Miracle-dz/UniFAR-FTUs huggingface dataset:
Logistic regression when the outcome is measured with uncertainty.

In epidemiologic research, logistic regression is often used to estimate the odds of some outcome of interest as a function of predictors. However, in some datasets, the outcome of interest is measured with imperfect sensitivity and specificity. It is well known that the misclassification induced by such an imperfect diagnostic test will lead to biased estimates of the odds ratios and their variances. In this paper, the authors show that when the sensitivity and specificity of a diagnostic test are known, it is straightforward to incorporate this information into the fitting of logistic regression models. An EM algorithm that produces unbiased estimates of the odds ratios and their variances is described. The resulting odds ratio estimates tend to be farther from the null but have greater variance than estimates found by ignoring the imperfections of the test. The method can be extended to the situation where the sensitivity and specificity differ for different study subjects, i.e., nondifferential misclassification. The method is useful even when the sensitivity and specificity are not known, as a way to see the degree to which various assumptions about sensitivity and specificity affect one's estimates. The method can also be used to estimate sensitivity and specificity under certain assumptions or when a validation subsample is available. Several examples are provided to compare the results of this method with those obtained by standard logistic regression. A SAS macro that implements the method is available on the World Wide Web at http:@som1.ab. umd.edu/Epidemiology/software.h tml.
From the Cover: A macroporous hydrogel for the coculture of neural progenitor and endothelial cells to form functional vascular networks in vivo

Vascularization is vital for tissue function. A microvascular network is critical for oxygen delivery, nutrient exchange, and, ultimately, for the long-term survival of tissue cells. Whereas the overall size and specific application of engineered tissues depend on the ability to create stable and functional microvascular networks (1, 2), vascularization has proven difficult to achieve. Approaches for engineering de novo microvascular networks have included the delivery of angiogenic growth factors from polymer constructs (3–5), implanting biodegradable matrices seeded with endothelial cells or their progenitors (6–9), and combining growth factors and cells (4). Although these approaches have shown promise, the long-term stability and function of microvascular networks remains a challenge. Recent work has implicated a strong functional interaction between neural progenitor cells (NPCs) and endothelial cells (10) and has shown spatial proximity between established neural and vascular networks (11). We sought to capitalize on this potential interaction to tissue engineer a functional vascular network. Our goal was to design a scaffold that would support the development of microvessels by providing a spatial environment that enabled neural progenitor cells to interact with endothelial cells during tube formation. Hydrogels, because of their highly water-saturated nature, are well suited for the transport of soluble factors, nutrients, and waste (12, 13). One of the challenges with hydrogels has been to obtain controlled pore architectures. The use of light to cross-link, inscribe, or remove material has been studied as a means to obtain distinct pore architectures in hydrogels (14, 15). These techniques lead to two-dimensional patterns of high-density and low-density regions. An alternative approach by using the dissolution of polycaprolactone fibers has also been used to create a similar pore architecture (16). However, to develop functional microvascular networks that are integral to tissue and organ function, a three-dimensional pore architecture is required. Our goal in these experiments was to engineer a three-dimensional scaffold that is suitable for microvascular networks in engineered tissues and to test the hypothesis that coculture of endothelial cells and NPCs would promote the stabilization of microvascular networks in vivo. We have developed a two-component enzymatically degradable hydrogel that is cast around a hydrolytically degraded polymer scaffold to create the requisite architecture. Our findings show that the resulting macroporous hydrogel supports the coculture of endothelial cells and neural progenitor cells. Furthermore, these cocultures encourage endothelial cell tube formation and the development of stable functional microvascular networks as confirmed after 6 weeks of implantation in the mouse.
Potential for the Use of the Solitaire Stent for Recanalization of Middle Cerebral Artery Occlusion without a Susceptibility Vessel Sign

BACKGROUND AND PURPOSE: Absence of the MCA susceptibility vessel sign (negative MCA susceptibility vessel sign) on gradient recalled-echo MR imaging in acute stroke is commonly associated with in situ stenosis and thrombotic occlusion. We evaluated the effectiveness and safety of the Solitaire stent as the first-line device for the recanalization of MCA occlusion with a negative MCA susceptibility vessel sign. MATERIALS AND METHODS: Thirty-eight consecutive patients presenting with acute ischemic stroke due to MCA occlusion were treated by using the Solitaire AB stent alone or combined with thrombolytic drugs. Among these patients, 11 (7 men and 4 women; median age, 70 years; range, 49–89 years) who underwent multimodal stroke MR imaging before the endovascular procedure and had no MCA susceptibility vessel sign on the initial gradient recalled-echo MR imaging were included in this study. The primary end point was the recanalization of the occluded artery evaluated by the arterial occlusive lesion score. Clinical outcome was assessed at discharge and 90 days, as was the degree of residual MCA stenosis or reocclusion. RESULTS: Successful recanalization (arterial occlusive lesion score ≥ II) without balloon angioplasty was obtained in 9 patients (81.8%). Six patients (54.5%) had an mRS score of ≤2 at 90 days. After a median of 147 days, no patient showed reocclusion on follow-up imaging. There were no symptomatic intracerebral hemorrhages. CONCLUSIONS: The Solitaire stent is a feasible tool as the first-line device for multimodal endovascular recanalization therapy in acute ischemic stroke with a negative MCA susceptibility vessel sign. It has a good rate of successful and complete recanalization and is a fast yet safe procedure.
Developing an Automated System, Based on Remtoly-Sensed Data, for Recognizing the Effect of Climate on the Morphology of Urban Open Spaces

Urban form reflects cultural, socio-economical and environmental parameters and constraints. An important environmental generator of urban form is climate. The majority of existing research that deals with the influence of climate on the development of urban form tends to present vernacular (traditional) urban form as a successful combination of architecture, urban design and climate. This assumption is supported by the claim that vernacular settlements adapted to the harsh climatic conditions through a process of trial and error. Selected cases of vernacular settlements are often presented to support this claim. This paper introduces the first part of an ongoing research which develops a model that investigates this claim through a quantitative based analysis. An automated system is under development, which will assist in studying the effect of prevailing climatic conditions on the development of urban form, particularly the development of vernacular urban form in hot-arid regions. This system combines: a) automated recognition of urban open spaces and b) automated recognition of morphological patterns and their analysis based on local climatic conditions. The system is based on remotely-sensed images with very-high spatial resolution and integrates image processing tools with Geographic Information Systems (GIS) spatial analysis.
Complex Co-localization of Chromogranins and Neurohormones in the Human Gastrointestinal Tract

Co-localization of chromogranin (Cg) A, B, and C has been studied in different neuroendocrine cell types in histologically normal mucosa from human gastrointestinal tract (corpus, antrum, duodenum, ileum, and colon) using single-, double-, and triple-immunofluorescence stainings. Virtually all enterochromaffin (EC) cells contained CgA, and those in the luminal two thirds of the antral mucosa and villi of small intestine often also contained CgB. A few EC cells in the duodenal crypts contained CgC. Most gastrin cells harbored both CgB and CgA, although rather more CgB than CgA, but some gastrin cells contained all three types, i.e., also CgC. Some CCK cells also contained all three chromogranins. Enteroglucagon cells in the duodenal villi contained CgA and some CgB. CgA (but not B or C) was found in some secretin, GIP, enteroglucagon/peptide YY, and neurotensin cells. A few somatostatin cells contained CgA but neither CgB nor CgC. CgA and C were found mainly in the basal cell region, whereas CgB occurred more diffusely throughout the cytoplasm. This varying distribution suggests that not all secretory granules contain CgA, or that CgB may occur in a nongranular form. The varying composition of the different chromogranins may reflect their complex functional roles in the widespread neuroendocrine system.
Simple value ordering heuristic in frequency assignment problem

In this paper, we introduce one simple heuristic for value ordering in solving frequency assignment problem. Our approach is based on a special container to organize the values selection by jumping between two sides of domain. In order to reduce the time and space complexities of algorithm, we change the current value selection with last unchecked element in the domain, and put all the inconsistent values after it. Then domain is managed by the increasing of acceptable level of values. Different from static value ordering scheme, our approach is dynamically selection the values during the constraint propagation.
Experimental control of matrix converter for active generator

This paper presents the control design for a matrix converter, which interfaces a power generator to a passive charge. Matrix converters, which are direct power electronic converters, are able to provide important benefits such as bidirectional power flow and great potential for size reduction. On the other hand, the complexity of the matrix converter topology makes the study and the determination of suitable control strategies a difficult task. A matrix converter is used as an alternative concept to avoid the need for a gearbox upstream the generator in an electrical energy production process. This work also includes a real-time control of the matrix converter, control scheme and experimental results are presented too.
Estimation of neural dynamics from MEG/EEG cortical current density maps: application to the reconstruction of large-scale cortical synchrony

There is a growing interest in elucidating the role of specific patterns of neural dynamics-such as transient synchronization between distant cell assemblies-in brain functions. Magnetoencephalography (MEG)/electroencephalography (EEG) recordings consist in the spatial integration of the activity from large and multiple remotely located populations of neurons. Massive diffusive effects and poor signal-to-noise ratio (SNR) preclude the proper estimation of indices related to cortical dynamics from nonaveraged MEG/EEG surface recordings. Source localization from MEG/EEG surface recordings with its excellent time resolution could contribute to a better understanding of the working brain. We propose a robust and original approach to the MEG/EEG distributed inverse problem to better estimate neural dynamics of cortical sources. For this, the surrogate data method is introduced in the MEG/EEG inverse problem framework. We apply this approach on nonaveraged data with poor SNR using the minimum norm estimator and find source localization results weakly sensitive to noise. Surrogates allow the reduction of the source space in order to reconstruct MEG/EEG data with reduced biases in both source localization and time-series dynamics. Monte Carlo simulations and results obtained from real MEG data indicate it is possible to estimate noninvasively an important part of cortical source locations and dynamic and, therefore, to reveal brain functional networks.
Diosmin reduces cell viability of A431 skin cancer cells through apoptotic induction

Objectives: Aim of the present study was to evaluate the in vitro cytotoxic potential of the diosmin in A431 skin cancer cells. Materials and Methods: The cytotoxic (anti-cell proliferative) potential of diosmin in A431 cells was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay (cell viability), dual staining (apoptotic induction), dichloro-dihydro-fluorescein diacetate assay (reactive oxygen species [ROS] generation), DNA fragmentation study, Western blotting analysis (apoptotic markers expression) and flow cytometry (cell cycle arrest). Results: Diosmin reduced the cell viability of A431 cells in a dose-dependent fashion and the inhibitory concentration 50% value was attained at 45 μg/ml using MTT assay. Diosmin at a concentration of 45 μg/ml generated excessive ROS in A431 cells, as compared to untreated cells. Diosmin treated A431 cells also revealed multiple DNA fragments than the untreated cells. Diosmin upregulated the expression of p53, caspases 3 and 9 and downregulated the expression of Bcl-2, matrix metalloproteinases-2 and 9 in A431 cells. Conclusion: The cytotoxic or anti-cell proliferative potential of diosmin is due to its ROS-mediated apoptotic induction potential, as well as due to its role in the inhibition of invasion in the A431 cells.
Advanced glycation end-products and insulin signaling in granulosa cells

Advanced glycation end-products (AGEs) may interfere with insulin intracellular signaling and glucose transport in human granulosa cells, potentially affecting ovarian function, follicular growth, linked with diminished fertility. The potential interaction of AGEs with insulin signaling pathways and glucose transport was investigated in human granulosa KGN cells. KGN cells were cultured with variable concentrations of human glycated albumin (HGA, 50–200 µg/mL) or insulin (100 ng/mL). Combined treatments of KGN cells with insulin (100 ng/mL) and HGA (200 µg/mL) were also performed. p-AKT levels and glucose transporter type 4 (Glut-4) translocation analysis were performed by Western blot. Phosphatidylinositol-3-kinase (PI3K)-specific signaling was checked by using the PI3K-inhibitor, LY294002. p-AKT levels were significantly increased following insulin treatment compared to basal levels or HGA exposure. This insulin-mediated AKT-phosphorylation was PI3K-specific and it was inhibited after combined treatment of insulin and HGA. Furthermore, Glut-4 translocation from the cytoplasm to the membrane compartments of KGN cells was remarkably reduced after the combined treatment of insulin and HGA. The present findings support that AGEs interfere with insulin signaling in granulosa cells and prevent Glut-4 membrane translocation suggesting that intra ovarian AGEs accumulation, from endogenous or exogenous sources, may contribute to the pathophysiology of states characterized with anovulation and insulin resistance such as polycystic ovary syndrome.
Mia40 and MINOS act in parallel with Ccs1 in the biogenesis of mitochondrial Sod1

Superoxide dismutase 1 (Sod1) is a major superoxide‐scavenging enzyme in the eukaryotic cell, and is localized in the cytosol and intermembrane space of mitochondria. Sod1 requires its specific chaperone Ccs1 and disulfide bond formation in order to be retained in the intermembrane space. Our study identified a pool of Sod1 that is present in the reduced state in mitochondria that lack Ccs1. We created yeast mutants with mutations in highly conserved amino acid residues corresponding to human mutations that cause amyotrophic lateral sclerosis, and found that some of the mutant proteins were present in the reduced state. These mutant variants of Sod1 were efficiently localized in mitochondria. Localization of the reduced, Ccs1‐independent forms of Sod1 relied on Mia40, an essential component of the mitochondrial intermembrane space import and assembly pathway that is responsible for the biogenesis of intermembrane space proteins. Furthermore, the mitochondrial inner membrane organizing system (MINOS), which is responsible for mitochondrial membrane architecture, differentially modulated the presence of reduced Sod1 in mitochondria. Thus, we identified novel mitochondrial players that are possibly involved in pathological conditions caused by changes in the biogenesis of Sod1.
Irritable bowel syndrome subtypes according to bowel habit: revisiting the alternating subtype

Background Disturbed bowel habit, diarrhoea or constipation is a key manifestation of irritable bowel syndrome (IBS). In some patients, diarrhoea and constipation alternate, giving rise to the so-called alternating subtype. Aims To assess IBS subtype breakdown (constipation (C-IBS), diarrhoea (D-IBS) or alternating (A-IBS)) according to the Rome II criteria and patients’ self-assessment, the predominance in the alternating subtype (i.e. constipation, diarrhoea or neither), and the medical and personal impact, including health-related quality of life (HRQoL), of the different IBS subtypes. Subjects and methods Two thousand individuals selected randomly to represent the general population were classified as potential IBS subjects (n = 281) or as non-potential IBS subjects (n = 1719) according to a validated questionnaire. Bowel habit classification was determined using the Rome II IBS supportive symptoms. Results Among 201 subjects meeting the Rome I criteria, 15% presented with D-IBS, 44% presented with C-IBS, 19% presented with A-IBS, and 22% presented with normal bowel habit. Among the 63 subjects meeting the Rome II criteria, 23% presented with A-IBS. According to the subjects’ self-assessment, of those meeting the Rome I criteria, 16% considered themselves to have D-IBS, 66% to have C-IBS and 18% to have A-IBS. In subjects meeting the Rome II criteria, 24% considered themselves to have A-IBS. Among those classified with A-IBS by the Rome II criteria, most considered themselves to be constipated. Regardless of the subtype self-classification, most subjects reported a normal frequency of bowel movements. Clinical manifestations in A-IBS were very similar to those of C-IBS but with the added presence of defecatory urgency. Abdominal discomfort/pain and frequency of visits to physicians were greater in the A-IBS subtype than in the other two IBS subtypes. HRQoL was affected similarly in all IBS subtypes. Conclusions Approximately one-quarter of subjects with IBS belong to the A-IBS subtype by the Rome II criteria, although the majority consider themselves to be constipated; indeed, clinical manifestations are more akin to the C-IBS subtype than to the D-IBS subtype. Abdominal discomfort/pain and frequency of visits to physicians are greater in the A-IBS subtype than in the other two IBS subtypes, while HRQoL is impaired similarly.
Complete Genome Sequence of Edwardsiella piscicida Isolate S11-285 Recovered from Channel Catfish (Ictalurus punctatus) in Mississippi, USA

ABSTRACT Edwardsiella piscicida is a recently described Gram-negative facultative anaerobe and an important pathogen to many wild and cultured fish species worldwide. Here, we report the complete and annotated genome of E. piscicida isolate S11-285 recovered from channel catfish (Ictalurus punctatus), consisting of a chromosome of 3,923,603 bp and 1 plasmid.
Exploring the motivations of White racial justice activist involved in education.

Whiteness’ studies in the United States of America and South Africa have explored both the concepts of ‘white’ privilege, as well as ‘white’ racial identity. In post-apartheid South Africa, the literature reveals that in many instances, ‘white’ South Africans are constructing identities around victimhood and colour-blind narratives that can support their privilege. However, there are few studies which seek to understand ‘white’ South Africans who are attempting to embrace more positive alternative narrative identities. This study aims to understand what narratives ‘white’ people who are actively seeking racial justice in South Africa are embracing. Using critical race theory and theories of narrative identity and social action, as well as drawing on previous studies of ‘white’ identity in South Africa and the USA, this qualitative study explores the narratives of ‘white’ racial justice activists in education from a South African perspective. All participants were English speaking and involved in the field of education, ranging from those who primarily see themselves as educators to those who primarily see themselves as activists. The analysis showed that the majority of participants were constructing their identities around narratives of “educator,” “Christian,” and “caring individual,” which were rooted in larger narratives. These larger narratives provided the underlying framework for the creation of narrative identities and moral action. In terms of their racial identity, it appeared that the majority of participants in this study were constructing their identities along the lines of Steyn’s (2001) Whiter Shade of White narrative, which highlights national, transcendent, or individual identities and avoids or denies the present implications of ‘whiteness’ in the post-apartheid context. This narrative shows a definite move away from overt prejudice and is a sincere attempt to positively engage with the “new South Africa” by finding common ground through aspects of shared identities; however, by not engaging with race at all, it is a way to avoid the guilt of continued racial
Evolution of Sleep Quantity, Sleep Deprivation, Mood Disturbances, Empathy, and Burnout among Interns

Purpose To explore the relationships between sleep deprivation and the evolution of mood disturbances, empathy, and burnout among a cohort of interns. Method In 2002–03, 47 interns in the internal medicine resident program at the University of Pennsylvania School of Medicine completed the following instruments at baseline and at year end: sleep quantities, Epworth Sleepiness Scale, the Beck Depression Inventory–Short Form, the Interpersonal Reactivity Index, and the Maslach Burnout Inventory-Human Services Survey. The prevalences of acute and chronic sleep deprivation, subjective sleepiness, burnout, empathy, and depression at the beginning of the year were compared to prevalences at the end of internship. Associations between sleep deprivation and mood, empathy, or burnout were explored. Results The prevalence of chronic sleep deprivation, depression, burnout, and empathy increased from baseline to year end. Specifically, the prevalence of "high" scores changed for chronic sleep deprivation (9% to 43%, p = .0001). The prevalence of moderate depression increased from 4.3% to 29.8% (p = .0002). Only 4.3% reported a high level of burnout initially compared with 55.3% at year end (p < .0001). Scores that were originally more favorable than general population norms (p < .001) approached norms at the end of the year for empathic concern (p = .15). There was an association between becoming chronically sleep deprived and becoming depressed (OR = 7, p = .014). Conclusions Given the association between chronic sleep deprivation and mood disturbances during internship, outcome assessment is warranted to see if duty-hour reform will translate into more hours slept or fewer hours worked, coincident with improved mood.