Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of estrogen plus progestin on breast cancer and mammography in healthy postmenopausal women: the Women's Health Initiative Randomized Trial.

CONTEXT The Women's Health Initiative trial of combined estrogen plus progestin was stopped early when overall health risks, including invasive breast cancer, exceeded benefits. Outstanding issues not previously addressed include characteristics of breast cancers observed among women using hormones and whether diagnosis may be influenced by hormone effects on mammography. OBJECTIVE To determine the relationship among estrogen plus progestin use, breast cancer characteristics, and mammography recommendations. DESIGN, SETTING, AND PARTICIPANTS Following a comprehensive breast cancer risk assessment, 16 608 postmenopausal women aged 50 to 79 years with an intact uterus were randomly assigned to receive combined conjugated equine estrogens (0.625 mg/d) plus medroxyprogesterone acetate (2.5 mg/d) or placebo from 1993 to 1998 at 40 clinical centers. Screening mammography and clinical breast examinations were performed at baseline and yearly thereafter. MAIN OUTCOME MEASURES Breast cancer number and characteristics, and frequency of abnormal mammograms by estrogen plus progestin exposure. RESULTS In intent-to-treat analyses, estrogen plus progestin increased total (245 vs 185 cases; hazard ratio [HR], 1.24; weighted P<.001) and invasive (199 vs 150 cases; HR, 1.24; weighted P =.003) breast cancers compared with placebo. The invasive breast cancers diagnosed in the estrogen plus progestin group were similar in histology and grade but were larger (mean [SD], 1.7 cm [1.1] vs 1.5 cm [0.9], respectively; P =.04) and were at more advanced stage (regional/metastatic 25.4% vs 16.0%, respectively; P =.04) compared with those diagnosed in the placebo group. After 1 year, the percentage of women with abnormal mammograms was substantially greater in the estrogen plus progestin group (716 [9.4%] of 7656) compared with placebo group (398 [5.4%] of 7310; P<.001), a pattern which continued for the study duration. CONCLUSIONS Relatively short-term combined estrogen plus progestin use increases incident breast cancers, which are diagnosed at a more advanced stage compared with placebo use, and also substantially increases the percentage of women with abnormal mammograms. These results suggest estrogen plus progestin may stimulate breast cancer growth and hinder breast cancer diagnosis.
Excessive Hip Flexion During Gait in Patients With Static Encephalopathy: An Examination of Contributing Factors

Background Excessive hip flexion in gait is thought to be associated with hip flexion contracture, but has also been associated with excessive anterior pelvic tilt, knee flexion, internal hip rotation, and muscular factors. The purpose of this study was to examine the contributors to excessive hip flexion during gait in children with cerebral palsy, with and without hip flexion contractures. Methods A retrospective chart review was conducted of 155 children with cerebral palsy. Potential contributors to excessive hip flexion in stance were evaluated, including static and dynamic range of motion, strength measurements, and patient factors including age, previous surgery, distribution of involvement (hemiplegia, diplegia, and quadriplegia), and Gross Motor Function Classification System level. Univariate analysis was performed using simple linear regression and analysis of variance, with appropriate post-hoc tests. All variables were then included in a stepwise linear regression using forward selection. Results Univariate analysis demonstrated a significant relationship (P<0.05) between excessive hip flexion in stance and all predictive variables except static dorsiflexion range of motion with the knee flexed and maximum dorsiflexion in stance. Results of stepwise regression revealed that 3 variables accounted for 65% of the variance: passive hip extension range of motion, average pelvic tilt during the gait cycle, and knee extension achieved in the stance phase of gait. Twenty-two of 45 (49%) exhibiting hip flexion contractures of greater than 10 degrees did not exhibit excessive hip flexion in stance phase. Conclusions Hip extension in stance in children with static encephalopathy depends primarily on hip extension passive range of motion, the amount of pelvic tilt, and knee extension in stance phase. These 3 variables account for 65% of variance in these 155 patients, whereas other factors (age, dorsiflexion in stance, and hamstring range) each account for only 2% to 3% of the variance. Careful clinical examination, including computerized gait analysis when available, is recommended before surgical intervention to determine whether excessive hip flexion is a primary or compensatory deviation. Level of Evidence Level IV, case series.
Design and Validation of a Microarray for Detection, Hemagglutinin Subtyping, and Pathotyping of Avian Influenza Viruses

ABSTRACT Continuing threats of devastating outbreaks in poultry and of human infections caused by highly pathogenic avian influenza virus (HPAIV) H5N1 emphasize the need for the further development of rapid and reliable methods of virus detection and characterization. Here we report on the design and comprehensive validation of a low-density microarray as a diagnostic tool for the detection and typing of avian influenza virus (AIV). The array consists of one probe for the conserved matrix gene and 97 probes targeting the HA0 cleavage-site region. Following fragment amplification by a generic PCR approach, the array enables AIV detection, hemagglutinin (HA) subtyping, and pathotyping within a single assay. For validation, a panel of 92 influenza A viruses which included 43 reference strains representing all 16 HA subtypes was used. All reference strains were correctly typed with respect to their HA subtypes and pathotypes, including HPAIV H5N1/Asia, which caused outbreaks in Germany in 2006 and 2007. In addition, differentiation of strains of the Eurasian and North American lineages of the H5 and H7 subtypes was possible. The sensitivity of the microarray for the matrix gene is comparable to that of real-time reverse transcription-PCR (RT-PCR). It is, however, 10- to 100-fold lower than that of real-time RT-PCR with respect to HA subtyping and pathotyping. The specificity of the array was excellent, as no pathogens relevant for differential diagnosis yielded a positive reaction. Validation with field samples included 19 cloacal swab specimens from wild and domestic birds. Influenza A virus was verified in all samples, whereas the HA subtypes could be determined for 14 samples. The results demonstrate that the microarray assay described complements current methods and can accelerate the diagnosis and characterization of AIV.
Marker Development for Phylogenomics: The Case of Orobanchaceae, a Plant Family with Contrasting Nutritional Modes

Phylogenomic approaches, employing next-generation sequencing (NGS) techniques, have revolutionized systematic and evolutionary biology. Target enrichment is an efficient and cost-effective method in phylogenomics and is becoming increasingly popular. Depending on availability and quality of reference data as well as on biological features of the study system, (semi-)automated identification of suitable markers will require specific bioinformatic pipelines. Here, we established a highly flexible bioinformatic pipeline, BaitsFinder, to identify putative orthologous single copy genes (SCGs) and to construct bait sequences in a single workflow. Additionally, this pipeline has been constructed to be able to cope with challenging data sets, such as the nutritionally heterogeneous plant family Orobanchaceae. To this end, we used transcriptome data of differing quality available for four Orobanchaceae species and, as reference, SCG data from monkeyflower (Erythranthe guttata, syn. Mimulus g.; 1,915 genes) and tomato (Solanum lycopersicum; 391 genes). Depending on whether gaps were permitted in initial blast searches of the four Orobanchaceae species against the reference, our pipeline identified 1,307 and 981 SCGs with average length of 994 bp and 775 bp, respectively. Automated bait sequence construction (using 2× tiling) resulted in 38,170 and 21,856 bait sequences, respectively. In comparison to the recently published MarkerMiner 1.0 pipeline BaitsFinder identified about 1.6 times as many SCGs (of at least 900 bp length). Skipping steps specific to analyses of Orobanchaceae, BaitsFinder was successfully used in a group of non-parasitic plants (three Asteraceae species and, as reference, SCG data from Arabidopsis thaliana based on previously compiled SCGs). Thus, BaitsFinder is expected to be broadly applicable in groups, where only transcriptomes or partial genome data of differing quality are available.
Localized Construction of Bounded Degree and Planar Spanner for Wireless Ad Hoc Networks

We propose a novel localized algorithm that constructs a bounded degree and planar spanner for wireless ad hoc networks modeled by unit disk graph (UDG). Every node only has to know its 2-hop neighbors to find the edges in this new structure. Our method applies the Yao structure on the local Delaunay graph [1] in an ordering that are computed locally. This new structure has the following attractive properties: (1) it is a planar graph; (2) its node degree is bounded from above by a positive constant $$19+\lceil\frac{2\pi}{\alpha}\rceil$$; (3) it is a t-spanner (given any two nodes u and v, there is a path connecting them in the structure such that its length is no more than $$t\leq {\rm max}\{\frac{\pi}{2},\pi {\rm sin}\frac{\alpha}{2}+1\} $$ · Cdel times of the shortest path in the unit disk graph); (4) it can be constructed locally and is easy to maintain when the nodes move around; (5) moreover, we show that the total communication cost is O(n log n) bits, where n is the number of wireless nodes, and the computation cost of each node is at most O(d log d), where d is its 2-hop neighbors in the original unit disk graph. Here Cdel is the spanning ratio of the Delaunay triangulation, which is at most $$\frac{4\sqrt{3}}{9}\pi$$. And the adjustable parameter α satisfies 0 < α ≤ π/3.
Bond strength of a composite luting agent to alumina ceramic surfaces

Objective. The purpose of this study was to evaluate the shear bond strength (SBS) of a dental luting agent to alumina ceramics after different surface pretreatment. Material and Methods. Specimens (n=50) of pressed blocks (10×0×5 mm) of alumina ceramic (Procera AllCeram) were divided into untreated specimens (AF) as provided by the manufacturer and polished specimens (AP). Five groups of specimens (n=5×10) with different surface pretreatments were prepared. Groups 1 and 2: AF and AP without any pretreatment; Group 3: AF treated with silane, (AF-s); Group 4: AF treated with RF plasma spray (AF-RF); Group 5: AF treated with low fusing porcelain (AF-p) glass pearls. Composite cylinders (5×5 mm) were cemented to the test specimens with a resin luting agent. The specimens were loaded to failure in shear mode using a universal testing machine. Recorded loads were used to calculate SBS in MPa. The results were analyzed using one-way ANOVA and the Tukey HSD multiple comparison test at α = 0.05. Scanning electron microscopic micrographs (SEM) were used to characterize surfaces of interest. Results. Polished surfaces had significantly lower SBS (p < 0.05) compared with untreated specimens (AP vs AF). Silanated, non-polished surfaces (AF-s) revealed lower SBS, even though the result was not significantly different from that of AF-s without silane treatment. Plasma treatment improved SBS by a factor of 2 (p<0.05) and treatment with low-fusing porcelain micro pearls increased SBS by a factor of 3 compared to untreated surfaces (p<0.05). The layer of glass pearls did not exceed 5 µm (SEM). Conclusions. Within the limitation of the conditions of this study, treatment of alumina oxide ceramic surfaces with a plasma spray coating or a low-fusing porcelain pearl layer significantly increased the SBS of a resin luting agent to the ceramic surface.
A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol

Thymine glycol (Tg) is a common product of oxidation and ionizing radiation, including that used for cancer treatment. Although Tg is a poor mutagenic lesion, it has been shown to present a strong block to both repair and replicative DNA polymerases. The 2.65-Å crystal structure of a binary complex of the replicative RB69 DNA polymerase with DNA shows that the templating Tg is intrahelical and forms a regular Watson–Crick base pair with the incorporated A. The C5 methyl group protrudes axially from the ring of the damaged pyrimidine and hinders stacking of the adjacent 5′ template guanine. The position of the displaced 5′ template guanine is such that the next incoming nucleotide cannot be incorporated into the growing primer strand, and it explains why primer extension past the lesion is prohibited even though DNA polymerases can readily incorporate an A across from the Tg lesion.
Polarimetric decomposition for forest biomass retrieval

In this paper, the decomposition of fully polarimetric SAR data into three canonical scattering mechanisms is investigated with respect to forest biomass retrieval. It is demonstrated that the dominant backscattering contribution depends strongly on the frequency, incidence angle, and stand condition. The relation between in-situ biomass measurements and the individual decomposition components is examined.
Systematic Knowledge Acquisition for Question Analysis

For the task of turning a natural language question into an explicit intermediate representation of the complexity in question answering systems, all published works so far use rulebased approach to the best of our knowledge. We believe it is because of the complexity of the representation and the variety of question types and also there are no publicly available corpus of a decent size. In these rule-based approaches, the process of creating rules is not discussed. It is clear that manually creating the rules in an ad-hoc manner is very expensive and error-prone. In this paper, we focus on the process of creating those rules manually, in a way that consistency between rules is maintained and the effort to create a new rule is independent of the size of the current rule set. Experimental results are promising where our system achieves better performance and requires much less time and cognitive load compared to previous work.
The Westervelt equation for nonlinear propagation: Numerical simulations and experimental validation of ultrasonic fields produced by array transducers

The purpose of this work is to validate the ability of the Westervelt equation to predict the behavior of ultrasound beams generated by steered phased array transducers. To this end, the Westervelt equation is solved numerically and the results obtained are compared with experimental measurements. The comparison of simulated and measured ultrasonic fields is performed for a modified 32-element linear array transducer. It is demonstrated that the developed code is capable of correctly predicting the behavior of the main lobe, side lobes, and grating lobes in the cases of zero and nonzero steering angles for both the fundamental and the 2nd harmonic components.
Mechanics of vibration-assisted entrapment with application to design

The phenomenon of vibration-assisted entrapment is analyzed in the context of a vibratory parts feeder - the SONY automated parts orienting system (APOS). Entrapment is treated as an energy minimization process. Mechanisms of energy increase and decrease are described. Conditions that lead to failure of entrapment are discussed for a planar part-relief system.
Effect of carvacrol on various cytokines genes expression in splenocytes of asthmatic mice

Objective(s): With regard to pharmacological effects of carvacrol on the respiratory system, its effect on cytokines genes expression in splenocytes of asthmatic mice was examined in this study. Materials and Methods: Splenocytes were isolated from non-sensitized (control group), sensitized mice to ovalbumin (OVA) (group S), and S animals treated with dexamethasone, and three concentrations of carvacrol. IL-4, IFN-γ, TGF-β, FOXP3, and IL-17 genes expression were carried out in cultured splenocytes using the real-time PCR method. Results: Compared to the control group, IFN-γ and FOXP3 genes expression were significantly decreased (P<0.001 for both cases), but IL-4 and IL-17 genes expression were significantly increased in the S group (P<0.001 and P<0.05, respectively). IL-4 gene expression due to treatment of all concentrations of carvacrol, TGF-β gene expression due to its two higher concentrations, and IL-17 gene expression due to its high concentration were significantly decreased compared to group S (P<0.01 to P<0.001). IFN-γ gene expression was significantly increased due to last carvacrol concentration (300 µg/ml, P<0.01), and FOXP3 due to its two last concentrations (150 and 300 µg/ml, P<0.05 and P<0.001, respectively) in treated S splenocytes. Dexamethasone treatment of sensitized splenocytes only showed significant inhibitory effect on IL-4 and TGF-β genes expression (P<0.001 for both cases). Conclusion: These results showed the immunomodulatory effect of carvacrol indicating increased IFN-γ and FOXP3 but decreased IL-4, TGF-β, and IL-17 genes expression, which was more selective than the effect of dexamethasone in sensitized mice splenocytes, which indicates its possible therapeutic value in allergy, autoimmunity, and infectious diseases.
Passive mode locking by using nonlinear polarization evolution in a polarization-maintaining erbium-doped fiber.

By using a new simple cavity design, in which both linear and nonlinear polarization evolution are reproducibly controlled, we demonstrate passive mode locking in a Fabry–Perot-type erbium fiber laser. The laser generates stable trains of pulses as short as 200 fs with an energy content of 70 pJ at repetition rates as high as 100 MHz.
HoLiSwap: Reducing Wire Energy in L1 Caches

This paper describes HoLiSwap a method to reduce L1 cache wire energy, a significant fraction of total cache energy, by swapping hot lines to the cache way nearest to the processor. We observe that (i) a small fraction (<3%) of cache lines (hot lines) serve over 60% of the L1 cache accesses and (ii) the difference in wire energy between the nearest and farthest cache subarray can be over 6$\times$. Our method exploits this difference in wire energy to dynamically identify hot lines and swap them to the nearest physical way in a set-associative L1 cache. This provides up to 44% improvement in the wire energy (1.82% saving in overall system energy) with no impact on the cache miss rate and 0.13% performance drop. We also show that HoLiSwap can simplify way-prediction.
Iminodibenzyl class antipsychotics for schizophrenia: a systematic review and meta-analysis of carpipramine, clocapramine, and mosapramine

Background We conducted a meta-analysis of the iminodibenzyl antipsychotics carpipramine, clocapramine, and mosapramine, which are classified as second-generation antipsychotics (SGAs) for schizophrenia treatment. Methods We searched data that had been published in PubMed, the Cochrane Library databases, PsycINFO, CiNii, and the Japan Medical Abstracts Society up to August 29, 2014. Randomized controlled trials that compared iminodibenzyl antipsychotics with other antipsychotics in patients with schizophrenia were included. Odds ratios and standardized mean differences were evaluated. Results We included four randomized controlled trials on carpipramine (number of patients [n]=290), six on clocapramine (n=1,048), and five on mosapramine (n=986) in the meta-analysis. There were no significant differences in the response rates or in the discontinuation rates either between carpipramine and the other pooled antipsychotics or between clocapramine and the other pooled antipsychotics. On the Positive and Negative Syndrome Scale, mosapramine’s positive subscale scores were superior to those of the other pooled antipsychotics (standard mean of difference =−0.22); however, on that same scale, there were no significant differences in total scores, negative scores, general subscale scores, response rates, or the discontinuation rates between mosapramine and the other pooled antipsychotics. Furthermore, the incidences of extrapyramidal symptoms and of hyperprolactinemia were significantly greater with mosapramine than with the other pooled antipsychotics. Conclusion The pharmacological profiles of carpipramine and clocapramine, which are classified as SGAs, were similar to those of first-generation antipsychotics because there were no significant differences in efficacy and safety outcomes. However, mosapramine was associated with a greater risk of extrapyramidal symptoms and hyperprolactinemia than the other SGAs were, although it may be beneficial for the improvement of positive symptoms.
Collaborative Filtering Recommendation Model based on Convolutional Denoising Auto Encoder

Sparse matrix problem and cold-start problem have been major challenges for recommendation systems. Many approaches take advantage of the combination of Denosing Auto Encoder (DAE) and Collaborative Filtering (CF) methods to address the above problems. However, most DAE-based algorithms adopt the bag-of-words model to process input texts, which loses the latent features of the context information. Therefore, this paper proposes a novel collaborative filtering recommendation model CDA-MF (Convolutional Denoising Auto Encoder-Matrix Factorization), which combines the Convolutional Neural Network (CNN) with the DAE and integrates into the Matrix Factorization algorithm so as to fully explore the latent context features. The experiments over real data verification show that CDA-MF model outperforms the state-of-the-art approaches and gracefully solves the cold-start problem on sparse matrices.
Pharmacokinetics of Isoniazid, Pyrazinamide, and Ethambutol in Newly Diagnosed Pulmonary TB Patients in Tanzania

Exposure to lower-than-therapeutic levels of anti-tuberculosis drugs is likely to cause selection of resistant strains of Mycobacterium tuberculosis and treatment failure. The first-line anti-tuberculosis (TB) regimen consists of rifampicin, isoniazid, pyrazinamide, and ethambutol, and correct management reduces risk of TB relapse and development of drug resistance. In this study we aimed to investigate the effect of standard of care plus nutritional supplementation versus standard care on the pharmacokinetics of isoniazid, pyrazinamide and ethambutol among sputum smear positive TB patients with and without HIV. In a clinical trial in 100 Tanzanian TB patients, with or without HIV infection, drug concentrations were determined at 1 week and 2 months post initiation of anti-TB medication. Data was analysed using population pharmacokinetic modelling. The effect of body size was described using allometric scaling, and the effects of nutritional supplementation, HIV, age, sex, CD4+ count, weight-adjusted dose, NAT2 genotype, and time on TB treatment were investigated. The kinetics of all drugs was well characterised using first-order elimination and transit compartment absorption, with isoniazid and ethambutol described by two-compartment disposition models, and pyrazinamide by a one-compartment model. Patients with a slow NAT2 genotype had higher isoniazid exposure and a lower estimate of oral clearance (15.5 L/h) than rapid/intermediate NAT2 genotype (26.1 L/h). Pyrazinamide clearance had an estimated typical value of 3.32 L/h, and it was found to increase with time on treatment, with a 16.3% increase after the first 2 months of anti-TB treatment. The typical clearance of ethambutol was estimated to be 40.7 L/h, and was found to decrease with age, at a rate of 1.41% per year. Neither HIV status nor nutritional supplementations were found to affect the pharmacokinetics of these drugs in our cohort of patients.