bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria
Authors: Hobley Laura , Lerner Thomas R , Williams Laura E , Lambert Carey , Till Rob , Milner David S , Basford Sarah M , Capeness Michael J , Fenton Andrew K , Atterbury Robert J , Harris Maximilian ATS , Sockett R Elizabeth 
Published: November 2012

Abstract

Background
Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

Results
To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

Conclusions
The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.
Evaluation of adhesion forces of Staphylococcus aureus along the length of Candida albicanshyphae
Authors: Ovchinnikova Ekaterina S , Krom Bastiaan P , Busscher Henk J , van der Mei Henny C 
Published: November 2012

Abstract

Background

Candida albicans is a human fungal pathogen, able to cause both superficial and serious, systemic diseases and is able to switch from yeast cells to long, tube-like hyphae, depending on the prevailing environmental conditions. Both morphological forms of C. albicans are found in infected tissue, often in combination with Staphylococcus aureus. Although bacterial adhesion to the different morphologies of C. albicans has been amply studied, possible differences in staphylococcal adhesion forces along the length of C. albicans hyphae have never been determined. In this study, we aim to verify the hypothesis that the forces mediating S. aureus NCTC8325-4GFP adhesion to hyphae vary along the length of C. albicans SC5314 and MB1 hyphae, as compared with adhesion to yeast cells.

Results

C. albicans hyphae were virtually divided into a “tip” (the growing and therefore youngest part of the hyphae), a “middle” and a so-called “head” region (the yeast cell from which germination started). Adhesion forces between S. aureus NCTC8325-4GFP and the different regions of C. albicans SC5314 hyphae were measured using atomic force microscopy. Strong adhesion forces were found at the tip and middle regions of C. albicans hyphae (−4.1 nN and −4.0 nN, respectively), while much smaller adhesion forces were measured at the head region (−0.3 nN). Adhesion forces exerted by the head region were comparable with the forces arising from budding yeast cells (−0.5 nN). A similar regional dependence of the staphylococcal adhesion forces was found for the clinical isolate involved in this study, C. albicans MB1.

Conclusions
This is the first time that differences in adhesion forces between S. aureus and different regions of C. albicans hyphae have been demonstrated on a quantitative basis, supporting the view that the head region is different from the remainder of the hyphae. Notably it can be concluded that the properties of the hyphal head region are similar to those of budding yeast cells. These novel findings provide new insights in the intricate interkingdom interaction between C. albicans and S. aureus.
Electrocardiogram features of premature ventricular contractions/ventricular tachycardia originating from the left ventricular outflow tract and the treatment outcome of radiofrequency catheter ablation
Authors: Ge Bei , Ji Kang-Ting , Ye Hai-Ge , Li Jia , Li Yue-Chun , Yin Ri-Peng , Lin Jia-Feng 
Published: November 2012

Abstract

Background
Radiofrequency catheter ablation (RFCA) has been used for the ablation of premature ventricular contractions (PVCs) or ventricular tachycardia (VT). To date, the mapping and catheter ablation of the arrhythmias originating from the left ventricular outflow tract (LVOT) has not been specified. This study investigates the electrocardiogram (ECG) feature of PVCs or VT originating from the LVOT. Moreover, the treatment outcome of RFCA is analyzed.

Methods
Mapping and ablation were performed on the supravalvular or subvalvular aorta in 52 cases with PVCs/VT originating from the LVOT. The data were compared with those from 104 patients with PVCs/VT originating from the right ventricular outflow tract (RVOT). A differential procedure was prepared based on the comparison of the ECG features of PVCs/VT originating from the RVOT, LVOT, and their different parts.

Results
Among 52 cases with PVCs originating from the LVOT, 47 were successfully treated by RFCA, with a success rate of 90.38%. Several differences among the 12-lead ECG features were observed from the RVOT and LVOT in the left and right coronary sinus groups, as well as under the left coronary sinus group (left fibrous trigone): (1) If the precordial leads transition <V3 plus the precordial leads transitional index >0 are considered as the diagnostic parameters of PVCs/VT originating from the LVOT, then the sensitivity, specificity, as well as positive and negative predictive values are 94.12%, 93.00%, 87.27%, and 96.88%, respectively; (2) The analysis of different subgroups of the LVOT are as follows: (a) A mainly positive wave of r or m pattern was recorded in the lead I in 72.73% of patients in the right coronary sinus group, versus 12.90% of patients in the left coronary sinus group, and 0% in the under left coronary sinus group. (b) All patients in the right coronary sinus group presented waves of RII>RIII and QSaVR>QSaVL, whereas most patients in the other two groups showed waves of RIII>RII and QSaVL>QSaVR. (c) Most patients in the under left coronary sinus group in lead V1 had a mainly positive wave (R) (77.78%), whereas those in the right (81.82%) and left (62.50%) coronary sinus groups had mainly negative waves (rS).

Conclusions
RFCA is a safe and effective curative therapy for PVCs/VT originating from the LVOT. The 12-lead ECG features of the LVOT from different origins exhibit certain distinctions.
Crusted scabies-associated immune reconstitution inflammatory syndrome
Authors: Fernández-Sánchez Mónica , Saeb-Lima Marcela , Alvarado-de la Barrera Claudia , Reyes-Terán Gustavo 
Published: November 2012

AbstractBackgroundDespite the widely accepted association between crusted scabies and human immunodeficiency virus (HIV)-infection, crusted scabies has not been included in the spectrum of infections associated with immune reconstitution inflammatory syndrome in HIV-infected patients initiating antiretroviral therapy.Case presentationWe report a case of a 28-year-old Mexican individual with late HIV-infection, who had no apparent skin lesions but soon after initiation of antiretroviral therapy, he developed an aggressive form of crusted scabies with rapid progression of lesions. Severe infestation bySarcoptes scabieiwas confirmed by microscopic examination of the scale and skin biopsy. Due to the atypical presentation of scabies in a patient responding to antiretroviral therapy, preceded by no apparent skin lesions at initiation of antiretroviral therapy, the episode was interpreted for the first time as “unmasking crusted scabies-associated immune reconstitution inflammatory syndrome”.ConclusionThis case illustrates that when crusted scabies is observed in HIV-infected patients responding to antiretroviral therapy, it might as well be considered as a possible manifestation of immune reconstitution inflammatory syndrome. Patient context should be considered for adequate diagnosis and treatment of conditions exacerbated by antiretroviral therapy-induced immune reconstitution.
Validation of the Oxford classification of IgA nephropathy for pediatric patients from China
Authors: Le Weibo , Zeng Cai-Hong , Liu Zhangsuo , Liu Dong , Yang Qing , Lin Rui-Xia , Xia Zheng-Kun , Fan Zhong-Min , Zhu Guanghua , Wu Ying , Xu Hong , Zhai Yihui , Ding Ying , Yang Xiaoqing , Liang Shaoshan , Chen Hao , Xu Feng , Huang Qian , Shen Hongbing , Wang Jianming , Fogo Agnes B , Liu Zhi-Hong 
Published: November 2012

Abstract

Background
The Oxford classification of IgA nephropathy (IgAN) provides a useful tool for prediction of renal prognosis. However, the application of this classification in children with IgAN needs validation in different patient populations.

Methods
A total of 218 children with IgAN from 7 renal centers in China were enrolled. The inclusion criteria was similar to the original Oxford study.

Results
There were 98 patients (45%) with mesangial proliferation (M1), 51 patients (23%) with endocapillary proliferation (E1), 136 patients (62%) with segmental sclerosis/adhesion lesion (S1), 13 patients (6%) with moderate tubulointerstitial fibrosis (T1 26-50% of cortex scarred), and only 2 patients (1%) with severe tubulointerstitial fibrosis (T2, >50% of cortex scarred). During a median follow-up duration of 56 months, 24 children (12.4%) developed ESRD or 50% decline in renal function. In univariate COX analysis, we found that tubular atrophy/interstitial fibrosis (HR 4.3, 95%CI 1.8-10.5, P < 0.001) and segmental glomerulosclerosis (HR 9.2 1.2-68.6, P = 0.03) were significant predictors of renal outcome. However, mesangial hypercellularity, endocapillary proliferation, crescents, and necrosis were not associated with renal prognosis. In the multivariate COX regression model, none of these pathologic lesions were shown to be independent risk factors of unfavorable renal outcome except for tubular atrophy/interstitial fibrosis (HR 2.9, 95%CI 1.0-7.9 P = 0.04).

Conclusions
We confirmed tubular atrophy/interstitial fibrosis was the only feature independently associated with renal outcomes in Chinese children with IgAN.
Profound tumor-specific Th2 bias in patients with malignant glioma
Authors: Shimato Shinji , Maier Lisa M , Maier Richard , Bruce Jeffrey N , Anderson Richard CE , Anderson David E 
Published: November 2012

Abstract

Background
Vaccination against tumor-associated antigens is one promising approach to immunotherapy against malignant gliomas. While previous vaccine efforts have focused exclusively on HLA class I-restricted peptides, class II-restricted peptides are necessary to induce CD4+ helper T cells and sustain effective anti-tumor immunity. In this report we investigated the ability of five candidate peptide epitopes derived from glioma-associated antigens MAGE and IL-13 receptor α2 to detect and characterize CD4+ helper T cell responses in the peripheral blood of patients with malignant gliomas.

Methods
Primary T cell responses were determined by stimulating freshly isolated PBMCs from patients with primary glioblastoma (GBM) (n = 8), recurrent GBM (n = 5), meningioma (n = 7), and healthy controls (n = 6) with each candidate peptide, as well as anti-CD3 monoclonal antibody (mAb) and an immunodominant peptide epitope derived from myelin basic protein (MBP) serving as positive and negative controls, respectively. ELISA was used to measure IFN-γ and IL-5 levels, and the ratio of IFN-γ/IL-5 was used to determine whether the response had a predominant Th1 or Th2 bias.

Results
We demonstrate that novel HLA Class-II restricted MAGE-A3 and IL-13Rα2 peptides can detect T cell responses in patients with GBMs as well as in healthy subjects. Stimulation with a variety of peptide antigens over-expressed by gliomas is associated with a profound reduction in the IFN-γ/IL-5 ratio in GBM patients relative to healthy subjects. This bias is more pronounced in patients with recurrent GBMs.

Conclusions
Therapeutic vaccine strategies to shift tumor antigen-specific T cell response to a more immunostimulatory Th1 bias may be needed for immunotherapeutic trials to be more successful clinically.
Expression of aurora kinase A is associated with metastasis-free survival in node-negative breast cancer patients
Authors: Siggelkow Wulf , Boehm Daniel , Gebhard Susanne , Battista Marco , Sicking Isabel , Lebrecht Antje , Solbach Christine , Hellwig Birte , Rahnenführer Jörg , Koelbl Heinz , Gehrmann Mathias , Marchan Rosemarie , Cadenas Cristina , Hengstler Jan G , Schmidt Marcus 
Published: November 2012

AbstractBackgroundInhibitors targeting the cell cycle-regulated aurora kinase A (AURKA) are currently being developed. Here, we examine the prognostic impact of AURKA in node-negative breast cancer patients without adjuvant systemic therapy (n = 766).MethodsAURKA was analyzed using microarray-based gene-expression data from three independent cohorts of node-negative breast cancer patients. In multivariate Cox analyses, the prognostic impact of age, histological grade, tumor size, estrogen receptor (ER), and HER2 were considered.ResultsPatients with higher AURKA expression had a shorter metastasis-free survival (MFS) in the Mainz (HR 1.93; 95% CI 1.34 – 2.78; P < 0.001), Rotterdam (HR 1.95; 95% CI 1.45– 2.63; P<0.001) and Transbig (HR 1.52; 95% CI 1.14–2.04; P=0.005) cohorts. AURKA was also associated with MFS in the molecular subtype ER+/HER2- carcinomas (HR 2.10; 95% CI 1.70–2.59; P<0.001), but not in ER-/HER2- nor in HER2+ carcinomas. In the multivariate Cox regression adjusted to age, grade and tumor size, AURKA showed independent prognostic significance in the ER+/HER2- subtype (HR 1.73; 95% CI 1.24–2.42; P=0.001). Prognosis of patients in the highest quartile of AURKA expression was particularly poor. In addition, AURKA correlated with the proliferation metagene (R=0.880; P<0.001), showed a positive association with grade (P<0.001), tumor size (P<0.001) and HER2 (P<0.001), and was inversely associated with ER status (P<0.001).ConclusionsAURKA is associated with worse prognosis in estrogen receptor positive breast carcinomas. Patients with the highest AURKA expression (>75% percentile) have a particularly bad prognosis and may profit from therapy with AURKA inhibitors.
Association analysis of cigarette smoking with onset of primary open-angle glaucoma and glaucoma-related biometric parameters
Authors: Wang Degui , Huang Yuqiang , Huang Chukai , Wu Pengfei , Lin Jianwei , Zheng Yuqian , Peng Yi , Liang Yuanbo , Chen Jian-Huan , Zhang Mingzhi 
Published: November 2012

Abstract

Background
To date, studies on the role played by cigarette smoking in primary open-angle glaucoma (POAG) remains controversial. The current study evaluated cigarette smoking as a risk factor of POAG and its relationships with vertical cup-to-disc ratio (VCDR), central corneal thickness (CCT) and intraocular pressure (IOP) in a Chinese cohort.

Methods
In a total of 248 unrelated individuals including 30 juvenile-onset POAG (JOAG), 92 adult-onset POAG (AOAG) and 126 sex-matched senile cataract controls, underwent comprehensive ophthalmic examination. Their smoking was obtained and documented by questionnaire. Association of cigarette smoking with POAG was performed using logistic regression controlled for age and sex. Effects of cigarette smoking on VCDR, IOP and CCT were analyzed with multiple linear regression.

Results
In either JOAG or AOAG, no association of cigarette smoking was found with disease onset (P = 0.692 and 0.925 respectively). In controls and JOAG, no significant effects of smoking were found on VCDR, IOP or CCT (all P > 0.05). Smoking was found to be correlated with decreased CCT in AOAG and combined POAG (JOAG + AOAG) (P = 0.009 and 0.003), but no association with VCDR or IOP was observed (P > 0.05).

Conclusions
Although cigarette smoking was not found to be risk factor for onset of POAG, it was correlated with CCT in AOAG, and thus might still play a role in the disease course, especially for AOAG.
Analysis of orthopedic surgery of bone metastases in breast cancer patients
Authors: Wegener Bernd , Schlemmer Marcus , Stemmler Joachim , Jansson Volkmar , Dürr Hans Roland , Pietschmann Matthias F 
Published: November 2012

Abstract

Background
Breast cancer is the most common malignancy and the second leading cause of death in women. Because bone metastases are a common finding in patients with breast cancer, they are of major clinical concern.

Methods
In 115 consecutive patients with bone metastases secondary to breast cancer, 132 surgical procedures were performed. Medical records and imaging procedures were reviewed for age, treatment of the primary tumor, clinical symptoms, surgical treatment, complications, and survival.

Results
The overall survival of patients with metastatic breast cancer was dependent on the site and the amount of the metastases. Age was not a prognostic factor for survival. If the result of the orthopaedic surgery was a wide resection (R0) survival was significantly better than in the R1 (marginal resection – tumor resection in sane tissue) or R2 (intralesional resection) situation. Concerning the orthopaedic procedures there was no survival difference.

Conclusion
In conclusion a wide (R0) resection and the absence of pathological fracture and visceral metastases were predictive for longer survival in univariate analysis. Age and the type of orthopaedic surgery had no impact on survival in multivariate analysis. The resection margins lost significance. The standard of care for patients with metastatic breast cancer to the bone requires a multidisciplinary approach.
Terpenic fraction of Pterodon pubescens inhibits nuclear factor kappa B and extracellular signal-regulated protein Kinase 1/2 activation and deregulates gene expression in leukemia cells
Authors: Pereira Monica Farah , Martino Thiago , Dalmau Sergio Ranto , Paes Márcia Cristina , Barja-Fidalgo Christina , Albano Rodolpho Mattos , Coelho Marsen Garcia Pinto , Sabino Kátia Costa de Carvalho 
Published: November 2012

Abstract

Background
Plant derived compounds have been shown to be important sources of several anti-cancer agents. As cell cycle deregulation and tumor growth are intimately linked, the discovery of new substances targeting events in this biochemical pathway would be of great value. The anti-leukemic effect of an ethanolic extract of Pterodon pubescens seeds (EEPp) has been previously demonstrated and now we show that a terpenic subfraction (SF5) of EEPp containing farnesol, geranylgeraniol and vouacapan derivatives induces apoptosis in the human chronic myelogenous leukemia cell line K562. This work addresses SF5’s antiproliferative mechanisms in these cells since they are still unclear.

Methods
DNA synthesis in K562 cells was assessed by [3H]-methyl-thymidine incorporation and cell cycle status by flow cytometry. The expression of cyclins D1 and E2, of the cell cycle inhibitor p21 and of the proto-oncogene c-myc was evaluated by semi-quantitative RT-PCR. Extracellular-signal-regulated kinases (ERK) 1/2 and nuclear factor kappa B (NF-κB) activation was evaluated by western blotting.

Results
In K562 cells, SF5 treatment induced a higher inhibition of DNA synthesis and cell growth than the original EEPp hexanic fraction from which SF5 originated, and also arrested the cell cycle in G1. Exposure of these cells to SF5 led to a decrease in cyclin E2 and c-myc expression while p21 mRNA levels were increased. Furthermore, SF5 inhibited the activation of mitogen-activated protein kinase (MAPK) ERK 1/2 and NF-κB.

Conclusions
This work suggests that the anti-leukemic action of SF5 is linked to the inhibition of ERKs, NF-κB and c-myc signaling pathways resulting in reduced cyclin E2 mRNA expression and cell cycle arrest in the G1 phase.
Complementary and alternative medicine (CAM) providers’ views of chronic low back pain patients’ expectations of CAM therapies: a qualitative study
Authors: Schafer Lisa M , Hsu Clarissa , Eaves Emery Rose , Ritenbaugh Cheryl , Turner Judith , Cherkin Daniel C , Sims Colette , Sherman Karen J 
Published: November 2012

Abstract

Background
Some researchers think that patients with higher expectations for CAM therapies experience better outcomes and that enthusiastic providers can enhance treatment outcomes. This is in contrast to evidence suggesting conventional medical providers often reorient patient expectations to better match what providers believe to be realistic. However, there is a paucity of research on CAM providers’ views of their patients’ expectations regarding CAM therapy and the role of these expectations in patient outcomes.

Methods
To better understand how CAM providers view and respond to their patients’ expectations of a particular therapy, we conducted 32 semi-structured, qualitative interviews with acupuncturists, chiropractors, massage therapists and yoga instructors identified through convenience sampling. Interviews were recorded, transcribed and analyzed thematically using Atlas ti version 6.1.

Results
CAM providers reported that they attempt to ensure that their patients’ expectations are realistic. Providers indicated they manage their patients’ expectations in a number of domains— roles and responsibilities of providers and patients, treatment outcomes, timeframe for improvement, and treatment experience. Providers reported that patients’ expectations change over time and that they need to continually manage these expectations to enhance patient engagement and satisfaction with treatment.

Conclusions
Providers of four types of CAM therapies viewed patients’ expectations as an important component of their experiences with CAM therapy and indicated that they try to align patient expectations with reality. These findings suggest that CAM providers are similar in this respect to conventional medical providers.