bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatic mutations of STK11 gene in human papillomavirus positive and negative penile cancer
Authors: Annunziata Clorinda , Buonaguro Luigi , Losito Simona , Buonaguro Franco M , Tornesello Maria Lina 
Published: January 2013

Abstract

Background
Human papillomavirus (HPV) infection accounts for about 40-50% of all cases of penile carcinoma suggesting that other factors, including host genetic status, are involved in neoplastic transformation. In this perspective, STK11 gene, which has been found frequently mutated in HPV-related cervical carcinoma, has been analyzed in HPV-positive and HPV-negative invasive penile cancers to establish its mutational status and the possible correlation of HPV infection with specific genetic alterations.

Methods
Genomic DNAs extracted from 26 cases of penile squamous cell carcinoma were analyzed for genetic alterations in the exons 1 to 9 of STK11 gene by quantitative real-time PCR. Ratios of potentially deleted and non-deleted exons were indicative of specific loss of STK11 coding regions. DNA samples of 5 cancer cases were subjected to standard PCR amplification of STK11 exons 1 to 9 and analyzed for somatic mutations by direct nucleotide sequencing analysis.

Results
Heterozygous deletions of STK11 exon 1 and 2 were identified in 2 out of 14 HPV-positive (14.3%) and 1 out of 12 HPV-negative cases (8.3%). Complete nucleotide sequencing analysis of exons 1 to 9 showed a single nucleotide change upstream the exon 2 coding region in 1 out of 5 penile carcinoma samples.

Conclusions
The present results suggest that single nucleotide mutations and/or deletions of STK11 gene are rare events in penile cancer. Moreover, no significant association was observed between STK11 alterations and HPV infection in these tumors.
Protocol for a systematic review on the extent of non-publication of research studies and associated study characteristics
Authors: Portalupi Susan , von Elm Erik , Schmucker Christine , Lang Britta , Motschall Edith , Schwarzer Guido , Gross Isabel T , Scherer Roberta W , Bassler Dirk , Meerpohl Joerg J 
Published: January 2013

Abstract

Background
Methodological research has found that non-published studies often have different results than those that are published, a phenomenon known as publication bias. When results are not published, or are published selectively based on the direction or the strength of the findings, healthcare professionals and consumers of healthcare cannot base their decision-making on the full body of current evidence.

Methods
As part of the OPEN project (http://www.open-project.eu) we will conduct a systematic review with the following objectives:

To determine the proportion and/or rate of non-publication of studies by systematically reviewing methodological research projects that followed up a cohort of studies that

received research ethics committee (REC) approval,

were registered in trial registries, or

were presented as abstracts at conferences.

To assess the association of study characteristics (for example, direction and/or strength of findings) with likelihood of full publication.

To identify reports of relevant methodological research projects we will conduct electronic database searches, check reference lists, and contact experts. Published and unpublished projects will be included. The inclusion criteria are as follows:

RECs: methodological research projects that examined the subsequent proportion and/or rate of publication of studies that received approval from RECs;

Trial registries: methodological research projects that examine the subsequent proportion and/or rate of publication of studies registered in trial registries;

Conference abstracts: methodological research projects that examine the subsequent proportion and/or rate of full publication of studies which were initially presented at conferences as abstracts.

Primary outcomes: Proportion/rate of published studies; time to full publication (mean/median; cumulative publication rate by time).
Secondary outcomes: Association of study characteristics with full publication.
The different questions (a, b, and c) will be investigated separately. Data synthesis will involve a combination of descriptive and statistical summaries of the included methodological research projects.

Discussion
Results are expected to be publicly available in mid 2013.
How bioinformatics influences health informatics: usage of biomolecular sequences, expression profiles and automated microscopic image analyses for clinical needs and public health
Authors: Kuznetsov Vladimir , Lee Hwee Kuan , Maurer-Stroh Sebastian , Molnár Maria Judit , Pongor Sandor , Eisenhaber Birgit , Eisenhaber Frank 
Published: January 2013

AbstractAbstractThe currently hyped expectation of personalized medicine is often associated with just achieving the information technology led integration of biomolecular sequencing, expression and histopathological bioimaging data with clinical records at the individual patients’ level as if the significant biomedical conclusions would be its more or less mandatory result. It remains a sad fact that many, if not most biomolecular mechanisms that translate the human genomic information into phenotypes are not known and, thus, most of the molecular and cellular data cannot be interpreted in terms of biomedically relevant conclusions. Whereas the historical trend will certainly be into the general direction of personalized diagnostics and cures, the temperate view suggests that biomedical applications that rely either on the comparison of biomolecular sequences and/or on the already known biomolecular mechanisms have much greater chances to enter clinical practice soon. In addition to considering the general trends, we exemplarily review advances in the area of cancer biomarker discovery, in the clinically relevant characterization of patient-specific viral and bacterial pathogens (with emphasis on drug selection for influenza and enterohemorrhagicE. coli) as well as progress in the automated assessment of histopathological images. As molecular and cellular data analysis will become instrumental for achieving desirable clinical outcomes, the role of bioinformatics and computational biology approaches will dramatically grow.Author summaryWith DNA sequencing and computers becoming increasingly cheap and accessible to the layman, the idea of integrating biomolecular and clinical patient data seems to become a realistic, short-term option that will lead to patient-specific diagnostics and treatment design for many diseases such as cancer, metabolic disorders, inherited conditions, etc. These hyped expectations will fail since many, if not most biomolecular mechanisms that translate the human genomic information into phenotypes are not known yet and, thus, most of the molecular and cellular data collected will not lead to biomedically relevant conclusions. At the same time, less spectacular biomedical applications based on biomolecular sequence comparison and/or known biomolecular mechanisms have the potential to unfold enormous potential for healthcare and public health. Since the analysis of heterogeneous biomolecular data in context with clinical data will be increasingly critical, the role of bioinformatics and computational biology will grow correspondingly in this process.
iPathCaseKEGG: An iPad interface for KEGG metabolic pathways
Authors: Johnson Stephen R , Qi Xinjian , Cicek A Ercument , Ozsoyoglu Gultekin 
Published: January 2013

Abstract

Background
Kyoto Encyclopedia of Genes and Genomes (KEGG) is an online and integrated molecular database for several organisms. KEGG has been a highly useful site, helping domain scientists understand, research, study, and teach metabolisms by linking sequenced genomes to higher level systematic functions. KEGG databases are accessible through the web pages of the system, but the capabilities of the web interface are limited. Third party systems have been built over the KEGG data to provide extensive functionalities. However, there have been no attempts towards providing a tablet interface for KEGG data. Recognizing the rise of mobile technologies and the importance of tablets in education, this paper presents the design and implementation of iPathCaseKEGG, an iPad interface for KEGG data, which is empowered with multiple browsing and visualization capabilities.

Results
iPathCaseKEGG has been implemented and is available, free of charge, in the Apple App Store (locatable by searching for “Pathcase” in the app store). The application provides browsing and interactive visualization functionalities on the KEGG data. Users can pick pathways, visualize them, and see detail pages of reactions and molecules using the multi-touch interface of iPad.

Conclusions
iPathCaseKEGG provides a mobile interface to access KEGG data. Interactive visualization and browsing functionalities let users to interact with the data in multiple ways. As the importance of tablets and their usage in research education continue to rise, we think iPathCaseKEGG will be a useful tool for life science instructors and researchers.
Co-enrollment of critically ill patients into multiple studies: patterns, predictors and consequences
Authors: Cook Deborah , McDonald Ellen , Smith Orla , Zytaruk Nicole , Heels-Ansdell Diane , Watpool Irene , McArdle Tracy , Matte Andrea , Clarke France , Vallance Shirley , Finfer Simon , Galt Pauline , Crozier Tim , Fowler Rob , Arabi Yaseen , Woolfe Clive , Orford Neil , Hall Richard , Adhikari Neill KJ , Ferland Marie-Clauide , Marshall John , Meade Maureen ,   The PROTECT Research Coordinators,   PROTECT Investigators,   Canadian Critical Care Trials Group and the Australian and New Zealand Intensive Care Society Clinical Trials Group
Published: January 2013

Abstract
Introduction
Research on co-enrollment practices and their impact are limited in the ICU setting. The objectives of this study were: 1) to describe patterns and predictors of co-enrollment of patients in a thromboprophylaxis trial, and 2) to examine the consequences of co-enrollment on clinical and trial outcomes.

Methods
In an observational analysis of an international thromboprophylaxis trial in 67 ICUs, we examined the co-enrollment of critically ill medical-surgical patients into more than one study, and examined the clinical and trial outcomes among co-enrolled and non-co-enrolled patients.

Results
Among 3,746 patients enrolled in PROTECT (Prophylaxis for ThromboEmbolism in Critical Care Trial), 713 (19.0%) were co-enrolled in at least one other study (53.6% in a randomized trial, 37.0% in an observational study and 9.4% in both). Six factors independently associated with co-enrollment (all P < 0.001) were illness severity (odds ratio (OR) 1.35, 95% confidence interval (CI) 1.19 to 1.53 for each 10-point Acute Physiology and Chronic Health Evaluation (APACHE) II score increase), substitute decision-makers providing consent, rather than patients (OR 3.31, 2.03 to 5.41), experience of persons inviting consent (OR 2.67, 1.74 to 4.11 for persons with > 10 years' experience compared to persons with none), center size (all ORs > 10 for ICUs with > 15 beds), affiliation with trials groups (OR 5.59, 3.49 to 8.95), and main trial rather than pilot phase (all ORs > 8 for recruitment year beyond the pilot). Co-enrollment did not influence clinical or trial outcomes or risk of adverse events.

Conclusions
Co-enrollment was strongly associated with features of the patients, research personnel, setting and study. Co-enrollment had no impact on trial results, and appeared safe, acceptable and feasible. Transparent reporting, scholarly discourse, ethical analysis and further research are needed on the complex topic of co-enrollment during critical illness.
Recyclable Pd-Incorporated Perovskite-Titanate Catalysts Synthesized in Molten Salts for the Liquid-Phase Oxidation of Alcohols with Molecular Oxygen
Authors: Adilina Indri Badria , Hara Takayoshi , Ichikuni Nobuyuki , Kumada Nobuhiro , Shimazu Shogo 
Published: January 2013

Abstract
A series of Pd-incorporated titanate catalysts (Pd/KSTO) were synthesized by the intercalation of Pd(NO3)2 into layered potassium titanate (KTO), which proceeded via a cation-exchange reaction in molten salts. Perovskite phases of Pd/KSTO for catalysis were synthesized at 600 °C and above, whereas a lepidocrocite-type layered titanate structure, similar to that of the parent KTO, was retained when a lower temperature of 400 °C was used during synthesis. In both cases, the Pd species exists as divalent Pd. The synthesized Pd/KSTO catalysts were then applied to the liquid-phase oxidation of alcohols using molecular oxygen without any additives. The perovskite-type Pd/KSTO catalyst displayed superior activity when compared to that of the lepidocrocite-type, yielding a high turnover number of 800 in the aerobic oxidation of 1-phenylethanol with no loss of catalytic activity after three runs in catalyst recycling experiments.
Gaming in Air Pollution Data? Lessons from China
Authors: Chen Yuyu , Jin Ginger Zhe , Kumar Naresh , Shi Guang 
Published: January 2013

Abstract
Protecting the environment during economic growth is a challenge facing every country. This paper focuses on two regulatory measures that China has adopted to incentivize air quality improvement: publishing a daily air pollution index (API) for major cities since 2000 and linking the API to performance evaluations of local governments. In particular, China defines a day with an API at or below 100 as a blue sky day. Starting in 2003, a city with at least 80% blue sky days in a calendar year (among other criteria) qualified for the “national environmental protection model city” award. This cutoff was increased to 85% in 2007.Using officially reported API data from 37 large cities during 2000-2009, we find a significant discontinuity at the threshold of 100 and this discontinuity is of a greater magnitude after 2003. Moreover, we find that the model cities were less likely to report API right above 100 when they were close to the targeted blue sky days in the fourth quarter of the year when or before they won the model city award. That being said, we also find significant correlation of API with two alternative measures of air pollution – namely visibility as reported by the China Meteorological Administration (CMA) and Aerosol Optical Depth (AOD), corrected for meteorological conditions, from NASA satellites. The discontinuity around 100 suggests that count of blue sky days could have been subject to data manipulation; nevertheless, API does contain useful information about air pollution.
The meaning of aluminium exposure on human health and aluminium-related diseases
Authors: Crisponi Guido , Fanni Daniela , Gerosa Clara , Nemolato Sonia , Nurchi Valeria M. , Crespo-Alonso Miriam , Lachowicz Joanna I. , Faa Gavino 
Published: January 2013

AbstractThe aim of this review is to attempt to answer extremely important questions related to aluminium-related diseases. Starting from an overview on the main sources of aluminium exposure in everyday life, the principal aspects of aluminium metabolism in humans have been taken into consideration in an attempt to enlighten the main metabolic pathways utilised by trivalent metal ions in different organs. The second part of this review is focused on the available evidence concerning the pathogenetic consequences of aluminium overload in human health, with particular attention to its putative role in bone and neurodegenerative human diseases.
Additional diagnostic and prognostic value of copeptin ultra-sensitive for diagnosis of non-ST-elevation myocardial infarction in older patients presenting to the emergency department1)
Authors: Bahrmann Philipp , Bahrmann Anke , Breithardt Ole-A. , Daniel Werner G. , Christ Michael , Sieber Cornel C. , Bertsch Thomas 
Published: January 2013

Abstract

Background: Identifying older patients with non-ST- elevation myocardial infarction (NSTEMI) within the very large proportion with elevated high-sensitive cardiac troponin T (hs-cTnT) is a diagnostic challenge because they often present without clear symptoms or electrocardiographic features of acute coronary syndrome to the emergency department (ED). We prospectively investigated the diagnostic and prognostic performance of copeptin ultra-sensitive (copeptin-us) and hs-cTnT compared to hs-cTnT alone for NSTEMI at prespecified cut-offs in unselected older patients.

Methods: We consecutively enrolled 306 non-surgical patients ≥70 years presenting to the ED. In addition to clinical examination, copeptin-us and hs-cTnT were measured at admission. Two cardiologists independently adjudicated the final diagnosis of NSTEMI after reviewing all available data. All patients were followed up for cardiovascular-related death within the following 12 months.

Results: NSTEMI was diagnosed in 38 (12%) patients (age 81±6 years). The combination of copeptin-us ≥14 pmol/L and hs-cTnT ≥0.014 µg/L compared to hs-cTnT ≥0.014 µg/L alone had a positive predictive value of 21% vs. 19% to rule in NSTEMI. The combination of copeptin-us <14 pmol/L and hs-cTnT <0.014 µg/L compared to hs-cTnT <0.014 µg/L alone had a negative predictive value of 100% vs. 99% to rule out NSTEMI. Hs-cTnT ≥0.014 µg/L alone was significantly associated with outcome. When copeptin-us ≥14 pmol/L was added, the net reclassification improvement for outcome was not significant (p=0.809).

Conclusions: In unselected older patients presenting to the ED, the additional use of copeptin-us at predefined cut-offs may help to reliably rule out NSTEMI but may not help to increase predicted risk for outcome compared to hs-cTnT alone.
Serum levels of cancer biomarkers in diabetic and non-diabetic proteinuric patients: a preliminary study
Authors: Turgutalp Kenan , Ozhan Onur , Helvacı İlter , Ata Alper , Arican Ali , Boztepe Burcu , Kıykım Ahmet 
Published: January 2013

Abstract

Background: Cancer biomarkers (CBs) can be used in early detection of several cancers as well as in detection of recurrence and following response to treatment. We aimed to investigate the levels of CBs in proteinuric patients with primary glomerular disease (PGD) and diabetes mellitus, and compare them with healthy controls.

Methods: One hundred and two patients with untreated PGD, 62 proteinuric patients with diabetic nephropathy, and 84 healthy controls were enrolled. Levels of cancer antigen 125 (CA 125), cancer antigen 15–3 (CA 15–3), carcinoembriogenic antigen (CEA), α-fetoprotein (AFP), total prostate specific antigen (TPSA), free prostate specific antigen (FPSA) and carbohydrate antigen 19–9 (CA 19–9) were measured.

Results: Compared to healthy controls, levels of CA 125, CA 15–3 and CA 19–9 were higher in patients with PGD and diabetic patients (all p<0.05), while levels of TPSA, FPSA, AFP and CEA were lower (all p<0.05). There was no correlation between levels of cancer biomarkers and serum fibrinogen and serum amyloid A protein levels (all p>0.05). Both urinary protein excretion rate and serum albumin levels were correlated with all CBs (all p<0.05).

Conclusions: CBs levels seem to be changed in different proteinuric patients. This condition should be kept in mind when evaluating CBs levels in proteinuric patients.
Suitability of quality control materials for prostate-specific antigen (PSA) measurement: inter-method variability of common tumor marker control materials
Authors: Vucetic Zivjena , Dnistrian Ann , Nilsson Olle , Lilja Hans G. , Plebani Mario 
Published: January 2013

Abstract

Background: Quality control materials with minimal inter-assay differences and clinically relevant proportions of different molecular forms of the analyte are needed to optimize intra- and inter-laboratory accuracy and precision.

Methods: We assessed if clinically relevant total prostate-specific antigen (tPSA) levels were present in seven commercially available Multi Constituent Tumor Marker Controls (MC-TMC). Further, we determined the concentration of free PSA (fPSA) and calculated the percentage of free PSA (%fPSA) in all materials. Finally, we determined variability of TMC materials across several commonly used PSA platforms.

Results: All MC-TMC materials contained at least one concentration of tPSA in normal and pathologic range. Control materials varied in the amount of fPSA and %fPSA, with most controls consisting of fPSA only and only one MC-TMC containing medically relevant levels of around 35% fPSA. Only a minority of MC-TMC materials showed minimal variability across four PSA methods while the majority of PSA controls showed wide inter-method differences.

Conclusions: Use of many commercially available controls for PSA could lead to biased PSA measurements because they contain medically irrelevant proportions of fPSA and show significant variation among different PSA assay platforms.
Coffee consumption, serum γ-glutamyltransferase, and glucose tolerance status in middle-aged Japanese men
Authors: Hiramatsu Tatsuo , Tajima Osamu , Uezono Kousaku , Tabata Shinji , Abe Hiroshi , Ohnaka Keizo , Kono Suminori 
Published: January 2013

AbstractBackground:Recently, coffee consumption has been related to decreased risk of type 2 diabetes mellitus (DM) among those with high levels of serum γ-glutamyltransferase (GGT). We examined the association between coffee and glucose tolerance, determined by a 75 g oral glucose tolerance test, and the effect modification of serum GGT on the association.Methods:The study subjects were 5320 men aged 46–60 years who received a health examination at two Self-Defense Forces hospitals from January 1997 to March 2004. Those medicated for DM were excluded. Coffee consumption was classified into <1, 1–2, 3–4, and ≥5 cups/day. Statistical adjustment was made for age, body mass index, smoking, alcohol use, leisure-time physical activity, green tea consumption, parental diabetes, hospital, and rank in the Self-Defense Forces.Results:Men with normal glucose tolerance, isolated impaired fasting glucose (IFG), isolated impaired glucose tolerance (IGT), combined IFG/IGT, and type 2 DM numbered 3384, 398, 790, 348, and 400, respectively. The prevalence odds of isolated IGT, combined IFG/IGT, and type 2 DM, but not of isolated IFG, decreased with increasing consumption of coffee. An inverse association with coffee was observed for isolated IGT in both low (≤40 IU/L) and high (>40 IU/L) GGT groups, and for combined IFG/IGT and type 2 DM in the latter group.Conclusions:Coffee drinking is protective against glucose intolerance. A possible effect modification of GGT on the coffee-DM association warrants further studies.
Orbital hemorrhage as a primary manifestation of disseminated intravascular coagulation (DIC) associated with intrauterine fetal death and placental abruption
Authors: Mayer-Pickel Karoline , Mörtl Manfred Georg , Jetzl Jörg , Lang Uwe , Schlembach Dietmar 
Published: January 2013

Abstract

Introduction: Disseminated intravascular coagulation (DIC) is a serious complication of obstetric emergencies, and its clinical manifestation occurs in various organs and tissues. Ocular and orbital involvement has been reported only rarely.

Presentation of the case: A 15-year-old primigravida complained about loss of vision in the right eye for 3 days. Magnetic resonance imaging showed a retrobulbar hemorrhage. A first diagnosis of pregnancy (estimated gestational age of 23 weeks) was made, and intrauterine fetal death was diagnosed by ultrasound examination. Laboratory workup revealed the diagnosis of DIC. Due to massive vaginal bleeding a cesarean section was performed, and placental abruption was diagnosed intraoperatively.

Discussion: The concomitance of intrauterine fetal death and other obstetric complications such as placental abruption might induce a fulminant coagulopathy with severe consequences even with uncommon organ localization.