bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Analysis of the Role of Pseudomonas aeruginosa Penicillin-Binding Protein 5 in β-Lactam Resistance
Authors: Smith Jeffrey D. , Kumarasiri Malika , Zhang Weilie , Hesek Dusan , Lee Mijoon , Toth Marta , Vakulenko Sergei , Fisher Jed F. , Mobashery Shahriar , Chen Yu 
Published: April 2013

ABSTRACT

Penicillin-binding protein 5 (PBP5) is one of the most abundant PBPs in
Pseudomonas aeruginosa
. Although its main function is that of a cell wall
dd
-carboxypeptidase, it possesses sufficient β-lactamase activity to contribute to the ability of
P. aeruginosa
to resist the antibiotic activity of the β-lactams. The study of these dual activities is important for understanding the mechanisms of antibiotic resistance by
P. aeruginosa
, an important human pathogen, and to the understanding of the evolution of β-lactamase activity from the PBP enzymes. We purified a soluble version of
P. aeruginosa
PBP5 (designated Pa sPBP5) by deletion of its C-terminal membrane anchor. Under
in vitro
conditions, Pa sPBP5 demonstrates both
dd
-carboxypeptidase and expanded-spectrum β-lactamase activities. Its crystal structure at a 2.05-Å resolution shows features closely resembling those of the class A β-lactamases, including a shortened loop spanning residues 74 to 78 near the active site and with respect to the conformations adopted by two active-site residues, Ser101 and Lys203. These features are absent in the related PBP5 of
Escherichia coli
. A comparison of the two Pa sPBP5 monomers in the asymmetric unit, together with molecular dynamics simulations, revealed an active-site flexibility that may explain its carbapenemase activity, a function that is absent in the
E. coli
PBP5 enzyme. Our functional and structural characterizations underscore the versatility of this PBP5 in contributing to the β-lactam resistance of
P. aeruginosa
while highlighting how broader β-lactamase activity may be encoded in the structural folds shared by the PBP and serine β-lactamase classes.
Human Monoclonal Antibodies against Clostridium difficile Toxins A and B Inhibit Inflammatory and Histologic Responses to the Toxins in Human Colon and Peripheral Blood Monocytes
Authors: Koon Hon Wai , Shih David Q. , Hing Tressia C. , Yoo Jun Hwan , Ho Samantha , Chen Xinhua , Kelly Ciarán P. , Targan Stephan R. , Pothoulakis Charalabos 
Published: April 2013

ABSTRACTClostridium difficileinfection (CDI) is a common and debilitating nosocomial infection with high morbidity and mortality.C. difficilemediates diarrhea and colitis by releasing two toxins, toxin A and toxin B. Since both toxins stimulate proinflammatory signaling pathways in human colonocytes and both are involved in the pathophysiology of CDI, neutralization of toxin A and B activities may represent an important therapeutic approach against CDI. Recent studies indicated that human monoclonal antibodies (MAbs) against toxins A and B reduce their cytotoxic and secretory activities and prevent CDI in hamsters. Moreover, anti-toxin A and anti-toxin B MAbs together with antibiotics also effectively reduced recurrent CDI in humans. However, whether these MAbs neutralize toxin A- and toxin B-associated immune responses in human colonic mucosa or human peripheral blood monocyte cells (PBMCs) has never been examined. We used fresh human colonic biopsy specimens and peripheral blood monocytes to evaluate the effects of these antibodies against toxin A- and B-associated cytokine release, proinflammatory signaling, and histologic damage. Incubation of anti-toxin A (MK3415) or anti-toxin B (MK6072) MAbs with human PBMCs significantly inhibited toxin A- and toxin B-mediated tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β) expression. MK3415 and MK6072 also diminished toxin A- and toxin B-mediated NF-κB p65 phosphorylation in human monocytes, respectively, and significantly reduced toxin A- and B-induced TNF-α and IL-1β expression as well as histologic damage in human colonic explants. Our results underline the effectiveness of MK3415 and MK6072 in blockingC. difficiletoxin A- and toxin B-mediated inflammatory responses and histologic damage.
Borrelia burgdorferi bba66
Gene Inactivation Results in Attenuated Mouse Infection by Tick Transmission
Authors: Patton Toni G. , Brandt Kevin S. , Nolder Christi , Clifton Dawn R. , Carroll James A. , Gilmore Robert D. 
Published: April 2013

ABSTRACT

The impact of the
Borrelia burgdorferi
surface-localized immunogenic lipoprotein BBA66 on vector and host infection was evaluated by inactivating the encoding gene,
bba66
, and characterizing the mutant phenotype throughout the natural mouse-tick-mouse cycle. The BBA66-deficient mutant isolate, Bb
ΔA66
, remained infectious in mice by needle inoculation of cultured organisms, but differences in spirochete burden and pathology in the tibiotarsal joint were observed relative to the parental wild-type (WT) strain.
Ixodes scapularis
larvae successfully acquired Bb
ΔA66
following feeding on infected mice, and the organisms persisted in these ticks through the molt to nymphs. A series of tick transmission experiments (
n
= 7) demonstrated that the ability of Bb
ΔA66
-infected nymphs to infect laboratory mice was significantly impaired compared to that of mice fed upon by WT-infected ticks.
trans
-complementation of Bb
ΔA66
with an intact copy of
bba66
restored the WT infectious phenotype in mice via tick transmission. These results suggest a role for BBA66 in facilitating
B. burgdorferi
dissemination and transmission from the tick vector to the mammalian host as part of the disease process for Lyme borreliosis.
Anaplasma phagocytophilum Inhibits Apoptosis and Promotes Cytoskeleton Rearrangement for Infection of Tick Cells
Authors: Ayllón Nieves , Villar Margarita , Busby Ann T. , Kocan Katherine M. , Blouin Edmour F. , Bonzón-Kulichenko Elena , Galindo Ruth C. , Mangold Atilio J. , Alberdi Pilar , Pérez de la Lastra José M. , Vázquez Jesús , de la Fuente José 
Published: April 2013

ABSTRACT

Anaplasma phagocytophilum
causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects gene expression in both the vertebrate host and the tick vector,
Ixodes scapularis
. Here, we identified new genes, including spectrin alpha chain or alpha-fodrin (CG8) and voltage-dependent anion-selective channel or mitochondrial porin (T2), that are involved in
A. phagocytophilum
infection/multiplication and the tick cell response to infection. The pathogen downregulated the expression of CG8 in tick salivary glands and T2 in both the gut and salivary glands to inhibit apoptosis as a mechanism to subvert host cell defenses and increase infection. In the gut, the tick response to infection through CG8 upregulation was used by the pathogen to increase infection due to the cytoskeleton rearrangement that is required for pathogen infection. These results increase our understanding of the role of tick genes during
A. phagocytophilum
infection and multiplication and demonstrate that the pathogen uses similar strategies to establish infection in both vertebrate and invertebrate hosts.
Phylogeographic Origin of Helicobacter pylori Determines Host-Adaptive Responses upon Coculture with Gastric Epithelial Cells
Authors: Sheh Alexander , Chaturvedi Rupesh , Merrell D. Scott , Correa Pelayo , Wilson Keith T. , Fox James G. 
Published: April 2013

ABSTRACT

While
Helicobacter pylori
infects over 50% of the world's population, the mechanisms involved in the development of gastric disease are not fully understood. Bacterial, host, and environmental factors play a role in disease outcome. To investigate the role of bacterial factors in
H. pylori
pathogenesis, global gene expression of six
H. pylori
isolates was analyzed during coculture with gastric epithelial cells. Clustering analysis of six Colombian clinical isolates from a region with low gastric cancer risk and a region with high gastric cancer risk segregated strains based on their phylogeographic origin. One hundred forty-six genes had increased expression in European strains, while 350 genes had increased expression in African strains. Differential expression was observed in genes associated with motility, pathogenicity, and other adaptations to the host environment. European strains had greater expression of the virulence factors
cagA
,
vacA
, and
babB
and were associated with increased gastric histologic lesions in patients. In AGS cells, European strains promoted significantly higher interleukin-8 (IL-8) expression than did African strains. African strains significantly induced apoptosis, whereas only one European strain significantly induced apoptosis. Our data suggest that gene expression profiles of clinical isolates can discriminate strains by phylogeographic origin and that these profiles are associated with changes in expression of the proinflammatory and protumorigenic cytokine IL-8 and levels of apoptosis in host epithelial cells. These findings support the hypothesis that bacterial factors determined by the phylogeographic origin of
H. pylori
strains may promote increased gastric disease.
Obesity in young men, and individual and combined risks of type 2 diabetes, cardiovascular morbidity and death before 55 years of age: a Danish 33-year follow-up study
Authors: Schmidt Morten , Johannesdottir Sigrun A , Lemeshow Stanley , Lash Timothy L , Ulrichsen Sinna P , Bøtker Hans Erik , Toft Sørensen Henrik 
Published: April 2013

ObjectivesTo examine the association between body mass index (BMI) in young adulthood and cardiovascular risks, including venous thromboembolism, before 55 years of age.DesignCohort study using population-based medical databases.SettingOutcomes registered from all hospitals in Denmark from 1977 onwards.Participants6502 men born in 1955 and eligible for conscription in Northern Denmark.Main outcome measuresFollow-up began at participants’ 22nd birthday and continued until death, emigration or 55 years of age, whichever came first. Using regression analyses, we calculated the risks and HRs, adjusting for cognitive test score and years of education.Results48% of all obese young men (BMI ≥30 kg/m2) were either diagnosed with type 2 diabetes, hypertension, myocardial infarction, stroke or venous thromboembolism or died before reaching 55 years of age. Comparing obese men with normal weight men (BMI 18.5 to <25.0 kg/m2), the risk difference for any outcome was 28% (95% CI 19% to 38%) and the HR was 3.0 (95% CI 2.3 to 4.0). Compared with normal weight, obesity was associated with an event rate that was increased more than eightfold for type 2 diabetes, fourfold for venous thromboembolism and twofold for hypertension, myocardial infarction and death.ConclusionsIn this cohort of young men, obesity was strongly associated with adverse cardiometabolic events before 55 years of age, including venous thromboembolism. Compared with those of normal weight, young obese men had an absolute risk increase for type 2 diabetes, cardiovascular morbidity or premature death of almost 30%.
Batch Effects and Pathway Analysis: Two Potential Perils in Cancer Studies Involving DNA Methylation Array Analysis
Authors: Harper Kristin N. , Peters Brandilyn A. , Gamble Mary V. 
Published: April 2013

AbstractBackground: DNA methylation microarrays have become an increasingly popular means of studying the role of epigenetics in cancer, although the methods used to analyze these arrays are still being developed and existing methods are not always widely disseminated among microarray users.Methods: We investigated two problems likely to confront DNA methylation microarray users: (i) batch effects and (ii) the use of widely available pathway analysis software to analyze results. First, DNA taken from individuals exposed to low and high levels of drinking water arsenic were plated twice on Illumina's Infinium 450 K HumanMethylation Array, once in order of exposure and again following randomization. Second, we conducted simulations in which random CpG sites were drawn from the 450 K array and subjected to pathway analysis using Ingenuity's IPA software.Results: The majority of differentially methylated CpG sites identified in Run One were due to batch effects; few sites were also identified in Run Two. In addition, the pathway analysis software reported many significant associations between our data, randomly drawn from the 450 K array, and various diseases and biological functions.Conclusions: These analyses illustrate the pitfalls of not properly controlling for chip-specific batch effects as well as using pathway analysis software created for gene expression arrays to analyze DNA methylation array data.Impact: We present evidence that (i) chip-specific effects can simulate plausible differential methylation results and (ii) popular pathway analysis software developed for expression arrays can yield spurious results when used in tandem with methylation microarrays. Cancer Epidemiol Biomarkers Prev; 22(6); 1052–60. ©2013 AACR.
Chromosomal Instability, DNA Index, Dysplasia, and Subsite in Oral Premalignancy as Intermediate Endpoints of Risk of Cancer
Authors: Giaretti Walter , Monteghirfo Stefano , Pentenero Monica , Gandolfo Sergio , Malacarne Davide , Castagnola Patrizio 
Published: April 2013

Abstract
Background: Chromosomal instability and aneuploidy may represent biomarkers of oral exposure to damaging agents and early signs of clinical disease according to the theory of “oral field cancerization.”
Methods: The hypothesis was tested that the DNA index (DI) values, obtained by high-resolution DNA flow cytometry (DNA-FCM), may potentially contribute to oral cancer risk prediction. For this purpose, the DI of oral fields of normal-appearing mucosa and oral potentially malignant disorders (OPMDs) in 165 consecutive patients was tested for association with dysplasia and/or the oral subsites of tongue and floor of the mouth taken as high-risk intermediate endpoints surrogate of cancer clinical endpoints. The association was evaluated by logistic regression using patient gender, age, tobacco, cigarette smoking habit, and alcohol abuse as confounding variables.
Results: Different DI models provided evidence of statistical significant associations. Subdividing the DI values in diploid, near-diploid aneuploid, and high or multiple aneuploid from both OPMDs and oral normal-appearing mucosa, ORs, respectively, of 1, 4.3 (P = 0.001), and 18.4 (P &lt; 0.0005) were obtained.
Conclusion: Routine DI analysis by high-resolution DNA-FCM seems potentially useful to complement dysplasia and subsite analysis for assessment of oral cancer risk prediction and for a better management of the patients with OPMDs. Work is in progress to validate the present findings in a prospective study with clinical endpoints.
Impact: Identifying DNA abnormalities in oral premalignancy may lead to biomarkers of oral exposure and cancer risk and potentially to more effective prevention measures. Cancer Epidemiol Biomarkers Prev; 22(6); 1133–41. ©2013 AACR.
Prolonged Inhibition of Glioblastoma Xenograft Initiation and Clonogenic Growth following In Vivo Notch Blockade
Authors: Chu Qian , Orr Brent A. , Semenkow Samantha , Bar Eli E. , Eberhart Charles G. 
Published: April 2013

Abstract
Purpose: To examine the effects of clinically relevant pharmacologic Notch inhibition on glioblastoma xenografts.
Experimental Design: Murine orthotopic xenografts generated from temozolomide-sensitive and -resistant glioblastoma neurosphere lines were treated with the γ-secretase inhibitor MRK003. Tumor growth was tracked by weekly imaging, and the effects on animal survival and tumor proliferation were assessed, along with the expression of Notch targets, stem cell, and differentiation markers, and the biology of neurospheres isolated from previously treated xenografts and controls.
Results: Weekly MRK003 therapy resulted in significant reductions in growth as measured by imaging, as well as prolongation of survival. Microscopic examination confirmed a statistically significant reduction in cross-sectional tumor area and mitotic index in a MRK003-treated cohort as compared with controls. Expression of multiple Notch targets was reduced in the xenografts, along with neural stem/progenitor cell markers, whereas glial differentiation was induced. Neurospheres derived from MRK003-treated xenografts exhibited reduced clonogenicity and formed less aggressive secondary xenografts. Neurospheres isolated from treated xenografts remained sensitive to MRK003, suggesting that therapeutic resistance does not rapidly arise during in vivo Notch blockade.
Conclusions: Weekly oral delivery of MRK003 results in significant in vivo inhibition of Notch pathway activity, tumor growth, stem cell marker expression, and clonogenicity, providing preclinical support for the use of such compounds in patients with malignant brain tumors. Some of these effects can persist for some time after in vivo therapy is complete. Clin Cancer Res; 19(12); 3224–33. ©2013 AACR.
Are any biocompatible coatings capable of attenuating the deleterious effects of cardiopulmonary bypass?
Authors: Marcoux JE , Mycyk TR 
Published: April 2013

Background: Biocompatible circuits (BCC) are intended to decrease the activation of blood to the artificial cardiopulmonary bypass (CPB) surface. Typically, the coatings are made of various inert substances or molecules physiologically similar to endothelium. Thromboelastography (TEG) graphically represents clot formation, strength of clotting and fibrinolysis. TEG analysis was undertaken to determine if coagulation could be preserved by the BCC. Methods: Five different BCC were studied in clinical applications. These five coated circuits were then compared to an identical circuit where only the oxygenator was coated. A pre- and post-bypass TEG was done for comparison. Six well-studied parameters of TEG analysis were compared: R time, Angle, K, Maximum Amplitude (MA), LY30% and Clot Index (CI). Postoperative bleeding and transfusion requirements were compared to TEG results for comparison. Results: All postoperative TEG results were significantly different from preoperative parameters except LY30%. No BCC circuit was able to prevent the significant disruption of the observed TEG coagulation parameters R, K, angle, MA and CI. Of note, the postoperative TEG parameters resulting from the Control and Trillium™ groups – which had the same type of oxygenator – were practically identical. The oxygenator, which represents the largest surface area in the CPB circuit, is the single most important factor influencing coagulation. Conclusion: While not harmful, BCC are ineffective in preserving TEG coagulation parameters post CPB. Clinical findings support laboratory TEG results in that there were no differences in bleeding or transfusion requirements between groups.
A question prompt list for patients with advanced cancer in the final year of life: Development and cross-cultural evaluation
Authors: Walczak Adam , Mazer Benjamin , Butow Phyllis N , Tattersall Martin HN , Clayton Josephine M , Davidson Patricia M , Young Jane , Ladwig Susan , Epstein Ronald M 
Published: April 2013

Background: Clinicians and patients find prognosis and end-of-life care discussions challenging. Misunderstanding one’s prognosis can contribute to poor decision-making and end-of-life quality of life. A question prompt list (booklet of questions patients can ask clinicians) targeting these issues may help overcome communication barriers. None exists for end-of-life discussions outside the palliative care setting. Aim: To develop/pilot a question prompt list facilitating discussion/planning of end-of-life care for oncology patients with advanced cancer from Australia and the United States and to explore acceptability, perceived benefits/challenges of using the question prompt list, suggestions for improvements and the necessity of country-specific adaptations. Design: An expert panel developed a question prompt list targeting prognosis and end-of-life issues. Australian/US semi-structured interviews and one focus group elicited feedback about the question prompt list. Transcribed data were analysed using qualitative methods. Setting/participants: Thirty-four patients with advanced cancer (15 Australian/19 US) and 13 health professionals treating such patients (7 Australian/6 US) from two Australian and one US cancer centre participated. Results: Most endorsed the entire question prompt list, though a minority queried the utility/appropriateness of some questions. Analysis identified four global themes: (1) reinforcement of known benefits of question prompt lists, (2) appraisal of content and suggestions for further developments, (3) perceived benefits and challenges in using the question prompt list and (4) contrasts in Australian/US feedback. These contrasts necessitated distinct Australian/US final versions of the question prompt list. Conclusions: Participants endorsed the question prompt list as acceptable and useful. Feedback resulted in two distinct versions of the question prompt list, accommodating differences between Australian and US approaches to end-of-life discussions, highlighting the appropriateness of tailoring communication aides to individual populations.
Impact of a palliative care initiative on end-of-life care in the general wards: A before-and-after study
Authors: Tan Adeline , Seah Angeline , Chua Gerald , Lim Tow Keang , Phua Jason 
Published: April 2013

Background: Data on deaths in the general wards of our hospital in 2007 revealed infrequent discussions on end-of-life care and excessive burdensome interventions. Aim: A physician order form to withhold inappropriate life-sustaining interventions was initiated in 2009. The use of the form was facilitated by staff educational sessions and a palliative care consult service. This study aims to evaluate the impact of these interventions in 2010. Design: Retrospective medical chart review with comparisons was made for the following: baseline patient characteristics, orders concerning life-sustaining therapies, treatment provided in last 24 h of life, and discussion of specific life-sustaining therapies with patients and families. Settings/participants: This study included all adult patients who died in our hospital’s general wards in 2007 ( N = 683) versus 2010 ( N = 714). Results: There was an increase in orders to withhold life-sustaining therapies, such as cardiopulmonary resuscitation (66.2%–80.0%). There was a decrease in burdensome interventions such as antibiotics (44.9%–24.9%) and a small increase in palliative treatments such as analgesia (29.1%–36.7%). There were more discussions on the role of cardiopulmonary resuscitation with conversant patients (4.6%–10.2%) and families (56.5%–79.8%) ( p-value all < 0.05). On multivariate analysis, the physician order form independently predicted orders to withhold cardiopulmonary resuscitation. Conclusions: A multifaceted intervention of a physician order form, educational sessions, and palliative care consult service led to an improvement in documentation of end-of-life discussions and was associated with an increase in such discussions and less burdensome treatments. There were small improvements in the proportion of palliative treatments administered.