Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between Human Genetic Variants and the Vaginal Bacteriome of Pregnant Women

Knowledge about the influence of host genetics on the vaginal bacteriome in pregnancy is still limited. Although a number of environmental and behavioral factors may exert influences on the structure of vaginal bacterial communities, the vaginal bacteriome often undergoes a relatively fixed transition to a more stable and less diverse state as the menstrual cycle stops, which raises questions on the effects of human genetics. ABSTRACT The influence of human genetic variants on the vaginal bacterial traits (VBTs) of pregnant women is still unknown. Using a genome-wide association approach based on the 16S rRNA bacteriome analysis, a total of 72 host genetic variant (single nucleotide polymorphisms [SNPs], indels, or copy number variations [CNVs])-VBT associations were found that reached the genome-wide significance level (P < 5 × 10−8) with an acceptable genomic inflation factor λ of <1.1. The majority of these SNPs that reached the genome-wide significance level had a relatively low minor allele frequency (MAF), and only seven of them had MAFs greater than 0.05. rs303212, located at the IFIT1 gene on chromosome 10, was the most eye-catching variant, which had a genome-wide association with the relative abundance (RAB) of Actinobacteria and Bifidobacteriaceae and also had a suggestive association with the RAB of a few common vaginal bacteria including Actinobacteriota, Firmicutes, Lactobacillus, and Gardnerella vaginalis and the beta diversity weighted UniFrac (P < 1 × 10−5). The findings of the study suggest that the vaginal bacteriome may be influenced by a number of genetic variants across the human genome and that interferon signaling may have an important influence on vaginal bacterial communities during pregnancy. IMPORTANCE Knowledge about the influence of host genetics on the vaginal bacteriome in pregnancy is still limited. Although a number of environmental and behavioral factors may exert influences on the structure of vaginal bacterial communities, the vaginal bacteriome often undergoes a relatively fixed transition to a more stable and less diverse state as the menstrual cycle stops, which raises questions on the effects of human genetics. We utilized a genome-wide approach to identify the associations between genetic variants and multiple VBTs and performed enrichment analyses. The human genetics during pregnancy may be involved in multiple pathways. The results may disclose innate functional factors involved in shaping the vaginal bacteriome during pregnancy and provide insight into the establishment of specific strategies for prevention and clinical treatment of pregnancy complications.
“We Want to Sign It, But We Can't Do It”

This study aimed to clarify the experiences of family members of older adult residents regarding the signing of an advance directive in the context of a Chinese culture. Twenty family members of older residents in a long-term care facility participated in face-to-face interviews, and the researchers conducted a thematic analysis of observation field notes and interview transcripts. A content analysis of the interviews revealed 4 themes concerning the refusal to sign advance directives: resident decision, group decision, not entitled to decide, and random decision. Health providers may serve as mediators and pass on the residents' views regarding their end-of-life care to their families after holding discussions with residents and their families separately to ensure that an agreeable decision regarding the modes and objectives of EOL care is reached and that such a decision respects the right of the patient to choose.
Association of County-Level Availability of Pediatricians With Emergency Department Visits

Supplemental digital content is available in the text. Objectives The relationship between pediatrician availability and emergency department (ED) attendance is uncertain. We determined whether children in counties with more pediatricians had fewer ED visits. Methods We conducted a cross-sectional study of all ED visits among children younger than 18 years from 6 states. We obtained ED visit incidences by county and assessed the relationship to pediatrician density (pediatricians per 1000 children). Possible confounders included state, presence of an urgent care facility in the county, urban-rural status, and quartile of county-level characteristics: English-speaking, Internet access, White race, socioeconomic status, and public insurance. We estimated county-level changes in incidence by pediatrician density adjusting for state and separately for all possible confounders. Results Each additional pediatrician per 1000 children was associated with a 13.7% (95% confidence interval, −19.6% to −7.5%) decrease in ED visits in the state-adjusted model. In the full model, there was no association (−1.4%, 95% confidence interval, −7.2% to 4.8%). The presence of an urgent care, higher socioeconomic status score, urban status, and higher proportions of White race and nonpublic insurance were each associated with decreased ED visit rates. Conclusions Pediatrician density is not associated with decreased ED visits after adjusting for other county demographic factors. Increasing an area's availability of pediatricians may not affect ED attendance.
The impact of dengue illness on social distancing and caregiving behavior

Background Human mobility among residential locations can drive dengue virus (DENV) transmission dynamics. Recently, it was shown that individuals with symptomatic DENV infection exhibit significant changes in their mobility patterns, spending more time at home during illness. This change in mobility is predicted to increase the risk of acquiring infection for those living with or visiting the ill individual. It has yet to be considered, however, whether social contacts are also changing their mobility, either by socially distancing themselves from the infectious individual or increasing contact to help care for them. Social, or physical, distancing and caregiving could have diverse yet important impacts on DENV transmission dynamics; therefore, it is necessary to better understand the nature and frequency of these behaviors including their effect on mobility. Methodology and principal findings Through community-based febrile illness surveillance and RT-PCR infection confirmation, 67 DENV positive (DENV+) residents were identified in the city of Iquitos, Peru. Using retrospective interviews, data were collected on visitors and home-based care received during the illness. While 15% of participants lost visitors during their illness, 22% gained visitors; overall, 32% of all individuals (particularly females) received visitors while symptomatic. Caregiving was common (90%), particularly caring by housemates (91%) and caring for children (98%). Twenty-eight percent of caregivers changed their behavior enough to have their work (and, likely, mobility patterns) affected. This was significantly more likely when caring for individuals with low “health-related quality of well-being” during illness (Fisher’s Exact, p = 0.01). Conclusions/Significance Our study demonstrates that social contacts of individuals with dengue modify their patterns of visitation and caregiving. The observed mobility changes could impact a susceptible individual’s exposure to virus or a presymptomatic/clinically inapparent individual’s contribution to onward transmission. Accounting for changes in social contact mobility is imperative in order to get a more accurate understanding of DENV transmission.
On Second-Order Roll Motions of Ships

More and more vessels for offshore engineering applications have a roll period beyond 20 seconds in order to avoid the wave frequency excitations on the roll motion. That is particularly true for the latest drilling vessels. However, this will lead to an unexpected second-order roll motion of the ships. This paper will present a new methodology to evaluate the second-order roll motions of the ships in random seas. The higher-order boundary element method (HOBEM) has been utilized to generate the second order difference-frequency roll excitations on the ships and the second-order ship roll motions were predicted by a frequency-domain method. A series of model tests have been conducted and the test results have a good agreement with the numerical predictions. Therefore, this new method has been verified and validated.Copyright © 2003 by ASME
Optimisation of Fixed-Outlet and Flow-Modulated Pressure Reduction Measures in Looped Water Distribution Networks Constrained by Fire-Fighting Capacity Requirements

Pressure management is a pivotal component when reducing leakages from water distribution networks, and can be achieved by sub-dividing existing networks into partitions where the pressure can be reduced effectively. There is a need to develop methods that aid in the identification of cost-effective partitions for pressure reduction, while simultaneously verifying that the topological changes entailed in these solutions do not compromise reliability and (fire-fighting) capacity requirements, especially in systems where the capacity is ensured through looped networks. This paper presents a method that can be used to this end, in which a novel combination of hydraulic simulations and graph theory is used to determine the maximal potential for (dynamic and static) pressure reduction, and this is used as a constraint for multi-objective optimization of pressure reduction measures. Trondheim, Norway, has been used as a case study area, and it is demonstrated how the developed method aids in the process of achieving leakage reduction in Trondheim. The results for Trondheim show that an economically optimal solution for pressure management is predicted to lead to a reduction from 28 to 22% water loss volume, and furthermore that effective pressure management will rely heavily on active (dynamic) regulation in this particular system.
Breastfeeding: How is it related to food insecurity and other factors among low-income mothers?

Abstract A cross-sectional study was conducted to (1) examine breastfeeding initiation and continuation rates, and; (2) investigate association between food insecurity and breastfeeding status, among low-income mothers. Mothers of infants two-months or younger were recruited from a local pediatric clinic serving primarily low-income families. Upon giving consent, mothers were interviewed in-person or over the phone in either English or Spanish. Of the total 92 mothers interviewed, 90% initiated breastfeeding, but only 24% were doing exclusive breastfeeding at 2 months of infant’s age. After controlling for socio-demographics, it was found that food-insecure mothers were less likely to continue with breastfeeding (β = −1.51, p = .024). Future research is warranted to understand pathways through which food insecurity affects breastfeeding and how this disparity can be prevented to ensure a safe and secure start for infants worldwide.
Analysis of Physiological Response during Cardiopulmonary Resuscitation with Personal Protective Equipment: A Randomized Crossover Study

The use of personal protective equipment (PPE) is required for the self-protection of healthcare workers during cardiopulmonary resuscitation (CPR) in patients at risk of aerosol transmission of infectious agents. The aim of this study was to analyze the impact of personal protective equipment on physiological parameters during CPR. A randomized, quasi-experimental, crossover design was used. The study was carried out in a training and simulation emergency box and the total sample consisted of 20 healthcare professionals. Two CPR tests were compared with the recommended sequence of 30 chest compressions and 2 ventilations. The duration of each test was 20 min. One of the CPR tests was carried out without using any PPE (CPR_control), i.e., performed with the usual clothing of each rescuer. The other test was carried out using a CPR test with PPE (i.e., CPR_PPE). The main variables of interest were: CPR quality, compressions, ventilations, maximum heart rate, body fluid loss, body temperature, perceived exertion index, comfort, thermal sensation and sweating. The quality of the CPR was similar in both tests. The maximum heart rate was higher in the active intervals (compressions + bag-valve-mask) of the test with PPE. CPR_PPE meant an increase in the perceived effort, temperature at the start of the thermal sensation test, thermal comfort and sweating, as opposed to CPR performed with usual clothing. Performing prolonged resuscitation with PPE did not influence CPR quality, but caused significant physiological demands. Rescuers were more fatigued, sweated more and their thermal comfort was worse. These results suggest that physical preparation should be taken into account when using PPE and protocols for physiological recovery after use should also be established.
Shedding Light on Cast Shadows: An Investigation of Perceived Ground Contact in AR and VR

Virtual objects in augmented reality (AR) often appear to float atop real world surfaces, which makes it difficult to determine where they are positioned in space. This is problematic as many applications for AR require accurate spatial perception. In the current study, we examine how the way we render cast shadows–which act as an important monocular depth cue for creating a sense of contact between an object and the surface beneath it–impacts spatial perception. Over two experiments, we evaluate people's sense of surface contact given both traditional and non-traditional shadow shading methods in optical see-through augmented reality (OST AR), video see-through augmented reality (VST AR), and virtual reality (VR) head-mounted displays. Our results provide evidence that nontraditional shading techniques for rendering shadows in AR displays may enhance the accuracy of one's perception of surface contact. This finding implies a possible tradeoff between photorealism and accuracy of depth perception, especially in OST AR displays. However, it also supports the use of more stylized graphics like non-traditional cast shadows to improve perception and interaction in AR applications.
Renal Resistive Index as a Predictor of Acute Kidney Injury and Mortality in COVID-19 Critically Ill Patients

Background: Acute kidney injury (AKI) in patients with COVID-19 can be caused by multiple mechanisms. Renal resistive index (RRI) is a noninvasive instrument to evaluate kidney hemodynamics, and it is obtained by analysis of intrarenal arterial waves using Doppler ultrasound. This study aimed to determine the role of RRI in predicting AKI and adverse outcomes in critically ill patients with COVID-19. Methods: This cross-sectional study included 65 patients with confirmed SARS-CoV-2 pneumonia admitted to the critical care unit from April 1, 2020, to June 20, 2020. Informed consent was obtained from all individual participants included in the study. Cardiac, pulmonary, and kidney ultrasonographic evaluations were performed in a protocolized way. Results: In this cohort, 65 patients were included, mean age was 53.4 years, 79% were male, and 35% were diabetic. Thirty-four percent of patients developed AKI, 12% required RRT, and 35% died. Of the patients who developed AKI, 68% had RRI ≥ 0.7. Also, 75% of the patients who required RRT had RRI ≥ 0.7. In the adjusted Cox model, the RRI ≥ 0.7 was associated with higher mortality (HR 2.86, 95% CI: 1.19–6.82, p = 0.01). Conclusions: Critical care ultrasonography is a noninvasive, reproducible, and accurate bedside method that has proven its usefulness. An elevated RRI may have a role in predicting AKI, RRT initiation, and mortality in patients with severe SARS-CoV-2 pneumonia.
The extrafoveal preview paradigm as a measure of predictive, active sampling in visual perception

A key feature of visual processing in humans is the use of saccadic eye movements to look around the environment. Saccades are typically used to bring relevant information, which is glimpsed with extrafoveal vision, into the high-resolution fovea for further processing. With the exception of some unusual circumstances, such as the first fixation when walking into a room, our saccades are mainly guided based on this extrafoveal preview. In contrast, the majority of experimental studies in vision science have investigated “passive” behavioral and neural responses to suddenly appearing and often temporally or spatially unpredictable stimuli. As reviewed here, a growing number of studies have investigated visual processing of objects under more natural viewing conditions in which observers move their eyes to a stationary stimulus, visible previously in extrafoveal vision, during each trial. These studies demonstrate that the extrafoveal preview has a profound influence on visual processing of objects, both for behavior and neural activity. Starting from the preview effect in reading research we follow subsequent developments in vision research more generally and finally argue that taking such evidence seriously leads to a reconceptualization of the nature of human visual perception that incorporates the strong influence of prediction and action on sensory processing. We review theoretical perspectives on visual perception under naturalistic viewing conditions, including theories of active vision, active sensing, and sampling. Although the extrafoveal preview paradigm has already provided useful information about the timing of, and potential mechanisms for, the close interaction of the oculomotor and visual systems while reading and in natural scenes, the findings thus far also raise many new questions for future research.
Correlation between peripheral blood automated hematopoietic progenitor cell counts and flow cytometric CD34+ cell counts differs according to diagnosis in patients undergoing autologous peripheral blood stem cell transplantation

An automated hematopoietic progenitor cell count measurement in Sysmex XN analyzer (XN‐HPC) has been developed to assist flow cytometry CD34+ cell count measurement, which requires technical expertise and a long turnaround time. Here, we evaluated the correlation between XN‐HPC count and flow cytometric CD34+ cell count in pre‐harvest peripheral blood (PB) samples from patients undergoing autologous peripheral blood stem cell (PBSC) transplantation according to diagnosis and investigated the possible cause of the decreased correlation in plasma cell neoplasm patients.
The Prognostic Role of DSM-5 Alcohol Use Disorder Severity and Age of Onset in Treatment Outcome Among Adults Aged 60+

Aims To investigate among older adults with DSM-5 alcohol use disorder (AUD) the relevance of (1) baseline DSM-5 AUD severity, (2) age of DSM-5 AUD onset, and (3) the interactions of DSM-5 AUD severity*treatment condition and age of DSM-5 AUD onset*treatment condition for the prediction of AUD treatment outcomes. Methods The international multicenter RCT “ELDERLY-Study” compared outpatient motivational enhancement therapy (4 sessions) with outpatient motivational enhancement therapy followed by community reinforcement approach for seniors (8 sessions) in adults aged 60+ with DSM-5 AUD. Baseline and 1-, 3-, and 6-month follow-up data from the German and Danish ELDERLY-sites (n = 544) were used (6-month participation rate: 75.9%). DSM-5 AUD diagnoses were obtained using the Mini International Neuropsychiatric Interview and alcohol use using Form 90. Associations between DSM-5 AUD severity and age of onset and AUD treatment outcomes were investigated using multiple logistic regression and generalized linear models. Results The sample was diverse in AUD severity (severe: 54.9%, moderate: 28.2%, mild: 16.9%) and age of onset (median: 50 years; 12–78 years). Overall, with few exceptions, neither AUD severity, nor age of onset, nor their respective interactions with treatment condition significantly predicted drinking outcomes at the different follow-ups (P ≥ 0.05). Conclusions No indication was found for the need to tailor treatment content according to DSM-5 AUD severity and earlier onset in older adults.
Direct Regulons of AtxA, the Master Virulence Regulator of Bacillus anthracis

Bacillus anthracis is the Gram-positive bacterial species that causes anthrax. Anthrax is still prevalent in countries mainly in Asia and Africa, where it causes economic damage and remains a public health issue. ABSTRACT AtxA, the master virulence regulator of Bacillus anthracis, regulates the expression of three toxins and genes for capsule formation that are required for the pathogenicity of B. anthracis. Recent transcriptome analyses showed that AtxA affects a large number of genes on the chromosome and plasmids, suggesting a role as a global regulator. However, information on genes directly regulated by AtxA is scarce. In this work, we conducted genome-wide analyses and cataloged the binding sites of AtxA in vivo and transcription start sites on the B. anthracis genome. By integrating these results, we detected eight genes as direct regulons of AtxA. These consisted of five protein-coding genes, including two of the three toxin genes, and three genes encoding the small RNAs XrrA and XrrB and a newly discovered 95-nucleotide small RNA, XrrC. Transcriptomes from single-knockout mutants of these small RNAs revealed changes in the transcription levels of genes related to the aerobic electron transport chain, heme biosynthesis, and amino acid metabolism, suggesting their function for the control of cell physiology. These results reveal the first layer of the gene regulatory network for the pathogenicity of B. anthracis and provide a data set for the further study of the genomics and genetics of B. anthracis. IMPORTANCE Bacillus anthracis is the Gram-positive bacterial species that causes anthrax. Anthrax is still prevalent in countries mainly in Asia and Africa, where it causes economic damage and remains a public health issue. The mechanism of pathogenicity is mainly explained by the three toxin proteins expressed from the pXO1 plasmid and by proteins involved in capsule formation expressed from the pXO2 plasmid. AtxA is a protein expressed from the pXO1 plasmid that is known to upregulate genes involved in toxin production and capsule formation and is thus considered the master virulence regulator of B. anthracis. Therefore, understanding the detailed mechanism of gene regulation is important for the control of anthrax. The significance of this work lies in the identification of genes that are directly regulated by AtxA via genome-wide analyses. The results reveal the first layer of the gene regulatory network for the pathogenicity of B. anthracis and provide useful resources for a further understanding of B. anthracis.