bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiplexing high‐side load switch using adaptive well biasing
Authors: Dilello A. , Rumberg B. , Graham D.W.
Published: April 2016

A high‐side load switch is presented for applications that require multiplexing the supply terminal to multiple voltage sources that are different, unknown, and/or dynamic. The design incorporates p‐channel switches with adaptive n‐well biasing to ensure that no junction is forward biased. Measured results are presented from a circuit that has been fabricated in a standard 0.35 μm CMOS process. The circuit is also demonstrated in an application of programming non‐volatile memory.
Load disturbance observer‐based control method for sensorless PMSM drive
Authors: Xiaoquan Lu , Heyun Lin , Junlin Han
Published: April 2016

This study proposes a sensorless control method for the permanent magnet synchronous machine (PMSM) drive that is robust against load torque variations. The proposed method is based on the disturbance observer‐based control (DOBC) method, and involves the use of a back electromotive force observer and a torque observer to estimate rotor position and compensate for load torque disturbance, respectively. This mechanism is simple to implement and requires no state vector derivation. The gains of the two observers are carefully selected to improve estimation accuracy and dynamic performance. The performance of the proposed load DOBC for sensorless PMSM drives was tested through a simulation, where the sensorless estimation error was considered to determine the adjustment laws for the proposed observer gains. Furthermore, results of evaluative experiments verified the effectiveness of the proposed method for high‐performance sensorless control and torque disturbance rejection for the PMSM drive.
Eigenvalue‐based relative parameter sensitivity analysis for optimised performance of sensorless induction motor drives
Authors: Kumar Rakesh , Das Sukanta
Published: April 2016

The formulation of a suitable control scheme for induction motor (IM) drive capable of working in a wide speed range including low and zero speed regions is a challenging task as the system parameters are prone to vary significantly due to temperature rise, skin effect and associated factors. The present study proposes eigenvalue sensitivity‐based generalised analytic approach for identifying the dominant motor parameter(s) which affect(s) the estimated speed most severely in the speed sensorless IM drive system. Once such parameter(s) is/are identified, a compensation scheme can be adopted for the same without worrying to the effect of the other motor parameters on the estimated speed. This not only reduce(s) the drive's complexity but also improves the reliability of the overall system. To validate the proposed approach, two different model reference adaptive systems are considered for the speed sensorless IM drive. All the relevant study is done in MATLAB/Simulink. The experimental results as obtained by a dSPACE‐1104‐based laboratory prototype also justify the analysis.
Modelling the operation strategies of storages and hydro resources in adequacy analysis of power systems in presence of wind farms
Authors: Shariatkhah Mohammad‐Hossein , Haghifam Mahmoud‐Reza , Chicco Gianfranco , Parsa‐Moghaddam Mohsen
Published: April 2016

This study addresses the adequacy of a generating system considering the impact of operation strategies of storages and hydro energy resources. It is assumed that the installed storage capacity of a system can be assigned for two purposes: first, economical operation which adopts storage to shift electric energy and smooth the load curve; and the second, reliability‐based operation, which deploys storage to avoid load curtailments. The economical operation strategy is represented by starting from time domain data and using the load curve modification method to synthesise the overall impact of storage. The reliability‐based operation is modelled with a new method based on Markov chain model that considers the dynamic behaviour of storage during time. Moreover, a novel state reduction method is presented for decreasing the number of Markov states in applications to large systems. The effectiveness of the presented methods is evaluated by running several simulation scenarios with results presented on three test systems. The results demonstrate that evaluating the system reliability in the presence of energy storage by considering the frequency and duration of system states is more effective than using methods based on the Capacity Outage Probability Table (COPT).
Overshoot effects of electron on efficiency droop in InGaN/GaN MQW light-emitting diodes
Authors: Huang Yang , Liu Zhiqiang , Yi Xiaoyan , Guo Yao , Wu Shaoteng , Yuan Guodong , Wang JunXi , Wang Guohong , Li Jinmin
Published: April 2016

To evaluate electron leakage in InGaN/GaN multiple quantum well (MQW) light emitting diodes (LEDs), analytic models of ballistic and quasi-ballistic transport are developed. With this model, the impact of critical variables effecting electron leakage, including the electron blocking layer (EBL), structure of multiple quantum wells (MQWs), polarization field, and temperature are explored. The simulated results based on this model shed light on previously reported experimental observations and provide basic criteria for suppressing electron leakage, advancing the design of InGaN/GaN LEDs.
Impacts of high intensity crop rotation and N management on oilseed rape productivity in Germany
Authors: Hegewald Hannes , Koblenz Barbara , Wensch-Dorendorf Monika , Christen Olaf
Published: April 2016

A rotational field experiment was established in the year 2002 at the experimental farm Etzdorf in the Hercynian dry region of central Germany. Since 2005 field measured datasets were used to determine the effect of different preceding crop combinations and different nitrogen (N) fertilisation treatments on the seed yield, oil content, oil yield and N-use efficiency of oilseed rape (Brassica napus L.). The preceding crop combinations compared were winter wheat (Triticum aestivum L.)-winter wheat (WW), WW-oilseed rape (OSR), OSR-OSR and an OSR monoculture. In addition to the preceding crop combination, N fertiliser treatments with either 120 kg N ha–1 or 180 kg N ha–1 were established in the year 2013.
Overall the results demonstrated that seed yield, oil yield and N-use efficiency all declined with an increased cropping intensity for the period 2005–2012. Higher N rates in the 2013–2014 seasons increased seed yield and oil yield when OSR followed WW-WW pre-crops. OSR monoculture had lowest yield independent of applied N. Seed yield declined from 4.61 t ha–1 (OSR following WW-WW) to 4.28 t ha–1 in the OSR monoculture with 120 kg N ha–1, and from 4.81 t ha–1 (following WW-WW) to 4.42 t ha–1 in the OSR monoculture with 180 kg N ha–1. Higher N rates generally reduced N-use efficiency, with highest N-efficiency for WW-WW-OSR (38.4 kg kg–1), and lowest for continuous OSR receiving 180 kg N ha–1 (24.5 kg kg–1).
These results emphasise the importance of crop rotation to maintain seed yield and oil yield of oilseed rape, and to maximise the response to applied N. A reduced N rate increased N-use efficiency and reduced the risk of high N surpluses without a significant/equivalent decrease of the seed yield when the rotation was optimised.
Resourcing an evolution of roles in general-practice: a study to determine the validity and reliability of tools to assist nurses and patients to assess physical activity
Authors: Dutton Shona N. , Bauman Adrian , Dennis Sarah M. , Zwar Nicholas , Harris Mark F.
Published: April 2016

Traditionally, GPs have been responsible for physical activity (PA) assessment within the general practice setting. Multiple questionnaires are available to support uptake of PA assessment but less than 30% of patients are assessed. A range of barriers hamper uptake. Evidence indicates that practice nurses (PNs) and patients are resourceful members of the general practice team but have been underutilised. This study assessed the validity and reliability of two instruments for assessing PA, administered by PNs and patients. The study aimed to identify robust tool(s) to support the evolving role of PNs and patients in prevention and management strategies in general practice. A purposive sample of PNs and patients from general practices in Sydney was invited to participate. The results of the PN- or patient-administered general practice physical activity questionnaire (GPPAQ) and the three-question physical activity questionnaire (3Q) were compared against accelerometer activity. The study examined agreement in classification of PA levels according to Australian PA recommendations. Validity showed low–moderate correlations between accelerometer and GPPAQ (rho=0.26), 3Q (rho=0.45). Seven-day test-retest reliability intraclass correlation coefficients (ICCs) were 0.82–0.95 for GGPAQ and 0.94–0.98 for 3Q. Agreement with PA recommendations was moderate for GPPAQ (kappa 0.73, 95% CI, 0.56–0.85) and fair for 3Q (kappa 0.62, 95% CI, 0.47–0.78). Although 3Q demonstrated higher correlation with accelerometry, GPPAQ demonstrated higher agreement with PA guidelines. Given GPPAQ showed reasonable rigour, it may prove useful for PN and patient use.
Canonical and noncanonical intraflagellar transport regulates craniofacial skeletal development
Authors: Noda Kazuo , Kitami Megumi , Kitami Kohei , Kaku Masaru , Komatsu Yoshihiro
Published: April 2016

Significance

Intraflagellar transport (IFT) plays a critical role in assembling primary cilia that mediate growth factor signaling. The disruption or dysfunction of IFT components can generate multiple diseases, including skeletal dysplasia. However, the mechanism by which IFT regulates skeletogenesis remains elusive. In the present study, we show that neural crest-specific deletion of the gene that encodes intraflagellar transport 20 (IFT20) in mice compromises ciliogenesis and the intracellular transport of collagen, leading to osteopenia in the face. Our findings highlight a unique function of IFT beyond its role in cilium assembly during craniofacial development, suggesting that IFT20 is indispensable for the regulation of not only ciliogenesis but also the intracellular trafficking of collagen in the unique multipotent stem cell population of cranial neural crests.
Human DDX3 protein is a valuable target to develop broad spectrum antiviral agents
Authors: Brai Annalaura , Fazi Roberta , Tintori Cristina , Zamperini Claudio , Bugli Francesca , Sanguinetti Maurizio , Stigliano Egidio , Esté José , Badia Roger , Franco Sandra , Martinez Miguel A. , Martinez Javier P. , Meyerhans Andreas , Saladini Francesco , Zazzi Maurizio , Garbelli Anna , Maga Giovanni , Botta Maurizio
Published: April 2016

Significance

Human DEAD-box polypeptide 3 (DDX3) is an ATPase/RNA helicase involved in the replication of many viral pathogens. We reported herein the first inhibitor, to our knowledge, of the helicase binding site of DDX3 endowed with a broad spectrum antiviral activity [HIV-1 WT, HIV drug-resistant strains, Hepatitis C virus (HCV), Dengue virus (DENV), and West Nile virus (WNV)]. The good toxicity profile suggests that the DDX3 activity, although essential for viruses, could be dispensable to the cells, validating DDX3 as a pharmaceutical target. Our results clearly showed that DDX3 inhibitors could be exploited to treat HIV/HCV coinfections, emerging infectious diseases (such as DENV and WNV), and HIV-1 patients carrying drug-resistant strains. Each of these three medical conditions currently represents a major challenge for clinical treatment.
Single-enzyme biomineralization of cadmium sulfide nanocrystals with controlled optical properties
Authors: Dunleavy Robert , Lu Li , Kiely Christopher J. , McIntosh Steven , Berger Bryan W.
Published: April 2016

Significance

Biomineralization is a promising, yet complex, route toward the scalable and green biomanufacturing of functional nanomaterials, involving multiple biomolecules acting in unison to control mineralization and crystal structure. Unraveling the interdependent complexity of biomineralization is a barrier to completely realize this approach. We distill this complexity to a single enzyme that both catalyzes the formation of the reactive precursors required for mineralization and templates nanocrystal growth in solution. This is the first report of a single enzyme capable of providing all of the required functionality for active biomineralization from otherwise unreactive solution. This work provides insight into the mechanism of metal sulfide biomineralization and is an example of the elegance in green functional material synthesis achievable through engineered biomineralization.
Appreciation for Analysis of how Levonorgestrel Works and Reservations with the use of Meloxicam as Emergency Contraception
Authors: Schneider A. Patrick , Kubat Christopher , Zainer Christine M.
Published: April 2016

This paper is a response to Dr. Kathleen Raviele's recent article on her critical analysis of the use of levonorgestrel given to women postsexual assault and her suggestion that the use of Meloxicam may be an ethical alternative.
Objects but not concepts modulate the size of the attended region
Authors: Goodhew Stephanie C. , Edwards Mark
Published: April 2016

Here we investigated the types of stimuli that modulate the size of the attentional spotlight. In particular, it has been previously shown that conceptual cues that either directly refer to or are semantically related to particular spatial locations can shift attention to that location (known as “ conceptual cueing”). For example, reading the word sun or joy can shift attention upward whereas the word boot or hostile can shift attention downward. Here, therefore, we tested whether words could modulate the size of the attended area. Across five experiments, we found that words that either directly referred to, or were abstractly associated with, particular sizes (small versus large) did not change the size of the attentional spotlight, whereas the presence of differently sized stimuli did, as evidenced by faster responses to targets when the spotlight is small than when it is large. This suggests that physical but not conceptual inducers can modulate the size of the attentional spotlight. This highlights an important difference between the regulation of spotlight size and shifts of attention, supporting the notion that they are subserved by distinct mechanisms.
TnT: a set of libraries for visualizing trees and track-based annotations for the web
Authors: Pignatelli Miguel
Published: April 2016

Summary: There is an increasing need for rich and dynamic biological data visualizations in bioinformatic web applications. New standards in web technologies, like SVG or Canvas, are now supported by most modern web browsers allowing the blossoming of powerful visualizations in biological data analysis. The exploration of different ways to visualize genomic data is still challenging due to the lack of flexible tools to develop them. Here, I present a set of libraries aimed at creating powerful tree- and track-based visualizations for the web. Its modularity and rich API facilitate the development of many different visualizations ranging from simple species trees to complex visualizations comprising per-node data annotations or even simple genome browsers.

Availability and Implementation: The TnT libraries have been written in Javascript, licensed under the APACHE 2.0 license and hosted at https://github.com/tntvis.

Contact:  mp@ebi.ac.uk
Estimating IBD tracts from low coverage NGS data
Authors: Vieira Filipe G. , Albrechtsen Anders , Nielsen Rasmus
Published: April 2016

Motivation: The amount of IBD in an individual depends on the relatedness of the individual’s parents. However, it can also provide information regarding mating system, past history and effective size of the population from which the individual has been sampled.

Results: Here, we present a new method for estimating inbreeding IBD tracts from low coverage NGS data. Contrary to other methods that use genotype data, the one presented here uses genotype likelihoods to take the uncertainty of the data into account. We benchmark it under a wide range of biologically relevant conditions and show that the new method provides a marked increase in accuracy even at low coverage.

Availability and implementation: The methods presented in this work were implemented in C/C ++ and are freely available for non-commercial use from https://github.com/fgvieira/ngsF-HMM.

Contact:  fgvieira@snm.ku.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases
Authors: Queralt-Rosinach Núria , Piñero Janet , Bravo Àlex , Sanz Ferran , Furlong Laura I.
Published: April 2016

Motivation: DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web. Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected linked open data.

Availability and implementation:  http://rdf.disgenet.org/

Contact:  support@disgenet.org
CaFE: a tool for binding affinity prediction using end-point free energy methods
Authors: Liu Hui , Hou Tingjun
Published: April 2016

Summary: Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters.

Availability and implementation: CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin. It is a VMD plugin written in Tcl and the usage is platform-independent.

Contact:  tingjunhou@zju.edu.cn
BRAT-nova: fast and accurate mapping of bisulfite-treated reads
Authors: Harris Elena Y. , Ounit Rachid , Lonardi Stefano
Published: April 2016

Summary: In response to increasing amounts of sequencing data, faster and faster aligners need to become available. Here, we introduce BRAT-nova, a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq). BRAT-nova is very fast and accurate. On the human genome, BRAT-nova is 2–7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2–8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy and space efficiency.

Availability and implementation: The software is available in the public domain at http://compbio.cs.ucr.edu/brat/

Contact:  elenah@cs.ucr.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
densityCut: an efficient and versatile topological approach for automatic clustering of biological data
Authors: Ding Jiarui , Shah Sohrab , Condon Anne
Published: April 2016

Motivation : Many biological data processing problems can be formalized as clustering problems to partition data points into sensible and biologically interpretable groups.

Results : This article introduces densityCut, a novel density-based clustering algorithm, which is both time- and space-efficient and proceeds as follows: densityCut first roughly estimates the densities of data points from a K -nearest neighbour graph and then refines the densities via a random walk. A cluster consists of points falling into the basin of attraction of an estimated mode of the underlining density function. A post-processing step merges clusters and generates a hierarchical cluster tree. The number of clusters is selected from the most stable clustering in the hierarchical cluster tree. Experimental results on ten synthetic benchmark datasets and two microarray gene expression datasets demonstrate that densityCut performs better than state-of-the-art algorithms for clustering biological datasets. For applications, we focus on the recent cancer mutation clustering and single cell data analyses, namely to cluster variant allele frequencies of somatic mutations to reveal clonal architectures of individual tumours, to cluster single-cell gene expression data to uncover cell population compositions, and to cluster single-cell mass cytometry data to detect communities of cells of the same functional states or types. densityCut performs better than competing algorithms and is scalable to large datasets.

Availability and Implementation : Data and the densityCut R package is available from https://bitbucket.org/jerry00/densitycut_dev .

Contact : condon@cs.ubc.ca or sshah@bccrc.ca or jiaruid@cs.ubc.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Identifying visual search patterns in eye gaze data; gaining insights into physician visual workflow
Authors: Fong Allan , Hoffman Daniel J , Zachary Hettinger A , Fairbanks Rollin J , Bisantz Ann M
Published: April 2016

Importance and Objectives As health information technologies become more prevalent in physician workflow, it is increasingly important to understand how physicians are using and interacting with these systems. This includes understanding how physicians search for information presented through health information technology systems. Eye tracking technologies provide a useful technique to understand how physicians visually search for information. However, analyzing eye tracking data can be challenging and is often done by measuring summative metrics, such as total time looking at a specific area and first-order transitions.

Methods In this paper, we propose an algorithmic approach to identify different visual search patterns. We demonstrate this approach by identifying common visual search patterns from physicians using a simulated prototype emergency department patient tracking system.

Results and Conclusions We evaluate and compare the visual search pattern results to first-order transition results. We discuss the benefits and limitations of this approach and insights from this initial evaluation.
Development, use, and integration of a nationally-distributed HIV/AIDS electronic health information system
Authors: Milberg John A
Published: April 2016

Background The management of HIV infection requires extensive, longitudinal information record-keeping and coordination to ensure optimal monitoring and outcomes of care and treatment.

Objective Agencies funded by The Ryan White HIV/AIDS Treatment Modernization Act are increasingly required to monitor the quality of their HIV care and generate reports for funding agencies. To assist in their data collection and reporting capacity, the HIV/AIDS Bureau in the Health Resources and Services Administration released its first version of a software application called CAREWare in 2000.

Methods This report describes the development of the application, the agencies that use it, how it is used, and overall satisfaction. The role of CAREWare in the larger health information technology landscape affecting HIV primary care providers is also discussed.

Results and Conclusion CAREWare has evolved significantly in functionality and use, including the capacity to run in a real-time network connecting multiple service providers, generate performance measures, and import data in multiple formats. The application is the source of over half of the Bureau s data, is used regularly by most providers and is installed in nearly every state. Ongoing enhancements will be essential to ensure that CAREWare stays current in a rapidly-changing environment of health information technology and data exchange.
Applying probabilistic temporal and multisite data quality control methods to a public health mortality registry in Spain: a systematic approach to quality control of repositories
Authors: Sáez Carlos , Zurriaga Oscar , Pérez-Panadés Jordi , Melchor Inma , Robles Montserrat , García-Gómez Juan M
Published: April 2016

Objective To assess the variability in data distributions among data sources and over time through a case study of a large multisite repository as a systematic approach to data quality (DQ).

Materials and Methods Novel probabilistic DQ control methods based on information theory and geometry are applied to the Public Health Mortality Registry of the Region of Valencia, Spain, with 512 143 entries from 2000 to 2012, disaggregated into 24 health departments. The methods provide DQ metrics and exploratory visualizations for (1) assessing the variability among multiple sources and (2) monitoring and exploring changes with time. The methods are suited to big data and multitype, multivariate, and multimodal data.

Results The repository was partitioned into 2 probabilistically separated temporal subgroups following a change in the Spanish National Death Certificate in 2009. Punctual temporal anomalies were noticed due to a punctual increment in the missing data, along with outlying and clustered health departments due to differences in populations or in practices.

Discussion Changes in protocols, differences in populations, biased practices, or other systematic DQ problems affected data variability. Even if semantic and integration aspects are addressed in data sharing infrastructures, probabilistic variability may still be present. Solutions include fixing or excluding data and analyzing different sites or time periods separately. A systematic approach to assessing temporal and multisite variability is proposed.

Conclusion Multisite and temporal variability in data distributions affects DQ, hindering data reuse, and an assessment of such variability should be a part of systematic DQ procedures.
Electronic medical record phenotyping using the anchor and learn framework
Authors: Halpern Yoni , Horng Steven , Choi Youngduck , Sontag David
Published: April 2016

Background Electronic medical records (EMRs) hold a tremendous amount of information about patients that is relevant to determining the optimal approach to patient care. As medicine becomes increasingly precise, a patient’s electronic medical record phenotype will play an important role in triggering clinical decision support systems that can deliver personalized recommendations in real time. Learning with anchors presents a method of efficiently learning statistically driven phenotypes with minimal manual intervention.

Materials and Methods We developed a phenotype library that uses both structured and unstructured data from the EMR to represent patients for real-time clinical decision support. Eight of the phenotypes were evaluated using retrospective EMR data on emergency department patients using a set of prospectively gathered gold standard labels.

Results We built a phenotype library with 42 publicly available phenotype definitions. Using information from triage time, the phenotype classifiers have an area under the ROC curve (AUC) of infection 0.89, cancer 0.88, immunosuppressed 0.85, septic shock 0.93, nursing home 0.87, anticoagulated 0.83, cardiac etiology 0.89, and pneumonia 0.90. Using information available at the time of disposition from the emergency department, the AUC values are infection 0.91, cancer 0.95, immunosuppressed 0.90, septic shock 0.97, nursing home 0.91, anticoagulated 0.94, cardiac etiology 0.92, and pneumonia 0.97.

Discussion The resulting phenotypes are interpretable and fast to build, and perform comparably to statistically learned phenotypes developed with 5000 manually labeled patients.

Conclusion Learning with anchors is an attractive option for building a large public repository of phenotype definitions that can be used for a range of health IT applications, including real-time decision support.
Public preferences for electronic health data storage, access, and sharing — evidence from a pan-European survey
Authors: Patil Sunil , Lu Hui , Saunders Catherine L , Potoglou Dimitris , Robinson Neil
Published: April 2016

Objective To assess the public’s preferences regarding potential privacy threats from devices or services storing health-related personal data.

Materials and Methods A pan-European survey based on a stated-preference experiment for assessing preferences for electronic health data storage, access, and sharing.

Results We obtained 20 882 survey responses (94 606 preferences) from 27 EU member countries. Respondents recognized the benefits of storing electronic health information, with 75.5%, 63.9%, and 58.9% agreeing that storage was important for improving treatment quality, preventing epidemics, and reducing delays, respectively. Concerns about different levels of access by third parties were expressed by 48.9% to 60.6% of respondents.

On average, compared to devices or systems that only store basic health status information, respondents preferred devices that also store identification data (coefficient/relative preference 95% CI = 0.04 [0.00-0.08], P = 0.034) and information on lifelong health conditions (coefficient = 0.13 [0.08 to 0.18], P < 0.001), but there was no evidence of this for devices with information on sensitive health conditions such as mental and sexual health and addictions (coefficient = −0.03 [−0.09 to 0.02], P = 0.24). Respondents were averse to their immediate family (coefficient = −0.05 [−0.05 to −0.01], P = 0.011) and home care nurses (coefficient = −0.06 [−0.11 to −0.02], P = 0.004) viewing this data, and strongly averse to health insurance companies (coefficient = −0.43 [−0.52 to 0.34], P < 0.001), private sector pharmaceutical companies (coefficient = −0.82 [−0.99 to −0.64], P < 0.001), and academic researchers (coefficient = −0.53 [−0.66 to −0.40], P < 0.001) viewing the data.

Conclusions Storing more detailed electronic health data was generally preferred, but respondents were averse to wider access to and sharing of this information. When developing frameworks for the use of electronic health data, policy makers should consider approaches that both highlight the benefits to the individual and minimize the perception of privacy risks.
Ten key considerations for the successful optimization of large-scale health information technology
Authors: Cresswell Kathrin M , Bates David W , Sheikh Aziz
Published: April 2016

Implementation and adoption of complex health information technology (HIT) is gaining momentum internationally. This is underpinned by the drive to improve the safety, quality, and efficiency of care. Although most of the benefits associated with HIT will only be realized through optimization of these systems, relatively few health care organizations currently have the expertise or experience needed to undertake this. It is extremely important to have systems working before embarking on HIT optimization, which, much like implementation, is an ongoing, difficult, and often expensive process. We discuss some key organization-level activities that are important in optimizing large-scale HIT systems. These include considerations relating to leadership, strategy, vision, and continuous cycles of improvement. Although these alone are not sufficient to fully optimize complex HIT, they provide a starting point for conceptualizing this important area.
Health information exchange in the wild: the association between organizational capability and perceived utility of clinical event notifications in ambulatory and community care
Authors: Vest Joshua R , Ancker Jessica S
Published: April 2016

Objective: Event notifications are real-time, electronic, automatic alerts to providers of their patients’ health care encounters at other facilities. Our objective was to examine the effects of organizational capability and related social/organizational issues upon users’ perceptions of the impact of event notifications on quality, efficiency, and satisfaction.

Materials and methods: We surveyed representatives (n = 49) of 10 organizations subscribing to the Bronx Regional Health Information Organization’s event notification services about organizational capabilities, notification information quality, perceived usage, perceived impact, and organizational and respondent characteristics. The response rate was 89%. Average item scores were used to create an individual domain summary score. The association between the impact of event notifications and organizational characteristics was modeled using random-intercept logistic regression models.

Results: Respondents estimated that organizations followed up on the majority (83%) of event notifications. Supportive organizational policies were associated with the perception that event notifications improved quality of care (odds ratio [OR] = 2.12; 95% CI, = 1.05, 4.45), efficiency (OR = 2.06; 95% CI = 1.00, 4.21), and patient satisfaction (OR = 2.56; 95% CI = 1.13, 5.81). Higher quality of event notification information was also associated with a perceived positive impact on quality of care (OR = 2.84; 95% CI = 1.31, 6.12), efficiency (OR = 3.04; 95% CI = 1.38, 6.69), and patient satisfaction (OR = 2.96; 95% CI = 1.25, 7.03).

Conclusions: Health care organizations with appropriate processes, workflows, and staff may be better positioned to use event notifications. Additionally, information quality remains critical in users’ assessments and perceptions.
A national report of nursing home information technology: year 1 results
Authors: Alexander Gregory L , Madsen Richard W , Miller Erin L , Schaumberg Melissa K , Holm Allison E , Alexander Rachel L , Wise Keely K , Dougherty Michelle L , Gugerty Brian
Published: April 2016

Objective

To provide a report on year 1 results of a national study investigating nursing home information technology (IT) adoption, called IT sophistication.

Methods

A reliable and valid survey was used to measure IT sophistication. The target goal was 10% from each state in the United States, 1570 nursing homes. A random sample of homes from each state was recruited from Nursing Home Compare.

Results

The team reached 2627 nursing home administrators, among whom 1799 administrators agreed to participate and were sent a survey. A total of 815 surveys were completed (45.3% response rate), which was below the goal. Facilities in the participating sample have similar demographic characteristics (ownership, total population in a location, and bed size) to the remaining homes not participating. There are greater IT capabilities in resident care and administrative activities, less in clinical support. The extent of use of these capabilities appears to be highest in administrative activities and lowest in clinical support. IT in resident care appears to be the most integrated with internal and external stakeholders. IT capabilities appear to be greater than IT extent of use in all health domains, with the greatest difference in resident care.

Discussion

National evaluations of nursing home IT are rare. Measuring trends in IT adoption in a nationally representative sample provides meaningful analytics that could be more useful for policy makers and nursing home leaders in the future.

Conclusion

Discovering national baseline assessments is a first step toward recognizing nursing home trends in IT adoption.
Mass constraint for a planet in a protoplanetary disk from the gap width
Authors: Kanagawa Kazuhiro D. , Muto Takayuki , Tanaka Hidekazu , Tanigawa Takayuki , Takeuchi Taku , Tsukagoshi Takashi , Momose Munetake
Published: April 2016

A giant planet creates a gap in a protoplanetary disk, which might explain the observed gaps in protoplanetary disks. The width and depth of the gaps depend on the planet mass and disk properties. We have performed two-dimensional hydrodynamic simulations for various planet masses, disk aspect ratios, and viscosities, to obtain an empirical formula for the gap width. The gap width is proportional to the square root of the planet mass, −3/4 the power of the disk aspect ratio and −1/4 the power of the viscosity. This empirical formula enables us to estimate the mass of a planet embedded in the disk from the width of an observed gap. We have applied the empirical formula for the gap width to the disk around HL Tau, assuming that each gap observed by the Atacama Large Millimeter/submillimeter Array (ALMA) observations is produced by planets, and discussed the planet masses within the gaps. The estimate of planet masses from the gap widths is less affected by the observational resolution and dust filtration than that by the gap depth.
Possible identification of massive and evolved galaxies at z ≳ 5
Authors: Mawatari Ken , Yamada Toru , Fazio Giovanni G. , Huang Jia-Sheng , Ashby Matthew L. N.
Published: April 2016

We report on the identification of the old stellar population galaxy candidates at z ≳ 5. We developed a new infrared color selection scheme to isolate galaxies with the strong Balmer breaks at z ≳ 5, and applied it to the ultra-deep and wide infrared survey data from the Spitzer Extended Deep Survey (SEDS) and the UKIRT Infrared Deep Sky Survey. The eight objects satisfying K − [3.6] > 1.3 and K − [3.6] > 2.4([3.6] − [4.5]) + 0.6 are selected in the 0.34 deg2 SEDS Ultra Deep Survey field. Rich multi-wavelength imaging data from optical to far-infrared are also used to reject blending sources and strong nebular line emitters, and we finally obtained the three most likely evolved galaxies at z ≳ 5. Their stacked spectral energy distribution is fitted well with the old stellar population template with M* = (7.5 ± 1.5) × 1010 M⊙, star formation rate = 0.9 ± 0.2 M⊙ yr−1, dust AV < 1, and age =0.7 ± 0.4 Gyr at z = 5.7 ± 0.6, where the dusty star-forming galaxies at z ∼ 2.8 are disfavored because of the faintness in the 24 μm. The stellar mass density of these evolved galaxy candidates, (6 ± 4) × 104 M⊙ Mpc−3, is much lower than that of star-forming galaxies, but the non-zero fraction suggests that initial star-formation and quenching have been completed by z ∼ 6.
Modulation of cellular redox homeostasis by the endocannabinoid system
Authors: Lipina Christopher , Hundal Harinder S.
Published: April 2016

The endocannabinoid system (ECS) and reactive oxygen species (ROS) constitute two key cellular signalling systems that participate in the modulation of diverse cellular functions. Importantly, growing evidence suggests that cross-talk between these two prominent signalling systems acts to modulate functionality of the ECS as well as redox homeostasis in different cell types. Herein, we review and discuss evidence pertaining to ECS-induced regulation of ROS generating and scavenging mechanisms, as well as highlighting emerging work that supports redox modulation of ECS function. Functionally, the studies outlined reveal that interactions between the ECS and ROS signalling systems can be both stimulatory and inhibitory in nature, depending on cell stimulus, the source of ROS species and cell context. Importantly, such cross-talk may act to maintain cell function, whereas abnormalities in either system may propagate and undermine the stability of both systems, thereby contributing to various pathologies associated with their dysregulation.
Molecular assessment of the effect of light and heterotrophy in the scleractinian coral
Stylophora pistillata
Authors: Levy Oren , Karako-Lampert Sarit , Ben-Asher Hiba Waldman , Zoccola Didier , Pagès Gilles , Ferrier-Pagès Christine
Published: April 2016

Corals acquire nutrients via the transfer of photosynthates by their endosymbionts (autotrophy), or via zooplankton predation by the animal (heterotrophy). During stress events, corals lose their endosymbionts, and undergo starvation, unless they increase their heterotrophic capacities. Molecular mechanisms by which heterotrophy sustains metabolism in stressed corals remain elusive. Here for the first time, to the best of our knowledge, we identified specific genes expressed in heterotrophically fed and unfed colonies of the scleractinian coral
Stylophora pistillata
, maintained under normal and light-stress conditions. Physiological parameters and gene expression profiling demonstrated that fed corals better resisted stress than unfed ones by exhibiting less oxidative damage and protein degradation. Processes affected in light-stressed unfed corals (HLU), were related to energy and metabolite supply, carbohydrate biosynthesis, ion and nutrient transport, oxidative stress, Ca
2+
homeostasis, metabolism and calcification (carbonic anhydrases, calcium-transporting ATPase, bone morphogenetic proteins). Two genes (
cp2u1
and
cp1a2
), which belong to the cytochrome P450 superfamily, were also upregulated 249 and 10 times, respectively, in HLU corals. In contrast, few of these processes were affected in light-stressed fed corals (HLF) because feeding supplied antioxidants and energetic molecules, which help repair oxidative damage. Altogether, these results show that heterotrophy helps prevent the cascade of metabolic problems downstream of oxidative stress.
Activated Ras/JNK driven Dilp8 in imaginal discs adversely affects organismal homeostasis during early pupal stage inDrosophila, a new checkpoint for development
Authors: Ray Mukulika , Lakhotia Subhash C.
Published: April 2016

Background

Dilp8-mediated inhibition of ecdysone synthesis and pupation in holometabolous insects maintains developmental homeostasis through stringent control of timing and strength of moulting signals. We examined reasons for normal pupation but early pupal death observed in certain cases.

Results

Over-expression of activated Ras in developing eye/wing discs inhibited Ptth expression in brain via up-regulated JNK signaling mediated Dilp8 secretion from imaginal discs, which inhibited ecdysone synthesis in prothoracic glandafterpupariation, leading to death of ~25-30 Hr old pupae. Inhibition of elevated Ras signaling completely rescued early pupal death while post-pupation administration of ecdysone to organisms with elevated Ras signaling in eye discs partially rescued their early pupal death. Unlike the earlier known Dilp8 action in delaying pupation, hyperactivated Ras mediated elevation of pJNK signaling in imaginal discs caused Dilp8 secretionafterpupariation. Ectopic expression of certain other transgene causing pupal lethality similarly enhanced pJNK and early pupal Dilp8. Sub-optimal ecdysone levels after 8 Hr of pupation prevented the early pupal metamorphic changes and caused organismal death.

Conclusions

Our results reveal early pupal stage as a novel Dilp8 mediated post-pupariation checkpoint and provide further evidence for inter-organ signaling during development, wherein a peripheral tissue influences the CNS driven endocrine function.
Radical amino acid mutations persist longer in the absence of sex
Authors: Sharbrough Joel , Luse Meagan , Boore Jeffrey L. , Logsdon John M. , Neiman Maurine
Published: April 2016

Harmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related sexual and asexual taxa provide a particularly powerful setting to study deleterious mutation elimination because sexual reproduction should facilitate mutational clearance by reducing selective interference between sites and by allowing the production of offspring with different mutational complements than their parents. Here, we compared the rate of removal of conservative (i.e., similar biochemical properties) and radical (i.e., distinct biochemical properties) nonsynonymous mutations from mitochondrial genomes of sexualvs. asexualPotamopyrgus antipodarum, a New Zealand freshwater snail characterized by coexisting and ecologically similar sexual and asexual lineages. Our analyses revealed that radical nonsynonymous mutations are cleared at higher rates than conservative changes and that sexual lineages eliminate radical changes more rapidly than asexual counterparts. These results are consistent with reduced efficacy of purifying selection in asexual lineages allowing harmful mutations to remain polymorphic longer than in sexual lineages. Together, these data illuminate some of the population-level processes contributing to mitochondrial mutation accumulation and suggest that mutation accumulation could influence the outcome of competition between sexual and asexual lineages.
Olfactory perception of chemically diverse molecules
Authors: Keller Andreas , Vosshall Leslie B.
Published: April 2016

Background: Understanding the relationship between a stimulus and how it is perceived reveals fundamental principles about the mechanisms of sensory perception. While this stimulus-percept problem is mostly understood for color vision and tone perception, it is not currently possible to predict how a given molecule smells. While there has been some progress in predicting the pleasantness and intensity of an odor, perceptual data for a larger number of diverse molecules are needed to improve current predictions. Towards this goal, we tested the olfactory perception of 480 structurally and perceptually diverse molecules at two concentrations using a panel of 55 healthy human subjects.

Results: For each stimulus, we collected data on perceived intensity, pleasantness, and familiarity. In addition, subjects were asked to apply 20 semantic odor quality descriptors to these stimuli, and were offered the option to describe the smell in their own words. Using this dataset, we replicated several previous correlations between molecular features of the stimulus and olfactory perception. The number of sulfur atoms in a molecule was highly correlated with the descriptors “garlic” “fish” “decayed,” and large and structurally complex molecules were perceived to be more pleasant. We discovered a number of strong correlations in intensity perception between molecules, which suggests a shared mechanism for perceiving these molecules. We show that familiarity had a strong effect on the ability of subjects to describe a smell. Many subjects used commercial products to describe familiar odors, highlighting the role of prior experience in biasing verbal report of perceived smells. Nonspecific descriptors like “chemical” were applied frequently to unfamiliar smells, and unfamiliar odors were generally rated as neither pleasant nor unpleasant.

Conclusions: We present a very large psychophysical dataset and use this to correlate molecular features of a stimulus to olfactory percept. Our work reveals robust correlations between molecular features and perceptual qualities, and highlights the dominant role of familiarity and experience in assigning verbal descriptors to smells.