Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear Bud Formation: A Novel Manifestation of Zidovudine Genotoxicity

Normal diploid somatic mammalian cell division generates 2 daughter cells as a result of a strict and well-controlled mitotic process. However, some defects during the progression of that process could generate an unbalanced distribution of chromosomes, aneuploidy and eventually, a malignant phenotype. Previous observations using a transgenic mouse model with diminished DNA repair capacity revealed the presence of nuclear buds (NBs) induced in vitro by the nucleoside analog zidovudine (Retrovir®, 3′-azido-3′-deoxythymidine, AZT). Here we used bone marrow mesenchymal cells, taken from mice with the Xpa–/–Trp53+/– genotype, that were cultured and exposed to 0 and 100 µM AZT for 24 hours. Fixed and denatured cells were processed by fluorescence in situ hybridization (FISH) with whole chromosome painting probes used to identify chromosomes in cells growing on glass chamber slides (2 probes/slide). A variety of sizes and shapes of NBs were observed. Some NBs had a large connection with the main nucleus (>¼ of the NB diameter), others hada smaller connection (<¼ of the NB diameter), some were circular and positioned close to the nucleus, while some resided in the cytoplasm separated from the nucleus or connected by a thin chromatin strand. We had hypothesized that NBs would progress in the process of budding until separation occurred, but this was not proven by time-lapse photography studies performed for 20 hours. From 1,126 cells scored in the unexposed cultures, 10.39 % of cells carried NBs, while from 1,108 cells scored in the AZT-exposed cultures 29.16% of cells carried NBs (p = 0.001). In AZT-exposed cells there were a total of 322 NBs scored; 46.6% or 150 NBs contained positive signals for one or both probes used, while 53% or 172 NBs had no probe signal. In addition, FISH analysis showed no preferential localization of any chromosome within the NBs. Among the NBs that carried no probe signal, the presence of positive signals with inversion of DAPI imaging demonstrated centromeric content. It has been hypothesized that NBs occur as a result of expulsion of amplified DNA from the main nucleus; however, this data demonstrates that NBs may contain any chromosome, suggesting that NBs do not consist of just amplified DNA.
Lung cancer in radon-exposed miners and estimation of risk from indoor exposure.

BACKGROUND Radioactive radon is an inert gas that can migrate from soils and rocks and accumulate in enclosed areas, such as homes and underground mines. Studies of miners show that exposure to radon decay products causes lung cancer. Consequently, it is of public health interest to estimate accurately the consequences of daily, low-level exposure in homes to this known carcinogen. Epidemiologic studies of residential radon exposure are burdened by an inability to estimate exposure accurately, low total exposure, and subsequent small excess risks. As a result, the studies have been inconclusive to date. Estimates of the hazard posed by residential radon have been based on analyses of data on miners, with recent estimates based on a pooling of four occupational cohort studies of miners, including 360 lung cancer deaths. PURPOSE To more fully describe the lung cancer risk in radon-exposed miners, we pooled original data from 11 studies of radon-exposed underground miners, conducted a comprehensive analysis, and developed models for estimating radon-associated lung cancer risk. METHODS We pooled original data from 11 cohort studies of radon-exposed underground miners, including 65,000 men and more than 2700 lung cancer deaths, and fit various relative risk (RR) regression models. RESULTS The RR relationship for cumulative radon progeny exposure was consistently linear in the range of miner exposures, suggesting that exposures at lower levels, such as in homes, would carry some risk. The exposure-response trend for never-smokers was threefold the trend for smokers, indicating a greater RR for exposure in never-smokers. The RR from exposure diminished with time since the exposure occurred. For equal total exposure, exposures of long duration (and low rate) were more harmful than exposures of short duration (and high rate). CONCLUSIONS In the miners, about 40% of all lung cancer deaths may be due to radon progeny exposure, 70% of lung cancer deaths in never-smokers, and 39% of lung cancer deaths in smokers. In the United States, 10% of all lung cancer deaths might be due to indoor radon exposure, 11% of lung cancer deaths in smokers, and 30% of lung cancer deaths in never-smokers. This risk model estimates that reducing radon in all homes exceeding the U. S. Environmental Protection Agency's recommended action level may reduce lung cancer deaths about 2%-4%. These estimates should be interpreted with caution, because concomitant exposures of miners to agents such as arsenic or diesel exhaust may modify the radon effect and, when considered together with other differences between homes and mines, might reduce the generalizability of findings in miners.
Risk Factors for Invasive Pulmonary Aspergillosis and Hospital Mortality in Acute-On-Chronic Liver Failure Patients: A Retrospective-Cohort Study

Background: Invasive pulmonary aspergillosis (IPA) in acute-on-chronic liver failure (ACLF) patients is associated with a high mortality. But the clinical characteristics of and the risk factors for IPA among patients with ACLF remains unclear. This study was aimed at assessing clinical manifestation, the risk factors and antifungal medications for as well as the mortality due to IPA in ACLF patients at the First Affiliated Hospital, College of Medicine, Zhejiang University. Patients and Methods: Patients with ACLF who were diagnosed with proven or probable IPA by clinical and laboratory parameters from 1 December 2008 to 1 May 2012 were retrospectively evaluated to determine the risk factors for IPA and the clinical outcomes. The follow-up ended on 30 July 2012. Multivariate analysis was performed to identify the risk factors for mortality and the development of IPA. Results: In total, 787 patients with ACLF were enrolled, and 39 of these patients developed IPA. Thirty seven of these 39 patients died in spite of treatment with antifungal drugs. Controls included 48 patients who did not have a pulmonary infection. The survival rate of patients with IPA was significantly lower than that of those without IPA. IPA was found to be independently associated with age (p = 0.021), encephalopathy (p = 0.002), and steroid use (p = 0.000). There was significant difference in the prognosis between the patients treated with either voriconazole or itraconazole and those without antifungal treatment. Conclusions: Patients with ACLF and IPA have a high mortality rate. Patients with ACLF who present with encephalopathy should avoid steroids, as they increase the mortality rate. Azoles may prolong the survival time.
Effects of Rosiglitazone with Insulin Combination Therapy on Oxidative Stress and Lipid Profile in Left Ventricular Muscles of Diabetic Rats

Purpose. In this study, we tested the hypothesis that rosiglitazone (RSG) with insulin is able to quench oxidative stress initiated by high glucose through prevention of NAD(P)H oxidase activation. Methods and Materials. Male albino Wistar rats were randomly divided into an untreated control group (C), a diabetic group (D) that was treated with a single intraperitoneal injection of streptozotocin (45 mgkg−1), and rosiglitazone group that was treated with RSG twice daily by gavage and insulin once daily by subcutaneous injection (group B). HbA1c and blood glucose levels in the circulation and malondialdehyde and 3-nitrotyrosine levels in left ventricular muscle were measured. Result. Treatment of D rats with group B resulted in a time-dependent decrease in blood glucose. We found that the lipid profile and HbA1c levels in group B reached the control group D rat values at the end of the treatment period. There was an increase in 3-nitrotyrosine levels in group D compared to group C. Malondialdehyde and 3-nitrotyrosine levels were found to be decreased in group B compared to group D (P < 0.05). Conclusion. Our data suggests that the treatment of diabetic rats with group B for 8 weeks may decrease the oxidative/nitrosative stress in left ventricular tissue of rats. Thus, in diabetes-related vascular diseases, group B treatment may be cardioprotective.
High-fat diet-induced juvenile obesity leads to cardiomyocyte dysfunction and upregulation of Foxo3a transcription factor independent of lipotoxicity and apoptosis

Background Obesity is associated with dyslipidemia, which leads to elevated triglyceride and ceramide levels, apoptosis and compromised cardiac function. Methods To determine the role of high-fat diet-induced obesity on cardiomyocyte function, weanling male Sprague–Dawley rats were fed diets incorporating 10% of kcal or 45% of kcal from fat. Mechanical function of ventricular myocytes was evaluated including peak shortening (PS), time-to-PS (TPS), time-to-90% relengthening (TR90) and maximal velocity of shortening and relengthening (± dl/dt). Intracellular Ca2+ properties were assessed using fluorescent microscopy. Results High-fat diet induced hyperinsulinemic insulin-resistant obesity with depressed PS, ± dl/dt, prolonged TPS/TR90 reduced intracellular Ca2+ release and Ca2+ clearing rate in the absence of hypertension, diabetes, lipotoxicity and apoptosis. Myocyte responsiveness to increased stimulus frequency and extracellular Ca2+ was compromised. SERCA2a and phospholamban levels were increased, whereas phosphorylated phospholamban and potassium channel (Kv1,2) were reduced in high-fat diet group. High-fat diet upregulated the forkhead transcription factor Foxo3a, and suppressed mitochondrial aconitase activity without affecting expression of the caloric sensitive gene silent information regulator 2 (Sir2), protein nitrotyrosine formation, lipid peroxidation and apoptosis. Levels of endothelial nitric oxide synthase (NOS), inducible NOS, triglycerides and ceramide were similar between the two groups. Conclusions Collectively, our data show that high-fat diet-induced obesity resulted in impaired cardiomyocyte function, upregulated Foxo3a transcription factor and mitochondrial damage without overt lipotoxicity or apoptosis.
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks

Motivation: The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of transcription factors, chromatin proteins and epigenetic mechanisms. High-throughput experimental data for genome wide in vivo protein–DNA interactions and epigenetic marks are becoming available from large projects, such as the model organism ENCyclopedia Of DNA Elements (modENCODE) and from individual labs. Dissemination and visualization of these datasets in an explorable form is an important challenge. Results: To support research on Drosophila melanogaster transcription regulation and make the genome wide in vivo protein–DNA interactions data available to the scientific community as a whole, we have developed a system called Flynet. Currently, Flynet contains 101 datasets for 38 transcription factors and chromatin regulator proteins in different experimental conditions. These factors exhibit different types of binding profiles ranging from sharp localized peaks to broad binding regions. The protein–DNA interaction data in Flynet was obtained from the analysis of chromatin immunoprecipitation experiments on one color and two color genomic tiling arrays as well as chromatin immunoprecipitation followed by massively parallel sequencing. A web-based interface, integrated with an AJAX based genome browser, has been built for queries and presenting analysis results. Flynet also makes available the cis-regulatory modules reported in literature, known and de novo identified sequence motifs across the genome, and other resources to study gene regulation. Contact: grossman@uic.edu Availability: Flynet is available at https://www.cistrack. org/flynet/. Supplementary information: Supplementary data are available at Bioinformatics online.
Two distinct Epichloë species symbiotic with Achnatherum inebrians, drunken horse grass

Achnatherum inebrians, colloquially known as drunken horse grass, is associated with livestock toxicity in northern China. Epichloë gansuensis (Eg) was described from endophyte isolates from A. inebrians in Sunan County, Gansu Province, whereas a morphologically distinct variety, E. gansuensis var. inebrians (Ei), was described based on two isolates from A. inebrians seeds collected in Urumqi County, Xinjiang Province. Genome sequencing and alkaloid analyses also distinguish these taxa; the Ei isolates produce neurotropic lysergic acid amides (ergot alkaloids), and an Eg isolate produces paxilline (an indole-diterpene alkaloid). To better elucidate the taxonomic diversity of Epichloë spp. symbiotic with A. inebrians, we surveyed eight populations in Xinjiang, Gansu and Inner Mongolia provinces of China and analyzed their genotypes by multiplex PCR for alkaloid biosynthesis genes and mating-type genes. Genotypes consistent with Ei were present in all eight populations, of which they dominated seven. The Ei isolates were all mating type A and tested positive for the ergot alkaloid gene, dmaW. In contrast Eg isolates were all mating type B and had the indole-diterpene gene, idtG. The genome was sequenced from an Ei isolate from seeds collected in Xiahe County, Gansu, and compared to that of the varietal ex type isolate from Urumqi. Alkaloid genes and four different housekeeping genes were nearly identical between the two sequenced Ei isolates and were distinct from a sequenced Eg isolate. Phylogenetic analysis placed Ei, Eg and Epichloë sibirica into respective subclades of a clade that emanated from the base of the Epichloë phylogeny. Given its chemotypic, genotypic, morphological and phylogenetic distinctiveness, its widespread occurrence in rangelands of northern China, and its importance in livestock toxicity, we propose raising Ei to species rank as Epichloë inebrians.
MetaSync: File Synchronization Across Multiple Untrusted Storage Services

Cloud-based file synchronization services, such as Drop-box, are a worldwide resource for many millions of users. However, individual services often have tight resource limits, suffer from temporary outages or even shutdowns, and sometimes silently corrupt or leak user data. We design, implement, and evaluate MetaSync, a secure and reliable file synchronization service that uses multiple cloud synchronization services as untrusted storage providers. To make MetaSync work correctly, we devise a novel variant of Paxos that provides efficient and consistent updates on top of the unmodified APIs exported by existing services. Our system automatically redistributes files upon reconfiguration of providers. Our evaluation shows that MetaSync provides low update latency and high update throughput while being more trustworthy and available. MetaSync outperforms its underlying cloud services by 1.2-10×on three realistic workloads.
The Association Between Insomnia and Increased Future Cardiovascular Events: A Nationwide Population-Based Study

Objectives Insomnia may increase the risk of cardiovascular disease (CVD), but the reported magnitude of the associations between sleep characteristics and CVD is inconsistent. We investigated the association between insomnia and the risk of developing acute myocardial infarction (AMI) and/or stroke by using a nationwide, population-based cohort database in Taiwan. Methods The analyses were conducted using information from a random sample of 1 million people enrolled in the nationally representative Taiwan National Health Insurance Research Database. A total of 44,080 individuals who were 20 years or older, including 22,040 people who had diagnosis of insomnia during the study period and an age-, sex-, comorbidity-matched group of 22,040 people without insomnia, were enrolled in our study. The study end points were the occurrence of cardiovascular events including AMI or stroke during follow-up. Results During a 10-year follow-up, 302 AMI events and 1049 stroke events were identified. The insomnia group had a higher incidence of AMI (2.25 versus 1.08 per 1000 person-years) and stroke (8.01 versus 3.69 per 1000 person-years, p < .001). Cox proportional hazard regression model analysis showed that insomnia was independently associated with a higher risk of future AMI (hazard ratio [HR] = 1.68, 95% confidence interval [CI] = 1.31–2.16, p < .001), stroke (HR = 1.85, 95% CI = 1.62–2.12, p < .001), and the composite event index (HR = 1.81, 95% CI = 1.61–2.05, p < .001), after adjusting for age, sex, and comorbidities. Conclusions Insomnia is associated with an increased risk of future cardiovascular events.
Fault resilience of the algebraic multi-grid solver

As HPC system sizes grow to millions of cores and chip feature sizes continue to decrease, HPC applications become increasingly exposed to transient hardware faults. These faults can cause aborts and performance degradation. Most importantly, they can corrupt results. Thus, we must evaluate the fault vulnerability of key HPC algorithms to develop cost-effective techniques to improve application resilience. We present an approach that analyzes the vulnerability of applications to faults, systematically reduces it by protecting the most vulnerable components and predicts application vulnerability at large scales. Weinitially focus on sparse scientific applications and apply our approachin this paper to the Algebraic Multi Grid (AMG) algorithm. We empirically analyze AMG's vulnerability to hardware faults in both sequential and parallel (hybrid MPI/OpenMP) executions on up to 1,600 cores and propose and evaluate the use of targeted pointer replication to reduce it. Our techniques increase AMG's resilience to transient hardware faults by 50-80% and improve its scalability on faulty computational environments by 35%. Further, we show how to model AMG's scalability in fault-prone environments to predict execution times of large-scale runs accurately.
A fusion tag enabling optical marking and tracking of proteins and cells by FRET‐acceptor photobleaching

Combined time‐lapse imaging with optical marking of fluorescent proteins (FPs) is a widely used method in studies of the dynamic behaviour of proteins, organelles and cell populations. Most of the approaches have specific limitations as they do not permit simultaneous observation of marked and non‐marked molecules, require co‐expression of two FP‐tagged proteins or rely on oligomerizing FPs. Here we provide a strategy to overcome such limitations with a fluorescence resonance energy transfer‐competent tandem fusion tag composed of two FPs. We combine optical marking by acceptor photobleaching with spectral imaging to discriminate between marked and non‐marked molecules. Such ‘bleach‐labelling’ may be employed in a broad range of studies for robust real‐time tracking of proteins, organelles and cells.
Mobile Forensics Development of Mobile Banking Application using Static Forensic

Modern society often conducts transactions through the banking system in many purposes. Suppose transfers between accounts or between banks, monthly subscription payments, and so forth. To facilitate such transactions, many banks provide a service to customers in the form of mobile banking applications. But the increasingly sophisticated technology used in providing the service, the greater the threat of cybercrime in the world around customers. By way of forensic analysis forensic data with the static method expected to obtain important information or data that can be used as digital evidence. Suppose the access log, transaction records, customer profiles, and so on. Because the important information that can be misused as a security loophole to carry out illegal access. This study focused on the analysis of the log data mobile banking application, expected results reached 80%. After testing and analysis of the mobile banking application, there is no important information that can be used for unauthorized access. And the security level applied modern enough to secure from unauthorized access action.
An efficient method for flux weakening control of an induction motor drive system

The paper presents a speed-sensorless induction motor drive system operated into deep flux weakening region. An efficient direct control method based on the stator flux control is detailed. The speed-sensorless proposed algorithm is based on the induction motor's mathematic model and is suitable for low cost industrial applications. Simulations and experimental results based on this algorithm are also presented. The experimental tests were performed based on a dSPACE DS 1103 platform controlling an inverter fed 4 kW induction motor.
Structure and properties of high dielectric constant CaCu/sub 3/Ti/sub 4/O/sub 12/ ceramics

The structure and dielectric properties of CaCu/sub 3/Ti/sub 4/O/sub 12/ ceramics have been investigated. The starting CaCu/sub 3/Ti/sub 4/O/sub 12/ powders were synthesized by a modified glycine nitrate process. The ceramics obtained exhibit a cubic perovskite structure. Dielectric constant up to 57,200 and dielectric loss of 4.4% at 1 kHz have been observed at room temperature. The dielectric properties have been investigated using an impedance spectroscopy technique. The effect of processing and microstructure on the dielectric properties has been discussed.
Overcoming the Barrier in Special Education: A Qualitative Investigation Into the Need for Speech and Language Therapists in St. Lucia

There has been serious under-representation of speech and language therapists in St. Lucia even with the genesis and augmentation of this service in the Western world. A qualitativestudy was conducted to investigate the need for this service in St. Lucia. The few related personnel in the area of speech and language therapy were contacted. In addition, the researcher met with speech and language therapists in Barbados to explore what was being done in the region. All data was collected via personal interviews, online interviews, telephone interviews, and e-mail. Findings suggest that the government is not doing enough to provide speech and language services to the children of St. Lucia who need them.
Effect of storage of red blood cells on alloimmunization

Red blood cells (RBCs) undergo changes during storage. Various studies have suggested a higher risk of adverse and often multifactorial clinical outcomes associated with older‐stored RBCs. Our aim therefore was to examine if storage of transfused RBCs is also associated with the risk of RBC‐specific alloantibody formation.
Improved iterative detection and achieved throughputs of OFDM systems under imperfect channel estimation

Assuming imperfect channel estimation, we propose an improved detector for orthogonal frequency-division multiplexing (OFDM) systems over a frequency-selective fading channel. By adopting a Bayesian approach involving the statistics of the channel estimation errors, we formulate an improved maximum-likelihood (ML) detection metric taking into account the characteristics of the channel estimates. As a first step, we propose a modified iterative detector based on a maximum a posteriori receiver formulation which reduces the impact of channel uncertainty on the decoder performance, by an appropriate use of this metric. The results are compared to those obtained by using a detector based on a mismatched ML metric, which uses the channel estimate as if it was the perfect channel. In a second step, we calculate the information rates achieved by both the improved and mismatched ML detectors, in terms of achievable outage rates. These outage rates are compared to those provided by a theoretical (not practical) decoder defined as the best decoder in the presence of channel estimation errors. Numerical results over both uncorrelated Rayleigh fading channels and realistic ultra wideband channels show that the improved detector outperforms the classically-used mismatched approach in terms of bit error rate and achievable outage rates, without any increase in the receiver complexity.