bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination
Authors: Carlos Camila , Pires Mathias M , Stoppe Nancy C , Hachich Elayse M , Sato Maria IZ , Gomes Tânia AT , Amaral Luiz A , Ottoboni Laura MM 
Published: June 2010

Abstract

Background

Escherichia coli strains are commonly found in the gut microflora of warm-blooded animals. These strains can be assigned to one of the four main phylogenetic groups, A, B1, B2 and D, which can be divided into seven subgroups (A0, A1, B1, B22, B23, D1 and D2), according to the combination of the three genetic markers chuA, yjaA and DNA fragment TspE4.C2. Distinct studies have demonstrated that these phylo-groups differ in the presence of virulence factors, ecological niches and life-history. Therefore, the aim of this work was to analyze the distribution of these E. coli phylo-groups in 94 human strains, 13 chicken strains, 50 cow strains, 16 goat strains, 39 pig strains and 29 sheep strains and to verify the potential of this analysis to investigate the source of fecal contamination.

Results
The results indicated that the distribution of phylogenetic groups, subgroups and genetic markers is non-random in the hosts analyzed. Strains from group B1 were present in all hosts analyzed but were more prevalent in cow, goat and sheep samples. Subgroup B23 was only found in human samples. The diversity and the similarity indexes have indicated a similarity between the E. coli population structure of human and pig samples and among cow, goat and sheep samples. Correspondence analysis using contingence tables of subgroups, groups and genetic markers frequencies allowed the visualization of the differences among animal samples and the identification of the animal source of an external validation set. The classifier tools Binary logistic regression and Partial least square -- discriminant analysis, using the genetic markers profile of the strains, differentiated the herbivorous from the omnivorous strains, with an average error rate of 17%.

Conclusions
This is the first work, as far as we are aware, that identifies the major source of fecal contamination of a pool of strains instead of a unique strain. We concluded that the analysis of the E. coli population structure can be useful as a supplementary bacterial source tracking tool.
Primary myxofibrosarcoma of the parotid: case report
Authors: Li Xu , Chen Xin , Shi Zhao-Hui , Chen Yang , Ye Jing , Qiao Li , Qiu Jian-Hua 
Published: June 2010

Abstract

Background
Myxofibrosarcoma is common in the extremities of elderly people and is characterized by a high frequency of local recurrence.

Case presentation
We report a 37 year old female who presented with a 4-month history of facial pain and a 3-month history of painful progressive swelling in the preauricular area. She underwent a total parotidectomy. The tumor was histopathologically and immunohistochemically diagnosed as a low-grade myxofibrosarcoma. The patient was free of disease 9 months after surgery with uneventful post-operative clinical course.

Conclusions
Parotid area swelling should always alert doctors. To our knowledge, this is the first case of parotid myxofibrosarcoma. It should be added to the differential diagnosis of diseases of the parotid. We have to recognize this disease and seek adequate treatment for it.
Rapid Health and Needs assessments after disasters: a systematic review
Authors: Korteweg Helena A , van Bokhoven Irene , Yzermans CJ , Grievink Linda 
Published: June 2010

Abstract

Background
Publichealth care providers, stakeholders and policy makers request a rapid insight into health status and needs of the affected population after disasters. To our knowledge, there is no standardized rapid assessment tool for European countries. The aim of this article is to describe existing tools used internationally and analyze them for the development of a workable rapid assessment.

Methods
A review was conducted, including original studies concerning a rapid health and/or needs assessment. The studies used were published between 1980 and 2009. The electronic databasesof Medline, Embase, SciSearch and Psychinfo were used.

Results
Thirty-three studies were included for this review. The majority of the studies was of US origin and in most cases related to natural disasters, especially concerning the weather. In eighteen studies an assessment was conducted using a structured questionnaire, eleven studies used registries and four used both methods. Questionnaires were primarily used to asses the health needs, while data records were used to assess the health status of disaster victims.

Conclusions
Methods most commonly used were face to face interviews and data extracted from existing registries. Ideally, a rapid assessment tool is needed which does not add to the burden of disaster victims. In this perspective, the use of existing medical registries in combination with a brief questionnaire in the aftermath of disasters is the most promising. Since there is an increasing need for such a tool this approach needs further examination.
Positive Association between Aspirin-Intolerant Asthma and Genetic Polymorphisms of FSIP1: a Case-Case Study
Authors: Kim Jason Yongha , Kim Jeong Hyun , Park Tae Joon , Bae Joon Seol , Lee Jin Sol , Pasaje Charisse Flerida , Park Byung Lae , Cheong Hyun Sub , Park Jong-Sook , Park Sung-Woo , Uh Soo-Taek , Kim Mi-Kyeong , Choi Inseon S , Cho Sang Heon , Choi Byoung Whui , Park Choon-Sik , Shin Hyoung Doo 
Published: June 2010

Abstract

Background
Aspirin-intolerant asthma (AIA), which is caused by non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin, causes lung inflammation and reversal bronchi reduction, leading to difficulty in breathing. Aspirin is known to affect various parts inside human body, ranging from lung to spermatogenesis. FSIP1, also known as HDS10, is a recently discovered gene that encodes fibrous sheath interacting protein 1, and is regulated by amyloid beta precursor protein (APP). Recently, it has been reported that a peptide derived from APP is cleaved by α disintegrin and metalloproteinase 33 (ADAM33), which is an asthma susceptibility gene. It has also been known that the FSIP1 gene is expressed in airway epithelium.

Objectives
Aim of this study is to find out whether FSIP1 polymorphisms affect the onset of AIA in Korean population, since it is known that AIA is genetically affected by various genes.

Methods
We conducted association study between 66 single nucleotide polymorphisms (SNPs) of the FSIP1 gene and AIA in total of 592 Korean subjects including 163 AIA and 429 aspirin-tolerant asthma (ATA) patients. Associations between polymorphisms of FSIP1 and AIA were analyzed with sex, smoking status, atopy, and body mass index (BMI) as covariates.

Results
Initially, 18 SNPs and 4 haplotypes showed associations with AIA. However, after correcting the data for multiple testing, only one SNP showed an association with AIA (corrected P-value = 0.03, OR = 1.63, 95% CI = 1.23-2.16), showing increased susceptibility to AIA compared with that of ATA cases. Our findings suggest that FSIP1 gene might be a susceptibility gene for aspirin intolerance in asthmatics.

Conclusion
Although our findings did not suggest that SNPs of FSIP1 had an effect on the reversibility of lung function abnormalities in AIA patients, they did show significant evidence of association between the variants in FSIP1 and AIA occurrence among asthmatics in a Korean population.
The transcription factor 7-like 2 (TCF7L2) polymorphism may be associated with focal arteriolar narrowing in Caucasians with hypertension or without diabetes: the ARIC Study
Authors: Yan Yu , Klein Ronald , Heiss Gerardo , Girman Cynthia J , Lange Ethan M , Klein Barbara E , Rose Kathryn M , Boerwinkle Eric , Pankow James S , Brancati Frederick L , Ballantyne Christie M , Köttgen Anna , North Kari E 
Published: June 2010

Abstract

Background
Transcription factor 7-like 2 (TCF7L2) has emerged as a consistently replicated susceptibility gene for type 2 diabetes, however, whether the TCF7L2 gene also has similar effects on the retinal microvasculature is less clear. We therefore aimed to investigate the association between the transcription factor 7-like 2 (TCF7L2) rs7903146 polymorphism and retinal microvascular phenotypes in the Atherosclerosis Risk in Communities (ARIC) Study (1993-1995).

Methods
This was a population-based, cross-sectional study of 10,320 middle-aged African American (n = 2,199) and Caucasian (n = 8,121) men and women selected from four United States communities to examine the association between TCF7L2 rs7903146 polymorphism and retinal microvascular signs (retinopathy, focal arteriolar narrowing, arteriovenous nicking, arteriolar and venular calibers). Photographs on one randomly selected eye were graded for presence of retinal microvascular signs and used to measure retinal vessel calibres.

Results
After adjusting for age, sex, study center, mean arterial blood pressure, total serum cholesterol, triglycerides, and other covariates, few associations of TCF7L2 rs7903146 and retinal microvascular signs were noted. TCF7L2 rs7903146 T risk allele was significantly associated with focal arteriolar narrowing in Caucasians with hypertension [odds ratio (OR)CT vs. CC (95% CI) = 1.25 (1.09-1.44); ORTT vs. CC = 1.56 (1.18-2.06); P = 0.002] and in Caucasians without diabetes [OR CT vs. CC = 1.18 (1.06-1.32); OR TT vs. CC = 1.40 (1.12, 1.75); P = 0.003]. No significant association of the TCF7L2 rs7903146 polymorphism and retinal vascular signs was noted among African American individuals.

Conclusions

TCF7L2 rs7903146 is not consistently associated with retinal microvascular signs. However, we report an association between the TCF7L2 rs7903146 polymorphism and focal arteriolar narrowing in Caucasians with hypertension or without diabetes. Further research in other large, population-based studies is needed to replicate these findings.
High cell density cultivation and recombinant protein production with Escherichia coli in a rocking-motion-type bioreactor
Authors: Glazyrina Julia , Materne Eva-Maria , Dreher Thomas , Storm Dirk , Junne Stefan , Adams Thorsten , Greller Gerhard , Neubauer Peter 
Published: June 2010

Abstract

Background
Single-use rocking-motion-type bag bioreactors provide advantages compared to standard stirred tank bioreactors by decreased contamination risks, reduction of cleaning and sterilization time, lower investment costs, and simple and cheaper validation. Currently, they are widely used for cell cultures although their use for small and medium scale production of recombinant proteins with microbial hosts might be very attractive. However, the utilization of rocking- or wave-induced motion-type bioreactors for fast growing aerobic microbes is limited because of their lower oxygen mass transfer rate. A conventional approach to reduce the oxygen demand of a culture is the fed-batch technology. New developments, such as the BIOSTAT® CultiBag RM system pave the way for applying advanced fed-batch control strategies also in rocking-motion-type bioreactors. Alternatively, internal substrate delivery systems such as EnBase® Flo provide an opportunity for adopting simple to use fed-batch-type strategies to shaken cultures. Here, we investigate the possibilities which both strategies offer in view of high cell density cultivation of E. coli and recombinant protein production.

Results
Cultivation of E. coli in the BIOSTAT® CultiBag RM system in a conventional batch mode without control yielded an optical density (OD600) of 3 to 4 which is comparable to shake flasks. The culture runs into oxygen limitation. In a glucose limited fed-batch culture with an exponential feed and oxygen pulsing, the culture grew fully aerobically to an OD600 of 60 (20 g L-1 cell dry weight). By the use of an internal controlled glucose delivery system, EnBase® Flo, OD600 of 30 (10 g L-1 cell dry weight) is obtained without the demand of computer controlled external nutrient supply. EnBase® Flo also worked well in the CultiBag RM system with a recombinant E. coli RB791 strain expressing a heterologous alcohol dehydrogenase (ADH) to very high levels, indicating that the enzyme based feed supply strategy functions well for recombinant protein production also in a rocking-motion-type bioreactor.

Conclusions
Rocking-motion-type bioreactors may provide an interesting alternative to standard cultivation in bioreactors for cultivation of bacteria and recombinant protein production. The BIOSTAT® Cultibag RM system with the single-use sensors and advanced control system paves the way for the fed-batch technology also to rocking-motion-type bioreactors. It is possible to reach cell densities which are far above shake flasks and typical for stirred tank reactors with the improved oxygen transfer rate. For more simple applications the EnBase® Flo method offers an easy and robust solution for rocking-motion-systems which do not have such advanced control possibilities.
Reptin is required for the transcription of telomerase reverse transcriptase and over-expressed in gastric cancer
Authors: Li Wenjuan , Zeng Jiping , Li Qiao , Zhao Li , Liu Tiantian , Björkholm Magnus , Jia Jihui , Xu Dawei 
Published: June 2010

Abstract

Background
Telomerase is activated in oncogenesis, which confers an immortal phenotype to cancer cells. The AAA + ATPase Reptin is required for telomerase biogenesis by maintaining telomerase RNA (hTER) stability and is aberrantly expressed in certain cancers. Given its role in chromatin remodeling and transcription regulation, we determined the effect of Reptin on the transcription of the telomerase reverse transcriptase (hTERT) gene, a key component of the telomerase complex and its expression in gastric cancer.

Results
Knocking down Reptin or its partner Pontin using small interfering RNA in gastric and cervical cancer cells led to significant decreases in hTERT mRNA, but hTERT promoter activity was inhibited in only Reptin-depleted cells. Reptin interacted with the c-MYC oncoprotein and its stimulatory effect on the hTERT promoter was significantly dependent on functional E-boxes in the promoter. Moreover, Reptin bound to the hTERT proximal promoter and the loss of the Reptin occupancy led to dissociation of c-MYC from the hTERT promoter in Reptin-depleted cells. Reptin inhibition dramatically impaired clonogenic potential of gastric cancer cells by inducing cell growtharrest and over-expression of Reptin was observed in primary gastric cancer specimens.

Conclusions
The hTERT gene is a direct target of Reptin, and hTERT transcription requires constitutive expression of Reptin and its cooperation with c-MYC. Thus, Reptin regulates telomerase at two different levels. This finding, together with the requirementof Reptin for the clonogenic potential of cancer cells and its over-expression in gastriccancer and other solid tumors, suggests that Reptin may be a putative therapeutic target.
Knock down of HIF-1α in glioma cells reduces migration in vitro and invasion in vivo and impairs their ability to form tumor spheres
Authors: Méndez Olga , Zavadil Jiri , Esencay Mine , Lukyanov Yevgeniy , Santovasi Daniel , Wang Shu-Chi , Newcomb Elizabeth W , Zagzag David 
Published: June 2010

Abstract

Background
Glioblastoma (GBM) is the most common and malignant primary intracranial human neoplasm. GBMs are characterized by the presence of extensive areas of necrosis and hypoxia. Hypoxia and its master regulator, hypoxia inducible factor 1 (HIF-1) play a key role in glioma invasion.

Results
To further elucidate the functional role of HIF-1α in glioma cell migration in vitro and in invasion in vivo, we used a shRNA approach to knock down HIF-1α expression complemented with genome-wide expression profiling, performed in both normoxic and hypoxic conditions. Our data show that knock down of HIF-1α in glioma cells significantly impairs their migration in vitro as well as their ability to invade into the brain parenchyma in vivo. Next, we assessed the role that HIF-1α plays in maintaining the characteristics of cancer stem cells (CSCs). By using the tumor sphere forming assay, we demonstrate that HIF-1α plays a role in the survival and self-renewal potential of CSCs. Finally, expression profiling experiments in glioma cells provided detailed insight into a broad range of specific biological pathways and processes downstream of HIF-1α. We discuss the role of these processes in the migratory and invasive properties, as well as the stem cell biology of glioblastomas

Conclusions
Our data show that knock down of HIF-1α in human and murine glioma cells impairs their migration in vitro and their invasion in vivo. In addition, our data suggest that HIF-1α plays a role in the survival and self-renewal potential of CSCs and identify genes that might further elucidate the role of HIF-1α in tumor migration, invasion and stem cell biology.
Measuring the neighborhood environment: associations with young girls' energy intake and expenditure in a cross-sectional study
Authors: Leung Cindy W , Gregorich Steven E , Laraia Barbara A , Kushi Lawrence H , Yen Irene H 
Published: June 2010

Abstract

Background
Neighborhood environments affect children's health outcomes. Observational methods used to assess neighborhoods can be categorized as indirect, intermediate, or direct. Direct methods, involving in-person audits of the neighborhoods conducted by trained observers, are recognized as an accurate representation of current neighborhood conditions. The authors investigated the associations of various neighborhood characteristics with young girls' diet and physical activity.

Methods
This study is based on a subset of participants in the Cohort Study of Young Girls' Nutrition, Environment and Transitions (CYGNET). In-person street audits were conducted within 215 girls' residential neighborhoods using a modified St. Louis Audit Tool. From the street audit data, exploratory factor analysis revealed five neighborhood scales: "mixed residential and commercial," "food and retail," "recreation," "walkability," and "physical disorder." A Neighborhood Deprivation Index was also derived from census data. The authors investigated if the five neighborhood scales and the Neighborhood Deprivation Index were associated with quartiles of total energy intake and expenditure (metabolic equivalent (MET) hours/week) at baseline, and whether any of these associations were modified by race/ethnicity.

Results
After adjustment for demographic characteristics, there was an inverse association between prevalence of "food and retail" destinations and total energy intake (for a one quartile increase, OR = 0.84, 95% CI 0.74, 0.96). Positive associations were also observed between the "recreation" and "walkability" scales with physical activity among Hispanic/Latina girls (for a one quartile increase in MET, OR = 1.94, 95% CI 1.31, 2.88 for recreation; OR = 1.71, 95% CI 1.11, 2.63 for walkability). Among African-American girls, there was an inverse association between "physical disorder" and physical activity (OR = 0.31, 95% CI 0.12, 0.80).

Conclusions
These results suggest that neighborhood food and retail availability may be inversely associated with young girls' energy intakes in contrast to other studies' findings that focused on adults. There is considerable variation in neighborhoods' influences on young girls' physical activity behaviors, particularly for young girls of different racial/ethnic backgrounds.
5th International AIDS Society Conference on HIV Pathogenesis, Treatment and Prevention: summary of key research and implications for policy and practice – Basic sciences
Authors: Mascolinli Mark , Kort Rodney 
Published: June 2010

Basic science studies at the 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention (IAS 2009) provided important new information that has implications not only for treatment, but also for better understanding the complex dynamics of HIV infection, epidemiology, and the impact of biology and genetics on vulnerability to HIV infection, disease progression and the risk of vertical transmission. There was renewed interest in strategies on how to eliminate residual viremia, bolster the immune system and potentially achieve viral eradication given recent evidence that antiretroviral therapy (ART) is effective at minimizing viral reservoirs if administered early in acute infection.19‐22 July 2009, 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention (IAS 2009), Cape Town, South Africa
5th International AIDS Society Conference on HIV Pathogenesis, Treatment and Prevention: summary of key research and implications for policy and practice – Clinical sciences
Authors: Mascolinli Mark , Kort Rodney 
Published: June 2010

Studies in several sub‐Saharan African countries demonstrated that the expansion of antiretroviral therapy (ART) access is not only beneficial for people living with HIV, but also results in significant declines in tuberculosis and malaria incidence and prevalence, bolstering arguments for earlier and increased ART access and contributing to a growing understanding of co‐epidemic dynamics. Several studies demonstrated that using standard triple‐drug ART in resource‐limited settings can reduce vertical transmission by as much as less than 1% if continued throughout breastfeeding.The Nevirapine Resistance Study (NEVEREST) results provided proof of concept that nevirapine could be used as part of a paediatric second‐line regimen, despite exposure to nevirapine prophylaxis for vertical transmission, following successful suppression on a lopinavir/ritonavir‐based regimen. A South African study found that high pre‐treatment levels of inflammatory and coagulation markers were strong predictors of death, reflecting similar findings in high‐income countries and reinforcing the shift towards viewing HIV as a chronic, inflammatory disease. An early study of a new integrase inhibitor (S/GSK1349572) indicated strong potency and limited cross‐resistance with raltegravir, the only integrase inhibitor currently approved for treatment.19‐22 July 2009, 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention (IAS 2009), Cape Town, South Africa
Bedside measurement of changes in lung impedance to monitor alveolar ventilation in dependent and non-dependent parts by electrical impedance tomography during a positive end-expiratory pressure trial in mechanically ventilated intensive care unit patients
Authors: Bikker Ido G , Leonhardt Steffen , Reis Miranda Dinis , Bakker Jan , Gommers Diederik 
Published: June 2010

Abstract
Introduction
As it becomes clear that mechanical ventilation can exaggerate lung injury, individual titration of ventilator settings is of special interest. Electrical impedance tomography (EIT) has been proposed as a bedside, regional monitoring tool to guide these settings. In the present study we evaluate the use of ventilation distribution change maps (ΔfEIT maps) in intensive care unit (ICU) patients with or without lung disorders during a standardized decremental positive end-expiratory pressure (PEEP) trial.

Methods
Functional EIT (fEIT) images and PaO2/FiO2 ratios were obtained at four PEEP levels (15 to 10 to 5 to 0 cm H2O) in 14 ICU patients with or without lung disorders. Patients were pressure-controlled ventilated with constant driving pressure. fEIT images made before each reduction in PEEP were subtracted from those recorded after each PEEP step to evaluate regional increase/decrease in tidal impedance in each EIT pixel (ΔfEIT maps).

Results
The response of regional tidal impedance to PEEP showed a significant difference from 15 to 10 (P = 0.002) and from 10 to 5 (P = 0.001) between patients with and without lung disorders. Tidal impedance increased only in the non-dependent parts in patients without lung disorders after decreasing PEEP from 15 to 10 cm H2O, whereas it decreased at the other PEEP steps in both groups.

Conclusions
During a decremental PEEP trial in ICU patients, EIT measurements performed just above the diaphragm clearly visualize improvement and loss of ventilation in dependent and non-dependent parts, at the bedside in the individual patient.