bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression
Authors: Ramírez-Carrillo Elvia , Gaona Osiris , Nieto Javier , Sánchez-Quinto Andrés , Cerqueda-García Daniel , Falcón Luisa I. , Rojas-Ramos Olga A. , González-Santoyo Isaac 
Published: February 2020

AbstractIf you think you are in control of your behavior, think again. Evidence suggests that behavioral modifications, as development and persistence of depression, maybe the consequence of a complex network of communication between macro and micro-organisms capable of modifying the physiological axis of the host. Some parasites cause significant nutritional deficiencies for the host and impair the effectiveness of cognitive processes such as memory, teaching or non-verbal intelligence. Bacterial communities mediate the establishment of parasites and vice versa but this complexity approach remains little explored. We study the gut microbiota-parasite interactions using novel techniques of network analysis using data of individuals from two indigenous communities in Guerrero, Mexico. Our results suggest that Ascaris lumbricoides induce a gut microbiota perturbation affecting its network properties and also subnetworks of key species related to depression, translating in a loss of emergence. Studying these network properties changes is particularly important because recent research has shown that human health is characterized by a dynamic trade-off between emergence and self-organization, called criticality. Emergence allows the systems to generate novel information meanwhile self-organization is related to the system’s order and structure. In this way, the loss of emergence means a depart from criticality and ultimately loss of health.
Dung beetles response to livestock management in three different regional contexts
Authors: Guerra Alonso Celeste Beatriz , Zurita Gustavo Andrés , Bellocq M. Isabel 
Published: February 2020

AbstractThe response of biological communities to human disturbances depends on factors acting at local and regional scale and on the interaction between them. We compared the response of native forest dung beetle communities to cattle grazing under regional contexts differing on precipitation patterns (Atlantic forest and humid and dry Chaco). Through multivariate and GLMM analyses we contrasted richness and composition across regions and land uses and explored the role of local and regional variables accounting for those changes. We captured a total of 44101 individuals of 109 species. The interaction between local and regional variables influenced the response to livestock management. In the two wet regions (humid Chaco and Atlantic forest) diversity was similar in the native forest regardless of cattle presence but differs strongly in open pastures. In contrast, in the dry Chaco, differences between native forest and land use were not evident. Vegetation structure was a major determinant of species richness, whereas regional climate determined differences in species composition. We concluded that the response of dung beetles to livestock management cannot be generalized for all biomes. In dry ecosystems, dung beetles are probably pre-adapted to environmental conditions imposed by cattle ranching whereas in wet ecosystems the impact of cattle ranching is more significant.
Anxiolytic Drug FGIN-1-27 Ameliorates Autoimmunity by Metabolic Reprogramming of Pathogenic Th17 Cells
Authors: Singh Anju , Dashnyam Myagmarjav , Chim Bryan , Escobar Thelma M. , Dulcey Andrés E. , Hu Xin , Wilson Kelli M. , Koganti Prasanthi P. , Spinner Camille A. , Xu Xin , Jadhav Ajit , Southall Noel , Marugan Juan , Selvaraj Vimal , Lazarevic Vanja , Muljo Stefan A. , Ferrer Marc 
Published: February 2020

AbstractTh17 cells are critical drivers of autoimmune diseases and immunopathology. There is an unmet need to develop therapies targeting pathogenic Th17 cells for the treatment of autoimmune disorders. Here, we report that anxiolytic FGIN-1-27 inhibits differentiation and pathogenicity of Th17 cellsin vitroandin vivousing the experimental autoimmune encephalomyelitis (EAE) model of Th17 cell-driven pathology. Remarkably, we found that the effects of FGIN-1-27 were independent of translocator protein (TSPO), the reported target for this small molecule, and instead were driven by a metabolic switch in Th17 cells that led to the induction of the amino acid starvation response and altered cellular fatty acid composition. Our findings suggest that the small molecule FGIN-1-27 can be re-purposed to relieve autoimmunity by metabolic reprogramming of pathogenic Th17 cells.
Asc-1 Transporter (SLC7A10): Homology Models And Molecular Dynamics Insights Into The First Steps Of The Transport Mechanism
Authors: Mikou Afaf , Cabayé Alexandre , Goupil Anne , Bertrand Hugues-Olivier , Mothet Jean-Pierre , Acher Francine C. 
Published: February 2020

AbstractThe alanine-serine-cysteine transporter Asc-1 regulates the synaptic availability of d-serine and glycine (the two co-agonists of the NMDA receptor) and is regarded as an important drug target. To shuttle the substrate from the extracellular space to the cytoplasm, this transporter undergoes multiple distinct conformational states. In this work, homology modeling, substrate docking and molecular dynamics simulations were carried out to learn more about the transition between the “outward-open” and “outward-open occluded” states. We identified a transition state involving the highly-conserved unwound TM6 region in which the Phe243 flips close to the d-serine substrate without major movements of TM6. This feature and those of other key residues are proposed to control the binding site and substrate translocation. Competitive inhibitors ACPP, LuAE00527 and SMLC were docked and their binding modes at the substrate binding site corroborated the key role played by Phe243 of TM6. For ACPP and LuAE00527, strong hydrophobic interactions with this residue hinder its mobility and prevent the uptake and the efflux of substrates. As for SMLC, the weaker interactions maintain the flexibility of Phe243 and the efflux process. Overall, we propose a molecular basis for the inhibition of substrate translocation of the Asc-1 transporter that should be valuable for rational drug design.
High-resolution profiling of human cytomegalovirus cell-free DNA in human plasma highlights its exceptionally fragmented nature
Authors: Peddu Vikas , Bradley Benjamin T. , Casto Amanda M. , Shree Raj , Colbert Brice G. , Xie Hong , Santo Tracy K. , Huang Meei-Li , Cheng Edith Y. , Konnick Eric , Salipante Stephen J. , Jerome Keith R. , Lockwood Christina M. , Greninger Alexander L. 
Published: February 2020

AbstractHuman cytomegalovirus (CMV) infections comprise a leading cause of newborn impairments worldwide and are pervasive concerns among the immunocompromised. Quantification of CMV viral loads is increasingly used to guide definitions of CMV disease but standardization of CMV quantitation remains problematic, mostly due to differences in qPCR amplicon sizes between clinical laboratories. Here, we used plasma cfDNA sequencing data from 2,208 samples sent for non-invasive prenatal aneuploidy screening to detect CMV and precisely measure the length of CMV fragments in human plasma. CMV reads were identified in 120 (5.4%) samples. Median cfDNA fragment size derived from CMV was significantly shorter than cfDNA derived from human chromosomes (103 vs 172 bp, p < 0.0001), corresponding to the 3rdpercentile of human cfDNA. Sequencing of cfDNA from seven plasma samples from transplant patients positive for CMV confirmed the extraordinarily short nature of CMV cfDNA fragment size with a median length of 149 bp. We further show that these high-resolution measurements of CMV DNA fragment size accurately predict measured discrepancies in serum viral load measurements by different qPCR assays. These results highlight the exceptionally fragmented nature of CMV cfDNA and illustrate the promise of plasma cfDNA sequencing for quantitating viral loads through detection of fragments that would be unrecoverable by qPCR.
Quality comparison of “Laba” garlic processed by High Hydrostatic Pressure and High Pressure Carbon Dioxide
Authors: Tao Dandan , Li Fangwei , Hu Xiaosong , Liao Xiaojun , Zhang Yan 
Published: February 2020

AbstractThe production of “Laba” garlic is limited to the homemade method with long processing time and non-uniform color quality. Innovative food processing technologies including high hydrostatic pressure (HHP) and high pressure carbon dioxide (HPCD) were applied to the processing of “Laba” garlic. Products prepared at different treatment pressures (200, 350 and 500 MPa of HHP; 4, 7 and 10 MPa of HPCD) were compared by evaluating the texture, color, flavor and sensory qualities. The results indicated that HHP treatment at 200 MPa was optimal for retaining the textural quality of “Laba” garlic, which was mainly attributed to the compacted cells and the increased Ca2+-cross linked cell-cell adhesion. HHP had greater effect on facilitating the formation of the attractive green color of “Laba” garlic than HPCD. The flavor profiles of “Laba” garlic were modified after treatments, with pungent compounds decreased to non-detectable. The results from sensory study confirmed that “Laba” garlic treated by HHP at 200 MPa was most acceptable to consumers. Moreover, considering the treatment capacity and feasibility of commercialization, HHP would be a promising technology in production of “Laba” garlic with improved quality and efficiency.
Epidemiology of Anosmia in South Korea: A Nationwide Population-Based Study
Authors: Kang Jeong Wook , Lee Young Chan , Han Kyungdo , Kim Sung Wan , Lee Kun Hee 
Published: February 2020

AbstractResearch about the epidemiology of olfactory dysfunction in Asians was not enough. The purpose of this study was to assess the prevalence and incidence rate of olfactory disorders in Koreans and to evaluate demographic risk factors. We analyzed clinical data of patients with anosmia using Korean National Health Insurance Service data from 2006 to 2016. The data includes medical insurance claim data and medical records of almost 50,000,000 people in Korea. The 30-39 age group showed the highest prevalence (19.25 per 10,000 per year). Their incidence rate was also high comparing other age groups (13.30 per 10,000 per year). The prevalence and the incidence increased from 7.10 to 13.74 and from 5.66 to 9.54 between 2006 and 2016. In the seasonal analysis, the incidence rate was high in spring and autumn. The high-income population showed about 1.4-folds higher incidence rate than the low-income population. We thought that the socioeconomic status could generally affect the rate of hospital visit in the anosmia population. Anosmia can be frequently underdiagnosed in the clinical environment because the elderly and the low-income people easily underestimate their anosmia symptom and ignore the severity due to their economic problem. Therefore careful attention and further studies for anosmia are needed.
The hemodynamic complexities underlying transient ischemic attacks in early-stage Moyamoya disease: an exploratory CFD study
Authors: Rashad Sherif , Saqr Khalid M. , Fujimura Miki , Niizuma Kuniyasu , Tominaga Teiji 
Published: February 2020

AbstractMoyamoya disease (MMD) is a rare cerebro-occlusive disease with unknown etiology that can cause both ischemic and hemorrhagic stroke. MMD is characterized by progressive stenosis of the terminal internal carotid artery (ICA) and development of basal brain collaterals. Early-stage MMD is known to cause hemodynamic insufficiency despite mild or moderate stenosis of the intracranial arteries, but the exact mechanism underlying this pathophysiological condition is undetermined. We used high-resolution Large Eddy Simulations to investigate multiple complex hemodynamic phenomena that led to cerebral ischemia in five patients with early-stage MMD. The effects of transitional flow, coherent flow structures and blood shear-thinning properties through regions of tortuous and stenosed arteries were explored and linked to symptomatology. It is evidently shown that in some cases complex vortex structures, such as Rankine-type vortices, redirects blood flow away from some arteries causing significant reduction in blood flow. Moreover, partial blood hammer (PBH) phenomenon was detected in some cases and led to significant hemodynamic insufficiency. PBH events were attributed to the interaction between shear-thinning properties, transitional flow structures and loss of upstream pressure-velocity phase lag. We clearly show that the hemodynamic complexities in early-stage MMD could induce ischemia and explain the non-responsiveness to antiplatelet therapy.
Impact of sunflower (Helianthus annuus L.) plastidial lipoyl synthases genes expression in glycerolipids composition of transgenic Arabidopsis plants
Authors: Martins-Noguerol Raquel , Moreno-Pérez Antonio Javier , Sebastien Acket , Troncoso-Ponce Manuel Adrián , Garcés Rafael , Thomasset Brigitte , Salas Joaquín J. , Martínez-Force Enrique 
Published: February 2020

AbstractLipoyl synthases are key enzymes in lipoic acid biosynthesis, a co-factor of several enzyme complexes involved in central metabolism. Plant pyruvate dehydrogenase complex (PDH), located in mitochondria and plastids, catalyses the first step of fatty acid biosynthesis in these organelles. Among their different components, the E2 subunit requires the lipoic acid prosthetic group to be active. De novo lipoic acid biosynthesis is achieved by the successive action of two enzymes on octanoyl-ACP: octanoyltransferase (LIP2) and lipoyl synthase (LIP1). In this study, two plastidial lipoyl synthase genes from sunflower (Helianthus annuus L.) were identified (HaLIP1p1 and HaLIP1p2), sequenced and cloned in a heterologous production system (Escherichia coli). Gene expression studies revealed similar expression patterns for both isoforms, with a slight predominance of HaLIP1p1 in vegetative tissues and mature seeds. Tertiary structural models for these enzymes indicate they both have the same theoretical catalytic sites, using lipoyl-lys and 5-deoxyadenosine as docking substrates. The fatty acid profile of E. coli cells overexpressing HaLIP1p1 and HaLIP1p2 did not present major differences, and the in vivo activity of both proteins was confirmed by complementation of an E. coli JW0623 mutant in which lipoyl synthase is defective. Although no significant differences were detected in the total fatty acid composition of transgenic Arabidopsis thaliana seeds overexpressing any of both proteins, a lipidomic analysis revealed a redistribution of the glycerolipid species, accompanied with increased phosphatidylethanolamine (PE) content and a decrease in diacyglycerols (DAG) and phosphatidylcholine (PC). Depletion of the SAM co-factor caused by HaLIP1p1 and HaLIP1p2 overexpression in transgenic plants could explain this remodelling through its effects on PC synthesis.
Impact of acute kidney injury in elderly versus young deceased donors on post-transplant outcomes: A multicenter cohort study
Authors: Park Woo Yeong , Kim Jeong Ho , Ko Eun Jung , Min Ji-Won , Ban Tae Hyun , Yoon Hye-Eun , Kim Young Soo , Jin Kyubok , Han Seungyeup , Yang Chul Woo , Chung Byung Ha 
Published: February 2020

AbstractWe investigated the impact of acute kidney injury (AKI) in elderly deceased-donors (DDs) vs. AKI in young DDs on post-transplant clinical outcomes. A total of 709 kidney transplant recipients (KTRs) from 602 DDs at four transplant centers were enrolled. KTRs were divided into young-DDKT and elderly-DDKT groups according to the age of DD of 60 years. Both groups were subdivided into non-AKI-KT and AKI-KT subgroups according to AKI in DDs. We investigated short-term and long-term clinical outcomes of non-AKI-DDKT and AKI-DDKT subgroups within young-DDKT and elderly-DDKT groups. The incidence of DGF in the AKI-DDKT subgroup was higher and the allograft function within 12 months after KT in the AKI-DDKT subgroup was lower than those in the non-AKI-DDKT subgroup in both young-DDKT and elderly-DDKT groups. Death-censored allograft survival rate was significantly lower in the AKI-elderly-DDKT subgroup than that in the non-AKI-elderly-DDKT subgroup, but it did not differ between AKI-young-DDKT and non-AKI-young-DDKT subgroup. In multivariable analysis, AKI-elderly-DDKT was an independent risk factor for allograft failure (hazard ratio: 2.648, 95% CI: 1.170–5.994, p = 0.019) and a significant interaction between AKI and old age in DDs on allograft failure was observed (p = 0.001). AKI in elderly DDs, but not in young DDs, can significantly affect long-term allograft outcomes of KTRs.
In situ identification of polyhydroxyalkanoate (PHA)-accumulating microorganisms in mixed microbial cultures under feast/famine conditions
Authors: Sruamsiri Donhatai , Thayanukul Parinda , Suwannasilp Benjaporn Boonchayaanant 
Published: February 2020

AbstractThe accumulation of plastic waste in the environment has become a serious environmental problem worldwide. Biodegradable plastics, such as polyhydroxyalkanoate (PHA), could serve as green alternatives to petroleum-based plastics. In this study, a mixed microbial culture was enriched under feast/famine conditions using a sequencing batch reactor (SBR) with acetate as a carbon source. The enrichment could accumulate a maximum PHA concentration of 32.3% gPHA/g mixed liquor suspended solids (MLSS) in the 12th cycle of SBR operation. The microbial community in this sludge sample was analyzed using 16 S rRNA gene amplicon sequencing (MiSeq). The results showed the dominance of Proteobacteria, represented by Alphaproteobacteria (13.26% of total sequences), Betaproteobacteria (51.37% of total sequences), and Gammaproteobacteria (23.44% of total sequences). Thauera (Betaproteobacteria) had the highest relative abundance, accounting for 48.88% of the total sequences. PHA-accumulating microorganisms in the enrichment were detected using fluorescence in situ hybridization (FISH) and a fluorescent dye, Nile blue A. Alphaproteobacteria and Betaproteobacteria were capable of accumulating PHA, while no Gammaproteobacteria were detected. Thauera spp. from Betaproteobacteria constituted 80.3% of the total PHA accumulating cells.
Ultrasensitive detection of saccharides using terahertz sensor based on metallic nano-slits
Authors: Qin Jianyuan , Cheng Wei , Han Baojuan , Du Yong , Han Zhanghua , Zhao Zongshan 
Published: February 2020

AbstractUnambiguous identification of trace amounts of biochemical molecules in a complex background using terahertz spectroscopy is extremely challenging owing to the extremely small absorption cross sections of these molecules in the terahertz regime. Herein, we numerically propose a terahertz nonresonant nano-slits structure that serves as a powerful sensor. The structure exhibits strongly enhanced electric field in the slits (five orders of magnitude), as well as high transmittance over an extra-wide frequency range that covers the characteristic frequencies of most molecules. Fingerprint features of lactose and maltose are clearly detected using this slits structure, indicating that this structure can be used to identify different saccharides without changing its geometrical parameters. The absorption signal strengths of lactose and maltose with a thickness of 200 nm are strongly enhanced by factors of 52.5 and 33.4, respectively. This structure is very sensitive to thin thickness and is suitable for the detection of trace sample, and the lactose thickness can be predicted on the basis of absorption signal strength when the thickness is less than 250 nm. The detection of a mixture of lactose and maltose indicates that this structure can also achieve multi-sensing which is very difficult to realize by using the resonant structures.
Neuronal contact guidance and YAP signaling on ultra-small nanogratings
Authors: Tonazzini Ilaria , Masciullo Cecilia , Savi Eleonora , Sonato Agnese , Romanato Filippo , Cecchini Marco 
Published: February 2020

AbstractContact interaction of neuronal cells with extracellular nanometric features can be exploited to investigate and modulate cellular responses. By exploiting nanogratings (NGs) with linewidth from 500 nm down to 100 nm, we here study neurite contact guidance along ultra-small directional topographies. The impact of NG lateral dimension on the neuronal morphotype, neurite alignment, focal adhesion (FA) development and YAP activation is investigated in nerve growth factor (NGF)-differentiating PC12 cells and in primary hippocampal neurons, by confocal and live-cell total internal reflection fluorescence (TIRF) microscopy, and at molecular level. We demonstrate that loss of neurite guidance occurs in NGs with periodicity below 400 nm and correlates with a loss of FA lateral constriction and spatial organization. We found that YAP intracellular localization is modulated by the presence of NGs, but it is not sensitive to their periodicity. Nocodazole, a drug that can increase cell contractility, is finally tested for rescuing neurite alignment showing mild ameliorative effects. Our results provide new indications for a rational design of biocompatible scaffolds for enhancing nerve-regeneration processes.
Knowledge status and sampling strategies to maximize cost-benefit ratio of studies in landscape genomics of wild plants
Authors: Santos Alesandro Souza , Gaiotto Fernanda Amato 
Published: February 2020

AbstractTo avoid local extinction due to the changes in their natural ecosystems, introduced by anthropogenic activities, species undergo local adaptation. Landscape genomics approach, through genome–environment association studies, has helped evaluate the local adaptation in natural populations. Landscape genomics, is still a developing discipline, requiring refinement of guidelines in sampling design, especially for studies conducted in the backdrop of stark socioeconomic realities of the rainforest ecologies, which are global biodiversity hotspots. In this study we aimed to devise strategies to improve the cost-benefit ratio of landscape genomics studies by surveying sampling designs and genome sequencing strategies used in existing studies. We conducted meta-analyses to evaluate the importance of sampling designs, in terms of (i) number of populations sampled, (ii) number of individuals sampled per population, (iii) total number of individuals sampled, and (iv) number of SNPs used in different studies, in discerning the molecular mechanisms underlying local adaptation of wild plant species. Using the linear mixed effects model, we demonstrated that the total number of individuals sampled and the number of SNPs used, significantly influenced the detection of loci underlying the local adaptation. Thus, based on our findings, in order to optimize the cost-benefit ratio of landscape genomics studies, we suggest focusing on increasing the total number of individuals sampled and using a targeted (e.g. sequencing capture) Pool-Seq approach and/or a random (e.g. RAD-Seq) Pool-Seq approach to detect SNPs and identify SNPs under selection for a given environmental cline. We also found that the existing molecular evidences are inadequate in predicting the local adaptations to climate change in tropical forest ecosystems.