bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Expression Analysis of Nonproliferating Intracellular Salmonella enterica Serovar Typhimurium Unravels an Acid pH-Dependent PhoP-PhoQ Response Essential for Dormancy
Authors: Núñez-Hernández Cristina , Tierrez Alberto , Ortega Álvaro D. , Pucciarelli M. Graciela , Godoy Marta , Eisman Blanca , Casadesús Josep , García-del Portillo Francisco 
Published: October 2012

ABSTRACT

Genome-wide expression analyses have provided clues on how
Salmonella
proliferates inside cultured macrophages and epithelial cells. However,
in vivo
studies show that
Salmonella
does not replicate massively within host cells, leaving the underlying mechanisms of such growth control largely undefined.
In vitro
infection models based on fibroblasts or dendritic cells reveal limited proliferation of the pathogen, but it is presently unknown whether these phenomena reflect events occurring
in vivo
. Fibroblasts are distinctive, since they represent a nonphagocytic cell type in which
S. enterica
serovar Typhimurium actively attenuates intracellular growth. Here, we show in the mouse model that
S
. Typhimurium restrains intracellular growth within nonphagocytic cells positioned in the intestinal lamina propria. This response requires a functional PhoP-PhoQ system and is reproduced in primary fibroblasts isolated from the mouse intestine. The fibroblast infection model was exploited to generate transcriptome data, which revealed that ∼2% (98 genes) of the
S
. Typhimurium genome is differentially expressed in nongrowing intracellular bacteria. Changes include metabolic reprogramming to microaerophilic conditions, induction of virulence plasmid genes, upregulation of the pathogenicity islands SPI-1 and SPI-2, and shutdown of flagella production and chemotaxis. Comparison of relative protein levels of several PhoP-PhoQ-regulated functions (PagN, PagP, and VirK) in nongrowing intracellular bacteria and extracellular bacteria exposed to diverse PhoP-PhoQ-inducing signals denoted a regulation responding to acidic pH. These data demonstrate that
S
. Typhimurium restrains intracellular growth
in vivo
and support a model in which dormant intracellular bacteria could sense vacuolar acidification to stimulate the PhoP-PhoQ system for preventing intracellular overgrowth.
Toward an Understanding of Changes in Diversity Associated with Fecal Microbiome Transplantation Based on 16S rRNA Gene Deep Sequencing
Authors: Shahinas Dea , Silverman Michael , Sittler Taylor , Chiu Charles , Kim Peter , Allen-Vercoe Emma , Weese Scott , Wong Andrew , Low Donald E. , Pillai Dylan R. 
Published: October 2012

ABSTRACT

Fecal microbiome transplantation by low-volume enema is an effective, safe, and inexpensive alternative to antibiotic therapy for patients with chronic relapsing
Clostridium difficile
infection (CDI). We explored the microbial diversity of pre- and posttransplant stool specimens from CDI patients (
n
= 6) using deep sequencing of the 16S rRNA gene. While interindividual variability in microbiota change occurs with fecal transplantation and vancomycin exposure, in this pilot study we note that clinical cure of CDI is associated with an increase in diversity and richness. Genus- and species-level analysis may reveal a cocktail of microorganisms or products thereof that will ultimately be used as a probiotic to treat CDI.

IMPORTANCE
Antibiotic-associated diarrhea (AAD) due to
Clostridium difficile
is a widespread phenomenon in hospitals today. Despite the use of antibiotics, up to 30% of patients are unable to clear the infection and suffer recurrent bouts of diarrheal disease. As a result, clinicians have resorted to fecal microbiome transplantation (FT). Donor stool for this type of therapy is typically obtained from a spouse or close relative and thoroughly tested for various pathogenic microorganisms prior to infusion. Anecdotal reports suggest a very high success rate of FT in patients who fail antibiotic treatment (>90%). We used deep-sequencing technology to explore the human microbial diversity in patients with
Clostridium difficile
infection (CDI) disease after FT. Genus- and species-level analysis revealed a cocktail of microorganisms in the
Bacteroidetes
and
Firmicutes
phyla that may ultimately be used as a probiotic to treat CDI.
Effects of Crude Oil, Dispersant, and Oil-Dispersant Mixtures on Human Fecal Microbiota in an
In Vitro
Culture System
Authors: Kim Jong Nam , Kim Bong-Soo , Kim Seong-Jae , Cerniglia Carl E. 
Published: October 2012

ABSTRACT

The Deepwater Horizon oil spill of 2010 raised concerns that dispersant and dispersed oil, as well as crude oil itself, could contaminate shellfish and seafood habitats with hazardous residues that had potential implications for human health and the ecosystem. However, little is known about the effects of crude oil and dispersant on the human fecal microbiota. The aim of this research was to evaluate the potential effects of Deepwater Horizon crude oil, Corexit 9500 dispersant, and their combination on human fecal microbial communities, using an
in vitro
culture test system. Fecal specimens from healthy adult volunteers were made into suspensions, which were then treated with oil, dispersant, or oil-dispersant mixtures under anaerobic conditions in an
in vitro
culture test system. Perturbations of the microbial community, compared to untreated control cultures, were assessed using denaturing gradient gel electrophoresis (DGGE), real-time PCR, and pyrosequencing methods. DGGE and pyrosequencing analysis showed that oil-dispersant mixtures reduced the diversity of fecal microbiota from all individuals. Real-time PCR results indicated that the copy numbers of 16S rRNA genes in cultures treated with dispersed oil or oil alone were significantly lower than those in control incubations. The abundance of the
Bacteroidetes
decreased in crude oil-treated and dispersed-oil-treated cultures, while the
Proteobacteria
increased in cultures treated with dispersed oil. In conclusion, the human fecal microbiota was affected differently by oil and dispersed oil, and the influence of dispersed oil was significantly greater than that of either oil or dispersant alone compared to control cultures.

IMPORTANCE
There have been concerns whether human health is adversely affected by exposure to spilled crude oil, which contains regulated carcinogens, such as polycyclic aromatic hydrocarbons. In this study, we determined the effect of BP Deepwater Horizon crude oil and oil dispersant on the human intestinal microbiota, since there is the potential that low-level residues of petrochemicals could contaminate seafood. The results of this study will increase our understanding of the ecophysiological changes in the microbial communities of the human gastrointestinal tract with respect to crude oil exposure.
Peripheral vascular structure and function in hypertrophic cardiomyopathy
Authors: Rowley Nicola Jayne , Green Daniel J , George Keith , Thijssen Dick H J , Oxborough David , Sharma Sanjay , Somauroo John D , Jones Julia , Sheikh Nabeel , Whyte Greg 
Published: October 2012

BackgroundHypertrophic cardiomyopathy (HCM) is characterised by idiopathic cardiac enlargement and represents the most frequent cause of sudden cardiac death in athletes under the age of 35 years. Differentiation between physiological (ie, exercise-related) and pathological (ie, HCM-related) cardiac remodelling is challenging. In line with cardiac remodelling, vascular structure and function are altered following training, but little is known about peripheral vascular adaptations in HCM. We hypothesised that, while HCM patients and athletes would exhibit similar cardiac characteristics, differences would be apparent in their brachial and carotid arteries.MethodsIn age-matched groups of HCM patients (n=18, 39±15 years), highly competitive athletes (n=18, 38±12 years) and recreational controls (n=10, 37±14 years), we used high-resolution ultrasound to assess the diameter and wall thickness of the carotid and brachial arteries, with flow-mediated dilator function (FMD) of the brachial arteries also assessed.ResultsA significant difference between athletes and HCM was evident in arterial wall thickness (carotid 519±60 vs 586±102 µm, p<0.05; brachial 345±80 vs 456±76 µm, p<0.05) and the brachial artery peak blood flow response following forearm ischaemia, an index of resistance artery remodelling (998±515 vs 725±248 ml/min, p<0.05). Similar differences were noted between athletes and controls, while controls and HCM did not differ. Brachial FMD% was not different between groups.ConclusionsAthletes and HCM subjects, who can be difficult to differentiate on the basis of cardiac measures, exhibit differences in indices of arterial structure. While this may be a disease-related effect, we cannot discount a generic impact of physical activity on arterial structure, as the athlete's arteries were also different to untrained control subjects. Future studies should assess artery function and structure in athletic HCM subjects.
Whole slide images as a platform for initial diagnostics in histopathology in a medium-sized routine laboratory
Authors: Al-Janabi Shaimaa , Huisman André , Nap Marius , Clarijs Ruud , van Diest Paul J 
Published: October 2012

IntroductionWhole slide imaging is the process of digitizing glass slides and the creation of Whole Slide Images (WSI), which enable the examination of pathology samples on a computer screen in a manner comparable to light microscopy. WSI have been used for different applications in pathology but their use for primary diagnostics is still limited. Implementing WSI for primary diagnostics would be a turning point necessitating extensive validation to unravel pitfalls and difficulties that could be encountered within the routine workflow. This article is aimed to describe the gradual integration of WSI into routine pathology diagnostics in a medium-sized routine pathology laboratory.MethodsThis project was started with optimizing the digital work environment including the setting up of validation studies, scanning preferences, storing WSI and the implemented adjustments to the workflow for the laboratory and the pathologist. Afterwards scanning glass slides was initiated in the department of pathology at the Atrium Medical Center, Heerlen, The Netherlands, for performing primary diagnostics of breast biopsies. Later this was extended to other specimen types including resections.ResultsThe validation studies yielded a high concordance rate between WSI and conventional diagnoses. Routine primary WSI based diagnosis was possible in 82.1% of cases. Failure of digital diagnosis was mainly related to poor image quality and logistic problems.ConclusionThe quality of the currently produced WSI is sufficient for primary diagnostics in 82.1% of the cases. Improving image quality, adequate retrieval and controlling scanning error will definitely encourage the wide adaptation in routine diagnostics.
Republished: The relationship between serum TSH and free T4 in older people
Authors: Clark Penny M , Holder Roger L , Haque Sayeed M , Hobbs F D Richard , Roberts Lesley M , Franklyn Jayne A 
Published: October 2012

Abstract
The frequency distribution of serum thyroid stimulating hormone (TSH) shows a skewed pattern that may change with age. The set point of the hypothalamic-pituitary-thyroid axis for an individual is thought to be genetically determined and has been described as a log-linear relationship of serum TSH to free thyroxine (T4); however, the validity of this hypothesis has yet to be established in older people. The aim of the study was to describe the relationship between serum TSH and free T4 in older people and define factors influencing this relationship. We conducted a cross-sectional, observational study of thyroid function in a community population of older subjects over 65 years of age. The relationship between serum TSH and free T4 was not linear as previously described, but is best described as a fourth-order polynomial. Both gender and smoking status affected the relationship. This suggests that more complex modelling is required when investigating the hypothalamic-pituitary-thyroid axis.
Community pharmacy and cash reward: a winning combination for chlamydia screening?
Authors: Currie Marian J , Deeks Louise S , Cooper Gabrielle M , Martin Sarah J , Parker Rhian M , Del Rosario Rendry , Hocking Jane S , Bowden Francis J 
Published: October 2012

ObjectivesTo date, the uptake of chlamydia screening in community pharmacies has been limited. The objective of this cross-sectional study was to determine if a cash reward, offered to both the provider and the consumer of chlamydia screening, increased the uptake of screening in community pharmacies.MethodsDuring 4 weeks in 2011, chlamydia screening and education were offered in four city and two suburban pharmacies to people aged 16–30 years. Those who provided a urine sample for testing, contact details, and completed a brief questionnaire were rewarded with $A10. Positive participants, and their nominated contacts, were offered treatment.ResultsOver a period of 751.5 h, 979 testing kits were requested, and 900 (93%) urine samples returned. Using probabilistic linkage methods, we determined that 671/900 (75%) urine samples were from unique individuals. 0.9 unique samples were obtained/hour of screening, 63% of which were provided by men. 19/671 (2.8%; 95% CI 1.7% to 4.4%) people tested positive, 5.2% (95% CI 2.8% to 8.8%) of women, and 1.4% (1.4 0.5 to 3.1) of men. 11/19 (58%) people were contacted and treated—two for suspected pelvic inflammatory disease.ConclusionsProviding a cash reward to encourage chlamydia screening in community pharmacies resulted in greater participation rates than previously reported pharmacy-based studies, particularly among men. Easily implemented mechanisms to reduce inappropriate repeat screening, incorrect contact details and effects on pharmacy work flow may enhance the efficiency of this approach.
A Novel Therapeutic Regimen to Eradicate Established Solid Tumors with an Effective Induction of Tumor-Specific Immunity
Authors: Tysome James R. , Li Xiaozhu , Wang Shengdian , Wang Pengju , Gao Dongling , Du Pan , Chen Dong , Gangeswaran Rathi , Chard Louisa S. , Yuan Ming , Alusi Ghassan , Lemoine Nicholas R. , Wang Yaohe 
Published: October 2012

AbstractPurpose: The efficacy of oncolytic viruses depends on multiple actions including direct tumor lysis, modulation of tumor perfusion, and stimulation of tumor-directed immune responses. In this study, we investigated whether a sequential combination of immunologically distinct viruses might enhance antitumor efficacy through the induction of tumor-specific immunity and circumvention or mitigation of antiviral immune responses.Experimental Design: The Syrian hamster as an immune-competent model that supports replication of both adenovirus and vaccinia virus was evaluated in vitro and in vivo. The antitumor efficacy of either virus alone or sequential combination of the two viruses was examined in pancreatic and kidney cancer models. The functional mechanism of the regimen developed here was investigated by histopathology, immunohistochemistry staining, CTL assay, and T-cell depletion.Results: The Syrian hamster is a suitable model for assessment of oncolytic adenovirus and vaccinia virus. Three low doses of adenovirus followed by three low doses of vaccinia virus resulted in a superior antitumor efficacy to the reverse combination, or six doses of either virus alone, against pancreatic and kidney tumors in Syrian hamsters. A total of 62.5% of animals bearing either tumor type treated with the sequential combination became tumor-free, accompanied by the induction of effective tumor-specific immunity. This enhanced efficacy was ablated by CD3+ T-cell depletion but was not associated with humoral immunity against the viruses.Conclusion: These findings show that sequential treatment of tumors with oncolytic adenovirus and vaccinia virus is a promising approach for cancer therapy and that T-cell responses play a critical role. Clin Cancer Res; 18(24); 6679–89. ©2012 AACR.
Do Imaging Biomarkers Relate to Outcome in Patients Treated with VEGF Inhibitors?
Authors: O'Connor James P.B. , Jayson Gordon C. 
Published: October 2012

AbstractThe management of solid tumors has been transformed by the advent of VEGF pathway inhibitors. Early clinical evaluation of these drugs has used pharmacodynamic biomarkers derived from advanced imaging such as dynamic MRI, computed tomography (CT), and ultrasound to establish proof of principle. We have reviewed published studies that used these imaging techniques to determine whether the same biomarkers relate to survival in renal, hepatocellular, and brain tumors in patients treated with VEGF inhibitors. Data show that in renal cancer, pretreatment measurements of Ktrans and early pharmacodynamic reduction in tumor enhancement and density have prognostic significance in patients treated with VEGF inhibitors. A weaker, but significant, relationship is seen with subtle early size change (10% in one dimension) and survival. Data from high-grade glioma suggest that pretreatment fractional blood volume and Ktrans were prognostic of overall survival. However, lack of control data with other therapies prevents assessment of the predictive nature of these biomarkers, and such studies are urgently required. Clin Cancer Res; 18(24); 6588–98. ©2012 AACR.
Cabazitaxel: More Than a New Taxane for Metastatic Castrate-Resistant Prostate Cancer?
Authors: Mita Alain C. , Figlin Robert , Mita Monica M. 
Published: October 2012

Abstract
The taxanes are recognized as a major class of chemotherapeutic agents; however, mechanisms of innate and acquired resistance can limit their usefulness. Cabazitaxel, a novel taxane with microtubule-stabilizing potency similar to docetaxel, exhibits activity against tumor cell lines resistant to paclitaxel and docetaxel. Cabazitaxel showed linear pharmacokinetics and a terminal elimination half-life comparable with that of docetaxel, findings which support dosing as a single infusion in three-week treatment cycles. Dose-ranging studies recommended doses of 20 or 25 mg/m2 every three weeks. Antitumor activity was shown in patients with advanced cancer and chemotherapy failure (including taxane failure). Other early studies investigated the efficacy of cabazitaxel in pretreated metastatic breast cancer, either as a single agent or in combination with capecitabine. Objective antitumor response rates of up to 24% and sustained tumor stabilizations were also observed. The TROPIC phase III study, conducted in patients with metastatic castrate-resistant prostate cancer previously treated with docetaxel, established cabazitaxel as the first chemotherapeutic agent to offer a survival advantage in this patient population. Across these studies, the dose-limiting hematologic toxicity was neutropenia (including febrile neutropenia), usually controllable with colony-stimulating factor/granulocyte-colony stimulating factor support. Clin Cancer Res; 18(24); 6574–9. ©2012 AACR.
Frequent Mutational Activation of the PI3K-AKT Pathway in Trastuzumab-Resistant Breast Cancer
Authors: Chandarlapaty Sarat , Sakr Rita A. , Giri Dilip , Patil Sujata , Heguy Adriana , Morrow Monica , Modi Shanu , Norton Larry , Rosen Neal , Hudis Clifford , King Tari A. 
Published: October 2012

Abstract
Purpose: HER2-amplified breast cancer is sometimes clinically insensitive to HER2-targeted treatment with trastuzumab. Laboratory models of resistance have causally implicated changes in HER2 expression and activation of the phosphoinositide 3-kinase (PI3K)–AKT pathway. We conducted a prospective tissue acquisition study to determine if there is evidence for these lesions in metastatic tumors that have progressed on trastuzumab-containing therapy.
Experimental Design: From 2/2007 to 11/2011, 63 patients with HER2-amplified breast cancer with recurrence of disease after adjuvant trastuzumab therapy or World Health Organization–defined progression of metastatic disease on a trastuzumab-containing regimen were prospectively enrolled and underwent tumor biopsy. Specimens were analyzed for activating mutations in PIK3CA and HER2 by Sequenom and analyzed for HER2 and PTEN status by immunohistochemistry.
Results: In 53/60 cases (88%, 3 cases not evaluable for HER2), HER2 overexpression persisted in the metastatic tumor following trastuzumab exposure. Among the 7 cases lacking HER2 overexpression, repeat analysis of the pretreatment tumor failed to confirm HER2 overexpression in five cases. Among cases evaluable for PTEN (56) or PI3K mutation (45), absent or significantly diminished PTEN expression was noted in 33 (59%) and activating mutations in PIK3CA in 13 (29%). The combined rate of PTEN loss and PIK3CA mutation in the trastuzumab-refractory tumors was 71% compared with 44% (P = 0.007) in an unexposed cohort of 73 HER2-amplified tumors.
Conclusions: In this series of prospectively collected trastuzumab-refractory human breast cancers, loss of HER2 overexpression was rare, whereas activation of the PI3K-AKT pathway through loss of PTEN or PIK3CA mutation was frequently observed. Clin Cancer Res; 18(24); 6784–91. ©2012 AACR.
Sequence Dependence of MEK Inhibitor AZD6244 Combined with Gemcitabine for the Treatment of Biliary Cancer
Authors: Xu Junyao , Knox Jennifer J. , Ibrahimov Emin , Chen Eric , Serra Stefano , Tsao Ming , Cao Pinjiang , Vines Douglass , Green David E. , Metran-Nascente Cristiane , McNamara Mairead G. , Hedley David W. 
Published: October 2012

Abstract
Purpose: MEK inhibition has clinical activity against biliary cancers and might therefore be successfully combined with gemcitabine, one of the most active chemotherapy agents for these cancers. As gemcitabine is active in S-phase, and the extracellular signal-regulated kinase (ERK) pathway has a major role driving cell-cycle progression, concurrent use of a MEK inhibitor could potentially antagonize the effect of gemcitabine. We therefore tested the sequence dependence of the combination of gemcitabine and the MEK inhibitor AZD6244 using a series of biliary cancer models.
Experimental Design: Primary xenografts were established from patients with gallbladder and distal bile duct cancer and grown in severe combined immunodeficient (SCID) mice at the subcutaneous site. Plasma and tumor drug levels and the time course for recovery of ERK signaling and S-phase were measured in tumor-bearing mice treated for 48 hours with AZD6244 and then monitored for 48 hours off treatment. On the basis of these results, two different treatment schedules combining AZD6244 with gemcitabine were tested in four different biliary cancer models.
Results: DNA synthesis was suppressed during treatment with AZD6244, and reentry into S-phase was delayed by approximately 48 hours after treatment. Strong schedule dependence was seen in all four biliary cancer models tested, suggesting that combined treatment with AZD6244 plus gemcitabine would be more active in patients with biliary cancer when gemcitabine is given following a 48-hour interruption in AZD6244 dosing, rather than concurrently.
Conclusions: The combination of AZD6244 plus gemcitabine is highly schedule dependent, and predicted to be more effective in the clinic using sequential rather than simultaneous dosing protocols. Clin Cancer Res; 19(1); 118–27. ©2012 AACR.