bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Overview of Atmospheric Features Over the Western North Atlantic Ocean and North American East Coast – Part 1: Analysis of Aerosols, Gases, and Wet Deposition Chemistry
Authors: Corral Andrea F. , Braun Rachel A. , Cairns Brian , Gorooh Vesta Afzali , Liu Hongyu , Ma Lin , Mardi Ali Hossein , Painemal David , Stamnes Snorre , van Diedenhoven Bastiaan , Wang Hailong , Yang Yang , Zhang Bo , Sorooshian Armin 
Published: January 2021

AbstractThe Western North Atlantic Ocean (WNAO) and adjoining East Coast of North America are of great importance for atmospheric research and have been extensively studied for several decades. This broad region exhibits complex meteorological features and a wide range of conditions associated with gas and particulate species from many sources regionally and other continents. As Part 1 of a 2‐part paper series, this work characterizes quantities associated with atmospheric chemistry, including gases, aerosols, and wet deposition, by analyzing available satellite observations, ground‐based data, model simulations, and reanalysis products. Part 2 provides insight into the atmospheric circulation, boundary layer variability, three‐dimensional cloud structure, properties, and precipitation over the WNAO domain. Key results include spatial and seasonal differences in composition along the North American East Coast and over the WNAO associated with varying sources of smoke and dust and meteorological drivers such as temperature, moisture, and precipitation. Spatial and seasonal variations of tropospheric carbon monoxide and ozone highlight different pathways toward the accumulation of these species in the troposphere. Spatial distributions of speciated aerosol optical depth and vertical profiles of aerosol mass mixing ratios show a clear seasonal cycle highlighting the influence of different sources in addition to the impact of intercontinental transport. Analysis of long‐term climate model simulations of aerosol species and satellite observations of carbon monoxide confirm that there has been a significant decline in recent decades among anthropogenic constituents owing to regulatory activities.
Three‐Dimensional Distribution of Groundwater Residence Time Metrics in the Glaciated United States Using Metamodels Trained on General Numerical Simulation Models
Authors: Starn J. J. , Kauffman L. J. , Carlson C. S. , Reddy J. E. , Fienen M. N. 
Published: January 2021

AbstractResidence time distribution (RTD) is a critically important characteristic of groundwater flow systems; however, it cannot be measured directly. RTD can be inferred from tracer data with analytical models (few parameters) or with numerical models (many parameters). The second approach permits more variation in system properties but is used less frequently than the first because large‐scale numerical models can be resource intensive. Using a novel automated approach, a set of 115 inexpensive general simulation models (GSMs) was used to create RTD metrics (fraction of young groundwater, defined as <65 years old; mean travel time of young fraction; median travel time of old fraction; and mean path length). GSMs captured the general trends in measured tritium concentrations in 431 wells. Boosted Regression Tree metamodels were trained to predict these RTD metrics using available wall‐to‐wall hydrogeographic digital sets as explanatory features. The metamodels produced a three‐dimensional distribution of predictions throughout the glacial system that generally matched with the numerical model RTD metrics. In addition to the expected importance of aquifer thickness and recharge rate in predicting RTD metrics, two new data sets, Multi‐Order Hydrologic Position (MOHP) and hydrogeologic terrane were important predictors. These variables by themselves produced metamodels with Nash‐Sutcliffe efficiency close to the full metamodel. Metamodel predictions showed that the volume of young groundwater stored in the glaciated United States is about 6,000 km3, or about 0.5% of globally stored young groundwater.
DNA Tracer Transport Through Porous Media—The Effect of DNA Length and Adsorption
Authors: Zhang Yuran , Hartung Marshall B. , Hawkins Adam J. , Dekas Anne E. , Li Kewen , Horne Roland N. 
Published: January 2021

AbstractArtificial tracer testing is an effective technique to identify fluid flow pathways and characterize subsurface hydrological properties. Synthetic DNA tracers, available in virtually unlimited number of unique variations, enable multiwell tracer testing and have the potential to improve the characterization of groundwater flowpaths enormously. This study investigated the effect of DNA length (i.e., number of base pairs) and adsorption on DNA tracer transport via well‐controlled laboratory experiments. Nine unique synthetic double‐stranded DNA tracers were designed with varying lengths (90–200 base pairs) and flowed with reference solute tracers (bromide and lithium) through columns packed with glass beads or Ottawa sand. The peak arrivals of DNA tracers were earlier than bromide in the glass‐bead column test, yet significantly retarded in the sand column test. In a given porous medium, DNA length did not have noticeable effects on peak arrival or tracer dispersion. However, DNA tracer recovery increased with increasing DNA length in the glass‐bead column test but decreased with increasing DNA length in the sand column test, likely resulting from the corresponding trends in partition coefficients as revealed by tracer transport modeling. Such reversed trends in different porous media likely resulted from the different likelihoods for longer DNA to have multisegment attachment during transport. Our findings suggest that both DNA length and the surface properties of the porous medium have notable effects on DNA tracer transport and hence need to be considered carefully in future tracer test designs in terms of site selection, DNA sequence design and data interpretation.
Aberrant role of ALK in tau proteinopathy through autophagosomal dysregulation
Authors: Park Jisu , Choi Hyunwoo , Kim Young Doo , Kim Seo-Hyun , Kim Youbin , Gwon Youngdae , Lee Dong Young , Park Sung-Hye , Heo Won Do , Jung Yong-Keun 
Published: January 2021

AbstractProteinopathy in neurodegenerative diseases is typically characterized by deteriorating activity of specific protein aggregates. In tauopathies, including Alzheimer’s disease (AD), tau protein abnormally accumulates and induces dysfunction of the affected neurons. Despite active identification of tau modifications responsible for tau aggregation, a critical modulator inducing tau proteinopathy by affecting its protein degradation flux is not known. Here, we report that anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase, is crucial for the tau-mediated AD pathology. ALK caused abnormal accumulation of highly phosphorylated tau in the somatodendritic region of neurons through its tyrosine kinase activity. ALK-induced LC3-positive axon swelling and loss of spine density, leading to tau-dependent neuronal degeneration. Notably, ALK activation in neurons impaired Stx17-dependent autophagosome maturation and this defect was reversed by a dominant-negative Grb2. In a Drosophila melanogaster model, transgenic flies neuronally expressing active Drosophila Alk exhibited the aggravated tau rough eye phenotype with retinal degeneration and shortened lifespan. In contrast, expression of kinase-dead Alk blocked these phenotypes. Consistent with the previous RNAseq analysis showing upregulation of ALK expression in AD [1], ALK levels were significantly elevated in the brains of AD patients showing autophagosomal defects. Injection of an ALK.Fc-lentivirus exacerbated memory impairment in 3xTg-AD mice. Conversely, pharmacologic inhibition of ALK activity with inhibitors reversed the memory impairment and tau accumulation in both 3xTg-AD and tauC3 (caspase-cleaved tau) transgenic mice. Together, we propose that aberrantly activated ALK is a bona fide mediator of tau proteinopathy that disrupts autophagosome maturation and causes tau accumulation and aggregation, leading to neuronal dysfunction in AD.
Prediction of short-term antidepressant response using probabilistic graphical models with replication across multiple drugs and treatment settings
Authors: Athreya Arjun P. , Brückl Tanja , Binder Elisabeth B. , John Rush A. , Biernacka Joanna , Frye Mark A. , Neavin Drew , Skime Michelle , Monrad Ditlev , Iyer Ravishankar K. , Mayes Taryn , Trivedi Madhukar , Carter Rickey E. , Wang Liewei , Weinshilboum Richard M. , Croarkin Paul E. , Bobo William V. 
Published: January 2021

AbstractHeterogeneity in the clinical presentation of major depressive disorder and response to antidepressants limits clinicians’ ability to accurately predict a specific patient’s eventual response to therapy. Validated depressive symptom profiles may be an important tool for identifying poor outcomes early in the course of treatment. To derive these symptom profiles, we first examined data from 947 depressed subjects treated with selective serotonin reuptake inhibitors (SSRIs) to delineate the heterogeneity of antidepressant response using probabilistic graphical models (PGMs). We then used unsupervised machine learning to identify specific depressive symptoms and thresholds of improvement that were predictive of antidepressant response by 4 weeks for a patient to achieve remission, response, or nonresponse by 8 weeks. Four depressive symptoms (depressed mood, guilt feelings and delusion, work and activities and psychic anxiety) and specific thresholds of change in each at 4 weeks predicted eventual outcome at 8 weeks to SSRI therapy with an average accuracy of 77% (p = 5.5E-08). The same four symptoms and prognostic thresholds derived from patients treated with SSRIs correctly predicted outcomes in 72% (p = 1.25E-05) of 1996 patients treated with other antidepressants in both inpatient and outpatient settings in independent publicly-available datasets. These predictive accuracies were higher than the accuracy of 53% for predicting SSRI response achieved using approaches that (i) incorporated only baseline clinical and sociodemographic factors, or (ii) used 4-week nonresponse status to predict likely outcomes at 8 weeks. The present findings suggest that PGMs providing interpretable predictions have the potential to enhance clinical treatment of depression and reduce the time burden associated with trials of ineffective antidepressants. Prospective trials examining this approach are forthcoming.
Acclimation and adaptation to elevated pCO2 increase arsenic resilience in marine diatoms
Authors: Xu Dong , Schaum Charlotte-Elisa , Li Bin , Chen Yanan , Tong Shanying , Fu Fei-Xue , Hutchins David A , Zhang Xiaowen , Fan Xiao , Han Wentao , Wang Yitao , Ye Naihao 
Published: January 2021

Abstract
Arsenic pollution is a widespread threat to marine life, but the ongoing rise pCO2 levels is predicted to decrease bio-toxicity of arsenic. However, the effects of arsenic toxicity on marine primary producers under elevated pCO2 are not well characterized. Here, we studied the effects of arsenic toxicity in three globally distributed diatom species (Phaeodactylum tricornutum, Thalassiosira pseudonana, and Chaetoceros mulleri) after short-term acclimation (ST, 30 days), medium-term exposure (MT, 750 days), and long-term (LT, 1460 days) selection under ambient (400 µatm) and elevated (1000 and 2000 µatm) pCO2. We found that elevated pCO2 alleviated arsenic toxicity even after short acclimation times but the magnitude of the response decreased after mid and long-term adaptation. When fed with these elevated pCO2 selected diatoms, the scallop Patinopecten yessoensis had significantly lower arsenic content (3.26–52.83%). Transcriptomic and biochemical analysis indicated that the diatoms rapidly developed arsenic detoxification strategies, which included upregulation of transporters associated with shuttling harmful compounds out of the cell to reduce arsenic accumulation, and upregulation of proteins involved in synthesizing glutathione (GSH) to chelate intracellular arsenic to reduce arsenic toxicity. Thus, our results will expand our knowledge to fully understand the ecological risk of trace metal pollution under increasing human activity induced ocean acidification.
Bodo saltans(Kinetoplastida) is dependent on a novelParacaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems
Authors: Midha Samriti , Rigden Daniel J , Siozios Stefanos , Hurst Gregory D D , Jackson Andrew P 
Published: January 2021

AbstractBacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protist Bodo saltans (Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that the endosymbiont is located adjacent to the nuclear membrane, and a detailed model of its intracellular niche is generated using serial block-face scanning electron microscopy. Phylogenomic analysis shows that the endosymbiont belongs to the Holosporales, most closely related to other α-proteobacterial endosymbionts of ciliates and amoebae. Comparative genomics indicates that it has a limited metabolism and is nutritionally host-dependent. However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems. We show that these systems are actively transcribed and hypothesize they represent a mechanism by which B. saltans becomes addicted to its endosymbiont. Consistent with this idea, attempts to cure Bodo of endosymbionts led to rapid and uniform cell death. This study adds kinetoplastid flagellates to ciliates and amoebae as hosts of Paracaedibacter-like bacteria, suggesting that these antagonistic endosymbioses became established very early in Eukaryotic evolution.
Environmental stress destabilizes microbial networks
Authors: Hernandez Damian J , David Aaron S , Menges Eric S , Searcy Christopher A , Afkhami Michelle E 
Published: January 2021

Abstract
Environmental stress is increasing worldwide, yet we lack a clear picture of how stress disrupts the stability of microbial communities and the ecosystem services they provide. Here, we present the first evidence that naturally-occurring microbiomes display network properties characteristic of unstable communities when under persistent stress. By assessing changes in diversity and structure of soil microbiomes along 40 replicate stress gradients (elevation/water availability gradients) in the Florida scrub ecosystem, we show that: (1) prokaryotic and fungal diversity decline in high stress, and (2) two network properties of stable microbial communities—modularity and negative:positive cohesion—have a clear negative relationship with environmental stress, explaining 51–78% of their variation. Interestingly, pathogenic taxa/functional guilds decreased in relative abundance along the stress gradient, while oligotrophs and mutualists increased, suggesting that the shift in negative:positive cohesion could result from decreasing negative:positive biotic interactions consistent with the predictions of the Stress Gradient Hypothesis. Given the crucial role microbiomes play in ecosystem functions, our results suggest that, by limiting the compartmentalization of microbial associations and creating communities dominated by positive associations, increasing stress in the Anthropocene could destabilize microbiomes and undermine their ecosystem services.
A likelihood ratio approach for identifying three-quarter siblings in genetic databases
Authors: Galván-Femenía Iván , Barceló-Vidal Carles , Sumoy Lauro , Moreno Victor , de Cid Rafael , Graffelman Jan 
Published: January 2021

AbstractThe detection of family relationships in genetic databases is of interest in various scientific disciplines such as genetic epidemiology, population and conservation genetics, forensic science, and genealogical research. Nowadays, screening genetic databases for related individuals forms an important aspect of standard quality control procedures. Relatedness research is usually based on an allele sharing analysis of identity by state (IBS) or identity by descent (IBD) alleles. Existing IBS/IBD methods mainly aim to identify first-degree relationships (parent–offspring or full siblings) and second degree (half-siblings, avuncular, or grandparent–grandchild) pairs. Little attention has been paid to the detection of in-between first and second-degree relationships such as three-quarter siblings (3/4S) who share fewer alleles than first-degree relationships but more alleles than second-degree relationships. With the progressively increasing sample sizes used in genetic research, it becomes more likely that such relationships are present in the database under study. In this paper, we extend existing likelihood ratio (LR) methodology to accurately infer the existence of 3/4S, distinguishing them from full siblings and second-degree relatives. We use bootstrap confidence intervals to express uncertainty in the LRs. Our proposal accounts for linkage disequilibrium (LD) by using marker pruning, and we validate our methodology with a pedigree-based simulation study accounting for both LD and recombination. An empirical genome-wide array data set from the GCAT Genomes for Life cohort project is used to illustrate the method.
Platoon control design for unmanned surface vehicles subject to input delay
Authors: Liang Xiaoling , Zhang Yuexin , Yang Guotao 
Published: January 2021

AbstractVessel train formation as a new trend has been raised in cooperative control for multiple vessels. This paper addresses formation control design for a group of unmanned surface vehicles platoon considering input delay. To account for connectivity-preserving and collision-avoiding, Barrier Lyapunov function is incorporated into the constraints design of line-of-sight range and bearing. To alleviate the computational burden, neural dynamic model is employed to simplify the control design and smooth the input signals. Besides, input control arising from time delay due to mechanisms and communication is considered in the marine vessels. Within the framework of the backstepping technique, distributed coordination is accomplished in finite time and the uniformly ultimately boundness of overall system is guaranteed via rigorous stability analysis. Finally, the simulation is performed to verify the effectiveness of the proposed control method.
Influence of forest stand characteristics on physical, mechanical properties and chemistry of chestnut wood
Authors: Marini Francesco , Manetti Maria Chiara , Corona Piermaria , Portoghesi Luigi , Vinciguerra Vittorio , Tamantini Swati , Kuzminsky Elena , Zikeli Florian , Romagnoli Manuela 
Published: January 2021

AbstractSite conditions and forest management affect dendrometric parameters of chestnut (Castanea sativaMill.) coppices, but there is modest knowledge on the effect of stand dendrometric characters on physical and mechanical wood characteristics. The aim of this study was to verify these relationships in chestnut coppices that were 12–14 years old. Wood density, compression and bending strength, shrinkages were measured on shoots of five different stand in a vulcanic site in Monte Amiata (Central – Italy). Investigated stands differ in number of stools/ha and dominant height, diameter/basal area of the shoots. The main difference in the physical characters among the stands is density. The initial results of the study showed that physical, mechanical wood characters are more dependent by the shoot than by the site. There is a positive relationships between the number of stools/ha and density and a negative one among shoot dominant height and basal area with wood density. Spectroscopic profile by FTIR has not showed relevant differences among the stands. Wood anatomy has showed the breakpoint at cellular level.
Assessing the efficacy of eDNA metabarcoding for measuring microbial biodiversity within forest ecosystems
Authors: Ladin Zachary S. , Ferrell Barbra , Dums Jacob T. , Moore Ryan M. , Levia Delphis F. , Shriver W. Gregory , D’Amico Vincent , Trammell Tara L. E. , Setubal João Carlos , Wommack K. Eric 
Published: January 2021

AbstractWe investigated the nascent application and efficacy of sampling and sequencing environmental DNA (eDNA) in terrestrial environments using rainwater that filters through the forest canopy and understory vegetation (i.e., throughfall). We demonstrate the utility and potential of this method for measuring microbial communities and forest biodiversity. We collected pure rainwater (open sky) and throughfall, successfully extracted DNA, and generated over 5000 unique amplicon sequence variants. We found that several taxa including Mycoplasma sp., Spirosoma sp., Roseomonas sp., and Lactococcus sp. were present only in throughfall samples. Spiroplasma sp., Methylobacterium sp., Massilia sp., Pantoea sp., and Sphingomonas sp. were found in both types of samples, but more abundantly in throughfall than in rainwater. Throughfall samples contained Gammaproteobacteria that have been previously found to be plant-associated, and may contribute to important functional roles. We illustrate how this novel method can be used for measuring microbial biodiversity in forest ecosystems, foreshadowing the utility for quantifying both prokaryotic and eukaryotic lifeforms. Leveraging these methods will enhance our ability to detect extant species, describe new species, and improve our overall understanding of ecological community dynamics in forest ecosystems.
Diabetic condition induces hypertrophy and vacuolization in glomerular parietal epithelial cells
Authors: Kawaguchi Takahisa , Hasegawa Kazuhiro , Yasuda Itaru , Muraoka Hirokazu , Umino Hiroyuki , Tokuyama Hirobumi , Hashiguchi Akinori , Wakino Shu , Itoh Hiroshi 
Published: January 2021

AbstractDiabetic nephropathy (DN) is accompanied by characteristic changes in the glomerulus, but little is known about the effect of diabetes on parietal epithelial cells (PECs). In this study, a descriptive analysis of PECs was undertaken in diabetic db/db mice and in diabetic patients. PEC hypertrophy was significantly more prominent in diabetic mice than in nondiabetic mice, and this was evident even at the early stage. Additionally, the number of vacuoles in PECs was markedly increased in diabetic mice, suggesting the presence of cellular injury in PECs in DN. Although rare, binuclear cells were observed in mice with early diabetes. In cultured PECs, a high glucose condition, compared with normal glucose condition, induced cellular hypertrophy and apoptosis. Flow cytometry showed that some PECs in the G0 phase reentered the cell cycle but got arrested in the S phase. Finally, in human diabetic subjects, hypertrophy and vacuolization were observed in the PECs. Our data showed that PECs undergo substantial changes in DN and may participate in rearrangement for differentiation into podocytes.