bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-conventional pathways enable pennycress (Thlaspi arvense L.) embryos to achieve high efficiency of oil biosynthesis
Authors: Tsogtbaatar Enkhtuul , Cocuron Jean-Christophe , Alonso Ana Paula 
Published: January 2020

AbstractPennycress (Thlaspi arvense L.) accumulates oil up to 35% of the total seed biomass, and its overall fatty acid composition is suitable for aviation fuel. However, for this plant to become economically viable, its oil production needs to be improved. In vivo culture conditions that resemble the development of pennycress embryos in planta were developed based on the composition of the liquid endosperm. Then, substrate uptake rates and biomass accumulation were measured from cultured pennycress embryos, revealing a biosynthetic efficiency of 93%, which is one of the highest in comparison with other oilseeds to date. Additionally, the ratio of carbon in oil to CO2 indicated that non-conventional pathways are likely to be responsible for such a high carbon conversion efficiency. To identify the reactions enabling this phenomenon, parallel labeling experiments with 13C-labeled substrates were conducted in pennycress embryos. The main findings of these labeling experiments include: (i) the occurrence of the oxidative reactions of the pentose phosphate pathway in the cytosol; (ii) the reversibility of isocitrate dehydrogenase; (iii) the operation of the plastidic NADP-dependent malic enzyme; and (iv) the refixation of CO2 by Rubisco. These reactions are key providers of carbon and reductant for fatty acid synthesis and elongation.
Evolving Populations in Biofilms Contain More Persistent Plasmids
Authors: Stalder Thibault , Cornwell Brandon , Lacroix Jared , Kohler Bethel , Dixon Seth , Yano Hirokazu , Kerr Ben , Forney Larry J , Top Eva M 
Published: January 2020

AbstractBacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid–bacteria coevolution is solely based on studies done in well-mixed liquid cultures, even though biofilms represent the main way of bacterial life on Earth and are responsible for most infections. The spatial structure and the heterogeneity provided by biofilms are known to lead to increased genetic diversity as compared with well-mixed liquids. Therefore, we expect that growth in this complex environment could affect the evolutionary trajectories of plasmid–host dyads. We experimentally evolved Shewanella oneidensis MR-1 with plasmid pBP136Gm in biofilms and chemostats and sequenced the genomes of clones and populations. Biofilm populations not only maintained a higher diversity of mutations than chemostat populations but contained a few clones with markedly more persistent plasmids that evolved via multiple distinct trajectories. These included the acquisition of a putative toxin–antitoxin transposon by the plasmid and chromosomal mutations. Some of these genetic changes resulted in loss of plasmid transferability or decrease in plasmid cost. Growth in chemostats led to a higher proportion of variants with decreased plasmid persistence, a phenomenon not detected in biofilms. We suggest that the presence of more stable plasmid–host dyads in biofilms reflects higher genetic diversity and possibly unknown selection pressures. Overall, this study underscores the importance of the mode of growth in the evolution of antibiotic-resistant bacteria.
The impact of comorbid chronic kidney disease and diabetes on health-related quality-of-life: a 12-year community cohort study
Authors: Wyld Melanie L R , Morton Rachael L , Aouad Leyla , Magliano Dianna , Polkinghorne Kevan R , Chadban Steve 
Published: January 2020

Abstract

Background
Quality-of-life is an essential outcome for clinical care. Both chronic kidney disease (CKD) and diabetes have been associated with poorer quality-of-life. The combined impact of having both diseases is less well understood. As diabetes is the most common cause of CKD, it is imperative that we deepen our understanding of their joint impact.

Methods
This was a prospective, longitudinal cohort study of community-based Australians aged ≥25 years who participated in the Australian Diabetes, Obesity and Lifestyle study. Quality-of-life was measured by physical component summary (PCS) and mental component summary sub-scores of the Short Form (36) Health Survey. Univariate and multivariate linear mixed effect regressions were performed.

Results
Of the 11 081 participants with quality-of-life measurements at baseline, 1112 had CKD, 1001 had diabetes and of these 271 had both. Of the 1112 with CKD 421 had Stage 1, 314 had Stage 2, 346 had Stage 3 and 31 had Stages 4/5. Adjusted linear mixed effect models showed baseline PCS was lower for those with both CKD and diabetes compared with either disease alone (P &lt; 0.001). Longitudinal analysis demonstrated a more rapid decline in PCS in those with both diseases.

Conclusions
The combination of CKD and diabetes has a powerful adverse impact on quality-of-life, and participants with both diseases had significantly poorer quality-of-life than those with one condition.
Empathy: An Integral Model in Clinical Social Work
Authors: Clark Arthur J , Butler Carrie M 
Published: January 2020

AbstractEmpathy has held a vital and enduring standing in the theory and practice of clinical social work. Defining and conceptualizing empathy is a continuing challenge in social work and across the human services. A multitude of definitions of empathy exist in the therapeutic literature, creating confusion relating to research findings and treatment processes. Recent trends emphasize an overarching and expansive way of conceiving empathic understanding in the therapeutic relationship and informing treatment practice. Multiple perspectives of empathy facilitate a broad and wide-ranging engagement of the practitioner and the client in the therapeutic process. With significant implications for clinical social workers, an integral model capitalizes on the engagement of empathy from multiple ways of knowing: subjective, objective, and interpersonal. Numerous clinical examples illustrate applications of the tripartite model in social work practice. The integral empathy model is amenable to research and training across therapeutic contexts in social work and related fields.
Spectral differentiation of oak wilt from foliar fungal disease and drought is correlated with physiological changes
Authors: Fallon Beth , Yang Anna , Lapadat Cathleen , Armour Isabella , Juzwik Jennifer , Montgomery Rebecca A , Cavender-Bares Jeannine 
Published: January 2020

Abstract
Hyperspectral reflectance tools have been used to detect multiple pathogens in agricultural settings and single sources of infection or broad declines in forest stands. However, differentiation of any one disease from other sources of tree stress is integral for stand and landscape-level applications in mixed species systems. We tested the ability of spectral models to differentiate oak wilt, a fatal disease in oaks caused by Bretziella fagacearum ``Bretz'', from among other mechanisms of decline. We subjected greenhouse-grown oak seedlings (Quercus ellipsoidalis ``E.J. Hill'' and Quercus macrocarpa ``Michx.'') to chronic drought or inoculation with the oak wilt fungus or bur oak blight fungus (Tubakia iowensis ``T.C. Harr. & D. McNew''). We measured leaf and canopy spectroscopic reflectance (400–2400 nm) and instantaneous photosynthetic and stomatal conductance rates, then used partial least-squares discriminant analysis to predict treatment from hyperspectral data. We detected oak wilt before symptom appearance, and classified the disease with high accuracy in symptomatic leaves. Classification accuracy from spectra increased with declines in photosynthetic function in oak wilt-inoculated plants. Wavelengths diagnostic of oak wilt were only found in non-visible spectral regions and are associated with water status, non-structural carbohydrates and photosynthetic mechanisms. We show that hyperspectral models can differentiate oak wilt from other causes of tree decline and that detection is correlated with biological mechanisms of oak wilt infection and disease progression. We also show that within the canopy, symptom heterogeneity can reduce detection, but that symptomatic leaves and tree canopies are suitable for highly accurate diagnosis. Remote application of hyperspectral tools can be used for specific detection of disease across a multi-species forest stand exhibiting multiple stress symptoms.
Effect of initial gravimetric water content and cyclic wetting-drying on soil-water characteristic curves of disintegrated carbonaceous mudstone
Authors: Zeng Ling , Li Fan , Liu Jie , Gao Qianfeng , Bian Hanbing 
Published: January 2020

Abstract
The soil-water characteristic curve (SWCC) is often used to estimate unsaturated soil properties (e.g. strength, permeability, volume change, solute and thermal diffusivity). The SWCC of soil samples is significantly affected by cyclic wetting-drying. To examine how water content and cyclic wetting-drying affect the SWCC of disintegrated carbonaceous mudstone (DCM), SWCC tests were implemented using a pressure-plate apparatus. In addition, SWCC models for DCM considering the initial gravimetric water content and cyclic wetting-drying were developed. The test results showed that the volumetric water content (θ) of the DCM first decreased rapidly and then became stable as matric suction (s) increased. The initial water content affected the SWCC by altering the pore structure of the DCM. For a given number of wetting-drying cycles, the higher the initial water content, the higher the stabilized θ. At a given s value, θ decreased as the number of wetting-drying cycles increased, which suggests that cyclic wetting-drying reduces the water-holding capacity of DCM. The Gardner model for DCM was constructed considering initial water content and cyclic wetting-drying, and was effective at describing and predicting the SWCC model for DCM.
Society for Developmental and Behavioral Pediatrics Clinical Practice Guideline for the Assessment and Treatment of Children and Adolescents with Complex Attention-Deficit/Hyperactivity Disorder
Authors: Barbaresi William J. , Campbell Lisa , Diekroger Elizabeth A. , Froehlich Tanya E. , Liu Yi Hui , O'Malley Eva , Pelham William E. , Power Thomas J. , Zinner Samuel H. , Chan Eugenia 
Published: January 2020

ABSTRACT:
Attention-deficit/hyperactivity disorder (ADHD) is the most common childhood neurodevelopmental disorder and is associated with an array of coexisting conditions that complicate diagnostic assessment and treatment. ADHD and its coexisting conditions may impact function across multiple settings (home, school, peers, community), placing the affected child or adolescent at risk for adverse health and psychosocial outcomes in adulthood. Current practice guidelines focus on the treatment of ADHD in the primary care setting. The Society for Developmental and Behavioral Pediatrics has developed this practice guideline to facilitate integrated, interprofessional assessment and treatment of children and adolescents with “complex ADHD” defined by age (<4 years or presentation at age >12 years), presence of coexisting conditions, moderate to severe functional impairment, diagnostic uncertainty, or inadequate response to treatment.
Linear and nonlinear thermosolutal instabilities in an inclined porous layer
Authors: Kumar Gautam , Narayana Puranam Anantha Lakshmi , Sahu Kirti Chandra 
Published: January 2020

We investigate the double-diffusive instability in an inclined porous layer with a concentration-based internal heat source by conducting linear instability and nonlinear energy analyses. The effects of different dimensionless parameters, such as the thermal (
Ra
T
) and solutal (
Ra
S
) Rayleigh numbers, the angle of inclination (
ϕ
), the Lewis number (
Le
) and the concentration-based internal heat source (
Q
) are examined. A comparison between the linear and nonlinear thresholds for the longitudinal and transverse rolls provides the region of subcritical instability. We found that the system becomes more unstable when the thermal diffusivity is greater than the solute and the internal heat source strength increases. It is observed that the system is stabilized by increasing the angle of inclination. While the longitudinal roll remains stationary without the region of subcritical instability, as the angle of inclination increases, the transverse roll switches from stationary-oscillatory-stationary mode. Our numerical results show that for
Ra
S
< 0, for all
Q
values, the subcritical instability only exists for transverse rolls. For
Ra
S
≥ 0, however, the subcritical instability appears only for
Q
= 0 and
Q
≥ 0, respectively, for longitudinal and transverse rolls.
Reduced loss aversion in subclinical negative symptoms and hypomania
Authors: Klaus Federica , Chumbley Justin , Seifritz Erich , Kaiser Stefan , Hartmann-Riemer Matthias 
Published: January 2020

AbstractLoss aversion is a behavioral phenomenon that describes a higher sensitivity to losses than to gains and influences decisions. Decision-making is altered in several psychopathologic states, such as in the two symptom dimensions of hypomania and negative symptoms. It has been argued that progress in our understanding of psychopathology requires a reorientation from the traditional, syndrome-based perspective to a more detailed study of individual constituent symptoms. In the present study, we made careful efforts to dissociate the relationship of loss aversion to negative symptoms, from its relationship with hypomanic symptoms. We selected a sample of 45 subjects from a healthy student population (n = 835) according to psychopathologic scales for hypomania and negative symptoms and stratified them into a control group (n = 15), a subclinical hypomania group (n = 15) and a negative symptoms group (n = 15). Participants completed a loss aversion task consisting of forced binary choices between a monetary gamble and a riskless choice with no gain or loss. We found, that these two symptom dimensions of hypomania and negative symptoms have a similar inverse relation to loss aversion as demonstrated by analysis of variance. Further research is warranted to describe the underlying psychological and neurobiological mechanisms at play. Given the partially opposing nature of hypomania and negative symptoms it further needs to be elucidated whether they are linked to loss aversion via dissociable mechanisms.
Projections between visual cortex and pulvinar nucleus in the rat
Authors: Scholl Leo R. , Foik Andrzej T. , Lyon David C. 
Published: January 2020

AbstractThe extrageniculate visual pathway, which carries visual information from the retina through the superficial layers of the superior colliculus and the pulvinar nucleus, is poorly understood. The pulvinar is thought to modulate information flow between cortical areas, and has been implicated in cognitive tasks like directing visually guided actions. In order to better understand the underlying circuitry, we performed retrograde injections of modified rabies virus in the visual cortex and pulvinar of the Long-Evans rat. We found a relatively small population of cells projecting to primary visual cortex (V1), compared to a much larger population projecting to higher visual cortex. Reciprocal corticothalamic projections showed a similar result, implying that pulvinar does not play as big a role in directly modulating V1 activity as previously thought.
Framework for Identifying Drug Repurposing Candidates from Observational Healthcare Data
Authors: Ozery-Flato Michal , Goldschmidt Yaara , Shaham Oded , Ravid Sivan , Yanover Chen 
Published: January 2020

AbstractObjectiveObservational medical databases, such as electronic health records and insurance claims, track the healthcare trajectory of millions of individuals. These databases provide real-world longitudinal information on large cohorts of patients and their medication prescription history. We present an easy-to-customize framework that systematically analyzes such databases to identify new indications for on-market prescription drugs.Materials and MethodsOur framework provides an interface for defining study design parameters and extracting patient cohorts, disease-related outcomes, and potential confounders in two observational databases, covering more than 150 million patients. It then applies causal inference methodology to emulate hundreds of randomized controlled trials (RCTs) for prescribed drugs, while adjusting for confounding and selection biases. After correcting for multiple testing, it outputs the estimated effects and their statistical significance in each database.ResultsWe demonstrate the utility of the framework in a case study of Parkinson’s disease (PD) and evaluate the effect of 259 drugs on various PD progression measures. The results of these emulated trials reveal a remarkable agreement between the two observational medical databases for the most promising candidates.DiscussionEstimating drug effects from observational data is challenging due to data biases and noise. To tackle this challenge, we integrate causal inference methodology with domain knowledge and compare the estimated effects in two separate databases.ConclusionOur framework enables a systematic search for drug repurposing candidates by emulating RCTs that use observational data. The high level of agreement in the results obtained in two separate databases provides an internal validation of identified effects.
CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation
Authors: Dumont Emmanuel LP , Tycko Benjamin , Do Catherine 
Published: January 2020

AbstractSummaryMethods for quantifying the imbalance in CpG methylation between alleles genome-wide have been described but their algorithmic time complexity is quadratic and their practical use requires painstaking attention to infrastructure choice, implementation, and execution. To solve this problem, we developed CloudASM, a scalable, ultra-efficient, turn-key, portable pipeline on Google Cloud Computing (GCP) that uses a novel pipeline manager and GCP’s serverless enterprise data warehouse.Availability and ImplementationCloudASM is freely available in the GitHub repositoryhttps://github.com/TyckoLab/CloudASMand a sample dataset and its results are also freely available athttps://console.cloud.google.com/storage/browser/cloudasm.Contactemmanuel.dumont@hmh-cdi.orgSupplementary informationNone.
Modelling the Replay of Dynamic Memories from Cortical Alpha Oscillations with the Sync-Fire / deSync Model
Authors: Parish George , Michelmann Sebastian , Hanslmayr Simon , Bowman Howard 
Published: January 2020

ABSTRACTWe here propose a neural network model to explore how neural oscillations might regulate the replay of memory traces. We simulate the encoding and retrieval of a series of events, where temporal sequences are uniquely identifiable by analysing population activity, as several recent EEG/MEG studies have shown. Our model comprises three parts, each considering distinct hypotheses. A cortical region actively represents sequences through the disruption of an intrinsically generated alpha rhythm, where a desynchronisation marks information-rich operations as the literature predicts. A binding region converts each event into a discrete index, enabling repetitions through a sparse encoding of events. We also instantiate a temporal region, where an oscillatory “ticking-clock” made up of hierarchical synfire chains discretely indexes a moment in time. By encoding the absolute timing between events, we show how one can use cortical desynchronisations to dynamically detect unique temporal signatures as they are replayed in the brain.
Vaccination withSchistosoma mansonicholinesterases reduces parasite burden and egg viability in a mouse model of schistosomiasis
Authors: Tedla Bemnet A. , Pickering Darren , Becker Luke , Loukas Alex , Pearson Mark S. 
Published: January 2020

AbstractSchistosomiasis is a neglected tropical disease which kills 300,000 people every year in developing countries and there is no vaccine. Recently, we have shown that cholinesterases (ChEs) - enzymes that regulate neurotransmission - fromSchistosoma mansoniare expressed on the tegument and present in the excretory/secretory products of schistosomula and adult worms, and are essential for parasite survival in the definitive host, highlighting their utility as potential schistosomiasis vaccine targets. When treatedin vitrowith anti-SmChE IgG, both schistosomula and adult worms displayed significantly decreased ChE activity, which eventually resulted in parasite death. Vaccination with individual SmChEs, or a combination of all three SmChEs, significantly reduced worm burdens in two independent trials compared to controls. Liver egg burdens were significantly decreased for all vaccinated mice across both trials (13% - 46%) except for those vaccinated withSmAChE1 in trial 1. Egg viability, as determined by egg hatching from liver homogenates, was significantly reduced in the groups vaccinated with theSmChE cocktail (40%) andSmAChE2 (46%). Further, surviving worms from each vaccinated group were significantly stunted and depleted of glycogen stores, compared to controls. These results suggest thatSmChEs could be incorporated into a vaccine against schistosomiasis to reduce the pathology and transmission of this debilitating disease.
Rethinking the role of lipids in lager yeast cells during beer fermentation from a transcriptome and systems biology perspective
Authors: Bonatto Diego 
Published: January 2020

AbstractBrewing lager yeast (Saccharomyces pastorianus) is exposed to stressful conditions during beer fermentation, including ethanol toxicity. In response to ethanol toxicity, various biological mechanisms are modulated, including lipid biosynthesis. It is well known that during beer fermentation, the composition of yeast membranes changes in response to ethanol toxicity, making it less fluid and permeable. Additionally, neutral lipids and lipid droplets (LDs) are produced in response to ethanol toxicity. LDs are membranous organelles that transport lipids and proteins, acting as hubs for inter-organellar communication and modulating the activity of mechanisms necessary for ethanol tolerance, such as proteostasis and autophagy. Unfortunately, little is known about the interplay between autophagy, lipid metabolism, and proteostasis (ALP) in lager cells during beer fermentation. Therefore, transcriptome analyses using publicly available DNA microarray data obtained from lager yeast cells were used to identify all the ALP-associated genes that were upregulated during beer fermentation compared to yeast biomass propagation. Thereafter, a top-down systems biology analysis was applied, involving constructing an ALP-associated shortest-pathway protein–protein interaction network (ALP network), identifying important nodes and communities within the ALP network, and identifying the overrepresented biological processes and cellular components using a Gene Ontology (GO) analysis. The transcriptome analyses indicated the upregulation of 204 non-redundant ALP-associated genes during beer fermentation, whose respective proteins interact in the shortest-pathway ALP network. Thirteen communities were selected from the ALP network, and they were associated with multiple overrepresented GO biological processes and cellular components, such as mitophagy, cytoplasm-to-vacuole transport, piecemeal microautophagy of the nucleus, endoplasmic reticulum (ER) stress, ergosterol and lipid biosynthesis, LDs, ER membrane, and phagophore assembly. These results indicate that ethanol tolerance in lager yeasts could be due to the modulation of proteostasis and various forms of autophagy by lipid biosynthesis and LDs, thus highlighting the importance of lipids for beer fermentation.