Monday, March 2, 2015

Published During February

We are pleased to announce the publication of the following peer reviewed papers. Sign up to receive email alerts to receive immediate notification of new papers.

Advances in Tumor Virology
Chronic Inflammation in Cancer: The Role of Human Viruses

Analytical Chemistry Insights
Determination of Chlorophenoxy Acid Methyl Esters and Other Chlorinated Herbicides by GC High-resolution QTOFMS and Soft lionization

Biochemistry Insights
Production, Purification, and Identification of Cholest-4-en-3-one Produced by Cholesterol Oxidase from Rhodococcus sp. in Aqueous/Organic Biphasic System

Bioinformatics and Biology Insights
Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum

Bone and Tissue Regeneration Insights
Future of Bone Repair

Cancer Informatics

Pathway-based Biomarkers for Breast Cancer in Proteomics

An Improved Version of Logistic Bayesian LASSO for Detecting Rare Haplotype-Environment Interactions with Application to Lung Cancer

Regulation of Epithelial-Mesenchymal Transition in Breast Cancer Cells by Cell Contact and Adhesion

Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer

Extending Information Retrieval Methods to Personalized Genomic-Based Studies of Disease

Toolbox for Mobile-Element Insertion Detection on Cancer Genomes

Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping

Mapping Splicing Quantitative Trait Loci in RNA-Seq

Introductory Editorial: Array Platform Modeling and Analysis (A)

Network Analysis of Circular Permutations in Multidomain Proteins Reveals Functional Linkages for Uncharacterized Proteins

What Tumor Dynamics Modeling Can Teach us About Exploiting the Stem-Cell View for Better Cancer Treatment

Comprehensive Evaluation of Composite Gene Features in Cancer Outcome Prediction

Clinical Medicine Insights: Arthritis and Musculoskeletal Disorders
Ultrasonographic Tendon Alteration in Relation to Parathyroid Dysfunction in Chronic Hemodialysis Patients.

Joint Instability and Osteoarthritis

Predictive Factors Related to the Efficacy of Golimumab in Patients with Rheumatoid Arthritis


The Use of Carbon-Fiber-Reinforced (CFR) PEEK Material in Orthopedic Implants: A Systematic Review

Clinical Medicine Insights: Cardiology
Fatty Acid-Binding Protein 4 (FABP4): Pathophysiological Insights and Potent Clinical Biomarker of Metabolic and Cardiovascular Diseases

Clinical Utility of Exercise Training in Heart Failure with Reduced and Preserved Ejection Fraction

Echocardiographic Manifestation of Esophagitis Mimicking a Posterior Mediastinal Mass


Transpopliteal Balloon-Assisted Excimer-Laser Atherectomy for the Treatment of Chronic Femoropopliteal Occlusions: Feasibility and Initial Results


Characterizing Heart Failure in the Ventricular Volume Domain

Clinical Medicine Insights: Case Reports
A Case of Tuberculous Cellulitis

Biliary Stent Migration to Hepatic Duct-Case Report of a Late Complication

Three Adult Cases of HPV-B19 Infection with Concomitant Leukopenia and Low Platelet Counts

Life Threatening Hemoperitoneum and Liver Injury as a Result of Chest Tube Thoracostomy

Clinical Medicine Insights: Ear, Nose and Throat
Selective Neck Dissection (IIa, III): A Rational Replacement for Extended Supraomohyoid Neck Dissection in Patients with N0 Supraglottic and Glottic Squamous Cell Carcinoma

Clinical Medicine Insights: Endocrinology and Diabetes
Unhealthy Weight Control Practices: Culprits and Clinical Recommendations

Clinical Medicine Insights: Oncology
Intraperitoneal Follicular Dendritic Cell Sarcoma: Role of Chemotherapy and Bone Marrow Allotransplantation in Locally Advanced Disease?

Development of Interpretable Predictive Models for BPH and Prostate Cancer

Clinical Medicine Insights: Pediatrics
Intravenous Lipids for Preterm Infants: A Review

Cyclopia: A Rare Condition with Unusual Presentation - A Case Report

Decreased Plasma Myeloperoxidase Associated with Probiotic Therapy in Autistic Children

Clinical Medicine Insights: Urology
Advances in the Treatment of Urinary Incontinence in Women

Environmental Health Insights
Evaluation of Pulmonary and Systemic Toxicity of Oil Dispersant (COREXIT EC9500A®) Following Acute Repeated Inhalation Exposure

Workplace Exercise for Control of Occupational Neck/Shoulder Disorders: A Review of Prospective Studies

Evolutionary Bioinformatics
windex: Analyzing Convergent Evolution Using the Wheatsheaf Index in R

A Novel Approach to Identify Candidate Prognostic Factors for Hepatitis C Treatment Response Integrating Clinical and Viral Genetic Data

Apparent microRNA-Target-specific Histone Modification in Mammalian Spermatogenesis

Healthy Aging & Clinical Care in the Elderly
Pragmatic Language Changes During Normal Aging: Implications for Health Care

Infectious Diseases: Research and Treatment
Lack of Correlation between Bristol Stool Scale and Quantitative Bacterial Load in Clostridium difficile Infection

International Journal of Tryptophan Research
The Aryl Hydrocarbon Receptor: A Review of Its Role in the Physiology and Pathology of the Integument and Its Relationship to the Tryptophan Metabolism

Journal of Experimental Neuroscience
Molecular and Physiological Factors of Neuroprotection in Hypoxia-tolerant Models: Pharmacological Clues for the Treatment of Stroke

Journal of Medical Education and Curricular Development
Pedagogy Rules: Open Mindset in Adopting Fit-for-Purpose Educational Tools in Teaching Dispersed Medical Students

Student Perceived Value of Anatomy Pedagogy, Part I: Prosection or Dissection?

Student Perceived Value of Anatomy Pedagogy, Part II: Clinical Practice and Assessment

Palliative Care: Research and Treatment
Death in Long-term Care: A Brief Report Examining Factors Associated with Death within 31 Days of Assessment

Perspectives in Medicinal Chemistry
New Approaches to Treating Alzheimer's Disease

Substance Abuse: Research and Treatment
Gasoline Abuse in a 10-Year-Old Child with Mental Retardation: A Case Report

What is the Association of Cannabis Use and Cardiovascular Complications?

 

Friday, February 27, 2015

Published This Week (23rd February - 27th February)

We are pleased to announce the publication of the following peer reviewed papers.  Sign up to receive email alerts to receive immediate notification of new papers.

Cancer Informatics

What Tumor Dynamics Modeling Can Teach us About Exploiting the Stem-Cell View for Better Cancer Treatment

Comprehensive Evaluation of Composite Gene Features in Cancer Outcome Prediction

Clinical Medicine Insights: Arthritis and Musculoskeletal Disorders

The Use of Carbon-Fiber-Reinforced (CFR) PEEK Material in Orthopedic Implants: A Systematic Review

Clinical Medicine Insights: Cardiology

Echocardiographic Manifestation of Esophagitis Mimicking a Posterior Mediastinal Mass

Transpopliteal Balloon-Assisted Excimer–Laser Atherectomy for the Treatment of Chronic Femoropopliteal Occlusions: Feasibility and Initial Results

Characterizing Heart Failure in the Ventricular Volume Domain

Clinical Medicine Insights: Case Reports

Three Adult Cases of HPV-B19 Infection with Concomitant Leukopenia and Low Platelet Counts

Life Threatening Hemoperitoneum and Liver Injury as a Result of Chest Tube Thoracostomy

Clinical Medicine Insights: Oncology

Development of Interpretable Predictive Models for BPH and Prostate Cancer

Clinical Medicine Insights: Urology

Advances in the Treatment of Urinary Incontinence in Women

Environmental Health Insights

Workplace Exercise for Control of Occupational Neck/Shoulder Disorders: A Review of Prospective Studies

Evolutionary Bioinformatics

A Novel Approach to Identify Candidate Prognostic Factors for Hepatitis C Treatment Response Integrating Clinical and Viral Genetic Data

Apparent microRNA-Target-specific Histone Modification in Mammalian Spermatogenesis

Healthy Aging & Clinical Care in the Elderly

Pragmatic Language Changes During Normal Aging: Implications for Health Care

Infectious Diseases: Research and Treatment

Lack of Correlation between Bristol Stool Scale and Quantitative Bacterial Load in Clostridium difficile Infection

Journal of Experimental Neuroscience

Molecular and Physiological Factors of Neuroprotection in Hypoxia-tolerant Models: Pharmacological Clues for the Treatment of Stroke

Journal of Medical Education and Curricular Development

Pedagogy Rules: Open Mindset in Adopting Fit-for-Purpose Educational Tools in Teaching Dispersed Medical Students

Student Perceived Value of Anatomy Pedagogy, Part I: Prosection or Dissection?

Student Perceived Value of Anatomy Pedagogy, Part II: Clinical Practice and Assessment

Tuesday, February 24, 2015

Interview with Dr Jafaar Makki

This author interview is by Dr Jafaar Makki, of Queen Elizabeth Hospital, Malaysia.  Dr Makki's full paper, Expression distribution of cancer stem cell, epithelial to mesenchymal transition and telomerase activity in breast cancer and their association with clinicopathological characteristic, is available for download in Clinical Medicine Insights: Pathology.

Please summarise for readers the content of your article.

My research deals with three novel concepts in breast cancer biology. These concepts (Cancer stem cells, Epithelial to Mesenchymal transition and Telomerase activity) are responsible for the initiation, propagation, invasion, progression and metastasis of breast carcinoma. It is important to study and identify these cancer cells to find new markers and proteins.  These could help invent a new therapeutic agent that could target tumor cells with CSC and EMT phenotypes at various stage of differentiation, sparing normal stem cells and reducing side effects.

How did you come to be involved in your area of study?

It is related to my daily practice as histopathologist.

What was previously known about the topic of your article?

Most of the previous research deals with animal inoculated specimens or cell lines. This study was performed on clinical human specimens and supports the relationship between cancer stem cells and epithelial to mesenchymal transition suggested by those previous non-clinical trials.

How has your work in this area advanced understanding of the topic?

By using three new medical technique ( IHC, IF, and flowcytometry) to highlight, verify and validate our results.

What do you regard as being the most important aspect of the results reported in the article?

It proved the claim from previous studies about the relationship and association between cancer stem cells and epithelial to mesenchymal transition.

Friday, February 13, 2015

Published This Week (9th Feb - 13th Feb)

We are pleased to announce the publication of the following peer reviewed papers. Sign up to receive email alerts to receive immediate notification of new papers.

Analytical Chemistry Insights
Determination of Chlorophenoxy Acid Methyl Esters and Other Chlorinated Herbicides by GC High-resolution QTOFMS and Soft lionization

Bioinformatics and Biology Insights
Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum

Bone and Tissue Regeneration Insights

Future of Bone Repair

Cancer Informatics

Pathway-based Biomarkers for Breast Cancer in Proteomics

An Improved Version of Logistic Bayesian LASSO for Detecting Rare Haplotype-Environment Interactions with Application to Lung Cancer

Regulation of Epithelial-Mesenchymal Transition in Breast Cancer Cells by Cell Contact and Adhesion


Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer

Extending Information Retrieval Methods to Personalized Genomic-Based Studies of Disease

Toolbox for Mobile-Element Insertion Detection on Cancer Genomes

Clinical Medicine Insights: Cardiology

Clinical Utility of Exercise Training in Heart Failure with Reduced and Preserved Ejection Fraction

Clinical Medicine Insights: Case Reports
A Case of Tuberculous Cellulitis

Clinical Medicine Insights: Ear, Nose and Throat
Selective Neck Dissection (IIa, III): A Rational Replacement for Extended Supraomohyoid Neck Dissection in Patients with N0 Supraglottic and Glottic Squamous Cell Carcinoma

Clinical Medicine Insights: Oncology
Intraperitoneal Follicular Dendritic Cell Sarcoma: Role of Chemotherapy and Bone Marrow Allotransplantation in Locally Advanced Disease?

Clinical Medicine Insights: Pediatrics
Intravenous Lipids for Preterm Infants: A Review

Cyclopia: A Rare Condition with Unusual Presentation - A Case Report

Environmental Health Insights
Evaluation of Pulmonary and Systemic Toxicity of Oil Dispersant (COREXIT EC9500A®) Following Acute Repeated Inhalation Exposure

Evolutionary Bioinformatics
windex: Analyzing Convergent Evolution Using the Wheatsheaf Index in R

International Journal of Tryptophan Research

The Aryl Hydrocarbon Receptor: A Review of Its Role in the Physiology and Pathology of the Integument and Its Relationship to the Tryptophan Metabolism

Perspectives in Medicinal Chemistry
New Approaches to Treating Alzheimer's Disease

Substance Abuse: Research and Treatment
Gasoline Abuse in a 10-Year-Old Child with Mental Retardation: A Case Report

 

Interview with Amgad N. Makaryus

This author interview is by Dr Amgad N. Makaryus, of North Shore-LIJ Health System. Dr Makaryus' full paper, Multi-Detector Coronary CT Imaging for the Identification of Coronary Artery Stenoses in a "Real-World" Population, is available for download in Clinical Medicine Insights: Cardiology.

First please summarise for readers the content of your article.
Multi-detector computed tomography (MDCT) has emerged as a modality for the non-invasive assessment of coronary artery disease (CAD) and is now an integral part of our diagnostic toolset. Prior studies looking at MDCT have selected specific patients for evaluation and have excluded many of the "real-world" patients commonly encountered in daily practice. These highly selected patients do not represent a "real-world" clini¬cal population of patients. These prior studies have excluded many patients with irregular heart rates, patients with contraindications to beta-blockers where they could have employed other rate-control methods, and many patients with prior history of CAD. Therefore, the aim of our study was to compare MDCT to conven¬tional coronary angiography (CA) to investigate the accuracy of MDCT in determining significant coronary stenoses in a "real-world" clinical population at a busy tertiary care center performing a large number of coronary CT angiography. A total of 1,818 consecutive patients referred for MDCT were evaluated. Patients in whom MDCT results prompted CA investigation were further evaluated, and results of the two diagnostic modalities were compared. A total of 164 coronary arteries and 410 coronary segments were evaluated and the overall per-vessel sensitivity, specificity, positive predictive value, negative predictive value, and accuracy were assessed compared to the gold standard of coronary angiography. We found that MDCT is an accurate imaging tool that allows a non-invasive assessment of significant CAD with a high diagnostic accuracy in a "real-world" population of patients.

How did you come to be involved in your area of study?
North Shore University Hospital in Manhasset, New York, USA, is a busy tertiary care hospital performing a large number of cardiac MDCT in clinical practice. I became involved in this study while directing the cardiology MDCT program at our hospital to evaluate the diagnostic accuracy of MDCT in these patients.

What was previously known about the topic of your article?
Prior studies looking at MDCT have selected specific patients for evaluation and have excluded many of the "real-world" patients commonly encountered in daily practice. These highly selected patients do not represent a "real-world" clini¬cal population of patients. These prior studies have excluded many patients with irregular heart rates (atrial fibrillation, atrial premature contractions, and ventricular premature contractions), patients with contraindications to beta-blockers where they could have employed other rate-control methods, and many patients with prior history of CAD.

How has your work in this area advanced understanding of the topic?
We found that MDCT is an accurate imaging tool that allows a non-invasive assessment of significant CAD with a high diagnostic accuracy in a "real-world" population of patients. The sensitivity and specificity that we noted are not as high as those in prior reports of idealized selected patients.

What do you regard as being the most important aspect of the results reported in the article?
Our report seems to be more realistic of an unselected patient population that is typically encountered in common clinical practice and therefore is more indicative of "real world" results.

Where can readers learn more about your work?
Hospital Webpage: https://www.northshorelij.com/find-care/find-a-doctor/internal-medicine/dr-amgad-nihad-makaryus-md-11317737
LinkedIN: https://www.linkedin.com/in/amgadmakaryus

Thursday, February 5, 2015

Identifying Legitimate Journals: A Guide for Scholars

This is a summary of a paper I recently published in Learned Publishing, the journal of the Association of Learned and Professional Society Publishers.  The full article is available to download here.

Until recently scholarly publishing had gone largely unchanged by the advent of the Internet.  However it has recently been disrupted by open access, which has grown in popularity amongst readers and authors.  

In keeping with what frequently happens when a new industry is in a state of development, many new OA publishers have recently entered the industry, some of which of lower quality than others.  In the long term it is likely that many of these newer players will either drop out of the industry or merge with other firms, but in the meantime scholars are faced with the new challenge of having to identify and avoid lower quality publishers, and to distinguish them from legitimate but inevitably imperfect publishers as well as those that are legitimate but pursuing innovative publishing models such as post-publication peer review. 

Here I offer a brief set of criteria to enable scholars to meet this challenge.  This list is intended to be short enough to be memorable and applicable to a large range of journals, and also to allow for legitimate variation amongst publishers.  

Point 1: who is the customer?

Legitimate scholarly publishers should demonstrate a focus on both authors and readers.  Does the publisher provide services that are not directed towards attracting submissions and therefore article publishing fees from authors?  Look for most or all of the following:

• New article notification services, including opted-in email services, RSS feeds, social media channels or other functions

• Article citation exportation functions

• Commenting and discussion functions

• A policy on the publication of corrections, expressions of concern, and retractions

• Use of digital object identifiers

• A clear statement on the copyright license in each article

• Pre-submission consultation and manuscript matching services

• Involvement in permanent article archiving services

• Multiple available communication channels including but not limited to email: phone, fax, postal address details, ‘live chat’ and other channels 

Point 2: inclusion in databases and indexes

Many indexes such as Pubmed and DOAJ impose strict editorial evaluations as a condition of inclusion, and inclusion of journals in them is a good indication of a journal’s quality.  Newer journals and publishers may not be involved in prominent databases for good reasons: it can sometimes require a considerable period fo time for eligible journals to complete evaluation or a title may not be within the scope of the database.  

Point 3: awareness of ethical and legal issues

Legitimate publishers must take steps to ensure that authors meet ethical and legal obligation to maintain the integrity of the literature:

• The publisher must have a policy on how it guards against plagiarism which must involve plagiarism scanning

• Membership of bodies such as COPE and ICMJE that provide guidance on how to address common ethical problems

• Membership of industry bodies that require compliance with ethical standards such as OASPA

• Clear criteria on what constitutes authorship and contributorship and a section in each published paper containing a clear statement delinating types of contributions made by each author

• A policy on declaration of funding sources and potential competing interests.  This should also be included in published articles.

• A policy on ethical requirements around human and animal study participants

• Although difficult to validate, every named author should be asked to provide signed consent that the paper bearing his/her name is fully compliant with ethical and legal requirements

Point 4: awareness of open access conventions

The publisher or journal should have a clear statement on all applicable fees.  It’s a commonly accepted principle of open access that publishers should provide a fee waiver and/or discount policy.  Authors should also be permitted to archive their work in external depositories under a commonly recognized Creative Commons license.  There should also be no access barriers to articles.  

Point 5: peer review and editorial procedures

The confidential nature of the peer review process can make it difficult to determine the integrity of the process being used.  Considerations such as an assessment of the quality of recently published papers or inclusion of the journal in databases resulting from expert assessment of published papers such as Pubmed or DOAJ can be strongly suggestive of the integrity of the process used.

The provision of information on the nature of the peer review process and conduct guidelines for reviewers are also good indicative factors.  Promises of very fast peer review should be treated with caution: 18-21 days is the minimum needed for reviewers to complete their work, and of course any guarantees of peer review outcome are clear indicators of illegitimacy.  

Tom Hill is the CEO of Libertas Academica

Download the full text of this article


Published Recently (27th January - 6th February)

We are pleased to announce the publication of the following peer reviewed papers. Sign up to receive email alerts to receive immediate notification of new papers.

Advances in Tumor Virology
Chronic Inflammation in Cancer: The Role of Human Viruses

Air, Soil and Water Research
Inhibition of Nodulation and Nitrogen Nutrition of Leguminous Crops by Selected Heavy Metals

Biomarkers in Cancer
Trisomy 8 Acute Myeloid Leukemia Analysis Reveals New Insights of DNA Methylome with Identification of HHEX as Potential Diagnostic Marker

Biomarker Insights
Perchlorate Exposure is Associated with Oxidative Stress and Indicators of Serum Iron Homeostasis Among NHANES 2005-2008 Subjects

Cancer Growth and Metastasis
Wound Healing and Cancer Stem Cells: Inflammation as a Driver of Treatment Resistance in Breast Cancer

Cancer Informatics
Inferring Active and Prognostic Ligand-Receptor Pairs with Interactions in Survival Regression Models

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data

Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays

Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival

Prognostic Gene Signature Identification Using Causal Structure Learning: Applications in Kidney Cancer

Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping

linical Medicine Insights: Arthritis and Musculoskeletal Disorders
Ultrasonographic Tendon Alteration in Relation to Parathyroid Dysfunction in Chronic Hemodialysis Patients.

Clinical Medicine Insights: Cardiology
Corrigendum to "Effects of Fibrosis Morphology on Reentrant Ventricular Tachycardia Inducibility and Simulation Fidelity in Patient-Derived Models"

Hypertrophic Cardiomyopathy: A Review Cardiology

Recent Advances in the Diagnosis and Management of Cirrhosis-Associated Cardiomyopathy in Liver Transplant Candidates: Advanced Echo Imaging, Cardiac Biomarkers, and Advanced Heart Failure Therapies

Fatty Acid-Binding Protein 4 (FABP4): Pathophysiological Insights and Potent Clinical Biomarker of Metabolic and Cardiovascular Diseases

Clinical Medicine Insights: Gastroenterology
Management of Loose, Frequent Stools and Fecal Incontinence in a Chronic Mesenteric Ischemia Patient with Oral Serum-derived Bovine Immunoglobulin

Clinical Medicine Insights: Pediatrics
Decreased Plasma Myeloperoxidase Associated with Probiotic Therapy in Autistic Children

Clinical Medicine Insights: Trauma and Intensive Medicine
The Role of Pelvic Packing for Hemodynamically Unstable Pelvic Ring Injuries

Environmental Health Insights
Houston's Novel Strategy to Control Hazardous Air Pollutants: A Case Study in Policy Innovation and Political Stalemate

Evolutionary Bioinformatics
Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier

International Journal of Insect Science
Assessment of Navel Oranges, Clementine Tangerines, and Rutaceous Fruits as Hosts of Bactrocera cucurbitae and Bactrocera latifrons (Diptera: Tephritidae)

Journal of Medical Education and Curricular Development
Attitudes to Organ Donation and Knowledge of Donation and Transplantation among University of Auckland Medical Students
Lymphoma and Chronic Lymphocytic Leukemias
Mantle Cell Lymphoma: Individualizing Therapy

Ophthalmology and Eye Diseases
Glycosaminoglycans in the Human Cornea: Age-Related Changes

Palliative Care: Research and Treatment
Death in Long-term Care: A Brief Report Examining Factors Associated with Death within 31 Days of Assessment

Substance Abuse: Research and Treatment
What is the Association of Cannabis Use and Cardiovascular Complications?

Published During January

We are pleased to announce the publication of the following peer reviewed papers. Sign up to receive email alerts to receive immediate notification of new papers.

Air, Soil and Water Research
Inhibition of Nodulation and Nitrogen Nutrition of Leguminous Crops by Selected Heavy Metals

Biomarkers in Cancer
Trisomy 8 Acute Myeloid Leukemia Analysis Reveals New Insights of DNA Methylome with Identification of HHEX as Potential Diagnostic Marker

Biomarker Insights
Perchlorate Exposure is Associated with Oxidative Stress and Indicators of Serum Iron Homeostasis Among NHANES 2005-2008 Subjects

Prednisolone-Induced Predisposition to Femoral Head Separation and the Accompanying Plasma Protein Changes in Chickens

Breast Cancer: Basic and Clinical Research
An Interesting Pathological Diagnosis - Adenoid Cystic Carcinoma in an Adolescent Girl

Cancer Growth and Metastasis
Wound Healing and Cancer Stem Cells: Inflammation as a Driver of Treatment Resistance in Breast Cancer

Cancer Informatics
Detection of Pancreatic Cancer Biomarkers Using Mass Spectrometry

Network-Constrained Group Lasso for High-Dimensional Multinomial Classification with Application to Cancer Subtype Prediction

Practical Issues in Screening and Variable Selection in Genome-Wide Association Analysis

Inferring Active and Prognostic Ligand-Receptor Pairs with Interactions in Survival Regression Models

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data

Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays

Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival

Prognostic Gene Signature Identification Using Causal Structure Learning: Applications in Kidney Cancer

Clinical Medicine Insights: Arthritis and Musculoskeletal Disorders
Knee Osteoarthritis Injection Choices: Platelet-Rich Plasma (PRP) Versus Hyaluronic Acid (A one-year randomized clinical trial)

Clinical Medicine Insights: Cardiology
Multi-Detector Coronary CT Imaging for the Identification of Coronary Artery Stenoses in a "Real-World" Population

Transthyretin Cardiac Amyloidosis: Pathogenesis, Treatments, and Emerging Role in Heart Failure with Preserved Ejection Fraction

Investigating Cardiac MRI Based Right Ventricular Contractility As A Novel Non-Invasive Metric of Pulmonary Arterial Pressure

Inflammation, Atherosclerosis, and Coronary Artery Disease: PET/CT for the Evaluation of Atherosclerosis and Inflammation

Corrigendum to "Effects of Fibrosis Morphology on Reentrant Ventricular Tachycardia Inducibility and Simulation Fidelity in Patient-Derived Models"

Hypertrophic Cardiomyopathy: A Review Cardiology

Recent Advances in the Diagnosis and Management of Cirrhosis-Associated Cardiomyopathy in Liver Transplant Candidates: Advanced Echo Imaging, Cardiac Biomarkers, and Advanced Heart Failure Therapies

Clinical Medicine Insights: Case Reports
A Case of Successful Laparoscopic Surgery for Tubal Stump Pregnancy After Tubectomy

Skin Squamous Cell Carcinoma Presenting as Cellulitis

Clinical Medicine Insights: Endocrinology and Diabetes
Combination of Linagliptin and Metformin for the Treatment of Patients with Type 2 Diabetes

Clinical Medicine Insights: Gastroenterology
Surgical Management of Adenocarcinoma of the Pancreatic Uncinate Process in a Cancer Hospital in Egypt

Management of Loose, Frequent Stools and Fecal Incontinence in a Chronic Mesenteric Ischemia Patient with Oral Serum-derived Bovine Immunoglobulin

Clinical Medicine Insights: Oncology
Cisplatin, Cetuximab, and Radiation in Locally Advanced Head and Neck Squamous Cell Cancer: A Retrospective Review

Clinical Medicine Insights: Pathology
Expression Distribution of Cancer Stem Cells, Epithelial to Mesenchymal Transition, and Telomerase Activity in Breast Cancer and Their Association with Clinicopathologic Characteristics

Clinical Medicine Insights: Pediatrics
Hepatic Dysfunction in Asphyxiated Neonates: Prospective Case-Controlled Study

A Case of Hydrometrocolpos and Polydactyly

Clinical Medicine Reviews in Therapeutics
Safety and Efficacy of Buprenorphine Patch in the Management of Chronic Pain

Evolutionary Bioinformatics
Correction to: "In Silico Detection of Virulence Gene Homologues in the Human Pathogen Sphingomonas Spp."

Clinical Medicine Insights: Trauma and Intensive Medicine
The Role of Pelvic Packing for Hemodynamically Unstable Pelvic Ring Injuries

Environmental Health Insights
Sexual Harassment and Feeding Inhibition Between Two Invasive Dengue Vectors

Houston's Novel Strategy to Control Hazardous Air Pollutants: A Case Study in Policy Innovation and Political Stalemate

Evolutionary Bioinformatics
Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana

Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier

Glycobiology Insights
Role of Galectin-3 in Cancer Metastasis

International Journal of Insect Science
Assessment of Navel Oranges, Clementine Tangerines, and Rutaceous Fruits as Hosts of Bactrocera cucurbitae and Bactrocera latifrons (Diptera: Tephritidae)

International Journal of Tryptophan Research
Enantiomeric Separation of Monosubstituted Tryptophan Derivatives and Metabolites by HPLC with a Cinchona Alkaloid-Based Zwitterionic Chiral Stationary Phase and Its Application to the Evaluation of the Optical Purity of Synthesized 6-Chloro-L-Tryptophan

Japanese Clinical Medicine
A Case of Fetal Intestinal Volvulus Without Malrotation Causing Severe Anemia

Journal of Medical Education and Curricular Development
Attitudes to Organ Donation and Knowledge of Donation and Transplantation among University of Auckland Medical Students

Lymphoma and Chronic Lymphocytic Leukemias
Mantle Cell Lymphoma: Individualizing Therapy

Ophthalmology and Eye Diseases
Glycosaminoglycans in the Human Cornea: Age-Related Changes

Palliative Care: Research and Treatment
Death in Long-term Care: A Brief Report Examining Factors Associated with Death within 31 Days of Assessment

Particle Physics Insights
Electroweak Radiative Corrections to h0 Production in Association with a Pair of Tau-sneutrino at e+ e- Linear Colliders

Tuesday, February 3, 2015

Interview with Dr Steve Klotz

This author interview is by Dr Steve Klotz, of University of Arizona. Dr Klotz's full paper, Kissing Bugs in the United States: Risk for Vector-Borne Disease in Humans, is available for download in Environmental Health Insights.

First please summarise for readers the content of your article.
This article gives the authors' perspective on the risk of the kissing bug species that are found in the United States causing an epidemic of Trypanosoma cruzi infections in man. This is certainly a "potential threat" but not realized to date. For an epidemic to occur, major changes must occur in the behavior of the insects. We discuss in great detail the kissing bug species found in the US including their behavior, physiology and carriage of T. cruzi. In addition, we also address significant issues such as allergies to kissing bug bites and methods of deterring bites as well as measures one can take to keep kissing bugs out of the home.

How did you come to be involved in your area of study?
We became interested in kissing bugs because numerous patients in the Tucson area came to clinic complaining of anaphylaxis to kissing bug bites as well as fear of Chagas disease in persons bitten numerous times by kissing bugs. Kissing bugs are common in the foothill areas of Tucson where man has moved into their territories and constructed houses. We were initially interested in determining why there were so few autochthonous cases of Chagas in US residents and implemented experiments to test questions such as how often kissing bugs defecated after feeding and did the defecation occur on the host.

What was previously known about the topic of your article?
There are 7 documented cases of autochthonous human Chagas in the US and a recent serological survey of blood donors may have found 16 other presumed autochthonous cases. Given the number of humans living in kissing bug home territories (the entire southern and south western states) this is an extremely small number. Simultaneous with the expansion of humans into the home ranges of kissing bugs is global warming and its role in the expansion of kissing bug home ranges. The question now being asked is, "what is the risk of an epidemic of Chagas occurring?"

How has your work in this area advanced understanding of the topic?
We designed experiments to determine how often wild or sylvan kissing bugs feed on humans and found to our surprise that the sylvan insects feed very often on humans. We have found a community where kissing bugs appear to have colonized homes and if documented, this would represent a significant change in behavior among US kissing bugs. We are currently working on deterrents to feeding of kissing bugs as measures to reduce the risk of significant allergies, such as anaphylaxis, in home owners.

What do you regard as being the most important aspect of the results reported in the article?
The article was a review of many different contributions by ourselves and other researchers that may bear upon the possibility of increasing numbers of US residents becoming infected with T. cruzi.

Friday, January 23, 2015

Interview with Jie Zheng

This author interview is by Dr Jie Zheng, of Nanyang Technological University, Singapore. Dr Zheng's full paper, In Silico Prediction of Synthetic Lethality by Meta-Analysis of Genetic Interactions, Functions, and Pathways in Yeast and Human Cancer, is available for download in Cancer Informatics.


Please summarise for readers the content of your article.
A pair of genes is called synthetic lethality (SL) if mutations of both genes will kill a cell while mutation of either gene alone will not. Hence, a gene in SL interactions with a cancer-specific mutated gene will be a promising drug target with anti-cancer selectivity. As wet-lab screening approaches are still expensive, computational methods are important for large-scale discovery of SL interactions.

In this article, we proposed a computational approach named MetaSL for predicting yeast SL, which integrates 17 genomic and proteomic features and the outputs of 10 classification methods. We also conducted analysis for feature ranking output by MetaSL, which provided biological insights into the observed SL in yeast. Moreover, through orthologous mapping from yeast to human genes, we then predicted several lists of candidate SL pairs in human cancer.

How did you come to be involved in your area of study?
When I was a postdoc researcher at USA National Institutes of Health, I worked on recombination hotspots in human genomes. After moving to Singapore as a junior faculty, I continued to work on this topic, but started to connect recombination directly with human diseases, especially cancer, for the critical roles of homologous recombination in genome instability and DNA damage repair. Through exploration of the literature, I came to know the new anti-cancer strategy of synthetic lethality. Based on this study, I applied for a grant on computational methods to understand and predict new SL gene pairs as potential cancer drug targets, and got awarded by the Ministry of Education, Singapore. This paper is part of this project.

What was previously known about the topic of your article?
There are several studies working on computational prediction for SL pairs. However, most of them focused on using individual features or single machine learning models. For example, Li et al. used protein domain as the main type of features and support vector machine (SVM) for SL prediction (Ref. [12] in the main text).

How has your work in this area advanced understanding of the topic?
Our work can shed light on both computational and biological aspects of SL prediction. Firstly, meta-analysis methods have been shown to improve the prediction accuracy by data integration and model combination. Secondly, we observed that similarity based features (e.g. relation between two proteins) are more important than lethality based features (e.g., characteristics for individual proteins). Thirdly, study of sig¬nalling pathways will be promising to understand and inter¬pret the underlying mechanisms of SL, as our manually collected SL pairs tend to occur in the same pathways.

What do you regard as being the most important aspect of the results reported in the article?
By comparing three types of human SL pairs (as shown in Table 6 in the main text of our article), our manually collected SL pairs are more likely to be involved in the same pathways than those predicted from yeast SL pairs. These results indicate that we may derive more features from signaling pathways for SL prediction. Our next step is to study the topological and dynamic properties of signaling pathways (e.g. crosstalk) to further improve the prediction of SL gene pairs.

http://www.ntu.edu.sg/home/zhengjie/

Friday, January 16, 2015

Published This Week (12th Jan - 16th Jan)

We are pleased to announce the publication of the following peer reviewed papers. Sign up to receive email alerts to receive immediate notification of new papers.

Biomarker Insights
Prednisolone-Induced Predisposition to Femoral Head Separation and the Accompanying Plasma Protein Changes in Chickens

Breast Cancer: Basic and Clinical Research
An Interesting Pathological Diagnosis - Adenoid Cystic Carcinoma in an Adolescent Girl

Cancer Informatics
Network-Constrained Group Lasso for High-Dimensional Multinomial Classification with Application to Cancer Subtype Prediction

Practical Issues in Screening and Variable Selection in Genome-Wide Association Analysis

Clinical Medicine Insights: Case Reports
A Case of Successful Laparoscopic Surgery for Tubal Stump Pregnancy After Tubectomy

Skin Squamous Cell Carcinoma Presenting as Cellulitis

Clinical Medicine Insights: Gastroenterology
Surgical Management of Adenocarcinoma of the Pancreatic Uncinate Process in a Cancer Hospital in Egypt

Clinical Medicine Insights: Pediatrics
Hepatic Dysfunction in Asphyxiated Neonates: Prospective Case-Controlled Study

A Case of Hydrometrocolpos and Polydactyly

Clinical Medicine Reviews in Therapeutics
Safety and Efficacy of Buprenorphine Patch in the Management of Chronic Pain

Evolutionary Bioinformatics
Correction to: "In Silico Detection of Virulence Gene Homologues in the Human Pathogen Sphingomonas Spp."

Glycobiology Insights
Role of Galectin-3 in Cancer Metastasis

Monday, January 12, 2015

Interview with Author Dr David Johnson

This author interview is by Dr David Johnson, of Imperial College London.  Dr Johnson's full paper, Semantically Linking In Silico Cancer Models, is available for download in Cancer Informatics.

Please summarise for readers the content of your article.

Our paper describes a new approach to thinking about the informatics behind cancer models. We think of computational models as any other data, which can be linked to metadata. We use connected property graphs as a means to representing data in such a way that meaningful questions can be asked of a database containing many cancer models. Models can be composed into larger models, even where different research groups have developed them. What our property-graph approach enables is a way of exploring possible model combinations based on semantic links, primarily through computaitonal interfaces, where compatibilities may be reasoned based on common units, computaional types, and biological concepts. The actual composition of models would still require a lot of rework and validation. In our paper we show two examples of describing cancer models as property graphs: one based on an EGFR-ERK pathway module, the other on a decomposed vascular tumour growth modelling framework.

How did you come to be involved in your area of study?

I have worked on life science and biological informatics since beginning my postdoctoral research, initially working on developing software for phylogenetics (the study of evolutionary relationships among populations and species) research in Professor Mark Pagel's Evolutionary Biology Group at the Univeresity of Reading, UK. Following this, I was appointed to the University of Oxford's Computing Laboratory (now called the Department of Computer Science) to work on the ‘Transatlantic Tumor Model Repositories' project developing interoperable databases between the US and Europe. This body of work eventually led to the work described in our contributions in this paper.

What was previously known about the topic of your article?

The idea of using linked data is not novel - in fact in biology in general, relating data and models to domain knowledge is commonplace, where there is a mature ecosytem of biological standards and ontologies to manage the diversity of data in biomedical sciences. There are established Web standards, such as RDF, OWL and SPARQL, are used to link datasets together. However these technologies primary purpose is to enable interoperation across distributed systems on the Web. Our approach is to link data in the first instance, within a cancer model database.

How has your work in this area advanced understanding of the topic?

Biological data management is creating new use cases for ‘NoSQL' databases including those that adopt the property graph data model, such as Neo4j that we used in our study. What we have proven is that linking model data, in particular model interfaces (input and output parameters) has the potential to create a system by which we can explore cancer model compositions. The challenge now is to use property graphs to build up a comprehensive resource of cancer models linked to metadata, to hopefully have an environment by which we can discover new candidate model compositions that could steer multiscale model research.

What do you regard as being the most important aspect of the results reported in the article?

Linking cancer models to metadata is a first step to producing an ecosystem of models and data. What we envisage is that we could link datasets into our property graphs, where not only model compositions could be inferred, but data-model combinations that may have previously not been identified could be found. Our focus was very much on the data management aspect of cancer informatics that we hope will in-turn help further the science in cancer research.

If you would like to include a link to a departmental webpage, LinkedIn profile, or other webpage where readers can learn more about your work paste it below:

There is a live demo of some of the work presented in the paper available here: http://gist.neo4j.org/?6038a7b526bfa48da2c0

LinkedIn: http://uk.linkedin.com/in/drdavidjohnson

Twitter: @NuDataScientist

ORCiD: http://orcid.org/0000-0002-2323-6847

Friday, January 9, 2015

Published This Week (5th Jan - 9th Jan)

We are pleased to announce the publication of the following peer reviewed papers. Sign up to receive email alerts to receive immediate notification of new papers.

Cancer Informatics
Detection of Pancreatic Cancer Biomarkers Using Mass Spectrometry

Clinical Medicine Insights: Arthritis and Musculoskeletal Disorders
Knee Osteoarthritis Injection Choices: Platelet-Rich Plasma (PRP) Versus Hyaluronic Acid (A one-year randomized clinical trial)

Clinical Medicine Insights: Cardiology
Multi-Detector Coronary CT Imaging for the Identification of Coronary Artery Stenoses in a "Real-World" Population

Transthyretin Cardiac Amyloidosis: Pathogenesis, Treatments, and Emerging Role in Heart Failure with Preserved Ejection Fraction

Investigating Cardiac MRI Based Right Ventricular Contractility As A Novel Non-Invasive Metric of Pulmonary Arterial Pressure

Inflammation, Atherosclerosis, and Coronary Artery Disease: PET/CT for the Evaluation of Atherosclerosis and Inflammation

Clinical Medicine Insights: Endocrinology and Diabetes
Combination of Linagliptin and Metformin for the Treatment of Patients with Type 2 Diabetes

Clinical Medicine Insights: Oncology
Cisplatin, Cetuximab, and Radiation in Locally Advanced Head and Neck Squamous Cell Cancer: A Retrospective Review

Clinical Medicine Insights: Pathology
Expression Distribution of Cancer Stem Cells, Epithelial to Mesenchymal Transition, and Telomerase Activity in Breast Cancer and Their Association with Clinicopathologic Characteristics

Environmental Health Insights
Sexual Harassment and Feeding Inhibition Between Two Invasive Dengue Vectors

Evolutionary Bioinformatics
Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana

International Journal of Tryptophan Research
Enantiomeric Separation of Monosubstituted Tryptophan Derivatives and Metabolites by HPLC with a Cinchona Alkaloid-Based Zwitterionic Chiral Stationary Phase and Its Application to the Evaluation of the Optical Purity of Synthesized 6-Chloro-L-Tryptophan

Japanese Clinical Medicine
A Case of Fetal Intestinal Volvulus Without Malrotation Causing Severe Anemia

Particle Physics Insights
Electroweak Radiative Corrections to h0 Production in Association with a Pair of Tau-sneutrino at e+ e- Linear Colliders

Wednesday, January 7, 2015

Public Science Insights: Nanotechnology and the organ donation shortage?

The world is facing a growing crisis as the number of patients on organ donation waiting lists far outpaces the number of adequate organs available for transplantation. Increased vital organ failure in the aging population of the West, twinned with rapidly improving post transplantation survival rates, have served to compound this issue. For example, in the US alone more than 120,000 people are currently on the transplant waiting list; on average 18 people die everyday while waiting for a transplant, and every 10 minutes another name is added to the list1.

An often cited solution to this growing problem is the promise of Tissue Engineering; the process of replacing, engineering or regenerating human cells, tissues or organs to restore or establish normal function. A basic schematic of a typical Tissue Engineering approach (Figure 1) sees cells isolated from a patients injured tissue and cultivated in the lab before being seeded on a specialised scaffold and re-implanted into the body. Tissue Engineering has received a lot of recent press due to the pioneering advances made by the likes of Robert Langer and Anthony Atala; the latter having successfully tissue engineered bladders and vaginal organs2. The key is to isolate undifferentiated cells, expand them to sufficient quantities and then use a scaffold to direct their differentiation into the cell type of choice. For example, in engineering a blood vessel you might isolate endothelial-progenitor cells to form the inner lining and mesenchymal stem cells for the outer connective tissue. You may then create a cylindrical scaffold that resembles a blood vessel and seed endothelial-progenitors on the inside and mesenchymal stem cells on the outside. If you had created a scaffold that resembled their normal biological environment closely enough, the cells may be ‘tricked' into forming a new section of blood vessel, which could be implanted into the patient.

Biologists and material scientists now know a great deal about the features of basic structures such as a blood vessel. We know that endothelial cells are more likely to be happy if seeded onto a very smooth surface and so this is how we would manufacture a tissue-engineered substitute. We also know that if endothelial cells are subjected to flow they will produce a factor known as VEGF, which promotes blood vessel formation, and so they may be cultured in a flow chamber. The tough connective tissue on the outside of the vessel, however, requires nanoscale ridges for differentiating fibroblasts to ‘hang on' to. By providing these biomimetic nanoscale features, successful tissue engineering becomes a step closer.

Cells exist in a nanoscale environment, and it is only by understanding and replicating the nanoscale features of their environment that we will be able to engineer very complex tissues, such as the solid organs. It may be a long way off, but there is a chance that new technologies such as those developed by Anthony Atala could solve the growing crisis in organ transplantation.

Figure 1 - Provided by the author

Schematic illustrating the typical stages involved in Tissue Engineering. First a tissue biopsy is taken from the patient. Cells of interest are isolated or derived according to literature best practices. Once bulked up, cells can be seeded onto a biomimetically-designed scaffold and cultured in a bioreactor designed to mimic the in vivo environment. The cell populated scaffold can then be grafted onto tissues of interest in the patient where they can help repair or augment organ function.

References
1. Department of Health and Human Services. U.S. Government Information on Organ and Tissue Donation and Transplantation. (2014). at
2. TEDMED. Growing new organs. (2009). at
3. Cassidy, J. W. Nanotechnology in the Regeneration of Complex Tissues. Bone Tissue Regen. Insights 25 (2014). doi:10.4137/BTRI.S12331

Dr John W Cassidy is author of the recently published paper Nanotechnology in the Regeneration of Complex Tissues, available for download now in Bone and Tissue Regeneration Insights