Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinctive Profiles of Infection and Pathology in Hamsters Infected with Clostridium difficile Strains 630 and B1

ABSTRACT Currently, the Golden Syrian hamster is widely considered an important model of Clostridium difficile disease, as oral infection of this animal pretreated with antibiotics reproduces many of the symptoms observed in humans. Two C. difficile strains, B1 and 630, showed significant differences in the progression and severity of disease in this model. B1-infected hamsters exhibited more severe pathology and a shorter time to death than hamsters infected with 630. Histological changes in the gut did not correlate with absolute numbers of C. difficile bacteria, but there were clear differences in the distribution of bacteria within gut tissues. Light, scanning, and transmission electron microscopy revealed high numbers of B1 bacteria at the mucosal surface of the tissue, whereas 630 bacteria were more frequently associated with the crypt regions. Both B1 and 630 bacteria were frequently observed within polymorphonuclear leukocytes, although, interestingly, a space frequently separated B1 bacteria from the phagosome wall, a phenomenon not observed with 630. However, pilus-like structures were detected on 630 located in the crypts of the gut tissue. Furthermore, B1 bacteria, but not 630 bacteria, were found within nonphagocytic cells, including enterocytes and muscle cells.
Differentiation of neuroblastoma cells induced by an inhibitor of mevalonate synthesis: Relation of neurite outgrowth and acetylcholinesterase activity to changes in cell proliferation and blocked isoprenoid synthesis

Mevinolin, a competitive inhibitor of 3‐hydroxy‐3‐methylglutaryl coenzyme A (HMG‐CoA) reductase, stimulates neurite outgrowth and acetylcholinesterase (ACE) activity in C1300 (Neuro‐2A) murine neuroblastoma cells. Sprouting of neurites began within 4–8 h, before changes in cell proliferation could be detected by [3H]thymidine incorporation or flow cytometry. In contrast, the increase in ACE activity was temporally correlated with suppression of DNA synthesis, which occurred after 8 h. The activity of the membrane marker enzyme phosphodiesterase I was not stimulated by mevinolin. Suppression of protein synthesis with cycloheximide blocked the induction of ACE activity but only partially inhibited neurite outgrowth in the mevinolin‐treated cultures. When mevinolin was removed from the culture medium, most of the cells retracted their neurites within 2 h, but ACE activity did not decline until DNA synthesis began to return to control levels after 10 h. Similarly, retraction of neurites in differentiated cells exposed to colchicine was not accompanied by a decrease in ACE activity. DNA histograms suggested that mevinolin arrests neuroblastoma cells in both the G1 and G2/M compartments of the cell cycle. Other cytostatic drugs that arrest cells at different stages of the cell cycle did not cause Neuro‐2A cells to form neurites such as those seen in the mevinolin‐treated cultures. When incorporation of [3H]acetate into isoprenoid compounds was studied in cultures containing mevinolin in concentrations ranging from 0.25 μM to 25 μM, the labeling of cholesterol, dolichol, and ubiquinone was suppressed by 90% or more at all concentrations. However, significant growth arrest and cell differentiation were observed only at the highest concentrations of mevinolin. Supplementing the medium with 100 μM mevalonate prevented the cellular response to mevinolin, but additions of cholesterol, dolichol, ubiquinone, or isopentenyl adenine were generally ineffective. The cholesterol content of neuroblastoma cells incubated with 25 μM mevinolin for 24 h was not diminished, and protein glycosylation, measured by [3H]mannose incorporation, was decreased only after 24 h at high mevinolin concentration. These studies suggest that the stimulation of neurite outgrowth and the increase in ACE activity induced by mevinolin are independent phenomena. Whereas neurite outgrowth is not related directly to the effects of mevinolin on cell cycling, the induction of ACE is correlated with the inhibition of cell proliferation. The cellular changes produced by blocking mevalonate synthesis do not appear to be causally linked to depletion of total cellular cholesterol or perturbation of glycoprotein synthesis. However, the possibility that depletion of ubiquinone or novel isoprenoid proteins triggers the arrest of cell proliferation and the expression of differentiated properties has not been ruled out.
An Exploration of the Genetic Robustness Landscape of Surface Protein Families in the Human Protozoan Parasite Trypanosoma Cruzi

The ability of genes to be robust to mutations at the codon level has been suggested as a key factor for understanding adaptation features. It has been proposed that genes relevant to host-parasite interactions will tend to exhibit high volatility or "antirobust" patterns, which may be related to the capacity of the parasite to evade the host immune system. We compared two superfamilies of surface proteins, trans-sialidase (TS)-like proteins and putative surface protein dispersed gene family-1 (DGF-1), in the parasite Trypanosoma cruzi in terms of a measure of gene volatility. We proposed alternative codon robustness indicators based on cross entropy and impurity of amino acids encoded by point-mutations, which were compared to a volatility estimator previously published. This allowed us to present a more detailed description of the differences between families. A significant difference was observed in terms of these scores, with the TS-MVarl and the DGF-1 families showing the highest and lowest gene volatility values respectively. The cross entropy and impurity estimators suggest that the MVarl levels of volatility are linearly correlated with their capacity to generate diverse sets of amino acids as a consequence of potential mutations. This study indicates the feasibility of applying different measures of genetic robustness to detect variations between potential drug targets at the protein level.
Ethnic favoritism in primary education in Kenya: effects of coethnicity with the president

ABSTRACT This study measures the effect of ethnic favoritism on primary education using data from the Kenya Demographic and Health Survey. In line with previous studies, this study confirms that having a coethnic president is expected to improve the likelihood of completing primary education. This study demonstrates that ethnic favoritism operates at the district level but not in the ethnic dimension, as only coethnics living in coethnic districts can benefit from it. Ethnic favoritism in the job market influences a demand-side mechanism of education by increasing the expectation of educational returns among coethnics in coethnic districts.
US inflation and inflation uncertainty over 200 years

This article uses historical US inflation data covering over two centuries to examine the impact of the establishment of the US Federal Reserve on average US inflation and inflation uncertainty. We find that the founding of the Fed is associated with higher average US inflation and lower inflation uncertainty. Critically, these results are not driven by the post-1980 period, where the Fed policy is characterised by the dual mandate. Other important results are that the gold standard period is associated with both lower inflation and inflation uncertainty, and that banking and stock market crises are a positive determinant of inflation uncertainty and perhaps inflation. World Wars I and II and the US Civil War are associated with both higher inflation and higher inflation uncertainty. In addition, we find that the central bank has responded to increasing inflation uncertainty in a stabilising manner in support of the Holland hypothesis.
Allowing for Genotyping Error in Analysis of Unmatched Case‐Control Studies

A commonly‐used method for testing for association between disease and a single‐nucleotide polymorphism (SNP) is to compare the frequencies of the SNP genotypes in a sample of unrelated cases to those in a sample of unrelated controls drawn from the same population (an unmatched case‐control study). A drawback of such a study is that it is impossible to detect genotyping errors, and few methods have been developed to allow for the presence of undetected genotyping errors. In this paper, we obtain analytic formulae for estimates of genotypic relative risks in terms of error probability (e). In general, e will be unknown. We investigate the effect of assuming both correct and incorrect values of e on power and type I error, and also on the genotypic relative risk estimates. The choice of e was found to have no effect on power or Type I error probability (provided a 2df test was used, allowing relative risks of homozygotes and heterozygotes to differ). However, overestimating e in the presence of a true association was found in general to bias relative risk estimates away from the null, with underestimates of e having the opposite effect. Although e is unknown, it may be estimated from an external “validation” study, such as genotyping a sample of unrelated individuals twice and counting the discrepancies. Simulation results suggest that, for such a study, 25 individuals would be sufficient to give approximately unbiased estimates of relative risks.
Graphs, Tables, and Scientific Illustrations: Visualisation as the Science of Seeing Gerontology*

RÉSUMÉ Une caractéristique essentielle de la découverte scientifique est l’utilisation d’inscriptions visuelles (p. ex. graphiques, illustrations) facilitant l’analyse des données, leur interprétation et leur communication (p. ex. Latour, 1990 ; Lynch, 1985). L’objectif de cette recherche était d’examiner les types d’inscriptions visuelles utilisés pour la présentation de données dans les revues scientifiques en gérontologie. Nous avons comparé 357 articles publiés entre 1995 et 2009 qui ont été échantillonnés à partir de 24 revues de gérontologie avec comités de pairs. Approximativement 11 pour cent de l’espace d’impression était consacré à la présentation de données ; les tableaux occupaient comparativement plus d’espace (9,13 %) que les graphiques (2,32 %). L’utilisation des graphiques dans les articles en gérontologie était inférieure à celle observée pour les articles en psychologie (6,6 % de l’espace d’impression), mais supérieure à celle retrouvée en criminologie ou en justice criminelle (1,7 % de l’espace d’impression). À l’instar de Latour (1990), nous soutenons que les figures représentent un résumé accessible de données complexes, permettant ainsi une présentation efficace de résultats multidimensionnels. Lorsque les inscriptions visuelles sont utilisées dans la dissémination des résultats, les chercheurs deviennent moins dépendants du jargon statistique et peuvent communiquer plus aisément avec divers publics (chercheurs, professionnels de la santé, clients). ABSTRACT Visual inscriptions (e.g., graphs, illustrations) are a defining feature of scientific discovery to aid in data analysis, interpretation, and communication (e.g., Latour, 1990; Lynch, 1985). Our purpose was to examine how visual inscriptions are used to present data in gerontology journals. We compared 357 articles sampled from 24 peer-reviewed gerontology journals published between 1995 and 2009. Approximately 11 per cent of page space was dedicated to data presentation with more page space occupied by tables (9.13%) than graphs (2.32%). Graph use in gerontology was lower than in psychology (6.6% of page space) and higher than in criminology and criminal justice (1.7% of page space). Following Latour (1990), we argue that visualisations provide an understandable summary of complex data by effectively presenting multifaceted results. When inscriptions are used in dissemination, researchers become less reliant on complex statistical jargon and can communicate easily with a diverse audience (researchers, health care practitioners, clients).
A new measure of home care patients' dignity at the end of life: The Palliative Patients' Dignity Scale (PPDS)

ABSTRACT Objective: This study aimed to develop a new and brief instrument to be employed in dignity measurement, one based on the perceptions of patients, relatives, and professionals about dignity. Method: Surveys of patients receiving palliative care, family caregivers, and palliative care professionals were first carried out (sample 1). In the second step, palliative care patients were surveyed with a pilot questionnaire (sample 2). Finally, a survey design was used to assess patients admitted into a home care unit (sample 3). Sample 1 included 78 subjects, including patients, family caregivers, and professionals. Some 20 additional palliative patients participated in sample 2. Finally, 70 more patients admitted to a home care unit participated were surveyed (sample 3). Together with the Palliative Patients' Dignity Scale (PPDS), our survey included other measures of dignity, anxiety, depression, resilient coping, quality of life, spirituality, and social support. Results: After analyzing data from steps 1 and 2, an eight-item questionnaire was presented for validation. The new scale showed appropriate factorial validity (χ2(19) = 21.43, p = 0.31, CFI = 0.99, GFI = 0.92, SRMR = 0.07, and RMSEA = 0.04), reliability (internal consistency estimations of 0.75 and higher), criterial validity (significant correlations with the hypothesized related variables), and a cutoff criteria of 50 on the overall scale. Significance of Results: The new PPDS has appropriate psychometric properties that, together with its briefness, encourages its applicability for dignity assessment at the end of life.
Aortic medial changes associated with bicuspid aortic valve: myth or reality?

OBJECTIVE To determine whether aortic medial changes are more severe in patients who require aortic valve replacement of congenitally bicuspid aortic valves (BAV) than in patients who require replacement of tricuspid aortic valves and acquired valvular disease (AVD). DESIGN Aortas from autopsies of 14 patients with BAV and 25 with AVD were histologically assessed by two 'blinded' cardiovascular pathologists and analyzed independently with computer-aided morphometry. The aortic valves were examined for valvular fibrosis and calcification. SETTING The patient population was from a tertiary-care facility. PATIENTS Patients were selected by retrospective review of autopsy records for patient deaths after aortic valve replacement, over the period 1984 to 1995. RESULTS There were no significant differences in age (P=0.89), sex (P=0.94), prevalence of systemic arterial hypertension (P=0.37), valvular degenerative changes (P=0.10 and P=1.0) or heart weights (P=0.60) between the two groups. Histological scores for aortic medial degenerative changes including elastic fragmentation, fibrosis and medionecrosis were not statistically different between the groups. However, morphometry demonstrated less elastic tissue in patients with BAV (P=0.003). CONCLUSION Routine microscopy shows no significant difference in the degree of aortic medial degenerative changes between patients with BAV and AVD. However, morphometry shows less elastic tissue in the aortas of BAV patients. This may explain the anecdotal increase in aortic fragility and propensity for aortic dissection in these patients.
Characteristics and outcome of patients with Philadelphia chromosome negative, bcr/abl negative chronic myelogenous leukemia

Up to 5% of patients with chronic myelogenous leukemia (CML) do not have the Philadelphia (Ph) translocation t(9;22)(q34;q11) or a bcr/abl molecular rearrangement. Although the diagnostic criteria of this entity are still under debate, there is general agreement that patients with Ph negative, bcr/abl negative CML have a severe clinical course that is not affected significantly by current treatment options.
Thyroid transcription factor‐1 expression is an independent predictor of recurrence and correlates with the IASLC/ATS/ERS histologic classification in patients with stage I lung adenocarcinoma

In the current study, the authors investigated whether thyroid transcription factor‐1 (TTF‐1) expression is correlated with the International Association for the Study of Lung Cancer (IASLC)/American Thoracic Society (ATS)/European Respiratory Society (ERS) classification and whether it stratifies patients with stage I lung adenocarcinoma with respect to disease recurrence.
Technology Diffusion and Environmental Regulation: The Adoption of Scrubbers by Coal-Fired Power Plants

Abstract Title IV of the 1990 Clean Air Act Amendments implemented a pollution permit system for sulfur dioxide (SO2) emissions that departs from state command-and-control regulations that were in place prior to and during its implementation. This paper develops a technology diffusion model, relying on rank effects or firm heterogeneity, to explain the adoption of scrubbers, a SO2 abatement technology. Using survival analysis, empirical results show that generating units regulated under Phase I of Title IV, units facing more stringent state regulations, and units with low expected installation costs are much more likely to install a scrubber. In addition, there is evidence of positive scale effects of adoption, meaning larger units are more likely to adopt because expected installation costs are lower. Tradable permit systems should give firms more flexibility in choosing abatement technologies, but results show that when command-and-control regulations overlap with a market-based system, the technology choice is restricted. http://dx.doi. org/10.5547/01956574.34. 1.8
Synergistic activity of clarithromycin and minocycline in an animal model of acute experimental toxoplasmosis

The efficacy of clarithromycin in a murine model of acute toxoplasmosis was studied. Clarithromycin was administered alone and concurrently with minocycline, and efficacy was assessed by survival rates and sequential determination of parasite burden in blood, brains, and lungs. Limited protection resulted from administration of each drug alone, whereas a remarkable synergistic effect followed concurrent administration. Survival of mice treated with 200 mg of clarithromycin plus 20 mg of minocycline per kg of body weight daily was 95%; that of mice treated with 50 mg of clarithromycin plus 50 mg of minocycline per kg daily was 93%. The parasite burden in the blood and organ tissues of these mice was markedly reduced compared with that in mice treated with a single agent. In mice treated with 200 mg of clarithromycin plus 50 mg of minocycline per kg per day, survival was 100% during the 30-day experiment; no parasites were found in blood and tissues.
An independent brain-computer interface based on covert shifts of non-spatial visual attention

Modulation of steady-state visual evoked potential (SSVEP) by directing gaze to targets flickering at different frequencies has been utilized in many brain-computer interface (BCI) studies. However, this paradigm may not work with patients suffering from complete locked-in syndrome or other severe motor disabilities that do not allow conscious control of gaze direction. In this paper, we present a novel, independent BCI paradigm based on covert shift of non-spatial visual selective attention. Subjects viewed a display consisting of two spatially overlapping sets of randomly positioned dots. The two dot sets differed in color, motion and flickering frequency. Two types of motion, rotation and linear motion, were investigated. Both, the SSVEP amplitude and phase response were modulated by selectively attending to one of the two dot sets. Offline analysis revealed a predicted online classification accuracy of 69.3±10.2% for the rotating dots, and 80.7±10.4% for the linearly moving dots.
Endotoxin-Induced Gamma Interferon Production: Contributing Cell Types and Key Regulatory Factors

ABSTRACT Gamma interferon (IFN-γ) is an important mediator of endotoxin (lipopolysaccharide [LPS])-induced immune responses. However, the specific cell types that produce IFN-γ in response to LPS and the cellular factors that regulate LPS-induced IFN-γ production have not been fully determined. The present studies were undertaken to characterize the cell populations that produce IFN-γ after LPS challenge in the spleens of mice and to determine the regulatory factors that modulate LPS-induced production of IFN-γ. Our studies show that the levels of splenic IFN-γ mRNA and protein production peak at 6 and 8 h, respectively, after systemic LPS challenge. Approximately 60% of IFN-γ-producing cells are natural killer (NK) cells (CD3−DX5+) and 25% are NKT cells (CD3+DX5+). Most of the remaining IFN-γ-producing cells are T cells (CD3+DX5−), macrophages, and dendritic cells. Functionally, interleukin-12 (IL-12) is the major IFN-γ-stimulating factor after LPS challenge, with costimulation provided by IL-15, IL-18, and B7 proteins. IL-10 is a major inhibitor of LPS-induced IFN-γ production. Unlike intact heat-killed gram-negative and gram-positive bacteria, the class II major histocompatibility complex did not play a functional role in LPS-induced IFN-γ production. LPS is a potent stimulus for splenic IL-10, IL-12 p40, and IL-15 mRNA expression, whereas IL-12 p35 and IL-18 mRNAs, as well as B7 proteins, are constitutively expressed in the mouse spleen. Of the factors studied, IL-18 serves as the most potent costimulus with IL-12 for IFN-γ production, followed by IL-15 and B7 proteins. These data demonstrate that NK cells and NKT cells are the most abundant IFN-γ-producing cells in the mouse spleen after LPS challenge and that IL-10 and IL-12 are key functional regulators of LPS-induced IFN-γ production.
Knockdown of Fbxo7 reveals its regulatory role in proliferation and differentiation of haematopoietic precursor cells

Fbxo7 is an unusual F-box protein because most of its interacting proteins are not substrates for ubiquitin-mediated degradation. Fbxo7 directly binds p27 and Cdk6, enhances the level of cyclin D–Cdk6 complexes, and its overexpression causes Cdk6-dependent transformation of immortalised fibroblasts. Here, we test the ability of Fbxo7 to transform haematopoietic pro-B (Ba/F3) cells which, unexpectedly, it was unable to do despite high levels of Cdk6. Instead, reduction of Fbxo7 expression increased proliferation, decreased cell size and shortened G1 phase. Analysis of cell cycle regulators showed that cells had decreased levels of p27, and increased levels of S phase cyclins and Cdk2 activity. Also, Fbxo7 protein levels correlated inversely with those of CD43, suggesting direct regulation of its expression and, therefore, of B cell maturation. Alterations to Cdk6 protein levels did not affect the cell cycle, indicating that Cdk6 is neither rate-limiting nor essential in Ba/F3 cells; however, decreased expression of Cdk6 also enhanced levels of CD43, indicating that expression of CD43 is independent of cell cycle regulation. The physiological effect of reduced levels of Fbxo7 was assessed by creating a transgenic mouse with a LacZ insertion into the Fbxo7 locus. Homozygous Fbxo7LacZ mice showed significantly increased pro-B cell and pro-erythroblast populations, consistent with Fbxo7 having an anti-proliferative function and/or a role in promoting maturation of precursor cells.