bluuebunny/crossref_metadata_2025_split huggingface dataset:
The
Staphylococcus aureus
Lipoprotein SitC Colocalizes with Toll-Like Receptor 2 (TLR2) in Murine Keratinocytes and Elicits Intracellular TLR2 Accumulation
Authors: Müller P. , Müller-Anstett M. , Wagener J. , Gao Q. , Kaesler S. , Schaller M. , Biedermann T. , Götz F. 
Published: August 2010

ABSTRACT

SitC is one of the predominant lipoproteins in
Staphylococcus aureus
. Recently, SitC was shown to be capable of stimulating Toll-like receptor 2 (TLR2), but the mechanism of TLR2 activation by SitC has not been analyzed in detail so far. In this study, we purified C-terminally His-tagged SitC (SitC-His) from
Staphylococcus aureus
. SitC-His induced interleukin-6 (IL-6) and tumor necrosis factor alpha (TNF-α) release in human monocytes and also NF-κB activation in TLR2-transfected HEK293 cells, indicating TLR2-specific activation. SitC not only induced a TLR2-dependent release of IL-6 in primary murine keratinocytes (MKs) but also induced intracellular accumulation of TLR2, which was time and concentration dependent. Cy2-labeled SitC-His colocalized specifically with TLR2 in MKs and was also internalized in TLR2 knockout MKs, suggesting a TLR2-independent uptake. Neither activation nor colocalization of SitC-His was observed with TLR4 or Nod2. The results show that the native lipoprotein SitC-His specifically colocalizes with TLR2, is internalized by host cells, induces proinflammatory cytokines, and triggers intracellular accumulation of TLR2.
Identification of the TcpP-Binding Site in the
toxT
Promoter of
Vibrio cholerae
and the Role of ToxR in TcpP-Mediated Activation
Authors: Goss Thomas J. , Seaborn Craig P. , Gray Miranda D. , Krukonis Eric S. 
Published: August 2010

ABSTRACT

ToxR-dependent recruitment of TcpP to the
toxT
promoter facilitates
toxT
transcription in
Vibrio cholerae
, initiating a regulatory cascade that culminates in cholera toxin expression and secretion. Although TcpP usually requires ToxR to activate the
toxT
promoter, TcpP overexpression can circumvent the requirement for ToxR in this process. To define nucleotides critical for TcpP-dependent promoter recognition and activation, a series of
toxT
promoter derivatives with single-base-pair transversions spanning the TcpP-binding site were generated and used as plasmid-borne
toxT-lacZ
fusions, as DNA mobility shift targets, and as allelic replacements of the chromosomal
toxT
promoter. When present in Δ
toxR V. cholerae
overexpressing TcpP, several transversions affecting nucleotides within two direct repeats present in the TcpP-binding region (TGTAA-N
6
-TGTAA) caused defects in TcpP-dependent
toxT-lacZ
fusion activation and toxin production. Electrophoretic mobility shift assays demonstrated that these same transversions reduced the affinity of the
toxT
promoter for TcpP. The presence of ToxR suppressed transcription activation defects associated with most, but not all, transversions. Particularly, the central thymine nucleotide of both pentameric repeats was essential for efficient
toxT
activation, even in the presence of ToxR. These results suggest that the
toxT
promoter recognition function provided by ToxR can facilitate the interaction of TcpP with the
toxT
promoter but is insufficient for promoter activation when the TcpP-binding site has been severely compromised by mutation. Thus, the interaction of TcpP with nucleotides of the direct repeat sequences appears to be a prerequisite for
toxT
promoter activation.
Overcoming the Heme Paradox: Heme Toxicity and Tolerance in Bacterial Pathogens
Authors: Anzaldi Laura L. , Skaar Eric P. 
Published: August 2010

ABSTRACTVirtually all bacterial pathogens require iron to infect vertebrates. The most abundant source of iron within vertebrates is in the form of heme as a cofactor of hemoproteins. Many bacterial pathogens have elegant systems dedicated to the acquisition of heme from host hemoproteins. Once internalized, heme is either degraded to release free iron or used intact as a cofactor in catalases, cytochromes, and other bacterial hemoproteins. Paradoxically, the high redox potential of heme makes it a liability, as heme is toxic at high concentrations. Although a variety of mechanisms have been proposed to explain heme toxicity, the mechanisms by which heme kills bacteria are not well understood. Nonetheless, bacteria employ various strategies to protect against and eliminate heme toxicity. Factors involved in heme acquisition and detoxification have been found to contribute to virulence, underscoring the physiological relevance of heme stress during pathogenesis. Herein we describe the current understanding of the mechanisms of heme toxicity and how bacterial pathogens overcome the heme paradox during infection.
Impact of Serum Hepatocyte Growth Factor on Treatment Response to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors in Patients with Non–Small Cell Lung Adenocarcinoma
Authors: Kasahara Kazuo , Arao Tokuzo , Sakai Kazuko , Matsumoto Kazuko , Sakai Asao , Kimura Hideharu , Sone Takashi , Horiike Atsushi , Nishio Makoto , Ohira Tatsuo , Ikeda Norihiko , Yamanaka Takeharu , Saijo Nagahiro , Nishio Kazuto 
Published: August 2010

Abstract
Purpose: The epidermal growth factor receptor (EGFR) mutation status has emerged as a validated biomarker for predicting the response to treatment with EGFR-tyrosine kinase inhibitors (EGFR-TKI) in patients with non–small cell lung cancer. However, the responses to EGFR-TKIs vary even among patients with EGFR mutations. We studied several other independently active biomarkers for EGFR-TKI treatment.
Experimental Design: We retrospectively analyzed the serum concentrations of 13 molecules in a cohort of 95 patients with non–small cell lung adenocarcinoma who received EGFR-TKI treatment at three centers. The pretreatment serum concentrations of amphiregulin, β-cellulin, EGF, EGFR, epiregulin, fibroblast growth factor-basic, heparin-binding EGF-like growth factor, hepatocyte growth factor (HGF), platelet-derived growth factor β polypeptide, placental growth factor, tenascin C, transforming growth factor-α, and vascular endothelial growth factor (VEGF) were measured using enzyme-linked immunosorbent assay and a multiplex immunoassay system. The associations between clinical outcomes and these molecules were evaluated.
Results: The concentrations of HGF and VEGF were significantly higher among patients with progressive disease than among those without progressive disease (P &lt; 0.0001). HGF and VEGF were strongly associated with progression-free survival (PFS) and overall survival (OS) in a univariate Cox analysis (all tests for hazard ratio showed P &lt; 0.0001). A stratified multivariate Cox model according to EGFR mutation status (mutant, n = 20; wild-type, n = 23; unknown, n = 52) showed that higher HGF levels were significantly associated with a shorter PFS and OS (P &lt; 0.0001 for both PFS and OS). These observations were also consistent in the subset analyses.
Conclusions: Serum HGF was strongly related to the outcome of EGFR-TKI treatment. Our results suggest that the serum HGF level could be used to refine the selection of patients expected to respond to EGFR-TKI treatment, warranting further prospective study. Clin Cancer Res; 16(18); 4616–24. ©2010 AACR.
Angiotensin-Converting Enzyme 2 Suppresses Pathological Hypertrophy, Myocardial Fibrosis, and Cardiac Dysfunction
Authors: Zhong JiuChang , Basu Ratnadeep , Guo Danny , Chow Fung L. , Byrns Simon , Schuster Manfred , Loibner Hans , Wang Xiu-hua , Penninger Josef M. , Kassiri Zamaneh , Oudit Gavin Y. 
Published: August 2010

Background—Angiotensin-converting enzyme 2 (ACE2) is a pleiotropic monocarboxypeptidase capable of metabolizing several peptide substrates. We hypothesized that ACE2 is a negative regulator of angiotensin II (Ang II)–mediated signaling and its adverse effects on the cardiovascular system.Methods and Results—Ang II infusion (1.5 mg · kg−1· d−1) for 14 days resulted in worsening cardiac fibrosis and pathological hypertrophy in ACE2 knockout (Ace2−/y) mice compared with wild-type (WT) mice. Daily treatment of Ang II–infused wild-type mice with recombinant human ACE2 (rhACE2; 2 mg · kg−1· d−1IP) blunted the hypertrophic response and expression of hypertrophy markers and reduced Ang II–induced superoxide production. Ang II–mediated myocardial fibrosis and expression of procollagen type Iα1, procollagen type IIIα1, transforming growth factor-β1, and fibronectin were also suppressed by rhACE2. Ang II–induced diastolic dysfunction was inhibited by rhACE2 in association with reduced plasma and myocardial Ang II and increased plasma Ang 1-7 levels. rhACE2 treatment inhibited Ang II–mediated activation of protein kinase C-α and protein kinase C-β1 protein levels and phosphorylation of the extracellular signal-regulated 1/2, Janus kinase 2, and signal transducer and activator of transcription 3 signaling pathways in wild-type mice. A subpressor dose of Ang II (0.15 mg · kg−1· d−1) resulted in a milder phenotype that was strikingly attenuated by rhACE2 (2 mg · kg−1· d−1IP). In adult ventricular cardiomyocytes and cardiofibroblasts, Ang II–mediated superoxide generation, collagen production, and extracellular signal-regulated 1/2 signaling were inhibited by rhACE2 in an Ang 1-7–dependent manner. Importantly, rhACE2 partially prevented the development of dilated cardiomyopathy in pressure-overloaded wild-type mice.Conclusions—Elevated Ang II induced hypertension, myocardial hypertrophy, fibrosis, and diastolic dysfunction, which were exacerbated by ACE2 deficiency, whereas rhACE2 attenuated Ang II– and pressure-overload–induced adverse myocardial remodeling. Hence, ACE2 is an important negative regulator of Ang II–induced heart disease and suppresses adverse myocardial remodeling.
Alpha Oscillations Correlate with the Successful Inhibition of Unattended Stimuli
Authors: Händel Barbara F. , Haarmeier Thomas , Jensen Ole 
Published: August 2010

AbstractBecause the human visual system is continually being bombarded with inputs, it is necessary to have effective mechanisms for filtering out irrelevant information. This is partly achieved by the allocation of attention, allowing the visual system to process relevant input while blocking out irrelevant input. What is the physiological substrate of attentional allocation? It has been proposed that alpha activity reflects functional inhibition. Here we asked if inhibition by alpha oscillations has behavioral consequences for suppressing the perception of unattended input. To this end, we investigated the influence of alpha activity on motion processing in two attentional conditions using magneto-encephalography. The visual stimuli used consisted of two random-dot kinematograms presented simultaneously to the left and right visual hemifields. Subjects were cued to covertly attend the left or right kinematogram. After 1.5 sec, a second cue tested whether subjects could report the direction of coherent motion in the attended (80%) or unattended hemifield (20%). Occipital alpha power was higher contralateral to the unattended side than to the attended side, thus suggesting inhibition of the unattended hemifield. Our key finding is that this alpha lateralization in the 20% invalidly cued trials did correlate with the perception of motion direction: Subjects with pronounced alpha lateralization were worse at detecting motion direction in the unattended hemifield. In contrast, lateralization did not correlate with visual discrimination in the attended visual hemifield. Our findings emphasize the suppressive nature of alpha oscillations and suggest that processing of inputs outside the field of attention is weakened by means of increased alpha activity.
Driver Acceptance of False Alarms to Simulated Encroachment
Authors: Smith Kip , Källhammer Jan-Erik 
Published: August 2010

Objective: We investigated driver acceptance of alerts to left-turn encroachment incidents that do not produce a crash. If an event that produces a crash is the criterion for a “true” alert, all the alerts we studied are technically false alarms. Our aim was to inform the design of intersection-assist active safety systems. Background: The premise of this study is that it may be possible to overcome driver resistance to alerts that are false alarms by designing systems to issue alerts when and only when drivers would expect and accept them. Method: Participants were passengers in a driving simulator that presented left-turn encroachment incidents. Participant point of view, the direction of encroachment, and postencroachment time (PET) were manipulated to produce 36 near-crash incidents. After viewing each incident, the participant rated the relative acceptability of a hypothetical alert to it. Results: Repeated-measures ANOVA and logistic regression indicate that acceptability varies inversely with PET. At PET intervals less than 2.2 s, driver point of view and encroachment direction interact. At PET intervals more than 2.2 s, alerts to lateral encroachments are more acceptable than alerts to oncoming encroachments. Conclusion: Driver acceptance of alerts by active safety systems will be sensitive to context. Application: This study demonstrates the utility of eliciting subjective criteria to inform system design to match driver (user) expectations. Intersection-assist active safety systems will need to be designed to adapt to the interaction of driver point of view, the direction of encroachment, and PET.
An Eye Movement Analysis of the Effect of Interruption Modality on Primary Task Resumption
Authors: Ratwani Raj , Trafton J. Gregory 
Published: August 2010

Objective: We examined the effect of interruption modality (visual or auditory) on primary task (visual) resumption to determine which modality was the least disruptive. Background: Theories examining interruption modality have focused on specific periods of the interruption timeline. Preemption theory has focused on the switch from the primary task to the interrupting task. Multiple resource theory has focused on interrupting tasks that are to be performed concurrently with the primary task. Our focus was on examining how interruption modality influences task resumption. We leverage the memory-for-goals theory, which suggests that maintaining an associative link between environmental cues and the suspended primary task goal is important for resumption. Method: Three interruption modality conditions were examined: auditory interruption with the primary task visible, auditory interruption with a blank screen occluding the primary task, and a visual interruption occluding the primary task. Reaction time and eye movement data were collected. Results: The auditory condition with the primary task visible was the least disruptive. Eye movement data suggest that participants in this condition were actively maintaining an associative link between relevant environmental cues on the primary task interface and the suspended primary task goal during the interruption. Conclusion: These data suggest that maintaining cue association is the important factor for reducing the disruptiveness of interruptions, not interruption modality. Application: Interruption-prone computing environments should be designed to allow for the user to have access to relevant primary task cues during an interruption to minimize disruptiveness.
The Impact of Adversity in Childhood on Outcomes in Adulthood
Authors: Davidson Gavin , Devaney John , Spratt Trevor 
Published: August 2010

• Summary: Current UK Government policy is concerned with the possible connections between childhood adversity, social exclusion and negative outcomes in adulthood. Understanding the impact of adverse childhood experiences on outcomes in adulthood is therefore key to informing effective policy and practice. In this article, the research on the impact of childhood adversity on outcomes in adulthood is reviewed in the broad categories of: mental health and social functioning; physical health; offending; service use; and economic impact. The literature on resilience that focuses on those who experience adversity, but do not have associated negative outcomes is also briefly considered. The strengths and limitations of the range of research methods used are then examined. • Findings: Previous studies have tended to focus on specific forms of adversity, predominantly abuse and neglect, and either: specific populations and specific outcomes; specific populations and general outcomes; or general populations and specific outcomes. This means there may be incomplete understanding of the inputs (the range of adverse experiences in childhood), the processes (how these may affect people) and the outcomes (across domains in adulthood). • Applications : It is concluded that it is important for social work researchers to engage in the current debate about how to prevent harmful childhood adversity and there is an important gap in the research for more interdisciplinary large-scale general population studies that consider the full range of childhood adversity and associated impacts across time and the possible processes involved.
Generation of human induced pluripotent stem cells by simple transient transfection of plasmid DNA encoding reprogramming factors
Authors: Si-Tayeb Karim , Noto Fallon K , Sepac Ana , Sedlic Filip , Bosnjak Zeljko J , Lough John W , Duncan Stephen A 
Published: August 2010

Abstract

Background
The use of lentiviruses to reprogram human somatic cells into induced pluripotent stem (iPS) cells could limit their therapeutic usefulness due to the integration of viral DNA sequences into the genome of the recipient cell. Recent work has demonstrated that human iPS cells can be generated using episomal plasmids, excisable transposons, adeno or sendai viruses, mRNA, or recombinant proteins. While these approaches offer an advance, the protocols have some drawbacks. Commonly the procedures require either subcloning to identify human iPS cells that are free of exogenous DNA, a knowledge of virology and safe handling procedures, or a detailed understanding of protein biochemistry.

Results
Here we report a simple approach that facilitates the reprogramming of human somatic cells using standard techniques to transfect expression plasmids that encode OCT4, NANOG, SOX2, and LIN28 without the need for episomal stability or selection. The resulting human iPS cells are free of DNA integration, express pluripotent markers, and form teratomas in immunodeficient animals. These iPS cells were also able to undergo directed differentiation into hepatocyte-like and cardiac myocyte-like cells in culture.

Conclusions
Simple transient transfection of plasmid DNA encoding reprogramming factors is sufficient to generate human iPS cells from primary fibroblasts that are free of exogenous DNA integrations. This approach is highly accessible and could expand the use of iPS cells in the study of human disease and development.
Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes
Authors: Ratnakumar Abhirami , McWilliam Sean , Barris Wesley , Dalrymple Brian P 
Published: August 2010

Abstract

Background
The advent of cheap high through-put sequencing methods has facilitated low coverage skims of a large number of organisms. To maximise the utility of the sequences, assembly into contigs and then ordering of those contigs is required. Whilst sequences can be assembled into contigs de novo, using assembled genomes of closely related organisms as a framework can considerably aid the process. However, the preferred search programs and parameters that will optimise the sensitivity and specificity of the alignments between the sequence reads and the framework genome(s) are not necessarily obvious. Here we demonstrate a process that uses paired-end sequence reads to choose an optimal program and alignment parameters.

Results
Unlike two single fragment reads, in paired-end sequence reads, such as BAC-end sequences, the two sequences in the pair have a known positional relationship in the original genome. This provides an additional level of confidence over match scores and e-values in the accuracy of the positional assignment of the reads in the comparative genome. Three commonly used sequence alignment programs: MegaBLAST, Blastz and PatternHunter were used to align a set of ovine BAC-end sequences against the equine genome assembly. A range of different search parameters, with a particular focus on contiguous and discontiguous seeds, were used for each program. The number of reads with a hit and the number of read pairs with hits for the two end sequences in the tail-to-tail paired-end configuration were plotted relative to the theoretical maximum expected curve. Of the programs tested, MegaBLAST with short contiguous seed lengths (word size 8-11) performed best in this particular task. In addition the data also provides estimates of the false positive and false negative rates, which can be used to determine the appropriate values of additional parameters, such as score cut-off, to balance sensitivity and specificity. To determine whether the approach also worked for the alignment of shorter reads, the first 240 bases of each BAC end sequence were also aligned to the equine genome. Again, contiguous MegaBLAST performed the best in optimising the sensitivity and specificity with which sheep BAC end reads map to the equine and bovine genomes.

Conclusions
Paired-end reads, such as BAC-end sequences, provide an efficient mechanism to optimise sequence alignment parameters, for example for comparative genome assemblies, by providing an objective standard to evaluate performance.
Fish oil supplementation reverses the effect of cholesterol on apoptotic gene expression in smooth muscle cells
Authors: Perales Sonia , Alejandre Ma José , Morales Rogelio Palomino , Torres Carolina , Linares Ana 
Published: August 2010

Abstract

Background
Nutritional control of gene regulation guides the transformation of smooth muscle cells (SMC) into foam cells in atherosclerosis. Oxidative stress has been reported in areas of lipid accumulation, activating proliferation genes. Suppression of oxidative stress by antioxidant administration reduces this activation and the progression of lesions. We hypothesized that fish oil consumption may protect against atherosclerotic vascular disease. The study objective was to determine the effects of dietary cholesterol and fish-oil intake on the apoptotic pathways induced by 25-hydroxycholesterol (25-HC) in SMC cultures.

Methods
An in vivo/in vitro cell model was used, culturing SMC isolated from chicks exposed to an atherogenic cholesterol-rich diet with 5% of cholesterol (SMC-Ch) alone or followed by an anti-atherogenic fish oil-rich diet with 10% of menhaden oil (SMC-Ch-FO) and from chicks on standard diet (SMC-C). Cells were exposed to 25-HC, studying apoptosis levels by flow cytometry (Annexin V) and expressions of caspase-3, c-myc, and p53 genes by quantitative real-time reverse transcriptase-polymerase chain reaction. Results: Exposure to 25-HC produced apoptosis in all three SMC cultures, which was mediated by increases in caspase-3, c-myc, and p53 gene expression. Changes were more marked in SMC-Ch than in SMC-C, indicating that dietary cholesterol makes SMC more susceptible to 25-HC-mediated apoptosis. Expression of p53 gene was elevated in SMC-Ch-FO. This supports the proposition that endogenous levels of p53 protect SMC against apoptosis and possibly against the development of atherosclerosis. Fish oil attenuated the increase in c-myc levels observed in SMC-C and SMC-Ch, possibly through its influence on the expression of antioxidant genes.

Conclusion
Replacement of a cholesterol-rich diet with a fish oil-rich diet produces some reversal of the cholesterol-induced changes, increasing the resistance of SMC to apoptosis.