bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple testing for gene sets from microarray experiments
Authors: Sohn Insuk , Owzar Kouros , Lim Johan , George Stephen L , Mackey Cushman Stephanie , Jung Sin-Ho 
Published: May 2011

Abstract

Background
A key objective in many microarray association studies is the identification of individual genes associated with clinical outcome. It is often of additional interest to identify sets of genes, known a priori to have similar biologic function, associated with the outcome.

Results
In this paper, we propose a general permutation-based framework for gene set testing that controls the false discovery rate (FDR) while accounting for the dependency among the genes within and across each gene set. The application of the proposed method is demonstrated using three public microarray data sets. The performance of our proposed method is contrasted to two other existing Gene Set Enrichment Analysis (GSEA) and Gene Set Analysis (GSA) methods.

Conclusions
Our simulations show that the proposed method controls the FDR at the desired level. Through simulations and case studies, we observe that our method performs better than GSEA and GSA, especially when the number of prognostic gene sets is large.
Fasting plasma glucose is an independent predictor for severity of H1N1 pneumonia
Authors: Wang Wei , Chen Hong , Li Qiang , Qiu Bo , Wang Jiajun , Sun Xiwen , Xiang Ying , Zhang Jinchao 
Published: May 2011

Abstract

Background
The pandemic influenza A (H1N1) virus emerged during 2009 and has spread worldwide. This virus can cause injuries to the lungs, liver, and heart. However, data regarding whether this influenza virus can affect pancreatic islets are limited. We investigated the effects of influenza A (H1N1) pneumonia on fasting plasma glucose (FPG) and islet function, and evaluated possible correlations between biochemical test results and the severity of H1N1 pneumonia.

Methods
We performed a retrospective analysis of patients either diagnosed with or suspected of having H1N1 pneumonia who were admitted to our hospital in 2009. Possible associations between FPG levels and H1N1 virus infection were assessed by logistic regression. Correlation and regression analyses were used to assess relationships between FPG and biochemical test results. Associations between admission days and significant data were assessed by single factor linear regression. To evaluate effects of H1N1 on pancreatic β-cell function, results of a resistance index (homa-IR), insulin function index (homa-β), and insulin sensitivity index (IAI) were compared between a H1N1 group and a non-H1N1 group by t-tests.

Results
FPG was significantly positively associated with H1N1 virus infection (OR = 1.377, 95%CI: 1.062-1.786; p = 0.016). FPG was significantly correlated with AST (r = 0.215; p = 0.039), LDH (r = 0.400; p = 0.000), BUN (r = 0.28; p = 0.005), and arterial Oxygen Saturation (SaO2; r = -0.416; p = 0.000) in the H1N1 group. H1N1 patients who were hypoxemic (SaO2<93%) had higher FPG levels than those who were not hypoxic (9.82 ± 4.14 vs. 6.64 ± 1.78; p < 0.05). FPG was negatively correlated with SaO2 in the H1N1 group with hypoxia (SaO2<93; r = -0.497; p = 0.041). SaO2 levels in patients with high FPG levels (≥7 mmol/L) were significantly lower than those of H1N1 patients with low FPG levels (<5.6 mmol/L). There were no significant differences in homa-IR, homa-β, or IAI between the H1N1 and non-H1N1 groups after adjusting for age, sex, and BMI.

Conclusions
FPG on admission could be an independent predictor for the severity of H1N1 pneumonia. Elevated FPG induced by H1N1 pneumonia is not a result of direct damage to pancreatic β-cells, but arises from various factors' combinations caused by H1N1 virus infection.
Low penetrance of retinoblastoma for p.V654L mutation of the RB1 gene
Authors: Hung Chia-Cheng , Lin Shin-Yu , Lee Chien-Nan , Chen Chih-Ping , Lin Shuan-Pei , Chao Mei-Chyn , Chiou Shyh-Shin , Su Yi-Ning 
Published: May 2011

Abstract

Background
Retinoblastoma is caused by compound heterozygosity or homozygosity of retinoblastoma gene (RB1) mutations. In germline retinoblastoma, mutations in the RB1 gene predispose individuals to increased cancer risks during development. These mutations segregate as autosomal dominant traits with high penetrance (90%).

Methods
We screened 30 family members from one family using high resolution melting assay and DNA direct sequencing for mutations in the RB1 gene. We evaluate the phenotype and penetrance of germline mutations of the RB1 gene in a large Taiwanese family.

Results
The molecular analysis and clinical details of this family showed phenotypic variability associated with the p.V654L mutation in exon 19 of the RB1 gene in 11 family members. The phenotype varied from asymptomatic to presence of a unilateral tumor. Only four individuals (2 males and 2 females) developed unilateral retinoblastoma, which resulted in calculated low penetrance of 36% (4/11). The four individuals with retinoblastoma were diagnosed before the age of three years. None of their relatives exhibited variable severity or bilateral retinoblastoma.

Conclusions
The diseased-eye ratio for this family was 0.36, which is lower than current estimates. This suggests that the RB1 p.V654L mutation is a typical mutation associated with low penetrance.
Systemic chemotherapy for treatment of advanced small bowel adenocarcinoma with prognostic factor analysis: retrospective study
Authors: Koo Dong Hoe , Yun Sung-Cheol , Hong Yong Sang , Ryu Min-Hee , Lee Jae-Lyun , Chang Heung-Moon , Ryoo Baek-Yeol , Kang Yoon-Koo , Kim Tae Won 
Published: May 2011

Abstract

Background
We sought to evaluate prognostic factors affecting overall survival (OS), and to investigate the role of palliative chemotherapy using propensity score-based weighting, in patients with advanced small bowel adenocarcinoma (SBA).

Methods
Data from a total of 91 patients diagnosed with advanced SBA at the Asan Medical Center between January 1989 and December 2009 were retrospectively analyzed. Patients were split into two groups, those who did and did not receive palliative chemotherapy.

Results
Overall, 81 patients (89.0%) died, at a median survival time of 6.6 months (95% confidence interval [CI], 5.5 - 7.5 months). The 40 patients receiving chemotherapy showed overall response and disease control rates of 11.1% and 37.0%, respectively, with OS and progression-free survival (PFS) of 11.8 months (95% CI, 4.6 - 19.0 months) and 5.7 months (95% CI, 3.5 - 8.0 months), respectively. The 41 patients who did not receive chemotherapy had an OS of 4.1 months (95% CI, 3.1 - 5.1 months) and a PFS of 1.3 months (95% CI, 0.8 - 1.7 months). Multivariate analysis showed that lack of tumor resection, non-prescription of chemotherapy, liver metastasis, and intra-abdominal lymph node metastasis, were all independently associated with poor survival outcomes. After inverse probability of treatment weighting (IPTW) adjustment, the group that did not receive chemotherapy was at a significantly higher risk of mortality (HR 3.44, 95% CI 2.03 - 5.83, p < 0.001) than were patients receiving chemotherapy.

Conclusion
Palliative chemotherapy may improve survival outcomes in patients with advanced SBA.
Cement leakage causes potential thermal injury in vertebroplasty
Authors: Lai Po-Liang , Tai Ching-Lung , Chen Lih-Huei , Nien Nai-Yuan 
Published: May 2011

AbstractBackgroundPercutaneous vertebroplasty by injecting PMMA bone cement into the fractured vertebrae has been widely accepted in treatment of spinal compression fracture. However, the exothermic polymerization of bone cement may cause osseous or neural tissue injury. This study is thus designed to evaluate the potential risk of thermal damage in percutaneous vertebroplasty.MethodTwelve porcine vertebrae were immersed in 37°C saline for the experiment. In the first stage of the study, vertebroplasty without cement leakage (control group, n = 6) was simulated. The anterior cortex, foramen, posterior cortex and the center of the vertebral body were selected for temperature measurement. Parameters including peak temperature and duration above 45°C were recorded. In the second stage, a model (n = 6) simulating bone cement leaking into the spinal canal was designed. The methods for temperature measurement were identical to those used in the first stage.ResultsIn Stage 1 of the study (vertebroplasty of the porcine vertebral body in the absence of cement leakage), the average maximal temperature at the anterior cortex was 42.4 ± 2.2°C; at the neural foramen 39.5 ± 2.1°C; at the posterior cortex 40.0 ± 2.5°C and at the vertebral center, 68.1 ± 3.4°C. The average time interval above 45°C was 0 seconds at the anterior cortex; at the neural foramen, 0 seconds; at the posterior cortex, 0 seconds and at the vertebral center, 223 seconds. Thus, except at the core of the bone cement, temperatures around the vertebral body did not exceed 45°C. In Stage 2 of the study (cement leakage model), the average maximal temperature at the anterior cortex was 42.7 ± 2.4°C; at the neural foramen, 41.1 ± 0.4°C; at the posterior cortex, 59.1 ± 7.6°C and at the vertebral center, 77.3 ± 5.7°C. The average time interval above 45°C at the anterior cortex was 0 seconds; at the neural foramen, 0 seconds; at the posterior cortex, 329.3 seconds and at the vertebral center, 393.2 seconds. Based on these results, temperatures exceeded 45°C at the posterior cortex and at the vertebral center.ConclusionsThe results indicated that, for bone cement confined within the vertebra, curing temperatures do not directly cause thermal injury to the nearby soft tissue. If bone cement leaks into the spinal canal, the exothermic reaction at the posterior cortex might result in thermal injury to the neural tissue.
1,2-propanediol-trehalose mixture as a potent quantitative real-time PCR enhancer
Authors: Horáková Helena , Polakovičová Iva , Shaik Gouse M , Eitler Jiří , Bugajev Viktor , Dráberová Lubica , Dráber Petr 
Published: May 2011

Abstract

Background
Quantitative real-time PCR (qPCR) is becoming increasingly important for DNA genotyping and gene expression analysis. For continuous monitoring of the production of PCR amplicons DNA-intercalating dyes are widely used. Recently, we have introduced a new qPCR mix which showed improved amplification of medium-size genomic DNA fragments in the presence of DNA dye SYBR green I (SGI). In this study we tested whether the new PCR mix is also suitable for other DNA dyes used for qPCR and whether it can be applied for amplification of DNA fragments which are difficult to amplify.

Results
We found that several DNA dyes (SGI, SYTO-9, SYTO-13, SYTO-82, EvaGreen, LCGreen or ResoLight) exhibited optimum qPCR performance in buffers of different salt composition. Fidelity assays demonstrated that the observed differences were not caused by changes in Taq DNA polymerase induced mutation frequencies in PCR mixes of different salt composition or containing different DNA dyes. In search for a PCR mix compatible with all the DNA dyes, and suitable for efficient amplification of difficult-to-amplify DNA templates, such as those in whole blood, of medium size and/or GC-rich, we found excellent performance of a PCR mix supplemented with 1 M 1,2-propanediol and 0.2 M trehalose (PT enhancer). These two additives together decreased DNA melting temperature and efficiently neutralized PCR inhibitors present in blood samples. They also made possible more efficient amplification of GC-rich templates than betaine and other previously described additives. Furthermore, amplification in the presence of PT enhancer increased the robustness and performance of routinely used qPCRs with short amplicons.

Conclusions
The combined data indicate that PCR mixes supplemented with PT enhancer are suitable for DNA amplification in the presence of various DNA dyes and for a variety of templates which otherwise can be amplified with difficulty.
Development of a context model to prioritize drug safety alerts in CPOE systems
Authors: Riedmann Daniel , Jung Martin , Hackl Werner O , Stühlinger Wolf , van der Sijs Heleen , Ammenwerth Elske 
Published: May 2011

Abstract

Background
Computerized physician order entry systems (CPOE) can reduce the number of medication errors and adverse drug events (ADEs) in healthcare institutions. Unfortunately, they tend to produce a large number of partly irrelevant alerts, in turn leading to alert overload and causing alert fatigue. The objective of this work is to identify factors that can be used to prioritize and present alerts depending on the 'context' of a clinical situation.

Methods
We used a combination of literature searches and expert interviews to identify and validate the possible context factors. The internal validation of the context factors was performed by calculating the inter-rater agreement of two researcher's classification of 33 relevant articles.

Results
We developed a context model containing 20 factors. We grouped these context factors into three categories: characteristics of the patient or case (e.g. clinical status of the patient); characteristics of the organizational unit or user (e.g. professional experience of the user); and alert characteristics (e.g. severity of the effect). The internal validation resulted in nearly perfect agreement (Cohen's Kappa value of 0.97).

Conclusion
To our knowledge, this is the first structured attempt to develop a comprehensive context model for prioritizing drug safety alerts in CPOE systems. The outcome of this work can be used to develop future tailored drug safety alerting in CPOE systems.
Function modification of SR-PSOX by point mutations of basic amino acids
Authors: Liu Weiwei , Yin Lan , Chen Chunxia , Dai Yalei 
Published: May 2011

Abstract

Background
Atherosclerosis (AS) is a common cardiovascular disease. Transformation of macrophages to form foam cells by internalizing modified low density-lipoprotein (LDL) via scavenger receptor (SR) is a key pathogenic process in the onset of AS. It has been demonstrated that SR-PSOX functions as either a scavenger receptor for uptake of atherogenic lipoproteins and bacteria or a membrane-anchored chemokine for adhesion of macrophages and T-cells to the endothelium. Therefore, SR-PSOX plays an important role in the development of AS. In this study the key basic amino acids in the chemokine domain of SR-PSOX have been identified for its functions.

Results
A cell model to study the functions of SR-PSOX was successfully established. Based on the cell model, a series of mutants of human SR-PSOX were constructed by replacing the single basic amino acid residue in the non-conservative region of the chemokine domain (arginine 62, arginine 78, histidine 80, arginine 82, histidine 85, lysine 105, lysine 119, histidine 123) with alanine (designated as R62A, R78A, H80A, R82A, H85A, K105A, K119A and H123A, respectively). Functional studies showed that the mutants with H80A, H85A, and K105A significantly increased the activities of oxLDL uptake and bacterial phagocytosis compared with the wild-type SR-PSOX. In addition, we have also found that mutagenesis of either of those amino acids strongly reduced the adhesive activity of SR-PSOX by using a highly non-overlapping set of basic amino acid residues.

Conclusion
Our study demonstrates that basic amino acid residues in the non-conservative region of the chemokine domain of SR-PSOX are critical for its functions. Mutation of H80, H85, and K105 is responsible for increasing SR-PSOX binding with oxLDL and bacteria. All the basic amino acids in this region are important in the cells adhesion via SR-PSOX. These findings suggest that mutagenesis of the basic amino acids in the chemokine domain of SR-PSOX may contribute to atherogenesis.
Synchronous gastric adenocarcinoma and gastrointestinal stromal tumor (GIST) of the stomach: A case report
Authors: Theodosopoulos Theodosios , Dellaportas Dionysios , Psychogiou Vasiliki , Gennatas Konstantinos , Kondi-Pafiti Agathi , Gkiokas Georgios , Papaconstantinou Ioannis , Polymeneas Georgios 
Published: May 2011

Abstract
Gastrointestinal stromal tumors (GISTs) are rare mesenchymal neoplasms of the gastrointestinal tract (1%), and stomach is the most common location involved. However, the co-existence of gastric adenocarcinoma and GIST is very rare. A case of an 80-year-old male with a simultaneous presentation of a gastric adenocarcinoma and GIST is presented. Various hypotheses have been proposed in order to explain this rare simultaneous development, but even though it's cause has not been proven yet.
Executive Summary: Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus
Authors: Sacks David B , Arnold Mark , Bakris George L , Bruns David E , Horvath Andrea Rita , Kirkman M Sue , Lernmark Ake , Metzger Boyd E , Nathan David M 
Published: May 2011

BACKGROUND
Multiple laboratory tests are used in the diagnosis and management of patients with diabetes mellitus. The quality of the scientific evidence supporting the use of these assays varies substantially.

APPROACH
An expert committee compiled evidence-based recommendations for the use of laboratory analysis in patients with diabetes. A new system was developed to grade the overall quality of the evidence and the strength of the recommendations. A draft of the guidelines was posted on the Internet, and the document was modified in response to comments. The guidelines were reviewed by the joint Evidence-Based Laboratory Medicine Committee of the AACC and the National Academy of Clinical Biochemistry and were accepted after revisions by the Professional Practice Committee and subsequent approval by the Executive Committee of the American Diabetes Association.

CONTENT
In addition to the long-standing criteria based on measurement of venous plasma glucose, diabetes can be diagnosed by demonstrating increased hemoglobin A1c (Hb A1c) concentrations in the blood. Monitoring of glycemic control is performed by the patients measuring their own plasma or blood glucose with meters and by laboratory analysis of Hb A1c. The potential roles of noninvasive glucose monitoring, genetic testing, and measurement of autoantibodies, urine albumin, insulin, proinsulin, C-peptide, and other analytes are addressed.

SUMMARY
The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.
Synthesis of superheavy elements by cold fusion
Authors: Hofmann S. 
Published: May 2011

AbstractThe new elements fromZ = 107 to 112 were synthesized in cold fusion reactions based on targets of lead and bismuth. The principle physical concepts are presented which led to the application of this reaction type in search experiments for new elements. Described are the technical developments from early mechanical devices to experiments with recoil separators. An overview is given of present experiments which use cold fusion for systematic studies and synthesis of new isotopes. Perspectives are also presented for the application of cold fusion reactions in synthesis of elements beyond element 113, the so far heaviest element produced in a cold fusion reaction. Further, the transition of hot fusion to cold fusion is pointed out, which occurs in reactions for synthesis of elements nearZ = 126 using actinide targets and beams of neutron rich isotopes of elements from iron to germanium.
Relativistic electronic structure studies on the heaviest elements
Authors: Pershina Valeria 
Published: May 2011

AbstractSpectacular developments in relativistic quantum theory and computational algorithms in the last two decades allowed for accurate predictions of properties of the heaviest elements and their experimental behaviour. The most recent works in this area of investigations are overviewed. Preference is given to those related to experimental research. The role of relativistic effects is elucidated.
Aqueous-phase chemistry of the transactinides
Authors: Kratz Jens Volker 
Published: May 2011

AbstractThe experimental techniques developed to perform rapid chemical separations of the heaviest elements in the aqueous phase are presented. In general, these include transport of the nuclear reaction products to a separation device by the gas-jet technique and dissolution in an aqueous solution containing inorganic ligands for complex formation. The complexes are chemically characterized by a partition method which can be liquid–liquid extraction, ion-exchange- or reversed-phase extraction chromatography. The separated fractions are quickly evaporated to dryness for the preparation of samples forα-particle spectroscopy. Comments are given on the special situation in which chemistry has to be studied with single atoms. Theoretical predictions of chemical properties are compared to the presently known chemical behaviour of rutherfordium, Rf (element 104), dubnium, Db (element 105), seaborgium, Sg (element 106), and hassium, Hs (element 108) and to that of their lighter homologs in the Periodic Table in order to assess the role of relativistic effects in the chemistry of the heaviest elements.
Modulating Hydrogen Tunnelling in Ascorbate Proton-Coupled Electron Transfers
Authors: Sajenko Ivana , Pilepić Viktor , Uršić Stanko 
Published: May 2011

Abstract
The oxidation of ascorbate with 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) radical in water and in water-acetonitrile (1:1 v/v) mixed solvent has been demonstrated to be a proton-coupled electron transfer (PCET) process, involving hydrogen tunnelling at room temperature. The observations of significant changes in isotope effect on the Arrhenius pre-factor, A
H/A
D caused by the presence of tetraethylammonium ions in the reaction clearly suggest changes in tunnelling regime in the reaction. The evidence comprises: a) the spectroscopic and kinetic evidence for the interaction of ascorbate and TEMPO; b) the observation of KIEs k
H/k
D of 25.4(0.3) in water-acetonitrile (1:1 v/v) without tetraethylammonium ions and 23.3(0.1) in presence of teraethylammonium ions; c) the observation of k
H/k
D of 21.9(0.2) in water in presence of tetraethylammonium ions; d) the observation of isotope effect on the Arrhenius pre-factor, A
H/A
D of 0.82(0.10) in the reaction in water-acetonitrile (1:1 v/v) without tetraethylammonium ions; e) the observation of isotope effect on the Arrhenius pre-factor, A
H/A
D of 0.22(0.03) in the reaction in water-acetonitrile (1:1 v/v) in the presence of tetraethylammonium ions; f) the observation of isotope effect on the Arrhenius pre-factor, A
H/A
D of 1.34(0.15) in the reaction in water in the presence of tetraethylammonium ions; g) the observation of isotope differences in the enthalpies of activation in water and D2O, in presence of tetraethylammonium ions Δr
H
‡ (in H2O) = 33.7(0.4) kJ/mol, Δ r
H
‡ (in D2O) = 40.7(0.1) kJ/mol; h) the observation of isotope differences in the enthalpies of activation in water-acetonitrile (1:1 v/v) and D2O-acetonitrile (1:1 v/v) in absence of tetraethylammonium ions, Δ r
H
‡ (in H2O-acetonitrile) = 31.1(0.1) kJ/mol, Δ r
H
‡ (in D2O-acetonitrile) = 39.5(0.4) kJ/mol; i) the observation of isotope differences in the enthalpies of activation in water-acetonitrile (1:1 v/v) and D2O-acetonitrile (1:1 v/v) in presence of tetraethylammonium ions, Δ r
H
‡ (in H2O-acetonitrile) = 29.4(0.3) kJ/mol, Δ r
H
‡ (in D2O-acetonitrile) = 41.0(0.4) kJ/mol. These results were discussed following a framework of Marcus-like tunnelling model, taking into account dynamical features of the systems.