bluuebunny/crossref_metadata_2025_split huggingface dataset:
Economics of U.S. catfish farming practices: Profitability, economies of size, and liquidity
Authors: Kumar Ganesh , Engle Carole , Hegde Shraddha , van Senten Jonathan 
Published: June 2020

AbstractEvolution of the U.S, catfish industry, forged by dynamic market forces, has resulted in the development of an array of farming practices. This comparative economic study was developed with data from 325 ponds on 38 commercial catfish farms (Alabama, Arkansas, and Mississippi) and provides concurrent estimates of the cost of production, profitability, and indicators of farm liquidity for the most common catfish growout strategies. Detailed enterprise budgets were developed for nine different catfish production strategies and analyzed on three different farm scales (32, 124, and 592 ha). Profitability differed across catfish farming practices. The split‐pond system using hybrid catfish was the least‐cost production strategy ($1.97/kg), followed by the multiple‐batch system employing channel catfish with increased aeration rates and intensively aerated ponds using hybrid catfish. Long‐term profitability of catfish farming practices increased with increases in farm size. Although seven of the nine production strategies discussed here were profitable in the long‐run on medium (124‐ha) and large (592‐ha) catfish farms, only split and intensively aerated ponds (hybrid catfish and multiple‐batch production with channel catfish with increased aeration rates) were profitable in the long‐run on small farms (32‐ha). Low‐intensity strategies involving channel catfish in single‐ or multiple‐batch systems were not profitable on any scale. High‐yielding strategies resulted in an increased cash flow coverage ratio and decreased debt‐servicing ratios, indicating lower liquidity risk. Economies of scale were evident throughout the analysis but stemmed from two different effects: (a) intensification of production in individual ponds; and (b) larger farm size. Changes in cost structures and economic conditions have changed the degree of profitability of farming practices. A number of previously profitable practices are no longer profitable. Newer, split pond, and intensively aerated farming practices were profitable but require greater attention to cost efficiencies.
Targeting extracellular vesicles‐mediated hepatic inflammation as a therapeutic strategy in liver diseases
Authors: Yang Dakai , Liu Jing 
Published: June 2020

AbstractExtracellular Vesicles (EVs) are nano‐ to micro‐sized membranous vesicles that can be produced by normal and diseased cells. As carriers of biologically active molecules including proteins, lipids and nucleic acids, EVs mediate cell‐to‐cell communication and execute diverse functions by delivering their cargoes to specific cell types. Hepatic inflammation caused by virus infection, autoimmunity and malignancy is a common driver of progressive liver fibrosis and permanent liver damage. Emerging evidence has shown that EVs‐mediated inflammation as critical player in the progression of liver diseases since they shuttle within the liver as well as between other tissues with inflammatory signals. Therefore, targeting inflammatory EVs could represent a potential therapeutic strategy in liver diseases. Moreover, EVs are emerging as a promising tool for intracellular delivery of therapeutic nucleic acid. In this review, we will discuss not only recent advances on the role of EVs in mediating hepatic inflammation and present strategies for targeted therapy on the context of liver diseases but also the challenging questions that need to be answered in the field.
Plasma metabolomic fingerprint of advanced cirrhosis stages among HIV/HCV‐coinfected and HCV‐monoinfected patients
Authors: Salgüero Sergio , Rojo David , Berenguer Juan , González‐García Juan , Fernández‐Rodríguez Amanda , Brochado‐Kith Oscar , Díez Cristina , Hontañon Victor , Virseda‐Berdices Ana , Martínez Javier , Ibañez‐Samaniego Luis , Llop‐Herrera Elba , Barbas Coral , Resino Salvador , Jiménez‐Sousa María A. ,   the Escorial Study Group
Published: June 2020

AbstractBackground & AimsHepatitis C virus (HCV), human immunodeficiency virus (HIV) and cirrhosis induce metabolic disorders. Here, we aimed to evaluate the association of plasma metabolites with Child‐Turcotte‐Pugh (CTP) score and hepatic decompensation in HIV/HCV‐coinfected and HCV‐monoinfected patients with advanced cirrhosis.MethodsA cross‐sectional study was carried out in 62 HIV/HCV‐coinfected and 28 HCV‐monoinfected patients. Metabolomics analysis was performed by gas chromatography‐mass spectrometry (GC‐MS) and liquid chromatography‐mass spectrometry (LC‐MS). The statistical association analysis was performed by partial least squares discriminant analysis (PLS‐DA) and generalized linear model (GLM) with binomial distribution (to analyse HIV coinfection, high alcohol intake, treatment with statins, previous HCV therapy failure and decompensation) and ordinal logistic regression (OLR) models to analyse different stages of cirrhosis (CTP score).ResultsThe statistical analysis identified plasma metabolites associated with HIV coinfection, high alcohol intake, CTP score and hepatic decompensation. Overall, fatty acids, bile acids, aromatic and sulphur amino acids, butyrate derivatives, oxidized phospholipids, energy‐related metabolites and bacterial fermentation‐related metabolites were increased in more advanced cirrhosis stages; while lysophosphatidylcholines and lysophosphatidylethanolamines, branched‐chain amino acids (BCAA) and metabolites of tricarboxylic acid cycle, among others, were decreased in more advanced cirrhosis. Most of the significant metabolites displayed a similar trend after stratifying for HIV/HCV‐ and HCV‐infected patients. Glycolic acid, LPC (16:0) and taurocholic acid had high accuracy for discriminating patients according to decompensated cirrhosis (CTP ≥ 7).ConclusionAltered plasma metabolomic profile was associated with advanced stages of cirrhosis in HIV/HCV‐coinfected and HCV‐monoinfected patients.
The molecular basis of venom resistance in a rattlesnake‐squirrel predator‐prey system
Authors: Gibbs H. Lisle , Sanz Libia , Pérez Alicia , Ochoa Alexander , Hassinger Alyssa T.B. , Holding Matthew L. , Calvete Juan J. 
Published: June 2020

AbstractUnderstanding how interspecific interactions mould the molecular basis of adaptations in coevolving species is a long‐sought goal of evolutionary biology. Venom in predators and venom resistance proteins in prey are coevolving molecular phenotypes, and while venoms are highly complex mixtures it is unclear if prey respond with equally complex resistance traits. Here, we use a novel molecular methodology based on protein affinity columns to capture and identify candidate blood serum resistance proteins (“venom interactive proteins” [VIPs]) in California Ground Squirrels (Otospermophilus beecheyi) that interact with venom proteins from their main predator, Northern Pacific Rattlesnakes (Crotalus o. oreganus). This assay showed that serum‐based resistance is both population‐ and species‐specific, with serum proteins from ground squirrels showing higher binding affinities for venom proteins of local snakes compared to allopatric individuals. Venom protein specificity assays identified numerous and diverse candidate prey resistance VIPs but also potential targets of venom in prey tissues. Many specific VIPs bind to multiple snake venom proteins and, conversely, single venom proteins bind multiple VIPs, demonstrating that a portion of the squirrel blood serum “resistome” involves broad‐based inhibition of nonself proteins and suggests that resistance involves a toxin scavenging mechanism. Analyses of rates of evolution of VIP protein homologues in related mammals show that most of these proteins evolve under purifying selection possibly due to molecular constraints that limit the evolutionary responses of prey to rapidly evolving snake venom proteins. Our method represents a general approach to identify specific proteins involved in co‐evolutionary interactions between species at the molecular level.
A protein phosphorylation module patterns the Bacillus subtilis spore outer coat
Authors: Freitas Carolina , Plannic Jarnaja , Isticato Rachele , Pelosi Assunta , Zilhão Rita , Serrano Mónica , Baccigalupi Loredana , Ricca Ezio , Elsholz Alexander K. W. , Losick Richard , O. Henriques Adriano 
Published: June 2020

AbstractAssembly of the Bacillus subtilis spore coat involves over 80 proteins which self‐organize into a basal layer, a lamellar inner coat, a striated electrodense outer coat and a more external crust. CotB is an abundant component of the outer coat. The C‐terminal moiety of CotB, SKRB, formed by serine‐rich repeats, is polyphosphorylated by the Ser/Thr kinase CotH. We show that another coat protein, CotG, with a central serine‐repeat region, SKRG, interacts with the C‐terminal moiety of CotB and promotes its phosphorylation by CotH in vivo and in a heterologous system. CotG itself is phosphorylated by CotH but phosphorylation is enhanced in the absence of CotB. Spores of a strain producing an inactive form of CotH, like those formed by a cotG deletion mutant, lack the pattern of electrondense outer coat striations, but retain the crust. In contrast, deletion of the SKRB region, has no major impact on outer coat structure. Thus, phosphorylation of CotG by CotH is a key factor establishing the structure of the outer coat. The presence of the cotB/cotH/cotG cluster in several species closely related to B. subtilis hints at the importance of this protein phosphorylation module in the morphogenesis of the spore surface layers.
PuHox52‐mediated hierarchical multilayered gene regulatory network promotes adventitious root formation inPopulus ussuriensis
Authors: Wei Ming , Liu Quangang , Wang Zhanchao , Yang Jingli , Li Wenlong , Chen Yingxi , Lu Han , Nie Jinfu , Liu Baoguang , Lv Kaiwen , Mao Xuliang , Chen Su , Sanders Jennifer , Wei Hairong , Li Chenghao 
Published: June 2020

SummaryAdventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive.Here, we report the identification of a poplar homeobox gene,PuHox52, which was induced rapidly (within 15 min) at the basal ends of stems upon cutting and played a key regulatory role in adventitious rooting. We demonstrated that overexpression ofPuHox52significantly increased the number of ARs while suppression ofPuHox52had the opposite effect.A multilayered hierarchical gene regulatory network (ML‐hGRN) mediated by PuHox52 was reverse‐engineered and demonstrated to govern AR formation. PuHox52 regulated AR formation through upregulation of nine hub regulators, including a jasmonate signaling pathway gene,PuMYC2, and an auxin signaling pathway gene,PuAGL12. We also identified coherent type 4 feed‐forward loops within this ML‐hGRN; PuHox52 repressedPuHDA9, which encodes a histone deacetylase, and led to an increase in acetylation and presumably expression of three hub regulators,PuWRKY51,PuLBD21andPuIAA7.Our results indicate that the ML‐hGRN mediated by PuHox52 governs AR formation at the basal ends of stem cuttings from poplar trees.
TLR4 agonist protects against Trypanosoma cruzi acute lethal infection by decreasing cardiac parasite burdens
Authors: Villanueva‐Lizama Liliana E. , Cruz‐Chan Julio V. , Versteeg Leroy , Teh‐Poot Christian F. , Hoffman Kristyn , Kendricks April , Keegan Brian , Pollet Jeroen , Gusovsky Fabian , Hotez Peter J. , Bottazzi Maria Elena , Jones Kathryn M. 
Published: June 2020

AbstractE6020 is a synthetic agonist of Toll‐like receptor‐4 (TLR4). The purpose of this study was to evaluate the effect of different doses of E6020‐SE on Trypanosoma cruzi‐specific immune responses and its ability to confer protection against acute lethal infection in mice. Forty female BALB/c were infected with 500 trypomastigotes of T cruzi H1 strain, divided into four groups (n = 10) and treated at 7‐ and 14‐day post‐infection (dpi) with different doses of E6020‐SE or PBS (control). Survival was followed for 51 days, mice were euthanized and hearts were collected to evaluate parasite burden, inflammation and fibrosis. We found significantly higher survival and lower parasite burdens in mice injected with E6020‐SE at all doses compared to the control group. However, E6020‐SE treatment did not significantly reduce cardiac inflammation or fibrosis. On the other hand, E6020‐SE modulated Th1 and Th2 cytokines, decreasing IFN‐γ and IL‐4 in a dose‐dependent manner after stimulation with parasite antigens. We conclude that E6020‐SE alone increased survival by decreasing cardiac parasite burdens in BALB/c mice acutely infected with T cruzi but failed to prevent cardiac damage. Our results suggest that for optimal protection, a vaccine antigen is necessary to balance and orient a protective immune response.
Application of theLeishmania infantum21‐kDa recombinant protein for the development of an immunochromatographic test
Authors: Karimi Kakh Mansoureh , Golchin Mehdi , Kazemi Arababadi Mohammad , Daneshvar Hamid 
Published: June 2020

AbstractBackgroundVisceral leishmaniasis (VL), caused byLeishmania infantum, is a systemic parasitic disease and presents a global health problem which can be fatal if not diagnosed and treated. Dogs are the main hosts and provide reservoirs for the transmission of the disease to humans.MethodsIn this study, the gene encoding a 21‐kDa protein was cloned and expressed as a fusion protein inEscherichia colistrain BL21 (DE3) for developing a rapid immunochromatographic test (ICT) to identify infected dogs. The expression of the recombinant 21‐kDa protein (r21) was investigated using SDS‐PAGE and Western blot methods. The purified r21‐kDa protein was spotted onto ICT strips and tested by sera from experimentally infected, naturally infected and uninfected dogs.ResultsThe SDS‐PAGE and Western blot methods showed the successful expression of r21‐kDa protein. The ICT strip test revealed that the r21‐kDa protein was detected by the sera of experimentally and naturally infected dogs. The specificity tests also confirmed no cross‐reactivity with animals infected withTrypanosoma cruzi,Toxoplasma gondiiandEhrlichia canis.ConclusionsBased on these findings, the new r21‐kDa protein may be a suitable target for developing a new simple, specific and rapid serological method to detect VL in infected dogs.
Inter‐individual genetic variation in the temperature response of Leptosphaeria species pathogenic on oilseed rape
Authors: Newbery Fay , Ritchie Faye , Gladders Peter , Fitt Bruce D. L. , Shaw Michael W. 
Published: June 2020

AbstractIt is important to understand the likely response of plant pathogens to increased temperatures due to anthropogenic climate change. This includes evolutionary change due to selection on genetically based variation in growth rate with temperature. We attempted to quantify this in two ways. First, radial mycelial growth rates in agar culture were determined for a collection of 44 English isolates of Leptosphaeria maculans and 17 isolates of L. biglobosa, at 14 temperatures. For L. maculans the genotypic variances in four parameters were measured: minimum temperature allowing growth, optimum temperature, growth rate at the optimum temperature, and growth rate at the highest usable temperature, 31.8°C. The standard deviations were 0.068°C, 1.28°C, 0.21 mm/day, and 0.31 mm⋅day−1⋅°C−1, respectively. For L. biglobosa, these figures were, respectively: immeasurably small, 1.31°C, 0.053 mm/day, and 0.53 mm⋅day−1⋅°C−1. In addition, the incidence and severity of phoma stem canker in planta over a natural growing cycle at four temperatures (16, 20, 24, and 28°C) around the average culture optimum were determined. There was no correlation between in vitro and in planta growth, and the decrease in pathogen measures either side of the optimum temperature was much less for in planta growth than for in vitro growth. We conclude that both pathogens have the capacity to evolve to adapt to changes in environmental conditions, but that predictions of the effect of this adaptation, or estimates of heritability in natural conditions, cannot be made from measurements in vitro.
Who Should We Count as Citizens? Categorizing People in Public Administration Research
Authors: Roberts Alasdair 
Published: June 2020

AbstractCitizenship is a core concept in public administration research. This article examines how the concept was employed in 29 research articles published in Public Administration Review since 2009. It finds two difficulties. The first is a tendency to omit an explicit definition of the concept, contrary to good practice. The second is a tendency to adopt an implied definition of citizenship that encompasses all of the general population. The article considers possible justifications for current practice. Research would be improved by using the concept less frequently, defining it explicitly, adopting a definition that is closer to ordinary usage, and attending more carefully to the ways in which attitudes and behavior are influenced by a person's status within a jurisdiction.
Different Processes, Different Outcomes? Assessing the Individual‐Level Impacts of Public Participation
Authors: Jo Suyeon , Nabatchi Tina 
Published: June 2020

AbstractThis article empirically investigates the relative efficacy of different direct participation processes. Specifically, it compares the effects of three types of participatory processes (public meetings, focus groups, and citizen juries) on participants' issue awareness, competence, empowerment, and trust in service professionals. The authors hypothesize that all three participatory processes will positively affect these individual outcomes but that the magnitudes of effects will differ across the three processes. Using data from field experiments, the authors test and find general support for the hypotheses. This study contributes to understanding of public participation, particularly in terms of the relationship between participatory design and outcomes.
Zeroth‐order conservation laws of two‐dimensional shallow water equations with variable bottom topography
Authors: Bihlo Alexander , Popovych Roman O. 
Published: June 2020

AbstractWe classify zeroth‐order conservation laws of systems from the class of two‐dimensional shallow water equations with variable bottom topography using an optimized version of the method of furcate splitting. The classification is carried out up to equivalence generated by the equivalence group of this class. We find additional point equivalences between some of the listed cases of extensions of the space of zeroth‐order conservation laws, which are inequivalent up to transformations from the equivalence group. Hamiltonian structures of systems of shallow water equations are used for relating the classification of zeroth‐order conservation laws of these systems to the classification of their Lie symmetries. We also construct generating sets of such conservation laws under action of Lie symmetries.
Clinical relevance of major histocompatibility complex class I chain–related molecule A (MICA) antibodies in live donor renal transplantation – Indian Experience
Authors: Baranwal Ajay Kumar , Bhat Deepali K. , Goswami Sanjeev , Agarwal Sanjay Kumar , Kaur Gurvinder , Mehra Narinder 
Published: June 2020

AbstractAntibody‐mediated rejections (AMR) in the absence of circulating anti‐HLA‐DSA have highlighted the role of non‐HLA antibodies, particularly those directed against endothelial cells. Of these, MICA (major histocompatibility complex class I chain–related molecule A) antibodies are the most notable and important because of their potential in promoting graft rejections. Limited studies have focused on the impact of MICA donor‐specific antibodies (DSA) on graft outcome as compared to those that are not donor‐specific (NDSA). We evaluated pre‐ and post‐transplant sera at POD 7, 30, 90, 180 and the time of biopsy from 206 consecutive primary live donor renal transplant recipients for anti‐MICA and anti‐HLA antibodies using single antigen bead assay on a Luminex platform. Recipients who developed MICA antibodies and their donors were phenotyped for MICA alleles. For the purpose of antibody analysis, patients were categorized into three major groups: biopsy‐proven AMR, acute cellular rejection (ACR) and those with no rejection episodes (NRE). During the mean follow‐up period of 17.37 ± 6.88 months, 16 of the 206 recipients developed AMR, while ACR was observed in only 13 cases. A quarter (25%) of the AMR cases had anti‐MICA antibodies as compared to 7.7% of those experiencing ACR and 6.2% of the NRE group. Allelic typing revealed that all MICA Ab +ve AMR cases were due to the presence of donor‐specific antibodies. MICA‐DSA even in the absence of HLA‐DSA was significantly associated with AMR but not with ACR when compared with the NRE group (P = <.01).
Associations among state‐level physical distancing measures and suicidal thoughts and behaviors among U.S. adults during the early COVID‐19 pandemic
Authors: Bryan Craig J. , Bryan AnnaBelle O. , Baker Justin C. 
Published: June 2020

AbstractPurposeThe purpose of this study was to identify leading sources of stress, describe rates of mental health outcomes, and examine their associations among U.S. adults during the first months of the COVID‐19 pandemic.MethodIn a cross‐sectional, general population survey conducted from March 18 to April 4, 2020, U.S. adults (n = 10,625) were recruited through Qualtrics Panels using quota sampling methods.ResultsLife stressors, probable depression, past‐month suicide ideation, and past‐month suicide attempts were not elevated among participants subject to state‐level stay‐at‐home orders and/or large gathering bans. Multiple life stressors were associated with increased rates of probable depression. Past‐month suicide ideation was significantly higher among participants reporting ongoing arguments with a partner and serious legal problems. Past‐month suicide attempt was significantly higher among participants reporting concerns about a life‐threatening illness or injury, but was significantly lower among participants reporting an unexpected bill or expense.ConclusionsResults failed to support the conclusion that physical distancing measures are correlated with worse mental health outcomes. Concerns about life‐threatening illness or injury were uniquely associated with increased risk of suicide attempt.
Thwarted belongingness and perceived burdensomeness explain the associations of COVID‐19 social and economic consequences to suicide risk
Authors: Gratz Kim L. , Tull Matthew T. , Richmond Julia R. , Edmonds Keith A. , Scamaldo Kayla M. , Rose Jason P. 
Published: June 2020

AbstractObjectiveThe social and economic consequences of COVID‐19 and related public health interventions aimed at slowing the spread of the virus have been proposed to increase suicide risk. However, no research has examined these relations. This study examined the relations of two COVID‐19 consequences (i.e., stay‐at‐home orders and job loss) to suicide risk through thwarted belongingness, perceived burdensomeness, and loneliness.MethodOnline data from a nationwide community sample of 500 adults (mean age = 40) from 45 states were collected between March 27 and April 5, 2020. Participants completed measures assessing thwarted belongingness, perceived burdensomeness, loneliness, and suicide risk, as well as whether they (a) were currently under a stay‐at‐home order and (b) had experienced a recent job loss due to the pandemic.ResultsResults revealed a significant indirect relation of stay‐at‐home order status to suicide risk through thwarted belongingness. Further, whereas recent job loss was significantly correlated with suicide risk, neither the direct relation of job loss to suicide risk (when accounting for their shared relations to perceived burdensomeness) nor the indirect relation through perceived burdensomeness was significant.ConclusionsResults highlight the potential benefits of interventions targeting thwarted belongingness and perceived burdensomeness to offset suicide risk during this pandemic.