bluuebunny/crossref_metadata_2025_split huggingface dataset:
Medical Record Documentation About Opioid Tapering: Examining Benefit-to-Harm Framework and Patient Engagement
Authors: Buonora Michele , Perez Hector R , Stumph Jordan , Allen Robert , Nahvi Shadi , Cunningham Chinazo O , Merlin Jessica S , Starrels Joanna L 
Published: January 2020

Abstract

Objective
Guidelines recommend that clinicians make decisions about opioid tapering for patients with chronic pain using a benefit-to-harm framework and engaging patients. Studies have not examined clinician documentation about opioid tapering using this framework.

Design and Setting
Thematic and content analysis of clinician documentation about opioid tapering in patients’ medical records in a large academic health system.

Methods
Medical records were reviewed for patients aged 18 or older, without cancer, who were prescribed stable doses of long-term opioid therapy between 10/2015 and 10/2016 then experienced an opioid taper (dose reduction ≥30%) between 10/2016 and 10/2017. Inductive thematic analysis of clinician documentation within six months of taper initiation was conducted to understand rationale for taper, and deductive content analysis was conducted to determine the frequencies of a priori elements of a benefit-to-harm framework.

Results
Thematic analysis of 39 patients’ records revealed 1) documented rationale for tapering prominently cited potential harms of continuing opioids, rather than observed harms or lack of benefits; 2) patient engagement was variable and disagreement with tapering was prominent. Content analysis found no patients’ records with explicit mention of benefit-to-harm assessments. Benefits of continuing opioids were mentioned in 56% of patients’ records, observed harms were mentioned in 28%, and potential harms were mentioned in 90%.

Conclusions
In this study, documentation of opioid tapering focused on potential harms of continuing opioids, indicated variable patient engagement, and lacked a complete benefit-to-harm framework. Future initiatives should develop standardized ways of incorporating a benefit-to-harm framework and patient engagement into clinician decisions and documentation about opioid tapering.
Living and Dying in a Disparate Health Care System: Rationale and Strategies for Cultural Humility in Palliative and Hospice Care Physical Therapy
Authors: Barnes Christopher , Mueller Karen , Fawcett Lubayna , Wagner Barbara 
Published: January 2020

Background:
Disparities in diversity, equity and inclusivity are endemic in American society, and in the United States (US) healthcare system. As US population diversity increases, physical therapists (PTs) must be able to provide equitable care for all people, regardless of their cultural or personal identity. Culturally-humble Hospice and palliative Care (HPC) PT practice, with vigilant awareness of cultural complexities and commitment to approaching cultural understanding with humility, is essential to provide optimal end of life care for all persons.

Purpose:
This Perspective paper will 1) provide an overview of the role of PT in HPC, 2) describe culturally-related disparities in HPC, and 3) suggest evidence-based strategies for cultural humility in HPC PT best practice. Specific challenges in the delivery of culturally-humble end of life care will be discussed, including advanced care planning, truth telling, and death beliefs/practices.
Improving Engagement in HIV Care Using a Data-to-Care and Patient Navigation System in Louisiana, United States
Authors: Anderson Susannah , Henley Catherine , Lass Katherine , Burgess Samuel , Jenner Eric 
Published: January 2020

Abstract
An estimated 57% of persons living with HIV (PLWH) in the United States are not connected to regular medical care or have lapsed from regular care (Centers for Disease Control and Prevention, 2018), increasing risk of HIV progression and transmission and delaying viral suppression. The state of Louisiana has consistently ranked in the top five US states for HIV case rates. We evaluated the impact of a combined data-to-care and patient navigation system that was implemented in 3 cities in Louisiana from 2013 to 2015. The program, LA Links, used a surveillance system to identify PLWH who were not in regular health care and connected them to a patient navigator. During the intervention period, persons who lapsed from care were 17% more likely to reengage in care than persons in the comparison group, and persons newly diagnosed during the intervention period were 56% more likely to link to care.
Fecal Markers of Inflammation and Disease Activity in Pediatric Crohn Disease
Authors: Leach Steven T. , Day Andrew S. , Messenger Rachel , Walters Thomas D. , Navas‐López Victor M. , Sladek Malgorzata , Brückner Annecarin , Yerushalmi Baruch , Saeed Shehzad , Otley Anthony , Mack David , Gavish Matan , Turner Dan , Griffiths Anne M. , Lemberg Daniel A. ,   ImageKids study group
Published: January 2020

ABSTRACTBackground:Noninvasive and accurate methods to monitor inflammatory bowel disease are required. As a planned ancillary study of the prospective ImageKids cohort, we aimed to assess the performance of fecal calprotectin (FC) with comparison to 3 fecal inflammatory markers; S100A12 (FA12), tumor pyruvate kinase isoenzyme type M2 (FM2PK) and fecal osteoprotegerin (FOPG) as indicators of a number of disease characteristics.Methods:The ImageKids study was a multicenter study designed to develop 2 magnetic resonance enterography–based measures for children with Crohn disease (6–18 years old). All patients underwent magnetic resonance enterography, a complete ileocolonoscopic evaluation and provided a fecal sample. Fecal samples were assay for FC, FA12, FM2PK, and FOPG by ELISA.Results:One‐hundred fifty‐six children provided 190 fecal samples. Median (interquartile range) for fecal makers were FC, 602 (181–1185) μg/g; FA12, 21 (3–109) μg/g; FM2PK, 16 (2–20) U/mL; and FOPG, 125 (125–312) μg/g. All markers correlated with simple endoscopic severity index for Crohn disease and with other constructs of disease activity, but FC had the highest overall correlations. FA12, however, predicted mucosal healing with significantly higher specificity (87% vs 70%, P = 0.004) and equivalent sensitivity (91% vs 90%) compared to FC.Conclusion:This study has confirmed that FC is useful, and overall best, marker to monitor mucosal inflammation in inflammatory bowel disease. FA12, however, appears to be a more suitable maker for prediction of mucosal healing in children.
Lineage Functional Types (LFTs): Characterizing functional diversity to enhance the representation of ecological behavior in Earth System Models
Authors: Griffith Daniel M. , Osborne Colin , Edwards Erika J. , Bachle Seton , Beerling David J. , Bond William J. , Gallaher Timothy , Helliker Brent R. , Lehmann Caroline E.R. , Leatherman Lila , Nippert Jesse B. , Pau Stephanie , Qiu Fan , Riley William J. , Smith Melinda D. , Strömberg Caroline , Taylor Lyla , Ungerer Mark , Still Christopher J. 
Published: January 2020

SummaryProcess-based vegetation models attempt to represent the wide range of trait variation in biomes by grouping ecologically similar species into plant functional types (PFTs). This approach has been successful in representing many aspects of plant physiology and biophysics, but struggles to capture biogeographic history and ecological dynamics that determine biome boundaries and plant distributions. Grass dominated ecosystems are broadly distributed across all vegetated continents and harbor large functional diversity, yet most Earth System Models (ESMs) summarize grasses into two generic PFTs based primarily on differences between temperate C3grasses and (sub)tropical C4grasses. Incorporation of species-level trait variation is an active area of research to enhance the ecological realism of PFTs, which form the basis for vegetation processes and dynamics in ESMs. Using reported measurements, we developed grass functional trait values (physiological, structural, biochemical, anatomical, phenological, and disturbance-related) of dominant lineages to improve ESM representations. Our method is fundamentally different from previous efforts, as it uses phylogenetic relatedness to create lineage-based functional types (LFTs), situated between species-level trait data and PFT-level abstractions, thus providing a realistic representation of functional diversity and opening the door to the development of new vegetation models.
Antibiotics-induced alterations in gut microbiol composition leads to blood-brain barrier permeability increase in rhesus monkeys
Authors: Wu Qiong , Zhang Yingqian , Zhang Yinbing , Xia Chunchao , Lai Qi , Dong Zaiquan , Kuang Weihong , Yang Cheng , Su Dan , Li Hongxia , Zhong Zhihui 
Published: January 2020

ABSTRACTBlood-brain barrier (BBB) contributes to maintenance of brain homeostasis. Gut microbiome composition affected BBB development and expression of tight junction proteins in rodents. However, we still do not know if there’s any direct effect of gut microbiol composition on BBB permeability and function in normal adult animals. In current study, we determined temporal and spatial change of BBB permeability in rhesus monkeys receiving either oral or intravenous amoxicillin-clavulanic acid (AC), by monitoring CSF/serum albumin ratio (AR) and the volume transfer constant (Ktrans). We showed that oral, but not intravenous AC led to a significant alteration in gut microbiol composition and increase of BBB permeability in all monkeys, especially in thalamus area. Acetic acid and propionic acid might play a pivotal role in this newly found communication between gut and central nervous system. Antibiotics-induced gut microbiol composition change, especially the decreasing of acetic and propionic acid producing phyla and genera, leads to increase of BBB permeability, which may contribute to a variety of neurological and psychological diseases.
Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum
Authors: Chakraborty Priyanka , George Jason T , Tripathi Shubham , Levine Herbert , Jolly Mohit Kumar 
Published: January 2020

AbstractThe Epithelial-mesenchymal transition (EMT) is a cellular process implicated in embryonic development, wound healing, and pathological conditions such as cancer metastasis and fibrosis. Cancer cells undergoing EMT exhibit enhanced aggressive behavior characterized by drug resistance, tumor-initiation potential, and the ability to evade immune system. Recentin silico, in vitro, andin vivoevidence indicates that EMT is not an all-or-none process; instead, cells stably acquire one or more hybrid epithelial/mesenchymal (E/M) phenotypes which often can be more aggressive than purely epithelial or mesenchymal cell populations. Thus, the EMT status of cancer cells can prove to be a critical estimate of patient prognosis. Recent attempts have employed different transcriptomics signatures to quantify EMT status in cell lines and patient tumors. However, a comprehensive comparison of these methods, including their accuracy in identifying cells in the hybrid E/M phenotype(s), is lacking. Here, we compare three distinct metrics that score EMT on a continuum, based on the transcriptomics signature of individual samples. Our results demonstrate that these methods exhibit good concordance among themselves in quantifying the extent of EMT in a given sample. Moreover, scoring EMT using any of the three methods discerned that cells undergo varying extents of EMT across tumor types. Separately, our analysis also identified tumor types with maximum variability in terms of EMT and associated an enrichment of hybrid E/M signatures in these samples. Moreover, we also found that the multinomial logistic regression (MLR) based metric was capable of distinguishing between ‘pure’ individual hybrid E/M vs. mixtures of epithelial (E) and mesenchymal (M) cells. Our results, thus, suggest that while any of the three methods can indicate a generic trend in the EMT status of a given cell, the MLR method has two additional advantages: a) it uses a small number of predictors to calculate the EMT score, and b) it can predict from the transcriptomic signature of a population whether it is comprised of ‘pure’ hybrid E/M cells at the single-cell level or is instead an ensemble of E and M cell subpopulations.
Complex interactions between weather, and microbial and physiochemical water quality impact the likelihood of detecting foodborne pathogens in agricultural water
Authors: Weller Daniel , Brassill Natalie , Rock Channah , Ivanek Renata , Mudrak Erika , Roof Sherry , Ganda Erika , Wiedmann Martin 
Published: January 2020

AbstractAgricultural water is an important source of foodborne pathogens on produce farms. Managing water-associated risks does not lend itself to one-size-fits-all approaches due to the heterogeneous nature of freshwater environments, and because environmental conditions affect the likelihood of pathogen contamination and the relationship between indicator organism levels (e.g., E. coli) and pathogen presence. To improve our ability to develop location-specific risk management practices, a study was conducted in two produce-growing regions to (i) characterize the relationship between E. coli levels and pathogen presence in agricultural water, and (ii) identify environmental factors associated with pathogen detection. Three AZ and six NY waterways were sampled longitudinally using 10-L grab samples (GS) and 24-h Moore swabs (MS). Regression showed that the likelihood of Salmonella detection (Odds Ratio [OR]=2.18), and eaeA-stx codetection (OR=6.49) was significantly greater for MS compared to GS, while the likelihood of detecting L. monocytogenes was not. Regression also showed that eaeA-stx codetection in AZ (OR=50.2) and NY (OR=18.4), and Salmonella detection in AZ (OR=4.4) were significantly associated with E. coli levels, while Salmonella detection in NY was not. Random forest analysis indicated that interactions between environmental factors (e.g., rainfall, temperature, turbidity) (i) were associated with likelihood of pathogen detection and (ii) mediated the relationship between E. coli levels and likelihood of pathogen detection. Our findings suggest that (i) environmental heterogeneity, including interactions between factors, affects microbial water quality, and (ii) E. coli levels alone may not be a suitable indicator of the food safety risks. Instead, targeted methods that utilize environmental and microbial data (e.g., models that use turbidity and E. coli levels to predict when there is a high or low risk of surface water being contaminated by pathogens) are needed to assess and mitigate the food safety risks associated with preharvest water use. By identifying environmental factors associated with an increased likelihood of detecting pathogens in agricultural water, this study provides information that (i) can be used to assess when pathogen contamination of agricultural water is likely to occur, and (ii) facilitate development of targeted interventions for individual water sources, providing an alternative to existing one-size-fits-all approaches.
Effects of language experience on domain-general perceptual strategies
Authors: Jasmin Kyle , Sun Hui , Tierney Adam T. 
Published: January 2020

AbstractSpeech and music are highly redundant communication systems, with multiple acoustic cues signaling the existence of perceptual categories. This redundancy makes these systems robust to the influence of noise, but necessitates the development of perceptual strategies: listeners need to decide the importance to place on each source of information. Prior empirical work and modeling has suggested that cue weights primarily reflect within-task statistical learning, as listeners assess the reliability with which different acoustic dimensions signal a category and modify their weights accordingly. Here we present evidence that perceptual experience can lead to changes in cue weighting which extend across tasks and across domains, suggesting that perceptual strategies reflect both global biases and local (i.e. task-specific) learning. In two experiments, native speakers of Mandarin (N=45)—where pitch is a crucial cue to word identity—placed more importance on pitch and less importance on other dimensions compared to native speakers of non-tonal languages English (N=45) and Spanish (N=27), during the perception of both second language speech and musical beats. In a third experiment, we further show that Mandarin speakers are better able to attend to pitch and ignore irrelevant variation in other dimensions compared to English and Spanish speakers, and even struggle to ignore pitch when asked to attend to other dimensions. Thus, an individual’s idiosyncratic auditory perceptual strategies reflect a complex mixture of congenital predispositions, task-specific learning, and biases instilled by extensive experience in making use of important dimensions in their native language.
Inactivation of LCN2/EGR1 Promotes Oligodendrocyte Progenitor Cell Differentiation and Remyelination after White Matter Injury
Authors: Li Qiang , Ru Xufang , Yang Yang , Zhao Hengli , Qu Jie , Chen Weixiang , Pan Pengyu , Ruan Huaizhen , Li Chaojun , Feng Hua , Chen Yujie 
Published: January 2020

AbstractThe insufficient remyelination due to the impaired oligodendrocyte precursor cell differentiation and maturation is highly associated with irreversible white matter injury and neurological deficits. Consequently, inhibitory components and microenvironment for remyelination might serve as potential therapeutic targets for treating white matter injury after acute central nervous system injury and neurodegeneration diseases. Lipocalin-2 was recently reported to corelate with white matter in both atypical, acute white matter injured disease subarachnoid hemorrhage and typical, chronic white matter injured disease multiple sclerosis. To elucidate the role and underlying mechanism of Lipocalin-2 in oligodendrocyte precursor cell differentiation and remyelination, we used genetic inhibition and a constitutive conditional knockout model with subarachnoid hemorrhage or multiple sclerosis. We found that the genetic inhibition of the increase in Lipocalin-2 promoted oligodendrocyte precursor cell differentiation, remyelination, and functional recovery after subarachnoid hemorrhage or multiple sclerosis. Unexpectedly, the inhibition of Lipocalin-2 did not reduce glial activation and inflammation. Lipocalin-2 was shown to activate Early Growth Response Protein 1 in oligodendrocyte precursor cells, which is partly regulated by its receptor SLC22A17. In the conditional knockout of Early Growth Response Protein 1 in oligodendrocyte precursor cells, we discovered enhanced oligodendrocyte precursor cell differentiation in developing and injured white matter; consistently, the specific inactivation of Early Growth Response Protein 1 promoted remyelination and neurological recovery after subarachnoid hemorrhage or multiple sclerosis. Thus, we propose that following white matter injury in humans, the increase in Lipocalin-2 activates Early Growth Response Protein 1 and consequently impair oligodendrocyte precursor cell differentiation and myelin repair. Our results suggest that therapies specifically inactivating Lipocalin-2/ Early Growth Response Protein 1 signal in oligodendroglial lineage cells could represent a novel strategy to enhance differentiation and remyelination in white matter injury patients.
Structure-function analysis of interallelic complementation inROOTYtransheterozygotes
Authors: Brumos Javier , Bobay Benjamin G. , Clark Cierra A. , Alonso Jose M. , Stepanova Anna N. 
Published: January 2020

AbstractAuxin is a crucial plant growth regulator. Forward genetic screens for auxin-related mutants have led to the identification of key genes involved in auxin biosynthesis, transport, and signaling. Loss-of-function mutations in the genes involved in indole glucosinolate biosynthesis, a metabolically-related route that produces defense compounds from indolic precursors shared with the auxin pathway, result in auxin overproduction. We identified an allelic series of fertile, hypomorphic mutants for an essential indole glucosinolate route geneROOTY(RTY)that show a range of high-auxin defects. Genetic characterization of these lines uncovered phenotypic suppression bycyp79b2 b3,wei2, andwei7mutants and revealed the phenomenon of interallelic complementation in severalRTYtransheterozygotes. Structural modeling of RTY shed light on the structure-to-function relations in the RTY homo- and heterodimers and unveiled the likely structural basis of interallelic complementation. This work underscores the importance of employing true null mutants in genetic complementation studies.
A Point Mutation in the RNA Recognition Motif of CSTF2 Associated with Intellectual Disability in Humans Causes Defects in 3′ End Processing
Authors: Grozdanov Petar N. , Masoumzadeh Elahe , Kalscheuer Vera M. , Bienvenu Thierry , Billuart Pierre , Delrue Marie-Ange , Latham Michael P. , MacDonald Clinton C. 
Published: January 2020

SUMMARYCSTF2 encodes an RNA-binding protein that is essential for mRNA cleavage and polyadenylation (C/P). No disease-associated mutations have been described for this gene. Here, we report a mutation in the RNA recognition motif (RRM) of CSTF2 that changes an aspartic acid at position 50 to alanine (p.D50A), resulting in intellectual disability in male patients. In mice, this mutation was sufficient to alter polyadenylation sites in over 1,000 genes critical for brain development. Using a reporter gene assay, we demonstrated that C/P efficiency of CSTF2D50A was lower than wild type. To account for this, we determined that p.D50A changed locations of amino acid side chains altering RNA binding sites in the RRM. The changes modified the electrostatic potential of the RRM leading to a greater affinity for RNA. These results highlight the importance of 3′ end mRNA processing in correct expression of genes important for brain plasticity and neuronal development.
Differential reinforcement encoding along the hippocampal long axis helps resolve the explore/exploit dilemma
Authors: Dombrovski Alexandre Y. , Luna Beatriz , Hallquist Michael N. 
Published: January 2020

ABSTRACTWhen making decisions, should one exploit known good options or explore potentially better alternatives? Exploration of spatially unstructured options depends on the neocortex, striatum, and amygdala. In natural environments, however, better options often cluster together, forming structured value distributions. The hippocampus binds reward information into allocentric cognitive maps to support navigation and foraging in such spaces. Using a reinforcement learning task with a spatially structured reward function, we show that human posterior hippocampus (PH) invigorates exploration while anterior hippocampus (AH) supports the transition to exploitation. These dynamics depend on differential reinforcement representations in the PH and AH. Whereas local reward prediction error signals are early and phasic in the PH tail, global value maximum signals are delayed and sustained in the AH body. AH compresses reinforcement information across episodes, updating the location and prominence of the value maximum and displaying goal cell-like ramping activity when navigating toward it.