Miracle-dz/UniFAR-FTUs huggingface dataset:
PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression

Polycyclic aromatic hydrocarbons (PAHs) are among the most widespread natural and anthropogenic pollutants, and some PAHs are proven developmental toxicants. We chemically characterized clean and heavily polluted sites and exposed fish embryos to PAH polluted sediment extracts during four critical developmental stages. Embryos were collected from Fundulus heteroclitus populations inhabiting the clean and heavily polluted Superfund estuary. Embryos of parents from the clean sites are sensitive to PAH pollutants while those of parents from the heavily polluted site are resistant. Chemical analysis of embryos suggests PAH accumulation and pollution-induced toxicity among sensitive embryos during development that ultimately kills all sensitive embryos before hatching, while remarkably, the resistant embryos develop normally. The adverse effects on sensitive embryos are manifested as developmental delays, reduced heart rates, and severe heart, liver, and kidney morphological abnormalities. Gene expression analysis of early somitogenesis, heartbeat initiation, late organogenesis, and pre-hatching developmental stages reveals genes whose expression significantly differs between sensitive and resistant embryo populations and helps to explain mechanisms of sensitivity and resistance to polluted environments during vertebrate animal development.
Mitochondrial Pyruvate Carrier Subunits Are Essential for Pyruvate-Driven Respiration, Infectivity, and Intracellular Replication of Trypanosoma cruzi

Trypanosoma cruzi is the causative agent of Chagas disease. Pyruvate is the end product of glycolysis, and its transport into the mitochondrion is mediated by the mitochondrial pyruvate carrier (MPC) subunits. ABSTRACT Pyruvate is the final metabolite of glycolysis and can be converted into acetyl coenzyme A (acetyl-CoA) in mitochondria, where it is used as the substrate for the tricarboxylic acid cycle. Pyruvate availability in mitochondria depends on its active transport through the heterocomplex formed by the mitochondrial pyruvate carriers 1 and 2 (MPC1/MPC2). We report here studies on MPC1/MPC2 of Trypanosoma cruzi, the etiologic agent of Chagas disease. Endogenous tagging of T. cruzi MPC1 (TcMPC1) and TcMPC2 with 3×c-Myc showed that both encoded proteins colocalize with MitoTracker to the mitochondria of epimastigotes. Individual knockout (KO) of TcMPC1 and TcMPC2 genes using CRISPR/Cas9 was confirmed by PCR and Southern blot analyses. Digitonin-permeabilized TcMPC1-KO and TcMPC2-KO epimastigotes showed reduced O2 consumption rates when pyruvate, but not succinate, was used as the mitochondrial substrate, while α-ketoglutarate increased their O2 consumption rates due to an increase in α-ketoglutarate dehydrogenase activity. Defective mitochondrial pyruvate import resulted in decreased Ca2+ uptake. The inhibitors UK5099 and malonate impaired pyruvate-driven oxygen consumption in permeabilized control cells. Inhibition of succinate dehydrogenase by malonate indicated that pyruvate needs to be converted into succinate to increase respiration. TcMPC1-KO and TcMPC2-KO epimastigotes showed little growth differences in standard or low-glucose culture medium. However, the ability of trypomastigotes to infect tissue culture cells and replicate as intracellular amastigotes was decreased in TcMPC-KOs. Overall, T. cruzi MPC1 and MPC2 are essential for cellular respiration in the presence of pyruvate, invasion of host cells, and replication of amastigotes. IMPORTANCE Trypanosoma cruzi is the causative agent of Chagas disease. Pyruvate is the end product of glycolysis, and its transport into the mitochondrion is mediated by the mitochondrial pyruvate carrier (MPC) subunits. Using the CRISPR/Cas9 technique, we generated individual T. cruzi MPC1 (TcMPC1) and TcMPC2 knockouts and demonstrated that they are essential for pyruvate-driven respiration. Interestingly, although glycolysis was reported as not an important source of energy for the infective stages, MPC was essential for normal host cell invasion and intracellular replication.
Transcriptional Control of Parturition: Insights from Gene Regulation Studies in the Myometrium.

The onset of labour is a culmination of a series of highly coordinated and preparatory physiological events that take place throughout the gestational period. In order to produce the associated contractions needed for fetal delivery, smooth muscle cells in the muscular layer of the uterus (i.e. myometrium) undergo a transition from quiescent to contractile phenotypes. Here, we present the current understanding of the roles transcription factors play in critical labour-associated gene expression changes as part of the molecular mechanistic basis for this transition. Consideration is given to both transcription factors that have been well-studied in a myometrial context, i.e. activator protein 1 (AP-1), progesterone receptors (PRs), estrogen receptors (ERs), and nuclear factor kappa B (NF-κB), as well as additional transcription factors whose gestational event-driving contributions have been demonstrated more recently. These transcription factors may form pregnancy- and labour- associated transcriptional regulatory networks in the myometrium to modulate the timing of labour onset. A more thorough understanding of the transcription factor-mediated, labour-promoting regulatory pathways holds promise for the development of new therapeutic treatments that can be used for the prevention of preterm labour in at-risk women.
Evaluating the vaccination coverage: validity of household-hold vaccination booklet and caregiver’s recall

ABSTRACT Background We compared results from household data sources to medical record sources by using data from a vaccination coverage survey. Methods Vaccination coverage (VC) was calculated based on parental recall, household vaccination booklet, and Zhejiang provincial immunization information system (ZJIIS). We evaluated the accuracy of VC based on household sources (vaccination booklet and recall) assuming the medical record was accurate. Concordance, sensitivity, specificity, positive predictive value, and negative predictive value were estimated as well as the Kappa statistic was also used to evaluate the agreement between data sources. Results Among the 1,800 children identified in the household survey, all were registered in ZJIIS. VC estimated using the vaccination booklet alone was substantially lower than that based on medical records (net bias 3.4–16.7% in different age groups). VC based on parental recall ranged from 2.5% below (among children aged 1 year) to 16.7% points above (among children aged 6 years) than those based on medical records. Concordance was lowest for card estimates (32.5–45.5%). Sensitivity was <60% for all household sources, except for recall source. Specificity was lowest for recall estimates (14.5–42.6%). Positive predictive value was >75%, while negative predictive value was <50%, for all household sources. Kappa statistics generally indicated poor agreement between household and medical record sources. Conclusions Household-retained vaccination booklets and parental recall were insufficient sources for evaluating the VC. Our findings emphasized the importance of taking interventions to make the vaccination booklet more consistent with the records from medical resource.
Facebook Ads Manager as a Recruitment Tool for a Health and Safety Survey of Farm Mothers: Pilot Study

Background Social media platforms have experienced unprecedented levels of growth and usage over the past decade, with Facebook hosting 2.7 billion active users worldwide, including over 200 million users in the United States. Facebook users have been underutilized and understudied by the academic community as a resource for participant recruitment. Objective We performed a pilot study to explore the efficacy and cost-effectiveness of Facebook advertisements for the recruitment of an online agricultural health and safety survey. Methods We undertook a 1-week advertising campaign utilizing the integrated, targeted advertising platform of Facebook Ads Manager with a target-spending limit of US $294. We created and posted three advertisements depicting varying levels of agricultural safety adoption leading to a brief survey on farm demographics and safety attitudes. We targeted our advertisements toward farm mothers aged 21-50 years in the United States and determined cost-effectiveness and potential biases. No participant incentive was offered. Results We reached 40,024 users and gathered 318 advertisement clicks. Twenty-nine participants consented to the survey with 24 completions. Including personnel costs, the cost per completed survey was US $17.42. Compared to the distribution of female producers in the United States, our advertisements were unexpectedly overrepresented in the eastern United States and were underrepresented in the western United States. Conclusions Facebook Ads Manager represents a potentially cost-effective and timely method to recruit participants for online health and safety research when targeting a specific population. However, social media recruitment mirrors traditional recruitment methods in its limitations, exhibiting geographic, response, and self-selection biases that need to be addressed.
Entry of dengue virus serotypes and their geographic distribution in Brazilian federative units: a systematic review.

OBJECTIVE To describe the entry of Dengue virus (DENV) serotypes in Brazil and its federative units. METHODS A systematic review of studies published between 1980 and 2018 in databases and in the gray literature was performed using descriptors related to the years of entry of the DENV serotypes. Additionally, experts and official sources of information (Brazilian Ministry of Health) were consulted. RESULTS From 100 publications selected for the systematic review, 26 addressed the entry of DENV serotypes in the North region of the country, 33 in the Northeast, 24 in the Southeast, 14 in the Central-West, and five in the South. DENV-1 and DENV-4 were introduced in the North region in 1981. DENV-2 was introduced in the Southeast in 1990. DENV-3 was introduced in the North in 1999. CONCLUSION The rapid expansion of dengue throughout the Brazilian territory was verified from the second half of the 1980s, with the gradual entry of the four serotypes, which resulted in the emergence of epidemics of arbovirus, which are currently verified in the country. Considering the epidemiology of the disease, more information should be disseminated and published in the wide-ranging scientific literature for a better understanding of the spread and circulation of DENV serotypes.
The Role of Sleep in Young Children’s Development: A Review

Abstract This review article provides an overview of studies highlighting the importance of sleep in young children’s development and summarizes research-based strategies for implementing healthy sleep practices. Sleep problems are common among young children and is one of the most commonly expressed concerns reported by caregivers. Insufficient sleep, poor sleep quality, and irregular sleep schedules may affect children’s physical health, cognitive capacity, socioemotional processes, and behavioral functioning, with implications for children’s development and well-being. Family context and factors, confounded with cultural variables, play a critical role in children’s sleep behavior and practices. This article presents research-based recommendations to enhance knowledge about children’s sleep and to promote appropriate practices.
Diagnosis and treatment of cardiac amyloidosis. A position statement of the European Society of Cardiology Working Group on Myocardial and Pericardial Diseases

Cardiac amyloidosis is a serious and progressive infiltrative disease that is caused by the deposition of amyloid fibrils at the cardiac level. It can be due to rare genetic variants in the hereditary forms or as a consequence of acquired conditions. Thanks to advances in imaging techniques and the possibility of achieving a non‐invasive diagnosis, we now know that cardiac amyloidosis is a more frequent disease than traditionally considered. In this position paper the Working Group on Myocardial and Pericardial Disease proposes an invasive and non‐invasive definition of cardiac amyloidosis, addresses clinical scenarios and situations to suspect the condition and proposes a diagnostic algorithm to aid diagnosis. Furthermore, we also review how to monitor and treat cardiac amyloidosis, in an attempt to bridge the gap between the latest advances in the field and clinical practice.
The Uncounted Casualties of a Hidden COVID-19 Epidemic in China: Cross-sectional Study on Deaths Related to Overwork

Background During the COVID-19 response, nonclinical essential workers usually worked overtime and experienced significant work stress, which subsequently increased their risk of mortality due to cardiovascular diseases, stroke, and pre-existing conditions. Deaths on duty, including deaths due to overwork, during the COVID-19 response were usually reported on web-based platforms for public recognition and solidarity. Although no official statistics are available for these casualties, a list of on-duty deaths has been made publicly available on the web by crowdsourcing. Objective This study aims to understand the trends and characteristics of deaths related to overwork among the frontline nonclinical essential workers participating in nonpharmaceutical interventions during the first wave of COVID-19 in China. Methods Based on a web-based crowdsourced list of deaths on duty during the first wave of the COVID-19 response in China, we manually verified all overwork-related death records against the full-text web reports from credible sources. After excluding deaths caused by COVID-19 infection and accidents, a total of 340 deaths related to overwork among nonclinical essential workers were attributed to combatting the COVID-19 crisis. We coded the key characteristics of the deceased workers, including sex, age at death, location, causes of death, date of incidence, date of death, containment duties, working area, and occupation. The temporal and spatial correlations between deaths from overwork and COVID-19 cases in China were also examined using Pearson correlation coefficient. Results From January 20 to April 26, 2020, at least 340 nonclinical frontline workers in China were reported to have died as a result of overwork while combatting COVID-19. The weekly overwork mortality was positively correlated with weekly COVID-19 cases (r=0.79, P<.001). Two-thirds of deceased workers (230/340, 67.6%) were under 55 years old, and two major causes of deaths related to overwork were cardiovascular diseases (138/340, 40.6%) and cerebrovascular diseases (73/340, 21.5%). Outside of Hubei province, there were almost 2.5 times as many deaths caused by COVID-19–related overwork (308/340, 90.6%) than by COVID-19 itself (n=120). Conclusions The high number of deaths related to overwork among nonclinical essential workers at the frontline of the COVID-19 epidemic is alarming. Policies for occupational health protection against work hazards should therefore be prioritized and enforced.
Rational design, preparation and adsorption study of a magnetic molecularly imprinted polymer using a dummy template and a bifunctional monomer

In this study, a molecular docking method and solvation model in computer simulation were applied to simultaneously screen a dummy template and a bifunctional monomer in the rational design of a magnetic molecularly imprinted polymer. According to the results of computer simulation, quercetin as a dummy template and methacrylic acid and 4-vinylpyridine as bifunctional monomers could form hydrogen bonds and π–π interaction in a pre-assembly system, which contributes to the formation of highly selective molecular recognition sites and reduces the influence of the solvent on the system. Magnetic molecularly imprinted polymers of a bifunctional monomer as well as those of a monofunctional monomer were prepared and systematically evaluated via scanning electron microscopy, infrared spectroscopy, and vibrating sample magnetometry as well as adsorption kinetics, adsorption isotherms, and adsorption selectivity experiments. All the results strongly indicated that quercetin was suitable to be used as a dummy template, and the bifunctional monomer polymer showed good selectivity and affinity to the target molecule zearalenone, which can be applied in the extraction and purification of real samples. This novel study provides complete and valuable information on the rational design, preparation, and adsorption properties of a magnetic molecularly imprinted polymer using a dummy template and bi-functional monomers.
New Bounds For Distributed Mean Estimation and Variance Reduction

We consider the problem of distributed mean estimation (DME) , in which n machines are each given a local d -dimensional vector x v ∈ R d , and must cooperate to estimate the mean of their inputs µ = 1 n P nv =1 x v , while minimizing total communication cost. DME is a fundamental construct in distributed machine learning, and there has been considerable work on variants of this problem, especially in the context of distributed variance reduction for stochastic gradients in parallel SGD. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an error bound in terms of this norm. However, in many real applications, the input vectors are concentrated around the correct output µ , but µ itself has large norm. In such cases, previous output error bounds perform poorly. In this paper, we show that output error bounds need not depend on input norm. We provide a method of quantization which allows distributed mean estimation to be performed with solution quality dependent only on the distance between inputs , not on input norm, and show an analogous result for distributed variance reduction. The technique is based on a new connection with lattice theory. We also provide lower bounds showing that the communication to error trade-oﬀ of our algorithms is asymptotically optimal. As the lattices achieving optimal bounds under ‘ 2 -norm can be computationally impractical, we also present an extension which leverages easy-to-use cubic lattices, and is loose only up to a logarithmic factor in d . We show experimentally that our method yields practical improvements for common applications, relative to prior approaches.
Plasmin-resistant PSD-95 inhibitors resolve effect-modifying drug-drug interactions between alteplase and nerinetide in acute stroke

The plasma stability and neuroprotective effectiveness of nerinetide are enhanced by partially substituting l- to d-amino acids. Creating an effective duo The drug nerinetide exerts neuroprotective effects in stroke by interfering with the postsynaptic density protein PSD-95. However, in patients, nerinetide lost the therapeutic effects when administered with (or after) the tissue plasminogen activator alteplase. Here, Mayor-Nunez et al. investigated the interaction between nerinetide and alteplase in rodents and showed that plasmin, activated by alteplase, cleaved nerinetide. Administering nerinetide 30 min or more before alteplase avoided the cleavage and restored the therapeutic effect of nerinetide. Moreover, the authors developed a protease-insensitive nerinetide by changing the enantiomeric form of cleavage-sensitive amino acids. The results identified two feasible strategies that might improve the efficacy of nerinetide in combination with tissue plasminogen activators in patients after stroke. Neuroprotection for acute ischemic stroke is achievable with the eicosapeptide nerinetide, an inhibitor of the protein-protein interactions of the synaptic scaffolding protein PSD-95. However, nerinetide is subject to proteolytic cleavage if administered after alteplase, a standard-of-care thrombolytic agent that nullifies nerinetide’s beneficial effects. Here, we showed, on the basis of pharmacokinetic data consistent between rats, primates, and humans, that in a rat model of embolic middle cerebral artery occlusion (eMCAO), nerinetide maintained its effectiveness when administered before alteplase. Because of its short plasma half-life, it can be followed by alteplase within minutes without reducing its neuroprotective effectiveness. In addition, the problem of protease sensitivity is solved by substituting cleavage-prone amino acids from their l- to their d-enantiomeric form. Treatment of rats subjected to eMCAO with such an agent, termed d-Tat-l-2B9c, eliminated protease sensitivity and maintained neuroprotective effectiveness. Our data suggest that both the clinical-stage PSD-95 inhibitor nerinetide and protease-resistant agents such as d-Tat-l-2B9c may be practically integrated into existing stroke care workflows and standards of care.
Mitigating excessive vCPU spinning in VM-agnostic KVM

In virtualized environments, oversubscribing virtual CPUs (vCPUs) on physical CPUs (pCPUs) is common to utilize CPU resources efficiently. Unfortunately, excessive vCPU spinning, which occurs when a vCPU is waiting in a spin loop for an event from a descheduled vCPU, causes serious performance degradation. Usually, the VM-agnostic hypervisor tries to prevent excessive vCPU spinning by rescheduling vCPUs when an excessive spin is detected by hardware support for virtualization. This paper investigates the effectiveness of KVM vCPU scheduler and shows it fails to avoid excessive vCPU spinning in many opportunities. Our in-depth analysis reveals simple modifications to KVM (41 LOC) improve the mitigation of excessive vCPU spinning. We have identified three problems: 1) scheduler mismatch, 2) lost opportunity, and 3) overboost. The first problem comes from the mismatch between the KVM vCPU scheduler and the Linux scheduler. The second and third problems come from an inefficient algorithm for choosing the next candidate vCPU to be scheduled. Our simple modifications gracefully resolves the problems and the performance improves by up to 80 %. Our results imply the VM-agnostic hypervisor can resolve excessive vCPU spinning more gracefully than previously believed.
Potential use of a magnetic compass during long-distance dispersal in a subterranean rodent

Geomagnetic sensitivity is present in a variety of vertebrates, but only recently has attention focused on subterranean mammals. We report the potential use of a magnetic compass in wild Damaraland mole-rats (Fukomys damarensis) during dispersal at two sites in the Kalahari region of South Africa. When the distance traveled was greater than 250 m, males and females dispersed in opposite directions and females preferentially chose a predominantly northeastern direction. This directional choice likely is due to the differing dispersal tactics between sexes. This evidence suggests that Damaraland mole-rats employ a magnetic compass during aboveground dispersal to assist in locating mates or a new territory. This study provides evidence to show how magnetic compass use could be useful in dispersal, an important ecological process for mammals.
A Pattern and POS Auto-Learning Method for Terminology Extraction from Scientific Text

Abstract A lot of new scientific documents are being published on various platforms every day. It is more and more imperative to quickly and efficiently discover new words and meanings from these documents. However, most of the related works rely on labeled data, and it is quite difficult to deal with unlabeled new documents efficiently. For this, we have introduced an unsupervised method based on sentence patterns and part of speech (POS) sequences. Our method just needs a few initial learnable patterns to obtain the initial terminology tokens and their POS sequences. In this process, new patterns are constructed and can match more sentences to find more POS sequences of terminology. Finally, we use obtained POS sequences and sentence patterns to extract terminology terms in new scientific text. Experiments on paper abstracts from Web of Knowledge show that this method is practical and can achieve a good performance on our test data.