Miracle-dz/UniFAR-FTUs huggingface dataset:
Statewide Implementation of Universal Third-Trimester Repeat HIV Testing in Illinois

Abstract Objective This article aims to assess statewide uptake of HIV repeat testing in the first 2 years after the implementation of an amendment to the Illinois Perinatal HIV Prevention Act (IPHPA) mandating universal repeat HIV testing in the third trimester. Study Design This is a retrospective, population-based study of all birthing individuals in Illinois (2018–2019). Data were collected using the state-mandated closed system of perinatal HIV test reporting. We evaluated the incidence of mother–infant pairs with negative early tests and repeat third-trimester tests (RTTTs) performed in adherence with the law, as well as the timing of the performance of the RTTTs (outpatient vs. inpatient). Chi-square tests of trend by quarter were performed to ascertain sustainability. Results Of 138,805 individuals delivered in 2018, 80.6% presented with early test and RTTTs. In 2018, outpatient RTTTs improved from 71.8% (quarter 1) to 85.1% (quarter 4; p < 0.001). In 2018, the proportion of mother–infant dyads who received testing that was adherent to the IPHPA Amendment was 92.1, 95.5, 96.7, and 96.4% in quarters 1 through 4, respectively ( p < 0.001). In 2019, outpatient RTTTs performance remained high (87.4%) and stable ( p = 0.06). In 2019, 99.9% of mother–infant dyads had testing adherent to the mandate in quarters 1 through 4 ( p = 0.39). Of individuals who presented without RTTTs, 93.5% (2018) and 98.8% (2019) underwent inpatient testing before delivery. Conclusion Implementation of RTTTs in Illinois was rapid, successful, and sustained in its first 2 years. Public health methodologies from Illinois may benefit other states implementing RTTT programs. Key Points In 2018, Illinois enacted statewide RTTT for HIV among all parturients. In 2019, over 99% of mother–infant dyads had documentation of both early and repeat HIV testing before hospital discharge. Implementation of repeat third-trimester HIV testing in Illinois was rapid, successful, and sustained in its first 2 years. Public health methodologies from Illinois may benefit other states implementing similar programs.
Predicting Length of Stay in Colorectal Cancer Patients: A Monocentric Study in Italy

Colorectal cancer is associated with high healthcare costs, and reducing hospital length of stay (LOS) is a priority for hospitals. Our study aimed to predict LOS after surgical resection for colorectal cancer using demographic and clinical characteristics available in administrative data. We conducted a retrospective cohort study of patients discharged from Cardarelli Hospital, Naples, Italy, between 2019 and 2022. Multiple linear regression was used to model the relationship between demographic and clinical characteristics and LOS. The multiple regression model predicted postoperative LOS. Age and emergency department admission were significant predictors and positively correlated with postoperative LOS. Our findings suggest that age and emergency department admission may be useful predictors for identifying patients at risk for prolonged postoperative LOS after colorectal cancer surgery. These findings may inform resource allocation decisions in colorectal cancer surgery.
Modeling Interference for Individual Treatment Effect Estimation from Networked Observational Data

Estimating individual treatment effect (ITE) from observational data has attracted great interest in recent years, which plays a crucial role in decision-making across many high-impact domains such as economics, medicine, and e-commerce. Most existing studies of ITE estimation assume that different units at play are independent and do not influence each other. However, many social science experiments have shown that there often exist different levels of interactions between units in observational data, especially in a networked environment. As a result, the treatment assignment of one unit can affect the outcome of other units connected to it in the network, which is referred to as the interference or spillover effect. In this article, we study an important problem of ITE estimation from networked observational data by modeling the interference between different units and provide a principled framework to support such study. Methodologically, we propose a novel framework, SPNet, that first captures the influence of hidden confounders with the aid of graph convolutional network and then models the interference by introducing an environment summary variable and developing a masked attention mechanism. Experimental evaluations on several semi-synthetic datasets based on real-world networks corroborate the superiority of our proposed framework over state-of-the-art individual treatment effect estimation methods.
Effect of Childhood Trauma on PTSD and PTG among College Students: The Mediating Role of Attachment

This study used CTQ-SF, PLC-C, PTGI and AAS questionnaires to evaluate the mediating role of attachment from childhood trauma to PTSD and PTG among 1421 college students in 5 colleges in a province as subjects. Through correlation analysis by SPSS, structural equation modeling analysis and Bootstrap method by Mplus, the results highlighted that childhood trauma positively predicted PTSD directly and negatively predicted PTG directly. Furthermore, it could negatively predict PTSD and positively predict PTG under the mediation of closeness-dependence, and positively predict PTSD and negatively predict PTG under the mediation of attachment anxiety. Therefore, we concluded that college students' childhood trauma had an important influence on PTSD and PTG, and attachment played a partially mediating effect from childhood trauma to PTSD and PTG. Implications for future research and attachment-based clinical intervention are discussed.
GLEFFN: A Global-Local Event Feature Fusion Network for Micro-Expression Recognition

Micro-expressions are facial movements of short duration and low amplitude, which, upon analysis, can reveal genuine human emotions. However, the low frame rate of frame-based cameras hinders the further advancement of micro-expression recognition (MER). A novel technology, event-based cameras, boasting high frame rates and low latency, proves suitable for the MER task but remains challenging to obtain. In this article, a local event feature, namely the local count image, is proposed. This feature is calculated from up-sampled video using the SloMo method. Additionally, a global-local event feature fusion network is constructed, wherein the local count image and the global dense optical flow are merged to map deeper features and effectively address the MER task. Experimental results demonstrate that the proposed light-weighted method outperforms state-of-the-art approaches across multiple datasets. To our best knowledges that this work marks the first successful attempt to solve the MER task from an event perspective, thus facilitating the future promotion of event-based camera technology and providing inspiration for future research endeavors in related domains.
Rangeland experiments to parameterize the water erosion prediction project model: vegetation canopy cover effects.

The Water Erosion Prediction Project (WEPP) is a new water erosion prediction technology being developed by the USDA-Agricultural Research Service to replace the Universal Soil Loss Equation. Rangeland field experiments were designed to parameterize the WEPP rangeland erosion model. Included in the field experiments were plot treatments designed to separate direct from indirect effects of vegetation canopy on runoff and soil erosion. Nine rangeland sites from a wide range of soil and vegetation types were evaluated using rainfall simulation techniques. Natural versus clipped treatment surface characteristics and runoff and erosion responses were compared using regression analyses. These analyses showed that there were no significant differences between natural and clipped plot surface characteristics, runoff ratios, final infiltration rates, or initial rainfall abstractions. Erosion rates were different between treatments with the clipped plots having slightly less erosion than the natural plots. Results indicated that, under the rainfall conditions simulated, canopy cover was not directly contributing to initial abstractions through rainfall interception loss or significantly affecting runoff or erosion.
Technology use and clinical outcomes in a racial-ethnic minority cohort of children and adolescents with type 1 diabetes

Abstract Objectives Technology use has been shown to improve diabetes control, but minority youths tend to have low rates of technology use and exhibit suboptimal glycemic control. We examined the impact of continuous glucose monitors (CGM) and continuous subcutaneous insulin infusion (CSII) on glycemic control in a racial-ethnic minority cohort of children and adolescents with type 1 diabetes (T1D). Methods A cross-sectional study was conducted among 140 pediatric T1D patients seen at a multidisciplinary clinic. From January to November 2022, data on demographics and glycated hemoglobin (HbA1c) levels were collected. Patients were categorized as technology (CGM, CSII, or both) or non-technology users (finger stick meter (FS) and multiple daily injections (MDI)). Results The majority identified as Hispanic (79 %) and had public health insurance (71 %). Sixty-nine percent used technology. Compared with non-technology users, technology users had significantly lower mean HbA1c levels (9.60 vs. 8.40 %, respectively) (p=0.0024), though no group (CGM + CSII, CGM + MDI, FS + CSII, and FS + MDI) achieved a mean HbA1c level of <7.0 %. Regarding minority status, no significant differences in mean HbA1c levels existed between Hispanics and Blacks in the CGM + MDI and FS + CSII groups (p=0.2232 and p=0.9224, respectively). However, there was a significant difference in mean HbA1c levels between Hispanic and Black non-technology users (9.19 vs. 11.26 %, respectively) (p=0.0385). Conclusions Technology users demonstrated better glycemic control than non-technology users. Further research is needed to investigate factors affecting glycemic control in minority youths with T1D.
Novel Approach to Investigate the Effect of High-Dose Methylprednisolone on Erythrocyte Morphology: White Light Diffraction Microscopy

Abstract The present study focuses on quantitative phase imaging of erythrocytes with the aim to evaluate the effects of high-dose methylprednisolone (HDMP) on erythrocytes in vivo under physiological conditions in human blood samples. Samples from ten patients, prescribed to be treated with 1000 mg/day intravenous methylprednisolone for 5 days, were analyzed by white light diffraction phase microscopy (WDPM) for quantitative imaging. WDPM, an optical measurement technique, enables single shot measurement and low speckle noise using white light. Quantitative phase imaging performed with this experimental setup allowed the determination of erythrocyte morphology with 9 different parameters. In vivo quantitative analysis of erythrocytes by WDPM, which is a simple and reliable method, shows that HDMP treatment has no significant effect on erythrocyte morphology. With the developing technology, interdisciplinary studies on individuals under treatment should play an important role in elucidating the interaction between steroids and erythrocytes.
THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually necessitates access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast datasets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and crucial cofactor in primary metabolic pathways. We conducted a comprehensive search for THI1 information within public repositories with careful curation to achieve this. Our searches reveal an evolutionary trend of 702 THI1 homologs of Archaea and Eukarya, with a detailed focus on plants. The green lineage of these organisms preserved the THI4 protein domain throughout its diversification by incorporating the N-terminus and targeting chloroplasts. Furthermore, evolutionary pressures and lifestyle appear to be associated with retention of TPP-riboswitch sites and consequent dual post-transcriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even successive rounds of genome duplications. Additionally, we identified the diversification of cis-regulatory sites in plants with the conservation of biological processes associated with the initial stages of seed development and preservation of the transcriptional pattern during the diurnal cycle. Our data mining of 484 transcriptome datasets supports this finding and brings a new look at public repositories and evolutionary trends to THI1.
Antiviral capacity of the early CD8 T-cell response is predictive of natural control of SIV infection

While most individuals suffer progressive disease following HIV infection, a small fraction spontaneously controls the infection. Although CD8 T-cells have been implicated in this natural control, their mechanistic roles are yet to be established. Here, we combined mathematical modeling and analysis of data from 16 SIV-infected macaques, of which 12 were natural controllers, to elucidate the role of CD8 T-cells in natural control. For each macaque, we considered, in addition to the canonical in vivo plasma viral load and SIV DNA data, longitudinal ex vivo measurements of the virus suppressive capacity of CD8 T-cells. Available mathematical models do not allow analysis of such combined in vivo-ex vivo datasets. By explicitly modeling the ex vivo assay and integrating it with in vivo dynamics, we developed a new framework that enabled the analysis. Our model fit the data well and estimated that the recruitment rate and/or maximal killing rate of CD8 T-cells was up to 2-fold higher in controllers than non-controllers (p=0.013). Importantly, the cumulative suppressive capacity of CD8 T-cells over the first 4-6 weeks of infection was associated with virus control (Spearman’s ρ=- 0.51; p=0.05). Thus, our analysis identified the early cumulative suppressive capacity of CD8 T-cells as a predictor of natural control. Furthermore, simulating a large virtual population, our model quantified the minimum capacity of this early CD8 T-cell response necessary for long-term control. Our study presents new, quantitative insights into the role of CD8 T-cells in the natural control of HIV infection and has implications for remission strategies.
The genetic basis of novel trait gain in walking fish

A major goal in biology is to understand how organisms evolve novel traits. Multiple studies have identified genes contributing to regressive evolution, the loss of structures that existed in a recent ancestor. However, fewer examples exist for genes underlying constructive evolution, the gain of novel structures and capabilities in lineages that previously lacked them. Sea robins are fish that have evolved enlarged pectoral fins, six mobile locomotory fin rays (legs) and six novel macroscopic lobes in the central nervous system (CNS) that innervate the corresponding legs. Here, we establish successful husbandry and use a combination of transcriptomics, CRISPR-Cas9 editing, and behavioral assays to identify key transcription factors that are required for leg formation and function in sea robins. We also generate hybrids between two sea robin species with distinct leg morphologies and use allele-specific expression analysis and gene editing to explore the genetic basis of species-specific trait diversity, including a novel sensory gain of function. Collectively, our study establishes sea robins as a new model for studying the genetic basis of novel organ formation, and demonstrates a crucial role for the conserved limb gene tbx3a in the evolution of chemosensory legs in walking fish.
Liver size is predetermined in the neonate by adding lobules at the periphery

Organs vary in size between and within species to match organismal needs1,2. Decades-old theoretical work has proposed that scaling of organs and body parts relative to the body relies on the features of energy-transport systems, the vascular system in mammals3. Yet, experimental studies on whether or how vascularization helps determine organ size have lagged behind. The mammalian liver is a remarkable example, as liver size scales proportionally with high precision between individuals4. Here, we use quantitative clonal mapping, volumetric imaging, and genetic perturbations combined with novel molecular and genetic tools to identify the temporal and spatial constraints that establish mouse liver size. We find that adult liver size is predetermined during a neonatal period when new functional units, termed lobules, are added to the organ. New lobules are vascularized by prominent sprouting angiogenesis of the hepatic vein, restricted to the periphery of the organ. When Wnt signals are ablated in the single cell-layered mesothelium at the periphery, lobule growth fails, and the organ adopts a compromised size set point. Remarkably, within a week after birth and well before hepatocyte division stops, vein sprouting rapidly declines and lobule addition concludes, setting a limit on the final liver size. These findings posit that vascularization in the neonate constrains and helps determine adult liver size. Together, these results propose a novel, vasculature-centric experimental framework for studying organ size control and scaling in mammals.
Escherichia coli plasmidome maps the game of clones

Escherichia coli is a major human pathogen and the most widely studied microbe in history, but its extrachromosomal elements known as plasmids remain poorly delineated. Here we used long-read technology to high-resolution sequence the entire plasmidome and the corresponding host chromosomes from a longitudinal survey covering two decades and over 2,000 E. coli isolates. Separation of chromosomal and extrachromosomal DNA enabled us to reconstruct co-evolutionary trajectories of host lineages and their plasmids on a population-wide scale, demonstrating that plasmid evolution is markedly constrained contrary to the established dogma. We find that some plasmids have persisted in lineages for centuries, and provide a high-resolution map of recent vertical and horizontal evolutionary events in plasmids with key antibiotic resistance, competition and virulence determinants. We present genomic evidence of both chromosomal and plasmid-driven success strategies that represent convergent phenotypic evolution in distant lineages, and use in vitro experiments to verify the importance of bacteriocin-producing plasmids for clone success. Our study has general implications for understanding plasmid biology and bacterial evolutionary strategies, and informing development of future interventions against pathogens.
A comparative study on hybrid fatigue stress-life model of RC beams strengthened with NSM CFRP

Abstract Near Surface Mounted Carbon Fiber-reinforced Polymers (NSM FRP) are becoming widely used in the rehabilitation field of concrete structures. Several studies were conducted to evaluate the fatigue performance of Reinforced Concrete (RC) bridges strengthened with NSM FRP composite materials. Most stress-life (S-N) fatigue models of RC beams are based on fatigue testing that has been conducted in the region of load cycles ranging between 103 and 107. This might cause an inaccuracy in the stress-life predictions when the common S-N formulations are used. This paper presents a review of the recent research on the fatigue behavior of RC beams and proposes a hybrid fatigue stress-life model of RC beams strengthened with NSM CFRP. An analytical fatigue S-N model was developed based on experimental fatigue data of constant amplitude of tension-tension cyclic loading obtained from the literature. A hybrid formulation was used, combining both exponential and power regression analyses to enhance the accuracy of prediction in low and high cycle fatigue regions. Moreover, Muratov’s method was used to determine the endurance limit of strengthened RC beams. A three-dimensional finite element RC beam strengthened with NSM CFRP was modeled to investigate the accuracy of the proposed hybrid model. The RC beam was modeled in ANSYS with similar dimensions and material properties to experimental specimens in the literature. The hybrid model was compared to experimental and numerical data, and satisfactory precision was observed with a correlation coefficient of 0.86. The proposed hybrid model helps to provide comprehensive fatigue stress-life estimation for design purposes.
Antibacterial Activity of Isolated Compounds from Allophylus spicatus (Poir.) Radlk (Sapindacea)

Abstract Phytochemical investigation on the roots of Allophylus spicatus (Sapindacea) led to the isolation of four compounds, namely cleomiscosin A (1), cleomiscosin C (2), scopoletin (3) and 3-oxotirucalla-7,24-dien-24-oic acid (4). The structures of the compounds were established by spectroscopic analysis: UV, IR, 1D and 2D NMR, EI-MS and HR-EI-MS and compared with the literature. These compounds are reported for the first time from the plant. The compounds showed potent antibacterial activity, marked inhibition against most of the tested bacterial strains: Pseudomonas aeruginosa (ATCC 27853), Escherichia coli (ATCC 25922), Salmonella typhi (ATCC 25923), Klebsiella pneumonia (ATCC 13883), Streptococcus faecalis (ATCC 29212) and Micrococcus luteus (ATCC 10240), with a zone of inhibition between 0.7±0.35 - 16±0.46 mm as compared with the zone of inhibition of Streptomycin (20±0.34 - 31±0.29 mm), a known antibacterial drug used as the standard. The antibacterial activity of the isolated phytochemicals could be responsible for the plant ethno-medicinal uses. GRAPHICAL ABSTRACT
An Integrated Assessment of Vulnerability to Glacial Hazards

Abstract The Rio Santa valley in the Cordillera Blanca, Peru, has been repeatedly affected by severe glacial flood disasters in the past decades. The continuing high rate of glacier retreat has led to the formation and rapid growth of a large number of glacial lakes. Due to the risk of lake outburst floods, downstream communities are confronted with serious hazards. The regional capital of Huaraz is one of the major sites exposed to these hazards. Mainly due to a lack of resources, no systematic evaluation of the existing hazards and related risks has been performed so far, nor have adequate warning systems been installed. Strict financial limitations make a prioritization of mitigation measures a necessity. Vulnerability assessments are an effective tool to this end. In this article, we present a method to measure the vulnerability of Huaraz to hazards from glacial lake outbursts integrating both physical (ie hazards-related) and socioeconomic factors. The difficulty of quantifying socioeconomic variables and its combination with physical factors, as well as a lack of corresponding concepts, is a challenge for measuring vulnerability. The resulting map shows a high vulnerability for several parts of Huaraz. The results of this study thus make an important contribution to effectively addressing the identified protection deficit and to efficiently assigning the limited resources in the context of a developing country. However, this article also shows the strong need for more vulnerability research integrating both physical and social science components and related theoretical frameworks to be readily applied in practice.