Miracle-dz/UniFAR-FTUs huggingface dataset:
Misoprostol use in medical evacuation of spontaneous miscarriage: Pilot drug use evaluation study at the Women's Hospital in Qatar

Background: Misoprostol is a synthetic prostaglandin E1 that induces cervical effacement and uterine contractions at all gestational ages, thus facilitating uterine evacuation and pregnancy termination. Successful medical evacuation of spontaneous miscarriage with minimal adverse effects can be performed using misoprostol-only regimen if given as indicated and if the administered dose, frequency of the dosage, and number of total doses are appropriate. Aim: To conduct a drug use evaluation by investigating indications, appropriateness of dosing, and clinical outcome of misoprostol-only regimen when used for medical evacuation of spontaneous miscarriage at the Women's Hospital in Doha, Qatar. Materials and methods: A retrospective descriptive drug use evaluation was conducted on women with spontaneous miscarriage who received misoprostol for medical evacuation during August 2013. The current practice at the Women's Hospital was compared with the recommendation from the World Health Organization (WHO). Patients were stratified into three groups based on weeks of amenorrhea. Results: A total of 107 patients received misoprostol during August 2013, of which 33 (31%) were included in the study. In these patients, the main indication for misoprostol use was missed miscarriage (54.5%). In the group of patients at ≤ 9 weeks of gestation, 80% received an initial dose of 800 μg, 80% received frequency within the WHO recommendation, and the majority had surgical evacuation (80%). In the group of patients at 10–12 weeks of gestation, more than 80% received an initial dose of 800 μg, 6% received frequency within the WHO recommendation, and more than 75% had successful medical evacuation. In the group of patients at 13–22 weeks of gestation, more than 80% received an initial dose of 400 μg, more than 80% received frequency within the WHO recommendation, and 54% had successful medical evacuation. Overall, more than 70% of the patients received ≤ 3 total doses of misoprostol and more than 60% had successful medical evacuation as a clinical outcome. Conclusions: Despite the current practice at the Women's Hospital not always being in accordance with the WHO recommendation, successful medical evacuation was achieved in most patients.
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google. com/p/readdepth/.
3′ to 5′ Exonuclease Activity of Herpes Simplex Virus Type 1 DNA Polymerase Modulates Its Strand Displacement Activity

ABSTRACT Using a minicircle DNA primer-template, the wild-type catalytic subunit of herpes simplex virus type 1 (HSV-1) DNA polymerase (pol) was shown to lack significant strand displacement activity with or without its processivity factor, UL42. However, an exonuclease-deficient (exo−) pol (D368A) was capable of slow strand displacement. Although UL42 increased the rate (2/s) and processivity of strand displacement by exo− pol, the rate was slower than that for gap-filling synthesis. High inherent excision rates on matched primer-templates and rapid idling-turnover (successive rounds of excision and polymerization) of exo-proficient polymerases correlated with poor strand displacement activity. The results suggest that the exo activity of HSV-1 pol modulates its ability to engage in strand displacement, a function that may be important to the viability and genome stability of the virus.
Origin, Development and Regulation of Human Leydig Cells

Sex steroids are crucial regulators of sexual differentiation and the proper development of secondary sex characteristics and patterns of sexual behavior. Since Leydig cells are the primary major producers of these steroid hormones, maintenance of the normal functions of these cells determines the reproductive capacity and fertility of males. The present minireview discusses recent findings concerning endocrine and paracrine regulation of the proliferation, differentiation and involution of human Leydig cells. The physiology and function of the two distinct fetal and adult populations of human Leydig cells are described, with particular focus on the paracrine environment that triggers their differentiation and functional maturation. The roles of established and more recently discovered paracrine regulators of this maturation, including insulin-like factor 3, platelet-derived growth factor-α, desert hedgehog, ghrelin and leptin are considered. A brief description of the origin, ontogenesis and functional markers of human fetal and adult Leydig cells is presented.
Identification of chronic hepatitis C patients without hepatic fibrosis by a simple predictive model

Liver biopsy is required for staging hepatic fibrosis in patients with chronic hepatitis C, but it is an expensive procedure with occasional complications and poor patient acceptance. This cohort study was designed to assess the accuracy of a noninvasive method aimed to discriminate between patients with and without significant liver fibrosis (stages 2‐4 versus 0‐1). Clinically relevant variables were analyzed in a cohort of 476 consecutive untreated patients (estimation group, 351 patients; validation group, 125 patients) with chronic hepatitis C who underwent a liver biopsy. Multivariate analysis identified age, gamma glutamyl transpeptidase (GGT), cholesterol, platelet count, and prothrombin time as independent predictors of fibrosis. We constructed a model and a score system combining age, GGT, cholesterol, and platelet count that proved useful to identify patients without significant hepatic fibrosis. The area under the ROC curve was 0.86 for the estimation group and 0.81 for the validation group. Using the best cutoff score (less than 4.2), presence of significant fibrosis (F2 to F4) could be excluded with high accuracy (negative predictive value of 96%) in 125 (36%) of 351 patients. Similarly, it could be excluded with the same certainty in 49 (39%) of the 125 patients of the validation group. Only 2 patients with liver fibrosis stage 2 were incorrectly classified. In conclusion, a combination of easily accessible variables accurately predicts the absence of significant fibrosis and might render liver biopsy unnecessary in more than one third of patients with chronic hepatitis C.
Report on the August 2012 Brawley Earthquake Swarm in Imperial Valley, Southern California

The 2012 Brawley earthquake swarm occurred in the Brawley Seismic Zone (BSZ) within the Imperial Valley of southern California (Fig. 1). The BSZ is the northernmost extensional segment of the Pacific–North America plate boundary system. Johnson and Hill (1982) used the distribution of seismicity since the 1930s to outline the geographical extent of the BSZ, defining boundaries of the BSZ as shown in Figure 1. Its north–south extent ranges from the northern section of the Imperial fault, starting approximately 10 km north of the United States–Mexico international border and connecting to the southern end of the San Andreas fault, where it terminates in the Salton Sea. Larsen and Reilinger (1991), who defined a similar geographical extent of the BSZ, argued that the BSZ was migrating to the northwest, which they associated with the propagation of the Gulf of California rift system into the North American continent. During the seismically active period of the 1970s, the BSZ produced close to half of the earthquakes recorded in California (Johnson and Hill, 1982; Hutton et al., 2010). However, for two decades following the 1979 Imperial Valley mainshock M_w 6.4 and its aftershock sequence, the BSZ was much less active. In general, the BSZ seismicity is indicative of right-lateral strike-slip plate motion accompanied by crustal thinning as well as possible associated fluid movements in the crust (Chen and Shearer, 2011). The 2012 Brawley swarm produced more than 600 events recorded by the United States Geological Survey (USGS)–California Institute of Technology (Caltech) Southern California Seismic Network (SCSN). Other monitoring instruments in the region, such as the Global Positioning System (GPS) network, creepmeters, and the Wildlife Liquefaction Array (WLA) also recorded signals from the largest events. In addition, Interferometric Synthetic Aperture Radar (InSAR) satellites collected images from space.
Fast Iterative Graph Computation with Block Updates

Scaling iterative graph processing applications to large graphs is an important problem. Performance is critical, as data scientists need to execute graph programs many times with varying parameters. The need for a high-level, high-performance programming model has inspired much research on graph programming frameworks. In this paper, we show that the important class of computationally light graph applications - applications that perform little computation per vertex - has severe scalability problems across multiple cores as these applications hit an early "memory wall" that limits their speedup. We propose a novel block-oriented computation model, in which computation is iterated locally over blocks of highly connected nodes, significantly improving the amount of computation per cache miss. Following this model, we describe the design and implementation of a block-aware graph processing runtime that keeps the familiar vertex-centric programming paradigm while reaping the benefits of block-oriented execution. Our experiments show that block-oriented execution significantly improves the performance of our framework for several graph applications.
Conductivity in transparent oxide semiconductors

Despite an extensive research effort for over 60 years, an understanding of the origins of conductivity in wide band gap transparent conducting oxide (TCO) semiconductors remains elusive. While TCOs have already found widespread use in device applications requiring a transparent contact, there are currently enormous efforts to (i) increase the conductivity of existing materials, (ii) identify suitable alternatives, and (iii) attempt to gain semiconductor-engineering levels of control over their carrier density, essential for the incorporation of TCOs into a new generation of multifunctional transparent electronic devices. These efforts, however, are dependent on a microscopic identification of the defects and impurities leading to the high unintentional carrier densities present in these materials. Here, we review recent developments towards such an understanding. While oxygen vacancies are commonly assumed to be the source of the conductivity, there is increasing evidence that this is not a sufficient mechanism to explain the total measured carrier concentrations. In fact, many studies suggest that oxygen vacancies are deep, rather than shallow, donors, and their abundance in as-grown material is also debated. We discuss other potential contributions to the conductivity in TCOs, including other native defects, their complexes, and in particular hydrogen impurities. Convincing theoretical and experimental evidence is presented for the donor nature of hydrogen across a range of TCO materials, and while its stability and the role of interstitial versus substitutional species are still somewhat open questions, it is one of the leading contenders for yielding unintentional conductivity in TCOs. We also review recent work indicating that the surfaces of TCOs can support very high carrier densities, opposite to the case for conventional semiconductors. In thin-film materials/devices and, in particular, nanostructures, the surface can have a large impact on the total conductivity in TCOs. We discuss models that attempt to explain both the bulk and surface conductivity on the basis of bulk band structure features common across the TCOs, and compare these materials to other semiconductors. Finally, we briefly consider transparency in these materials, and its interplay with conductivity. Understanding this interplay, as well as the microscopic contenders for providing the conductivity of these materials, will prove essential to the future design and control of TCO semiconductors, and their implementation into novel multifunctional devices.
Dietary Folate Intake, MTHFR Genetic Polymorphisms, and the Risk of Endometrial Cancer among Chinese Women

Folate plays an important role in carcinogenesis. The enzyme 5,10-methylenetetrahydrofolate reductase (MTHFR), encoded by the MTHFR gene, is involved in this process. We investigated both the independent and joint effects of dietary folate and other methyl-related nutrients, as well as three polymorphisms of MTHFR (677C>T, 1298A>C, and 1793G>A), on endometrial cancer risk in a population-based case-control study. Between 1997 and 2003, 1,204 newly diagnosed endometrial cancer cases and 1,212 controls were recruited among women between the ages of 30 and 69 years in urban Shanghai, China. Information on dietary intake of folate and other methyl-related nutrients, including vitamin B2 (riboflavin), vitamin B6, vitamin B12, and methionine, was derived from a validated food frequency questionnaire. Genotyping was completed on 1,041 cases and 1,030 controls for MTHFR 677C>T (rs1801133), 1298A>C (rs1801131), and 1793 G>A (rs22749746). Haplotype estimation of the three single-nucleotide polymorphisms was performed using PHASE software. Odds ratios (OR) and 95% confidence intervals (95% CI) were calculated to evaluate associations of nutrients, MTHFR genotypes, and haplotypes with endometrial cancer risk. A significant inverse association between dietary folate intake and endometrial cancer risk was observed among all subjects and non–B vitamin supplement users. The greatest reduction in endometrial cancer risk was observed among non-users of supplements in the highest quartile of dietary folate intake (OR, 0.5; 95% CI, 0.4-0.7) as compared with those in the lowest quartile. Dietary intake of folate cofactors (methionine, vitamin B2, vitamin B6, and vitamin B12) was not related to risk of endometrial cancer. No association was observed between endometrial cancer and the MTHFR 677C>T, 1298 A>C, and 1793G>A polymorphisms or derived haplotypes. Among non-users of supplements, however, the 1298C and 1793A alleles were associated with a lower risk of endometrial cancer among women with high dietary folate intake but related to a higher risk among those with low dietary folate intake (Pinteraction = 0.08 and 0.03, respectively). Further analysis showed that the lowest risk (OR, 0.6; 95% CI, 0.4-1.1) was among women with the 1298C allele and the highest intake of both folate and riboflavin (Pinteraction = 0.04). A similar association was observed for the 1793A allele (Pinteraction = 0.03). Our findings suggest that folate intake may decrease the risk of endometrial cancer and modify the effect of MTHFR polymorphisms on risk. (Cancer Epidemiol Biomarkers Prev 2007;16(2):281–7)
Quantitative Determination of Nuclear and Cytoplasmic Epidermal Growth Factor Receptor Expression in Oropharyngeal Squamous Cell Cancer by Using Automated Quantitative Analysis

Background: Several lines of evidence support the epidermal growth factor receptor (EGFR) as a molecular target for therapy in head and neck squamous cell carcinomas (HNSCC). Determination of tumor EGFR levels by conventional immunohistochemistry has not always predicted antitumor efficacy. Quantitative assays may provide more accurate assessment of the level of EGFR receptor in the tumor, which may thus provide more reliable prognostic and predictive information. We studied the prognostic value of quantitative assessment of EGFR in oropharyngeal squamous cell cancers treated with radiotherapy. Experimental Design: We studied EGFR protein expression on a tissue microarray composed of 95 oropharyngeal cancer cases using an in situ molecular-based method of quantitative assessment of protein expression (AQUA) and correlated those with clinical and pathologic data. Automated, quantitative analysis uses cytokeratin to define pixels as cancer (tumor mask) within the array spot and measures intensity of EGFR expression using a Cy5-conjugated antibody within the mask. A continuous index score is generated, which is directly proportional to the number of molecules per unit area, and cases were defined as high expressing if they were above the median expression level. Results: The mean follow-up time for survivors was 44.9 months, and for the entire cohort was 34.8 months. Patients with high tumor EGFR expression levels had a local recurrence rate of 58% compared with 17% for patients with low EGFR tumor expression (P < 0.01). Similarly, patients with high nuclear EGFR expression had a local recurrence rate of 54% compared with 21% for patients with low EGFR nuclear expression (P < 0.05). Additionally, patients with high tumor and nuclear EGFR levels had inferior disease-free survival compared with low expressors (19% versus 43% and 19% versus 45%, respectively. P < 0.05 for each). In multivariate analysis adjusting for well-characterized prognostic variables, high tumor and nuclear EGFR expression levels retained their prognostic significance. Conclusion: The AQUA system provides a continuous measurement of EGFR on paraffin-embedded tissue and was able to reveal the association between EGFR expression and outcome expected from the biological role of EGFR. In the future, EGFR AQUA score may be useful in predicting response to EGFR-targeted therapies.
Direct Comparison of the Safety and Efficacy of Ferric Carboxymaltose versus Iron Dextran in Patients with Iron Deficiency Anemia

Several intravenous iron complexes are available for the treatment of iron deficiency anemia (IDA). Iron dextran (DEX) is associated with an elevated risk of potentially serious anaphylactic reactions, whereas others must be administered in several small infusions to avoid labile iron reactions. Ferric carboxymaltose (FCM) is a nondextran intravenous iron which can be administered in high single doses. A randomized, open label, and multicenter comparison of FCM to DEX in adults with IDA and baseline hemoglobin of ≤11.0 g/dL was conducted. A total of 160 patients were in the safety population (FCM n = 82; DEX n = 78). Adverse events, including immune system disorders (0% in FCM versus 10.3% in DEX, P = 0.003) and skin disorders (7.3% in FCM versus 24.4% in DEX, P = 0.004), were less frequently observed in the FCM group. A greater portion of patients in the FCM group experienced a transient, asymptomatic decrease in phosphate compared to patients in the DEX group (8.5% in FCM versus 0% in DEX, P = 0.014). In the FCM arm, the change in hemoglobin from baseline to the highest observed level was 2.8 g/dL, whereas the DEX arm displayed a change of 2.4 g/dL (P = 0.20). Treatment of IDA with FCM resulted in fewer hypersensitivity-related reactions than DEX.
Transforming growth factor‐βl as a regulator of the serpins/t‐PA axis in cerebral ischemia

The tissue type plasminogen activator (t‐PA) is a serine protease that is involved in neuronal plasticity and cell death induced by excitotoxins and ischemia in the brain. t‐PA activity in the central nervous system is regulated through the activation of serine protease inhibitors (serpins) such as the plasminogen activator inhibitor (PAI‐1), the protease nexin‐1 (PN‐1), and neuroserpin (NSP). Recently we demonstrated in vitro that PAI‐1 produced by astrocytes mediates the neuroprotective effect of the transforming growth factor‐β1 (TGF‐β1) in NMDA‐induced neuronal cell death. To investigate whether serpins may be involved in neuronal cell death after cerebral ischemia, we determined, by using semiquantitative RT‐PCR and in situ hybridization, that focal cerebral ischemia in mice induced a dramatic overexpression of PAI‐1 without any effect on PN‐1, NSP, or t‐PA. Then we showed that although the expression of PAI‐1 is restricted to astrocytes, PN‐1, NSP, and t‐PA are expressed in both neurons and astrocytes. Moreover, by using semiquantitative RT‐PCR and Western blotting, we observed that only the expression of PAI‐1 was modulated by TGF‐β1 treatment via a TGF‐β‐inducible element contained in the PAI‐1 promoter (CAGAbox). Finally, we compared the specificity of TGF‐β 1 action with other members of the TGF‐β family by using luciferase reporter genes. These data show that TGF‐β and activin were able to induce the overexpression of PAI‐1 in astrocytes, but that bone morphogenetic proteins, glial cell line‐derived neutrophic factor, and neurturin did not. These results provide new insights into the regulation of the serpins/t‐PA axis and the mechanism by which TGF‐β may be neuroprotective. —Docagne, F. , Nicole, O. , Marti, H. H. , MacKenzie, E. T. , Buisson, A. , Vivien, D. Transforming growth factor‐β1 as a regulator of the serpins/t‐PA axis in cerebral ischemia. FASEB J. 13, 1315–1324 (1999)
affeine potentiates methamphetamine-induced toxicity both in vitro and in vivo

Ya-Ba, a combination of the two potent psychostimulants methamphetamine (METH) and caffeine (CAF), is commonly used by drug abusers in Thailand and neighboring countries. While the neurotoxic effects of METH are well documented, the toxicity of this combination is mostly unknown. This study aimed to elucidate the effects of this particular drug combination using both in vitro and in vivo models. We found that combined treatment of METH and CAF at individually non-toxic concentrations significantly
Multiple-Description <formula formulatype="inline"> <tex Notation="TeX">$l_{1}$</tex></formula>-Compression

Multiple descriptions (MDs) is a method to obtain reliable signal transmissions on erasure channels. An MD encoder forms several descriptions of the signal and each description is independently transmitted across an erasure channel. The reconstruction quality then depends on the set of received descriptions. In this paper, we consider the design of redundant descriptions in an MD setup using l1-minimization with Euclidean distortion constraints. In this way we are able to obtain sparse descriptions using convex optimization. The proposed method allows for an arbitrary number of descriptions and supports both symmetric and asymmetric distortion design. We show that MDs with partial overlapping information corresponds to enforcing coupled constraints in the proposed convex optimization problem. To handle the coupled constraints, we apply dual decompositions which makes first-order methods applicable and thereby admit solutions for large-scale problems, e.g., coding entire images or image sequences. We show by examples that the proposed framework generates non-trivial sparse descriptions and non-trivial refinements. We finally show that the sparse descriptions can be quantized and encoded using off-the-shell encoders such as the set partitioning in hierarchical trees (SPIHT) encoder, however, the proposed method shows a rate-distortion loss compared to state-of-the-art image MD encoders.