bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physicochemical properties and isoflavone content of Chaga Cheonggukjang with Lactobacillus acidophilus KCTC 3925 starter
Authors: Na Ha Gyoon , Jang Eun Ho , Nam Dong Hun , Kim Min-Ah , Kim Mi-Ja , Sohn Eun Hwa , Kim Hyun Dong , Jang Ki-Hyo 
Published: October 2018

This study was conducted to investigate the quality characteristics and changes in isoflavone content of Cheonggukjang with added Chaga mushroom by secondary fermentation at 40℃ for 48 h with or without a starter, Lactobacillus acidophilus KCTC 3925. Cheonggukjang samples were divided into three groups: Control (unsterilized Cheonggukjang fermented without a starter), NS (unsterilized Cheonggukjang inoculated with L. acidophilus KCTC 3925), and YS (heat-sterilized Cheonggukjang inoculated with L. acidophilus KCTC 3925). The approximate composition of the three types of Cheonggukjang was 49.79-51.44% moisture, 4.54-4.72% crude ash, 43.21-44.37% crude protein, 11.58-13.65% crude fat, 37.41-40.07% carbohydrate, 31.92-33.82% dietary fiber. The mineral content included 5.43–9.64 mg% Na, 1,792.86–1,824.39 mg% K, 253.69–326.09 mg% Ca, 619.37–691.20 mg% P, 92.59–110.59 mg% Fe, and 0.01–0.02 mg% Cd. Free amino acid contents of NS (2,520.92 mg%) and YS (2,421.94 mg%) were significantly higher than that of the control (2,236.76 mg%). Amino-type nitrogen content for the three types of Cheonggukjang ranged from 837.20-920.27 mg% with no significant difference. Ammonia-type nitrogen content ranged from 137.09-169.36 mg%. Supplement of Cheonggukjang with L. acidophilus KCTC 3925 increased production of aglycone isoflavons compared to that of control. Therefore, our results show that fermenting Chaga Cheonggukjang with L. acidophilus KCTC 3925 leads to improved quality characteristics and increased isoflavone aglycone content.
Antioxidant and anti-inflammatory activities of Opuntia ficus-indica and Opuntia humifusa fruits ethanol extracts
Authors: Kim Dong-Gyu , Shin Jung-Hye , Kang Min-Jung 
Published: October 2018

Opuntia species have been used for centuries as food resources and in traditional folk medicine for their nutritional properties and their benefit in chronic diseases, particularly diabetes, obesity, cardiovascular diseases, and cancer. The aim of this study was to evaluate the antioxidant activities and anti-inflammatory effects of 75% ethanol extracts from Opuntia ficus-indica fruits (OFFE) and Opuntia humifusa fruits (OHFE). The total polyphenol and total flavonoid contents of OFFE were 17.07±0.08 and 8.65±0.08 mgQE/g, respectively, whereas those of OHFE were 9.41±0.14 and 2.03±0.08 mgQE/g, respectively. The antioxidant activities of OFFE and OHFE were determined based on various radical scavenging activities using 1,1-diphenyl-2-dipicrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging assays. The DPPH and ABTS radical scavenging activities of OFFE were significantly higher than those of OHFE. In addition, the release of nitric oxide (NO) and reactive oxygen species (ROS) were ameliorated by pretreatment with OFFE and OHFE in a dose-dependent manner. OFFE also suppressed the secretion of pro-inflammatory cytokines, including interleukin-1β (IL-1β) and interleukin-6(IL-6) but not tumor necrosis factor-α (TNF-α) from lipopolysaccharide (LPS)-stimulated RAW 264.7 cells, but the OHFE did not decrease cytokine expression. These results suggest that OFFE exhibits strong antioxidant activity and anti-inflammatory effects and can be developed as a potential therapeutic candidate for diseases involving oxidative stress and inflammation.
Evolutionarily conserved anatomical and physiological properties of olfactory pathway till fourth order neurons in a species of grasshopper(Hieroglyphus banian)
Authors: Singh Shilpi , Joseph Joby 
Published: October 2018

AbstractOlfactory systems of different species show variations in structure and physiology despite some conserved characteristics. We characterized the olfactory circuit of the grasshopperHieroglyphus banianof family Acrididae (subfamily: Hemiacridinae) and compared it to a well-studied species of locust,Schistocerca americana(subfamily: Cyrtacanthacridinae), also belonging to family Acrididae. We used in vivo electrophysiological, immunohistochemical and anatomical (bulk tract tracing) methods to elucidate the olfactory pathway from the second order neurons in antennal lobe to the fourth order neurons in β-lobe ofH. banian.We observe highly conserved anatomical and physiological characteristics till the fourth order neurons in the olfactory circuit ofH. banianandS. americana, though they are evolutionarily divergent (~57 million years ago). However, we found one major difference between the two species-there are four antennal lobe tracts inH. banianwhile only one is reported inS. americana. Besides, we are reporting for the first time, a new class of bilateral neurons which respond weakly to olfactory stimuli even though they innervate densely downstream of Kenyon cells.
The first draft genomes of the antFormica exsecta, and itsWolbachiaendosymbiont reveal extensive gene transfer from endosymbiont to host
Authors: Dhaygude Kishor , Nair Abhilash , Johansson Helena , Wurm Yannick , Sundström Liselotte 
Published: October 2018

AbstractThe wood antFormica exsecta(Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well established model for studies of ecological characteristics and evolutionary conflict. In this study, we sequenced and assembled draft genomes forFormica exsectaand its endosymbiontWolbachia. The draftF. exsectagenome is 277.7 Mb long; we identify 13,767 protein coding genes for which we provide gene ontology, and protein domain annotations. This is also the first report of aWolbachiagenome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) fromWolbachiatoF. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes. We expect that theF. exsectagenome will be valuable resource in further exploration of the molecular basis of the evolution of social organization.
Excitatory-inhibitory windows shape coherent neuronal dynamics driven by optogenetic stimulation in the primate brain
Authors: Shewcraft Ryan A. , Dean Heather L. , Fabiszak Margaret M. , Hagan Maureen A. , Wong Yan T. , Pesaran Bijan 
Published: October 2018

SummaryCoherent neuronal dynamics play an important role in complex cognitive functions. Optogenetic stimulation promises to provide new ways to test the functional significance of coherent neural activity. However, the mechanisms by which optogenetic stimulation drives coherent dynamics remain unclear, especially in the non-human primate brain. Here, we perform computational modeling and experiments to study the mechanisms of optogenetic-stimulation-driven coherent neuronal dynamics in non-human primates. Neural responses arise from stimulation-evoked temporal windows of excitatory and inhibitory activity. The temporal properties of the E-I windows generate coherent neuronal dynamics at varied frequencies and depend on optogenetic stimulation parameters. Experimental results agree with parameter dependent predictions from the computational models. These results demonstrate that responses to optogenetic stimulation are governed by local circuit properties that alter the timing of E-I activity. Transient imbalances in excitatory and inhibitory activity may provide a general mechanism for generating coherent neuronal dynamics.
Differentiating Genomic SNPs Using Allele Depth and Predicted Genotype
Authors: Hasan Saam 
Published: October 2018

AbstractDifferentiating between genomic SNPs and other types of single nucleotide variants becomes a key issue in research aimed at studying the importance of these variants of a particular type in biological processes. Here we present an R based method for differentiating between genomic single nucleotide polymorphisms (SNPs) and RNA editing sites. We use data from an earlier study of ours and target only the known dbsnp SNPs that we found in our study. Our method involves calculating the ratio of allele depth for ref and alt alleles and comparing that to the predicted genotype. We use the concept that editing levels should be different for each allele and thus should not reflect the ratio predicted by the genotype. The study yielded an accuracy rate ranging from 86 to over 90 percent at successfully predicted dbsnp entries as SNPs. Albeit this is in the absence of known RNA editing site vcf data to compare as a reference.
An averaging strategy to reduce variability in target-decoy estimates of false discovery rate
Authors: Keich Uri , Tamura Kaipo , Stafford Noble William 
Published: October 2018

AbstractDecoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed dataset analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, datasets or databases. In such cases, the nominal FDR might be 1% but the true proportion of false discoveries might be 10%. The averaged TDC protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. We provide a tutorial introduction to aTDC, describe an improved variant of the protocol that offers increased statistical power, and discuss how to deploy aTDC in practice using the Crux software toolkit.
Brain responses to anticipating and receiving beer: Comparing light, at-risk, and dependent alcohol users
Authors: Groefsema Martine M. , Engels Rutger C.M.E. , Voon Valerie , Schellekens Arnt F.A. , Luijten Maartje , Sescousse Guillaume 
Published: October 2018

ABSTRACTBackgroundImpaired brain processing of alcohol-related rewards has been suggested to play a central role in alcohol use disorder. Yet, evidence remains inconsistent, and mainly originates from studies in which participants passively observe alcohol cues or taste alcohol. Here we designed a protocol in which beer consumption was predicted by incentive cues and contingent on instrumental action, closer to real life situations. We predicted that anticipating and receiving beer (compared with water) would elicit activity in the brain reward network, and that this activity would correlate with drinking level across participants.MethodsThe sample consisted of 150 beer-drinking males, aged 18-25 years. Three groups were defined based on AUDIT scores: light drinkers (n=40), at-risk drinkers (n=63), and dependent drinkers (n=47). fMRI measures were obtained while participants engaged in the Beer Incentive Delay task involving beer- and water-predicting cues, followed by real sips of beer or water.ResultsDuring anticipation, outcome notification and delivery of beer compared with water, higher activity was found in a reward-related brain network including the medial prefrontal cortex, orbitofrontal cortex and amygdala. Yet, no activity was observed in the striatum, and no differences were found between the groups.ConclusionsOur results reveal that anticipating, obtaining and tasting beer activates parts of the brain reward network, but that these brain responses do not differentiate between different drinking levels. We speculate that other factors, such as cognitive control or sensitivity to social context, may be more discriminant predictors of drinking behaviour in young adults.
Sample-based regulatory intervention for managing risk within heterogeneous populations, with phytosanitary inspection of mixed consignments as a case study
Authors: Lane Stephen E. , Cannon Rob M. , Arthur Anthony D. , Robinson Andrew P. 
Published: October 2018

AbstractInspection of consignments of imported goods is commonly undertaken at national borders in order to prevent incursions of pests and diseases and deter malefactors. Inspection of the whole consignment is usually either impossible or inefficient, so inspection of a random sample is used instead.The size of the random sample for plant products is justified by appeal to International Standards for Phytosanitary Measures No. 31, “Methodologies for Sampling of Consignments”. ISPM 31 notes that “A lot to be sampled should be a number of units of a single commodity identifiable by its homogeneity […]” and “Treating multiple commodities as a single lot for convenience may mean that statistical inferences can not be drawn from the results of the sampling.”However, commonly consignments are heterogeneous, either because the same commodities have multiple sources or because there are several different commodities. The ISPM 31 prescription creates a substantial impost on border inspection because it suggests that heterogeneous populations must be split into homogeneous sub-populations from which separate samples of nominal size must be taken.We demonstrate that if consignments with known heterogeneity are treated as stratified populations and the random sample of units is allocated proportionally based on the number of units in each stratum, then the nominal sensitivity at the consignment level is achieved if our concern is the level of contamination in the entire consignment taken as a whole. We argue that unknown heterogeneity is no impediment to appropriate statistical inference. We conclude that the international standard is unnecessarily restrictive.
Diffusion Tensor Model links to Neurite Orientation Dispersion and Density Imaging at high b-value in Cerebral Cortical Gray Matter
Authors: Fukutomi Hikaru , Glasser Matthew F. , Murata Katsutoshi , Akasaka Thai , Fujimoto Koji , Yamamoto Takayuki , Autio Joonas A. , Okada Tomohisa , Togashi Kaori , Zhang Hui , Van Essen David C. , Hayashi Takuya 
Published: October 2018

AbstractDiffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) are widely used models to infer microstructural features in the brain from diffusion-weighted MRI. Several studies have recently applied both models to increase sensitivity to biological changes, however, it remains uncertain how these measures are associated. Here we show that cortical distributions of DTI and NODDI are associated depending on the choice of b-value, a factor reflecting strength of diffusion weighting gradient. We analyzed a combination of high, intermediate and low b-value data of multi-shell diffusion-weighted MRI (dMRI) in healthy 456 subjects of the Human Connectome Project using NODDI, DTI and a mathematical conversion from DTI to NODDI. Cortical distributions of DTI and DTI-derived NODDI metrics were remarkably associated with those in NODDI, particularly when applied highly diffusion-weighted data (b-value =3000 sec/mm2). This was supported by simulation analysis, which revealed that DTI-derived parameters with lower b-value datasets suffered from errors due to heterogeneity of cerebrospinal fluid fraction and partial volume. These findings suggest that high b-value DTI redundantly parallels with NODDI-based cortical neurite measures, but the conventional low b-value DTI does not reasonably characterize cortical microarchitecture.
Defoliation estimation of forest trees from ground-level images
Authors: Kälin Ursula , Lang Nico , Hug Christian , Gessler Arthur , Wegner Jan Dirk 
Published: October 2018

AbstractIn this paper, we propose to estimate tree defoliation from ground-level RGB photos with convolutional neural networks (CNN). Tree defoliation is usually assessed with field campaigns, where experts estimate multiple tree health indicators per sample site. Campaigns span entire countries to come up with a holistic, nation-wide picture of forest health. Surveys are very laborious, expensive, time-consuming and need a large number of experts. We aim at making the monitoring process more efficient by casting tree defoliation estimation as an image interpretation problem. What makes this task challenging is strong variance in lighting, viewpoint, scale, tree species, and defoliation types. Instead of accounting for each factor separately through explicit modelling, we learn a joint distribution directly from a large set of annotated training images following the end-to-end learning paradigm of deep learning. The proposed workflow works as follows: (i) Human experts visit individual trees in forests distributed all over Switzerland, (ii) acquire one photo per tree with an off-the-shelf, hand-held RGB camera and (iii) assign a defoliation value. The CNN approach is (iv) trained on a subset of the images with expert defoliation assessments and (v) tested on a hold-out part to check predicted values against ground truth. We evaluate our supervised method on three data sets with different level of difficulty acquired in Swiss forests and achieve an average mean absolute error (avgMAE) of 7.6% for the joint data set after cross-validation. Comparison to a group of human experts on one of the data sets shows that our CNN approach performs only 0.9 percent points worse. We show that tree defoliation estimation from ground-level RGB images with a CNN works well and achieves performance close to human experts.
A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)
Authors: Louro Bruno , De Moro Gianluca , Garcia Carlos , Cox Cymon J. , Veríssimo Ana , Sabatino Stephen J. , Santos António M. , Canário Adelino V. M. 
Published: October 2018

AbstractBackgroundThe European sardine (Sardina pilchardus Walbaum, 1792) has a high cultural and economic importance throughout its distribution. Monitoring studies of sardine populations report an alarming decrease in stocks due to overfishing and environmental change, which has resulted in historically low captures along the Iberian Atlantic coast. Consequently, there is an urgent need to better understand the causal factors of this continuing decrease in the sardine stock. Important biological and ecological features such as levels of population diversity, structure, and migratory patterns can be addressed with the development and use of genomics resources.FindingsThe sardine genome of a single female individual was sequenced using Illumina HiSeq X Ten 10X Genomics linked-reads generating 113.8 Gb of data. Three draft genomes were assembled: two haploid genomes with a total size of 935 Mbp (N50 103Kb) each, and a consensus genome with a total size of 950 Mbp (N50 97Kb). The genome completeness assessment captured 84% of Actinopterygii Benchmarking Universal Single-Copy Orthologs. To obtain a more complete analysis, the transcriptomes of eleven tissues were sequenced and used to aid the functional annotation of the genome, resulting in 40 777 genes predicted. Variant calling on nearly half of the haplotype genome resulted in the identification of more than 2.3 million phased SNPs with heterozygous loci.ConclusionsA draft genome was obtained with the 10X Genomics linked-reads technology, despite a high level of sequence repeats and heterozygosity that are expected genome characteristics of a wild sardine. The reference sardine genome and respective variant data are a cornerstone resource of ongoing population genomics studies to be integrated into future sardine stock assessment modelling to better manage this valuable resource.
Increased Epstein-Barr virus C-promoter activity with CTCF-binding site deletion is associated with elevated EBNA2 recruitment
Authors: Groves Ian J , Allday Martin J 
Published: October 2018

AbstractThe regulation of transcription from Epstein-Barr virus promoters is known to involve the association of the host CCCTC-binding factor (CTCF) protein. This control involves direct binding of CTCF across the EBV genome and the formation of three-dimensional loops between virus promoters and enhancers. We sought to address how the deletion of a CTCF binding site upstream of the C-promoter (Cp) affected viral transcription in infected lymphoblastoid cell lines (LCLs) and how binding of the EBV trans-activating protein EBNA2 was changed across this promoter. Transcript level from Cp was up-regulated with CTCF binding site deletion, and transcription from other promoters (Wp and Qp) was decreased, while transcript levels were largely unchanged by independent mutation of a Cp-RBPJκ binding site. In turn, expression of EBNA2 protein was also increased, likely driven by increases in polycistronic EBNA2-encoding transcripts. Finally, Cp up-regulation was associated with an 8-fold increase in EBNA2 enrichment across Cp, concomitant with increased association of the associated cellular factor RBPJκ, probably due to a more accessible three-dimensional chromatin conformation upstream of Cp. Overall, the data presented here confirm that binding of CTCF directly upstream of Cp is important for the regulation of transcription from this and other EBV promoters.
High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
Authors: Johnston Michael J , Nikolic Ana , Ninkovic Nicoletta , Guilhamon Paul , Cavalli Florence MG , Seaman Steven , Zemp Franz J , Lee John , Abdelkareem Aly , Ellestad Katrina , Murison Alex , Kushida Michelle M , Coutinho Fiona J , Ma Yussanne , Mungall Andrew J , Moore Richard , Marra Marco A , Taylor Michael D , Dirks Peter B , Pugh Trevor J , Morrissy Sorana , Croix Bradley St , Mahoney Douglas J , Lupien Mathieu , Gallo Marco 
Published: October 2018

SUMMARYWe investigated the role of 3D genome architecture in instructing functional properties of glioblastoma stem cells (GSCs) by generating the highest-resolution 3D genome maps to-date for this cancer. Integration of DNA contact maps with chromatin and transcriptional profiles identified specific mechanisms of gene regulation, including individual physical interactions between regulatory regions and their target genes. Residing in structurally conserved regions in GSCs was CD276, a gene known to play a role in immuno-modulation. We show that, unexpectedly, CD276 is part of a stemness network in GSCs and can be targeted with an antibody-drug conjugate to curb self-renewal, a key stemness property. Our results demonstrate that integrated structural genomics datasets can be employed to rationally identify therapeutic vulnerabilities in self-renewing cells.SIGNIFICANCEIn adult GBM, GSCs act as therapy-resistant reservoirs to nucleate tumor recurrence. New therapeutic approaches that target these cell populations hold the potential of significantly improving patient care and overall prognosis for this always-lethal cancer. Our work describes new links between 3D genome architecture and stemness properties in GSCs. In particular, through integration of multiple genomics and structural genomics datasets, we found an unexpected connection between immune-related genes and self-renewal programs in GBM. Among these, we show that targeting CD276 with knockdown strategies or specific antibody-drug conjugates achieve suppression of self-renewal. Strategies to target CD276+ cells are currently in clinical trials for solid tumors. Our results indicate that CD276-targeting agents could be deployed in GBM to specifically target GSC populations.HIGHLIGHTSWe generated high (sub-5 kb) resolution Hi-C maps for stem-like cells from GBM patients.Integration of Hi-C and genomics datasets dissects mechanisms of gene regulation.3D genomes poise immune-related genes, including CD276, for expression.Targeting CD276 curbs self-renewal properties of GBM cells.