective of this study was to prepare the drug-loaded filament by hot-melt extrusion technique. Indomethacin (IND) was used as a model drug and polyvinyl alcohol (PVA) was used to produce the filament. The IND-PVA filament had clear yellow color and rough surface. Drug loading in the filament that was determined from three segments of the filament was similar, indicating that IND was homogeneously distributed in the filament.This finding was confirmed by differential scanning calorimetry and powder X-ray diffraction. In addition, thermogravimetric analysis data suggested that the drug and polymer were not degraded at temperature used in extrusion process. The filament could be further developed as dosage form or applied as starting material for 3D-printed dosage forms.
SIndex: a scalable learned index for string keys

The learned index structures have reshaped our perspectives on the design of traditional data structures. With machine learning (ML) techniques, they can achieve better lookup performance than existing indexes. However, current learned indexes primarily focus on integer-key workloads and failed to efficiently index variable-length string keys. We introduce SIndex, a concurrent learned index specialized in variable-length string key workloads. To reduce the cost of model inference and data accesses, SIndex groups keys with shared prefixes and use each key's unique part for model training. We evaluate SIndex with both real-world and synthesized datasets. The result shows that SIndex can achieve up to 91% better performance compared with other state-of-the-art index structures. We have open-sourced our implementation1.
Infrared Spectrometry as a High-Throughput Phenotyping Technology to Predict Complex Traits in Livestock Systems

High-throughput phenotyping technologies are growing in importance in livestock systems due to their ability to generate real-time, non-invasive, and accurate animal-level information. Collecting such individual-level information can generate novel traits and potentially improve animal selection and management decisions in livestock operations. One of the most relevant tools used in the dairy and beef industry to predict complex traits is infrared spectrometry, which is based on the analysis of the interaction between electromagnetic radiation and matter. The infrared electromagnetic radiation spans an enormous range of wavelengths and frequencies known as the electromagnetic spectrum. The spectrum is divided into different regions, with near- and mid-infrared regions being the main spectral regions used in livestock applications. The advantage of using infrared spectrometry includes speed, non-destructive measurement, and great potential for on-line analysis. This paper aims to review the use of mid- and near-infrared spectrometry techniques as tools to predict complex dairy and beef phenotypes, such as milk composition, feed efficiency, methane emission, fertility, energy balance, health status, and meat quality traits. Although several research studies have used these technologies to predict a wide range of phenotypes, most of them are based on Partial Least Squares (PLS) and did not considered other machine learning (ML) techniques to improve prediction quality. Therefore, we will discuss the role of analytical methods employed on spectral data to improve the predictive ability for complex traits in livestock operations. Furthermore, we will discuss different approaches to reduce data dimensionality and the impact of validation strategies on predictive quality.
Breeding Biology of the Bridled Tern Sterna Anaethetus

Features of breeding Bridled Terns can be considered as either anti-predator or other adaptations. Each anti-predator feature acting by itself or with others can decrease the likelihood of gulls preying on eggs and/or chicks. Anti-predator features include nesting under cover, dispersion of nests, cryptic colour of eggs and chicks, behaviour of ohicks and adults, defeacating away from the nest and fast initial growth of chicks. However, other features can increase the likelihood of gulls preying on young. These include asynchronous laying and hatching and not removing egg shells from nests. Breeding success of Bridled Terns at One Tree Island, Great Barrier Reef was high because: (1) predation on their eggs and chicks was lower than on those of other terns, (2) their ability to fast for longer periods than, for example, Crested Tern Sterna bergii chicks buffered them from the effects of cyclonic weather. Growth rate of Bridled chicks may depend on the ability of, and the effort made by, their parents to transport food to them as well as the nutrient composition of their diet. We suggest that dietary differences are responsible for dif- ferences in the timing of adults' moulting in the Seychelles and Australia.
Differential Effects of K+ and Na+ on Oxygen Evolution Activity of Photosynthetic Membranes from Two Halophytes and Spinach

KCl reduced oxygen evolution by Sarcocornia quinqueflora thylakoids to well below the level of activity in the presence of NaCI. This inhibition occurred at both high and low pH. On the other hand, both KCl and NaCl induced almost indistinguishable effects on oxygen evolution in spinach thylakoids. Photosystem (PS) Il membranes from Avicennia marina showed a similar inhibition of oxygen evolution by KCl to S. quinqueflora thylakoids, but spinach PS Il particles were not inhibited by KCl. The KCl inhibition of oxygen evolution of halophytic thylakoids was localised to the oxygen-evolving complex and required little KCl, as significant inhibition occurred with only 25 mM. K2SO4 was also inhibitory, but Na2SO4 was not, indicating that K+ was the inhibitory ion. Na2SO4 was partly able to reverse this inhibition caused by KCl, suggesting the inhibition to be a function of the K+ /Na+ ratio. These results have implications concerning the ionic relations of the leaf cells of halophytes.
Matrix Metallopeptidase 14: A Candidate Prognostic Biomarker for Diffuse Large B-Cell Lymphoma

Background Matrix metallopeptidase 14 (MMP14) is an important gene in the regulation of T-cell function. However, the correlation between MMP14 expression, prognosis, and immune cell infiltration in diffuse large B-cell lymphoma (DLBCL) remains unclear. Methods We investigated the influence of MMP14 on clinical prognosis using data obtained from three Gene Expression Omnibus (GEO) database sets (GSE98588, GSE10846, and GSE4475). The expression of MMP14 was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA). The correlation between MMP14 and immune cell infiltration was investigated using the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and Tumor Immune Estimation Resource (TIMER) tools. In addition, the correlation between MMP14 expression and immune gene markers was analyzed by TIMER and GEPIA. Results MMP14 expression positively correlated with favorable progression-free survival (PFS; GSE98588, P = 0.02) and overall survival (OS; GSE98588, P = 0.003; GSE10846, P = 5.517e-05; and GSE4475, P = 9.85e-04). Moreover, MMP14 expression was higher in DLBCL tumors than in normal tissues. Regarding clinical characteristics, high MMP14 expression was found to be correlated with race. MMP14 expression was also correlated with immune cell infiltration and had a remarkable correlation with various immune marker sets. It was found that M0 macrophages were the immune cells most related to survival, decreasing with the increase in Ann Arbor clinical stage. The results especially showed that MMP14 was a prognostic biomarker and related to the macrophages M0. Conclusion The results suggest that MMP14 is a novel prognostic molecular marker for DLBCL and is related to the immune cell infiltration, especially related to the macrophages M0. Our study provides insights for understanding the potential roles of MMP14 in tumor immunology and its suitability as a prognosis biomarker in DLBCL.
Non-alcoholic Fatty Liver Disease and Alcohol-Related Liver Disease: Two Intertwined Entities

Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease worldwide, with a prevalence of 25–30%. Since its first description in 1980, NAFLD has been conceived as a different entity from alcohol-related fatty liver disease (ALD), despite that, both diseases have an overlap in the pathophysiology, share genetic–epigenetic factors, and frequently coexist. Both entities are characterized by a broad spectrum of histological features ranging from isolated steatosis to steatohepatitis and cirrhosis. Distinction between NAFLD and ALD is based on the amount of consumed alcohol, which has been arbitrarily established. In this context, a proposal of positive criteria for NAFLD diagnosis not considering exclusion of alcohol consumption as a prerequisite criterion for diagnosis had emerged, recognizing the possibility of a dual etiology of fatty liver in some individuals. The impact of moderate alcohol use on the severity of NAFLD is ill-defined. Some studies suggest protective effects in moderate doses, but current evidence shows that there is no safe threshold for alcohol consumption for NAFLD. In fact, given the synergistic effect between alcohol consumption, obesity, and metabolic dysfunction, it is likely that alcohol use serves as a significant risk factor for the progression of liver disease in NAFLD and metabolic syndrome. This also affects the incidence of hepatocellular carcinoma. In this review, we summarize the overlapping pathophysiology of NAFLD and ALD, the current data on alcohol consumption in patients with NAFLD, and the effects of metabolic dysfunction and overweight in ALD.
Profiling Detection and Classification of Lameness Methods in British Dairy Cattle Research: A Systematic Review and Meta-Analysis

Lameness is a serious concern in the dairy sector, reflecting its high incidence and impact on animal welfare and productivity. Research has provided figures on its frequency using different methodologies, making it difficult to compare results and hindering farm-level decision-making. The study's objectives were to determine the frequency levels of lameness in British dairy cattle through a meta-analysis approach, and to understand the chronological patterns of how lameness cases are detected and classified in scientific research. A systematic review was conducted using PRISMA-P guidelines for article selection. Random-effects models estimated the pooled frequency measure of lameness with heterogeneity managed through subgroup analysis and meta-regression. Sixty-eight papers were identified, 50 included prevalence and 36 incidence data. The pooled prevalence of lameness in British dairy cattle was estimated at 29.5% (95% CI 26.7–32.4%) whilst all-cause lameness incidence rate indicated 30.9 cases of lameness per 100 cow-years (95% CI 24.5–37.9). The pooled cause-specific lameness incidence rate per 100 cow-years was 66.1 (95% CI 24.1–128.8) for white line disease, 53.2 (95% CI 20.5–101.2) for sole ulcer, 53.6 (95% CI 19.2–105.34) for digital dermatitis, with 51.9 (95% CI 9.3–129.2) attributable to other lameness-related lesions. Heterogeneity levels remained high. Sixty-nine papers contributed to a chronological overview of lameness data source. Although the AHDB Dairy mobility scoring system (MSS) was launched in the UK in 2008 and adopted shortly after by the British Dairy sector as the standard tool for assessing lameness, other methods are used depending on the investigator. Automated lameness detection systems may offer a solution for the subjective nature of MSSs, yet it was utilized in one study only. Despite the recognition of under-reporting of lameness from farm records 22 (31.9%) studies used this data source. The diversity of lameness data collection methods and sources was a key finding. It limits the understanding of lameness burden and the refinement of policy making for lameness. Standardizing case definition and research methods would improve knowledge of and ability to manage lameness. Regardless of the measurement method lameness in British dairy cattle is high.
Pornography use and romantic relationships: A dyadic daily diary study

Pornography use is now considered a normative sexual activity, including for partnered individuals. Although there are documented positive and negative effects of pornography use on romantic relationships, studies to date suffer from key limitations, narrowing their clinical relevance. Most rely on vague recall measurement that may inadequately capture actual pornography use, and all are exclusively based on mixed-sex couples. This study used a 35-day dyadic daily diary design to examine the associations between an individual’s daily pornography use and their own and their partner’s relationship satisfaction, partnered sexual desire, and probability of partnered sexual activity in mixed-sex and same-sex couples (N = 217 couples). For women, regardless of partner’s sex, using pornography was associated with their own and their partner’s higher sexual desire and with higher odds of partnered sexual activity. For men, regardless of partner’s sex, using pornography was associated with their partner’s lower sexual desire; for men coupled with women, with lower odds of partnered sexual activity, and for men coupled with men, with higher odds of partnered sexual activity. For all participants, pornography use was unrelated to relationship satisfaction. The current study demonstrated that an individual’s pornography use is associated with same-day couple’s sexual dynamics, with different associations according to users’ and their partners’ sex.
Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure

Changes in chromatin structure, especially in histone modifications (HMs), linked with chromatin accessibility for transcription machinery, are considered to play significant roles in transcriptional regulation. Alveolar macrophages (AM) are important immune cells for protection against pulmonary pathogens, and must readily respond to bacteria and viruses that enter the airways. Mechanism(s) controlling AM innate response to different pathogen-associated molecular patterns (PAMPs) are not well defined in pigs. By combining RNA sequencing (RNA-seq) with chromatin immunoprecipitation and sequencing (ChIP-seq) for four histone marks (H3K4me3, H3K4me1, H3K27ac and H3K27me3), we established a chromatin state map for AM stimulated with two different PAMPs, lipopolysaccharide (LPS) and Poly(I:C), and investigated the potential effect of identified histone modifications on transcription factor binding motif (TFBM) prediction and RNA abundance changes in these AM. The integrative analysis suggests that the differential gene expression between non-stimulated and stimulated AM is significantly associated with changes in the H3K27ac level at active regulatory regions. Although global changes in chromatin states were minor after stimulation, we detected chromatin state changes for differentially expressed genes involved in the TLR4, TLR3 and RIG-I signaling pathways. We found that regions marked by H3K27ac genome-wide were enriched for TFBMs of TF that are involved in the inflammatory response. We further documented that TF whose expression was induced by these stimuli had TFBMs enriched within H3K27ac-marked regions whose chromatin state changed by these same stimuli. Given that the dramatic transcriptomic changes and minor chromatin state changes occurred in response to both stimuli, we conclude that regulatory elements (i.e. active promoters) that contain transcription factor binding motifs were already active/poised in AM for immediate inflammatory response to PAMPs. In summary, our data provides the first chromatin state map of porcine AM in response to bacterial and viral PAMPs, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the role of HMs, especially H3K27ac, in regulating transcription in AM in response to LPS and Poly(I:C).
Microbial Communities of the Shallow-Water Hydrothermal Vent Near Naples, Italy, and Chemosynthetic Symbionts Associated With a Free-Living Marine Nematode

Shallow-water hydrothermal vents are widespread, especially in the Mediterranean Sea, owing to the active volcanism of the area. Apart free microbial communities’ investigations, few biological studies have been leaded yet. Investigations of microbial communities associated with Nematoda, an ecologically important group in sediments, can help to improve our overall understanding of these ecosystems. We used a multidisciplinary-approach, based on microscopic observations (scanning electron microscopy: SEM and Fluorescence In Situ Hybridization: FISH) coupled with a molecular diversity analysis using metabarcoding, based on the 16S rRNA gene (V3-V4 region), to characterize the bacterial community of a free-living marine nematode and its environment, the shallow hydrothermal vent near Naples (Italy). Observations of living bacteria in the intestine (FISH), molecular and phylogenetic analyses showed that this species of nematode harbors its own bacterial community, distinct from the surrounding sediment and water. Metabarcoding results revealed the specific microbiomes of the sediment from three sites of this hydrothermal area to be composed mainly of sulfur oxidizing and reducing related bacteria.
A sport-specific optimization approach to mental wellness for youth in low-income neighborhoods

Psychiatric disorders, particularly substance use disorders, are an impactful and highly prevalent public health concern in youth from low-income neighborhoods (YLINs). Indeed, prevention and intervention programs for mental health disorders that have evidenced improvements in youth from general population are not well integrated into community resources of YLINs and appear to be a poor fit for YLINs. Along this vein, experts have indicated there is an immediate need to empirically refine existing evidence-based mental health programs to be less stigmatizing, more culturally sensitive, relevant, and engaging for YLINs. To assist in addressing this need, we describe an innovative sport-specific optimization approach to mental wellness that is tailored for use in YLINs. Derived from Family Behavior Therapy, The Optimum Performance Programme in Sports (TOPPS) was developed to be implemented within the umbrella of well-established sport organizations that are accepted within low-income communities (e.g. YMCA, Boys & Girls Club) or primary and secondary school systems. TOPPS is designed to address both prevention and intervention of mental health disorders through a focus on overall wellness and sport performance, and incorporation of engagement methods, significant others, sport/physical education, and evidence-supported methods of addressing culture. Given the absence of sport-specific mental health intervention for youth, TOPPS may be appropriate in this population. However, formal evaluation of TOPPS in youth samples is warranted.