Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycobacterial genotype is associated with disease phenotype in children.

OBJECTIVE To investigate the association between mycobacterial genotype and disease phenotype in children. METHODS We describe hospitalised children diagnosed with culture-confirmed tuberculosis (TB) in South Africa, a high TB burden setting. Disease phenotype was classified as intrathoracic or extrathoracic based on mycobacterial culture site. Mycobacterial genotyping was completed using spoligotyping. RESULTS We analysed 421 isolates from 392 children (median age 2 years, range 0.1-12). Intrathoracic disease was present in 294 (75%) children and extrathoracic disease in 98 (25%). The Beijing genotype was the most prevalent (32.9%), followed by the Latin American Mediterranean (LAM, 28.8%), and S genotypes (6.4%). Age was significantly associated with genotype. Children with the Beijing (OR = 2.36, 95%CI 1.21- 4.60) and S genotypes (OR = 3.47, 95%CI 1.26-9.56) were more likely to have extrathoracic disease compared to children infected with the LAM genotype, in analyses adjusted for age and drug resistance. CONCLUSIONS TB genotype and disease phenotype in children were associated. Beijing and S genotypes were more frequently cultured from extrathoracic cultures, indicating potential improved ability to disseminate. Strain-related phenotypes could explain different disease spectra in geographic settings where certain strains are successful. Studies of mycobacterial human interaction should consider host immune responses, clinical and epidemiological factors.
Female X-chromosome mosaicism for gp91phox expression diversifies leukocyte responses during endotoxemia

Objective:To test the hypothesis, using an animal model, whether female X-chromosome mosaicism for inflammatory gene expression could contribute to the gender dimorphic response during the host response. X-chromosome-linked genetic polymorphisms present a unique biological condition because females display heterozygous cellular mosaicism, due to the fact that either the maternal or the paternal X chromosomes are inactivated in each individual cell in females. This is in contrast with the conditions in males who carry exclusively the maternal X chromosome. Design:Prospective, randomized, laboratory investigation. Settings:University research laboratory. Subjects:Female mice deficient, heterozygous (mosaic) or WT for the X-linked gp91phox. Interventions:We compared selected inflammatory markers among heterozygous (mosaics), WT and homozygous deficient animals in response to in vivo lipopolysaccharide (Escherichia coli, 20 mg/kg body weight). To test individual mosaic subpopulations of polymorphonuclear neutrophil responses, we also developed a flow cytometry assay that identifies the active parental X chromosomes in individual cells, using gp91phox expression as a marker. Measurements and Main Results:Heterozygous mosaic mice presented white blood cell trafficking patterns similar to that observed in WT mice, despite the fact that the deficient subpopulation in mosaic animals displayed increased cell activation as reflected in elevated neutrophil CD11b expression and splenic infiltration. Mosaic animals also displayed splenic neutrophil infiltration, which was skewed toward the deficient subpopulation. Observations on splenic T-cell depletion and post lipopolysaccharide interleukin-10 responses indicated that the inflammatory response in mosaic animals does not simply display an average of the deficient and WT responses, but the mosaic subjects display a uniquely characteristic response. Conclusions:The study supports the notion that female X chromosome mosaicism for polymorphic gene expression represents a unique condition, which may contribute to the gender dimorphic character of the inflammatory response. Mosaicism for X-linked polymorphisms may have clinical significance and needs consideration in genetic association or gender-related clinical studies.
Forbidden subgraphs and forbidden substructures

Abstract The problem of the existence of a universal structure omitting a finite set of forbidden substructures is reducible to the corresponding problem in the category of graphs with a vertex coloring by two colors. It is not known whether this problem reduces further to the category of ordinary graphs. It is also not known whether these problems are decidable.
The effect of local cooling on pain perception during infiltration of local anaesthetic agents, a prospective randomised controlled trial *

The effect of pre‐infiltration local cooling of the site of inguinal herniorrhaphy on pain perception during infiltration of local anaesthetic was studied in a prospective randomised controlled trial. One hundred patients were randomly allocated to receive topical application of either a cooled saline bag (study group) or a saline bag at room temperature (control group) prior to injection of local anaesthetic. Pain scores were recorded using a visual analogue scale following application of the saline bags and again on completion of infiltration with local anaesthetic. There was no significant difference in pain scores following topical saline bag application. However, a highly significant difference (p = 0.0001, Mann–Whitney U) was observed between post‐infiltration pain scores of the study group (median = 2) and the control group (median = 6).
Long‐Term Epilepsy‐Associated Tumors

The term long‐term epilepsy associated tumor (LEAT) encompasses lesions identified in patients investigated for long histories (often 2 years or more) of drug‐resistant epilepsy. They are generally slowly growing, low grade, cortically based tumors, more often arising in younger age groups and in many cases exhibit neuronal in addition to glial differentiation. Gangliogliomas and dysembryoplastic neuroepithelial tumors predominate in this group. LEATs are further united by cyto‐architectural changes that may be present in the adjacent cortex which have some similarities to developmental focal cortical dysplasias (FCD); these are now grouped as FCD type IIIb in the updated International League Against Epilepsy (ILAE) classification. In the majority of cases, surgical treatments are beneficial from both perspectives of managing the seizures and the tumor. However, in a minority, seizures may recur, tumors may show regrowth or recurrence, and rarely undergo anaplastic progression. Predicting and identifying tumors likely to behave less favorably are key objectives of the neuropathologist. With immunohistochemistry and modern molecular pathology, it is becoming increasingly possible to refine diagnostic groups. Despite this, some LEATs remain difficult to classify, particularly tumors with “non‐specific” or diffuse growth patterns. Modification of LEAT classification is inevitable with the goal of unifying terminological criteria applied between centers for accurate clinico‐pathological‐molecular correlative data to emerge. Finally, establishing the epileptogenic components of LEAT, either within the lesion or perilesional cortex, will elucidate the cellular mechanisms of epileptogenesis, which in turn will guide optimal surgical management of these lesions.
Patient-Centered Care and Emergency Department Utilization

Increased emergency department (ED) overcrowding has renewed interest in identifying remedies for unnecessary ED utilization. One potential remedy receiving more attention is patient-centered care. Relatively little is known, however, about how patient-centered care might decrease ED utilizatiosn. This study examined two mediating processes by which four dimensions of patient-centered care may affect patients’ reported ED visits. Cross-sectional path analysis of 8,140 chronically ill patients found that patients reporting higher levels of patient-centered care were less likely to have experienced problems of care coordination, and in turn were associated with decreased likelihood of having delayed care and fewer ED visits. These findings suggest that understanding how care is delivered, and not simply whether it is available or provided, is an important consideration in understanding ED utilization. Our findings suggest that fostering more fair and respectful relationships between patients and providers may be a particularly important way of reducing ED utilization.
Shortwave direct radiative effects of above-cloud aerosols over global oceans derived from 8 years of CALIOP and MODIS observations

Abstract. In this paper, we studied the frequency of occurrence and shortwave direct radiative effects (DREs) of above-cloud aerosols (ACAs) over global oceans using 8 years (2007–2014) of collocated CALIOP and MODIS observations. Similar to previous work, we found high ACA occurrence in four regions: southeastern (SE) Atlantic region, where ACAs are mostly light-absorbing aerosols, i.e., smoke and polluted dust according to CALIOP classification, originating from biomass burning over the African Savanna; tropical northeastern (TNE) Atlantic and the Arabian Sea, where ACAs are predominantly windblown dust from the Sahara and Arabian deserts, respectively; and the northwestern (NW) Pacific, where ACAs are mostly transported smoke and polluted dusts from Asian. From radiative transfer simulations based on CALIOP–MODIS observations and a set of the preselected aerosol optical models, we found the DREs of ACAs at the top of atmosphere (TOA) to be positive (i.e., warming) in the SE Atlantic and NW Pacific regions, but negative (i.e., cooling) in the TNE Atlantic Ocean and the Arabian Sea. The cancellation of positive and negative regional DREs results in a global ocean annual mean diurnally averaged cloudy-sky DRE of 0.015 W m−2 (range of −0.03 to 0.06 W m−2) at TOA. The DREs at surface and within the atmosphere are −0.15 W m−2 (range of −0.09 to −0.21 W m−2), and 0.17 W m−2 (range of 0.11 to 0.24 W m−2), respectively. The regional and seasonal mean DREs are much stronger. For example, in the SE Atlantic region, the JJA (July–August) seasonal mean cloudy-sky DRE is about 0.7 W m−2 (range of 0.2 to 1.2 W m−2) at TOA. All our DRE computations are publicly available1. The uncertainty in our DRE computations is mainly caused by the uncertainties in the aerosol optical properties, in particular aerosol absorption, the uncertainties in the CALIOP operational aerosol optical thickness retrieval, and the ignorance of cloud and potential aerosol diurnal cycle. In situ and remotely sensed measurements of ACA from future field campaigns and satellite missions and improved lidar retrieval algorithm, in particular vertical feature masking, would help reduce the uncertainty. 1 https://drive.google. com/folderview? id=0B6gKx4dgNY0GMVYzcEd0bkZmRmc&usp=sharing
Patterns of alcohol consumption in bipolar patients comorbid for alcohol abuse or dependence.

OBJECTIVES Despite a high prevalence rate, patients with bipolar disorder and active alcohol use are routinely excluded from controlled clinical trials leaving clinicians with little evidence-based medicine to guide treatment. This report evaluates preliminary data of alcohol consumption patterns utilizing the Alcohol Timeline Followback (TLFB) method in actively drinking patients with bipolar disorder. METHODS A sample of 30 patients underwent a Structured Diagnostic Interview for DSM-IV (SCID-IV) as well as completing various measures of alcohol use and associated morbidity. RESULTS In the month prior to study entry, the TLFB reported 18.4/30+/-9.12 drinking days, 9.9+/-4.73 drinks per drinking day and 169.4+/-101.71 total standard drinks for this study group. There was a significant difference in the number of drinks per drinking day between those diagnosed with rapid cycling than non-rapid cycling bipolar disorder and those with a new diagnosis versus established diagnosis of bipolar disorder. DISCUSSION This study highlights heavy alcohol use in patients with bipolar disorder and alcohol comorbidity. The TLFB method provides 'real world' quantification of use. Further studies are encouraged to elucidate implications of heavy drinking patterns as found in our rapid cycling and newly diagnosed cohorts.
Direct, enzyme‐linked immunoassay for urinary deoxypyridinoline as a specific marker for measuring bone resorption

Several studies in recent years have shown that the pyridinium crosslinks of collagen provide good urinary markers of collagen degradation, primarily reflecting bone resorption. Most studies, however, were based on time‐consuming HPLC assays of the crosslinks. We now describe the development of an immunoassay (ELISA) based on a monoclonal antibody for free deoxypyridinoline (Dpd) and its use in healthy individuals and patients with bone‐related disorders to measure the urinary excretion of Dpd as an improved assessment of bone resorption rate. The Dpd antibody exhibited less than 1% cross‐reaction with free pyridinoline and was shown to react only with free Dpd in urine, having no significant interaction with peptide forms of the crosslinks. The intra‐ and interassay variations were less than 10 and 15%, respectively. A total of 402 urine samples from patients and healthy volunteers were analyzed by both the immunoassay and HPLC. The ELISA results were highly correlated with those for total Dpd measured by HPLC over the full range of sample groups (r = 0.95). In normal adults, the excretion of Dpd (mean + SD) was 4.7 + 1.6 nmol/mmol creatinine, with about fivefold higher excretion rates in children. For 31 osteoporotic patients, the ELISA Dpd values (median 6.7; range 3.0–13.5 nmol/mmol Cr) were significantly higher (p < 0.0001) than the corresponding values for age‐ and sex‐matched controls (median 4.0; range 1.8–7.4). The difference between the groups was similar for total Dpd by HPLC (osteoporotic: mean 12.8, range 4.8–30.7; controls: 6.6, range 3.0–18.1; p < 0.0001). For other patient groups, comparisons of the Dpd excretion with healthy controls revealed similar differences for both the immunoassay and total Dpd analyses in primary HPT (n = 23: p < 0.0001), Paget's disease (n = 28, p < 0.0001), renal dysfunction (n = 26, no significant difference), and breast cancer (n = 17, p < 0.0001). We conclude that the immunoassay constitutes a simpler, more direct way of assessing bone resorption rates that provides similar information to the more cumbersome HPLC methods.
Factors influencing oncology nurses' use of hazardous drug safe-handling precautions.

PURPOSE/OBJECTIVES To examine relationships among factors affecting nurses' use of hazardous drug (HD) safe-handling precautions, identify factors that promote or interfere with HD precaution use, and determine managers' perspectives on the use of HD safe-handling precautions. DESIGN Cross-sectional, mixed methods; mailed survey to nurses who handle chemotherapy and telephone interviews with managers. SETTING Mailed invitation to oncology centers across the United States. SAMPLE 165 nurses who reported handling chemotherapy and 20 managers of nurses handling chemotherapy. METHODS Instruments measured the use of HD precautions and individual and organizational factors believed to influence precaution use. Data analysis included descriptive statistics and hierarchical regression. Manager interview data were analyzed using content analysis. MAIN RESEARCH VARIABLES Chemotherapy exposure knowledge, self-efficacy, perceived barriers, perceived risk, interpersonal influences, and workplace safety climate. FINDINGS Nurses were well educated, experienced, and certified in oncology nursing. The majority worked in outpatient settings and administered chemotherapy to an average of 6.8 patients per day. Exposure knowledge, self-efficacy for using personal protective equipment, and perceived risk of harm from HD exposure were high; total precaution use was low. Nurse characteristics did not predict HD precaution use. Fewer barriers, better workplace safety climate, and fewer patients per day were independent predictors of higher HD precaution use. HD handling policies were present, but many did not reflect current recommendations. Few managers formally monitored nurses' HD precaution use. CONCLUSIONS Circumstances in the workplace interfere with nurses' use of HD precautions. IMPLICATIONS FOR NURSING Interventions should include fostering a positive workplace safety climate, reducing barriers, and providing appropriate nurse-patient ratios.
The one microgram adrenocorticotropin test in the assessment of hypothalamic-pituitary-adrenal function.

The possibility of assessing hypothalamic-pituitary-adrenal (HPA) function by the standard ACTH test (250 microg) has been widely discussed in the past years and compared with the role of the insulin tolerance test (ITT). Recently, it was shown that low doses of ACTH, such as 1 microg i.v. , induce a maximal adrenal response and, by reducing the discrepancies compared with the ITT also allow one to detect mild forms of secondary hypoadrenalism. In the present study the 1 microg ACTH test was performed in patients with hypothalamic-pituitary disease in order to assess adrenal function, and the results have been compared with those obtained after the insulin test. Fifty-seven patients (31 men and 26 women, aged 19-73 years) with hypothalamic-pituitary diseases were studied: 51 patients were affected with pituitary tumor and 6 patients had hypothalamic disorders. All these patients and 18 healthy volunteers (7 men and 11 women, aged 19-46 years) received 1 microg i.v. ACTH injection. In addition, the ITT (0.1-0.15 U/kg body weight) was performed in all patients. In normal subjects mean cortisol levels significantly (P<0.001) increased from a baseline of 393+/-43 nmol/l to a peak of 770+/-41 nmol/l after 1 microg ACTH. In 44 patients with hypothalamic-pituitary disease 1 microg ACTH caused a cortisol rise similar to that of normal subjects (from 332+/-17 to 769+/-24 nmol/l; P<0.001), while an impaired response (from 124+/-23 to 312+/-46 nmol/l) was observed in 13 cases (23%), 7 of them with low morning cortisol levels (10-127 nmol/l) and 6 with basal values at the lower limit of normality. The cortisol response to ITT was compared with that obtained after the 1 microg ACTH test: 10 patients failed both challenges, 4 patients who passed the ACTH test failed the ITT, while 3 patients who failed the ACTH test passed the ITT. The 23 out of 57 patients (40%) who showed a cortisol peak greater than 750 nmol/l after 1 microg ACTH had a normal response to ITT. A positive correlation between cortisol peaks after ACTH and after insulin was also found (r = 0.68, P<0.001). Assuming a 100% accuracy of ITT, the low dose ACTH test yielded a 71% sensitivity and a 93% specificity. In conclusion, the low-dose ACTH test is a useful, safe and inexpensive tool for the initial assessment of HPA function in patients with hypothalamic-pituitary disease. In fact, the ITT is unnecessary when cortisol peaks are greater than 750 nmol/l after 1 microg ACTH and also when very low cortisol basal levels indicate an overt hypoadrenalism. Within these limits the ITT is mandatory and its important role in the recognition of secondary adrenal failure is further confirmed.
Differential Involvement of Dendritic Cell Subsets During Acute Salmonella Infection1

Within murine CD11c+ dendritic cells (DC), CD8α+, CD8α−CD4+, and CD8α−CD4− subsets are defined. This study characterized the localization, number, and function of these subsets during acute Salmonella typhimurium infection. Immunohistochemical and flow cytometric analyses of spleens from mice orally infected with virulent S. typhimurium revealed that in situ redistribution and alteration in the absolute number and function of DC occurred in a subset-specific manner during infection. CD8α−CD4+ DC present at B cell follicle borders in the spleen of naive mice were absent 5 days post-Salmonella infection, despite no overall change in the absolute number of CD8α−CD4+ splenic DC. CD8α+ and CD8α−CD4− DC were prominently associated with the red pulp, and the frequency of these cells increased strikingly 5 days post-Salmonella infection. Significant quantitative increases in both CD8α+ and CD8α−CD4− subsets were associated with the in situ redistribution. Examination of Salmonella-infected TAP1−/−/β2-microglobulin−/− mice, which lack CD8α+ T cells, confirmed the differential subset-specific modulations in the DC populations both in situ and quantitatively. Ex vivo intracellular cytokine analysis showed significantly increased frequencies of CD8α+ DC producing TNF-α at days 2 and 5 postinfection. In contrast, CD4+ DC producing TNF-α were transiently increased followed by a significant reduction. No significant increase in IL-12p40 or IL-10 production by splenic DC was detected during the first 5 days post-S. typhimurium infection. Together these data reveal differential modulation of splenic DC subsets with regard to organization, number, and cytokine production during the course of acute Salmonella infection.
VS38: a new monoclonal antibody for detecting plasma cell differentiation in routine sections.

AIMS--To characterise a new mouse monoclonal antibody, VS38, which recognises an intracytoplasmic antigen of 64 kilodaltons present in normal and neoplastic plasma cells; and to establish its value as a diagnostic reagent for routine pathological practice. METHODS--A range of normal and neoplastic tissue sections, both frozen and routinely fixed, were immunostained, using the microwave method of antigen retrieval for routinely fixed specimens. The antibody was also tested on blood and bone marrow specimens and a range of human cell lines. The molecular weight of the antigen recognised by the antibody was obtained by western blot analysis. FACS analysis was used to demonstrate the cellular location of the antigen and its presence on tonsil cell suspensions and myeloma cases. RESULTS--VS38 recognised normal and neoplastic plasma cells in all of the tissues, including all routinely fixed plasma cell neoplasms tested. The antibody also weakly stained epithelial elements within the tissue but was absent from haemopoietic cells of other lineages. CONCLUSION--Antibody VS38 is of potential value in identifying myeloma or plasmacytoma in bone marrow or other tissues. It differentiates lymphoplasmacytoid lymphoma from lymphocytic and follicular lymphoma. It also subdivides large cell lymphomas into two groups which may be a more reliable method of separating these tumours than morphology alone.
Making e-books available through public libraries

This paper considers the results of an online questionnaire survey that collected user data on e-book collections held at Essex County Libraries over a two-year period between April 2004 and June 2006. The research was funded by the Laser Foundation, and specifically considered e-book collections held on Personal Digital Assistant (PDA) devices, as well as collections viewable on Personal Computers with Internet access. Questionnaire responses from 58 individuals indicated clearly that marketing of e-book collections needs serious consideration, that certain genres were popular with users (notably Science Fiction), and that the largest number of respondents were aged between 21 and 30. As we discuss, the findings of this questionnaire survey offer few insights into e-book usage that have not been reported in other research. However, what the findings do illustrate clearly is that publicity afforded to e-book and other electronic collections remains crucial. From perusal of the data, 47 of the 58 respondents found out about the e-book collections after browsing the website. Whilst this obviously indicates that the website is indeed useful, the fact that only nine respondents investigated the collections having seen publicity material tells another story.
Identification of binding domains on red blood cell glycophorins for Babesia divergens

Invasion of red blood cells (RBCs) is one of the critical points in the lifecycle of Babesia. The parasite does not invade other host cells. Earlier work has shown that GPA and GPB function as putative receptors during parasite invasion. The primary focus of this study was the delineation of parasite‐binding domains on GPA and GPB.