Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Immune Response and Th1/Th2 Cytokines in Human Neurocysticercosis: Lack of Immune Suppression

Some reports have suggested that human neurocysticercosis (NCC) induces immunosuppression. To test this hypothesis, we performed a study on active cases of NCC who had not received cestocidal or immunosuppressive treatments. We examined blood counts and specific T cell markers (CD3, CD4, and CD8) by flow cytometry and found no differences between patients with NCC and healthy individuals. Both groups responded to concanavalin A (Con A), and patients with NCC responded more to a parasite crude antigen than uninfected individuals. Peripheral blood mononuclear cells were examined for interleukin (IL)-2, interferon-γ, IL-10, and IL-4 mRNA. Regardless of infection status, more than 60% of individuals synthesized IL-2 mRNA and, less frequently, the other cytokines. These data suggest that immunosuppression does not occur in NCC patients.
Endobronchial ultrasound‐guided transbronchial needle aspirate (EBUS‐TBNA):A proposal for on‐site adequacy criteria

This is a retrospective study of 48 patients who underwent EBUS‐TBNA procedure between the periods January 2008 to September 2009 at Long Island Jewish Medical Center. The study was undertaken with the following objectives: First, to define practical and useful on‐site adequacy criteria for EBUS‐TBNA samples; Second, to understand the diagnostic pitfalls associated with accurate interpretation of EBUS‐TBNA samples. EBUS‐TBNA procedure was able to diagnose 24/48 (50%) patients with malignancy, 1/48 (2%) suspicious for malignancy, 9/48 (19%) with granulomatous process, and 9/48 (19%) negative for disease. Only five cases (10%) could not be diagnosed with this procedure. Based on our experience, any smear with presence of > 5 low power fields (×100) with ≥ 100 lymphocytes in each and containing < 2 groups of bronchial cells/low power field (×100) can be considered adequate for evaluation. Also, the presence of germinal center fragments renders a smear adequate for evaluation, irrespective of the above mentioned criteria. Adequacy criteria are to be applied only to the smears not showing any identifiable pathology such as malignancy or granuloma. An understanding of diagnostic pitfalls associated with accurate interpretation of EBUS‐TBNA samples is essential to avoid false‐positive and false‐negative diagnosis. To conclude, an effective communication between the clinician and cytologist, an algorithmic approach to diagnosis, and the on‐site adequacy criteria proposed in this study can markedly improve the diagnostic yield of the procedure. Diagn. Cytopathol. 2011. © 2010 Wiley Periodicals, Inc.
Role of Pseudomonas aeruginosa dinB-Encoded DNA Polymerase IV in Mutagenesis

ABSTRACT Pseudomonas aeruginosa is a human opportunistic pathogen that chronically infects the lungs of cystic fibrosis patients and is the leading cause of morbidity and mortality of people afflicted with this disease. A striking correlation between mutagenesis and the persistence of P. aeruginosa has been reported. In other well-studied organisms, error-prone replication by Y family DNA polymerases contributes significantly to mutagenesis. Based on an analysis of the PAO1 genome sequence, P. aeruginosa contains a single Y family DNA polymerase encoded by the dinB gene. As part of an effort to understand the mechanisms of mutagenesis in P. aeruginosa, we have cloned the dinB gene of P. aeruginosa and utilized a combination of genetic and biochemical approaches to characterize the activity and regulation of the P. aeruginosa DinB protein (DinB Pa ). Our results indicate that DinB Pa is a distributive DNA polymerase that lacks intrinsic proofreading activity in vitro. Modest overexpression of DinB Pa from a plasmid conferred a mutator phenotype in both Escherichia coli and P. aeruginosa. An examination of this mutator phenotype indicated that DinB Pa has a propensity to promote C→A transversions and −1 frameshift mutations within poly(dGMP) and poly(dAMP) runs. The characterization of lexA+ and ΔlexA::aacC1 P. aeruginosa strains, together with in vitro DNA binding assays utilizing cell extracts or purified P. aeruginosa LexA protein (LexA Pa ), indicated that the transcription of the dinB gene is regulated as part of an SOS-like response. The deletion of the dinB Pa gene sensitized P. aeruginosa to nitrofurazone and 4-nitroquinoline-1-oxide, consistent with a role for DinB Pa in translesion DNA synthesis over N 2 -dG adducts. Finally, P. aeruginosa exhibited a UV-inducible mutator phenotype that was independent of dinB Pa function and instead required polA and polC, which encode DNA polymerase I and the second DNA polymerase III enzyme, respectively. Possible roles of the P. aeruginosa dinB, polA, and polC gene products in mutagenesis are discussed.
System-Level Thermal Management of Pulsed Loads on an All-Electric Ship

With the Navy's development of the integrated electric warship, large amounts of electrical energy will be made available, thus allowing the addition of pulsed weaponry and sensors. Electromagnetic railguns will increase the thermal load on such a ship by an order of magnitude or more over a conventional gun. To represent the expected loads, a numerical model has been created to simulate the system-level energy balance for a capacitive-based railgun system and is currently in development for a rotating machine-based system. In order to better study the system-level effects of the increased thermal burden, multiple shot profiles and scenarios were used. The simulation outputs are used as inputs to a ship-based, thermal management architecture built in the dynamic thermal software package ProTRAX. Our analysis quantifies additional thermal management capacity that will be necessary for the future all-electric ship and provides the first step in simulating potential ship wide thermal management systems of pulsed loads in a dynamic sense
Structure-Function Analysis of the Enteroaggregative Escherichia coli Plasmid-encoded Toxin Autotransporter Using Scanning Linker Mutagenesis*

The plasmid-encoded toxin (Pet) from enteroaggregative Escherichia coli is a cytopathic serine protease, which is prototypical of a large family of bacterial autotransporter toxins. To further elucidate the structure-function relationships of this toxin, we employed transposon-based scanning linker mutagenesis. A subset of insertions throughout the Pet mature toxin (passenger) domain reduced secretion to the extracellular space. Many of these mutants were undetectable, but secretion of a subset of mutants with insertions in the N-terminal half of the toxin could be restored to wild type secretion levels if cultured in the presence of 0.1% Triton X-100. Secretion of two mutants with insertions at the extreme C terminus was partially restored when co-expressed with a minimal clone of EspP, a related autotransporter protein. Several well secreted mutants with insertions in the N-terminal third of the molecule reduced protease activity over 20-fold, suggesting that the protease domain is located within this N-terminal region of Pet. We have also identified two insertional mutants in the middle of the passenger domain that were proteolytic but no longer cytopathic; these mutants displayed decreased binding and internalization upon incubation with HEp-2 cells. Our data suggest the existence of separate functional domains mediating Pet proteolysis, secretion, and cell interaction.
Active Replication of HIV-1 at the Lymphoepithelial Surface of the Tonsil

From the Armed Forces Institute ofPathology and the Division of Retrovirology,* Department ofHIV Vaccine Development, Walter Reed Army Institute of Research, Rockville, Maryland; the Bernard-Nocht-Institute for Tropical Medicine,t Hamburg, Germany; the Department of Pathology,t Georgetown University Medical Center, Washington, DC; and the Laboratory of Cellular Physiology and Immunology,t Rockefeller University, New York, New York
Effect of the Er, Cr: YSGG Laser Parameters on Shear Bond Strength and Microstructure on Human Dentin Surface

Eun Mi Rhim1, Sungyoon Huh2, Duck Su Kim3, Sun-Young Kim4, Su-Jin Ahn5, Kyung Lhi Kang6 and Sang Hyuk Park4,7 1The Catholic University of Korea, St. Paul’s Hospital, Dept. of Conservative Dentistry, Seoul, 2Shingu University, Dept. of Dental Hygiene, Seongnam, 3Kyung Hee University, Dental Hospital, Dept. of Conservative Dentistry, Seoul 4Kyung Hee University, Dept. of Conservative Dentistry, Seoul, 5Kyung Hee University, Dental Hospital at Gandong, Dept. of Biomaterials & Prosthodontics, 6Kyung Hee University, Dental Hospital at Gandong, Dept. of Periodontology, 7Kyung Hee University Dental Hospital at Gandong, Dept. of Conservative Dentistry Korea
UTATION IN F AULT L OCALIZATION

Fault localization is time-consuming and difficult, which makes it the bottleneck of the debugging progress. To help facilitate this task, there exist many fault localization techniques that help narrow down the region of the suspicious code in a program. Better accuracy in fault localization is achieved from heavy computation cost. Fault localization techniques that can effectively locate faults also manifest slow response rate. In this paper, we promote the use of pre-computing to distribute the time-intensive computations to the idle period of coding phase, in order to speed up such techniques and achieve both low-cost and high accuracy. We raise the research problems of finding suitable techniques that can be pre-computed and adapt it to the pre-computing paradigm in a continuous integration environment. Further, we use an existing fault localization technique to demonstrate our research exploration, and shows visions and challenges of the related methodologies.
Elevated Depressive Symptoms, Antidepressant Use, and Diabetes in a Large Multiethnic National Sample of Postmenopausal Women

OBJECTIVE To examine elevated depressive symptoms and antidepressant use in relation to diabetes incidence in the Women’s Health Initiative. RESEARCH DESIGN AND METHODS A total of 161,808 postmenopausal women were followed for over an average of 7.6 years. Hazard ratios (HRs) estimating the effects of elevated depressive symptoms and antidepressant use on newly diagnosed incident diabetes were obtained using Cox proportional hazards models adjusted for known diabetes risk factors. RESULTS Multivariable-adjusted HRs indicated an increased risk of incident diabetes with elevated baseline depressive symptoms (HR 1.13 [95% CI 1.07–1.20]) and antidepressant use (1.18 [1.10–1.28]). These associations persisted through year 3 data, in which respective adjusted HRs were 1.23 (1.09–1.39) and 1.31 (1.14–1.50). CONCLUSIONS Postmenopausal women with elevated depressive symptoms who also use antidepressants have a greater risk of developing incident diabetes. In addition, longstanding elevated depressive symptoms and recent antidepressant medication use increase the risk of incident diabetes.
Reliability of radiographic measurement of small intestinal length

Objective The capacity for absorption of nutrients after small intestinal resection is related to the remaining length of intestine, and short bowel syndrome has major implications. Accurate pre‐operative determination of bowel length may be useful in conditions where further resection of small bowel is contemplated. The aim of this study is to evaluate the accuracy of small bowel length measured by barium follow‐through (BaFT) examination.
Novel topology and control of single inverter system for two permanent magnet synchronous machines

This paper proposes a novel topology which is capable of operate two permanent-magnet synchronous machines (PMSM) using a single 6-bridge inverter and its control method. In the conventional parallel connection method for this application, two motors can operate only at the same speed and have a high risk of loss of synchronism since the single voltage is applied to both motors. In other inverter topologies, the number of switches increases or implementation of inverter is complicated. On the other hand, the proposed topology can employ the conventional six bridge power module without any modification or addition and operate two motors at the different speeds using the superposition principle. The analysis of the proposed system is presented and the control method to independently operate two motors is proposed. It is verified through experimental results.
Aflatoxin levels in locally grown maize from Makueni District, Kenya.

OBJECTIVES Investigations were carried out to determine aflatoxin levels in household maize in Makueni District and to correlate aflatoxin levels to maize drying and storage practices. Also, aflatoxin exposure in villages that reported aflatoxicosis cases in 2005 was compared with that in villages that did not report cases to assess whether aflatoxin exposure levels could be used to identify high-risk villages for targeted prevention interventions. DESIGN A cross-sectional study. SETTING Three divisions of Makueni district, Kibwezi, Makindu and Mtito Andei in Eastern Province, Kenya. SUBJECTS Ninety six households were surveyed, and 104 maize samples were analysed for total aflatoxin levels from June to July 2005. The households were selected from high and low aflatoxicosis risk areas. RESULTS Out of the 104 maize samples collected from 96 households, 37 (35.5%) had aflatoxin levels above the World Health Organisation (WHO) recommended maximum limit of 20 ppb. All of these samples were homegrown or purchased. Twenty one samples (20.1%) had levels above 100 ppb. Eleven (10.6%) had extremely high levels above 1000 ppb. No relief supply maize had aflatoxin levels above the WHO maximum limit. CONCLUSION High levels of aflatoxin in homegrown and purchased maize suggested that aflatoxin exposure was widespread.
The Minicommunity Design to Assess Indirect Effects of Vaccination

Abstract We propose the minicommunity design to estimate indirect effects of vaccination. Establishing indirect effects of vaccination in unvaccinated subpopulations could have important implications for global vaccine policies. In the minicommunity design, the household or other small transmission unit serves as the cluster in which to estimate indirect effects of vaccination, similar to studies in larger communities to estimate indirect, total, and overall effects. Examples from the literature include studies in small transmission units to estimate indirect effects of pertussis, pneumococcal, influenza, and cholera vaccines. We characterize the minicommunity design by several methodologic considerations, including the assignment mechanism, ascertainment, the role of transmission outside the transmission unit, and the relation of the size of the transmission unit to number of people vaccinated. The minicommunity study for indirect effects is contrasted with studies to estimate vaccine effects on infectiousness and protective effects under conditions of household exposure within small transmission units. The minicommunity design can be easily implemented in individually randomized studies by enrolling and following-up members of households of the randomized individuals. The methodology for the minicommunity design for estimating indirect effects of vaccination deserves much future research.
"Evil habits" and "personal choices": assigning responsibility for health in the 20th century.

The 20th century began and ended with many of the nation's more affluent and better-educated citizens in a near-frenzied pursuit of better health through lifestyle modification. Americans sought and received health-enhancing and disease-preventing advice in books, newspapers, popular magazine articles, and government studies. They followed exercise regimes and bought self-improvement paraphernalia from “medicine balls” to elliptical machines in order to learn “How to Avoid Heart Troubles” (Groedel 1901) and, even more ambitiously, to stay Forever Young (Berger 1989). Upton Sinclair alerted early 20th-century Americans to the appalling conditions in the meatpacking industry (1906), and nearly a century later Eric Schlosser warned of the “Dark Side of the All-American Meal” (2001). Finally, San Franciscans, fretting about the nutritional dangers to their children's health, began the last century by banning “roving pie vendors” who catered to the “habitual pie-eating” habits of schoolchildren (Habitual Pie-Eating Ruining Health of Children 1910) and began this century by prohibiting the sale of soft drinks and other unhealthy snacks on school campuses (Delgado 2003).
Report of spores of Henneguya salminicola (Myxozoa) in human stool specimens: possible source of confusion with human spermatozoa

The spores of Henneguya salminicola, a common tissue parasite of salmonid fishes in the northern hemisphere, were observed in stool specimens from two different patients with diarrhea. The spores' superficial resemblance to human spermatozoa resulted, in one instance, in an incorrect report, leading to suspicion of sexual abuse. H. salminicola spores and human spermatozoa can be differentiated on the basis of size, morphology, and staining characteristics. Laboratory personnel who perform microscopic examinations of stool specimens for ova and parasites should be aware that spores of H. salminicola may be seen from time to time.
Facilitating online support groups for cancer patients: the learning experience of psycho‐oncology clinicians

Objective: Counsellor familiarity and engagement with technology‐mediated communication represents an important factor in the ability to implement support programs to cancer patients. This study describes the experiences of a cohort of expert psycho‐oncology counsellors who learned to facilitate online support groups (OSGs) and identifies the important elements of their learning experience that led to their engagement.
Effects of Budesonide on P38 MAPK Activation, Apoptosis and IL-8 Secretion, Induced by TNF-α and Haemophilus Influenzae in Human Bronchial Epithelial Cells

Non-typeable Haemophilus influenzae (NTHi) is one of the most frequently involved pathogens in bacterial exacerbations of chronic obstructive pulmonary disease (COPD). In the airways, the main tissue target of NTHi is bronchial epithelium, where this pathogen can further amplify the inflammatory and structural changes induced by proinflammatory cytokines such as tumour necrosis factor-α (TNF-α). Therefore, the aim of this study is to investigate, in primary cultures of human bronchial epithelial cells, the effects of NTHi on signal transduction pathways, apoptotic events and chemokine production activated by TNF-α. Moreover, we also evaluated the effects exerted on such cellular and molecular phenomena by a corticosteroid drug. p38 mitogen-activated protein kinase (MAPK) phosphorylation was analyzed by Western blotting, using an anti-phospho-p38 MAPK monoclonal antibody. Apoptosis was assayed by active caspase-3 expression. Interleukin-8 (IL-8/CXCL8) was detected in cell-free culture supernatants by ELISA. TNF-α induced a significant increase in p38 MAPK phosphorylation. NTHi was able to potentiate the stimulatory actions of TNF-α on caspase-3 expression and, to a lesser extent, on IL-8 secretion. These effects were significantly (P < 0.01) inhibited by a pharmacological pre-treatment with budesonide. These results suggest that TNF-a is able to stimulate, via activation of p38 MAPK signalling pathway, IL-8 release and airway epithelial cell apoptosis; the latter effect can be markedly potentiated by NTHi. Furthermore, budesonide can be very effective in preventing, through inhibition of p38 MAPK phosphorylation, both structural and proinflammatory changes elicited in bronchial epithelium by TNF-α and NTHi.
Infection, Viral Dissemination, and Antibody Responses of Rhesus Macaques Exposed to the Human Gammaretrovirus XMRV

ABSTRACT Xenotropic murine leukemia-related virus (XMRV) was identified in association with human prostate cancer and chronic fatigue syndrome. To examine the infection potential, kinetics, and tissue distribution of XMRV in an animal model, we inoculated five macaques with XMRV intravenously. XMRV established a persistent, chronic disseminated infection, with low transient viremia and provirus in blood lymphocytes during acute infection. Although undetectable in blood after about a month, XMRV viremia was reactivated at 9 months, confirming the chronicity of the infection. Furthermore, XMRV Gag was detected in tissues throughout, with wide dissemination throughout the period of monitoring. Surprisingly, XMRV infection showed organ-specific cell tropism, infecting CD4 T cells in lymphoid organs including the gastrointestinal lamina propria, alveolar macrophages in lung, and epithelial/interstitial cells in other organs, including the reproductive tract. Of note, in spite of the intravenous inoculation, extensive XMRV replication was noted in prostate during acute but not chronic infection even though infected cells were still detectable by fluorescence in situ hybridization (FISH) in prostate at 5 and 9 months postinfection. Marked lymphocyte activation occurred immediately postinfection, but antigen-specific cellular responses were undetectable. Antibody responses were elicited and boosted upon reexposure, but titers decreased rapidly, suggesting low antigen stimulation over time. Our findings establish a nonhuman primate model to study XMRV replication/dissemination, transmission, pathogenesis, immune responses, and potential future therapies.
Electroencephalographic Sleep Recordings and Depression in the Elderly *

Eighteen patients over the age of 60 who were experiencing a major depressive episode were studied on a Clinical Research Unit after they had been drug‐free for at least two weeks. All‐night electroencephalographic (EEG) recordings revealed considerable fragmentation of sleep, a mean sleep efficiency of 58 percent, and very little delta sleep. The findings of reduced sleep time, shortened REM latency, and high REM density were similar to those in depressed patients under the age of 60. These preliminary findings support the application of EEG sleep recordings as a tool for the differential diagnosis of depression in the elderly.
Improving Performance of Medical Images Retrieval by Combining Textual and Visual Information

This paper studies the combination of textual and visual information in a database of medical records in order to improve the performance of the multi-modal information retrieval system. The proposed model consists of two subsystems: a content-based information retrieval subsystem that performs the image retrieval and a textual information retrieval subsystem that performs the textual retrieval. The images and text are independently retrieved and then the partial resulting lists are mixed. A study of different weighting schemes has been accomplished and analyzed. The results obtained show that the proper integration of textual information improves conventional multi-modal systems.