Miracle-dz/UniFAR-FTUs huggingface dataset:
Stillbirths at a hospital in Nablus, 2010: a cohort study

Background Stillbirths are insufficiently reported in many countries. In Nablus, reporting has recently started; little is published in Palestine on the stillbirth rate and its risk factors. Objective To study the rate of stillbirths at Rafidia Hospital in 2010 and some of its risk factors. Design A retrospective cohort design. Methods Data were collected from the delivery registry for all births and we analysed those with a gestation of 28 weeks or more at Rafidia Hospital. Stillbirth rates were estimated for available determinants. Results In 2010, a total of 5,644 women gave birth to 5,782 babies, of whom 41 were stillbirths, that is, a stillbirth rate of 7.1/1,000 births (95% confidence interval 5.2–9.5). Premature babies had a higher risk of being a stillbirth. For small babies, the lower the birth weight the higher was the probability of being a stillbirth, and for babies weighing 4,500 g or more there was a higher risk of being stillborn. The risk of stillbirth was also higher among babies from mothers with high haemoglobin concentration, but low maternal haemoglobin was not associated with stillbirths. Conclusions The stillbirth rates at Rafidia hospital assessed in this study compares favourably with the reported national numbers, indicating a good reliability of the on-going registration. The rates were highest among premature births. Stillbirth was linked to low birth weight, foetal macrosomia, and maternal haemoconcentration. We believe the findings identify areas to address when designing antenatal care with the aim of improving perinatal mortality in the country.
Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23

The most consistent finding derived from the WTCCC GWAS for rheumatoid arthritis (RA) was association to a SNP at 6q23. We performed a fine-mapping of the region in order to search the 6q23 region for additional disease variants. 3962 RA patients and 3531 healthy controls were included in the study. We found 18 SNPs associated with RA. The SNP showing the strongest association was rs6920220 [P = 2.6 × 10−6, OR (95% CI) 1.22 (1.13–1.33)]. The next most strongly associated SNP was rs13207033 [P = 0.0001, OR (95% CI) 0.86 (0.8–0.93)] which was perfectly correlated with rs10499194, a SNP previously associated with RA in a US/European series. Additionally, we found a number of new potential RA markers, including rs5029937, located in the intron 2 of TNFAIP3. Of the 18 associated SNPs, three polymorphisms, rs6920220, rs13207033 and rs5029937, remained significant after conditional logistic regression analysis. The combination of the carriage of both risk alleles of rs6920220 and rs5029937 together with the absence of the protective allele of rs13207033 was strongly associated with RA when compared with carriage of none [OR of 1.86 (95% CI) (1.51–2.29)]. This equates to an effect size of 1.50 (95% CI 1.21–1.85) compared with controls and is higher than that obtained for any SNP individually. This is the first study to show that the confirmed loci from the GWA studies, that confer only a modest effect size, could harbour a significantly greater effect once the effect of additional risk variants are accounted for.
Safety assessment of selected medicinal food plants used in Ayurveda through CYP450 enzyme inhibition study.

BACKGROUND Andrographis paniculata, Bacopa monnieri and Centella asiatica are mentioned in Ayurveda for the management of neurodegenerative disorders. These plants and their phytomolecules, such as andrographolide, bacoside A and asiaticoside, were studied for their inhibition potential on pooled CYP450 as well as human CYP3A4, CYP2D6, CYP2C9 and CYP1A2 by CYP-CO complex assay and fluorogenic assay respectively followed by IC50 determination. Quantification of bioactive compounds present in the extracts was done by RP-HPLC. Heavy metal content in the selected medicinal plants was determined by atomic absorption spectroscopy. RESULT CYP-CO complex assay indicated significantly less inhibition potential than standard inhibitor (P < 0.05 and above). A. paniculata showed highest inhibitory activity against CYP3A4 and CYP2D6 (IC50 = 63.06 ± 1.35 µg mL-1 ; 88.80 ± 3.32 µg mL-1 ), whereas C. asiatica and B. monnieri showed least inhibitory activity against CYP1A2 (IC50 = 288.83 ± 1.61 µg mL-1 ) and CYP2C9 (184.68 ± 3.79 µg mL-1 ), respectively. In all cases the extract showed higher inhibition than the single bioactive compounds. The heavy metals content in the plant extracts were within the permissible limits. CONCLUSION The findings suggested that selected food plants and bioactive compounds contributed negligible interaction potential with CYP isozymes and may not possess any harmful effect with regard to their therapeutic application. © 2016 Society of Chemical Industry.
Fluid inclusion and isotope geochemistry of the Atebayue Sb deposit, South Tianshan Orogen, Kyrgyzstan

The Atebayue Sb deposit is hosted in the Silurian clastics in the South Tianshan Orogen in Kyrgyzstan. The Sb ores appear as veins/veinlets and disseminations, with stibnite being the main ore mineral. Gangue minerals comprise quartz, calcite, and clay minerals. The quartz at Atebayue only contains aqueous fluid inclusions with low homogenization temperature (215–336 °C) and salinity (3.4–6.9 wt.% NaCl equiv.), supporting an epizonogenic hydrothermal origin. The minimum trapping pressures estimated from the NaCl─H2O inclusions are 9–14 MPa, suggesting that the Sb mineralization mainly occurred at a depth of 0.9–1.4 km. Sulphur isotopes (δ34S = −0.4 to 6.2‰) suggest that the host rocks within the Silurian system to be a significant source of ore metals. The ores contain average 206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb values of 18.112, 15.547, and 38.064, respectively, and 2‐stage model ages of 337–381 Ma, indicating the ores were likely sourced from the Paleozoic strata. Integrating the data obtained from the studies including ore geology, fluid inclusion, and S─Pb isotope geochemistry, we conclude that that the Atebayue Sb deposit is best classified as epizonogenic type formed by the Tarim–Kazakhstan continent–continent collision.
Proinflammatory Chemokines in the Intestinal Lumen Contribute to Intestinal Dysfunction During Endotoxemia

ABSTRACT Intestinal failure is common in patients with septic shock, with dysfunction of the gut often manifesting as both a cause and consequence of their critical illness. Most studies investigating the pathogenesis of intestinal failure focus on the systemic aspect, although few data examine the inflammatory signaling in the intestinal lumen. Having previously demonstrated apical/luminal chemokine secretion in an in vitro model of intestinal inflammation, we hypothesized that endotoxemia would induce secretion of proinflammatory chemokines into the intestinal lumen. In addition, we examined the contribution of these mediators to intestinal dysmotility. C57/BL6 male mice were injected intraperitoneally with LPS. Serum, intestinal tissue, and intestinal luminal contents were harvested for cytokine analysis. For intestinal motility studies, a transit assay was performed after oral gavage of chemokines. Caco-2 cells grown on Transwell culture inserts were used to examine the role of the intestinal epithelium in chemokine secretion. Monocyte chemoattractant protein 1 (MCP-1/CCL2) and macrophage-derived chemokine (MDC/CCL22) were secreted into the lumen of multiple segments of the gut during endotoxemia in mice. In vitro work showed that the intestinal epithelium participates in monocyte chemoattractant protein 1 and MDC secretion and expresses the CCR2 and CCR4 receptors for these chemokines. Intestinal transit studies show that oral gavage of MDC results in impaired gut motility. This study demonstrates that the intestinal lumen is an active compartment in the gut’s inflammatory response. Proinflammatory chemokines are secreted into the intestinal lumen during endotoxemia. These intraluminal chemokines contribute to intestinal dysmotility, complicating intestinal failure.
Estimates of Parainfluenza Virus-Associated Hospitalizations and Cost Among Children Aged Less Than 5 Years in the United States, 1998-2010.

BACKGROUND Parainfluenza virus (PIV) is the second leading cause of hospitalization for respiratory illness in young children in the United States. Infection can result in a full range of respiratory illness, including bronchiolitis, croup, and pneumonia. The recognized human subtypes of PIV are numbered 1-4. This study calculates estimates of PIV-associated hospitalizations among U.S. children younger than 5 years using the latest available data. METHODS Data from the National Respiratory and Enteric Virus Surveillance System were used to characterize seasonal PIV trends from July 2004 through June 2010. To estimate the number of PIV-associated hospitalizations that occurred annually among U.S. children aged <5 years from 1998 through 2010, respiratory hospitalizations from the Healthcare Cost and Utilization Project Nationwide Inpatient Sample were multiplied by the proportion of acute respiratory infection hospitalizations positive for PIV among young children enrolled in the New Vaccine Surveillance Network. Estimates of hospitalization charges attributable to PIV infection were also calculated. RESULTS Parainfluenza virus seasonality follows type-specific seasonal patterns, with PIV-1 circulating in odd-numbered years and PIV-2 and -3 circulating annually. The average annual estimates of PIV-associated bronchiolitis, croup, and pneumonia hospitalizations among children aged <5 years in the United States were 3888 (0.2 hospitalizations per 1000), 8481 per year (0.4 per 1000 children), and 10,186 (0.5 per 1000 children), respectively. Annual charges for PIV-associated bronchiolitis, croup, and pneumonia hospitalizations were approximately $43 million, $58 million, and $158 million, respectively. CONCLUSIONS The majority of PIV-associated hospitalizations in young children occur among those aged 0 to 2 years. When vaccines for PIV become available, immunization would be most effective if realized within the first year of life.
Pilot Clinical Trial of Hedgehog Pathway Inhibitor GDC-0449 (Vismodegib) in Combination with Gemcitabine in Patients with Metastatic Pancreatic Adenocarcinoma

Purpose: The hedgehog (HH) signaling pathway is a key regulator in tumorigenesis of pancreatic adenocarcinoma and is upregulated in pancreatic adenocarcinoma cancer stem cells (CSCs). GDC-0449 is an oral small-molecule inhibitor of the HH pathway. This study assessed the effect of GDC-0449–mediated HH inhibition in paired biopsies, followed by combined treatment with gemcitabine, in patients with metastatic pancreatic adenocarcinoma. Experimental Design: Twenty-five patients were enrolled of which 23 underwent core biopsies at baseline and following 3 weeks of GDC-0449. On day 29, 23 patients started weekly gemcitabine while continuing GDC-0449. We evaluated GLI1 and PTCH1 inhibition, change in CSCs, Ki-67, fibrosis, and assessed tumor response, survival and toxicity. Results: On pretreatment biopsy, 75% of patients had elevated sonic hedgehog (SHH) expression. On posttreatment biopsy, GLI1 and PTCH1 decreased in 95.6% and 82.6% of 23 patients, fibrosis decreased in 45.4% of 22, and Ki-67 in 52.9% of 17 evaluable patients. No significant changes were detected in CSCs pre- and postbiopsy. The median progression-free and overall survival for all treated patients were 2.8 and 5.3 months. The response and disease control rate was 21.7% and 65.2%. No significant correlation was noted between CSCs, fibrosis, SHH, Ki-67, GLI1, PTCH1 (baseline values or relative change on posttreatment biopsy), and survival. Grade ≥3 adverse events were noted in 56% of patients. Conclusion: We show that GDC-0449 for 3 weeks leads to downmodulation of GLI1 and PTCH1, without significant changes in CSCs compared with baseline. GDC-0449 and gemcitabine were not superior to gemcitabine alone in the treatment of metastatic pancreatic cancer. Clin Cancer Res; 20(23); 5937–45. ©2014 AACR.
Patients' perceptions and experiences of the prevention of hospital-acquired thrombosis: a qualitative study

Objective To examine patients' understanding of hospital-associated thrombosis, and their experiences of thromboprophylaxis. Design Qualitative study using semi-structured interviews with 31 patients requiring venous thromboembolism (VTE) prophylaxis following a recent hospital admission. Interviews were audio-recorded, transcribed verbatim and analysed thematically using framework analysis. Setting 4 hospitals in Birmingham and Oxford. Results All the participants received thromboprophylaxis following surgical procedures. Participants were aware of a risk of blood clots; however, they lacked a good understanding of VTE and its components. Experiences of VTE prophylaxis were characterised with good adherence to heparin injections and poor adherence to elastic compression stockings, largely due to perceived lack of clarity in guidance from health professionals. Participants had limited knowledge of the signs and symptoms of VTE and would value improved education on VTE. Conclusions Findings suggest that patient education is often inadequate and impacts negatively on patients' involvement in VTE prevention. An enhanced patient education programme incorporating a consistent message on the appropriate use of elastic compression stockings and description of VTE symptoms is likely to optimise the effectiveness of the prevention of hospital-associated thrombosis. Physicians may use the results of this study to improve individual patient education.
Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.
The use of left ventricular end-ejection pressure and peak pressure in the estimation of the end-systolic pressure-volume relationship.

The end-systolic pressure-volume relationship (ESPVR) as derived from left ventricular pressure-volume loops has gained increasing acceptance as an index of ventricular contractile function. In animal experiments the ESPVR has been defined as a line connecting the upper left corners of several differently loaded pressure-volume (P-V) loops with a slope parameter Ees and a volume axis intercept parameter Vo. In the clinical setting, several variants of the ESPVR have been determined with use of peak left ventricular pressure, end-ejection pressure, and end-ejection volume. The maximum P-V ratio has also frequently been measured. We attempted to determine which of these alternatives resulted in good approximations of the reference ESPVR in eight isolated canine ventricles that ejected into a simulated arterial impedance system with resistance, compliance, and characteristic impedance. We determined various versions of the ESPVR from the same set of beats quickly obtained with little change in inotropic background. To vary ventricular pressure wave forms, each of the arterial impedance parameters was independently controlled at 50%, 100%, and 200% of normal. Against each of the nine combinations of the impedance parameters four P-V loops were obtained under four preloads and from each of the sets of four P-V loops, the reference ESPVR, linear regression of the peak pressure on end-ejection volume (ESPVRPP-EEV), and linear regression of end-ejection pressure on end-ejection volume (ESPVREEPV) were determined. In addition, the maximum P-V ratio (MPVR) was calculated for each P-V loop. (ABSTRACT TRUNCATED AT 250 WORDS)
A review on decision support for massive transfusion: understanding human factors to support the implementation of complex interventions in trauma

BACKGROUND: Critically bleeding trauma patients require coordinated and efficient decision‐making processes to ensure optimal management of their massive transfusion (MT) requirements. Human factors (HFs) is a discipline that investigates factors influencing work processes from the organizational, group, and individual levels. Given the complexity of trauma resuscitation, implementing any intervention for decision support in MT is challenging and may benefit from a HFs‐assisted approach.
Potential role of phenotypic mutations in the evolution of protein expression and stability

Phenotypic mutations (errors occurring during protein synthesis) are orders of magnitude more frequent than genetic mutations. Consequently, the sequences of individual protein molecules transcribed and translated from the same gene can differ. To test the effects of such mutations, we established a bacterial system in which an antibiotic resistance gene (TEM-1 β-lactamase) was transcribed by either a high-fidelity RNA polymerase or its error-prone mutant. This setup enabled the analysis of individual mRNA transcripts that were synthesized under normal or error-prone conditions. We found that an increase of ≈20-fold in the frequency of transcription errors promoted the evolution of higher TEM-1 expression levels and of more stable enzyme variants. The stabilized variants exhibited a distinct advantage under error-prone transcription, although under normal transcription they conferred resistance similar to wild-type TEM-1. They did so, primarily, by increasing TEM-1's tolerance to destabilizing deleterious mutations that arise from transcriptional errors. The stabilized TEM-1 variants also showed increased tolerance to genetic mutations. Thus, although phenotypic mutations are not individually subjected to inheritance and natural selection, as are genetic mutations, they collectively exert a direct and immediate effect on protein fitness. They may therefore play a role in shaping protein traits such as expression levels, stability, and tolerance to genetic mutations.
A Wideband and Compact EBG Structure With a Circular Defected Ground Structure

We propose a new analysis method to determine the bandgap characteristics of an electromagnetic bandgap structure with a defected ground structure (DGS). The proposed method is based on a 1-D segmented transmission line model and a piecewise linear approximation of Zo within a unit cell. Although the previous method is only applicable to rectangular DGSs (RDGSs), the proposed method is applicable to any DGS shapes. As an example, the proposed method is applied to a circular DGS and shows a good agreement with full-wave simulations of the unit cell and measurements of 11 × 11 unit cells. The circular DGS achieves a 15% improvement in the stopband bandwidth over the RDGS with the same perforation area. The proposed method allows us to explore a variety of DGS shapes in the search for better stopband characteristics. It also offers the basis for numerical optimization techniques to be used in synthesizing DGS shapes to meet required stopband characteristics.
CYP3A4 Mediates Growth of Estrogen Receptor-positive Breast Cancer Cells in Part by Inducing Nuclear Translocation of Phospho-Stat3 through Biosynthesis of (±)-14,15-Epoxyeicosatrienoic Acid (EET)*

CYP3A4 expression in breast cancer correlates with decreased overall survival, but the mechanisms are unknown. Cytochrome P450 gene profiling by RNAi silencing demonstrates that CYP3A or 2C8 gene expression is specifically required for growth of the breast cancer lines MCF7, T47D, and MDA-MB-231. CYP3A4 silencing blocks the cell cycle at the G2/M checkpoint and induces apoptosis in the MCF7 line, thereby inhibiting anchorage-dependent growth and survival. CYP3A4 was profiled for NADPH-dependent arachidonic acid (AA) metabolism and synthesized AA epoxygenase products (±)-8,9-, (±)-11,12-, and (±)-14,15-epoxyeicosatrienoic acid (EET) (total turnover of ∼2 pmol/pmol CYP3A4/min) but not hydroxylase products (±)-15-, (±)-19-, or 20-hydroxyeicosatetraenoic acid. Furthermore, eicosanoid profiling revealed that MCF7 cells synthesize EETs in a CYP3A4-dependent manner. The (±)-14,15-EET regioisomer selectively rescues breast cancer cells from CYP3A4 silencing in a concentration-dependent fashion and promotes mitogenesis and anchorage-dependent cloning. Stat3 (Tyr-705) phosphorylation was inhibited by CYP3A4 silencing, providing a potential mechanism for CYP3A4 involvement in breast cancer cell growth. Silencing Stat3 blocks breast cancer cell growth and abrogates (±)-14,15-EET-induced proliferation, indicating a Stat3 requirement for (±)-14,15-EET-mediated cell growth. Although silencing of CYP3A4 reduces nuclear Tyr(P)-705-Stat3, (±)-14,15-EET restores this signaling process and promotes Tyr(P)-705-Stat3 translocation to the nucleus, suggesting that (±)-14,15-EET may be involved in an autocrine/paracrine pathway driving cell growth. These studies indicate that CYP3A4 is a highly active AA epoxygenase that promotes Stat3-mediated breast cancer cell growth in part through (±)-14,15-EET biosynthesis. Furthermore, these studies indicate an essential role for Stat3 as a mediator of epoxygenase activity in breast cancer.
Correcting recognition errors via discriminative utterance verification

Utterance verification (UV) is a process by which the output of a speech recognizer is verified to determine if the input speech actually includes the recognized keyword(s). The output of the speech verifier is a binary decision to accept or reject the recognized utterance based on a UV confidence score. In this paper, we extend the notion of utterance verification to not only detect errors but also to selectively correct them. We perform error correction by flipping the hypotheses produced by an N-best recognizer in cases when the top candidate has a UV confidence score that is lower than that of the next candidate. We propose two measures for computing confidence scores and investigate the use of a hybrid confidence measure that combines the two measures into a single score. Using this hybrid confidence measure and an N-best algorithm, we obtained an 11% improvement in word-error rate on a connected digit recognition task. This improvement was achieved while still maintaining reliable detection of non-keyword speech and misrecognitions.