Miracle-dz/UniFAR-FTUs huggingface dataset:
Coronary atherosclerosis in noncardiac deaths: An autopsy study

Introduction: Atherosclerosis leading to ischemic heart disease (IHD) is the most common cause of cardiac deaths worldwide. To evaluate the prevalence of atherosclerosis, an autopsy-based study conducted on subjects who died of noncardiac causes can be a valuable tool. With this hypothesis, we conducted this study on the hearts of subjects who died of noncardiac causes. Materials and Methods: This study was conducted from August 2012 to February 2013 at Department of Pathology, BJ Medical College, Ahmedabad, Gujarat. The deceased patients who died of noncardiac causes and underwent autopsy at our hospital, their hearts were sent to our department for histopathological analysis. The hearts were fixed in 10% formalin, weighed, measured, and the three main coronary arteries were dissected out and carefully examined for any histological evidence of atherosclerotic plaques and associated pathological lesions and graded according to the classification given by American Heart Association. Results: A total of 250 autopsy cases were evaluated. Amongst them 113 were deaths due to noncardiac causes, of which 83 (73.45%) subjects had evidence of atherosclerosis. In the study, 68 (82%) were males and 15 (18%) were females. Left anterior descending artery (LADA; 69%) was the most commonly involved coronary artery. Triple vessel disease was found in 22% of subjects. Conclusion: The study showed alarmingly high prevalence of atherosclerosis. The pathogenesis of coronary atherosclerosis begins at a younger age in Indian population. Though the incidence of atherosclerosis is more common in males compared to females; coronary atherosclerosis is an important risk factor for IHDs in both sexes and screening for the same should begin at an early age.
Arrhythmia Phenotype During Fetal Life Suggests Long-QT Syndrome Genotype: Risk Stratification of Perinatal Long-QT Syndrome

Background— Fetal arrhythmias characteristic of long QT syndrome (LQTS) include torsades de pointes (TdP) and/or 2° atrioventricular block, but sinus bradycardia, defined as fetal heart rate <3% for gestational age, is most common. We hypothesized that prenatal rhythm phenotype might predict LQTS genotype and facilitate improved risk stratification and management. Method and Results— Records of subjects exhibiting fetal LQTS arrhythmias were reviewed. Fetal echocardiograms, neonatal ECG, and genetic testing were evaluated. We studied 43 subjects exhibiting fetal LQTS arrhythmias: TdP±2° atrioventricular block (group 1, n=7), isolated 2° atrioventricular block (group 2, n=4), and sinus bradycardia (group 3, n=32). Mutations in known LQTS genes were found in 95% of subjects tested. SCN5A mutations occurred in 71% of group 1, whereas 91% of subjects with KCNQ1 mutations were in group 3. Small numbers of subjects with KCNH2 mutations (n=4) were scattered in all 3 groups. Age at presentation did not differ among groups, and most subjects (n=42) were live-born with gestational ages of 37.5±2.8 weeks (mean±SD). However, those with TdP were typically delivered earlier. Prenatal treatment in group 1 terminated (n=2) or improved (n=4) TdP. The neonatal heart rate–corrected QT interval (mean±SE) of group 1 (664.7±24.9) was longer than neonatal heart rate–corrected QT interval in both group 2 (491.2±27.6; P=0.004) and group 3 (483.1±13.7; P<0.001). Despite medical and pacemaker therapy, postnatal cardiac arrest (n=4) or sudden death (n=1) was common among subjects with fetal/neonatal TdP. Conclusions— Rhythm phenotypes of fetal LQTS have genotype-suggestive features that, along with heart rate–corrected QT interval duration, may risk stratify perinatal management.
Bivariate Instantaneous Frequency and Bandwidth

The generalizations of instantaneous frequency and instantaneous bandwidth to a bivariate signal are derived. These are uniquely defined whether the signal is represented as a pair of real-valued signals or as one analytic and one anti-analytic signal. A nonstationary but oscillatory bivariate signal has a natural representation as an ellipse whose properties evolve in time, and this representation provides a simple geometric interpretation for the bivariate instantaneous moments. The bivariate bandwidth is shown to consist of three terms measuring the degree of instability of the time-varying ellipse: amplitude modulation with fixed eccentricity, eccentricity modulation, and orientation modulation or precession. An application to the analysis of data from a free-drifting oceanographic float is presented and discussed.
The combination of pivampicillin and pivmecillinam versus pivampicillin alone in the treatment of acute pyelonephritis.

96 patients with clinical symptoms of acute pyelonephritis were randomized to 2 weeks treatment with either a fixed combination of pivampicillin and pivmecillinam or to pivampicillin alone. If needed, treatment was first started with the respective parenteral equivalents of the drugs. Acute pyelonephritis was bacteriologically verified in 57 patients, in whom Escherichia coli was isolated in 80% of the cases, Klebsiella in 7% and Proteus mirabilis in 5%. 22 of the 39 patients excluded did not have significant bacteriuria (less than 10(8) c.f. u. /l). Combination treatment was superior to pivampicillin/ampicillin alone, in terms of clinical effect, with successful treatment being noted in 93% in the combination group and in 53% in the ampicillin group (p = 0.002). The combination was also more effective bacteriologically and it did not select resistant strains in the urinary tract. Ampicillin treatment alone, was, however, associated with a significant increase in urinary strains resistant to ampicillin and to mecillinam. Unsuccessful responders had a significantly higher mean age (p less than 0.01) than successful responders. No serious side-effects were noted.
Dose Response Effects of Insulin Glargine in Type 2 Diabetes Running Title: Dose Response Glargine

This is an uncopyedited electronic version of an article accepted for publication in Diabetes Care. The American Diabetes Association, publisher of Diabetes Care, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive publisherauthenticated version will be available in a future issue of Diabetes Care in print and online at http://care.diabetesjournals. org. Diabetes Care Publish Ahead of Print, published online March 31, 2010
Cohort profile: 1958 British birth cohort (National Child Development Study).

How did the study come about? The 1958 birth cohort or the National Child Development Study (NCDS) began as a study of Perinatal Mortality focussing on just over 17 000 births in a single week in 1958. To address concerns regarding the stillbirth rate not falling, the original study aimed to identify social and obstetric factors linked to stillbirth and neonatal death. The findings contributed to the improvement of maternity services in Britain and to a reduction in perinatal mortality. 1 The initial survey was not planned as a longitudinal study, but subsequently the National Children’s Bureau was commissioned by the Central Advisory Council for Education (The Plowden Committee) to retrace the cohort at age 7 and monitor their educational, physical, and social development. 2 Further surveys took place when children were aged 11 and 16. 3,4 This cohort was educated during a period when there was considerable debate about the nature of primary schooling, the selection for secondary school (the ‘eleven-plus’) was being abolished, and the comprehensive sector of secondary schooling was expanding. The school leaving age was raised to 16 yr in 1973 making cohort members part of the first year group required to stay on at school for an extra year. Divorce rates, though rising during the 1960s, were still relatively low and most of this cohort lived with both parents throughout their childhood. In other respects, the cohort grew up in an environment which differed from that experienced by children today, with proportionately more children living in houses that lacked basic amenities, although access to welfare provision, such as free school meals, was available. Breast-feeding was relatively common, and so too was maternal smoking in pregnancy. This generation was not exposed to the levels of childhood obesity seen nowadays and rates of teenage drug taking were low.
The Jurassic Yeba Formation in the Gangdese arc of S. Tibet: implications for upper plate extension in the Lhasa terrane

ABSTRACT The formation of the Jurassic Xiongcun porphyry copper deposit, within the Gangdese magmatic belt of southern Tibet, took place coincident with subduction of the Neotethyan oceanic lithosphere. Although the Yeba Formation (coeval and co-magmatic intrusions and volcanic rocks) in the eastern Gangdese magmatic belt formed at the same time as the Xiongcun deposit, the Yeba Formation is devoid of subduction-related porphyry Cu deposits. Here, we report detrital zircon U–Pb ages for sedimentary rocks of the Yeba and Bima Formations along with a summary of all published whole-rock geochemical data and zircon epsilon Hf isotopes for the volcanic rocks in the Yeba Formation. We use these data to re-evaluate the petrogenesis, magmatic source, and tectonic setting of the volcanic rocks. Detrital zircon ages from the sedimentary rocks reveal that the volcanic rocks of the Yeba and Bima Formations are the main source for their sedimentary interlayers. In addition, the Yeba sedimentary layers contain inherited zircons sourced from older country rocks whereas the Bima Formation is devoid of ancient zircons. Geochemically, the Yeba volcanic rocks resemble a bimodal volcanic suite. Geochemical data reveal that the Yeba volcanic rocks formed in a continental arc setting, while the mafic ones were derived from the partial melting of the mantle wedge above the subducting slab rather than from the melting of the descending oceanic slab. In addition, the mafic ensemble formed in a back-arc setting, indicative of subduction-related extension in the Lhasa terrane. In contrast, the felsic ensemble may originate from the melting of basaltic lower crust. Thus, the magma source and tectonic setting for the Yeba Formation are distinct from typical subduction-related Cu-hosted porphyry and volcanic rocks in a compressional setting.
Influence of significant weight loss on serum matrix metalloproteinase (MMP)-7 levels.

BACKGROUND Matrix metalloproteinases (MMPs) and their specific inhibitors (tissue inhibitor of metalloproteinases [TIMPs]), are involved in adipogenesis, angiogenesis and remodeling of extracellular matrix. MMPs and TIMPs have been shown to be associated with various diseases such as neurological disorders, malignancies and cardiovascular disease. MMPs and TIMPs are thought to play a major role in extensive reorganization of the adipose tissue in obesity. METHODS AND MATERIALS To test whether significant weight loss alters circulating MMPs and TIMPs, 18 morbidly obese women, who underwent bariatric surgery for weight loss, were investigated before and one year after surgery in a prospective design study. Body composition, glucose and lipid metabolism parameters were determined in all study subjects before and after weight loss. Circulating MMP-2, -3, -7 and TIMP-1, -2 and -4 serum levels were measured using commercially available, enzyme-linked immunoassays. RESULTS Pronounced weight loss was accompanied by improvements in glucose homeostasis and lipid parameters. In the mean time MMP-2 and MMP-3, as well as TIMP-1, -2 and TIMP-4 concentrations were not affected by significant weight loss, and circulating MMP-7 increased significantly after bariatric surgery, although without reaching the standard levels as determined in 18, lean, healthy women. CONCLUSION Our data indicate that reduced MMP-7 levels in obesity might be restored by significant weight loss, suggesting that the reorganization of adipose tissue in obesity might be partially reversible by weight reduction. We hypothesize that increased circulating MMP-7 might indicate enhanced adipocyte differentiation in subjects who had undergone bariatric surgery.
Mapping of Succinate Dehydrogenase Losses in 2258 Epithelial Neoplasms

Losses in the succinate dehydrogenase (SDH) complex characterize 20% to 30% of extra-adrenal paragangliomas and 7% to 8% of gastric GISTs, and rare renal cell carcinomas. This loss is reflected as lack of the normally ubiquitous immunohistochemical expression of the SDH subunit B (SDHB). In paragangliomas, SDHB loss correlates with homozygous loss of any of the SDH subunits, typically by loss-of-function mutations. The occurrence of SDHB losses in other epithelial malignancies is unknown. In this study, we immunohistochemically examined 2258 epithelial, mostly malignant neoplasms including common carcinomas of all sites. Among renal cell carcinomas, SDHB loss was observed in 4 of 711 cases (0.6%), including a patient with an SDHB-deficient GIST. Histologically, the SDHB-negative renal carcinomas varied. There was 1 clear cell carcinoma with a high nuclear grade, 1 papillary carcinoma type 2, 1 unclassified carcinoma with a glandular pattern, and 1 oncocytoid low-grade carcinoma as previously described for SDHB-negative renal carcinoma. None of these patients was known to have paragangliomas or had loss of SDHA expression in the tumor. Three of these patients had metastases at presentation (2 in the adrenal, 1 in the retroperitoneal lymph nodes). There were no cases with SDHB loss among 64 renal oncocytomas. SDHB losses were not seen in other carcinomas, except in 1 prostatic adenocarcinoma (1/57), 1 lymphoepithelial carcinoma of the stomach, and 1 (1/40) seminoma. On the basis of this study, SDHB losses occur in 0.6% of renal cell carcinomas and extremely rarely in other carcinomas. Some of these renal carcinomas may be clinically aggressive. The clinical significance and molecular genetics of these SDHB-negative tumors requires further study.
The Contribution of Home, Neighbourhood and School Environmental Factors in Explaining Physical Activity among Adolescents

The present study aimed at investigating the influence of home, neighbourhood and school environmental factors on adolescents' engagement in self-reported extracurricular physical activity and leisure time sports and on MVPA objectively measured by accelerometers. Environmental factors were assessed using questionnaires. Gender specific hierarchical regression analyses were conducted, with demographic variables entered in the first block, and environmental, psychosocial factors and interactions terms entered in the second block. Participation in extracurricular activities at school was positively related to the number of organized activities and the provision of supervision. Perceived accessibility of neighborhood facilities was not related to engagement in leisure time sports, whereas the availability of sedentary and physical activity equipment was. Findings were generally supportive of ecological theories stating that behaviors are influenced by personal and environmental factors that are constantly interacting.
Cutting Edge: Bone Morphogenetic Protein Antagonists Drm/Gremlin and Dan Interact with Slits and Act as Negative Regulators of Monocyte Chemotaxis12

Drm/Gremlin and Dan, two homologous secreted antagonists of bone morphogenic proteins, have been shown to regulate early development, tumorigenesis, and renal pathophysiology. In this study, we report that Drm and Dan physically and functionally interact with Slit1 and Slit2 proteins. Drm binding to Slits depends on its glycosylation and is not interfered with by bone morphogenic proteins. Importantly, Drm and Dan function as inhibitors for monocyte migration induced by stromal cell-derived factor 1α (SDF-1α) or fMLP. The inhibition of SDF-1α-induced monocyte chemotaxis by Dan is not due to blocking the binding of SDF-1α to its receptor. Thus, the results identify that Drm and Dan can interact with Slit proteins and act as inhibitors of monocyte chemotaxis, demonstrating a previously unidentified biological role for these proteins.
2 Correlated pairs of experiments from different projects :

1 Supplementary Methods 1.1 Treatment of replicate microarrays When a given experiment had more than one replicate, we only included the closest-to-average (CTA) replicate in analysis. The CTA replicate was the microarray in a set of replicates that was closest to the average of that set of replicates (minimum sum of absolute differences between the replicate and the average of replicates). If there were only two replicates for an experiment, one was chosen at random. TRNI performance using CTA replicate data was compared to two other treatments of replicates (including all chips or averaging replicate chips) in Supplementary Figure S2. We chose to use the CTA replicates for analysis in this work, as the CTA data performed better in correlation-based TRNI than including all replicates, and this approach avoids possible smoothing effects due to averaging. We conducted permutation tests for i.i. d. experiments following [2]. The n × n experiment correlation matrix was computed for the double standardized compendium. The first eigenvector of this matrix, v1, was calculated via singular value decomposition. If the experiments were indeed i.i. d. , the order of the values in v1 should be random with respect to the order of the experiments. To test this, a block statistic S(v) = v Bv (1) was computed for v = v1 and 5000 random permutations of v1, v = v1 *. The block operator B was the n × n matrix: B = h β h β h for h=1:number of projects (2) where β h is the n × 1 vector: β h = 1 for j in project h, j=1:n 0 otherwise. (3) The p-value of the test was then computed as the fraction of S(v1 *) exceeding S(v1).
A 500‐Year Tree Ring‐Based Reconstruction of Extreme Cold‐Season Precipitation and Number of Atmospheric River Landfalls Across the Southwestern United States

This study develops a reconstruction of the frequency of extreme cold‐season precipitation and the occurrence of landfalling atmospheric river (AR) storm tracks across the southwestern Unites States using a network of tree ring chronologies and the Living Blended Drought Atlas (LBDA), a 500‐year tree ring based reconstruction of the summer Palmer Drought Severity Index. The first two rotated empirical orthogonal functions of the LBDA across the Southwest are shown to relate well to previously identified patterns of regional AR activity. Accordingly, the rotated empirical orthogonal functions also record patterns of extreme precipitation associated with those ARs, albeit with some uncertainty introduced by nonextreme precipitation. A network of chronologies sensitive to cold‐season precipitation is then used to reconstruct the occurrence of landfalling ARs and extreme precipitation along the southern Californian coast, demonstrating for the first time the feasibility of reconstructing AR landfalls and extreme events in the Southwest based on spatial patterns in a network of dendroclimatic proxies.
Differences in Gene Expression Profiles of Diabetic and Nondiabetic Patients Undergoing Cardiopulmonary Bypass and Cardioplegic Arrest

Background—Diabetes mellitus is an independent risk factor for early postoperative mortality and complications after coronary artery bypass grafting (CABG). We sought to compare the cardiac gene expression responses to cardiopulmonary bypass (CPB) and cardioplegic arrest (C) in patients with and without diabetes. Methods and Results—Twenty atrial myocardium samples were harvested from 5 type II insulin-dependent diabetic and 5 matched nondiabetic patients undergoing CABG, before and after CPB/C. Oligonucleotide microarray analyses of 12625 genes were performed on the 10 sample pairs using matched pre-CPB tissues as controls. Array results were validated with Northern blotting and immunoblotting. Compared with pre-CPB/C, post-CPB/C myocardial tissues revealed 851 upregulated and 480 downregulated genes with a threshold P≤0.025 (signal-to-noise ratio, 4.04) in the diabetic group, compared with 480 upregulated and 626 downregulated genes (signal-to-noise ratio, 3.04) in the nondiabetic group (P<0.001). There were 18 genes that were upregulated >4-fold in diabetic and nondiabetic patients (including inflammatory/transcription activators FOS, CYR 61, and IL-6, apoptotic gene NR4A1, stress gene DUSP1, and glucose-transporter gene SLC2A3). However, 28 genes showed such marked upregulation in the diabetic group exclusively (including inflammatory/transcription activators MYC, IL8, IL-1&bgr;, growth factor vascular endothelial growth factor, amphiregulin, and glucose metabolism-involved gene insulin receptor substrate 1), and 27 genes in the nondiabetic group only, including glycogen-binding subunit PPP1R3C. Conclusions—Gene expression profile after CPB/C is quantitatively and qualitatively different in patients with diabetes. These results have important implications for the design of tailored myocardial protection and operative strategies for diabetic patients undergoing CPB/C.
LAND USE AND ITS RELATIONSHIP TO RIPARIAN ZONE ORGANIC CARBON STORAGE ON THE UPPER HUNTER RIVER

Anthropogenic influences and land use practices in eastern Australia over the past 200 years have resulted in vastly altered channel and catchment conditions. This has not only reduced geomorphic diversity but also vegetation diversity and ecological functioning. As such, identifying the impact of various land use regimes is highly important when developing future riparian zone management strategies. To investigate the influence land use (specifically grazing) has on the riparian zone and river system, 12 in-channel river deposits were studied on the Hunter River between Muswellbrook and Aberdeen. Three land use types were selected — i) never grazed, ii) crash grazed and iii) perennially grazed — and samples were taken at three study reaches (Aberdeen, Downstream Aberdeen and Dart Brook Mine). One hundred and eleven (111) soil samples were collected from bars and benches in order to determine organic carbon content and fine sediment retention. The soil samples were analysed using loss-on-ignition (LOI) testing to determine the percentage (%) of organic carbon (OC). The Malvern Mastersizer was used to analyse average grain size and to determine the dominant sediment fraction within each soil sample. Hand sieves (-4 phi and -1 phi) were used to determine the main sediment fractions as a measure of bar variability. Spatial and hydrologic analyses were undertaken to determine historical and recent changes in both vegetation and river geomorphology. Results from the sample analysis showed that sites that had never been grazed had an average increased OC concentration of 6.43% and were also comprised of the finest sediment (FS), at 108.7m. Study locations that had been subjected to controlled grazing (3.02% OC and FS 324.4m) fell on average between permanently grazed (2.68% OC and FS 376.4m) and never-grazed locations across most variables analysed. Riparian zone management is a prevalent and important topic and these results provide guidance for developing management strategies. It has been found that stock may be useful in removing exotic vegetation as part of a larger weed management program, however in doing so they may decrease the amount of carbon sequestered and fine sediment retained. Decreased organic carbon can affect the nutrient cycling and the removal of nitrogen and phosphorus from water prior to entering the stream. In addition, decreased fine sediment retention may result in increased turbidity and therefore decreased light availability throughout the water column. These results may also have implications on global carbon storage through the riparian zone and its associated role in mitigating climate change.