bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide recruitment to Polycomb-modified chromatin and activity regulation of the synovial sarcoma oncogene SYT-SSX2
Authors: Garcia Christina B , Shaffer Christian M , Eid Josiane E 
Published: May 2012

AbstractBackgroundSYT-SSX is the oncogene associated with synovial sarcoma (SS), a stem cell disease. SYT-SSX is thought to be responsible for sarcoma initiation and development. It interacts with components of Polycomb and SWI/SNF complexes, the two epigenetic controllers that maintain the heritable status of differentiation-specific genes in the stem/progenitor cell. Through these associations SYT-SSX is thought to alter gene expression programs by epigenetic mechanisms. Recently, we reported that SYT-SSX2 reprograms mesenchymal stem cells and myoblasts by dictating their commitment to the neural lineage while disrupting their normal differentiation. This reprogramming was due to the direct occupancy of proneural genes by the SYT-SSX2 nuclear complex. To gain a clear understanding of SYT-SSX2 control of gene expression networks, we conducted a thorough genome-wide analysis to determine the mechanism of its recruitment and identify signature sets of epigenetic markers that would predict its targeting and transcriptional activity.ResultsSYT-SSX2 was recruited to distinct loci across all chromosomes, and an overwhelming number of Polycomb-modified sites enriched with the trimethylated histone H3 on lysine 27 (H3K27me3) formed the main recruiting module for SYT-SSX2. Not all SYT-SSX2/H3K27me3-occupied genes had altered expression, denoting the requirement for additional signals upon oncogene binding. Differential binding and epigenetic patterns distinguished upregulated and downregulated genes. Most activated genes had SYT-SSX2 sites enriched with H3K27me3 within their body or near their transcription start site (TSS) whereas a majority of downregulated genes were characterized by SYT-SSX2/H3K27me3-rich regions at long-range, or by modifications associated with transcription activation within the gene body or near the TSS. Hierarchical and functional clustering identified H3K27me3 as the dominant epigenetic marker associated with SYT-SSX2 binding and gene expression. Notably, this analysis revealed a cluster of upregulated neuronal genes densely covered by H3K27me3, consistent with programming toward the neural lineage by SYT-SSX2 observed previously.ConclusionsThe data analysis revealed that Polycomb complexes or their modified chromatin and their stably silenced differentiation programs seem to be the main target for SYT-SSX2, suggesting that their perturbation is at the center of tumorigenesis driven by the oncogene. Further research into this mechanism is crucial to the full understanding of SS biology.
Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks
Authors: Ray Monika , Yunis Reem , Chen Xiucui , Rocke David M 
Published: May 2012

Abstract

Background
The growing use of imaging procedures in medicine has raised concerns about exposure to low-dose ionising radiation (LDIR). While the disastrous effects of high dose ionising radiation (HDIR) is well documented, the detrimental effects of LDIR is not well understood and has been a topic of much debate. Since little is known about the effects of LDIR, various kinds of wet-lab and computational analyses are required to advance knowledge in this domain. In this paper we carry out an “upside-down pyramid” form of systems biology analysis of microarray data. We characterised the global genomic response following 10 cGy (low dose) and 100 cGy (high dose) doses of X-ray ionising radiation at four time points by analysing the topology of gene coexpression networks. This study includes a rich experimental design and state-of-the-art computational systems biology methods of analysis to study the differences in the transcriptional response of skin cells exposed to low and high doses of radiation.

Results
Using this method we found important genes that have been linked to immune response, cell survival and apoptosis. Furthermore, we also were able to identify genes such as BRCA1, ABCA1, TNFRSF1B, MLLT11 that have been associated with various types of cancers. We were also able to detect many genes known to be associated with various medical conditions.

Conclusions
Our method of applying network topological differences can aid in identifying the differences among similar (eg: radiation effect) yet very different biological conditions (eg: different dose and time) to generate testable hypotheses. This is the first study where a network level analysis was performed across two different radiation doses at various time points, thereby illustrating changes in the cellular response over time.
Quantitative analysis of organelle distribution and dynamics in Physcomitrella patens protonemal cells
Authors: Furt Fabienne , Lemoi Kyle , Tüzel Erkan , Vidali Luis 
Published: May 2012

Abstract

Background
In the last decade, the moss Physcomitrella patens has emerged as a powerful plant model system, amenable for genetic manipulations not possible in any other plant. This moss is particularly well suited for plant polarized cell growth studies, as in its protonemal phase, expansion is restricted to the tip of its cells. Based on pollen tube and root hair studies, it is well known that tip growth requires active secretion and high polarization of the cellular components. However, such information is still missing in Physcomitrella patens. To gain insight into the mechanisms underlying the participation of organelle organization in tip growth, it is essential to determine the distribution and the dynamics of the organelles in moss cells.

Results
We used fluorescent protein fusions to visualize and track Golgi dictyosomes, mitochondria, and peroxisomes in live protonemal cells. We also visualized and tracked chloroplasts based on chlorophyll auto-fluorescence. We showed that in protonemata all four organelles are distributed in a gradient from the tip of the apical cell to the base of the sub-apical cell. For example, the density of Golgi dictyosomes is 4.7 and 3.4 times higher at the tip than at the base in caulonemata and chloronemata respectively. While Golgi stacks are concentrated at the extreme tip of the caulonemata, chloroplasts and peroxisomes are totally excluded. Interestingly, caulonemata, which grow faster than chloronemata, also contain significantly more Golgi dictyosomes and fewer chloroplasts than chloronemata. Moreover, the motility analysis revealed that organelles in protonemata move with low persistency and average instantaneous speeds ranging from 29 to 75 nm/s, which are at least three orders of magnitude slower than those of pollen tube or root hair organelles.

Conclusions
To our knowledge, this study reports the first quantitative analysis of organelles in Physcomitrella patens and will make possible comparisons of the distribution and dynamics of organelles from different tip growing plant cells, thus enhancing our understanding of the mechanisms of plant polarized cell growth.
Absence of Helicobacter pylori high tetracycline resistant 16S rDNA AGA926-928TTC genotype in gastric biopsy specimens from dyspeptic patients of a city in the interior of São Paulo, Brazil
Authors: Suzuki Rodrigo Buzinaro , Almeida Cristiane Maria , Sperança Márcia Aparecida 
Published: May 2012

Abstract

Background
Treatment effectiveness of Helicobacter pylori varies regionally and is decreasing worldwide, principally as a result of antibiotic resistant bacterium. Tetracycline is generally included in second line H. pylori eradication regimens. In Brazil, a high level of tetracycline resistance (TetR) is mainly associated with AGA926-928TTC 16 S rDNA nucleotide substitutions. As H. pylori culture is fastidious, we investigated the primary occurrence of H. pylori 16 S rDNA high level TetR genotype using a molecular approach directly on gastric biopsies of dyspeptic patients attending consecutively at Hospital das Clinicas of Marilia, São Paulo, Brazil.

Methods
Gastric biopsy specimens of 68 peptic ulcer disease (PUD) and 327 chronic gastritis (CG) patients with a positive histological diagnosis of H. pylori were investigated for TetR 16 S rDNA genotype through a molecular assay based on amplification of a 16 S rDNA 545 bp fragment by polymerase chain reaction and HinfI restriction fragment length polymorphism (PCR/RFLP). Through this assay, AGA926-928TTC 16 S rDNA TetR genotype resulted in a three DNA fragment restriction pattern (281, 227 and 37 bp) and its absence originated two DNA fragments (264 and 281 bp) due to a 16 S rDNA conserved Hinf I restriction site.

Results
The 545 bp 16 S rDNA PCR fragment was amplified from 90% of gastric biopsies from histological H. pylori positive patients. HinfI RFLP revealed absence of the AGA926–928TTC H. pylori genotype and PCR products of two patients showed absence of the conserved 16 S rDNA HinfI restriction site. BLASTN sequence analysis of four amplicons (two conserved and two with an unpredicted HinfI restriction pattern) revealed a 99% homology to H. pylori 16 S rDNA from African, North and South American bacterial isolates. A nucleotide substitution abolished the conserved HinfI restriction site in the two PCR fragments with unpredicted HinfI RFLP, resulting in an EcoRI restriction site.

Conclusions

H. pylori AGA926-928TTC 16 S rDNA gene substitutions were not found in our population. More research is required to investigate if H. pylori TetR has a different genetic background in our region and if the nucleotide substitutions of the uncultured H. pylori 16 S rRNA partial sequences have biological significance.
Evaluation of a hand-held far-ultraviolet radiation device for decontamination of Clostridium difficile and other healthcare-associated pathogens
Authors: Nerandzic Michelle M , Cadnum Jennifer L , Eckart Kevin E , Donskey Curtis J 
Published: May 2012

Abstract

Background
Environmental surfaces play an important role in transmission of healthcare-associated pathogens. There is a need for new disinfection methods that are effective against Clostridium difficile spores, but also safe and rapid. The Sterilray™ Disinfection Wand device is a hand-held room decontamination technology that utilizes far-ultraviolet radiation (185-230 nm) to kill pathogens.

Methods
We examined the efficacy of disinfection using the Sterilray device in the laboratory, in rooms of hospitalized patients, and on surfaces outside of patient rooms (i.e. keyboards and portable medical equipment). Cultures for C. difficile, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE) were collected from commonly-touched surfaces before and after use of the Sterilray device.

Results
On inoculated surfaces in the laboratory, application of the Sterilray device at a radiant dose of 100 mJ/cm2 for ~ 5 seconds consistently reduced recovery of C. difficile spores by 4.4 CFU log10, MRSA by 5.4 log10CFU and of VRE by 6.9 log10CFU. A >3 log10 reduction of MRSA and VRE was achieved in ~2 seconds at a lower radiant dose, but killing of C. difficile spores was significantly reduced. On keyboards and portable medical equipment that were inoculated with C. difficile spores, application of the Sterilray device at a radiant dose of 100 mJ/cm2 for ~ 5 seconds reduced contamination by 3.2 log10CFU. However, the presence of organic material reduced the lethal effect of the far-UV radiation. In hospital rooms that were not pre-cleaned, disinfection with the Sterilray device significantly reduced the frequency of positive C. difficile and MRSA cultures (P =0.007).

Conclusions
The Sterilray™ Disinfection Wand is a novel environmental disinfection technology that rapidly kills C. difficile spores and other healthcare-associated pathogens on surfaces. However, the presence of organic matter reduces the efficacy of far-UV radiation, possibly explaining the more modest results observed on surfaces in hospital rooms that were not pre-cleaned.
Ethics, patient rights and staff attitudes in Shanghai's psychiatric hospitals
Authors: Su Liang , Huang Jingjing , Yang Weimin , Li Huafang , Shen Yifeng , Xu Yifeng 
Published: May 2012

Abstract

Background
Adherence to ethical principles in clinical research and practice is becoming topical issue in China, where the prevalence of mental illness is rising, but treatment facilities remain underdeveloped. This paper reports on a study aiming to understand the ethical knowledge and attitudes of Chinese mental health professionals in relation to the process of diagnosis and treatment, informed consent, and privacy protection in clinical trials.

Methods
A self-administered survey was completed by 1110 medical staff recruited from Shanghai’s 22 psychiatric hospitals. Simple random selection methods were used to identify target individuals from the computerized registry of staff.

Results
The final sample for analysis consisted 1094 medical staff (including 523 doctors, 542 nurses, 8 pharmacologists and 21 other staff). The majority reported that their medical institutions had not established an Ethics Committee (87.8%) and agreed that Ethics Committees should be set up in their institutions (72.9%). Approximately half (52%) had not received systematic education in ethics, and almost all (89.1%) of the staff thought it was necessary. Nearly all participants (90.0%) knew the Shanghai Mental Health Regulations which was the first local regulations relating to mental health in China, but only 11% and 16.6% respectively knew of the Nuremberg Code and the Declaration of Helsinki. About half (51.8%) thought that the guardian should make the decision as to whether the patient participated in clinical trials or not.

Conclusions
The study indicates that most psychiatric hospitals in Shanghai have no Medical Ethics Committee. More than half the medical staff had not received systematic education and training in medical ethics and they have insufficient knowledge of the ethical issues related to clinical practice and trials. Training in ethics is recommended for medical staff during their training and as ongoing professional development.
Comparative effect of angiotensin II type I receptor blockers and calcium channel blockers on laboratory parameters in hypertensive patients with type 2 diabetes
Authors: Nishida Yayoi , Takahashi Yasuo , Nakayama Tomohiro , Asai Satoshi 
Published: May 2012

Abstract

Background
Both angiotensin II type I receptor blockers (ARBs) and calcium channel blockers (CCBs) are widely used antihypertensive drugs. Many clinical studies have demonstrated and compared the organ-protection effects and adverse events of these drugs. However, few large-scale studies have focused on the effect of these drugs as monotherapy on laboratory parameters. We evaluated and compared the effects of ARB and CCB monotherapy on clinical laboratory parameters in patients with concomitant hypertension and type 2 diabetes mellitus.

Methods
We used data from the Clinical Data Warehouse of Nihon University School of Medicine obtained between Nov 1, 2004 and July 31, 2011, to identify cohorts of new ARB users (n = 601) and propensity-score matched new CCB users (n = 601), with concomitant mild to moderate hypertension and type 2 diabetes mellitus. We used a multivariate-adjusted regression model to adjust for differences between ARB and CCB users, and compared laboratory parameters including serum levels of triglyceride (TG), total cholesterol (TC), non-fasting blood glucose, hemoglobin A1c (HbA1c), sodium, potassium, creatinine, alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyltransferase (GGT), hemoglobin and hematocrit, and white blood cell (WBC), red blood cell (RBC) and platelet (PLT) counts up to 12 months after the start of ARB or CCB monotherapy.

Results
We found a significant reduction of serum TC, HbA1c, hemoglobin and hematocrit and RBC count and a significant increase of serum potassium in ARB users, and a reduction of serum TC and hemoglobin in CCB users, from the baseline period to the exposure period. The reductions of RBC count, hemoglobin and hematocrit in ARB users were significantly greater than those in CCB users. The increase of serum potassium in ARB users was significantly greater than that in CCB users.

Conclusions
Our study suggested that hematological adverse effects and electrolyte imbalance are greater with ARB monotherapy than with CCB monotherapy.
Transcript and protein expression profile of PF11_0394, a Plasmodium falciparum protein expressed in salivary gland sporozoites
Authors: Schlarman Maggie S , Roberts Renee N , Kariuki Michael M , LaCrue Alexis N , Ou Ruguang , Beerntsen Brenda T 
Published: May 2012

Abstract

Background

Plasmodium falciparum malaria is a significant problem around the world today, thus there is still a need for new control methods to be developed. Because the sporozoite displays dual infectivity for both the mosquito salivary glands and vertebrate host tissue, it is a good target for vaccine development.

Methods
The P. falciparum gene, PF11_0394, was chosen as a candidate for study due to its potential role in the invasion of host tissues. This gene, which was selected using a data mining approach from PlasmoDB, is expressed both at the transcriptional and protein levels in sporozoites and likely encodes a putative surface protein. Using reverse transcription-polymerase chain reaction (RT-PCR) and green fluorescent protein (GFP)-trafficking studies, a transcript and protein expression profile of PF11_0394 was determined.

Results
The PF11_0394 protein has orthologs in other Plasmodium species and Apicomplexans, but none outside of the group Apicomplexa. PF11_0394 transcript was found to be present during both the sporozoite and erythrocytic stages of the parasite life cycle, but no transcript was detected during axenic exoerythrocytic stages. Despite the presence of transcript throughout several life cycle stages, the PF11_0394 protein was only detected in salivary gland sporozoites.

Conclusions
PF11_0394 appears to be a protein uniquely detected in salivary gland sporozoites. Even though a specific function of PF11_0394 has not been determined in P. falciparum biology, it could be another candidate for a new vaccine.
A new approach for cytokinin isolation from Arabidopsis tissues using miniaturized purification: pipette tip solid-phase extraction
Authors: Svačinová Jana , Novák Ondřej , Plačková Lenka , Lenobel René , Holík Josef , Strnad Miroslav , Doležal Karel 
Published: May 2012

Abstract

Background
We have developed a new analytical approach for isolation and quantification of cytokinins (CK) in minute amounts of fresh plant material, which combines a simple one-step purification with ultra-high performance liquid chromatography–fast scanning tandem mass spectrometry.

Results
Plant tissue samples (1–5 mg FW) were purified by stop-and-go-microextraction (StageTip purification), which previously has only been applied for clean-up and pre-concentration of peptides. We found that a combination of two reverse phases and one cation-exchange phase, was the best tool, giving a total extraction recovery higher than 80%. The process was completed by a single chromatographic analysis of a wide range of naturally occurring cytokinins (bases, ribosides, O- and N-glucosides, and nucleotides) in 24.5 minutes using an analytical column packed with sub-2-microne particles. In multiple reaction monitoring mode, the detection limits ranged from 0.05 to 5 fmol and the linear ranges for most cytokinins were at least five orders of magnitude. The StageTip purification was validated and optimized using samples of Arabidopsis thaliana seedlings, roots and shoots where eighteen cytokinins were successfully determined.

Conclusions
The combination of microextraction with one-step high-throughput purification provides fast, effective and cheap sample preparation prior to qualitative and quantitative measurements. Our procedure can be used after modification also for other phytohormones, depending on selectivity, affinity and capacity of the selected sorbents.
Novel therapeutic agents for cutaneous T-Cell lymphoma
Authors: Jain Salvia , Zain Jasmine , O’Connor Owen 
Published: May 2012

Abstract
Mycosis fungoides (MF) and Sezary Syndrome (SS) represent the most common subtypes of primary Cutaneous T-cell lymphoma (CTCL). Patients with advanced MF and SS have a poor prognosis leading to an interest in the development of new therapies with targeted mechanisms of action and acceptable safety profiles. In this review we focus on such novel strategies that have changed the treatment paradigm of this rare malignancy.
The effect of health education intervention on the home management of malaria among the caregivers of children aged under 5 years in Ogun State, Nigeria
Authors: Fatungase Kehinde O , Amoran Olorunfemi E , Alausa Kabir O 
Published: May 2012

Abstract

Background
Malaria is currently the most important cause of death and disability in children aged under 5 years in Africa. A health education interventional study of this nature is essential in primary control of an endemic communicable disease such as malaria. This study was therefore designed to determine the effect of health education on the home management of Malaria among the caregivers of children under 5 years old in Ogun State, Nigeria.

Methods
The study design was a quasi-experimental study carried out in Ijebu North Local Government Area of Ogun State. A multistage random sampling technique was used in choosing the required samples for this study and a semi-structured questionnaire was used to collect relevant information. The intervention consisted of a structured educational program based on a course content adapted from the national malaria control program. A total of 400 respondents were recruited into the study, with 200 each in both the experimental and control groups, and were followed up for a period of 3 months when the knowledge and uptake of insecticide treated net was reassessed.

Results
There was no statistically significant differences observed between the experimental and control groups in terms of sociodemographic characteristics such as age (P = 0.99), marital status (P = 0.48), religion (P = 0.1), and income (P = 0.51). The majority in both the experimental (75.0%) and control (71.5%) groups use arthemisinin-based combination therapy as first line home treatment drugs pre intervention. Post health education intervention, the degree of change in the knowledge of referral signs and symptoms in the experimental group was 52.8% (P < 0.0001) while it was 0.2% in the control group (P = 0.93). Tepid sponging improved by 45.0%, paracetamol use by 55.3%, and the use of herbs and other drugs were not significantly influenced in the experimental (P = 0.65 and 0.99) and control group (P = 0.89 and 0.88), respectively. Furthermore, there was a 55.7% (P = 0.001) increase in the proportion of respondents using the correct dose of arthemisinin-based combination therapy in the home management of malaria and 23.9% (P < 0.001) in the proportion using it for the required time.

Conclusions
The study concludes that there is a shift in the home management of malaria with the use of current and effective antimalarial drugs. It also demonstrated the effect of health education on the promptness of appropriate actions taken among the respondents for early diagnosis and treatment. Early diagnosis and appropriate treatment can be guaranteed if caregivers are knowledgeable on prompt actions to be taken in the home management of malaria.