Miracle-dz/UniFAR-FTUs huggingface dataset:
Metagenomes of Wastewater at Different Treatment Stages in Central Germany

Nine metagenomes derived from university hospital effluent, at different stages of wastewater treatment, and the river adjacent to the wastewater treatment plant in Göttingen, Germany, were analyzed. Bacteria was the dominant domain and mainly comprised Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. The microbiomes harbored a diverse microbial community with a site-specific structure. ABSTRACT Nine metagenomes derived from university hospital effluent, at different stages of wastewater treatment, and the river adjacent to the wastewater treatment plant in Göttingen, Germany, were analyzed. Bacteria was the dominant domain and mainly comprised Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. The microbiomes harbored a diverse microbial community with a site-specific structure.
Drought and heat wave impacts on grassland carbon cycling across hierarchical levels.

Droughts and heat waves are increasing in magnitude and frequency, altering the carbon cycle. However, understanding of the underlying response mechanisms remains poor, especially for the combination (hot drought). We conducted a 4-yr. field experiment to examine both individual and interactive effects of drought and heat wave on carbon cycling of a semiarid grassland across individual, functional group, community and ecosystem levels. Drought did not change below-ground biomass (BGB) or above-ground biomass (AGB) due to compensation effects between grass and non-grass functional groups. However, consistently decreased BGB under heat waves limited such compensation effects, resulting in reduced AGB. Ecosystem CO2 fluxes were suppressed by droughts, attributed to stomatal closure-induced reductions in leaf photosynthesis and decreased AGB of grasses, while CO2 fluxes were little affected by heat waves. Overall the hot drought produced the lowest leaf photosynthesis, AGB and ecosystem CO2 fluxes although the interactions between heat wave and drought were usually not significant. Our results highlight that the functional group compensatory effects that maintain community-level AGB rely on feedback of root system responses, and that plant adjustments at the individual level, together with shifts in composition at the functional group level, co-regulate ecosystem carbon sink strength under climate extremes. This article is protected by copyright. All rights reserved.
The evolutionary and transmission characteristic of HIV‐1 CRF07_BC in Nanjing, Jiangsu

To understand the epidemiology, evolutionary and transmission characteristics of HIV‐1 CRF07_BC in Nanjing, China. One hundred and fifty‐nine patients with HIV‐1 CRF07_BC were recruited. DNA sequencing, phylogenetic analysis, and molecular transmission cluster analysis were conducted to determine the molecular epidemiology and evolutionary characteristics. Of these HIV‐1‐infected patients, 95.6% were male, and men who sex with men (76.7%) were the main transmission route. Only 34.0% of these cases were born in Nanjing, and most of them (64.8%) reported having multiple sex partners in the last 6 months. The maximum likelihood phylogenetic analyses of HIV‐1 CRF07_BC revealed two lineages. Overall, 67.3% of Nanjing sequences were connected to at least one other individual distributed in 11 clusters, and the average degree was 21.2 with range (1‐178). The clustered patients were more likely to be male. The time to a most recent common ancestor for the early HIV‐1 CRF07_BC circulating in Nanjing was estimated to be 1998.71[1997.36‐2001.07]. The mean estimated evolutionary rate for the epidemic cluster was slightly lower at 2.38[2.12‐2.65] × 10−3 per site per year with the relaxed exponential clock model. HIV‐1 CRF07_BC was transmitted into Nanjing more than 20 years ago from Yunnan and has become one of the most predominant subtypes with a higher evolutionary rate than before.
Recombinant Human Plasma Gelsolin Stimulates Phagocytosis while Diminishing Excessive Inflammatory Responses in Mice with Pseudomonas aeruginosa Sepsis

Plasma gelsolin (pGSN) is a highly conserved abundant circulating protein, characterized by diverse immunomodulatory activities including macrophage activation and the ability to neutralize pro-inflammatory molecules produced by the host and pathogen. Using a murine model of Gram-negative sepsis initiated by the peritoneal instillation of Pseudomonas aeruginosa Xen 5, we observed a decrease in the tissue uptake of IRDye®800CW 2-deoxyglucose, an indicator of inflammation, and a decrease in bacterial growth from ascitic fluid in mice treated with intravenous recombinant human plasma gelsolin (pGSN) compared to the control vehicle. Pretreatment of the murine macrophage line RAW264.7 with pGSN, followed by addition of Pseudomonas aeruginosa Xen 5, resulted in a dose-dependent increase in the proportion of macrophages with internalized bacteria. This increased uptake was less pronounced when cells were pretreated with pGSN and then centrifuged to remove unbound pGSN before addition of bacteria to macrophages. These observations suggest that recombinant plasma gelsolin can modulate the inflammatory response while at the same time augmenting host antibacterial activity.
Structure of the protective nematode protease complex H-gal-GP and its conservation across roundworm parasites

Roundworm parasite infections are a major cause of human and livestock disease worldwide and a threat to global food security. Disease control currently relies on anthelmintic drugs to which roundworms are becoming increasingly resistant. An alternative approach is control by vaccination and ‘hidden antigens’, components of the worm gut not encountered by the infected host, have been exploited to produce Barbervax, the first commercial vaccine for a gut dwelling nematode of any host. Here we present the structure of H-gal-GP, a hidden antigen from Haemonchus contortus, the Barber’s Pole worm, and a major component of Barbervax. We demonstrate its novel architecture, subunit composition and topology, flexibility and heterogeneity using cryo-electron microscopy, mass spectrometry, and modelling. Importantly, we demonstrate that complexes with the same architecture are present in other Strongylid roundworm parasites including human hookworm. This suggests a common ancestry and the potential for development of a unified hidden antigen vaccine.
Fruit-feeding and activity patterns of mountain gorillas (Gorilla beringei beringei) in Bwindi Impenetrable National Park, Uganda.

OBJECTIVES Availability of fruit is an important factor influencing variation in great ape foraging strategies and activity patterns. This study aims to quantify how frugivory influences activity budgets across age-sex classes of mountain gorillas in Bwindi Impenetrable National Park, Uganda. MATERIALS AND METHODS Daily proportions of fruit-feeding and activity budgets were calculated using 6 years of observational data on four habituated groups. We fitted generalized linear mixed models to test for age-sex differences in the amount of fruit-feeding, and to test whether these factors influence the proportion of time spent feeding, resting, and traveling. RESULTS Bwindi mountain gorillas spent on average 15% of feeding time consuming fruit, with monthly variation ranging from 0 to 70%. Greater amounts of fruit-feeding were associated with more time feeding and traveling, and less time resting. Immatures tended to spend more feeding time on fruit than adults, but less overall time feeding and more time traveling. There were no significant differences in the amount of fruit-feeding and overall feeding time between adult females and silverback males, despite differences in body size. DISCUSSION This study confirms that gorillas are frugivorous, and only the Virunga mountain gorilla population can be characterized as highly folivorous. Along with other frugivorous great apes, Bwindi mountain gorillas alter their activity patterns in response to varying amounts of fruit in their diet. A better understanding of how variable ecological conditions can drive diversity even within a subspecies has important implications for understanding relationships between ecology, body size, and foraging strategies in great apes.
Immunity status against tetanus in young migrants: a seroprevalence study

Background and aim of the work: Thanks to the highly effective vaccine, tetanus became sporadic in high-income countries with well-established primary childhood immunization programs, but it is common in low-income countries. The migrants, leaving countries with poor immunization programs or where vaccinations have been interrupted, may represent a new risk group for tetanus in host countries. A seroprevalence study was conducted to estimate the immunological status against tetanus in young migrants without vaccination documentation. Methods: After a careful assessment by vaccination services of the Local Health Authority, all migrants recently arrived in Italy were included in the serosurvey. Titers of anti-tetanus toxoid were measured using a commercial ELISA kit. Subjects were stratified by age and by WHO region. Antibody titers <0.10 IU/ml were considered to be seronegative, between 0.10 and 1.00 IU/ml as intermediate protection, and >1.00 IU/ml high protection. Results: From January 2004 to December 2019, 2,326 blood samples were collected. Mean age was 13.9 years with no differences between WHO regions. The percentage of the subjects without protective antibodies was 22.3%, with an intermediate level was 45.2%, with high titer was 32.5%. Among migrant coming from African and Eastern Mediterranean WHO regions, the highest percentages of seronegative titers and, at the same time, the low percentages of high protective levels were found. Titers decreased with age. Conclusions: The significant proportion of seronegative migrants and the decrease of protective titers increasing age, confirm the importance of the evaluation of the immunological status to employ the appropriate vaccination strategy.
Spatial-temporal trends and risk factors for undernutrition and obesity among children (<5 years) in South Africa, 2008–2017: findings from a nationally representative longitudinal panel survey

Objectives To assess space-time trends in malnutrition and associated risk factors among children (<5 years) in South Africa. Design Multiround national panel survey using multistage random sampling. Setting National, community based. Participants Community-based sample of children and adults. Sample size: 3254 children in wave 1 (2008) to 4710 children in wave 5 (2017). Primary outcomes Stunting, wasting/thinness and obesity among children (<5). Classification was based on anthropometric (height and weight) z-scores using WHO growth standards. Results Between 2008 and 2017, a larger decline nationally in stunting among children (<5) was observed from 11.0% to 7.6% (p=0.007), compared with thinness/wasting (5.2% to 3.8%, p=0.131) and obesity (14.5% to 12.9%, p=0.312). A geographic nutritional gradient was observed with obesity more pronounced in the east of the country and thinness/wasting more pronounced in the west. Approximately 73% of districts had an estimated wasting prevalence below the 2025 target threshold of 5% in 2017 while 83% and 88% of districts achieved the necessary relative reduction in stunting and no increase in obesity respectively from 2012 to 2017 in line with 2025 targets. African ethnicity, male gender, low birth weight, lower socioeconomic and maternal/paternal education status and rural residence were significantly associated with stunting. Children in lower income and food-insecure households with young malnourished mothers were significantly more likely to be thin/wasted while African children, with higher birth weights, living in lower income households in KwaZulu-Natal and Eastern Cape were significantly more likely to be obese. Conclusions While improvements in stunting have been observed, thinness/wasting and obesity prevalence remain largely unchanged. The geographic and sociodemographic heterogeneity in childhood malnutrition has implications for equitable attainment of global nutritional targets for 2025, with many districts having dual epidemics of undernutrition and overnutrition. Effective subnational-level public health planning and tailored interventions are required to address this challenge.
Physical fitness disparities among New York City public school youth using standardized methods, 2006-2017

Standardized physical fitness monitoring provides a more accurate proxy for youth health when compared with physical activity. Little is known about the utilization of broad-scale individual-level youth physical fitness testing to explore health disparities. We examined longitudinal trends in population-level fitness for 4th-12th grade New York City youth during 2006/7-2016/17 (average n = 510,293 per year). Analyses were performed in 2019. The primary outcome was whether or not youth achieved sex-/age-specific performance levels (called the Healthy Fitness Zone) on the aerobic capacity, muscular strength and muscular endurance tests using the NYC FITNESSGRAM. The Cooper Institute’s most recent Healthy Fitness Zone criteria were applied to all tests and years. Prevalence estimates were weighted, accounted for school clustering, adjusted for student-level sociodemographics, and run by sociodemographic subgroups and year. The overall prevalence for meeting 3 Healthy Fitness Zones increased from 15.5% (95%CI: 13.9%-17.0%) in 2006/7 to 23.3% (95%CI: 22.2%-24.4%) in 2016/17 for students in grades 4–12. Fitness for all student groups increased over time, although Hispanic and non-Hispanic black girls consistently had the lowest prevalence of meeting 3 Healthy Fitness Zones as compared to all other race/sex subgroups. Also, 9th-12th graders had a lower prevalence of meeting 3 Healthy Fitness Zones as compared to 4th-8th graders. Given forecasted sharp increases in cardiovascular disease prevalence, routine youth fitness surveillance using standardized, criterion referenced methods can identify important fitness disparities and inform interventions.
Cochlear Cell Death Induced Via Cisplatin or Gentamycin in Combination with Furosemide in Rodents

Ototoxic models of animal represent an elemental tool in basic otological research. In the present study, using guinea pigs we compared cochlear lesions mediated via cisplatin applied in terms of two regimens: consecutive application alone and in combination with furosemide. The influences of furosemide alone were also assessed; it was observed to result in temporary hearing loss and reversible damage to the stria vascularis. Consecutive administration of cisplatin alone tended to be disadvantageous because it bred progressive body weight loss and higher mortality compared with the combined regimen, which utilized a smaller cisplatin dose. The combined regimen brought about remarkable hair cell loss without corresponding lesion of spiral ganglion neurons. This difference suggests that the co-administered regimen did not mimic the damage to cochlear neuronal innervation caused by clinical application of cisplatin. In the meantime, we spread this method to the ototoxic model build in mice. Coadministration of gentamicin and furosemide caused marked hair cell loss as well as less mortality compared with consecutive application of gentamicin in mice. Due to different pharmacokinetics between cisplatin in guinea pigs and gentamicin in mice, the injection regimens of co-administration of furosemide cisplatin in guinea pigs and gentamicin – furosemide in mice were varied. Overall, the methods of co-administration of cisplatin/gentacimin and furosemide in rodents facilitate ototoxic model build.
Measuring Social Disparities: A Modified Approach to the Index of Child Well-Being (CWI) for Race-Ethnic, Immigrant-Generation, and Socioeconomic Groups with New Results for Whites, Blacks, and Hispanics

The FCD Index of Child Well-Being (CWI) provides a national composite measure for monitoring change in the quality of life of America’s children by indicating the average amount of change that children experience between a baseline year and a subsequent year (Land, Lamb, and Mustillo, 2001; Land, 2005a, 2005b). The method also has been implemented for Whites, Blacks, and Hispanics to assess trends for each group individually (Land, Lamb, and Mustillo, 2001). To assess disparities across groups, the gaps separating Whites from other race-ethnic groups have been calculated as a percentage of the baseline disparity in 1985 set to a value of 100 (Land, Lamb, and Mustillo, 2001; Lamb, Land, Meadows, Traylor, 2005), but this measure cannot show whether disparities have been eliminated, or how much change would be required to eliminate disparities. To overcome this limitation, research presented here offers a modified methodology that measures both levels and disparities in 1985, and from this starting point measures subsequent trends in levels and disparities. Future research will explore disparities among children distinguished by immigrant and socioeconomic circumstances of their families.
Disagreement Payoffs and Negotiated Prices: Evidence from out-of-Network Hospital Payments

Recent policy proposals seek to regulate the prices that hospitals can levy for care delivered outside of a patient’s insurance network. In this paper, we study the potential effects of such regulations on equilibrium in-network prices, network breadth, and hospital service line closures. The bulk of existing empirical work on insurer-provider negotiations assumes that no out-of-network transactions occur. We show that accounting for the presence of these transactions implies substantively larger hospital margins than those implied by canonical models from the literature. We operationalize this by proposing a novel, data-driven measure of off-contract prices paid by insurers to hospitals. Using our model, we conduct a series of counterfactuals to evaluate current policy proposals that would cap out-of-network reimbursements. In counterfactual simulations, reducing out-of-network reimbursements results in considerably lower negotiated prices with in-network hospitals, but at the cost of narrower networks and some outright service line closures. JEL codes: C78, I11, L13 ∗We thank Chris Garmon and seminar participants at RAND, DOJ, and the APPAM annual conference for helpful suggestions. Any errors are our own. Contact information: Prager: elena.prager@kellogg.northwestern. edu; Tilipman: tilipman@uic.edu
The JAK-STAT Pathway and Hematological Malignancy: Beyond Stats

The Janus kinase-signal transducers and activators of transcription (JAK-STAT) is an evolutionarily conserved signaling pathway that mediates cellular responses to dozens of cytokines and growth factors [1]. These responses, including proliferation, differentiation, migration, and apoptosis, are essential for the development and homeostasis of hematopoietic cells. The disruption of the normal homeostatic process arising from aberrant JAK-STAT activation leads to oncogenic consequences. Genetic lesions that cause constitutively active JAK-STAT signaling have been demonstrated in many chronic and acute hematologic malignancies [2]. Somatic JAK2 V617F mutations and other mutant alleles have been identified in most patients with myeloproliferative neoplasms (MPNs) [3]. IL-6 or IL-10/STAT3 signaling is required for the survival of activated B-cell like subtype of diffuse large B-cell lymphoma (ABC DLBCL) [4]. The auto-secretion of IL6 or IL10 in these cancer cells is due to oncogenic MYD88 L265P mutations, which are present in about a third of patients [5]. We and others have demonstrated that the chromosome 9p24 region that JAK2 resides is amplified in 30-50% of primary mediastinal and Hodgkin lymphoma [6]. The amplification results in increased expression of JAK2, whose activation is dependent on autocrine IL-13 cytokine stimulation.
Construction of the Idea of Active Ageing in Centres for Seniors

Current demographic trends are calling forth the need to redefi ne the meaning of old age and its place in society. The concept of active ageing can be seen as a reaction to these efforts to reconceptualise life in old age. This article fi rst briefl y describes the context that gave rise to the term ‘active ageing’ and how this concept is framed as ‘ageing well’ in national and international documents and in the discourse of gerontology. Based on ethnographic studies of two centres offering leisure activities for seniors (mainly using participant observation and in-depth and informal interviews with clients and employees), the article shows 1) how the idea of active ageing and generally of being active as an desirable or undesirable lifestyle in old age is constructed in the framework of the centre’s general operations, and 2) how the clients themselves relate to this idea. The objective of the article is to reveal the signifi cance of active ageing in the formation of a normative image of ‘ageing well’, which on the one hand helps seniors break away from stereotypical notions of ageing, but on the other hand generates new inequalities based on the ability or willingness to ‘age actively’.
Activity Detection in Untrimmed Videos Using Chunk-based Classifiers

Activity detection in untrimmed videos - the process of detecting and localizing human activities in potentially long videos - is a challenging problem in computer vision. We propose an algorithm which is based on the proposition that despite the differences between activity classification and detection, a strong classifier can still be used to achieve state-of-the-art performance in detection by breaking the video into multiple overlapping chunks and classifying each individually. We further introduce two new auxiliary tasks which we call chunk inclusion and localization. The outputs of these tasks, when carefully applied, can be used to dramatically improve performance. We call our method Chunk Aggregation. It is straight-forward to implement and use, and is agnostic to the backbone activity classification architecture used. We also demonstrate the effectiveness of chunk association by presenting results and a series of ablation experiments on the THUMOS’14 and ActEV datasets.
Lack of Skeletal Muscle IL-6 Affects Pyruvate Dehydrogenase Activity at Rest and during Prolonged Exercise

Pyruvate dehydrogenase (PDH) plays a key role in the regulation of skeletal muscle substrate utilization. IL-6 is produced in skeletal muscle during exercise in a duration dependent manner and has been reported to increase whole body fatty acid oxidation, muscle glucose uptake and decrease PDHa activity in skeletal muscle of fed mice. The aim of the present study was to examine whether muscle IL-6 contributes to exercise-induced PDH regulation in skeletal muscle. Skeletal muscle-specific IL-6 knockout (IL-6 MKO) mice and floxed littermate controls (control) completed a single bout of treadmill exercise for 10, 60 or 120 min, with rested mice of each genotype serving as basal controls. The respiratory exchange ratio (RER) was overall higher (P<0.05) in IL-6 MKO than control mice during the 120 min of treadmill exercise, while RER decreased during exercise independent of genotype. AMPK and ACC phosphorylation also increased with exercise independent of genotype. PDHa activity was in control mice higher (P<0.05) at 10 and 60 min of exercise than at rest but remained unchanged in IL-6 MKO mice. In addition, PDHa activity was higher (P<0.05) in IL-6 MKO than control mice at rest and 60 min of exercise. Neither PDH phosphorylation nor acetylation could explain the genotype differences in PDHa activity. Together, this provides evidence that skeletal muscle IL-6 contributes to the regulation of PDH at rest and during prolonged exercise and suggests that muscle IL-6 normally dampens carbohydrate utilization during prolonged exercise via effects on PDH.