Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Coupling between Replication and Packaging of Poliovirus Replicon RNA

ABSTRACT Poliovirus RNA genomes that contained deletions in the capsid-coding regions were synthesized in monkey kidney cells that constitutively expressed T7 RNA polymerase. These replication-competent subgenomic RNAs, or replicons (G. Kaplan and V. R. Racaniello, J. Virol. 62:1687–1696, 1988), were encapsidated intrans by superinfecting polioviruses. When superinfecting poliovirus resistant to the antiviral compound guanidine was used, the RNA replication of the replicon RNAs could be inhibited independently of the RNA replication of the guanidine-resistant helper virus. Inhibiting the replication of the replicon RNA also profoundly inhibited its trans-encapsidation, even though the capsid proteins present in the cells could efficiently encapsidate the helper virus. The observed coupling between RNA replication and RNA packaging could account for the specificity of poliovirus RNA packaging in infected cells and the observed effects of mutations in the coding regions of nonstructural proteins on virion morphogenesis. It is suggested that this coupling results from direct interactions between the RNA replication machinery and the capsid proteins. The coupling of RNA packaging to RNA replication and of RNA replication to translation (J. E. Novak and K. Kirkegaard, Genes Dev. 8:1726–1737, 1994) could serve as mechanisms for late proofreading of poliovirus RNA, allowing only those RNA genomes capable of translating a full complement of functional RNA replication proteins to be propagated.
Assessment of adult body composition using bioelectrical impedance: comparison of researcher calculated to machine outputted values

Objectives To explore the usefulness of Bioelectrical Impedance Analysis (BIA) for general use by identifying best-evidenced formulae to calculate lean and fat mass, comparing these to historical gold standard data and comparing these results with machine-generated output. In addition, we explored how to best to adjust lean and fat estimates for height and how these overlapped with body mass index (BMI). Design Cross-sectional observational study within population representative cohort study. Setting Urban community, North East England Participants Sample of 506 mothers of children aged 7–8 years, mean age 36.3 years. Methods Participants were measured at a home visit using a portable height measure and leg-to-leg BIA machine (Tanita TBF-300MA). Measures Height, weight, bioelectrical impedance (BIA). Outcome measures Lean and fat mass calculated using best-evidenced published formulae as well as machine-calculated lean and fat mass data. Results Estimates of lean mass were similar to historical results using gold standard methods. When compared with the machine-generated values, there were wide limits of agreement for fat mass and a large relative bias for lean that varied with size. Lean and fat residuals adjusted for height differed little from indices of lean (or fat)/height2. Of 112 women with BMI >30 kg/m2, 100 (91%) also had high fat, but of the 16 with low BMI (<19 kg/m2) only 5 (31%) also had low fat. Conclusions Lean and fat mass calculated from BIA using published formulae produces plausible values and demonstrate good concordance between high BMI and high fat, but these differ substantially from the machine-generated values. Bioelectrical impedance can supply a robust and useful field measure of body composition, so long as the machine-generated output is not used.
High-precision aspherical wavefront shaping with combined computer generated holograms

The problem of design and fabrication of metrological standards of aspherical wavefronts and aspherical surfaces is considered. Method for wavefront shaping by computer-generated hologram (CGH) is presented. The wavefront errors caused by fabrication process of CGH, substrate nonuniformity and misalignment against interferometer are considered and discussed in details. Practical results of design and fabrication of amplitude and phase combined CGHs for shaping of two functionally independent wavefronts are presented. It is experimentally shown that errors of wavefront are localized within 0.01 wavelength. It is shown that hologram of this kind allows to subtract from measurements results substrate non-uniformity and fabrication error.
Liver Stiffness Measurement-Based Scoring System for Significant Inflammation Related to Chronic Hepatitis B

Objectives Liver biopsy is indispensable because liver stiffness measurement alone cannot provide information on intrahepatic inflammation. However, the presence of fibrosis highly correlates with inflammation. We constructed a noninvasive model to determine significant inflammation in chronic hepatitis B patients by using liver stiffness measurement and serum markers. Methods The training set included chronic hepatitis B patients (n = 327), and the validation set included 106 patients; liver biopsies were performed, liver histology was scored, and serum markers were investigated. All patients underwent liver stiffness measurement. Results An inflammation activity scoring system for significant inflammation was constructed. In the training set, the area under the curve, sensitivity, and specificity of the fibrosis-based activity score were 0.964, 91.9%, and 90.8% in the HBeAg(+) patients and 0.978, 85.0%, and 94.0% in the HBeAg(−) patients, respectively. In the validation set, the area under the curve, sensitivity, and specificity of the fibrosis-based activity score were 0.971, 90.5%, and 92.5% in the HBeAg(+) patients and 0.977, 95.2%, and 95.8% in the HBeAg(−) patients. The liver stiffness measurement-based activity score was comparable to that of the fibrosis-based activity score in both HBeAg(+) and HBeAg(−) patients for recognizing significant inflammation (G ≥3). Conclusions Significant inflammation can be accurately predicted by this novel method. The liver stiffness measurement-based scoring system can be used without the aid of computers and provides a noninvasive alternative for the prediction of chronic hepatitis B-related significant inflammation.
Age Group and Gender Estimation in the Wild With Deep RoR Architecture

Automatically predicting age group and gender from face images acquired in unconstrained conditions is an important and challenging task in many real-world applications. Nevertheless, the conventional methods with manually-designed features on in-the-wild benchmarks are unsatisfactory because of incompetency to tackle large variations in unconstrained images. This difficulty is alleviated to some degree through convolutional neural networks (CNN) for its powerful feature representation. In this paper, we propose a new CNN-based method for age group and gender estimation leveraging residual networks of residual networks (RoR), which exhibits better optimization ability for age group and gender classification than other CNN architectures. Moreover, two modest mechanisms based on observation of the characteristics of age group are presented to further improve the performance of age estimation. In order to further improve the performance and alleviate over-fitting problem, RoR model is pre-trained on ImageNet first, and then it is fune-tuned on the IMDB-WIKI-101 data set for further learning the features of face images, finally, it is used to fine-tune on Adience data set. Our experiments illustrate the effectiveness of RoR method for age and gender estimation in the wild, where it achieves better performance than other CNN methods. Finally, the RoR-152+IMDB-WIKI-101 with two mechanisms achieves new state-of-the-art results on Adience benchmark.
Performance Enhancement in Uniaxial Strained Silicon-on-Insulator N-MOSFETs Featuring Silicon–Carbon Source/Drain Regions

We report the demonstration of a novel strained silicon-on-insulator N-MOSFET featuring silicon-carbon (Si1-yCy) source and drain (S/D) regions, tantalum nitride metal gate, and hafnium-aluminum oxide high-k gate dielectric. Due to the lattice mismatch between Si0.99C0. 01 S/D stressors and Si, a lateral tensile strain is induced in the transistor channel, leading to substantial electron mobility enhancement. At a fixed OFF-state leakage of 100 nA/mum, the Sii-j/C1-yCy S/D N-MOSFET having a width of 4.7 mum achieves a drive current Josat enhancement of 16% over a control N-MOSFET. This iDsat enhancement, which is primarily attributed to strain-induced mobility improvement, is found to increase with decreasing gate length LG due to an increased strain level in the transistor channel as the Si1-yCy S/D stressors are placed in closer proximity. Slightly improved series resistance with Si1-yCy S/D regions in a strained N-MOSFET accounted for approximately 2% IDsat gain. In addition, a reduction of device width is found to reduce the drive current enhancement of the N-MOSFETs due to the presence of a transverse compressive strain in the transistor channel induced by the isolation regions.
Blood Pressure Response to Main Renal Artery and Combined Main Renal Artery Plus Branch Renal Denervation in Patients With Resistant Hypertension

Background Single‐electrode ablation of the main renal artery for renal sympathetic denervation showed mixed blood pressure (BP)‐lowering effects. Further improvement of the technique seems crucial to optimize effectiveness of the procedure. Because sympathetic nerve fibers are closer to the lumen in the distal part of the renal artery, treatment of the distal main artery and its branches has been shown to reduce variability in treatment effects in preclinical studies and a recent randomized trial. Whether this optimized technique improves clinical outcomes remains uncertain. We report a 2‐center experience of main renal artery and combined main renal artery plus branches renal denervation in patients with resistant hypertension using a multielectrode catheter. Methods and Results Twenty‐five patients with therapy‐resistant hypertension underwent renal sympathetic denervation with combined main renal artery and renal branch ablation and were compared to matched controls undergoing an ablation of the main renal artery only. BP change was assessed by ambulatory measurement at baseline and after 3 months. At baseline, BP was balanced between the groups. After 3 months, BP changed significantly in the combined ablation group (systolic/diastolic 24‐hour mean and daytime mean BP −8.5±9.8/−7.0±10.7 and −9.4±9.8/−7.1±13.5 mm Hg, P<0.001/0.003 and <0.001/0.016, respectively), but not in patients with main artery treatment (−3.5±11.1/−2.0±7.6 and −2.8±10.9/−1.8±7.7 mm Hg, P=0.19/0.20 and 0.19/0.24, respectively). Systolic daytime BP was significantly more reduced in patients with combined ablation than in patients with main artery ablation (P=0.033). Conclusions Combined ablation of the main renal artery and branches appears to improve BP‐lowering efficacy and should be further investigated.
Seroprevalence of hepatitis A in Iranian adolescents: is it time to introduce a vaccine?

SUMMARY Universal vaccination of children for hepatitis A virus (HAV) has emerged as a cost-effective strategy to prevent this infection in regions with high incidence of symptomatic disease. Age-specific seroprevalence surveys are practical and reliable methods to estimate the rate of susceptibility in populations, and to help the implementation of vaccination policies. We surveyed the age-specific HAV seroprevalence in a nationally representative sample of Iranian adolescent students aged 10–18 years. Serum samples (n = 2494) were tested by enzyme immunoassay for total anti-HAV antibody. The overall rate of HAV seropositivity was 64% [95% confidence interval (CI), 62–66), which increased sharply from 14·8% (95% CI 7–23) at age 10 years to 72·9% (95% CI 68–78) at age 13 years, without a significant increase up to age 18 years. No significant difference in HAV seroprevalence was observed between males and females (63% vs. 65·1%), or urban and rural areas (63·4% vs. 65·2%); the seropositivity rate was similar in four different socioeconomic regions of Iran. We conclude that the seroconversion rate of HAV is high in Iranian adolescents and therefore mass vaccination of children may be necessary and should be considered by national health authorities.
Analysis of diabetic retinopathy data using shared inverse Gaussian frailty model

The dependence between individuals in a group is modeled by the group specific quantity, which can be interpreted as an unobserved covariates or “frailties” common to the individuals in the group and assumed to follow some distribution. We consider the shared frailty model in the frame work of parametric Cox proportional hazard model. The Cox regression model with the shared frailty factor allows for unobserved heterogeneity or for statistical dependence between the observed survival times. There are certain assumptions about the distribution of frailty and baseline distribution. The exponential distribution is the commonly used distribution for analyzing life time data. In this paper, we consider shared inverse Gaussian frailty model with bivariate exponential of Marshall-Olkin [20] distribution as baseline hazard for bivariate survival times. We fit the model to the real life bivariate survival data set of diabetic retinopathy data. Data are analyzed using Bayesian approach to the analysis of clustered survival data in which there is a dependence of failure time observations within the same group. The variance component estimation provides the estimated dispersion of the random effects. The problem of analyzing and estimating parameters of shared inverse Gaussian frailty for diabetic retinopathy data is the interest of this paper. Also, we carried out a test for independence using information criteria.
The roles of intrinsic disorder-based liquid-liquid phase transitions in the “Dr. Jekyll–Mr. Hyde” behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration

ABSTRACT Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the “Dr. Jekyll–Mr. Hyde” behavior of those proteins.
Tomato powder in laying hen diets: effects on concentrations of yolk carotenoids and lipid peroxidation

1. The effects of tomato powder supplementation on performance, egg quality, serum and egg yolk carotenoids, vitamins and malondialdehyde (MDA) concentrations in were investigated in laying hens in mid-lay. 2. A total of 90 laying hens, 49 weeks old, were divided into 3 groups consisting of 6 replicate cages, 5 birds per cage. Birds were randomly fed on one of three diets: basal diet and basal diet added with 5 or 10 g tomato powder per kg diet. 3. As tomato powder concentration increased, there were linear increases in feed intake, egg production, egg weight and yolk colour and a linear decrease in feed conversion. Shell weight, shell thickness and Haugh unit remained unchanged in response to dietary treatments. 4. Concentrations of serum and egg yolk lycopene, β-carotene, lutein and vitamin A increased for both diets including tomato powder, whereas MDA decreased linearly with increasing supplemental tomato powder concentration. 5. Tomato powder supplementation increased egg production persistency and increased carotenoids and vitamin A contents in egg yolk, accompanied by reduced yolk lipid peroxidation.
Learning to Rank

Algorithms for learning to rank Web documents, display ads, or other types of items constitute a fundamental component of search engines and more generally of online services. In such systems, when a user makes a request or visits a web page, an ordered list of items (e.g. documents or ads) is displayed; the user scans this list in order, and clicks on the first relevant item if any. When the user clicks on an item, the reward collected by the system typically decreases with the position of the item in the displayed list. The main challenge in the design of sequential list selection algorithms stems from the fact that the probabilities with which the user clicks on the various items are unknown and need to be learned. We formulate the design of such algorithms as a stochastic bandit optimization problem. This problem differs from the classical bandit framework: (1) the type of feedback received by the system depends on the actual relevance of the various items in the displayed list (if the user clicks on the last item, we know that none of the previous items in the list are relevant); (2) there are inherent correlations between the average relevance of the items (e.g. the user may be interested in a specific topic only). We assume that items are categorized according to their topic and that users are clustered, so that users of the same cluster are interested in the same topic. We investigate several scenarios depending on the available side-information on the user before selecting the displayed list: (a) we first treat the case where the topic the user is interested in is known when she places a request; (b) we then study the case where the user cluster is known but the mapping between user clusters and topics is unknown. For both scenarios, we derive regret lower bounds and devise algorithms that approach these fundamental limits.
Vaginal infections among pregnant women at Omdurman Maternity Hospital in Khartoum, Sudan.

INTRODUCTION Microbial infections of the vagina in pregnant women are health problems that lead to serious medical complications and consequences. This study aimed to investigate and determine antimicrobial susceptibilities of the causative agents of vaginal infections in pregnant women. METHODOLOGY A cross-sectional study of pregnant women (n = 200) was conducted between August and December 2008 at Omdurman Maternity Hospital, Khartoum, Sudan. Vaginal and cervical swabs were obtained from each subject and processed for isolation and identification of pathogenic microorganisms using standard methods of wet mount preparation, direct Gram smear, Nugent scoring system, direct immunofluorescence, and cultural techniques. Antimicrobial susceptibility testing of bacterial isolates was performed using standard procedures. Statistical analysis was done using SPSS program version 12.0. 1. A p value < 0.05 was considered statistically significant. RESULTS Of the 200 pregnant women enrolled, BV was detected in 49.8%, followed by Chlamydia trachomatis (31.3%) and Candida albicans (16.6%), with low frequencies of Neisseria gonorrhoeae (1.8%) and Trichomonas vaginalis (0.5%). Higher infection rates were recorded among subjects in the third trimester (71.6%) than in the second trimester of gestation (28.4%). No significant association (p = 0.7) between history of abortions and C. trachomatis infections was found. Gentamicin was the most active agent against Gram-positive and Gram-negative bacteria. Clarythromycin was the most active against Mycoplasma species. CONCLUSIONS Pregnant women with vaginal complaints revealed various positive microbiology results. Such cases may require specific medication. Routine culture of vaginal and cervical samples should be performed on all pregnant women during prenatal visits.
3-Dimensional Numerical Simulation of Open-Barrel Crimping Process

A study of an open-barrel crimping process of 7-stranded wire has been conducted using a full 3-dimensional non-linear explicit dynamic finite element model. 3D dynamic simulation of the crimping process allowed capturing parameters not available in commonly used 2D models, such as barrel and wire extrusion, effect of serrations, and effect of crimper geometry. The model was validated using experimental results. Numerical results indicate that elastic springback of the crimp, upon release of the tool pressure after crimping, is an essential design parameter engineered into a reliable crimped termination. The springback behavior was confirmed experimentally using metallurgical cross sections of terminals treated to reduce adhesion between the wire and the terminal.
Treatment Efficacy of NGF Nanoparticles Combining Neural Stem Cell Transplantation on Alzheimer’s Disease Model Rats

Background Alzheimer’s disease (AD) is the most common type of dementia. It causes progressive brain disorder involving loss of normal memory and thinking skills. The transplantation of neural stem cells (NSCs) has been reported to improve learning and memory function of AD rats, and protects basal forebrain cholinergic neurons. Nerve growth factor – poly (ethylene glycol) – poly (lactic-co-glycolic acid)-nanoparticles (NGF-PEG-PLGA-NPs) can facilitate the differentiation of NSCs in vitro. This study thus investigated the treatment efficacy of NGF-PEG-PLGA-NPs combining NSC transplantation in AD model rats. Material/Methods AD rats were prepared by injection of 192IgG-saporin into their lateral ventricles. Embryonic rat NSCs were separated, induced by NGF-PEG-PLGA-NPs in vitro, and were transplanted. The Morris water-maze test was used to evaluate learning and memory function, followed by immunohistochemical staining for basal forebrain cholinergic neurons, hippocampal synaptophysin, and acetylcholine esterase (AchE) fibers. Results Rats in the combined treatment group had significantly improved spatial learning ability compared to AD model animals (p<0.05). The number of basal forebrain cholinergic neurons, hippocampal synaptophysin, and AchE-positive fibers were all significantly larger than in the NSC-transplantation group, with no difference from control animals. Conclusions NGF-PEG-PLGA-NPs plus NSC transplantation can significantly improve learning and memory functions of AD rats, replenish basal forebrain cholinergic neurons, and help form hippocampal synapses and AchE-positive fibers. These findings may offer practical support for and insight into treatment of Alzheimer’s disease.