bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circadian rhythm phase shifts and endogenous free-running circadian period differ between African-Americans and European-Americans
Authors: Eastman Charmane I. , Suh Christina , Tomaka Victoria A. , Crowley Stephanie J. 
Published: February 2015

AbstractSuccessful adaptation to modern civilization requires the internal circadian clock to make large phase shifts in response to circumstances (e.g., jet travel and shift work) that were not encountered during most of our evolution. We found that the magnitude and direction of the circadian clock's phase shift after the light/dark and sleep/wake/meal schedule was phase-advanced (made earlier) by 9 hours differed in European-Americans compared to African-Americans. European-Americans had larger phase shifts, but were more likely to phase-delay after the 9-hour advance (to phase shift in the wrong direction). The magnitude and direction of the phase shift was related to the free-running circadian period and European-Americans had a longer circadian period than African-Americans. Circadian period was related to the percent Sub-Saharan African and European ancestry from DNA samples. We speculate that a short circadian period was advantageous during our evolution in Africa and lengthened with northern migrations out of Africa. The differences in circadian rhythms remaining today are relevant for understanding and treating the modern circadian-rhythm-based disorders which are due to a misalignment between the internal circadian rhythms and the times for sleep, work, school and meals.
Dimensional crossover and cold-atom realization of topological Mott insulators
Authors: Scheurer Mathias S. , Rachel Stephan , Orth Peter P. 
Published: February 2015

AbstractInteracting cold-atomic gases in optical lattices offer an experimental approach to outstanding problems of many body physics. One important example is the interplay of interaction and topology which promises to generate a variety of exotic phases such as the fractionalized Chern insulator or the topological Mott insulator. Both theoretically understanding these states of matter and finding suitable systems that host them have proven to be challenging problems. Here we propose a cold-atom setup where Hubbard on-site interactions give rise to spin liquid-like phases: weak and strong topological Mott insulators. They represent the celebrated paradigm of an interacting and topological quantum state with fractionalized spinon excitations that inherit the topology of the non-interacting system. Our proposal shall help to pave the way for a controlled experimental investigation of this exotic state of matter in optical lattices. Furthermore, it allows for the investigation of a dimensional crossover from a two-dimensional quantum spin Hall insulating phase to a three-dimensional strong topological insulator by tuning the hopping between the layers.
Involvement of dachshund and Distal-less in distal pattern formation of the cricket leg during regeneration
Authors: Ishimaru Yoshiyasu , Nakamura Taro , Bando Tetsuya , Matsuoka Yuji , Ohuchi Hideyo , Noji Sumihare , Mito Taro 
Published: February 2015

AbstractCricket nymphs have the remarkable ability to regenerate a functional leg following amputation, indicating that the regenerating blastemal cells contain information for leg morphology. However, the molecular mechanisms that underlie regeneration of leg patterns remain poorly understood. Here, we analyzed phenotypes of the tibia and tarsus (three tarsomeres) obtained by knockdown with regeneration-dependent RNA interference (rdRNAi) against Gryllus dachshund (Gb'dac) and Distal-less (Gb'Dll). We found that depletion of Gb'Dll mRNA results in loss of the tarsal segments, while rdRNAi against Gb'dac shortens the tibia at the two most distal tarsomeres. These results indicate that Gb'Dll expression is indispensable for formation of the tarsus, while Gb'dac expression is necessary for elongation of the tibia and formation of the most proximal tarsomere. These findings demonstrate that mutual transcriptional regulation between the two is indispensable for formation of the tarsomeres, whereas Gb'dac is involved in determination of tibial size through interaction with Gb'ds/Gb'ft.
Fear renewal preferentially activates ventral hippocampal neurons projecting to both amygdala and prefrontal cortex in rats
Authors: Jin Jingji , Maren Stephen 
Published: February 2015

AbstractAnxiety, trauma and stress-related disorders are often characterized by a loss of context-appropriate emotional responding. The contextual retrieval of emotional memory involves hippocampal projections to the medial prefrontal cortex and amygdala; however the relative contribution of these projections is unclear. To address this question, we characterized retrieval-induced Fos expression in ventral hippocampal (VH) neurons projecting to the prelimbic cortex (PL) and basal amygdala (BA) after the extinction of conditioned fear in rats. After extinction, freezing behavior (an index of learned fear) to the auditory conditioned stimulus was suppressed in the extinction context, but was “renewed” in another context. Hippocampal neurons projecting to either PL or BA exhibited similar degrees of context-dependent Fos expression; there were more Fos-positive neurons in each area after the renewal, as opposed, to suppression of fear. Importantly, however, VH neurons projecting to both PL and BA were more likely to express Fos during fear renewal than neurons projecting to either PL or BA alone. These data suggest that although projections from the hippocampus to PL and BA are similarly involved in the contextual retrieval of emotional memories, VH neurons with collaterals to both areas may be particularly important for synchronizing prefrontal-amygdala circuits during fear renewal.
A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples
Authors: Huang Yuqing , Zhang Zhiyong , Chen Hao , Feng Jianghua , Cai Shuhui , Chen Zhong 
Published: February 2015

AbstractNMR spectroscopy is a commonly used technique for metabolite analyses. Due to the observed macroscopic magnetic susceptibility in biological tissues, current NMR acquisitions in measurements of biological tissues are generally performed on tissue extracts using liquid NMR or on tissues using magic-angle spinning techniques. In this study, we propose an NMR method to achieve high-resolution J-resolved information for metabolite analyses directly from intact biological samples. A dramatic improvement in spectral resolution is evident in our contrastive demonstrations on a sample of pig brain tissue. Metabolite analyses for a postmortem fish from fresh to decayed statuses are presented to further reveal the capability of the proposed method. This method is a previously-unreported high-resolution 2D J-resolved spectroscopy for biological applications without specialised hardware requirements or complicated sample pretreatments. It provides a significant contribution to metabolite analyses of biological samples and may be potentially applicable to in vivo samples. Furthermore, this method also can be applied to measurements of semisolid and viscous samples.
Hierarchical Auxetic Mechanical Metamaterials
Authors: Gatt Ruben , Mizzi Luke , Azzopardi Joseph I. , Azzopardi Keith M. , Attard Daphne , Casha Aaron , Briffa Joseph , Grima Joseph N. 
Published: February 2015

AbstractAuxetic mechanical metamaterials are engineered systems that exhibit the unusual macroscopic property of a negative Poisson's ratio due to sub-unit structure rather than chemical composition. Although their unique behaviour makes them superior to conventional materials in many practical applications, they are limited in availability. Here, we propose a new class of hierarchical auxetics based on the rotating rigid units mechanism. These systems retain the enhanced properties from having a negative Poisson's ratio with the added benefits of being a hierarchical system. Using simulations on typical hierarchical multi-level rotating squares, we show that, through design, one can control the extent of auxeticity, degree of aperture and size of the different pores in the system. This makes the system more versatile than similar non-hierarchical ones, making them promising candidates for industrial and biomedical applications, such as stents and skin grafts.
Molten salt‐assisted template synthesis of lithium‐rich layered oxide 0.3Li2MnO3 ·0.7LiNi1/3Co1/3Mn1/3O2 nanorods as lithium‐ion battery cathode
Authors: Zhao Chenhao , Hu Zhibiao , Shen Qiang 
Published: February 2015

Lithium‐rich layered oxide 0.3Li2MnO3 ·0.7LiNi1/3Co1/3Mn1/3O2 nanorods have been prepared by a KCl molten salt‐assisted template route. The nanorods can well retain the rod‐like structure of a β‐MnO2 template, and have the length of several hundred nanometres and diameters of about one hundred nanometres. In comparison with the sample obtained from immediate solid‐state reaction, the molten salt treatment can help improve the phase purity and decrease the particle size. As a lithium‐ion battery cathode, the KCl‐treated nanorods deliver an initial discharge capacity of 242.9 mAh g−1 with a high Coulombic efficiency of 83.6% at a current density of 20 mA g−1 within 2.0–4.7 V. After 60 cycles, a discharge capacity of 150.8 mAh g−1 can be retained at 0.5 C. Even at a high charge–discharge rate of 4 C (800 mA g−1), a stable capacity of 104.2 mAh g−1 can be reached, while the sample obtained from solid‐state reaction only delivers an initial discharge capacity of 179.1 mAh g−1 at 20 mA g−1.
The Association between School Bonding and Smoking Amongst Chilean Adolescents
Authors: Gaete Jorge , Montgomery Alan , Araya Ricardo 
Published: February 2015

Background The objective of the research was to study the association between school bonding dimensions (school commitment and school attachment) and current adolescent smoking in Chile, controlling for confounding variables using the fifth Chilean School Population National Substance Use Survey, 2003 (CHSS-2003) data set. Methods The CHSS-2003 is a stratified cross-sectional survey that gathers information about personal, familial, peer, and school factors and cigarette use using a self-reported questionnaire. Complete data from 21,956 adolescent students for all the variables of interest were used in the analyses. An exploratory factor analysis (EFA) was performed in order to explore the construct validity of the questionnaire and create the main exposure and potential confounding variables. Multivariable logistic regression analyses were undertaken to study the association between school bonding and smoking. Results The construct validity of the school attachment and school commitment scales was mainly supported by the EFA. Multivariable analyses showed strong evidence that, after adjusting for factors from different domains, school commitment (student's good grades and school attendance) appears to have a clear inverse association with current smoking (odds ratio [OR] = 0.46, 95% confidence interval [CI]: 0.38–0.56). On the other hand, school attachment (their feelings towards their school and their teachers) was not associated with adolescent smoking (OR = 1.16, 95% CI: 0.88–1.53). Conclusions School commitment was strongly associated with current smoking. It is important to further study this variable with the aim of ascertaining whether or not interventions that improve school commitment may prevent or reduce smoking amongst adolescent students.
The use of Technology in Participant Tracking and Study Retention: Lessons Learned from a Clinical Trials Network Study
Authors: Mitchell Shannon Gwin , Schwartz Robert P. , Alvanzo Anika A. H. , Weisman Monique S. , Kyle Tiffany L. , Turrigiano Eva M. , Gibson Martha L. , Perez Livangelie , McClure Erin A. , Clingerman Sara , Froias Autumn , Shandera Danielle R. , Walker Robrina , Babcock Dean L. , Bailey Genie L. , Miele Gloria M. , Kunkel Lynn E. , Norton Michael , Stitzer Maxine L. 
Published: February 2015

Background The growing use of newer communication and Internet technologies, even among low-income and transient populations, require research staff to update their outreach strategies to ensure high follow-up and participant retention rates. This paper presents the views of research assistants on the use of cell phones and the Internet to track participants in a multisite randomized trial of substance use disorder treatment. Methods Preinterview questionnaires exploring tracking and other study-related activities were collected from 21 research staff across the 10 participating US sites. Data were then used to construct a semistructured interview guide that, in turn, was used to interview 12 of the same staff members. The questionnaires and interview data were entered in Atlas.ti and analyzed for emergent themes related to the use of technology for participant-tracking purposes. Results Study staff reported that most participants had cell phones, despite having unstable physical addresses and landlines. The incoming call feature of most cell phones was useful for participants and research staff alike, and texting proved to have additional benefits. However, reliance on participants’ cell phones also proved problematic. Even homeless participants were found to have access to the Internet through public libraries and could respond to study staff e-mails. Some study sites opened generic social media accounts, through which study staff sent private messages to participants. However, the institutional review board (IRB) approval process for tracking participants using social media at some sites was prohibitively lengthy. Internet searches through Google, national paid databases, obituaries, and judiciary Web sites were also helpful tools. Conclusions Research staff perceive that cell phones, Internet searches, and social networking sites were effective tools to achieve high follow-up rates in drug abuse research. Studies should incorporate cell phone, texting, and social network Web site information on locator forms; obtain IRB approval for contacting participants using social networking Web sites; and include Web searches, texting, and the use of social media in staff training as standard operating procedures.
Identifying homelessness using health information exchange data
Authors: Zech John , Husk Gregg , Moore Thomas , Kuperman Gilad J , Shapiro Jason S 
Published: February 2015

Abstract
Background Homeless patients experience poor health outcomes and consume a disproportionate amount of health care resources compared with domiciled patients. There is increasing interest in the federal government in providing care coordination for homeless patients, which will require a systematic way of identifying these individuals.
Objective We analyzed address data from Healthix, a New York City–based health information exchange, to identify patterns that could indicate homelessness.
Methods Patients were categorized as likely to be homeless if they registered with the address of a hospital, homeless shelter, place of worship, or an address containing a keyword synonymous with “homelessness.”
Results We identified 78 460 out of 7 854 927 Healthix patients (1%) as likely to have been homeless over the study period of September 30, 2008 to July 19, 2013. We found that registration practices for these patients varied widely across sites.
Conclusions The use of health information exchange data enabled us to identify a large number of patients likely to be homeless and to observe the wide variation in registration practices for homeless patients within and across sites. Consideration of these results may suggest a way to improve the quality of record matching for homeless patients. Validation of these results is necessary to confirm the homeless status of identified individuals. Ultimately, creating a standardized and structured field to record a patient’s housing status may be a preferable approach.
Cost-effectiveness analysis of a hospital electronic medication management system
Authors: Westbrook Johanna I , Gospodarevskaya Elena , Li Ling , Richardson Katrina L , Roffe David , Heywood Maureen , Day Richard O , Graves Nicholas 
Published: February 2015

AbstractObjective To conduct a cost–effectiveness analysis of a hospital electronic medication management system (eMMS).Methods We compared costs and benefits of paper-based prescribing with a commercial eMMS (CSC MedChart) on one cardiology ward in a major 326-bed teaching hospital, assuming a 15-year time horizon and a health system perspective. The eMMS implementation and operating costs were obtained from the study site. We used data on eMMS effectiveness in reducing potential adverse drug events (ADEs), and potential ADEs intercepted, based on review of 1 202 patient charts before (n = 801) and after (n = 401) eMMS. These were combined with published estimates of actual ADEs and their costs.Results The rate of potential ADEs following eMMS fell from 0.17 per admission to 0.05; a reduction of 71%. The annualized eMMS implementation, maintenance, and operating costs for the cardiology ward were A$61 741 (US$55 296). The estimated reduction in ADEs post eMMS was approximately 80 actual ADEs per year. The reduced costs associated with these ADEs were more than sufficient to offset the costs of the eMMS. Estimated savings resulting from eMMS implementation were A$63–66 (US$56–59) per admission (A$97 740–$102 000 per annum for this ward). Sensitivity analyses demonstrated results were robust when both eMMS effectiveness and costs of actual ADEs were varied substantially.Conclusion The eMMS within this setting was more effective and less expensive than paper-based prescribing. Comparison with the few previous full economic evaluations available suggests a marked improvement in the cost–effectiveness of eMMS, largely driven by increased effectiveness of contemporary eMMs in reducing medication errors.
Harmonizing and extending standards from a domain-specific and bottom-up approach: an example from development through use in clinical applications
Authors: Harris Marcelline R , Langford Laura Heermann , Miller Holly , Hook Mary , Dykes Patricia C , Matney Susan A 
Published: February 2015

Abstract
Objective Currently, the processes for harmonizing and extending standards by leveraging the knowledge within local documentation artifacts are not well described. We describe a collaborative project to develop common information models, terminology bindings, and term definitions based on nursing documentation systems, and carry the findings through to the adoption in standards development organizations (SDOs) and technical implementations in clinical applications.
Materials and Methods Nursing flowsheet documents from six large organizations were analyzed to generate a common information model and terminologies that fully expressed documentation across all systems, and were sufficient for evidence-based decision support, reporting, and analysis.
Results Significant gaps in existing standards were identified. The models and terminologies were submitted to and incorporated by SDOs, are published, implemented, and now serving as a foundation for an eMeasure.
Discussion There are few examples in the literature of success working through the standards development process from a bottom-up perspective. Subsequently, standards do not yet fully address the need for detailed clinical data that enables, for example, decision support as well as a range of reporting and analytic requirements. Recommendations from this project include transparent processes within SDOs, registries that make models and associated terminologies freely available, and coordinated governance processes.
Conclusion We demonstrated the feasibility of using documentation artifacts in a bottom-up approach to develop common models and sets of terms that are complete from the perspective of clinical implementation. Importantly, we demonstrated a process by which a community of practice can contribute to closing gaps in existing standards using SDO processes.
Feasibility and utility of applications of the common data model to multiple, disparate observational health databases
Authors: Voss Erica A , Makadia Rupa , Matcho Amy , Ma Qianli , Knoll Chris , Schuemie Martijn , DeFalco Frank J , Londhe Ajit , Zhu Vivienne , Ryan Patrick B 
Published: February 2015

Abstract
Objectives To evaluate the utility of applying the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) across multiple observational databases within an organization and to apply standardized analytics tools for conducting observational research.
Materials and methods Six deidentified patient-level datasets were transformed to the OMOP CDM. We evaluated the extent of information loss that occurred through the standardization process. We developed a standardized analytic tool to replicate the cohort construction process from a published epidemiology protocol and applied the analysis to all 6 databases to assess time-to-execution and comparability of results.
Results Transformation to the CDM resulted in minimal information loss across all 6 databases. Patients and observations excluded were due to identified data quality issues in the source system, 96% to 99% of condition records and 90% to 99% of drug records were successfully mapped into the CDM using the standard vocabulary. The full cohort replication and descriptive baseline summary was executed for 2 cohorts in 6 databases in less than 1 hour.
Discussion The standardization process improved data quality, increased efficiency, and facilitated cross-database comparisons to support a more systematic approach to observational research. Comparisons across data sources showed consistency in the impact of inclusion criteria, using the protocol and identified differences in patient characteristics and coding practices across databases.
Conclusion Standardizing data structure (through a CDM), content (through a standard vocabulary with source code mappings), and analytics can enable an institution to apply a network-based approach to observational research across multiple, disparate observational health databases.
Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network
Authors: Kim Taehyong , Dreher Kate , Nilo-Poyanco Ricardo , Lee Insuk , Fiehn Oliver , Lange Bernd Markus , Nikolau Basil J. , Sumner Lloyd , Welti Ruth , Wurtele Eve S. , Rhee Seung Y. 
Published: February 2015

AbstractMetabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.