Miracle-dz/UniFAR-FTUs huggingface dataset:
Description of Mycobacterium conceptionense sp. nov., a Mycobacterium fortuitum Group Organism Isolated from a Posttraumatic Osteitis Inflammation

ABSTRACT A nonpigmented rapidly growing mycobacterium was isolated from wound liquid outflow, bone tissue biopsy, and excised skin tissue from a 31-year-old woman who suffered an accidental open right tibia fracture and prolonged stay in a river. The three isolates grew in 3 days at 24 to 37°C. 16S rRNA sequence analyses over 1,483 bp showed that they were identical and shared 99.7% (4-bp difference) sequence similarity with that of Mycobacterium porcinum, the most closely related species. Partial rpoB (723 bp) sequence analyses showed that the isolates shared 97.0% sequence similarity with that of M. porcinum. Further polyphasic approaches, including biochemical tests, antimicrobial susceptibility analyses, and hsp65, sodA, and recA gene sequence analysis, as well as % G+C determination and cell wall fatty acid composition analysis supported the evidence that these isolates were representative of a new species. Phylogenetic analyses showed the close relationship with M. porcinum in the Mycobacterium fortuitum group. The isolates were susceptible to most antibiotics and exhibited evidence for penicillinase activity, in contrast to M. porcinum. We propose the name Mycobacterium conceptionense sp. nov. for this new species associated with posttraumatic osteitis. The type strain is D16T (equivalent to CIP 108544T and CCUG 50187T).
Strategies to Decrease Taxanes Toxicities in the Adjuvant Treatment of Early Breast Cancer

Taxanes are tubulin-targeting agents that are highly active in the treatment of breast cancer. The lack of cross-resistance and limited overlapping toxicities of taxanes with other agents, such as anthracycline, made it possible to incorporate them in the adjuvant treatment of early breast cancer. When used alone or in combination with other cytotoxic agents, taxanes significantly improved response rate, time to progression, disease-free and in some trials over-all survival in patients with advanced or metastatic breast cancer. Mature data are now emerging from the early randomized clinical trials that consistently demonstrate a clear survival benefit of taxanes when combined with anthracycline. However, increased toxicities, especially hematological toxicities, were also observed. Various strategies to decrease the taxanes toxicities have been explored, including appropriate dosing and scheduling to optimize the therapeutic index, sequential rather than concurrent use of anthracycline and taxanes, the use of growth factor support and the removal of anthracycline, with encouraging results. The development of novel taxanes with less toxicities and use of molecular markers to target patients with taxane-responsive tumors are in early clinical trials. This review focuses on safety issues of taxanes in the adjuvant treatment of early breast cancer. Strategies to reduce the taxane toxicity and future direction of taxane research in early breast cancer will be discussed.
GaInN Quantum Wells as Optochemical Transducers for Chemical Sensors and Biosensors

In this paper, investigations on gallium indium nitride (GaInN) quantum well structures as optochemical transducers in (bio)chemical sensing are presented. In contrast to the conventional electrical read-out of III-nitride-based sensors, a purely optical photoluminescence read-out is performed. A significant spectral shift of the quantum well photoluminescence is observed with varying surface modification. The spectral photoluminescence shift can be attributed to an externally induced quantum confined Stark effect caused by the adsorbed species deposited on the quantum well surface. In order to improve the sensitivity of the transducer elements, different chemical surface treatments are studied. In particular, optical sensing experiments with reducing and oxidizing gases are performed in order to investigate the quantum well photoluminescence response. Additionally, optical investigations of the iron-storage molecule ferritin with varying iron load are presented. The iron load of this molecule is generally considered as a superior biomarker for severe illnesses, such as Alzheimer's disease. In contrast to conventional fluorescent labels, GaInN quantum wells provide a much more stable luminescence signal, and hence, are promising candidates for next generation bioanalytical sensor structures.
Health performance of feeder calves sold at conventional auctions versus special auctions of vaccinated or conditioned calves in Ontario.

OBJECTIVE To compare health performance during the first 28 days in the feedlot for vaccinated or conditioned feeder calves sold through special auctions in Ontario with health performance for calves sold through conventional auctions in the province. DESIGN Cohort study. ANIMALS 12,313 calves sold through conventional and special auctions at the Keady Livestock Market during the fall of 1999 and 2000. PROCEDURE Buyers of calf groups were approached at the auction market or contacted by telephone and asked to record the number of calves requiring treatment for bovine respiratory tract disease (BRD) during the first 28 days after purchase. RESULTS 211 calf groups (> or = 20 calves/group) were followed up for 28 days after purchase. Multivariate logistic analysis indicated that vaccinated calves purchased through special auctions were 0.68 (95% confidence interval, 0.50 to 0.93) times as likely to receive treatment for BRD as were calves purchased at conventional auctions and that conditioned calves were 0.22 (95% confidence interval, 0.12 to 0.38) times as likely to receive treatment. Groups that received antimicrobials by injection on arrival at the feedlot were 0.64 (95% confidence interval, 0.43 to 0.96) times as likely to be treated as were groups that did not. CONCLUSIONS AND CLINICAL RELEVANCE Results suggest that vaccinated and conditioned calves were less likely to receive treatment for BRD during the first 28 days in the feedlot; however, there was no difference in mortality rate.
Expressomal approach for comprehensive analysis and visualization of ligand sensitivities of xenoestrogen responsive genes

Significance Cells change their mRNA expression in response to biologically active substances in a dose-dependent manner. Because different genes in a cell show distinct sensitivities to the same substance, changes in the genome-wide mRNA expression profile induced by low and high doses of a substance are essentially different, but this notion has been commonly overlooked in previously published studies. Using a human cell culture model and microarray, we performed genome-wide determinations of gene sensitivities to hormonally active substances with statistically rigorous approaches. Our study provides a conceptual and methodological framework for the systematic examination of gene sensitivities and demonstrates effective detection of nonmonotonic dose-dependent responses, introducing the importance of gene sensitivity analysis to pharmacogenomic and toxicogenomic research. Although biological effects of endocrine disrupting chemicals (EDCs) are often observed at unexpectedly low doses with occasional nonmonotonic dose–response characteristics, transcriptome-wide profiles of sensitivities or dose-dependent behaviors of the EDC responsive genes have remained unexplored. Here, we describe expressome analysis for the comprehensive examination of dose-dependent gene responses and its applications to characterize estrogen responsive genes in MCF-7 cells. Transcriptomes of MCF-7 cells exposed to varying concentrations of representative natural and xenobiotic estrogens for 48 h were determined by microarray and used for computational calculation of interpolated approximations of estimated transcriptomes for 300 doses uniformly distributed in log space for each chemical. The entire collection of these estimated transcriptomes, designated as the expressome, has provided unique opportunities to profile chemical-specific distributions of ligand sensitivities for large numbers of estrogen responsive genes, revealing that at low concentrations estrogens generally tended to suppress rather than to activate transcription. Gene ontology analysis demonstrated distinct functional enrichment between high- and low-sensitivity estrogen responsive genes, supporting the notion that a single EDC chemical can cause qualitatively distinct biological responses at different doses. Expressomal heatmap visualization of dose-dependent induction of Bisphenol A inducible genes showed a weak gene activation peak at a very low concentration range (ca. 0.1 nM) in addition to the main, strong gene activation peak at and above 100 nM. Thus, expressome analysis is a powerful approach to understanding the EDC dose-dependent dynamic changes in gene expression at the transcriptomal level, providing important information on the overall profiles of ligand sensitivities and nonmonotonic responses.
Hereditary influences on cognitive functioning in older men. A study of 4000 twin pairs.

OBJECTIVE To determine the contribution of genetic factors to cognitive functioning in older men. DESIGN Cognitive testing by telephone interview in an epidemiologically defined population. PARTICIPANTS 2077 monozygotic and 2225 dizygotic male twin pairs, all between the ages of 62 and 73 years, recruited from the National Academy of Sciences twin registry. MAIN OUTCOME MEASURES The Telephone Interview for Cognitive Status--Modified total score and factor scores were analyzed. The Falconer heritability statistic and maximum likelihood estimates of genetic and environmental components were computed. RESULTS Heritability of the total Telephone Interview for Cognitive Status--Modified score was estimated to be 30%. Shared environmental effects accounted for an additional 18% of the variance; most of this was related to years of education. Of the four cognitive factors derived, the language/attention factor had the highest heritability estimate. CONCLUSIONS Genetic factors and educational achievement together account for almost half of the variance in the cognitive functioning of older men. Studies of the genetics of dementing illnesses need to consider the degree to which cognitive capacities are themselves under genetic control.
Inhibition of acyl‐coenzyme A: cholesterol acyl transferase modulates amyloid precursor protein trafficking in the early secretory pathway

Amyloid β‐peptide (Aβ) has a central role in the pathogenesis of Alzheimer's disease (AD). Cellular cholesterol homeostasis regulates endoproteo‐ lytic generation of Aβ from the amyloid precursor protein (APP). Previous studies have identified acyl‐ coenzyme A: cholesterol acyltransferase (ACAT)’ an enzyme that regulates subcellular cholesterol distribu‐tion, as a potential therapeutic target for AD. Inhibition of ACAT activity decreases Aβ generation in cell‐ and animal‐based models of AD through an unknown mechanism. Here we show that ACAT inhibition retains a fraction of APP molecules in the early secretory pathway, limiting the availability of APP for secretase‐ mediated proteolytic processing. ACAT inhibitors delayed the trafficking of immature APP molecules from the endoplasmic reticulum (ER) as shown by metabolic labeling and live‐cell imaging. This resulted in partial ER retention of APP and enhanced ER‐associated deg‐radation of APP by the proteasome, without activation of the unfolded protein response pathway. The ratio of mature APP to immature APP was reduced in brains of mice treated with ACAT inhibitors’ and strongly correlated with reduced brain APP‐C99 and cerebrospinal fluid Aβ levels in individual animals. Our results identify a novel ACAT‐dependent mechanism that regulates secretory trafficking of APP, likely contributing to decreased Aβ generation in vivo. —Huttunen, H. J., Peach, C. , Bhattacharyya, R. , Barren, C. , Pettingell, W. , Hutter‐Paier, B. , Windisch, M. , Berezovska, O. , Kovacs, D. M. Inhibition of acyl‐coenzyme A: cholesterol acyl transferase modulates amyloid precursor protein trafficking in the early secretory pathway. FASEB J. 23, 3819‐3828 (2009). www.fasebj. org
Intrauterine xenotransplantation of human Wharton jelly-derived mesenchymal stem cells into the liver of rabbit fetuses: A preliminary study for in vivo expression of the human liver genes

Objective(s): End-stage hepatic failure is a potentially life-threatening condition for which orthotopic liver transplantation is the only effective treatment. However, a shortage of available donor organs for transplantation each year results in the death of many patients waiting for liver transplantation. Xenotransplantation, or the transplantation of cells, tissues, or organs between different species, was proposed as a possible solution to the worldwide shortage of human organs and tissues for transplantation. The purpose of this preliminary study was to reconstruct human liver tissue by xenotransplantation of human Wharton jelly mesenchymal stem cells (hWJ-MSCs) into fetal rabbit. Materials and Methods: Isolation and confirmation of hWJ-MSCs from human umbilical cord was performed. Eight rabbits at gestational day 14 were anesthetized. All rabbits carried pregnancies to term yielding 40 rabbit fetuses. Intrauterine injection of hWJ-MSCs was performed in 24 fetuses. Twenty-seven fetuses were born alive. Ten liver samples from injected fetuses were sampled, eight rabbits 3 days after birth and two rabbits 21 days after birth. The non-injected fetuses served as positive control. Fetuses of non-injected rabbits were negative controls. Using real-time polymerase chain reaction (RT-PCR), mRNA expression of albumin (ALB), α-fetoprotein (AFP), hepatic nuclear factor 4 (HNF4), and CYP2B6 (CYP) were detected in liver samples. Results: The human ALB, AFP, HNF4, and CYP mRNAs were expressed in the injected sampled fetuses by hWJ-MSCs into fetuses of rabbits in utero. Conclusion: Developing xenotransplantation of hWJ-MSCs into rabbit uterus can introduce an applied approach for producing human liver tissue in rabbits.
Evidence for the presence of endothelin ETA receptors in endothelial cells in situ on the aortic side of porcine aortic valve

1 In the present study, we determined whether ETA receptors are present on endothelial cells in situ, by use of front‐surface fluorometry of fura‐2‐loaded porcine aortic valvular strips and reverse transcription polymerase chain reaction (RT‐PCR). 2 Although endothelin‐1 (ET‐1) and endothelin‐3 (ET‐3) induced maximum elevations of cytosolic Ca2+ concentrations ([Ca2+]i) at 10−7 m, the peak elevations of [Ca2+]i induced by ET‐1 were much greater than those induced by ET‐3. 3 The application of ET‐1 after ET‐3 induced an additional increase in [Ca2+]i, while the application of ET‐3 after ET‐1 had no effect. A selective ETA receptor antagonist, BQ‐123, partially inhibited the ET‐1‐induced Ca2+ transient but had no effect on ET‐3‐induced Ca2+ transients. These experiments indicated the presence of functioning ETA receptors in addition to ETB receptors in endothelial cells in situ. 4 The sequence of pig lung ETA receptor complimentary DNA (cDNA) was determined by PCR. RT‐PCR, using specific primers for pig ETA receptor sequence and total RNA from endothelial cells on the aortic side of the aortic valve, gave the expected size of band. This PCR product was sequenced and was found to be identical to the sequence of the pig lung ETA receptor. 5 The partial sequence of the pig lung ETB receptor was also determined. RT‐PCR for the pig ETBreceptor revealed that endothelial cells of the aortic valve express ETB receptor messenger RNA (mRNA). 6 We confirmed that functioning ETA receptors and expression of ETA receptor mRNA exist in the endothelial cells on the aortic side of porcine aortic valves.
The human dendritic cell marker CD83 maps to chromosome 6p23

The chromosomal localization of the human CD83 gene was determined using somatic cell hybrids, a radiation hybrid mapping panel and FISH analysis on human metaphase chromosomes. PCR‐based analysis of a single chromosome hybrid panel identified the presence of the CD83 gene on human chromosome 6 and subsequent analysis of the Genebridge4 radiation panel located the gene between AFMa192wg9 and AFMb322wd1 with a lod score of 9.2. Finally, using FISH analysis the CD83 gene was localized to chromosome 6 band p23.
Genetic parameters of ascites-related traits in broilers: effect of cold and normal temperature conditions

1. Ascites syndrome is a growth-related disorder of broilers that occurs more often in fast-growing birds and at low temperatures. The objective of this study was to estimate genetic and phenotypic correlations among ascites-related traits measured either under cold or under normal temperature conditions, and to estimate genetic correlations between ascites-related traits measured under cold and normal conditions. 2. Several traits related to ascites were measured on more than 4000 chickens under cold conditions and on more than 700 chickens under normal conditions. 3. The heritability estimates for body weight (BW) measured under cold and normal conditions were 0·42 and 0·50, respectively, for haematocrit value 0·46 and 0·17, respectively, and for ratio of right to total ventricular weight 0·45 and 0·12, respectively. 4. The genetic correlation between BW and haematocrit value under cold conditions was −0·23 and between BW and ratio of right to total ventricular weight −0·27. Under normal conditions, however, these genetic correlations were 0·55 and 0·50, respectively. 5. These results demonstrate that the heritability estimates of ascites-related traits as well as genetic correlations between ascites-related traits and BW depend on the temperature conditions under which animals are kept. 6. Strong positive genetic correlations (around 0·8) were observed between total mortality, fluid in the abdomen and ratio of right to total ventricular weight under cold conditions. The genetic correlation between ratio of right to total ventricular weight under cold and normal conditions was 0·91. 7. These results suggest that the ratio of right to total ventricular weight measured under normal temperature conditions might serve as a good indicator trait for ascites.
Architectonics of the parietal and temporal association cortex in the strepsirhine primate Galago compared to the anthropoid primate Macaca

A number of higher order association areas have been described in the parietal and temporal cortex of large‐brained anthropoid primates such as Macaca. However, little is known about the evolution of these areas, and the existence of homologous areas has not yet been clearly demonstrated in other mammalian groups. We addressed this issue by comparing the myelo‐ and cytoarchitecture of posterior association cortex in the anthropoid Macaca to that of the small‐brained, strepsirhine (“prosimian”) primate Galag.
A diverse path set planning algorithm with a path set fitness function

A diverse path set generation method to solve the two-point boundary value problem is first proposed here. The diverse path set planning algorithm (DPSP) generates the probabilistic roadmap and extracts paths that connect a fixed start and a goal point from the roadmap. The roadmap is revised as the path is extracted. The path set is evaluated by the proposed path set fitness function with respect to the diversity and the lengths of the paths using the opposite Hausdorff distance metric. By replacing the least important path in the path set, the diversity of the path set is iteratively improved. Better performance enhancements are shown by simulations in the empty map and static obstacles map.
Bile Acids Modulate Signaling by Functional Perturbation of Plasma Membrane Domains*

Background: Bile acids (BAs) affect cellular membranes. Results: BAs stabilize domains in plasma membranes, leading to reorganization of membrane proteins and signaling perturbations. Conclusion: BAs affect cell function by modulating the stability of plasma membrane nanodomains. Significance: These results suggest mechanisms for regulation of functional membrane domains and nonreceptor-mediated BA signaling. Eukaryotic cell membranes are organized into functional lipid and protein domains, the most widely studied being membrane rafts. Although rafts have been associated with numerous plasma membrane functions, the mechanisms by which these domains themselves are regulated remain undefined. Bile acids (BAs), whose primary function is the solubilization of dietary lipids for digestion and absorption, can affect cells by interacting directly with membranes. To investigate whether these interactions affected domain organization in biological membranes, we assayed the effects of BAs on biomimetic synthetic liposomes, isolated plasma membranes, and live cells. At cytotoxic concentrations, BAs dissolved synthetic and cell-derived membranes and disrupted live cell plasma membranes, implicating plasma membrane damage as the mechanism for BA cellular toxicity. At subtoxic concentrations, BAs dramatically stabilized domain separation in Giant Plasma Membrane Vesicles without affecting protein partitioning between coexisting domains. Domain stabilization was the result of BA binding to and disordering the nonraft domain, thus promoting separation by enhancing domain immiscibility. Consistent with the physical changes observed in synthetic and isolated biological membranes, BAs reorganized intact cell membranes, as evaluated by the spatial distribution of membrane-anchored Ras isoforms. Nanoclustering of K-Ras, related to nonraft membrane domains, was enhanced in intact plasma membranes, whereas the organization of H-Ras was unaffected. BA-induced changes in Ras lateral segregation potentiated EGF-induced signaling through MAPK, confirming the ability of BAs to influence cell signal transduction by altering the physical properties of the plasma membrane. These observations suggest general, membrane-mediated mechanisms by which biological amphiphiles can produce their cellular effects.
High resolution imaging of the unsaturated and saturated zones of a gravel aquifer using full-waveform inversion

Full-waveform inversion can significantly improve imaging results of cross-hole GPR data compared to conventional ray-based inversion schemes. Recently, a 2D full-waveform finite difference time domain (FDTD) approach was used to invert cross-hole GPR data measured in the saturated zone of a gravel aquifer. Due to water table refractions and reflections, the upper part of the aquifer was not reliably imaged. Here, we reconstruct the upper part of the aquifer by imaging both the saturated and unsaturated zones. Estimating one effective wavelet, as was done for the saturated zone inversion alone, is insufficient because the effective wavelet strongly depends on the location of both the transmitter and receiver antennas. Therefore, four different source wavelets were estimated for the different combinations of antennas placement in the two zones, and the full-waveform inversion algorithm adapted accordingly. This resulted in improved images of the aquifer. In general, the observed and the synthetic traces show a good correspondence in both shape and amplitude. For the transmitters in the unsaturated domain, the amplitude fit was not optimum and can probably be improved by adjusting the conductivity starting model.