Miracle-dz/UniFAR-FTUs huggingface dataset:
Estrogen Degraders and Estrogen Degradation Pathway Identified in an Activated Sludge

ABSTRACT The environmental release and fate of estrogens are becoming an increasing public concern. Bacterial degradation has been considered the main process for eliminating estrogens from wastewater treatment plants. Various bacterial isolates are reportedly capable of aerobic estrogen degradation, and several estrogen degradation pathways have been proposed in proteobacteria and actinobacteria. However, the ecophysiological relevance of estrogen-degrading bacteria in the environment is unclear. In this study, we investigated the estrogen degradation pathway and corresponding degraders in activated sludge collected from the Dihua Sewage Treatment Plant, Taipei, Taiwan. Cultivation-dependent and cultivation-independent methods were used to assess estrogen biodegradation in the collected activated sludge. Estrogen metabolite profile analysis revealed the production of pyridinestrone acid and two A/B-ring cleavage products in activated sludge incubated with estrone (1 mM), which are characteristic of the 4,5-seco pathway. PCR-based functional assays detected sequences closely related to alphaproteobacterial oecC, a key gene of the 4,5-seco pathway. Metagenomic analysis suggested that Novosphingobium spp. are major estrogen degraders in estrone-amended activated sludge. Novosphingobium sp. strain SLCC, an estrone-degrading alphaproteobacterium, was isolated from the examined activated sludge. The general physiology and metabolism of this strain were characterized. Pyridinestrone acid and the A/B-ring cleavage products were detected in estrone-grown strain SLCC cultures. The production of pyridinestrone acid was also observed during the aerobic incubation of strain SLCC with 3.7 nM (1 μg/liter) estrone. This concentration is close to that detected in many natural and engineered aquatic ecosystems. The presented data suggest the ecophysiological relevance of Novosphingobium spp. in activated sludge. IMPORTANCE Estrogens, which persistently contaminate surface water worldwide, have been classified as endocrine disruptors and human carcinogens. We contribute new knowledge on the major estrogen biodegradation pathway and estrogen degraders in wastewater treatment plants. This study considerably advances the understanding of environmental estrogen biodegradation, which is instrumental for the efficient elimination of these hazardous pollutants. Moreover, this study substantially improves the understanding of microbial estrogen degradation in the environment.
Towards a bacterial treatment for armpit malodour

Axillary malodour is a frustrating condition for many people. It can lead to significant discomforts and various psychological effects. The underarm microbiome plays a major role in axillary malodour formation. Not only the bacteria on the epidermis, but also and especially those living in the sweat glands, sweat pores and hair follicles play a pivotal role in malodour development. To treat underarm malodour, this viewpoint article envisions a bacterial treatment. Replacing the autochthonous malodour‐causing microbiome with a non‐odour‐causing microbiome, through an armpit bacterial transplantation or direct application of probiotics/non‐odour‐causing bacteria, could resolve the condition. Selective steering of the microbiome with prebiotics, biochemicals or plant extracts can likewise greatly help in improving the underarm odour. Elimination/inhibition of the “bad bugs” and application/stimulation of the “good bugs” will be part of the future treatment for axillary body odour.
A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design

Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community. This 10-week summer program begins with one week of training on computational biology methods development, transitions to eight weeks of research, and culminates in one week at the Rosetta annual conference. To date, two cohorts of students have participated, tackling research topics including vaccine design, enzyme design, protein-based materials, glycoprotein modeling, crowd-sourced science, RNA processing, hydrogen bond networks, and amyloid formation. Students in the program report outcomes comparable to students who participate in similar in-person programs. These outcomes include the development of a sense of community and increases in their scientific self-efficacy, scientific identity, and science values, all predictors of continuing in a science research career. Furthermore, the program attracted students from diverse backgrounds, which demonstrates the potential of this approach to broaden the participation of young scientists from backgrounds traditionally underrepresented in computational biology.
Lazy release consistency for GPUs

The heterogeneous-race-free (HRF) memory model has been embraced by the Heterogeneous System Architecture (HSA) Foundation and OpenCLTM because it clearly and precisely defines the behavior of current GPUs. However, compared to the simpler SC for DRF memory model, HRF has two shortcomings. The first is that HRF requires programmers to label atomic memory operations with the correct scope of synchronization. This explicit labeling can save significant coherence overhead when synchronization is local, but it is tedious and error-prone. The second shortcoming is that HRF restricts important dynamic data sharing patterns like work stealing. Prior work on remote-scope promotion (RSP) attempted to resolve the second shortcoming. However, RSP further complicates the memory model and no scalable implementation of RSP has been proposed. For example, we found that the previously proposed RSP implementation actually results in slowdowns of up to 30% on large GPUs, compared to a naïve baseline system that forgoes work stealing and scopes. Meanwhile, DeNovo has been shown to offer efficient synchronization with an SC for DRF memory model, performing on average 21% better than our baseline system, but it introduces additional overheads to maintain ownership of all modified data. To resolve these deficiencies, we propose to adapt lazy release consistency - previously only proposed for homogeneous CPU systems - to a heterogeneous system. Our approach, called hLRC, uses a DeNovo-like mechanism to track ownership of synchronization variables, lazily performing coherence actions only when a synchronization variable changes locations. hLRC allows GPU programmers to use the simpler SC for DRF memory model without tracking ownership for all modified data. Our evaluation shows that lazy release consistency provides robust performance improvement across a set of work-stealing graph analysis applications - 29% on average versus the baseline system.
Measurements of Iron Compound Content in the Brain Using a Flexible Core Fluxgate Magnetometer at Room Temperature

It has been observed that patients with neurodegenerative diseases, e.g., Alzheimer’s and Parkinson’s diseases, accumulate metals and, specifically, iron compounds with a magnetic moment, in specific, anatomic regions of the central nervous systems. In this context, several techniques have been exploited in order to measure increased brain iron levels that, typically, accompany neurodegenerative diseases; these techniques include positron emission tomography (PET), magnetic resonance imaging (MRI) and measurement systems based on magnetic sensors (i.e., HTS or LTS SQUID magnetometers). In particular, the measurement approach based on MRI, unlike PET, does not require the use of radioactive tracers and affords superior spatial resolution. However, MRIs can be expensive and not suitable in patients with implanted devices. SQUID-based measurement techniques usually require a very controlled environment, with good compensation for ambient magnetic noise, and are expensive. In this paper, we investigate the possibility of using a flexible core residence time’s difference-fluxgate magnetometer as an alternative low-cost, room temperature solution for carrying out measurements of iron compound contents as observed in neurodegenerative diseases. Our experimental results appear promising enough that one can conclude that it is worth further pursuing this approach, namely, using a very simple sensor to detect ferromagnetic compounds that have accumulated in a localized area in the brain. Our results allow us to state, with good confidence, that monitoring the iron content in (at risk) patients might make it possible to detect the looming onset of some neurodegenerative disorders and could, in fact, be used as a diagnostic tool; all this can be accomplished with an inexpensive, room temperature magnetic field sensor that uses a neuromorphic readout in the time domain.
Exercise-induced adaptations to white and brown adipose tissue

ABSTRACT The beneficial effects of exercise on skeletal muscle and the cardiovascular system have long been known. Recent studies have focused on investigating the effects of exercise on adipose tissue and the effects that these exercise-induced adaptations have on overall metabolic health. Examination of exercise-induced adaptations in both white adipose tissue (WAT) and brown adipose tissue (BAT) has revealed marked differences in each tissue with exercise. In WAT, there are changes to both subcutaneous WAT (scWAT) and visceral WAT (vWAT), including decreased adipocyte size and lipid content, increased expression of metabolic genes, altered secretion of adipokines and increased mitochondrial activity. Adaptations specific to scWAT include lipidomic remodeling of phospholipids and, in rodents, the beiging of scWAT. The changes to BAT are less clear: studies evaluating the effect of exercise on the BAT of humans and rodents have revealed contradictory data, making this an important area of current investigation. In this Review, we discuss the exercise-induced changes to WAT and BAT that have been reported by different studies and highlight the current questions in this field. Summary: Discussion of studies examining the exercise-induced adaptations to white and brown adipose tissue, and the effects that these exercise-induced adaptations have on overall metabolic health.
Pembrolizumab-Induced Thyroiditis: Comprehensive Clinical Review and Insights Into Underlying Involved Mechanisms

Context Thyroid immune-related adverse events (irAEs) in patients treated with programmed death receptor-1 (PD-1) blockade are increasingly recognized as one of the most common adverse effects. Our aim was to determine the incidence and examine the potential mechanisms of anti-PD-1-induced thyroid irAEs. Design Single-center, retrospective cohort study. Patients and Measurements We studied 93 patients with advanced cancer (ages 24 to 82 years; 60% males) who received at least one infusion of pembrolizumab. Thyroid test results and thyroid imaging modalities were reviewed. Comprehensive 10-color flow cytometry of peripheral blood was performed. Results Thirteen (14%) thyroid irAEs were observed. Thyroiditis occurred in seven patients (54%), from which four recovered. New onset of hypothyroidism overt/subclinical developed in three patients. Levothyroxine dosing required doubling in three patients with a known history of hypothyroidism. Thyroperoxidase antibodies were positive in the minority of the patients [4/13 (31%)] and diffuse increased 18fludeoxyglucose uptake of the thyroid gland was observed in the majority [7/11 (64%)] of patients. We observed more circulating CD56+CD16+ natural killer (NK) cells and an elevated HLA-DR surface expression in the inflammatory intermediate CD14+CD16+ monocytes in anti-PD-1-treated patients. Conclusions Thyroid dysfunction is common in cancer patients treated with pembrolizumab. Reversible destructive thyroiditis and overt hypothyroidism are the most common clinical presentations. The mechanism of thyroid destruction appears independent of thyroid autoantibodies and may include T cell, NK cell, and/or monocyte-mediated pathways. Because the thyroid is a frequent target of anti-PD-1 therapies, patients with therapeutically refractory thyroid cancer may be ideal candidates for this treatment.
Prevalence of Extended Spectrum Beta Lactamase (ESBL) Producing Escherichia coli and Klebsiella pneumoniae Isolated from Raw Milk Samples in Al Jazirah State, Sudan

Milk play a major role in human sources of nutrition and remain as the most important prominent in the Sudanese diet. Escherichia coli and Klebsiella pneumoniae are humans and animals opportunistic pathogens, responsible for a wide range of infections. The aim of this study was to evaluate the quality of the commercial available milk and to detect ESBL producing E. coli and K. pneumoniae from raw milk samples of cow in Al Jazirah state, Sudan. Seventy fresh row cow milk samples were collected and examined using standard microbiological methods, ESBL detection was performed on all the isolates by Ceftazidime screening test, those shows positive results by screening method were subjected to ESBL confirmatory test using Double-Disk Synergy Test and Molecular base detection using conventional PCR. Out of the 70 collected samples, 58 (82.8%) showed positive isolating result, the highest prevalence of the isolates was K. pneumoniae 36 (62%) followed by E. coli 22 (38%). The most resistance antibiotics against isolates was Ampicillin (98%), ESBL production was detected among 17 out of the 22 isolated E. coli (29.3%) and 26 (44.8%) out of the 36 isolated K. pneumoniae. The ESBL gene encoding the ESBL isolates was CTX-M gene representing 61% fellows by SHV gene (23%) and TEM gene (16%). ESBL-producing bacteria may also be transferred via waste milk to calves, thus further spreading antibiotic resistance in the farm environment.
Students’ ability in science: Results from a test development study

Student’s ability to use and manipulate scientific concepts has been widely explored; however there is still a need to define the characteristics and nature of science ability. Also, the tests and performance scales that require minimal conceptual knowledge to measure this ability are relatively less common. The aim of this study was to develop an objective measure of science ability of gifted middle school students. In order to assess this ability, Science Ability Test Battery was developed by the researchers. The test battery was divided into two sub scales containing; a multiple choice questions achievement test (Science Ability Test) and a performance assessment (Science Performance Test). The initial Science Ability Test consisted of 23 multiple choice items with one correct answer that required students to use science process skills and reasoning. In the study, stratified sampling was used. The test was administered to 280 middle school students in Turkey and the missing data from 26 students were excluded. In order to obtain a proof of content validity, the researchers elicited feedback from five experts in the field of science education and gifted education and necessary corrections were made in accordance of their views and suggestions. This study will be followed by another research to further analyse validity and reliability of the test. Keywords: science ability, talent, gifted education
On the Stabilizing Effect of the Magnetic Fields in the Magnetic Rayleigh-Taylor Problem

We investigate the stabilizing effect of the vertical equilibrium magnetic field in the Rayleigh--Taylor (RT) problem for a nonhomogeneous incompressible viscous magnetohydrodynamic (MHD) fluid of zero resistivity in the presence of a uniform gravitational field in a horizontally periodic domain, in which the velocity of the fluid is nonslip on both upper and lower flat boundaries. When an initial perturbation around a magnetic RT equilibrium state satisfies some relations, and the strength $|m|$ of the vertical magnetic field of the equilibrium state is bigger than the critical number $m_C$, we can use the Bogovskii function in the standing-wave form and adapt a two-tier energy method in Lagrangian coordinates to show the existence of a unique global-in-time (perturbed) stability solution to the magnetic RT problem. For the case of $|m|<m_C$, we show that the nonlinear RT instability still occurs by developing a new analysis technique based on the method of bootstrap instability. The current result revea.
Fern Stomatal Responses to ABA and CO2 Depend on Species and Growth Conditions1[OPEN]

Growth conditions and species affect fern stomatal responsiveness to ABA and CO2. Changing atmospheric CO2 levels, climate, and air humidity affect plant gas exchange that is controlled by stomata, small pores on plant leaves and stems formed by guard cells. Evolution has shaped the morphology and regulatory mechanisms governing stomatal movements to correspond to the needs of various land plant groups over the past 400 million years. Stomata close in response to the plant hormone abscisic acid (ABA), elevated CO2 concentration, and reduced air humidity. Whether the active regulatory mechanisms that control stomatal closure in response to these stimuli are present already in mosses, the oldest plant group with stomata, or were acquired more recently in angiosperms remains controversial. It has been suggested that the stomata of the basal vascular plants, such as ferns and lycophytes, close solely hydropassively. On the other hand, active stomatal closure in response to ABA and CO2 was found in several moss, lycophyte, and fern species. Here, we show that the stomata of two temperate fern species respond to ABA and CO2 and that an active mechanism of stomatal regulation in response to reduced air humidity is present in some ferns. Importantly, fern stomatal responses depend on growth conditions. The data indicate that the stomatal behavior of ferns is more complex than anticipated before, and active stomatal regulation is present in some ferns and has possibly been lost in others. Further analysis that takes into account fern species, life history, evolutionary age, and growth conditions is required to gain insight into the evolution of land plant stomatal responses.
Bidirectional Associations Between Disordered Eating and Health-Related Quality of Life in Elementary School-Age Youth

Objective To examine longitudinal, bidirectional associations between disordered eating and physical/psychosocial health-related quality of life (HRQOL) in a nonclinical community sample of elementary school-age youth. Methods Participants included 130 children between the ages of 7 and 10 years ( M age = 8.62). Disordered eating and physical/psychosocial HRQOL were assessed using self-report measures at three time points. The potential bidirectional associations were examined using a longitudinal panel model. Results Higher disordered eating predicted lower psychosocial HRQOL during a 6-month period within the same academic year, and lower HRQOL predicted higher disordered eating during a 6-month period across academic years. Conclusion The current study found longitudinal, bidirectional associations between disordered eating and psychosocial, but not physical, HRQOL. The results provide evidence for psychosocial HRQOL as a potential predictor and consequence of disordered eating attitudes. Limitations, future directions, and implications of this research are discussed.
The Relation of Volunteering and Subsequent Changes in Physical Disability in Older Adults

Objectives To describe the association between initiating volunteering and changes in physical disability in older adults, and whether intensity and gender modify this relationship. Methods Employing propensity score weighted regression adjustment, we calculate changes in disability using a sample of U.S. adults (n = 7,135) in the Health and Retirement Study (1996-2012) not volunteering at baseline but later initiating volunteering (1-99 hr/year or 100+ hours per year) or remaining a nonvolunteer. Results Relative to continuous nonvolunteers, low-intensity volunteering is related to 34% lower disability in the low-intensity group (average treatment effect [ATE] = -0.12) and 63% lower in the higher-intensity group (ATE = -0.23). For men, progression was lower only in the highest intensity group (ATE = +0.02), but women experienced similarly less progression of disability (38%-39%) at either level of new engagement (ATE = -0.17 and -0.18). Discussion Initiating a new volunteer role in later life is related to decreased progression of disability, at low or high levels for women and only at higher levels for men. This study suggests that volunteer intervention programs may represent a major public health strategy to delay the progression of physical disability for older adults.
Role of Secondary Prophylaxis With Valganciclovir in the Prevention of Recurrent Cytomegalovirus Disease in Solid Organ Transplant Recipients

Background Cytomegalovirus (CMV) is a major contributor to morbidity and mortality in solid organ transplant recipients (SOTRs). Ganciclovir and valganciclovir are highly effective antiviral drugs with a well-established role in primary prophylaxis and treatment of CMV disease. Our objective in this study was to examine the effect of secondary prophylaxis (SP) on the risk of relapse in SOTRs following an episode of CMV disease. Methods We performed a retrospective cohort study of SOTRs from 1995 to 2015 and used propensity score-based inverse probability of treatment weighting methodology to control for confounding by indication. A weighted Cox model was created to determine the effect of SP on time to relapse within 1 year of treatment completion. Results Fifty-two heart, 34 liver, 79 kidney, and 5 liver-kidney transplant recipients who completed treatment for an episode of CMV infection/disease were included. A total of 120 (70.6%) received SP (median duration, 61 days; range, 5-365) and 39 (23%) relapsed. SP was protective against relapse from 0 to 6 weeks following treatment completion (hazard ratio [HR], 0.19; 95% confidence interval [CI], 0.05-0.69). However, after 6 weeks, risk of relapse did not significantly differ between the 2 groups (HR, 1.18; 95% CI, 0.46-2.99). Conclusions Our findings demonstrate that use of SP following treatment of CMV disease did not confer long-term protection against relapse, although it did delay relapse while patients were receiving antivirals. This suggests that SP has limited clinical utility in the overall prevention of recurrent CMV disease.
Negative Effects of Makeup Use on Perceptions of Leadership Ability Across Two Ethnicities

Cosmetics alter social perceptions, and prior work suggests that cosmetic use may aid female intrasexual competition, making women appear more dominant to other women but more prestigious to other men. It is unclear whether these findings reflect general improvements in perceptions of traits related to women’s dominance or if they are specific to mating contexts only. Here, across two ethnicities, we examined effects of cosmetics used for a social night out on perceptions of women’s leadership ability, a trait that denotes competence/high status outside of mating contexts. Participants of African and Caucasian ethnicity judged faces for leadership ability where half of the trials differed in ethnicity (own- vs. other-ethnicity face pairs) and the subtlety of the color manipulation (50% vs. 100%). Regardless of the participant’s sex or ethnicity, makeup used for a social night out had a negative effect on perceptions of women’s leadership ability. Our findings suggest that, in prior work, women are afforded traits related to dominance, as makeup enhances perceptions of traits that are important for successful female mating competition but not other components of social dominance such as leadership.