bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring pinyon-juniper cover and aboveground biomass across the Great Basin
Authors: Filippelli Steven K , Falkowski Michael J , Hudak Andrew T , Fekety Patrick A , Vogeler Jody C , Khalyani Azad Henareh , Rau Benjamin M , Strand Eva K
Published: January 2020

Since the mid-1800s pinyon-juniper (PJ) woodlands have been encroaching into sagebrush-steppe shrublands and grasslands such that they now comprise 40% of the total forest and woodland area of the Intermountain West of the United States. More recently, PJ ecosystems in select areas have experienced dramatic reductions in area and biomass due to extreme drought, wildfire, and management. Due to the vast area of PJ ecosystems, tracking these changes in woodland tree cover is essential for understanding their consequences for carbon accounting efforts, as well as ecosystem structure and functioning. Here we present a carbon monitoring, reporting, and verification (MRV) system for characterizing total aboveground biomass stocks and flux of PJ ecosystems across the Great Basin. This is achieved through a two-stage remote sensing approach by first using spatial wavelet analysis to rapidly sample tree cover from very high-resolution imagery (1 m), and then training a Random Forest model which maps tree cover across the region from 2000 to 2016 using temporally-segmented Landsat spectral indices obtained from the LandTrendr algorithm in Google Earth Engine. Estimates of cover were validated against field data from the SageSTEP project (R
2 = 0.67, RMSE = 10% cover). Biomass estimated from cover-based allometry was higher than estimates from the Forest Inventory and Analysis Program (FIA) at the plot-level (bias = 5 Mg ha−1 and RMSE = 15.5 Mg ha−1) due in part to differences in tree-level biomass allometrics. County-level aggregation of biomass closely matched estimates from the FIA (R
2 = 0.97) after correcting for bias at the plot level. Even after many previous decades of encroachment, we find forest area (i.e. areas with ≥10% cover) increasing at a steady rate of 0.46% per year, but 80% of the 9.86 Tg increase in biomass is attributable to infilling of existing forest. This suggests that the known consequences of encroachment such as reduced water availability, impacts to biodiversity, and risk of severe wildfire may have been increasing across the region in recent years despite the actions of sagebrush steppe restoration initiatives.
Subhourly rainfall in a convection-permitting model
Authors: Meredith Edmund P , Ulbrich Uwe , Rust Henning W
Published: January 2020

Convection-permitting models (CPMs)—the newest generation of high-resolution climate models—have been shown to greatly improve the representation of subdaily and hourly precipitation, in particular for extreme rainfall. Intense precipitation events, however, often occur on subhourly timescales. The distribution of subhourly precipitation, extreme or otherwise, during a rain event can furthermore have important knock-on effects on hydrological processes. Little is known about how well CPMs represent precipitation at the subhourly timescale, compared to the hourly. Here we perform multi-decadal CPM simulations centred over Catalonia and, comparing with a high temporal-resolution gauge network, find that the CPM simulates subhourly precipitation at least as well as hourly precipitation is simulated. While the CPM inherits a dry bias found in its parent model, across a range of diagnostics and aggregation times (5, 15, 30 and 60 min) we find no consistent evidence that the CPM precipitation bias worsens with shortening temporal aggregation. We furthermore show that the CPM excels in its representation of subhourly extremes, extending previous findings at the hourly timescale. Our findings support the use of CPMs for modelling subhourly rainfall and add confidence to CPM-based climate projections of future changes in subhourly precipitation, particularly for extremes.
Preparation and characterization of nano silver immobilized hydrochar derived from hydrothermal carbonization of tobacco stem
Authors: Liang Miao , Liu Xiangzhen , Wang Le , He Yuan , Huang Feng , Li Bin , Zhang Ke , Tian Haiying
Published: January 2020

In this present study, silver nanoparticles (AgNPs) immobilized hydrochar was prepared through a facile one-pot co-hydrothermal carbonization of tobacco stem and silver nitrate. The effect of concentration of silver precursor, hydrothermal temperature and reaction time on the chemical compositions, structural property, combustion performance, as well as gaseous products release behavior of the resultant AgNPs immobilized hydrochar were evaluated. The co-hydrothermal treatment decreased the volatile matter while increased the ash content of hydrochar. Single-phase AgNPs were successfully generated and evenly immobilized onto the hydrochar during the hydrothermal process. The immobilized AgNPs played a notable catalytic role during the char combustion stage, thereby decreased the ignition temperature, burnout temperature and maximum rate temperature for char combustion. Meanwhile, TG-FTIR analysis suggested that the emission amount of harmful gas CO during hydrochar combustion was reduced due to the catalytic effect of AgNPs. This phenomenon may indicate the appropriate amount of nanoparticles immobilization could enhance the combustion behavior of hydrochar fuel.
Experimental investigation on self-activated healing performance of thermosetting polyurethane prepared by tungsten (VI) chloride catalyst
Authors: Fereidoon Abdoulhossein , Ghasemi-Ghalebahman Ahmad , Amini-Nejad Reza , Golshan-Ebrahimi Nadereh
Published: January 2020

Polymers and polymeric composites are widely used for various applications due to their outstanding and wide range of properties. Polyurethanes, existing in different types, are novel and versatile polymers with excellent mechanical properties. Thermosetting polyurethane resins are among the most widely used polyurethanes wherein their manufacturing and developing have been introduced during the last few years. Self-healing materials have been inspired by biological systems in which damages provoke healing responses. It is almost cost-effective to use self-healing materials in commercial applications. This study investigates a novel self-activated approach in thermosetting polyurethane resins. A tungsten (VI) chloride (

WCl

6

) catalyst, a co-activator (phenylacetylene) and a dissolution agent (nonylphenol) were used for the onset of ring-opening metathesis polymerization of dicyclopentadiene. Here different percentages of a catalyst in polyurethane resins were used, the impacts of which on fracture toughness and healing efficiency were also studied. To examine healing efficiency, samples with tapered double-cantilever beam geometry were prepared and using the self-activated method, the development of thermosetting polyurethane self-healing was investigated. The results showed that the concentration of catalyst affects the basic properties of the material and healing efficiency of the composite. The highest healing efficiency of 97% was obtained for a 3 wt% catalyst.
Classifying superconductivity in ThH-ThD superhydrides/superdeuterides
Authors: Talantsev E F , Mataira R C
Published: January 2020

Satterthwaite and Toepke (1970 Phys. Rev. Lett.
25 741) discovered that Th4H15-Th4D15 superhydrides are superconducting but exhibit no isotope effect. As the isotope effect is a fundamental prediction of electron-phonon mediated superconductivity described by Bardeen, Cooper, and Schrieffer (BCS) its absence alludes to some other mechanism. Soon after this work, Stritzker and Buckel (1972 Zeitschrift für Physik A Hadrons and nuclei 257 1-8) reported that superconductors in the PdHx-PdDx system exhibit the reverse isotope effect. Yussouff et al (1995 Solid State Communications
94 549) extended this finding in PdHx-PdDx-PdTx systems. Renewed interest in hydrogen- and deuterium-rich superconductors is driven by the discovery of near-room-temperature superconductivity in highly-compressed H3S (Drozdov et al 2015 Nature
525 73) and LaH10 (Somayazulu et al 2019 Phys. Rev. Lett.
122 027001). Here we attempt to reaffirm or disprove our primary idea that the mechanism for near-room-temperature superconductivity in hydrogen-rich superconductors is not BCS electron-phonon mediated. To that end, we analyse the upper critical field data, B
c2(T), in Th4H15-Th4D15 (Satterthwaite and Toepke 1970 Phys. Rev. Lett.
25 741) as well as two recently discovered high-pressure hydrogen-rich phases of ThH9 and ThH10 (Semenok et al 2019 Materials Today, DOI: 10.1016/j.mattod.2019.10.005). We conclude that all known thorium super-hydrides/deuterides, to date, are unconventional superconductors—along with the heavy fermions, fullerenes, pnictides, cuprates—where we find they have T
c/T
F ratios within a range of 0.008 < T
c/T
F < 0.120, where T
c is the superconducting transition temperature and T
F is the Fermi temperature.
Optical and dielectric properties of electrochemically deposited p-Cu2O films
Authors: Ait Hssi A , Atourki L , Labchir N , Ouafi M , Abouabassi K , Elfanaoui A , Ihlal A , Bouabid K
Published: January 2020

A perfect crystalline phases of cuprous oxide were synthesized using electrochemical method at different duration ( 15, 30 and 60 min). The deposited samples were examined by XRD, SEM, UV–Vis absorption and Mott-Schottky measurements. The effect of the deposition time on the optical and dielectric properties of Cu2O was studied in detail. The x-ray diffraction indicated increasing of crystallinity and crystallite size with increasing of deposition time. SEM micrographs exhibited grains with three-faced pyramid shape and grains size increased with improvement of crystallinity. Optical study is performed to calculate optical band gap (Eg), absorption coefficient (α), extinction coefficient (k), refractive index (n), dielectric constants (ε), urbach energy (EU) and optical conductivity (σopt) using the transmittance and absorption spectra in the wavelength range of 400–1100 nm. Among all grown samples, the film deposited at 60 min shows interesting optical and dielectric properties. The Mott-Schottky analysis shows that the film deposited at 60 min has a low carrier density compared to samples deposited in other deposition times.
ZnO thin films grown at different plasma energies by the laser ablation of metallic Zn with a 532 nm wavelength
Authors: de León J A Guerrero , Pérez-Centeno A , Gómez-Rosas G , Camps E , Arias-Cerón J S , Santana-Aranda M A , Quiñones-Galvan J G
Published: January 2020

In this work, structural, optical and electrical properties of ZnO thin films grown by laser ablation of a Zn metallic target on oxygen atmosphere using the 532 nm emission of the second harmonic of a Nd:YAG laser, are studied. Different mean kinetic energies of the plasma (Ek) at fixed ion density (Np) were used as control parameters. X-ray diffraction profiles show the presence of a width (002) peak together with a peak associated with the (101) reflection. Changes in Ek affect the crystallinity of the samples. An intense PL emission in the visible range of the spectra associated with a majority intrinsic donor defects can be observed. The films showed an unusual low electrical resistivity as compared to the commonly reported values for undoped ZnO thin films.
Structural electronic and dynamic properties of Li3Bi and Li2NaBi
Authors: Erden Gulebaglan Sinem , Kilit Dogan Emel
Published: January 2020

We report a study of structural, electronic and dynamic properties of Li3Bi and Li2NaBi via density functional theory. It is found that Li3Bi and Li2NaBi show semiconducting property with an indirect electronic band gap. The calculated structural and electronic parameters (lattice parameters, bulk modulus, bulk modulus derivation) are in a good agreement with the available experimental data. Full phonon spectra of Li3Bi and Li2NaBi materials in the Rock Salt structure were collected using the linear response method. At 0 GPa pressure, Li3Bi is dynamically stable while Li2NaBi, which can be synthesized from Li3Bi by replacing one Bi atom with the Na atom, is unstable. In this study we searched to find the pressure value that makes Li2NaBi dynamically stable. Calculations showed that the Li2NaBi structure becomes stable when 8.62 GPa pressure is applied to the Li2NaBi structure. This study is thought to give direction to the future studies.
Optical anisotropy of one-dimensional perovskite C4N2H14PbI4 crystals
Authors: Cheng Xue , Ma Jiaqi , Zhou Yunxi , Fang Chen , Wang Jun , Li Junze , Wen Xinglin , Li Dehui
Published: January 2020

Optical anisotropy is essential for the polarization-sensitive optoelectronic devices. Recently, in-plane anisotropy is demonstrated in various 2D layered materials. It has been proved that organic-inorganic perovskites possess excellent optical properties; however, the anisotropy of organic-inorganic perovskites is rarely reported because of the in-plane isotropic structure. Here, we report a large optical anisotropy of one-dimensional organic lead iodine perovskites C4N2H14PbI4 crystals, including emission, excitation and reflection anisotropy. An emission linear dichroic ratio of 5.5 and an excitation linear dichroic ration of 7 are achieved respectively, which are much larger than the in-plane anisotropy of 2D layered materials. The large optical anisotropy can be ascribed to the anisotropic dipole moment in the unique 1D chain structure. In addition, the PL of the 1D C4N2H14PbI4 crystal is dominated by the broadband self-trapped exciton emission due to the quantum confinement effect and strong electron-phonon interaction. Our results advocate that 1D perovskites are promising in the application of broadband polarization-sensitive optoelectronic devices.
contamDE-lm: linear model-based differential gene expression analysis using next-generation RNA-seq data from contaminated tumor samples
Authors: Ji Yifan , Yu Chang , Zhang Hong
Published: January 2020

Motivation

Tumor and adjacent normal RNA samples are commonly used to screen differentially expressed genes between normal and tumor samples or among tumor subtypes. Such paired-sample design could avoid numerous confounders in differential expression (DE) analysis, but the cellular contamination of tumor samples can be an important noise and confounding factor, which can both inflate false-positive rate and deflate true-positive rate. The existing DE tools that use next-generation RNA-seq data either do not account for cellular contamination or are computationally extensive with increasingly large sample size.

Results

A novel linear model was proposed to avoid the problem that could arise from tumor–normal correlation for paired samples. A statistically robust and computationally very fast DE analysis procedure, contamDE-lm, was developed based on the novel model to account for cellular contamination, boosting DE analysis power through the reduction in individual residual variances using gene-wise information. The desired advantages of contamDE-lm over some state-of-the-art methods (limma and DESeq2) were evaluated through the applications to simulated data, TCGA database and Gene Expression Omnibus (GEO) database.

Availability and implementation

The proposed method contamDE-lm was implemented in an updated R package contamDE (version 2.0), which is freely available at https://github.com/zhanghfd/contamDE.

Supplementary information

Supplementary data are available at Bioinformatics online.
Safety of Antimicrobials During Pregnancy: A Systematic Review of Antimicrobials Considered for Treatment and Postexposure Prophylaxis of Plague
Authors: Yu Patricia A , Tran Emmy L , Parker Corinne M , Kim Hye-Joo , Yee Eileen L , Smith Paul W , Russell Zachary , Nelson Christina A , Broussard Cheryl S , Yu Yon C , Meaney-Delman Dana
Published: January 2020

Background

The safety profile of antimicrobials used during pregnancy is one important consideration in the decision on how to treat and provide postexposure prophylaxis (PEP) for plague during pregnancy.

Methods

We searched 5 scientific literature databases for primary sources on the safety of 9 antimicrobials considered for plague during pregnancy (amikacin, gentamicin, plazomicin, streptomycin, tobramycin, chloramphenicol, doxycycline, sulfadiazine, and trimethoprim-sulfamethoxazole [TMP-SMX]) and abstracted data on maternal, pregnancy, and fetal/neonatal outcomes.

Results

Of 13 052 articles identified, 66 studies (case-control, case series, cohort, and randomized studies) and 96 case reports were included, totaling 27 751 prenatal exposures to amikacin (n = 9), gentamicin (n = 345), plazomicin (n = 0), streptomycin (n = 285), tobramycin (n = 43), chloramphenicol (n = 246), doxycycline (n = 2351), sulfadiazine (n = 870), and TMP-SMX (n = 23 602). Hearing or vestibular deficits were reported in 18/121 (15%) children and 17/109 (16%) pregnant women following prenatal streptomycin exposure. First trimester chloramphenicol exposure was associated with an elevated risk of an undescended testis (odds ratio [OR] 5.9, 95% confidence interval [CI] 1.2–28.7). Doxycycline was associated with cardiovascular malformations (OR 2.4, 95% CI 1.2–4.7) in 1 study and spontaneous abortion (OR 2.8, 95% CI 1.9–4.1) in a separate study. First trimester exposure to TMP-SMX was associated with increased risk of neural tube defects (pooled OR 2.5, 95% CI 1.4–4.3), spontaneous abortion (OR 3.5, 95% CI 2.3–5.6), preterm birth (OR 1.5, 95% CI 1.1–2.1), and small for gestational age (OR 1.6, 95% CI 1.2–2.2). No other statistically significant associations were reported.

Conclusions

For most antimicrobials reviewed, adverse maternal/fetal/neonatal outcomes were not observed consistently. Prenatal exposure to streptomycin and TMP-SMX was associated with select birth defects in some studies. Based on limited data, chloramphenicol and doxycycline may be associated with adverse pregnancy or neonatal outcomes; however, more data are needed to confirm these associations. Antimicrobials should be used for treatment and PEP of plague during pregnancy; the choice of antimicrobials may be influenced by these data as well as information about the risks of plague during pregnancy.
PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants
Authors: Wu Wenyi , Wu Yan , Hu Dahui , Zhou Yincong , Hu Yanshi , Chen Yujie , Chen Ming
Published: January 2020

Non-coding RNAs (ncRNAs) are recognized as key regulatory molecules in many biological processes. Accumulating evidence indicates that ncRNA-related mechanisms play important roles in plant stress responses. Although abundant plant stress-responsive ncRNAs have been identified, these experimentally validated results have not been gathered into a single public domain archive. Therefore, we established PncStress by curating experimentally validated stress-responsive ncRNAs in plants, including microRNAs, long non-coding RNAs and circular RNAs. The current version of PncStress contains 4227 entries from 114 plants covering 48 biotic and 91 abiotic stresses. For each entry, PncStress has biological information and network visualization. Serving as a manually curated database, PncStress will become a valuable resource in support of plant stress response research.
GREG—studying transcriptional regulation using integrative graph databases
Authors: Mei Songqing , Huang Xiaowei , Xie Chengshu , Mora Antonio
Published: January 2020

A gene regulatory process is the result of the concerted action of transcription factors, co-factors, regulatory non-coding RNAs (ncRNAs) and chromatin interactions. Therefore, the combination of protein–DNA, protein–protein, ncRNA–DNA, ncRNA–protein and DNA–DNA data in a single graph database offers new possibilities regarding generation of biological hypotheses. GREG (The Gene Regulation Graph Database) is an integrative database and web resource that allows the user to visualize and explore the network of all above-mentioned interactions for a query transcription factor, long non-coding RNA, genomic range or DNA annotation, as well as extracting node and interaction information, identifying connected nodes and performing advanced graphical queries directly on the regulatory network, in a simple and efficient way. In this article, we introduce GREG together with some application examples (including exploratory research of Nanog’s regulatory landscape and the etiology of chronic obstructive pulmonary disease), which we use as a demonstration of the advantages of using graph databases in biomedical research.

Database URL: https://mora-lab.github.io/projects/greg.html, www.moralab.science/GREG/
Mortality burden in patients born with Ebstein’s anomaly: a 40-year nationwide cohort study
Authors: Eckerström Filip , Eriksson Peter , Dellborg Mikael , Lappas Georgios , Rosengren Annika , Hjortdal Vibeke Elisabeth , Mandalenakis Zacharias
Published: January 2020

Aims 

Survival rates for unoperated patients with Ebstein’s anomaly (EA) are unknown. We estimated overall long-term mortality in operated and unoperated EA patients, compared with the general population in Sweden.

Methods and results 

Using national medical registries, Swedish individuals born 1970–93 and diagnosed with EA between 1970 and 2011 were included. The hazard ratio for overall mortality for EA patients (n = 216) vs. the matched comparison cohort (n = 2160) was 43.7 [95% confidence interval (CI): 24.8–82.5]. Mortality risk for EA patients (vs. controls) decreased as birth period progressed, with hazard ratios declining from 63.6 (95% CI: 26.3–191.8) for those born in the 1970s to 34.4 (95% CI: 15.8–83.1) for those born in the 1980s and 20.2 (95% CI: 1.6–632.5) for those born at the beginning of 1990s. The overall mortality hazard ratios for unoperated and operated patients with EA (vs. controls) were 30.2 (95% CI: 13.8–73.3) and 63.7 (95% CI: 28.1–172.5), respectively. The risk of mortality among unoperated EA patients (vs. controls) declined with progressing birth period, with hazard ratios declining from 58.4 (95% CI: 15.1–415.2) in the 1970s to 22.9 (95% CI: 8.0–75.3) in the 1980s and 10.2 (95% CI: 0.3–395.9) in the 1990s.

Conclusion 

Overall all-cause mortality for patients with EA declined dramatically from 64 times to 20 times that of controls without EA, from the 1970s to the early 1990s. Unoperated patients with EA had better survival than did operated patients, possibly reflecting the higher severity of disease or more severe associated cardiac defects in patients undergoing surgery.
RETRACTED: From farm to fork: global surveillance trends of animal-food-human antimicrobial resistance
Authors: Ashaolu Tolulope J
Published: January 2020

Objectives

Global surveillance measures keep trending with antimicrobial resistance (AMR) from farm to the final consumer. It is intended to review these trends within the past few decades.

Materials and Methods

This short communication showcases AMR surveillance basics, methods, processes, technicalities and milestones within recent decades in relationship to AMR emergence from farm to fork.

Results and Conclusions

Antibiotics and antimicrobial agents contribute to AMR dynamics. Passive and active AMR surveillance strategies continuously render data-driven robust systems for monitoring resistance levels and thereof changes across all geographical regions.
Regularity Estimates for Nondivergence Parabolic Equations on Generalized Orlicz Spaces
Authors: Anh Bui The
Published: January 2020

In this paper, by using a new approach, we prove regularity estimates for the solution to the nondivergence parabolic equation on generalized Orlicz spaces. Our approach can be viewed as a combination of representation theorems in partial differential equations and harmonic analysis techniques.
Rotating Nightshift Work and Hematopoietic Cancer Risk in US Female Nurses
Authors: Zhang Yin , Birmann Brenda M , Papantoniou Kyriaki , Zhou Eric S , Erber Astrid C , Schernhammer Eva S
Published: January 2020

Background

Nightshift work is a plausible risk factor for hematologic cancer, but epidemiological evidence remains sparse, especially for individual subtypes. We prospectively examined the association of rotating nightshift work with hematopoietic cancer risk.

Methods

This cohort study included US women from the Nurses’ Health Study (NHS: n = 76 846, 1988–2012) and Nurses’ Health Study II (NHSII: n = 113 087, 1989–2013). Rotating nightshift work duration was assessed at baseline (both cohorts) and cumulatively updated (NHSII). Cox regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for overall hematopoietic cancer and specific histologic subtypes. All statistical tests were two-sided.

Results

We documented 1405 (NHS) and 505 (NHSII) incident hematopoietic cancer cases during follow-up. In NHS, compared with women who never worked rotating nightshifts, longer rotating nightshift work duration was associated with an increased risk of overall hematopoietic cancer (HR1–14y = 0.93, 95% CI = 0.83 to 1.04; HR≥15y = 1.28, 95% CI = 1.06 to 1.55; Ptrend = .009). In NHSII, results were similar though not statistically significant (HR1–14y = 0.99, 95% CI = 0.82 to 1.21; HR≥15y = 1.41, 95% CI = 0.88 to 2.26; Ptrend = .47). In the subtype analyses in the NHS, the association of history of rotating nightshift work with risk of diffuse large B-cell lymphoma varied by duration (HR1–14y = 0.71, 95% CI = 0.51 to 0.98; HR≥15y = 1.69, 95% CI = 1.07 to 2.67; Ptrend = .01) compared with those who never worked rotating nightshifts. Women reporting a longer history of rotating nightshifts also had suggestive (statistically nonsignificant) increased risks of overall non-Hodgkin lymphoma (HR≥15y = 1.19, 95% CI = 0.95 to 1.49), Hodgkin lymphoma (HR≥15y = 1.32, 95% CI = 0.43 to 4.06), and multiple myeloma (HR≥15y = 1.42, 95% CI = 0.85 to 2.39).

Conclusions

Longer duration (≥15 years) of rotating nightshift work was associated with increased risks of overall and several subtypes of hematopoietic cancer.
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

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.
The Search for a Functional Outcome Measure for Physical Therapy in Specialist Palliative Care: An Ongoing Journey
Authors: Looney Finola , Cobbe Sinead , Ryan Angela , Barriscale Isabel , McMahon Ailbhe , Real Shirley
Published: January 2020

A perspective article on the field testing of outcome measures and functional assessment tools by physical therapists working in specialist palliative care. Palliative care physical therapy is an evolving field, and there is a pressing need to evaluate interventions. The authors are members of a specialist palliative care physical therapy team in Ireland who evaluated their service by conducting several research and quality improvement activities. This involved trialing the use of a number of outcome measures, including functional, global, patient-specific, and quality-of-life scales. The following tools were piloted: the Edmonton Functional Assessment Tool, Second Version; an adjusted version of the Functional Independence Measure, Timed Up and Go test; Five Times Sit to Stand test; a self-devised Mobility Measure; distress thermometer; Patient-Specific Functional Scale; and EORTC-QLC C30. This article outlines the journey toward finding the most clinically useful outcome measure to use with palliative care patients. All the tools that were trialed had disadvantages, and many were not suitable for use on sizeable cohorts in our palliative care population. The team concluded that a functional outcome measure was the measure most suitable for measuring the effect of physical therapy interventions and that there was a need to devise a new functional measure specifically for palliative care. The next stage is to use pragmatic clinician input in devising a clinically useful tool in collaboration with research-based content experts to ensure acceptable psychometric properties. It is hoped that this approach will advance the evidence for physical therapy in specialist and general palliative care.
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

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

Background:

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

Process-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.
Dutch population structure across space, time and GWAS design
Authors: Byrne Ross P. , van Rheenen Wouter ,   Project MinE ALS GWAS Consortium, van den Berg Leonard H. , Veldink Jan H. , McLaughlin Russell L.
Published: January 2020

We studied fine-grained population genetic structure and demographic change across the Netherlands using genome-wide single nucleotide polymorphism data (1,626 individuals) with associated geography (1,422 individuals). We applied ChromoPainter/fineSTRUCTURE, identifying 40 haplotypic clusters exhibiting strong north/south variation and fine-scale differentiation within provinces. Clustering is tied to country-wide ancestry gradients from neighbouring lands and to locally restricted gene flow across major Dutch rivers. Despite superexponential population growth, north-south structure is temporally stable, with west-east differentiation more transient, potentially influenced by migrations during the middle ages. Within Dutch and international data, GWAS incorporating fine-grained haplotypic covariates are less confounded than standard methods.
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

Blood-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

The 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

Agricultural 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

Speech 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

The 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.