bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical element models in the SHARPn consortium
Authors: Oniki Thomas A , Zhuo Ning , Beebe Calvin E , Liu Hongfang , Coyle Joseph F , Parker Craig G , Solbrig Harold R , Marchant Kyle , Kaggal Vinod C , Chute Christopher G , Huff Stanley M 
Published: November 2015

Abstract
Objective The objective of the Strategic Health IT Advanced Research Project area four (SHARPn) was to develop open-source tools that could be used for the normalization of electronic health record (EHR) data for secondary use—specifically, for high throughput phenotyping. We describe the role of Intermountain Healthcare’s Clinical Element Models ([CEMs] Intermountain Healthcare Health Services, Inc, Salt Lake City, Utah) as normalization “targets” within the project.
Materials and Methods Intermountain’s CEMs were either repurposed or created for the SHARPn project. A CEM describes “valid” structure and semantics for a particular kind of clinical data. CEMs are expressed in a computable syntax that can be compiled into implementation artifacts. The modeling team and SHARPn colleagues agilely gathered requirements and developed and refined models.
Results Twenty-eight “statement” models (analogous to “classes”) and numerous “component” CEMs and their associated terminology were repurposed or developed to satisfy SHARPn high throughput phenotyping requirements. Model (structural) mappings and terminology (semantic) mappings were also created. Source data instances were normalized to CEM-conformant data and stored in CEM instance databases. A model browser and request site were built to facilitate the development.
Discussion The modeling efforts demonstrated the need to address context differences and granularity choices and highlighted the inevitability of iso-semantic models. The need for content expertise and “intelligent” content tooling was also underscored. We discuss scalability and sustainability expectations for a CEM-based approach and describe the place of CEMs relative to other current efforts.
Conclusions The SHARPn effort demonstrated the normalization and secondary use of EHR data. CEMs proved capable of capturing data originating from a variety of sources within the normalization pipeline and serving as suitable normalization targets.
The vulnerabilities of computerized physician order entry systems: a qualitative study
Authors: Slight Sarah P , Eguale Tewodros , Amato Mary G , Seger Andrew C , Whitney Diana L , Bates David W , Schiff Gordon D 
Published: November 2015

Abstract
Objective To test the vulnerabilities of a wide range of computerized physician order entry (CPOE) systems to different types of medication errors, and develop a more comprehensive qualitative understanding of how their design could be improved.
Materials and Methods The authors reviewed a random sample of 63 040 medication error reports from the US Pharmacopeia (USP) MEDMARX reporting system where CPOE systems were considered a “contributing factor” to errors and flagged test scenarios that could be tested in current CPOE systems. Testers entered these orders in 13 commercial and homegrown CPOE systems across 16 different sites in the United States and Canada, using both usual practice and where-needed workarounds. Overarching themes relevant to interface design and usability/workflow issues were identified.
Results CPOE systems often failed to detect and prevent important medication errors. Generation of electronic alert warnings varied widely between systems, and depended on a number of factors, including how the order information was entered. Alerts were often confusing, with unrelated warnings appearing on the same screen as those more relevant to the current erroneous entry. Dangerous drug-drug interaction warnings were displayed only after the order was placed rather than at the time of ordering. Testers illustrated various workarounds that allowed them to enter these erroneous orders.
Discussion and Conclusion The authors found high variability in ordering approaches between different CPOE systems, with major deficiencies identified in some systems. It is important that developers reflect on these findings and build in safeguards to ensure safer prescribing for patients.
Effects of health information technology on patient outcomes: a systematic review
Authors: Brenner Samantha K , Kaushal Rainu , Grinspan Zachary , Joyce Christine , Kim Inho , Allard Rhonda J , Delgado Diana , Abramson Erika L 
Published: November 2015

AbstractObjective To systematically review studies assessing the effects of health information technology (health IT) on patient safety outcomes.Materials and Methods The authors employed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement methods. MEDLINE, Cumulative Index to Nursing Allied Health (CINAHL), EMBASE, and Cochrane Library databases, from 2001 to June 2012, were searched. Descriptive and comparative studies were included that involved use of health IT in a clinical setting and measured effects on patient safety outcomes.Results Data on setting, subjects, information technology implemented, and type of patient safety outcomes were all abstracted. The quality of the studies was evaluated by 2 independent reviewers (scored from 0 to 10). A total of 69 studies met inclusion criteria. Quality scores ranged from 1 to 9. There were 25 (36%) studies that found benefit of health IT on direct patient safety outcomes for the primary outcome measured, 43 (62%) studies that either had non-significant or mixed findings, and 1 (1%) study for which health IT had a detrimental effect. Neither the quality of the studies nor the rate of randomized control trials performed changed over time. Most studies that demonstrated a positive benefit of health IT on direct patient safety outcomes were inpatient, single-center, and either cohort or observational trials studying clinical decision support or computerized provider order entry.Discussion and Conclusion Many areas of health IT application remain understudied and the majority of studies have non-significant or mixed findings. Our study suggests that larger, higher quality studies need to be conducted, particularly in the long-term care and ambulatory care settings.
Strategizing EHR use to achieve patient-centered care in exam rooms: a qualitative study on primary care providers
Authors: Zhang Jing , Chen Yunan , Ashfaq Shazia , Bell Kristin , Calvitti Alan , Farber Neil J , Gabuzda Mark T , Gray Barbara , Liu Lin , Rick Steven , Street Richard L , Zheng Kai , Zuest Danielle , Agha Zia 
Published: November 2015

Abstract
Objective Electronic health records (EHRs) have great potential to improve quality of care. However, their use may diminish “patient-centeredness” in exam rooms by distracting the healthcare provider from focusing on direct patient interaction. The authors conducted a qualitative interview study to understand the magnitude of this issue, and the strategies that primary care providers devised to mitigate the unintended adverse effect associated with EHR use.
Methods and Materials Semi-structured interviews were conducted with 21 healthcare providers at 4 Veterans Affairs (VAs) outpatient primary care clinics in San Diego County. Data analysis was performed using the grounded theory approach.
Results The results show that providers face demands from both patients and the EHR system. To cope with these demands, and to provide patient-centered care, providers attempt to perform EHR work outside of patient encounters and create templates to streamline documentation work. Providers also attempt to use the EHR to engage patients, establish patient buy-in for EHR use, and multitask between communicating with patients and using the EHR.
Discussion and Conclusion This study has uncovered the challenges that primary care providers face in integrating the EHR into their work practice, and the strategies they use to overcome these challenges in order to maintain patient-centered care. These findings illuminate the importance of developing “best” practices to improve patient-centered care in today’s highly “wired” health environment. These findings also show that more user-centered EHR design is needed to improve system usability.
Equiosmolar Solutions of Hypertonic Saline and Mannitol Do Not Impair Blood Coagulation During Elective Intracranial Surgery
Authors: Hernández-Palazón Joaquín , Fuentes-García Diego , Doménech-Asensi Paloma , Piqueras-Pérez Claudio , Falcón-Araña Luis , Burguillos-López Sebastián 
Published: November 2015

Background:
The authors investigated the effect of equiosmolar, equivolemic solutions of 3% hypertonic saline (HS) and 20% mannitol on blood coagulation assessed by rotational thromboelastometry (ROTEM) and standard coagulation tests during elective craniotomy.

Methods:
In a prospective, randomized, double-blind trial, 40 patients undergoing elective craniotomy were randomized to receive 5 mL/kg of either 20% mannitol or 3% HS for intraoperative brain relaxation. Fibrinogen, activated partial thromboplastin time, prothrombin time, hemoglobin, hematocrit, and platelet count were simultaneously measured intraoperatively with ROTEM for EXTEM, INTEM, and FIBTEM analysis. ROTEM parameters were: clotting time (CT), clot formation time (CFT), maximum clot firmness (MCF), and α-angle.

Results:
No significant differences between groups were found in ROTEM variables CT, CFT, MCF, α-angle (EXTEM and INTEM), and MCF (FIBTEM) nor standard coagulation tests. ROTEM parameters did not show changes after administration of hyperosmolar solutions relating to basal values, except for an increase of CFT EXTEM (118±28 vs. 128±26 s) and decrease of CT INTEM (160±18 vs. 148±15 s) with values within normal range. Significant decreases from baseline levels were observed for hematocrit (−7%), platelet count (−10%), and fibrinogen (−13%) after HS infusion, and hematocrit (−9%), platelet count (−13%), and fibrinogen (−9%) after mannitol infusion, but remaining normal.

Conclusions:
The use of 5 mL/kg of equiosmolar solutions of 3% HS and 20% mannitol applied to reach a brain relaxation during elective craniotomy does not induce coagulation impairment as evidenced by ROTEM and standard coagulation tests.
A Dopamine Pathway Gene Risk Score for Cognitive Recovery Following Traumatic Brain Injury: Methodological Considerations, Preliminary Findings, and Interactions With Sex
Authors: Myrga John M. , Failla Michelle D. , Ricker Joseph H. , Dixon C. Edward , Conley Yvette P. , Arenth Patricia M. , Wagner Amy K. 
Published: November 2015

Objectives:
With evidence of sexual dimorphism involving the dopamine (DA)-pathway, and the importance of DA pathways in traumatic brain injury (TBI) recovery, we hypothesized that sex × DA-gene interactions may influence cognition post-TBI.

Participants:
Adult survivors of severe TBI (n = 193) consecutively recruited from a level 1 trauma center.

Design:
Risk allele assignments were made for multiple DA pathway genes using a sex-specific stratified approach. Genetic risk alleles, and their impacts on cognition, were assessed at 6 and 12 months postinjury using unweighted, semiweighted, and weighted gene risk score (GRS) approaches.

Main Measures:
A cognitive composite score generated from 8 standardized neuropsychological tests targeting multiple cognitive domains.

Results:
A significant sex × gene interaction was observed at 6 and 12 months for ANKK1 rs1800497 (6M: P = .002, 12M: P = .001) and COMT rs4680 (6M: P = .048; 12M: P = .004); DRD2 rs6279 (P = .001) and VMAT rs363226 (P = .043) genotypes were independently associated with cognition at 6 months, with trends for a sex × gene interaction at 12 months. All GRS methods were significant predictors of cognitive performance in multivariable models. Weighted GRS multivariate models captured the greatest variance in cognition: R
2 = 0.344 (6 months); R
2 = 0.441 (12 months), significantly increasing the variance captured from the base prediction models.

Conclusions:
A sex-specific DA-pathway GRS may be a valuable tool when predicting cognitive recovery post-TBI. Future work should validate these findings and explore how DA-pathway genetics may guide therapeutic intervention.
Consistency of Recall for Deployment-Related Traumatic Brain Injury
Authors: Alosco Michael L. , Aslan Mihaela , Du Mengtian , Ko John , Grande Laura , Proctor Susan P. , Concato John , Vasterling Jennifer J. 
Published: November 2015

Objective:
To examine the temporal consistency of self-reported deployment-related traumatic brain injury (TBI) and its association with posttraumatic stress disorder (PTSD) symptom severity.

Setting:
In-person interviews at US Army installations (postdeployment); phone interviews (long-term follow-up).

Participants:
A total of 378 US Army soldiers and veterans deployed to Iraq; 14.3% (n = 54) reported TBI with loss of consciousness during an index deployment.

Design:
Participants were evaluated after returning from deployment and again 5 to 9 years later.

Main Measures:
Temporal consistency of TBI endorsement based on TBI screening interviews; PTSD Checklist, Civilian Version.

Results:
The concordance of deployment-related TBI endorsement from the postdeployment to long-term follow-up assessment was moderate (κ = 0.53). Of the 54 participants reporting (predominantly mild) TBI occurring during an index deployment, 32 endorsed TBI inconsistently over time. More severe PTSD symptoms at postdeployment assessment were independently associated with discordant reporting (P = .0004); each 10-point increase in PCL scores increasing odds of discordance by 69% (odds ratio = 1.69; 95% confidence interval, 1.26-2.26).

Conclusions:
Deployment-related TBI may not be reported reliably over time, particularly among war-zone veterans with greater PTSD symptoms. Results of screening evaluations for TBI history should be viewed with caution in the context of PTSD symptom history.
Summation of a Schlömilch type series
Authors: Asatryan A. A. 
Published: November 2015

The ability to accurately and efficiently characterize multiple scattering of waves of different nature attracts substantial interest in physics. The advent of photonic crystals has created additional impetus in this direction. An efficient approach in the study of multiple scattering originates from the Rayleigh method, which often requires the summation of conditionally converging series. Here summation formulae have been derived for conditionally convergent Schlömilch type series

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. These series arise in two-dimensional scattering problems on diffraction gratings with multiple inclusions per unit cell. It is shown that the Schlömilch series involving Hankel functions or Neumann functions can be expressed as an absolutely converging series of elementary functions and a finite sum of Lerch transcendent functions, while the Schlömilch series of Bessel functions can be transformed into a finite sum of elementary functions. The closed-form expressions for the Coates's integrals of integer order have also been found. The derived equations have been verified numerically and their accuracy and efficiency has been demonstrated.
Towards extracting supporting information about predicted protein-protein interactions
Authors: Roth Adam , Subramanian Sandeep , Ganapathiraju Madhavi K. 
Published: November 2015

AbstractOne of the goals of relation extraction is to identify protein-protein interactions (PPIs) in biomedical literature. Current systems are capturing binary relations and also the direction and type of an interaction. Besides assisting in the curation PPIs into databases, there has been little real-world application of these algorithms. We describe UPSITE, a text mining tool for extracting evidence in support of a hypothesized interaction. Given a predicted PPI, UPSITE uses a binary relation detector to check whether a PPI is found in abstracts in PubMed. If it is not found, UPSITE retrieves documents relevant to each of the two proteins separately, and extracts contextual information about biological events surrounding each protein, and calculates semantic similarity of the two proteins to provide evidential support for the predicted PPI. In evaluations, relation extraction achieved an Fscore of 0.88 on the HPRD50 corpus, and semantic similarity measured with angular distance was found to be statistically significant. With the development of PPI prediction algorithms, the burden of interpreting the validity and relevance of novel PPIs is on biologists. We suggest that presenting annotations of the two proteins in a PPI side-by-side and a score that quantifies their similarity lessens this burden to some extent.
Health and population effects of rare gene knockouts in adult humans with related parents
Authors: Narasimhan V. , Hunt K.A. , Mason D. , Baker C.L. , Karczewski K.J. , Barnes M.R. , Barnett A.H. , Bates C. , Bellary S. , Bockett N.A. , Giorda K. , Griffiths C.J. , Hemingway H. , Jia Z. , Kelly M.A. , Khawaja H.A. , Lek Monkol , McCarthy S. , McEachan R. , Paigen K. , Parisinos C. , Sheridan E. , Southgate Laura , Tee L. , Thomas M. , Xue Y. , Schnall-Levin M. , Petkov P.M. , Tyler-Smith C. , Maher E.R. , Trembath R.C. , MacArthur D.G. , Wright J. , Durbin R. , van Heel D.A. 
Published: November 2015

Abstract:Complete gene knockouts are highly informative about gene function. We exome sequenced 3,222 British Pakistani-heritage adults with high parental relatedness, discovering 1,111 rare-variant homozygous likely loss of function (rhLOF) genotypes predicted to disrupt (knockout) 781 genes. Based on depletion of rhLOF genotypes, we estimate that 13.6% of knockouts are incompatible with adult life, finding on average 1.6 heterozygous recessive lethal LOF variants per adult. Linking to lifelong health records, we observed no association of rhLOF genotypes with prescription- or doctor-consultation rate, and no disease-related phenotypes in 33 of 42 individuals with rhLOF genotypes in recessive Mendelian disease genes. Phased genome sequencing of a healthyPRDM9knockout mother, her child and controls, showed meiotic recombination sites localised away fromPRDM9-dependent hotspots, demonstratingPRDM9redundancy in humans.
DataJoint: managing big scientific data using MATLAB or Python
Authors: Yatsenko Dimitri , Reimer Jacob , Ecker Alexander S. , Walker Edgar Y. , Sinz Fabian , Berens Philipp , Hoenselaar Andreas , James Cotton R. , Siapas Athanassios S. , Tolias Andreas S. 
Published: November 2015

AbstractThe rise of big data in modern research poses serious challenges for data management: Large and intricate datasets from diverse instrumentation must be precisely aligned, annotated, and processed in a variety of ways to extract new insights. While high levels of data integrity are expected, research teams have diverse backgrounds, are geographically dispersed, and rarely possess a primary interest in data science. Here we describe DataJoint, an open-source toolbox designed for manipulating and processing scientific data under the relational data model. Designed for scientists who need a flexible and expressive database language with few basic concepts and operations, DataJoint facilitates multiuser access, efficient queries, and distributed computing. With implementations in both MATLAB and Python, DataJoint is not limited to particular file formats, acquisition systems, or data modalities and can be quickly adapted to new experimental designs. DataJoint and related resources are available athttp://datajoint.github.com.
A new model of human dispersal
Authors: Underwood Trevor G. 
Published: November 2015

AbstractAnalysis of previously unpublished allele counts obtained from the French-San-Neanderthal-Chimpanzee alignment of the high quality DNA sequence of a Neanderthal from the Altai Mountains raises significant questions about the currently accepted phylogenetic model of the origins of Europeans. Previous estimates of the proportion of Neanderthal ancestry in present-day Europeans ranged between 1.3% and 2.7% supporting a recent Out-of Africa dispersal model followed by a low level of admixture with Neanderthals. However, analysis of the allele counts indicates the existence of an unidentified third archaic ancestor of Europeans, which diverged from its common ancestor with sub-Saharan Africans around 900 thousand years ago. This analysis shows that the relative proportions of derived alleles in the 0.0826% of the European genome that is not shared with the common ancestor of humans and chimpanzee are 13.6% Neanderthal, 32.3% sub-Saharan African and 54.2% third archaic ancestor. This analysis together with anthropological and archaeological evidence suggests a new model of human dispersal based on a Eurasian lineage in the Levant, which admixed with Neanderthals and descendants of African mtDNA haplogroup L3, followed by radiation from a basal admixed population around 55–50 Kya, with no subsequent major contribution to the European genome.
Shared generative rules of locomotor behavior in arthropods and vertebrates
Authors: Gomez-Marin Alex , Oron Efrat , Gakamsky Anna , Valente Dan , Benjamini Yoav , Golani Ilan 
Published: November 2015

AbstractThe discovery of shared behavioral processes across phyla is an essential step in the establishment of a comparative study of behavior. We use immobility as an origin and reference for the measurement of locomotor behavior; speed, direction of walking and direction of facing as the three degrees of freedom shaping fly locomotor behavior; and cocaine as the parameter inducing a progressive transition in and out of immobility. In this way we expose and quantify the generative rules that shape part of fruit fly locomotor behavior, bringing about a gradual buildup of freedom during the transition from immobility to normal behavior and a precisely opposite narrowing down during the transition into immobility. During buildup the fly exhibits enhancement and then reduction to normal values of movement along each degree of freedom: first, body rotation in the horizontal plane, then path curvature and then speed of translation. Transition into immobility unfolds by narrowing down of the repertoire in the opposite sequential order, showing reciprocal relations during both buildup and narrowing down. The same generative rules apply to vertebrate locomotor behavior in a variety of contexts involving transition out and into immobility. Recent claims for deep homology between the arthropod central complex and the vertebrate basal ganglia provide an opportunity to examine whether the generative rules we discovered also share common descent. Neurochemical processes mediating the buildup of locomotor behavior in vertebrates could guide the search for equivalent processes in arthropods. The measurement methodology we use prompts the discovery of candidate behavioral homologies.Significance StatementDo flies and mice share the same behavior? By defining immobility as an intrinsic reference point for locomotor behavior we show that the rules that generate the transition from immobility to full blown normal behavior, and from full blown behavior to immobility are shared by fruit flies and mice. These rules constitute a much desired aim of evolutionary biology: the discovery of behavioral homologies across distant phyla. The methodology we use facilitates the discovery of cross-phyletic behavioral homologies, shedding light on the problem of the evolution of behavior.