Identifying Parkinson's Patients: A Functional Gradient Boosting Approach.

Parkinson's, a progressive neural disorder, is difficult to identify due to the hidden nature of the symptoms associated. We present a machine learning approach that uses a definite set of features obtained from the Parkinsons Progression Markers Initiative(PPMI) study as input and classifies them into one of two classes: PD(Parkinson's disease) and HC(Healthy Control). As far as we know this is the first work in applying machine learning algorithms for classifying patients with Parkinson's disease with the involvement of domain expert during the feature selection process.

Combined Effects of Irrigation Regime, Genotype, and Harvest Stage Determine Tomato Fruit Quality and Aptitude for Processing into Puree.

Industry tomatoes are produced under a range of climatic conditions and practices which significantly impact on main quality traits of harvested fruits. However, the quality of tomato intended for processing is currently addressed on delivery through color and Brix only, whereas other traits are overlooked. Very few works provided an integrated view of the management of tomato puree quality throughout the chain.

Monosomy 17 in potentially curable HER2-amplified breast cancer: prognostic and predictive impact.

Purpose: HER2 copy number by fluorescence in situ hybridization (FISH) is typically reported relative to the centromere enumeration probe 17 (CEP17). HER2/CEP17 ratio could be impacted by alterations in the number of chromosome 17 copies. Monosomy of chromosome 17 (m17) is found in ~ 1900 cases of early-stage HER2-positive breast cancer annually in the United States; however, the efficacy of HER2-directed trastuzumab therapy in these patients is not well characterized.

Applying family analyses to electronic health records to facilitate genetic research.

Motivation: Pedigree analysis is a longstanding and powerful approach to gain insight into the underlying genetic factors in human health, but identifying, recruiting and genotyping families can be difficult, time consuming and costly. Development of high throughput methods to identify families and foster downstream analyses are necessary.

Results: This paper describes simple methods that allowed us to identify 173 368 family pedigrees with high probability using basic demographic data available in most electronic health records (EHRs).

Methodological Considerations for Comparison of Brand Versus Generic Versus Authorized Generic Adverse Event Reports in the US Food and Drug Administration Adverse Event Reporting System (FAERS).

Background: The US Food and Drug Administration Adverse Event Reporting System (FAERS), a post-marketing safety database, can be used to differentiate brand versus generic safety signals.

Objective: To explore the methods for identifying and analyzing brand versus generic adverse event (AE) reports.

Methods: Public release FAERS data from January 2004 to March 2015 were analyzed using alendronate and carbamazepine as examples.

Treatment patterns and outcomes for patients with locally advanced basal cell carcinoma before availability of Hedgehog pathway inhibitors: a retrospective chart review.

Unlabelled: Understanding the molecular basis of basal cell carcinoma (BCC) has led to development of Hedgehog pathway inhibitors (HPIs) for patients with advanced forms of BCC (aBCC). A practical definition of aBCC as a distinct disease entity is unavailable, and epidemiological information is limited. To conduct the RONNIE study to describe characteristics, treatment patterns, and outcomes of patients with aBCC during the period preceding HPI introduction, as well as results from patients with locally advanced BCC (laBCC).

Pulmonary Mechanics and Mortality in Mechanically Ventilated Patients Without Acute Respiratory Distress Syndrome: A Cohort Study.

Background: Driving pressure has been proposed as a major determinant of outcome in patients with acute respiratory distress syndrome (ARDS), but there is little data examining the association between pulmonary mechanics, including driving pressure, and outcomes in mechanically ventilated patients without ARDS.

Methods: Secondary analysis from 1,705 mechanically ventilated patients enrolled in a clinical study that examined outcomes associated with the use of early lung-protective mechanical ventilation. The primary outcome was mortality and the secondary outcome was the incidence of ARDS.

A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications.

We present a simple text mining method that is easy to implement, requires minimal data collection and preparation, and is easy to use for proposing ranked associations between a list of target terms and a key phrase. We call this method KinderMiner, and apply it to two biomedical applications. The first application is to identify relevant transcription factors for cell reprogramming, and the second is to identify potential drugs for investigation in drug repositioning.

Early aspirin use and the development of cardiac allograft vasculopathy.

Background: Cardiac allograft vasculopathy (CAV) remains a leading cause of morbidity and mortality after orthotopic heart transplantation (OHT). Little is known about the influence of aspirin on clinical expression of CAV.

Methods: We followed 120 patients with OHT at a single center for a median of 7 years and categorized them by the presence or absence of early aspirin therapy post-transplant (aspirin treatment ≥6 months in the first year).

Biodegradation of pharmaceuticals and endocrine disruptors with oxygen, nitrate, manganese (IV), iron (III) and sulfate as electron acceptors.

Biodegradation of pharmaceuticals and endocrine disrupting compounds was examined in long term batch experiments for a period of two and a half years to obtain more insight into the effects of redox conditions. A mix including lipid lowering agents (e.g.

Comparison of brand versus generic antiepileptic drug adverse event reporting rates in the U.S. Food and Drug Administration Adverse Event Reporting System (FAERS).

Objective: Despite the cost saving role of generic anti-epileptic drugs (AEDs), debate exists as to whether generic substitution of branded AEDs may lead to therapeutic failure and increased toxicity. This study compared adverse event (AE) reporting rates for brand vs. authorized generic (AG) vs.

Unraveling the complexities of the velocity dependency of E. coli retention and release parameters in saturated porous media.

Escherichia coli transport and release experiments were conducted to investigate the pore-water velocity (v) dependency of the sticking efficiency (α), the fraction of the solid surface area that contributed to retention (S), the percentage of injected cells that were irreversibly retained (M), and cell release under different (10-300mM) ionic strength (IS) conditions. Values of α, S, and M increased with increasing IS and decreasing v, but the dependency on v was greatest at intermediate IS (30 and 50mM). Following the retention phase, successive increases in v up to 100 or 150mday and flow interruption of 24h produced negligible amounts of cell release.

Assessing fracture risk in early stage breast cancer patients treated with aromatase-inhibitors: An enhanced screening approach incorporating trabecular bone score.

Introduction: Aromatase-inhibitors (AIs) are commonly used for treatment of patients with hormone-receptor positive breast carcinoma, and are known to induce bone density loss and increase the risk of fractures. The current standard-of-care screening tool for fracture risk is bone mineral density (BMD) by dual-energy X-ray absorptiometry (DXA). The fracture risk assessment tool (FRAX®) may be used in conjunction with BMD to identify additional osteopenic patients at risk of fracture who may benefit from a bone-modifying agent (BMA).

Structure-Leveraged Methods in Breast Cancer Risk Prediction.

Predicting breast cancer risk has long been a goal of medical research in the pursuit of precision medicine. The goal of this study is to develop novel penalized methods to improve breast cancer risk prediction by leveraging structure information in electronic health records. We conducted a retrospective case-control study, garnering 49 mammography descriptors and 77 high-frequency/low-penetrance single-nucleotide polymorphisms (SNPs) from an existing personalized medicine data repository.

Defining Components of Team Leadership and Membership in Prehospital Emergency Medical Services.

Background: Teamwork is critical for patient and provider safety in high-stakes environments, including the setting of prehospital emergency medical services (EMS).

Objective: We sought to describe the components of team leadership and team membership on a single patient call where multiple EMS providers are present.

Methods: We conducted a two-day focus group with nine subject matter experts in crew resource management (CRM) and EMS using a structured nominal group technique (NGT).

Baseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data.

Computational Drug Repositioning (CDR) is the knowledge discovery process of finding new indications for existing drugs leveraging heterogeneous drug-related data. Longitudinal observational data such as Electronic Health Records (EHRs) have become an emerging data source for CDR. To address the high-dimensional, irregular, subject and time-heterogeneous nature of EHRs, we propose Baseline Regularization (BR) and a variant that extend the one-way fixed effect model, which is a standard approach to analyze small-scale longitudinal data.

Meioc maintains an extended meiotic prophase I in mice.

The meiosis-specific chromosomal events of homolog pairing, synapsis, and recombination occur over an extended meiotic prophase I that is many times longer than prophase of mitosis. Here we show that, in mice, maintenance of an extended meiotic prophase I requires the gene Meioc, a germ-cell specific factor conserved in most metazoans. In mice, Meioc is expressed in male and female germ cells upon initiation of and throughout meiotic prophase I.

Effect of aquifer storage and recovery (ASR) on recovered stormwater quality variability.

Aquifer Storage and Recovery (ASR) is increasingly being considered as a means of reusing urban stormwater to supplement available urban water resources. Storage of stormwater in an aquifer has been shown to affect water quality but it has also been claimed that storage will also decrease the stormwater quality variability making for improved predictability and management. This study is the first to document the changes in stormwater quality variability as a result of subsurface storage at four full scale ASR sites using advanced statistical techniques.

Computational Drug Repositioning Using Continuous Self-Controlled Case Series.

Computational Drug Repositioning (CDR) is the task of discovering potential new indications for existing drugs by mining large-scale heterogeneous drug-related data sources. Leveraging the patient-level temporal ordering information between numeric physiological measurements and various drug prescriptions provided in Electronic Health Records (EHRs), we propose a Continuous Self-controlled Case Series (CSCCS) model for CDR. As an initial evaluation, we look for drugs that can control Fasting Blood Glucose (FBG) level in our experiments.

Linear methods for reducing EMG contamination in peripheral nerve motor decodes.

Signals recorded from the peripheral nervous system (PNS) with high channel count penetrating microelectrode arrays, such as the Utah Slanted Electrode Array (USEA), often have electromyographic (EMG) signals contaminating the neural signal. This common-mode signal source may prevent single neural units from successfully being detected, thus hindering motor decode algorithms. Reducing this EMG contamination may lead to more accurate motor decode performance.

A preclinical screen to evaluate pharmacotherapies for the treatment of agitation in dementia.

Agitation associated with dementia is frequently reported clinically but has received little attention in preclinical models of dementia. The current study used a 7PA2 CM intracerebroventricular injection model of Alzheimer's disease (AD) to assess acute memory impairment, and a bilateral intrahippocampal (IH) injection model of AD (aggregated Aβ1-42 injections) and a bilateral IH injection model of dementia with Lewy bodies (aggregated NAC61-95 injections) to assess chronic memory impairment in the rat. An alternating-lever cyclic-ratio schedule of operant responding was used for data collection, where incorrect lever perseverations measured executive function (memory) and running response rates (RRR) measured behavioral output (agitation).

Two intermittent vismodegib dosing regimens in patients with multiple basal-cell carcinomas (MIKIE): a randomised, regimen-controlled, double-blind, phase 2 trial.

Background: Vismodegib, a first-in-class Hedgehog-pathway inhibitor, is approved for use in adults with advanced basal-cell carcinoma. Patients with multiple basal-cell carcinomas, including those with basal-cell nevus (Gorlin) syndrome, need extended treatment. We assessed the safety and activity of two long-term intermittent vismodegib dosing regimens in patients with multiple basal-cell carcinomas.