bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementing an EHR-based Screening and Referral System to Address Social Determinants of Health in Primary Care
Authors: Buitron de la Vega Pablo , Losi Stephanie , Sprague Martinez Linda , Bovell-Ammon Allison , Garg Arvin , James Thea , Ewen Alana M. , Stack Marna , DeCarvalho Heloisa , Sandel Megan , Mishuris Rebecca G. , Deych Stella , Pelletier Patrick , Kressin Nancy R. 
Published: May 2019

Background:
Social determinants affect health, yet there are few systematic clinical strategies in primary care that leverage electronic health record (EHR) automation to facilitate screening for social needs and resource referrals. An EHR-based social determinants of health (SDOH) screening and referral model, adapted from the WE CARE model for pediatrics, was implemented in urban adult primary care.

Objectives:
This study aimed to: (1) understand the burden of SDOH among patients at Boston Medical Center; and (2) evaluate the feasibility of implementing a systematic clinical strategy to screen new primary care patients for SDOH, use EHR technology to add these needs to the patient’s chart through autogenerated ICD-10 codes, and print patient language-congruent referrals to available resources upon patient request.

Research Design:
This observational study assessed the number of patients who were screened to be positive and requested resources for social needs. In addition, we evaluated the feasibility of implementing our SDOH strategy by determining the proportion of: eligible patients screened, providers signing orders for positive patient screenings, and provider orders for resource referral guides among patients requesting resource connections.

Results:
In total, 1696 of 2420 (70%) eligible patients were screened. Employment (12%), food insecurity (11%), and problems affording medications (11%) were the most prevalent concerns among respondents. In total, 367 of 445 (82%) patients with ≥1 identified needs (excluding education) had the appropriate ICD-10 codes added to their visit diagnoses. In total, 325 of 376 (86%) patients who requested resources received a relevant resource referral guide.

Conclusions:
Implementing a systematic clinical strategy in primary care using EHR workflows was successful in identifying and providing resource information to patients with SDOH needs.
The Use of a Mobile Application to Increase Access to Interpreters for Cancer Patients With Limited English Proficiency
Authors: Narang Bharat , Park So-Young , Norrmén-Smith Ingrid O. , Lange Michelle , Ocampo Alex J. , Gany Francesca M. , Diamond Lisa C. 
Published: May 2019

Background:
Language barriers can influence the quality of health care and health outcomes of limited English proficient patients with cancer. The use of medical interpretation services can be a valuable asset for improving communications in emergency care settings.

Objective:
To evaluate whether a mobile translation application increased call frequency to interpreter services among providers in an Urgent Care Center at a comprehensive cancer center and to assess provider satisfaction of the mobile application.

Research Design:
Prospective pre-post nonrandomized intervention of a mobile translation application with access to an over the phone interpreter (OPI) service at the push of a button and poststudy satisfaction survey.

Subjects:
Sixty-five clinicians working at the Urgent Care Center in a cancer center in New York City.

Measures:
Mean call frequency to OPI services, tested by the nonparametric Wilcoxon Mann Whitney test, and self-reported provider satisfaction descriptives.

Results:
The mobile application contributed to increasing the frequency of phone calls to OPI services during the intervention period (mean=12.8; P=0.001) as compared with the preintervention period (mean=4.3), and showed continued use during the postintervention period (mean=5.7). Most clinicians were satisfied with the use of the mobile application and access to the OPI services.

Conclusions:
The results suggest that mobile application tools contribute to increasing the use and ease of access to language services. This has the potential to improve the quality of communication between medical providers and limited English proficient patients in the delivery of cancer care in urgent care settings.
Novel Health Information Technology to Aid Provider Recognition and Treatment of Major Depressive Disorder and Posttraumatic Stress Disorder in Primary Care
Authors: Sorkin Dara H. , Rizzo Shemra , Biegler Kelly , Sim Susan Elliott , Nicholas Elisa , Chandler Maria , Ngo-Metzger Quyen , Paigne Kittya , Nguyen Danh V. , Mollica Richard 
Published: May 2019

Background:
Millions of traumatized refugees worldwide have resettled in the United States. For one of the largest, the Cambodian community, having their mental health needs met has been a continuing challenge. A multicomponent health information technology screening tool was designed to aid provider recognition and treatment of major depressive disorder and posttraumatic stress disorder (PTSD) in the primary care setting.

Methods:
In a clustered randomized controlled trial, 18 primary care providers were randomized to receive access to a multicomponent health information technology mental health screening intervention, or to a minimal intervention control group; 390 Cambodian American patients empaneled to participating providers were assigned to the providers’ randomized group.

Results:
Electronic screening revealed that 65% of patients screened positive for depression and 34% screened positive for PTSD. Multilevel mixed effects logistic models, accounting for clustering structure, indicated that providers in the intervention were more likely to diagnose depression [odds ratio (OR), 6.5; 95% confidence interval (CI), 1.48–28.79; P=0.013] and PTSD (OR, 23.3; 95% CI, 2.99–151.62; P=0.002) among those diagnosed during screening, relative to the control group. Providers in the intervention were more likely to provide evidence-based guideline (OR, 4.02; 95% CI, 1.01–16.06; P=0.049) and trauma-informed (OR, 15.8; 95% CI, 3.47–71.6; P<0.001) care in unadjusted models, relative to the control group. Guideline care, but not trauma-informed care, was associated with decreased depression at 12 weeks in both study groups (P=0.003), and neither was associated with PTSD outcomes at 12 weeks.

Conclusions:
This innovative approach offers the potential for training primary care providers to diagnose and treat traumatized patients, the majority of whom seek mental health care in primary care (ClinicalTrials.gov number, NCT03191929).
The Diagnostic Dilemma of Psychosis
Authors: Lingiardi Vittorio , Boldrini Tommaso 
Published: May 2019

AbstractThe term “pseudoneurotic schizophrenia” was introduced in 1949 by Hoch and Polatin to describe apparently neurotic patients showing formal thought disorders, emotional dysregulation, and transient psychotic symptoms. Even if this diagnostic entity is no longer included in modern diagnostic systems, its evolution is intertwined with the history of schizophrenia in the 20th century. This article retraces the development of pseudoneurotic (or “borderline”) schizophrenia in modern psychiatry, finding it a pioneering concept in psychopathology. In particular, we demonstrate that recent findings about the positive syndrome, good-outcome, type I “distress” subtype of schizophrenia (associated with high emotionality, including anxiety, depression, and sensitivity to stress) show surprising consistency with the clinical concept of pseudoneurotic schizophrenia. Finally, we discuss the historical development of pseudoneurotic schizophrenia in modern psychiatry as a meaningful example of the difficulty of confining severe psychological disturbances lying at the edge of full-blown schizophrenia within a widely accepted diagnostic category.
Factors Associated With Delirium Following Electroconvulsive Therapy
Authors: Tsujii Takashi , Uchida Takahito , Suzuki Takefumi , Mimura Masaru , Hirano Jinichi , Uchida Hiroyuki 
Published: May 2019

Objectives
Delirium following electroconvulsive therapy (ECT) has been a clinical challenge, which, however, has not been investigated through a systematic literature review. The objective of this study was to systematically synthesize available evidence regarding factors associated with post-ECT delirium.

Methods
We conducted a systematic literature search for any type of original investigations that reported risk factors of post-ECT delirium, using PubMed.

Results
The literature search identified 43 relevant articles. One study found an association between catatonic feature and increased risk of postictal delirium. Five studies reported that the presence of cerebrovascular disease, Parkinson disease, or dementia was related to higher incidence of post-ECT delirium. Incidence of post-ECT course delirium was increased with bitemporal stimulation (3 studies). One study showed that ultrabrief pulse ECT reduced reorientation time following seizure compared with brief pulse ECT. High stimulus intensity resulted in more prolonged reorientation time after ECT than lower stimulus intensity (2 studies). Longer seizure length was significantly associated with post-ECT delirium in 1 study. Eight studies that examined postictal delirium in association with medications used, including lithium, did not show any consistent finding in their relationships. Four studies showed decreased incidence of postictal delirium in those receiving dexmedetomidine.

Conclusions
Limited evidence suggests that catatonic feature, cerebrovascular disease, Parkinson disease, dementia, bitemporal electrode placement, high stimulus intensity, or longer seizure length are associated with an increased risk of post-ECT delirium. Moreover, dexmedetomidine and ultrabrief pulse ECT seem to have preventive effects of post-ECT delirium.
A sparse negative binomial classifier with covariate adjustment for RNA-seq data
Authors: Rahman Tanbin , Huang Hsin-En , Tai An-Shun , Hsieh Wen-Ping , Tseng George 
Published: May 2019

AbstractSupervised machine learning methods have been increasingly used in biomedical research and in clinical practice. In transcriptomic applications, RNA-seq data have become dominating and have gradually replaced traditional microarray due to its reduced background noise and increased digital precision. Most existing machine learning methods are, however, designed for continuous intensities of microarray and are not suitable for RNA-seq count data. In this paper, we develop a negative binomial model via generalized linear model framework with double regularization for gene and covariate sparsity to accommodate three key elements: adequate modeling of count data with overdispersion, gene selection and adjustment for covariate effect. The proposed method is evaluated in simulations and two real applications using cervical tumor miRNA-seq data and schizophrenia post-mortem brain tissue RNA-seq data to demonstrate its superior performance in prediction accuracy and feature selection.
Bridging the gap between theory and data: the Red Queen Hypothesis for sex
Authors: Park Sang Woo , Bolker Benjamin M 
Published: May 2019

AbstractSexual reproduction persists in nature despite its large cost. The Red Queen Hypothesis postulates that parasite pressure maintains sexual reproduction in the host population by selecting for the ability to produce rare genotypes that are resistant to infection. Mathematical models have been used to lay theoretical foundations for the hypothesis; empirical studies have confirmed these predictions. For example, Lively used a simple host-parasite model to predict that the frequency of sexual hosts should be positively correlated with the prevalence of infection. Lively et al. later confirmed the prediction through numerous field studies of snail-trematode systems in New Zealand. In this study, we fit a simple metapopulation host-parasite coevolution model to three data sets, each representing a different snail-trematode system, by matching the observed prevalence of sexual reproduction and trematode infection among hosts. Using the estimated parameters, we perform a power analysis to test the feasibility of observing the positive correlation predicted by Lively. We discuss anomalies in the data that are poorly explained by the model and provide practical guidance to both modelers and empiricists. Overall, our study suggests that a simple Red Queen model can only partially explain the observed relationships between parasite infection and the maintenance of sexual reproduction.
A new model for the implementation of positive and negative emotion recognition
Authors: Sorinas Jennifer , Fernandez-Troyano Juan C. , Val-Calvo Mikel , Ferrández Jose Manuel , Fernandez Eduardo 
Published: May 2019

ABSTRACTThe large range of potential applications, not only for patients but also for healthy people, that could be achieved by affective BCI (aBCI) makes more latent the necessity of finding a commonly accepted protocol for real-time EEG-based emotion recognition. Based on wavelet package for spectral feature extraction, attending to the nature of the EEG signal, we have specified some of the main parameters needed for the implementation of robust positive and negative emotion classification. 12 seconds has resulted as the most appropriate sliding window size; from that, a set of 20 target frequency-location variables have been proposed as the most relevant features that carry the emotional information. Lastly, QDA and KNN classifiers and population rating criterion for stimuli labeling have been suggested as the most suitable approaches for EEG-base emotion recognition. The proposed model reached a mean accuracy of 98% (s.d. 1.4) and 98.96% (s.d. 1.28) in a subject-dependent approach for QDA and KNN classifier, respectively. This new model represents a step forward towards real-time classification. Although results were not conclusive, new insights regarding subject-independent approximation have been discussed.
Actin chromobody imaging reveals sub-organellar actin dynamics
Authors: Schiavon Cara R. , Zhang Tong , Zhao Bing , Andrade Leonardo , Wu Melissa , Sung Tsung-Chang , Dayn Yelena , Feng Jasmine W. , Quintero Omar A. , Grosse Robert , Manor Uri 
Published: May 2019

AbstractThe actin cytoskeleton plays multiple critical roles in cells, from cell migration to organelle dynamics. The small and transient actin structures regulating organelle dynamics are difficult to detect with fluorescence microscopy. We developed an approach using fluorescent protein-tagged actin nanobodies targeted to organelle membranes to enable live cell imaging of sub-organellar actin dynamics with unprecedented spatiotemporal resolution. These probes reveal that ER-associated actin drives fission of multiple organelles including mitochondria, endosomes, lysosomes, peroxisomes, and the Golgi.
Role of Water-bridged Interactions in Metal Ion Coupled Protein Allostery
Authors: Guan Xingyue , Tan Cheng , Li Wenfei , Wang Wei , Thirumalai D. 
Published: May 2019

AbstractAllosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca2+ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca2+ binding helix-loop-helix motifs (EF-hands), we revealed the key role of water-bridged interactions in Ca2+ binding and protein allostery. The bridging water molecules between Ca2+ and binding residue reduces the ruggedness of ligand exchange landscape by acting as a lubricant, facilitating the Ca2+ coupled protein allostery.Calcium-induced rotation of the helices in the EF-hands, with the hydrophobic core serving as the pivot, leads to exposure of hydrophobic sites for target binding. Intriguingly, despite being structurally similar, the response of the two symmetrically arranged EF-hands upon Ca2+ binding is asymmetric. Breakage of symmetry is needed for efficient allosteric communication between the EF-hands. The key roles that water molecules play in driving allosteric transitions are likely to be general in other metal ion mediated protein allostery.
Mammalian retromer is an adaptable scaffold for cargo sorting from endosomes
Authors: Kendall Amy K. , Xie Boyang , Xu Peng , Wang Jue , Burcham Rodger , Frazier Meredith N. , Binshtein Elad , Wei Hui , Graham Todd R. , Nakagawa Terunaga , Jackson Lauren P. 
Published: May 2019

AbstractIn metazoans, retromer (VPS26/VPS35/VPS29) associates with sorting nexin (SNX) proteins to form coats on endosomal tubules and sort cargo proteins to the trans-Golgi network (TGN) or plasma membrane. This core complex is highly conserved from yeast to humans, but molecular mechanisms of metazoan retromer assembly remain undefined. Here we combine single particle cryo-electron microscopy with biophysical methods to uncover multiple oligomer structures formed by mammalian retromer. Two-dimensional class averages in ice reveal the retromer heterotrimer; dimers of trimers; tetramers of trimers; and flat chains. These species are further supported by biophysical studies in solution. We provide cryo-EM reconstructions of all species, including pseudo-atomic resolution detail for key sub-structures. Multi-body refinement demonstrates how retromer heterotrimers and dimers adopt a range of conformations. Our structures identify a flexible yet highly conserved electrostatic interface in dimers formed by interactions between VPS35 subunits. We generate a structure-based mutant to disrupt this key interface in vitro and introduce equivalent mutations into S. cerevisiae to demonstrate the mutant exhibits a cargo sorting defect. Together, structures and complementary functional data in budding yeast imply a conserved assembly interface across eukaryotes. These data further suggest mammalian retromer acts as an adaptable and plastic scaffold that accommodates interactions with different SNXs to sort multiple cargoes from endosomes their final destinations.
Bund removal to re-establish tidal flow, remove aquatic weeds and restore coastal wetland services – North Queensland, Australia
Authors: Abbott Brett N. , Wallace Jim , Nicholas David M. , Karim Fazlul , Waltham Nathan J. 
Published: May 2019

AbstractThe shallow tidal and freshwater coastal wetlands adjacent to the Great Barrier Reef lagoon provide a vital nursery and feeding complex that supports the life cycles of marine and freshwater fish, important native vegetation and vital bird habitat. Urban and agricultural development threaten these wetlands, with many of the coastal wetlands becoming lost or changed due to the construction of artificial barriers (e.g. bunds, roads, culverts and floodgates). Infestation by weeds has become a major issue within many of the wetlands that were modified (bunded) for ponded pasture growth last century. A range of expensive chemical and mechanical control methods has been used to try and restore some of these coastal wetlands, with limited success. This study describes an alternative approach to those methods, investigating the impact of tidal reinstatement after bund removal on weed infestation, associated changes in water quality, and fish biodiversity, in the Boolgooroo lagoon region of the Mungalla wetlands, East of Ingham in North Queensland. High resolution remote sensing, electrofishing and in-water logging was used to track changes over time – 1 year before and 4 years after removal of an earth bund. With tides only penetrating the wetland a few times yearly, gross changes towards a more natural system occurred within a relatively short timeframe, leading to a reduction in weed infestation, reappearance of native vegetation, improvements in water quality, and a tripling of fish diversity. Weed abundance and water quality does appear to oscillate however, dependent on summer rainfall, as changes in hydraulic pressure stops or allows tidal ingress (fresh/saline cycling). With an estimated 30% of coastal wetlands bunded in the Great Barrier Reef region, a passive remediation method such as reintroduction of tidal flow by removal of an earth bund or levee could provide a more cost effective and sustainable means of controlling freshwater weeds and improving coastal water quality into the future.
An intergenic non-coding RNA promoter required for histone modifications in the human β-globin chromatin domain
Authors: Debrand Emmanuel , Chakalova Lyubomira , Miles Joanne , Dai Yan-Feng , Goyenechea Beatriz , Dye Sandra , Osborne Cameron S. , Horton Alice , Harju-Baker Susanna , Pink Ryan C. , Caley Daniel , Carter David R. F. , Peterson Kenneth R. , Fraser Peter 
Published: May 2019

AbstractTranscriptome analyses show a surprisingly large proportion of the mammalian genome is transcribed; much more than can be accounted for by genes and introns alone. Most of this transcription is non-coding in nature and arises from intergenic regions, often overlapping known protein-coding genes in sense or antisense orientation. The functional relevance of this widespread transcription is unknown. Here we characterize a promoter responsible for initiation of an intergenic transcript located approximately 3.3 kb and 10.7 kb upstream of the adult-specific human β-globin genes. Mutational analyses in β-YAC transgenic mice show that alteration of intergenic promoter activity results in ablation of H3K4 di- and tri-methylation and H3 hyperacetylation extending over a 30 kb region immediately downstream of the initiation site, containing the adult δ- and β-globin genes. This results in dramatically decreased expression of the adult genes through position effect variegation in which the vast majority of definitive erythroid cells harbor inactive adult globin genes. In contrast, expression of the neighboring ε- and γ-globin genes is completely normal in embryonic erythroid cells, indicating a developmentally specific variegation of the adult domain. Our results demonstrate a role for intergenic non-coding RNA transcription in the propagation of histone modifications over chromatin domains and epigenetic control of β-like globin gene transcription during development.
Neural tube development depends on notochord-derived Sonic hedgehog released into the sclerotome
Authors: Kahane Nitza , Kalcheim Chaya 
Published: May 2019

AbstractSonic hedgehog (Shh), produced in notochord and floor plate, is necessary both for neural and mesodermal development. To reach the myotome, Shh has to traverse the sclerotome. By loss and gain of Shh function, and floor plate deletions, we report that sclerotomal Shh is also necessary for neural tube development. Reducing the amount of Shh in sclerotome by membrane-tethered hedgehog-interacting protein or by Patched1, but not by dominant active Patched, decreased motoneuron numbers while also compromising myotome differentiation. These effects were a specific and direct consequence of reducing Shh. In addition, grafting notochords in a basal, but not apical location vis-a-vis the tube, profoundly affected motoneuron development, suggesting that initial ligand presentation occurs at the basal side of epithelia corresponding to the sclerotome-neural tube interface.Collectively, our results reveal that the sclerotome is a potential site of a Shh gradient that coordinates development of mesodermal and neural progenitors.Summary statementShh that transits through the sclerotome is presented to the neuroepithelium from its basal aspect to affect motoneuron development.