Miracle-dz/UniFAR-FTUs huggingface dataset:
Gastroesophageal reflux and PPI exposure alter gut microbiota in very young infants

Importance Infants with symptomatic Gastroesophageal reflux are treated with pharmacological therapy that includes proton pump inhibitors (PPI) with clinical improvement. The alterations to gut microbiome profiles in comparison to infants without reflux is not known. Objective To determine the effect of PPI therapy on gut bacterial richness, diversity, and proportions of specific taxa in infants when compared to infants not exposed to acid suppressive therapy. Design, setting, and participants This cohort study was conducted at the Stony Brook Hospital in Stony Brook, NY between February 2016, and June 2019. Infants meeting inclusion criteria were enrolled in a consecutive fashion. Results A total of 76 Infants were recruited and 60 were enrolled in the study, Twenty nine infants met clinical criteria for reflux and were treated with PPI therapy: median [IQR] gestation: 38.0 weeks [34.7–39.6 weeks]; median [IQR] birthweight: 2.95 Kg [2.2–3.4]; 14 [46.7%] male) and 29 infant were healthy controls median [IQR] gestation: 39.1 weeks [38–40 weeks]; median [IQR] birthweight: 3.3 Kg [2.2–3.4]; 17 [58.6%] male); 58 stool samples from 58 infants were analyzed. There were differences in Shannon diversity between the reflux and control groups. The reflux group that was exposed to PPI therapy had increased relative abundance of a diverse set of genera belonging to the phylum Firmicutes. On the other hand, the control group microbiota was dominated by Bifidobacterium, and a comparatively lower level of enrichment and abundance of microbial taxa was observed in this group of infants. Conclusions and relevance We observed significant differences in both α- and β-diversity of the microbiome, when the two groups of infants were compared. The microbiome in the reflux group had more bacterial taxa and the duration of PPIs exposure was clearly associated with the diversity and abundance of gut microbes. These findings suggest that PPI exposure among infants results in early enrichment of the intestinal microbiome.
Histopathological and Molecular Analyses of Leptospira borgpetersenii and Leptospira interrogans in Bovine Kidneys in Kota Bharu, Kelantan, Malaysia

Leptospirosis is a zoonotic bacterial disease affecting both humans and animals. This is the first study aiming to detect the Leptospira spp. in bovine kidneys collected from selected wet markets in Kota Bharu, Kelantan and subsequently determine the predominant Leptospira species. Additionally, the pathological alterations to the bovine kidneys as a result of leptospirosis were also analyzed. A total of fifty bovine kidney samples (n=50) were collected from four wet markets within Kota Bharu town and the samples were tested using a polymerase chain reaction (PCR) assay. From the results, thirteen samples (n=13; 26%) were found to be positive for the 16S rRNA gene. DNA sequencing of the positive samples revealed the presence of Leptospira borgpetersenii (n=11) and Leptospira interrogans (n=1), which are known to be pathogenic Leptospira species in cattle and humans. One sample cannot be sequenced due to poor yield and quality. Furthermore, the kidneys that were PCR-positive showed significant histopathological lesions of bovine leptospirosis, consisting of interstitial nephritis, glomerular atrophy and tubular necrosis. In conclusion, the present study demonstrated the presence of L. borgpetersenii and L. interrogans in local cattle and this is an indisputable public health risk to the public considering that the samples were obtained from the local wet markets.
Pesticides affecting the diversity of pollinator insects in cocoa plantations (Theobroma cacao L.)

Pollinating insects play a significant role in the pollination process of cocoa flowers because unpollinated cocoa flowers will fall within 24 hours and fail to develop into fruit and seeds; on the other hand, the presence of pollinators in cacao plants is influenced by cultivation techniques such as the use of pesticides to against pest and disease attacks. This study aims to determine the diversity of pollinating insects in cacao plantations with and without pesticides. The study included field research on cocoa plantations in Rahmat Village, Palolo Sub-district, Sigi Regency. Insect identification was carried out at the Plant Pests and Diseases Laboratory, Faculty of Agriculture, Tadulako University, Palu. Sampling was carried out in 3 plots measuring 40×40 m² with treatments: application of Chlormite 505 EC insecticide at a dose of 20ml/15L water, Lamda Cyhalothrin 247 ZC insecticide at an amount of 10ml/15L water, and control. In each plot, ten trees were selected for observation. Insect pollinators and flower visitors were collected using yellow pant traps and direct observation. The results of this study found six species of pollinator insects, namely Forcipomyia sp. and Bactrocera sp. from the order Diptera, Lasius niger, Solenopsis invica, and Vespidae from the order Hymenoptera, and Melantis sp. from the order Lepidoptera. Insecticide application affects pollinating insect diversity.
ANOMALY DETECTION AND COMPARATIVE ANALYSIS OF HYDROTHERMAL ALTERATION MATERIALS TROUGH HYPERSPECTRAL MULTISENSOR DATA IN THE TURRIALBA VOLCANO

The aim of this work is the comparative study of the presence of hydrothermal alteration materials in the Turrialba volcano (Costa Rica) in relation with computed spectral anomalies from multitemporal and multisensor data adquired in spectral ranges of the visible (VIS), short wave infrared (SWIR) and thermal infrared (TIR). We used for this purposes hyperspectral and multispectral images from the HyMAP and MASTER airborne sensors, and ASTER and Hyperion scenes in a period between 2002 and 2010. Field radiometry was applied in order to remove the atmospheric contribution in an empirical line method. HyMAP and MASTER images were georeferenced directly thanks to positioning and orientation data that were measured at the same time in the acquisition campaign from an inertial system based on GPS/IMU. These two important steps were allowed the identification of spectral diagnostic bands of hydrothermal alteration minerals and the accuracy spatial correlation. Enviromental impact of the volcano activity has been studied through different vegetation indexes and soil patterns. Have been mapped hydrothermal materials in the crater of the volcano, in fact currently active, and their surrounding carrying out a principal components analysis differentiated for a high and low absorption bands to characterize accumulations of kaolinite, illite, alunite and kaolinite+smectite, delimitating zones with the presence of these minerals. Spectral anomalies have been calculated on a comparative study of methods pixel and subpixel focused in thermal bands fused with high-resolution images. Results are presented as an approach based on expert whose main interest lies in the automated identification of patterns of hydrothermal altered materials without prior knowledge or poor information on the area.
Caddisflies (Trichoptera) of Protected Calcareous Fen Habitats: Assemblages, Environmental Drivers, Indicator Species, and Conservation Issues

Simple Summary Calcareous fens, a unique and endangered type of peatland, harbour unique groups of little-studied aquatic insects. Caddisflies (Trichoptera), an amphibiotic insect group, have proven to be useful (at different levels of organisation) in describing various aspects of fens and their water bodies (pools and ditches). We focused on the evaluation of indicator species and the most important patterns and drivers of species distribution. A comprehensive approach including species, assemblages, functional groups, and ecological indices was recommended. In general, our findings provide a solid basis for analysing the potential of caddisflies in such habitats and present some useful tips for conservation practices and the management of these vulnerable ecosystems. Abstract The caddisflies (Trichoptera) of calcareous fen habitats, in contrast to those of other peatland types, have been poorly researched. We thus conducted a two-year study in south-eastern Poland encompassing four types of such habitats—drained and undrained fens and water bodies (pools and ditches) located within the fens—in order to define trichopteran reference assemblages (PCoA), indicator species (IndVal analysis), and the drivers (both natural and those associated with landscape management, including area protection) responsible for caddisfly species distribution (CCA). The most important environmental driver was habitat persistence. Distance-based RDA analysis revealed a distinct pattern in the distribution of species with or without diapause along the persistence gradient. Environmental drivers associated with plants were also crucial for both fens and water bodies. The key factor influencing the caddisfly assemblages of pools and ditches was the use and management of the surrounding land, whereas in the fens, it was the level of area protection. Physical and chemical water parameters had no statistically significant impact on the assemblages. Some factors can be modified by humans (e.g., water level regulation, vegetation, and landscape management) to maintain healthy ecosystems for aquatic insects.
Eulerian and Lagrangian statistics in the Bluelink numerical model and AVISO altimetry: Validation of model eddy kinetics

[1] We compare Eulerian and Lagrangian timescales, velocity autocorrelations, and spectra from 14 years of hindcast ocean model and satellite velocities with direct observations. Our main aim is to determine how well the model (Bluelink, version Bran 2.1) and satellite-derived currents (Archiving, Validation and Interpretation of Satellite Oceanographic data (AVISO)) simulate mesoscale eddy variability, which is important in mixing heat, salinity, and momentum and in controlling dispersion. Ocean Eulerian observations are from Topex-Poseidon (T/P) Crossover velocities, and Lagrangian observations are from Global Drifter Program (GDP) surface drifters. Eulerian spectra from Bluelink are similar to Eulerian spectra from Crossover velocities over the range of common frequencies (the ∼10-day sampling from T/P limits the comparison to low frequencies), and Eulerian timescales from Bluelink are slightly shorter than from the observations. Part of this difference may be an effect of the T/P sampling rate. In contrast, Lagrangian spectra from Bluelink are considerably steeper than spectra from GDP drifters, and consequently, Lagrangian timescales from Bluelink are longer than from the observations. Both Eulerian and Lagrangian spectra from AVISO are steeper than from observations so that both Eulerian and Lagrangian AVISO timescales are longer than observed. The real ocean is an ocean where the Eulerian-Lagrangian relationship described by Middleton (1985) is followed; the Tasman Sea averaged ratio of Lagrangian to Eulerian timescales is about 0.1 zonally and 0.15 meridionally. However, the Eulerian-Lagrangian relationship described by Middleton (1985) is not obeyed by Bluelink, and we believe that this behavior in Bluelink reflects a loss of short-wavelength eddies in the model.
A Spatio-Temporal Correlation Analysis of Water Quality and Economic Growth in the Jiulong River Basin

Based on the 1981-2009 dataset of the socio-economic and water environment of the Jiulong River Basin,an important region of the Western Taiwan Strait Economic Zone,the spatio-temporal relationship of river water quality with economic growth in the basin was analyzed,using statistical tools,GIS technique and environmental Kuznets curve(EKC) method.Compared with the rapidly growing secondary and tertiary industries,the slowly but steadily growing primary industry stood out in pollution creation.It increased first and then decreased in cultivated area,and showed a linear rise in mean N and P fertilization intensity.Its N ∶P ratio(on a net nutrient basis) in fertilization declined from 4 ∶1 in 1981 to 2 ∶1 in 2009,which led to changes in nutrient stoichiometry of the river water,thus increasing the risk of algal bloom in the river.Marked differences existed between counties(cities or districts) in structure of pollution sources.The changes in water quality and the distribution of pollution along the river were closely related to the disposition of the socio-economy in space.The overgrowth of animal husbandry in the northern part of the Jiulong River Basin and the cash crop-based agricultural structure and the highly intensive,but low-in-use-efficiency fertilization in the western part of the Jiulong River Basin,were the causes triggering degradation(eutrophication) of the water quality since the 1990s.So far,the EKC curve has not yet shown any apparent turning point,indicating that water quality of the basin will go on degrading unless the pollution from agriculture is effectively controlled.
Bacterial modelling of a rural tropical stream using the QUAL2K model.

Surface water is frequently contaminated by microorganisms from different sources such as farm animals and agriculture (Hyland et al., 2003; Pappas et al., 2008; Muyibi et al., 2008; Mishra et al., 2008), sewage (Gerba & Smith, 2005; Muyibi et al., 2008) and wild animals (Jiang et al., 2007). Contamination of surface water renders the water unsuitable for its designated purposes such as drinking, body contact recreation and it affects fish and shellfish quality due to the potential for human to be infected by pathogens. It has been reported that majority of diarrhoeal disease in the world (88%) and approximately 1.7 million deaths worldwide was attributable to unsafe water, sanitation and hygiene (WHO, 2003). In developing regions, drinking water is a major source of microbial pathogens (Ashbolt, 2004). Sewage exposed fish has been found to harbour drug resistant coliforms (Sanyal et al., 2011). The Serin River, a rural river located in south-western part of Sarawak, is an important river for the communities around the area. Its importance includes a drinking water source, fish aquaculture, laundry and recreation. But, landuse and settlement in the river basin have contributed to water quality contamination. Previous studies showed that the water and sediment along the river are contaminated with E. coli and levels are high near human settlement and animal farms (Ling et al., 2006; 2008; 2012; 2013). In order to reduce the contaminants so that the water is suitable for use according to its designated purposes, it is best that modelling be applied. In Malaysia, fecal coliform limit of National Water Standards for Class I (no treatment required), IIA and IIB are 10 count/100mL, 100 count/100mL and 400 counts/100mL respectively.
Microbially-Mediated Environmental Influences on Metazoan Colonization of Matground Ecosystems: Evidence from the Lower Cambrian Harkless Formation

Abstract Prior to the advent of widespread bioturbation during Cambro–Ordovician times, microbial mats may have covered large expanses of the continental shelf. Evidence of matgrounds in shallow-marine settings is provided by abundant wrinkle structures in Lower Cambrian strata of the Great Basin, United States. Wrinkle structures from the Lower Cambrian Harkless Formation commonly co-occur with a distinctive assemblage of invertebrate fossils, providing evidence for the possibility of selective metazoan colonization of matground substrates. Molds of linguliform brachiopods are abundant on many wrinkle surfaces. The agglutinated problematicum, Volborthella tenuis, also is found on wrinkle surfaces and in laminations beneath wrinkle-structure surfaces. Bedding-parallel trace fossils, such as Planolites, Diplichnites, and Taphrhelminthopsis, commonly crosscut wrinkle structures, while vertically oriented trace fossils are absent. Microbial mats containing layered microbial communities would have considerably compressed stratified redox zones beneath the sediment-water interface in marine-shelf settings. Sulfidic and anoxic conditions within and beneath microbial mats would have precluded habitation by many metazoans, while those that adapted to such conditions may have found matgrounds a unique, though temporally fleeting, ecological niche. The distinctive, low-diversity fossil assemblage found in association with the wrinkle structures in the Great Basin suggests that some early animals may have been adapted to hypoxic and sulfidic conditions found in matground substrates, while others may have been physiologically excluded from these environments.
AUTOMATIC LINKING AND FAST CALCULATION METHODS OF 1D/2D COUPLED MODEL

In order to use 1D/2D coupled model for flood prediction in a large area, we propose automatic linking and fast calculation methods. For fast calculation, we propose the Dynamic Domain Defining Method (Dynamic DDM), which defines the calculation domain to include wet cells and to exclude dry cells during the simulation. Because of the nearly optimal calculation domain, the calculation time is significantly reduced. For automatic linkage generation, we propose the Floodplain -River -Overflow Gluing (FROG) method. It defines a cell in the 2D model as either left or right side of a river, and connects it to the same side of the levee line in the 1D river model. The coupled model generated by the FROG method accurately simulated a flood disaster occurred in Takayama City (Japan). We applied the proposed methods for Kawasaki City (Japan). The 1D model is applied to the two river systems with 2 main rivers and 15 tributaries, and the 2D model is applied to the city (143 km 2 ). The FROG method generates 14,287 linkages between 1D and 2D models. The system working on a PC simulates a 27 hours event in less than 10 minutes. We conclude that the proposed methods are suitable for flood prediction.
Obstacles and facilitators to intimate bystanders reporting violent extremism or targeted violence

ABSTRACT The first people to suspect someone is planning an act of terrorism or violent extremism are often those closest to them. Encouraging friends or family to report an “intimate” preparing to perpetrate violence is a strategy for preventing violent extremist or targeted mass violence. We conducted qualitative-quantitative interviews with 123 diverse U.S. community members to understand what influences their decisions to report potential violent extremist or targeted mass violence. We used hypothetical scenarios adapted from studies in Australia, Canada, and the United Kingdom. Factors influencing reporting decisions include fears of causing harm to the potential violent actor, self, family, or relationships; not knowing when and how to report; mistrust of law enforcement; access to mental health services; and perceptions that law enforcement lacks prevention capabilities. White and non-White participants were concerned about law enforcement causing harm. Participants would contact professionals such as mental health before involving law enforcement and Black-identified participants significantly preferred reporting to non-law enforcement persons, most of whom are not trained in responding to targeted violence. However, participants would eventually involve law enforcement if the situation required. They preferred reporting in-person or by telephone versus on-line. We found no difference by the type of violent extremism or between ideologically motivated and non-ideologically motivated violence. This study informs intimate bystander reporting programmes in the U.S. To improve reporting, U.S. policymakers should attend to how factors like police violence shape intimate bystander reporting. Our socio-ecological model also situates intimate bystander reporting beside other population-based approaches to violence prevention.
An Examination of Positive and Negative Reciprocity Norms as to Serious Leisure Activities and Demographic Variables

Research conducted on positive and negative reciprocities mainly aims to determine the variables that impact this phenomenon. To this end, this study sought to ascertain the influence of participation in trekking and kickboxing as serious leisure activities along with several other variables on the positive and negative reciprocity attitudes. The study utilized a descriptive survey design and a random sampling method. The findings revealed a significant difference between the choice of serious leisure activities and demographic variables such as gender, age, and education level. Additionally, the mean scores of positive reciprocity attitudes increased proportionately to age and education level. Furthermore, the mean scores of positive reciprocity attitudes of the trekking participants were significantly higher than those of kickboxing participants.Keywords: Serious Leisure Activities, Positive and Negative Reciprocity, Kickboxing, Trekking
Trends and Projection of the Incidence of Active Pulmonary Tuberculosis in Southwestern China: Age-Period-Cohort Analysis

Background The control of pulmonary tuberculosis (PTB) is critical for achieving the vision of World Health Organization’s End TB goal. Objective This study analyzes the temporal trends in PTB incidence associated with age, period, and birth cohorts from 2006 to 2020 in Yunnan, China; projects the PTB burden till 2030; and explores the drivers of PTB incidence. Methods The aggregated PTB incidence rates between 2005 and 2020 were obtained from the National Notifiable Disease Reporting System. We used the age-period-cohort model to evaluate the age, period, and cohort effects on PTB incidence. We applied the Bayesian age-period-cohort model to project future PTB incidence from 2021 to 2030. We applied the decomposition algorithm to attribute the incidence trends to population aging, population growth, and age-specific changes from 2006 to 2030. Results From 2006 to 2020, the PTB incidence in Yunnan was relatively stable, although the absolute number showed an increase. The net drift was –1.56% (95% CI –2.41% to –0.70%). An M-shaped bimodal local drift and a longitudinal age curve were observed. The overall local drift was below zero for most age groups except for the age groups of 15-19 years (2.37%, 95% CI –0.28% to 5.09%) and 50-54 years (0.41%, 95% CI –1.78% to 2.64%). The highest risk of PTB incidence was observed in the age group of 65-69 years, and another peak was observed in the age group of 20-24 years. Downward trends were observed for both period and cohort effects, but the cohort effect trends were uneven. A higher risk was observed for the birth cohorts of 1961-1970 (rate ratio [RR]1961-1965=1.10, 95% CI 0.88-1.38; RR1966-1970=1.11, 95% CI 0.92-1.37) and 2001-2010 (RR2001-2005=0.92, 95% CI 0.63-1.34; RR2006-2010=0.84, 95% CI 0.45-1.58) than for the adjacent cohorts. The Bayesian age-period-cohort model projected that PTB incidence will continually increase from 2021 to 2030 and that PTB incidence in 2030 will be 2.28 times higher than that in 2006. The age-specific change was the leading cause for the growing PTB disease burden. Conclusions Although there are several levels and measures for PTB control, the disease burden is likely to increase in the future. To bridge the gap of TB-free vision, our study suggests that public health policies be put in place soon, including large-scale active case-finding, priority prevention policies for high-risk older adult and young adult populations, and reduction of possible grandparent-grandchildren transmission patterns.