bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli
Strain Nissle 1917 Ameliorates Experimental Colitis via Toll-Like Receptor 2- and Toll-Like Receptor 4-Dependent Pathways
Authors: Grabig A. , Paclik D. , Guzy C. , Dankof A. , Baumgart D. C. , Erckenbrecht J. , Raupach B. , Sonnenborn U. , Eckert J. , Schumann R. R. , Wiedenmann B. , Dignass A. U. , Sturm A. 
Published: June 2006

ABSTRACT

Toll-like receptors (TLRs) are key components of the innate immune system that trigger antimicrobial host defense responses. The aim of the present study was to analyze the effects of probiotic
Escherichia coli
Nissle strain 1917 in experimental colitis induced in TLR-2 and TLR-4 knockout mice. Colitis was induced in wild-type (wt), TLR-2 knockout, and TLR-4 knockout mice via administration of 5% dextran sodium sulfate (DSS). Mice were treated with either 0.9% NaCl or 10
7
E. coli
Nissle 1917 twice daily, followed by the determination of disease activity, mucosal damage, and cytokine secretion. wt and TLR-2 knockout mice exposed to DSS developed acute colitis, whereas TLR-4 knockout mice developed significantly less inflammation. In wt mice, but not TLR-2 or TLR-4 knockout mice,
E. coli
Nissle 1917 ameliorated colitis and decreased proinflammatory cytokine secretion. In TLR-2 knockout mice a selective reduction of gamma interferon secretion was observed after
E. coli
Nissle 1917 treatment. In TLR-4 knockout mice, cytokine secretion was almost undetectable and not modulated by
E. coli
Nissle 1917, indicating that TLR-4 knockout mice do not develop colitis similar to the wt mice. Coculture of
E. coli
Nissle 1917 and human T cells increased TLR-2 and TLR-4 protein expression in T cells and increased NF-κB activity via TLR-2 and TLR-4. In conclusion, our data provide evidence that
E. coli
Nissle 1917 ameliorates experimental induced colitis in mice via TLR-2- and TLR-4-dependent pathways.
EshA Accentuates ppGpp Accumulation and Is Conditionally Required for Antibiotic Production in
Streptomyces coelicolor
A3(2)
Authors: Saito Natsumi , Xu Jun , Hosaka Takeshi , Okamoto Susumu , Aoki Hiroyuki , Bibb Mervyn J. , Ochi Kozo 
Published: June 2006

ABSTRACT

Disruption of
eshA
, which encodes a 52-kDa protein that is produced late during the growth of
Streptomyces coelicolor
A3(2), resulted in elimination of actinorhodin production. In contrast, disruption of
eshB
, a close homologue of
eshA
, had no effect on antibiotic production. The
eshA
disruptant accumulated lower levels of ppGpp than the wild-type strain accumulated. The loss of actinorhodin production in the
eshA
disruptant was restored by expression of a truncated
relA
gene, which increased the ppGpp level to the level in the wild-type strain, indicating that the reduced ppGpp accumulation in the
eshA
mutant was solely responsible for the loss of antibiotic production. Antibiotic production was also restored in the
eshA
mutant by introducing mutations into
rpoB
(encoding the RNA polymerase β subunit) that bypassed the requirement for ppGpp, which is consistent with a role for EshA in modulating ppGpp levels. EshA contains a cyclic nucleotide-binding domain that is essential for its role in triggering actinorhodin production. EshA may provide new insights and opportunities to unravel the molecular signaling events that occur during physiological differentiation in streptomycetes.
FppA, a Novel
Pseudomonas aeruginosa
Prepilin Peptidase Involved in Assembly of Type IVb Pili
Authors: de Bentzmann Sophie , Aurouze Marianne , Ball Geneviève , Filloux Alain 
Published: June 2006

ABSTRACT

Several subclasses of type IV pili have been described according to the characteristics of the structural prepilin subunit. Whereas molecular mechanisms of type IVa pilus assembly have been well documented for
Pseudomonas aeruginosa
and involve the PilD prepilin peptidase, no type IVb pili have been described in this microorganism. One subclass of type IVb prepilins has been identified as the Flp prepilin subfamily. Long and bundled Flp pili involved in tight adherence have been identified in
Actinobacillus actinomycetemcomitans
, for which assembly was due to a dedicated machinery encoded by the
tad-rcp
locus. A similar
flp-tad-rcp
locus containing
flp
,
tad
, and
rcp
gene homologues was identified in the
P. aeruginosa
genome. The function of these genes has been investigated, which revealed their involvement in the formation of extracellular Flp appendages. We also identified a gene (designated by open reading frame PA4295) outside the
flp-tad-rcp
locus, that we named
fppA
, encoding a novel prepilin peptidase. This is the second enzyme of this kind found in
P. aeruginosa
; however, it appears to be truncated and is similar to the C-terminal domain of the previously characterized PilD peptidase. In this study, we show that FppA is responsible for the maturation of the Flp prepilin and belongs to the aspartic acid protease family. We also demonstrate that FppA is required for the assembly of cell surface appendages that we called Flp pili. Finally, we observed an Flp-dependent bacterial aggregation process on the epithelial cell surface and an increased biofilm phenotype linked to Flp pilus assembly.
Non-fatal occupational injuries in British agriculture
Authors: Solomon Christine , Poole Jason , Palmer Keith T , Coggon David 
Published: June 2006

Objectives:To investigate the incidence, nature and determinants of non-fatal occupational injuries in British agriculture.Methods:As part of a postal survey, data on lifetime histories of work in agriculture and occupational accidents were obtained from men born between 1933 and 1977 and residing in three rural areas of England and Wales. Incidence rates for different categories of accident were compared with those derived from statutory reporting. Associations with risk factors were explored by Poisson regression, and summarised by incidence rate ratios (IRRs).Results:Of the 10 765 responders (response rate = 31%), 3238 (30%) reported at least one occupational accident at the ages of 14–64 years, leading to absence from work for ⩾3 days, including 1492 accidents that could be linked to a specific job listed in the history of agricultural work. The reported incidence of injuries in agriculture was markedly higher than that derived from statutory reporting, particularly for self-employed farmers. During 1996–2003, the highest rates of agricultural accidents were from handling, lifting or carrying (4.9/1000 person-years), falls from a height (4.6/1000 person-years) and injury by animals (3.4/1000 person-years). After adjustment for calendar period and age, the risk of accidents was elevated in men who had only recently entered agricultural work (IRR 3.7, 95% CI 2.7 to 5.1 for men who had worked in agriculture for up to 1 year relative to those who had entered the industry >25 years earlier), and in those who carried out forestry (IRR 1.7, 95% CI 1.5 to 1.9).Conclusion:Our findings confirm the substantial underascertainment of serious accidental injuries in agriculture through statutory reporting, particularly for the self-employed. The risk of accidents is highest in new recruits to the industry and in those undertaking forestry, and these groups should be a target for further preventive action.
A Change of Heart: Moral Emotions, Transformation, and Moral Virtue
Authors: Stark Susan 
Published: June 2006

AbstractInspired in part by a renewed attention to Aristotle's moral philosophy, philosophers have acknowledged the important role of the emotions in morality. Nonetheless, precisely how emotions matter to morality has remained contentious. Aristotelians claim that moral virtue is constituted by correct action and correct emotion. But Kantians seem to require solely that agents do morally correct actions out of respect for the moral law. There is a crucial philosophical disagreement between the Aristotelian and Kantian moral outlooks: namely, is feeling the correct emotions necessary to virtue or is it an optional extra, which is permitted but not required. I argue that there are good reasons for siding with the Aristotelians: virtuous agents must experience the emotions appropriate to their situations. Moral virtue requires a change of heart.
c-Myc mediates pre-TCR-induced proliferation but not developmental progression
Authors: Dose Marei , Khan Irum , Guo Zhuyan , Kovalovsky Damian , Krueger Andreas , von Boehmer Harald , Khazaie Khashayarsha , Gounari Fotini 
Published: June 2006

AbstractConstitutive and cell-autonomous signals emanating from the pre-T-cell receptor (pre-TCR) promote proliferation, survival and differentiation of immature thymocytes. We show here that induction of pre-TCR signaling resulted in rapid elevation of c-Myc protein levels. Cre-mediated thymocyte-specific ablation of c-Myc in CD25+CD44- thymocytes reduced proliferation and cell growth at the pre-TCR checkpoint, resulting in thymic hypocellularity and a severe reduction in CD4+CD8+ thymocytes. In contrast, c-Myc deficiency did not inhibit pre-TCR-mediated differentiation or survival. Myc-/- double-negative (DN) 3 cells progressed to the double-positive (DP) stage and up-regulated TCRαβ surface expression in the absence of cell proliferation, in vivo as well as in vitro. These observations indicate that distinct signals downstream of the pre-TCR are responsible for proliferation versus differentiation, and demonstrate that c-Myc is only required for pre-TCR-induced proliferation but is dispensable for developmental progression from the DN to the DP stage.
Web-based analysis of the mouse transcriptome using Genevestigator
Authors: Laule Oliver , Hirsch-Hoffmann Matthias , Hruz Tomas , Gruissem Wilhelm , Zimmermann Philip 
Published: June 2006

Abstract

Background
Gene function analysis often requires a complex and laborious sequence of laboratory and computer-based experiments. Choosing an effective experimental design generally results from hypotheses derived from prior knowledge or experimentation. Knowledge obtained from meta-analyzing compendia of expression data with annotation libraries can provide significant clues in understanding gene and network function, resulting in better hypotheses that can be tested in the laboratory.

Description
Genevestigator is a microarray database and analysis system allowing context-driven queries. Simple but powerful tools allow biologists with little computational background to retrieve information about when, where and how genes are expressed. We manually curated and quality-controlled 3110 mouse Affymetrix arrays from public repositories. Data queries can be run against an annotation library comprising 160 anatomy categories, 12 developmental stage groups, 80 stimuli, and 182 genetic backgrounds or modifications. The quality of results obtained through Genevestigator is illustrated by a number of biological scenarios that are substantiated by other types of experimentation in the literature.

Conclusion
The Genevestigator-Mouse database effectively provides biologically meaningful results and can be accessed at https://www.genevestigator.ethz.ch.
The tip of the iceberg: a giant pelvic atypical lipoma presenting as a sciatic hernia
Authors: Skipworth Richard JE , Smith Graeme HM , Stewart Ken J , Anderson David N 
Published: June 2006

Abstract

Background
This case report highlights two unusual surgical phenomena: lipoma-like well-differentiated liposarcomas and sciatic hernias. It illustrates the need to be aware that hernias may not always simply contain intra-abdominal viscera.

Case presentation
A 36 year old woman presented with an expanding, yet reducible, right gluteal mass, indicative of a sciatic hernia. However, magnetic resonance imaging demonstrated a large intra- and extra-pelvic fatty mass traversing the greater sciatic foramen. The tumour was surgically removed through an abdomino-perineal approach. Subsequent pathological examination revealed an atypical lipomatous tumour (synonym: lipoma-like well-differentiated liposarcoma). The patient remains free from recurrence two years following her surgery.

Conclusion
The presence of a gluteal mass should always suggest the possibility of a sciatic hernia. However, in this case, the hernia consisted of an atypical lipoma spanning the greater sciatic foramen. Although lipoma-like well-differentiated liposarcomas have only a low potential for recurrence, the variable nature of fatty tumours demands that patients require regular clinical and radiological review.
Measles viral load may reflect SSPE disease progression
Authors: Kühne Simmonds M , Brown DWG , Jin L 
Published: June 2006

Abstract
Subacute sclerosing panencephalitis (SSPE) is a rare, slowly progressive neurological disorder caused by the persistent infection with measles virus (MV). Despite much research into SSPE, its pathology remains obscure. We examined autopsy tissues of eight SSPE patients by real time quantitative PCR, immunohistochemistry and immunoblotting to determine viral load. MV N, M and H gene RNA could be detected in the central nervous system (CNS) of all patients and in two non-CNS tissues of one patient. The viral burden between patients differed up to four-fold by quantitative PCR and corresponded with detection of MV protein. The level of both viral RNA and antigen in the brain may correlate with disease progression.
The distinct clinical profile of chronically critically ill patients: a cohort study
Authors: Estenssoro Elisa , Reina Rosa , Canales Héctor S , Saenz María Gabriela , Gonzalez Francisco E , Aprea María M , Laffaire Enrique , Gola Victor , Dubin Arnaldo 
Published: June 2006

Abstract
Introduction
Our goal was to describe the epidemiology, clinical profiles, outcomes, and factors that might predict progression of critically ill patients to chronically critically ill (CCI) patients, a still poorly characterized subgroup.

Methods
We prospectively studied all patients admitted to a university-affiliated hospital intensive care unit (ICU) between 1 July 2002 and 30 June 2005. On admission, we recorded epidemiological data, the presence of organ failure (multiorgan dysfunction syndrome (MODS)), underlying diseases (McCabe score), acute respiratory distress syndrome (ARDS) and shock. Daily, we recorded MODS, ARDS, shock, mechanical ventilation use, lengths of ICU and hospital stay (LOS), and outcome. CCI patients were defined as those having a tracheotomy placed for continued ventilation. Clinical complications and time to tracheal decannulation were registered. Predictors of progression to CCI were identified by logistic regression.

Results
Ninety-five patients (12%) fulfilled the CCI definition and, compared with the remaining 690 patients, these CCI patients were sicker (APACHE II, 21 ± 7 versus 18 ± 9 for non-CCI patients, p = 0.005); had more organ dysfunctions (SOFA 7 ± 3 versus 6 ± 4, p < 0.003); received more interventions (TISS 32 ± 10 versus 26 ± 8, p < 0.0001); and had less underlying diseases and had undergone emergency surgery more frequently (43 versus 24%, p = 0.001). ARDS and shock were present in 84% and 83% of CCI patients, respectively, versus 44% and 48% in the other patients (p < 0.0001 for both). CCI patients had higher expected mortality (38% versus 32%, p = 0.003), but observed mortality was similar (32% versus 35%, p = 0.59). Independent predictors of progression to CCI were ARDS on admission, APACHE II and McCabe scores (odds ratio (OR) 2.26, p < 0.001; OR 1.03, p < 0.01; and OR 0.34, p < 0.0001, respectively). Lengths of mechanical ventilation, ICU and hospital stay were 33 (24 to 50), 39 (29 to 55) and 55 (37 to 84) days, respectively. Tracheal decannulation was achieved at 40 ± 19 days.

Conclusion
CCI patients were a severely ill population, in which ARDS, shock, and MODS were frequent on admission, and who suffered recurrent complications during their stay. However, their prognosis was equivalent to that of the other ICU patients. ARDS, APACHE II and McCabe scores were independent predictors of evolution to chronicity.
Anti-Xa activity after subcutaneous administration of dalteparin in ICU patients with and without subcutaneous oedema: a pilot study
Authors: Rommers Mirjam K , Van Der Lely Netty , Egberts Toine CG , van den Bemt Patricia MLA 
Published: June 2006

Abstract
Introduction
Intensive care unit (ICU) patients often suffer from subcutaneous oedema, due to administration of large fluid volumes and the underlying pathophysiological condition. It is unknown whether the presence of subcutaneous oedema impairs the absorption of dalteparin, a low molecular weight heparin, when it is given by subcutaneous administration for venous thromboembolism prophylaxis. The objective of this study is to compare the anti-Xa activity of dalteparin after subcutaneous administration in ICU patients with and without subcutaneous oedema.

Methods
This non-randomized open parallel group follow-up pilot study was conducted in two mixed medical-surgical intensive care units at two teaching hospitals. Seven ICU patients with subcutaneous oedema (index group) and seven ICU patients without subcutaneous oedema (reference group) were studied. Anti-Xa activity was determined at 0, 3, 4, 6, 8, 12 and 24 hours after subcutaneous administration of 2,500 IU dalteparin. Plasma concentrations of factor anti-Xa activity were measured using a chromogenic factor Xa inhibition assay.

Results
The characteristics of the index group were: age, 58 years; male/female ratio, 5/2; body mass index at admission, 23.4 kg/m2 (at study day, 30.6 kg/m2). The characteristics of the reference group were: age, 49 years; male/female ratio, 6/1; body mass index at admission, 24.8 kg/m2 (at study day, 25.0 kg/m2). In the index group, creatinine clearance was lower compared to the reference group (71 versus 131 ml/minute, p = 0.003). Sequential organ failure assessment score did not differ between index and reference groups (4 versus 5). Mean arterial pressure was comparable between index and reference groups (91 versus 95 mmHg) and within the normal range. The mean Cmax value was not different between ICU patients with and without subcutaneous oedema (0.15 ± 0.02 versus 0.14 ± 0.02 IU/ml, p = 0.34). In the index group, the mean AUC(0–24 h) value was slightly higher compared with the reference group (1.50 ± 0.31 versus 1.15 ± 0.25 h·IU/ml, p = 0.31). This difference was not significant.

Conclusion
In this pilot study, there was no clinically relevant difference in anti-Xa activity after subcutaneous administration of 2,500 IU dalteparin for venous thromboembolism prophylaxis between ICU patients with and without subcutaneous oedema. Critically ill patients seem to have lower anti-Xa activity levels than healthy volunteers.
Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling
Authors: Zak Daniel E , Hao Haiping , Vadigepalli Rajanikanth , Miller Gregory M , Ogunnaike Babatunde A , Schwaber James S 
Published: June 2006

Abstract
Background
Identifying the gene regulatory networks governing physiological signal integration remains an important challenge in circadian biology. Epidermal growth factor receptor (EGFR) has been implicated in circadian function and is expressed in the suprachiasmatic nuclei (SCN), the core circadian pacemaker. The transcription networks downstream of EGFR in the SCN are unknown but, by analogy to other SCN inputs, we expect the response to EGFR activation to depend on circadian timing.

Results
We have undertaken a systems-level analysis of EGFR circadian time-dependent signaling in the SCN. We collected gene-expression profiles to study how the SCN response to EGFR activation depends on circadian timing. Mixed-model analysis of variance (ANOVA) was employed to identify genes with circadian time-dependent EGFR regulation. The expression data were integrated with transcription-factor binding predictions through gene group enrichment analyses to generate robust hypotheses about transcription-factors responsible for the circadian phase-dependent EGFR responses.

Conclusion
The analysis results suggest that the transcriptional response to EGFR signaling in the SCN may be partly mediated by established transcription-factors regulated via EGFR transription-factors (AP1, Ets1, C/EBP), transcription-factors involved in circadian clock entrainment (CREB), and by core clock transcription-factors (Rorα). Quantitative real-time PCR measurements of several transcription-factor expression levels support a model in which circadian time-dependent EGFR responses are partly achieved by circadian regulation of upstream signaling components. Our study suggests an important role for EGFR signaling in SCN function and provides an example for gaining physiological insights through systems-level analysis.
A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements
Authors: Wang Guandong , Zhang Weixiong 
Published: June 2006

AbstractThe comprehensive identification of cis-regulatory elements on a genome scale is a challenging problem. We develop a novel, steganalysis-based approach for genome-wide motif finding, called WordSpy, by viewing regulatory regions as a stegoscript with cis-elements embedded in 'background' sequences. We apply WordSpy to the promoters of cell-cycle-related genes of Saccharomyces cerevisiae and Arabidopsis thaliana, identifying all known cell-cycle motifs with high ranking. WordSpy can discover a complete set of cis-elements and facilitate the systematic study of regulatory networks.
Quality of Life Is Decreased after Treatment for Nonfunctioning Pituitary Macroadenoma
Authors: Dekkers O. M. , van der Klaauw A. A. , Pereira A. M. , Biermasz N. R. , Honkoop P. J. , Roelfsema F. , Smit J. W. A. , Romijn J. A. 
Published: June 2006

Abstract
Objective: Although a reduced quality of life (QoL) has been reported after long-term cure of functioning pituitary adenomas, the effect of successful treatment of nonfunctioning pituitary macroadenoma (NFMA) on QoL has not been fully addressed. Therefore, we evaluated a broad spectrum of QoL parameters in patients successfully treated for NFMA in our center.
Design: We conducted a case-control study.
Patients and Methods: We assessed QoL in 99 adult patients (mean age, 61.9 yr; range, 24–86 yr) in remission during long-term follow-up after surgical (n = 99) and additional radiotherapeutic (n = 37) treatment for NFMA by four validated health-related questionnaires (Hospital Anxiety and Depression Scale, Multidimensional Fatigue Index, Nottingham Health Profile, and Short Form-36). Patient outcomes were compared with 125 controls and with age-adjusted reference values derived from the literature.
Results: NFMA patients reported significantly impaired QoL in all questionnaires compared with the 125 controls and the age-adjusted reference values. All subscales of fatigue, assessed using the Multidimensional Fatigue Index (general fatigue, physical fatigue, reduction in activity, reduction in motivation, and mental fatigue) were impaired. The scores in the Nottingham Health Profile pointed toward reduced energy and affected emotional reaction. In several subscales of the Short Form-36 (social functioning, role limitations due to physical problems, role limitations due to emotional problems, and general health perception), NFMA patients reported a reduced QoL.
Conclusion: QoL is considerably reduced in patients after successful treatment of NFMA.