Miracle-dz/UniFAR-FTUs huggingface dataset:
Social Capital and Delinquency among Turkish Juveniles

This study examined the relationship between aspects of social capital and self-reported delinquency among Turkish juveniles by using a secondary dataset, which is a part of the European Youth Survey. The survey was conducted among tenth graders in 2007 in Bagcilar, Istanbul. The dependent variable of this study, delinquency, was divided into two groups, minor and major, according to the stipulations of the Turkish Penal Code. Social capital was measured by assessing adolescents’ reports of their direct interactions with their parents, peers and community. In order to predict the likelihood of major and minor delinquency independently, two different subsets (N: 1879 and 1837, respectively) of the data set were used. The findings of the multivariate analyses suggest that a low level of social capital contributed significantly to Turkish juveniles’ engagement in major and minor delinquent activities. Among the social capital items, adolescents’ affiliation with delinquent peers had the strongest correlation with both dependent variables.
Unraveling the SES health connection

While a debate rages on about competing reasons why SES may affect health, there is little recognition that the so-called reverse causation from health to economic status may be pretty fundamental as well. Even if the direction of causation is that SES mainly affects health, what dimensions of SES actually matter—the financial aspects such as income or wealth or non-financial dimensions like education? Finally, is there a life course component to the health gradient so that we may be mislead in trying to answer these questions by only looking at people of a certain age—say those past 50. This paper, which is divided into four sections, provides my answers to these questions. The first section examines the issue of reverse causation or whether a new health event has a significant impact on four dimensions of SES—out-of-pocket medical expenses, labor supply, household income, and household wealth. The next section switches the perspective by asking whether the so-called direct causation from SES to health really matters all that much. If the answer is yes and it will be, a sub-theme in this section concerns which dimensions of SES—income, wealth, or education—matter for individual health. Since the answer to that question turns out to be education, Section 3 deals with the very much more difficult issue of why education matters so much. The evidence in these first three sections relies on data for people above age 50. In the final section of the paper, I test the robustness of my answers to these basic questions of the meaning of the SES-health gradient using data that span the entire life-course.
Licensing Adaptive Immunity by NOD-Like Receptors

The innate immune system is composed of a diverse set of host defense molecules, physical barriers, and specialized leukocytes and is the primary form of immune defense against environmental insults. Another crucial role of innate immunity is to shape the long-lived adaptive immune response mediated by T and B lymphocytes. The activation of pattern recognition receptors (PRRs) from the Toll-like receptor family is now a classic example of innate immune molecules influencing adaptive immunity, resulting in effective antigen presentation to naïve T cells. More recent work suggests that the activation of another family of PRRs, the NOD-like receptors (NLRs), induces a different set of innate immune responses and accordingly, drives different aspects of adaptive immunity. Yet how this unusually diverse family of molecules (some without canonical PRR function) regulates immunity remains incompletely understood. In this review, we discuss the evidence for and against NLR activity orchestrating adaptive immune responses during infectious as well as non-infectious challenges.
The VEGF receptor Flt-1 spatially modulates Flk-1 signaling and blood vessel branching

Blood vessel formation requires the integrated regulation of endothelial cell proliferation and branching morphogenesis, but how this coordinated regulation is achieved is not well understood. Flt-1 (vascular endothelial growth factor [VEGF] receptor 1) is a high affinity VEGF-A receptor whose loss leads to vessel overgrowth and dysmorphogenesis. We examined the ability of Flt-1 isoform transgenes to rescue the vascular development of embryonic stem cell–derived flt-1−/− mutant vessels. Endothelial proliferation was equivalently rescued by both soluble (sFlt-1) and membrane-tethered (mFlt-1) isoforms, but only sFlt-1 rescued vessel branching. Flk-1 Tyr-1173 phosphorylation was increased in flt-1−/− mutant vessels and partially rescued by the Flt-1 isoform transgenes. sFlt-1–rescued vessels exhibited more heterogeneous levels of pFlk than did mFlt-1–rescued vessels, and reporter gene expression from the flt-1 locus was also heterogeneous in developing vessels. Our data support a model whereby sFlt-1 protein is more efficient than mFlt-1 at amplifying initial expression differences, and these amplified differences set up local discontinuities in VEGF-A ligand availability that are important for proper vessel branching.
Nominal Rigidities and the Dynamic Effects of a Shock to Monetary Policy

We present a model embodying moderate amounts of nominal rigidities that accounts for the observed inertia in inflation and persistence in output. The key features of our model are those that prevent a sharp rise in marginal costs after an expansionary shock to monetary policy. Of these features, the most important are staggered wage contracts that have an average duration of three quarters and variable capital utilization.
Linking trust in the principal to school outcomes

Purpose – The main purpose of this paper is to examine the effects of faculty's trust in the school principal on three school outcomes, namely, self‐reported in‐role job performance (IRP), organizational citizenship behaviour (OCB) and learning goal orientation (LGO). Furthermore, this paper aims to highlight the role of organizational identification (OID) and work engagement (Eng) in explaining the linkage between trust in the principal (TIP) and the three outcome variables.Design/methodology/approach – Survey data are collected from 130 high school teachers in Pakistan. Hierarchical multiple regression analyses are used to test the research hypotheses.Findings – The results of this paper revealed that OID and Eng fully mediated the relationship between TIP and IRP; whereas, they partially mediated the effects of TIP on OCB and LGO.Research limitations/implications – The data used in this paper are cross‐sectional and hence causation cannot be determined. Additionally, the data for this paper are collect.
Infected Patients with Antiretroviral Regimen Switches − Virus Using Administrative Claims Data to Estimate Virologic Failure Rates among Human Immunodeficiency

http://mdm.sagepub. com/content/32/1/118 The online version of this article can be found at: DOI: 10.1177/0272989X11403489 2012 32: 118 originally published online 21 April 2011 Med Decis Making Michael S. Broder, Timothy Juday, Eunice Y. Chang, Yonghua Jing and Tanya G. K. Bentley Infected Patients with Antiretroviral Regimen Switches − Virus Using Administrative Claims Data to Estimate Virologic Failure Rates among Human Immunodeficiency
Temporal bone fractures: Longitudinal or oblique? The case for oblique temporal bone fractures

Classical descriptions and illustrations of temporal bone fractures are misleading. Both oblique and longitudinal fractures produce a similar fracture line in the middle cranial fossa; however, externally, they are different. Oblique fractures cross the petrotympanic fissure while longitudinal fractures run within it. In a study of 150 temporal bone fractures, the majority were oblique. An array of fracture planes accounts for most of the fractures observed. Depending on the direction of trauma, fracture planes rotate around an anteroposterior axis. When they approach the horizontal (axial) plane, they result in oblique fractures. True longitudinal fractures are rare. They are vertical and perpendicular to the oblique planes.
Investigation of Urination Disorder in Parkinson's Disease

Background: Urination disorders are common in Parkinson's disease (PD) and respond poorly to medication. This study aimed to analyze the risk factors for urination disorders in PD. Methods: Ninety-one patients with PD (aged 34–83 years old) were recruited. Patients were assessed with the Unified PD Rating Scale (UPDRS), Hoehn and Yahr stage, Pittsburgh Sleep Quality Index (PSQI), Hamilton Depression Rating Scale (HAMD), and Hamilton Anxiety Scale (HAMA). Micturition number was recorded, and Type B ultrasound was used to evaluate residual urine. Statistics was performed using binary logistic regression, bivariate correlations, and Chi-square and t-tests. Results: Of 91 patients, urinary dysfunction occurred in 55.0%. Among these, 49.5% suffered with nocturia, 47.3% with pollakiuria. Nocturia number had a positive linear relationship with HAMA score (odds ratio [OR] = 0.340, P = 0.001), HAMD score (OR = 0.323, P = 0.002), duration of L-dopa medication (OR = 0.328, P = 0.001), dose of L-dopa (OR = 0.273, P = 0.009), UPDRS-II (OR = 0.402, P = 0.000), UPDRS-III score (OR = 0.291, P = 0.005), and PSQI score (OR = 0.249, P = 0.017). Micturition number over 24 h was positively associated with HAMA (OR = 0.303, P = 0.004) and UPDRS-II scores (OR = 0.306, P = 0.003). Of patients with residual urine, 79.3% had a volume of residual urine <50 ml. Residual urine was present in 44.4% of the patients with nocturia, 46.5% of the patients with pollakiuria, and 80.0% of the patients with dysuria. More men than women had residual urine (35.2% male vs. 13.3% female; P = 0.002). Conclusions: Nocturia and pollakiuria were common micturition symptoms in our participants with PD. Nocturia was associated with depression, anxiety, sleep problems, and severity of PD. Pollakiuria was associated with anxiety and severity of PD. Male patients were more prone to residual urine and pollakiuria.
Effect of protein binding on levels of ampicillin and cloxacillin in synovial fluid

The penetration of ampicillin and cloxacillin into synOVial fluid has been measured after oral administration of these penicillins to patients with osteoarthritis or rheumatoid arthritis. The results show that both penicillins diffuse readily into synovial i0int fluid and that concentrations inhibitory for bacteria commonly associated with septic arthritis can be readily attained in infected synOVial ioints following systemic administration of ampicillin or cloxacillin. The penicillins differed with respect to the levels appearing in the synovial fluid relative to the levels in serum; in the case of ampicillin (which is not highly bound to serum) the total levels in synovial fluid were similar to the total serum levels, whereas with cloxacillin (which is highly bound to serum) the total levels in synOVial fluid were notably lower than in serum. However, the unbound levels of cloxacillin in synOVial fluid and serum were similar, as with ampicillin, indicating that the degree of binding is imp01tant in distribution between serum and tissue.
UCSF Chimera—A visualization system for exploratory research and analysis

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real‐world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl. ucsf.edu/chimera/. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1605–1612, 2004
Treat Me Right

Introduction 1. Storytelling in Medicine 2. The Nature and Complexities of Narrative 3. Dimensions of Sickness 4. Sickness, Life Stories, and Self-Respect 5. Types of Stories about Sickness 6. Sick Roles: Practices and Life Plans 7. How Sickness Alters Experience 8. Sickness and Social Relations 9. Stories of Life with Disability 10. Maladaptive Ways of Being Sick 11. What is Narrative Ethics 12. How Does One Do Narrative Ethics 13. Rigor in Narrative Judgements 14. Ethics and the Life-Span Narrative 15. Conclusion: The Patient-Health Professional Relationship as a Narrative
Haldane's Rule in an Avian System: Using Cline Theory and Divergence Population Genetics to Test for Differential Introgression of Mitochondrial, Autosomal, and Sex-Linked Loci Across the Passerina Bunting Hybrid Zone

Abstract Using cline fitting and divergence population genetics, we tested a prediction of Haldane's rule: autosomal alleles should introgress more than z-linked alleles or mitochondrial haplotypes across the Passerina amoena/Passerina cyanea (Aves: Cardinalidae) hybrid zone. We screened 222 individuals collected along a transect in the Great Plains of North America that spans the contact zone for mitochondrial (two genes), autosomal (four loci) and z-linked (two loci) markers. Maximum-likelihood cline widths estimated from the mitochondrial (223 km) and z-linked (309 km) datasets were significantly narrower on average than the autosomal cline widths (466 km). We also found that mean coalescent-based estimates of introgression were larger for the autosomal loci (0.63 genes/generation, scaled to the mutation rate μ) than for both the mitochondrial (0.27) and z-linked loci (0.59). These patterns are consistent with Haldane's rule, but the among-locus variation also suggests many independently segregating loci are required to investigate introgression patterns across the genome. These results provide the first comprehensive comparison of mitochondrial, sex-linked, and autosomal loci across an avian hybrid zone and add to the body of evidence suggesting that sex chromosomes play an important role in the formation and maintenance of reproductive isolation between closely related species.
Human brain activation during sexual stimulation of the penis

Penile sensory information is essential for reproduction, but almost nothing is known about how sexually salient inputs from the penis are processed in the brain. We used positron emission tomography to measure regional cerebral blood flow (rCBF) during various stages of male sexual performance. Compared to a passive resting condition (without penile erection), sexual stimulation of the penis increased rCBF in an area of the right hemisphere encompassing the posterior insula and adjacent posterior part of the secondary somatosensory cortex (SII) and decreased rCBF in the right amygdala. No activation was observed in either the thalamus, genital part of primary somatosensory cortex (SI), or hypothalamus. Based on these results we put forward the concept that during sexual performance the salience of the stimulus, represented by activation of the insula and SII, is of greater significance than the exact location of the stimulus, encoded in SI. The absence of activation in the hypothalamus indicates that this region is more important for the onset of sexual arousal than for the resulting sexual performance. Deactivation of the amygdala during sexual stimulation of the penis corresponds with a decrease of vigilance during sexual performance. J. Comp. Neurol. 493:33–38, 2005. © 2005 Wiley‐Liss, Inc.
An experimental metagenome data management and analysis system

The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity for microbial communities, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context. IMG/M is available at http://img.jgi. doe.gov/m.
Identification of Helicobacter pylori DNA in Human Cholesterol Gallstones

Background: The gallbladder mucosa secretes hydrogen ions and is covered by mucus. The environmental conditions for bacterial colonization are similar to those in the stomach. Gallbladder stones often contain DNA from enteric bacteria, but no compelling evidence demonstrates that Helicobacter spp. have been present. The aim of this study was to establish bacterial DNA profiles in cholesterol gallstones with special reference to Helicobacter pylori. Methods: Cholesterol gallstones from 20 patients were subjected to polymerase chain reaction, bacterial profiling by temporal temperature gradient gel electrophoresis, automated DNA sequencing, and Southern blot analysis using a Helicobacter sp. specific primer. A nested ureI- PCR assay was used to discriminate between gastric and non-gastric H. pylori. Results: TTGE, partial 16S rDNA sequencing, and hybridization analysis revealed the presence of DNA presumably representing a mixed bacterial flora in cholesterol gallstones, including H. pylori in the gallstone centres in 11 out of 20 patients. In three cases, the ureI -PCR assay revealed non-gastric H. pylori. Conclusions: These data support the presence of DNA from a mixed bacterial population, including H. pylori in cholesterol gallstones, reflecting either that H. pylori is an indigenous part of a flora in the stone-containing gallbladder or, alternatively, that H. pylori colonization in the biliary tract predisposes to cholesterol gallstone formation.
Short-term effects of particulate air pollution on cardiovascular diseases in eight European cities

Study objective: As part of the APHEA project this study examined the association between airborne particles and hospital admissions for cardiac causes (ICD9 390–429) in eight European cities (Barcelona, Birmingham, London, Milan, the Netherlands, Paris, Rome, and Stockholm). All admissions were studied, as well as admissions stratified by age. The association for ischaemic heart disease (ICD9 410–413) and stroke (ICD9 430–438) was also studied, also stratified by age. Design: Autoregressive Poisson models were used that controlled for long term trend, season, influenza epidemics, and meteorology to assess the short-term effects of particles in each city. The study also examined confounding by other pollutants. City specific results were pooled in a second stage regression to obtain more stable estimates and examine the sources of heterogeneity. Main results: The pooled percentage increases associated with a 10 μg/m3 increase in PM10 and black smoke were respectively 0.5% (95% CI: 0.2 to 0.8) and 1.1% (95% CI: 0.4 to 1.8) for cardiac admissions of all ages, 0.7% (95% CI: 0.4 to 1.0) and 1.3% (95% CI: 0.4 to 2.2) for cardiac admissions over 65 years, and, 0.8% (95% CI: 0.3 to 1.2) and 1.1% (95% CI: 0.7 to 1.5) for ischaemic heart disease over 65 years. The effect of PM10 was little changed by control for ozone or SO2, but was substantially reduced (CO) or eliminated (NO2) by control for other traffic related pollutants. The effect of black smoke remained practically unchanged controlling for CO and only somewhat reduced controlling for NO2. Conclusions: These effects of particulate air pollution on cardiac admissions suggest the primary effect is likely to be mainly attributable to diesel exhaust. Results for ischaemic heart disease below 65 years and for stroke over 65 years were inconclusive.
Kinetics of Label Retaining Cells in the Developing Rat Kidneys

Background The kidney is a specialized low-regenerative organ with several different types of cellular lineages. The BrdU label-retaining cell (LRCs) approach has been used as part of a strategy to identify tissue-specific stem cells in the kidney; however, because the complementary base pairing in double-stranded DNA blocks the access of the anti-BrdU antibody to BrdU subunits, the stem cell marker expression in BrdU-labeled cells are often difficult to detect. In this study, we introduced a new cell labeling and detection method in which BrdU was replaced with 5-ethynyl-2-deoxyuridine (EdU) and examined the time-dependent dynamic changes of EdU-labeled cells and potential stem/progenitor markers in the development of kidney. Methods Newborn rats were intraperitoneally injected with EdU, and their kidneys were harvested respectively at different time points at 1 day, 3 days, 1 week, 2 weeks, and 6 weeks post-injection. The kidney tissues were processed for EdU and cellular markers by immunofluorescence staining. Results At the early stage, LRCs labeled by EdU were 2176.0 ± 355.6 cells at day one in each renal tissue section, but dropped to 168 ± 48.4 cells by week 6. As time increased, the numbers of LRCs were differentially expressed in the renal cortex and papilla. At the postnatal day one, nearly twice as many cells in the cortex were EdU-labeled as compared to the papilla (28.6 ± 3.6% vs. 15.6 ± 3.4%, P<0.05), while there were more LRCs within the renal papilla since the postnatal week one, and at the postnatal week 6, one third as many cells in the cortex were EdU-labeled as compared to the papilla (2.5 ± 0.1% vs. 7.7 ± 2.7%, P<0.05). The long-term LRCs at 6-week time point were associated exclusively with the glomeruli in the cortex and the renal tubules in the papilla. At 6 weeks, the EdU-labeled LRCs combined with expression of CD34, RECA-1, Nestin, and Synaptopodin were discretely but widely distributed within the glomeruli; Stro-1 around the glomeruli; and α-smooth muscle actin (SMA) in arteries. Conversely, co-expression of CD34, RECA-1, and Nestin with the long term EdU-labeled LRCs was significantly lower in renal tubules (P<0.01), while Stro-1 and Synaptopodin were not detected. Conclusion Our data found that at 6-week time point, EdU-labeled LRCs existing in the glomeruli expressed undifferentiated podocyte and endothelial markers at high rates, while those in the renal tubules expressed Nestin and vascular markers at low rates. To understand the characterization and localization of these EdU-LRCs, further studies will be needed to test cell lineage tracing, clonogenicity and differentiation potency, and the contributions to the regeneration of the kidney in response to renal injury/repair.