Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Genomic Studies of Uropathogenic Escherichia coli and Host Urothelial Cells when Intracellular Bacterial Communities Are Assembled*

Uropathogenic Escherichia coli (UPEC), the principal cause of urinary tract infection in women, colonizes the gut as well as the genitourinary tract. Studies of mice inoculated with UTI89, a sequenced isolate, have revealed a complex life cycle that includes formation of intracellular bacterial communities (IBCs) in bladder urothelial cells. To understand how UPEC adapts to life in IBCs, we have used GeneChips and/or quantitative reverse transcriptase PCR to study UTI89 recovered from the distal gut of gnotobiotic mice and from IBCs harvested by laser capture microdissection from the bladder urothelium of infected C3H/HeJ female mice. Host responses were characterized in laser capture microdissected urothelial cells that do or do not contain IBCs. The results reveal components of ferric iron acquisition systems in UTI89 that are expressed at significantly higher levels in IBCs compared with the intestine, including the hemin receptor chuA (1,390 ± 188-fold). Localized urothelial responses to IBCs help oppose bacterial salvage of host cell iron (e.g. up-regulation of Tfrc (transferrin receptor) and Lcn2 (lipocalin 2)), facilitate glucose import (e.g. Hk2 (hexokinase 2)), and maintain epithelial structural integrity (e.g. Ivl (involucrin) and Sbsn (suprabasin)). ΔchuA mutants produce significantly smaller IBCs compared with wild type UTI89. This difference was not observed in strains lacking sitA (ABC-type iron/manganese transporter subunit), iroN (salmochelin receptor), hlyA (α-hemolysin), or entF (enterobactin synthetase subunit). Together, these studies indicate that heme- and siderophore-associated iron play key roles in IBC development and provide a series of microbial and host biomarkers for comparing UPEC strains isolated from humans.
Heat-shock protein induction in adriamycin and picornavirus-infected cardiocytes.

BACKGROUND Both chemicals, such as the chemotherapy agent adriamycin, and viruses, such as the picornaviruses coxsackievirus B3 and encephalomyocarditis virus, cause metabolic injury in myocardial cells. This injury includes depression of cellular RNA and protein synthesis and production of oxygen free radicals which are known to induce increased expression of "heat-shock" or stress proteins (hsp). These hsp can stimulate potent T lymphocyte responses that may then contribute to cardiac damage associated with adriamycin therapy and picornavirus infections. EXPERIMENTAL DESIGN To determine whether adriamycin and the picornaviruses stimulate hsp expression, cultured neonatal myocardial cells from BALB/c Cum mice were treated with heat-shock, adriamycin and either infectious or ultraviolet irradiated (noninfectious) CVB3. The treated myocardial cell homogenates were subjected to polyacrylamide gel electrophoresis and Western blot analysis for 70 kilodalton hsp. To determine whether these treatments stimulated T lymphocyte responses (presumably to hsp), BALB/c Cum mice were injected with 0.1 ml complete Freund's adjuvant containing 0.1 mg of heat-killed mycobacterium tuberculosis, 10 mg/kg adriamycin or 5 x 10(4) plaque-forming units CVB3 intraperitoneally. Splenic lymphocytes obtained 7 days later from these animals were evaluated in a 51Cr release cytotoxicity assay to cultured myocytes treated with heat-shock, adriamycin or virus. Cytolytic T lymphocytes (CTL) were characterized as to T cell subset and T cell receptor (TcR) utilization treating CTL populations with anti-CD4 or anti-CD8 antibodies or with anti-alpha/beta TcR or anti-gamma/delta TcR antibodies. RESULTS Both adriamycin and infectious virus treatment of myocardial cells stimulated increased hsp expression. Ultraviolet irradiation of the virus prevents virus replication and failed to elicit hsp production in heart cells. Two types of CTL were detected. Animals injected with complete Freund's adjuvant virus, and adriamycin produced CD8+, gamma/delta TcR+ CTL that were not major histocompatibility complex antigen restricted since both CBA (H-2k) and BALB/c (H-2d) myocardial cells were lysed. Virus-specific CTL, belonging to the CD4+, alpha/beta TcR+ population, were detected in CVB3-infected mice. CONCLUSIONS Different agents that metabolically injure myocardial cells can induce increased expression of one or more hsp. CTL presumably directed to these hsp can cross-reactively lyse targets treated with any of the hsp inducing agents. This observation raises the question whether multiple exposures of individuals to dramatically different hsp-inducing agents might result in increasingly damaging immune responses.
A Survey of Quantitative Information Flow

Traditional information flow security policies declare that many useful and necessary programs are insecure. This results from the qualitative nature of these policies: either information flows, or it does not. A richer class of security properties that can express the degree of information flow is needed; we call these quantitative information flow policies. Such policies have recently become a research topic of active interest. This paper surveys work in the area.
Use of palivizumab with other infection control measures to control respiratory syncytial virus outbreaks in neonatal care units.

OBJECTIVE No guidelines exist on the use of palivizumab during outbreaks of Respiratory Syncytial Virus (RSV) in Neonatal Intensive Care Units (NICUs). We aimed to describe an outbreak of RSV in NICU settings and the role of palivizumab in controlling the outbreak. METHODS The index case was a 30-day-old premature infant. During the outbreak, 13 cases of RSV were confirmed by RT-PCR. All infants in the NICU received palivizumab after RSV diagnosis. RESULTS Of the 13 cases, seven were male; and the median (interquartile) of birth weight was 1585 (IQR: 1480-1705) g. All cases were premature under 34-weeks-gestation. Age at onset of disease varies between 10 and 160 days. Only four cases occurred after administering palivizumab and applying other infection control measures. CONCLUSION During nosocomial outbreaks of RSV, administration of palivizumab to all infants in NICU appears to be rational and may help contain outbreaks.
Transfer of bromocriptine across the blood‐brain barrier in man

The transfer of 14C‐bromocriptine across the blood‐brain barrier was studied in 10 patients using the double indicator single injection method. The extraction (E) of bromocriptine was 8 % (quartiles: 6 and 14 %). Based on the results the cerebral uptake velocity of bromocriptine was calculated assuming constant arterial drug concentration. Its T1/2 was found to be 12–24 minutes, depending on the tissue‐blood partition coefficient.
Zusammenhang von kognitiver Leistungsfähigkeit (LPS-2) und Arbeitsgedächtnis (Working Memory Span Tasks)

Zur Validierung des revidierten Leistungsprufsystem (LPS-2, Kreuzpointner, Lukesch & Horn, in Vorb.) wurde mit 48 Studierenden der Universitaten Regensburg neben dem LPS-2 die automated working memory span tasks (aWMT, Unsworth et al., 2005) durchgefuhrt. Das LPS-2 misst mit 11 Subtests die vier Intelligenz-Dimensionen Kristalline (Gc) und Fluide (Gf) Intelligenz, visuelle Wahrnehmung (Gv) und kognitive Geschwindigkeit (Gs) (nach Carroll, 2005), die zu einem g-Faktor zusammengefasst werden konnen. Die aWMT sind unterteilt in Rechen-, Lese- und Symmetrieaufgaben, „Buchstaben memorieren“ als Zweitaufgabe. Sorgfaltigkeit (richtiges Losen der aWMT-Aufgaben) und LPS-R stehen quasi in keinem Zusammenhang. Statistisch signifikant korrelieren die LPS-R-Dimensionen mit einigen Erinnerungsmasen (5 von 15) und mehreren Verarbeitungsgeschwindigkeitskomponenten (10 von 15). Werden in einer Regression mit g als abhangiger Variable die Erinnerungsmase und Geschwindigkeitsmase getrennt als unabhangige Variablen eingeschlossen, zeigt sich, dass der LPS-R-Gesamtscore vorwiegend durch die Verarbeitungsgeschwindigkeit (21 % spezifische Varianzklarung bzw. 28 % alleinige) und nur bedingt durch die Erinnerungskomponente (6 % bzw. 13 %) vorhergesagt wird.
An automated information system to ensure quality in higher education institutions

Despite the great efforts to assure quality in higher education institutions, the ambiguity of its related concepts and requirements constitute a big challenge when trying to implement it as an automated information system. The present work introduces a framework for an automated information system that manages the quality assurance in higher educations institutions. The aim of designing such a system is to provide an automation tool that avoids unnecessary and redundant tasks associated to quality in higher education institutions. In addition, the proposed system helps all higher education stockholders to handle and monitor their tasks. Moreover, it aims to help the quality assurance center in a higher education institution to apply its qualitys standards, and to make sure that they are being maintained and enhanced. This information system contains a core module and 17 sub-modules, which are described in this paper.
Informed Browsing: Scaling Up Co-Experienced Access to Digital Media

Recent progress in the ﬁeld of multi-touch interactive surfaces makes it imaginable that our daily environments will become interactive and acquire new functionalities provided by computing capabilities. For example, walls, doors and tables could double as displays and accept input. The spatial and social affordances of tables predestine them for sharing media artifacts with friends and family. Interactive tables are subject to different design constraints than conventional interfaces. In this paper I present individual interfaces as primary interaction style for tabletop multimedia applications. Furthermore, I present the concept of informed browsing as a mean to deal with large amounts of data in this context.
Pharmacological management of alcohol withdrawal. A meta-analysis and evidence-based practice guideline. American Society of Addiction Medicine Working Group on Pharmacological Management of Alcohol Withdrawal.

OBJECTIVE To provide an evidence-based practice guideline on the pharmacological management of alcohol withdrawal. DATA SOURCES English-language articles published before July 1, 1995, identified through MEDLINE search on "substance withdrawal--ethyl alcohol" and review of references from identified articles. STUDY SELECTION Articles with original data on human subjects. DATA ABSTRACTION Structured review to determine study design, sample size, interventions used, and outcomes of withdrawal severity, delirium, seizures, completion of withdrawal, entry into rehabilitation, adverse effects, and costs. Data from prospective controlled trials with methodologically sound end points corresponding to the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, were abstracted by 2 independent reviewers and underwent meta-analysis. DATA SYNTHESIS Benzodiazepines reduce withdrawal severity, reduce incidence of delirium (-4.9 cases per 100 patients; 95% confidence interval, -9.0 to -0.7; P=.04), and reduce seizures (-7.7 seizures per 100 patients; 95% confidence interval, -12.0 to -3.5; P=.003). Individualizing therapy with withdrawal scales results in administration of significantly less medication and shorter treatment (P<.001). beta-Blockers, clonidine, and carbamazepine ameliorate withdrawal severity, but evidence is inadequate to determine their effect on delirium and seizures. Phenothiazines ameliorate withdrawal but are less effective than benzodiazepines in reducing delirium (P=.002) or seizures (P<.001). CONCLUSIONS Benzodiazepines are suitable agents for alcohol withdrawal, with choice among different agents guided by duration of action, rapidity of onset, and cost. Dosage should be individualized, based on withdrawal severity measured by withdrawal scales, comorbid illness, and history of withdrawal seizures. beta-Blockers, clonidine, carbamazepine, and neuroleptics may be used as adjunctive therapy but are not recommended as monotherapy.
Arsenic Exposure and Type 2 Diabetes: A Systematic Review of the Experimental and Epidemiologic Evidence

Chronic arsenic exposure has been suggested to contribute to diabetes development. We performed a systematic review of the experimental and epidemiologic evidence on the association of arsenic and type 2 diabetes. We identified 19 in vitro studies of arsenic and glucose metabolism. Five studies reported that arsenic interfered with transcription factors involved in insulin-related gene expression: upstream factor 1 in pancreatic β-cells and peroxisome proliferative-activated receptor γ in preadipocytes. Other in vitro studies assessed the effect of arsenic on glucose uptake, typically using very high concentrations of arsenite or arsenate. These studies provide limited insight on potential mechanisms. We identified 10 in vivo studies in animals. These studies showed inconsistent effects of arsenic on glucose metabolism. Finally, we identified 19 epidemiologic studies (6 in high-arsenic areas in Taiwan and Bangladesh, 9 in occupational populations, and 4 in other populations). In studies from Taiwan and Bangladesh, the pooled relative risk estimate for diabetes comparing extreme arsenic exposure categories was 2.52 (95% confidence interval, 1.69–3.75), although methodologic problems limit the interpretation of the association. The evidence from occupational studies and from general populations other than Taiwan or Bangladesh was inconsistent. In summary, the current available evidence is inadequate to establish a causal role of arsenic in diabetes. Because arsenic exposure is widespread and diabetes prevalence is reaching epidemic proportions, experimental studies using arsenic concentrations relevant to human exposure and prospective epidemiologic studies measuring arsenic biomarkers and appropriately assessing diabetes should be a research priority.
Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen

Characterizing the activating and inhibiting effect of protein-protein interactions (PPI) is fundamental to gain insight into the complex signaling system of a human cell. A plethora of methods has been suggested to infer PPI from data on a large scale, but none of them is able to characterize the effect of this interaction. Here, we present a novel computational development that employs mitotic phenotypes of a genome-wide RNAi knockdown screen and enables identifying the activating and inhibiting effects of PPIs. Exemplarily, we applied our technique to a knockdown screen of HeLa cells cultivated at standard conditions. Using a machine learning approach, we obtained high accuracy (82% AUC of the receiver operating characteristics) by cross-validation using 6,870 known activating and inhibiting PPIs as gold standard. We predicted de novo unknown activating and inhibiting effects for 1,954 PPIs in HeLa cells covering the ten major signaling pathways of the Kyoto Encyclopedia of Genes and Genomes, and made these predictions publicly available in a database. We finally demonstrate that the predicted effects can be used to cluster knockdown genes of similar biological processes in coherent subgroups. The characterization of the activating or inhibiting effect of individual PPIs opens up new perspectives for the interpretation of large datasets of PPIs and thus considerably increases the value of PPIs as an integrated resource for studying the detailed function of signaling pathways of the cellular system of interest.
All liaisons are dangerous when all your friends are known to us

Abstract Online Social Networks (OSNs) are used by millions of users worldwide. Academically speaking, there is little doubt about the usefulness of demographic studies conducted on OSNs and, hence, methods to label unknown users from small labeled samples are very useful. However, from the general public point of view, this can be a serious privacy concern. Thus, both topics are tackled in this paper: First, a new algorithm to perform user profiling in social networks is described, and its performance is reported and discussed. Secondly, the experiments --conducted on information usually considered sensitive-- reveal that by just publicizing one's contacts privacy is at risk and, thus, measures to minimize privacy leaks due to social graph data mining are outlined.
Morphology of individual axons projecting from area V2 to MT in the macaque

Efferent axons from area V2 to the middle temporal area (MT) were anterogradely labeled by Phaseolus vulgaris ‐leucoagglutinin (PHA‐L) or biocytin and analyzed in serial reconstructions. Five of seven reconstructed axons had three arbors (each < 200 μm in diameter) in layers 3–4, separated by 200–600 jLm. Two axons terminated in what was apparently a single focus in layers 3–4. Of 15 additional single arbors analyzed, 12 were concentrated in layers 3–4, and measured 200–250 μm across at their widest point. Three of these arbors were more columnar in shape (about 400 μm in diameter), and extended from layer 4 toward layer 1. This system differs in several features from MT‐projecting axons originating from V1. Namely, V2 axons terminating in MT are thinner (∼ 1. 0 μm vs. 3. 0 gm), their terminal specializations are more delicate, and their arbors are concentrated in layer 4 and overlying layer 3, with no collaterals to layer 6. These differences may reflect the distinctive neuronal populations giving rise to these two connectional systems (different sizes of pyramidal neurons in layer 3 of V2, and a mix of pyramidal and spiny stellate cells in area V). Differences may have implications for timing factors; that is, impulses from V1, subserved by large‐caliber axons, may arrive in MT coincidentally with indirect connections via V2 to MT. Another consideration may be the functional architecture of MT. Regularly spaced clusters of neurons have been described in MT which have similar directionality preferences. The interarbor spacing of cortical efferents is consistent with a columnar organization, but the laminar specificity may indicate recruitment of different combinations of postsynaptic populations by V1 or V2 terminations.
Consensus Investor and Intertemporal Asset Pricing with Heterogeneous Beliefs ∗

This paper considers an intertemporal capital market with an arbitrary number of heterogeneous belief investors who maximise the expected utilities of their terminal wealths under their subject beliefs. By aggregating the heterogeneous beliefs of the investors, a consensus investor is constructed to characterise the market equilibrium under the heterogeneous beliefs. Applying this idea to logarithmic utility function case, the impact of the belief heterogeneity on the market equilibrium is examined explicitly and survival conditions of the heterogeneous agents are given.
An association and meta-analysis study of 4 SNPs from beta-2 adrenergic receptor (ADRB2) gene with risk of asthma in children.

BACKGROUND Although various case-control studies have been conducted to investigate the relationship between ADRB2 gene polymorphisms and asthma risk in different population groups, the results have been conflicting and inconclusive. OBJECTIVE We performed a case-control study to investigate the association of 4 SNPs in the ADRB2 gene with risk of asthma in children, and then conducted a meta-analysis by combining the previous studies. METHODS A total of 340 patients and 340 age-matched healthy controls were recruited. All of the subjects were genotyped using the PCR-based invader assay. The case-control study was performed to define the contribution of rs1042713, rs1042714, rs1800888, and rs1042711 to the predisposition of asthma. Additionally, we further conducted a meta-analysis of the study findings together with those of previously reported studies. RESULTS No significant association was found between the polymorphisms rs1042713, rs1042714, rs1800888, and rs1042711 and asthma in the current case-control study. The meta-analysis confirmed that there was no positive association of these SNPs with asthma in children in Asia, South America, Europe and the overall population. CONCLUSIONS None of the four polymorphisms in ADRB2 gene were associated with a risk of asthma in a current children population.
Influence of Rain Tree Pod Meal Supplementation on Rice Straw Based Diets Using In vitro Gas Fermentation Technique

The objective of this study was to determine the roughage to concentrate (R:C) ratio with rain tree pod meal (RPM) supplementation on in vitro fermentation using gas production technique. The experiment design was a 6×4 factorial arrangement in a CRD. Factor A was 6 levels of R:C ratio (100:0, 80:20, 60:40, 40:60, 20:80 and 0:100) and factor B was 4 levels of RPM (0, 4, 8 and 12 mg). It was found that gas kinetic, extent rate (c) was linearly increased (p<0.01) with an increasing level of concentrate while cumulative gas production (96 h) was higher in R:C of 40:60. In addition, interaction of R:C ratio and RPM level affected NH3-N and IVDMD and were highest in R:C of 0:100 with 0, 4 mg of RPM and 40:60 with 8 mg of RPM, respectively. Moreover, interaction of R:C ratio and RPM level significantly increased total volatile fatty acids and propionate concentration whereas lower acetate, acetate to propionate ratios and CH4 production in R:C of 20:80 with 8 mg of RPM. Moreover, the two factors, R:C ratio and RPM level influenced the protozoal population and the percentage of methanogens in the total bacteria population. In addition, the use of real-time PCR found that a high level of concentrate in the diet remarkably decreased three cellulolytic bacteria numbers (F. succinogenes, R. flavefaciens and R. albus). Based on this study, it is suggested that the ratio of R:C at 40:60 and RPM level at 12 mg could improve ruminal fluid fermentation in terms of reducing fermentation losses, thus improving VFA profiles and ruminal ecology.
Ground Steel Target Plates in Combination with Direct Transfer of Clinical Candida Isolates Improves Frequencies of Species-Level Identification by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry in Comparison with Polished Steel Target Plates

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identification (ID) of Candida yeast isolates is fast and reliable, but the optimal workflow is debated ([1][1], [2][2]). Two different steel target plates are available for the Microflex system (Bruker
Organ mapping using parelectric spectroscopy

Whenever physical methods are used in the field of diagnostics, it is necessary to find an unambiguous mapping of the properties of the tested tissues (e.g. normal or pathologic) to their answer to the respective analysis tool such as nuclear magnetic resonance (NMR), ultrasound, x-rays or the relatively new method of parelectric spectroscopy (PS). The well-established non-invasive NMR method has, by now, a sufficiently wide-spread atlas of such mappings. This has to be contrasted to the situation of the PS method where first experiments showed the fulfilment of conditions necessary for any reliable diagnosis, namely the uncertainties of the results being small compared to the differences between the normal and pathologic state of the tissues under test. To help close this gap, we present here results of the behaviour of 12 different organs of mice, taken 20 min after excision and give the dependence of the two most essential PS parameters, the dipole density Δϵ and the mobility f0, on the type of healthy organs. To be able to use tumorous tissues preserved in formaldehyde after excision for comparison purposes, we have been measuring the changes of some organs between the fresh state and the preserved state under formaldehyde for over 180 min each.