bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing complex geophysical geometries with chattering dust
Authors: Pyrak-Nolte Laura J. , Braverman William , Nolte Nicholas J. , Wright Alan J. , Nolte David D. 
Published: October 2020

AbstractThe modern energy economy and environmental infrastructure rely on the flow of fluids through fractures in rock. Yet this flow cannot be imaged directly because rocks are opaque to most probes. Here we apply chattering dust, or chemically reactive grains of sucrose containing pockets of pressurized carbon dioxide, to study rock fractures. As a dust grain dissolves, the pockets burst and emit acoustic signals that are detected by distributed sets of external ultrasonic sensors that track the dust movement through fracture systems. The dust particles travel through locally varying fracture apertures with varying speeds and provide information about internal fracture geometry, flow paths and bottlenecks. Chattering dust particles have an advantage over chemical sensors because they do not need to be collected, and over passive tracers because the chattering dust delineates the transport path. The current laboratory work has potential to scale up to near-borehole applications in the field.
Epigenetic regulation of gene expression improves Fusarium head blight resistance in durum wheat
Authors: Kumar Jitendra , Rai Krishan M. , Pirseyedi Seyedmostafa , Elias Elias M. , Xu Steven , Dill-Macky Ruth , Kianian Shahryar F. 
Published: October 2020

AbstractEight advanced durum-breeding lines were treated with 5-methyl-azacytidine to test the feasibility of generating sources of Fusarium head blight (FHB) resistance. Of the 800 treated seeds, 415 germinated and were advanced up to four (M4) generations by selfing. Thirty-two of the resulting 415 M4 lines were selected following preliminary screening and were further tested for FHB resistance for three years at two field locations, and in the greenhouse. Five of the 32 M4 lines showed less than 30% disease severity, as compared to the parental lines and susceptible checks. Fusarium-damaged kernels and deoxynivalenol analyses supported the findings of the field and greenhouse disease assessments. Two of the most resistant M4 lines were crossed to a susceptible parent, advanced to third generation (BC1:F3) and were tested for stability and inheritance of the resistance. About, one third of the BC1:F3 lines showed FHB resistance similar to their M4 parents. The overall methylation levels (%) were compared using FASTmC method, which did not show a significant difference between M4 and parental lines. However, transcriptome analysis of one M4 line revealed significant number of differentially expressed genes related to biosynthesis of secondary metabolites, MAPK signaling, photosynthesis, starch and sucrose metabolism, plant hormone signal transduction and plant-pathogen interaction pathways, which may have helped in improved FHB resistance.
A general theory of far-field optical microscopy image formation and resolution limit using double-sided Feynman diagrams
Authors: Fukutake Naoki 
Published: October 2020

AbstractOptical resolution of far-field optical microscopy is limited by the diffraction of light, while diverse light-matter interactions are used to push the limit. The image resolution limit depends on the type of optical microscopy; however, the current theoretical frameworks provide oversimplified pictures of image formation and resolution that only address individual types of microscopy and light-matter interactions. To compare the fundamental optical resolutions of all types of microscopy and to codify a unified image-formation theory, a new method that describes the influence of light-matter interactions on the resolution limit is required. Here, we develop an intuitive technique using double-sided Feynman diagrams that depict light-matter interactions to provide a bird’s-eye view of microscopy classification. This diagrammatic methodology also allows for the optical resolution calculation of all types of microscopy. We show a guidepost for understanding the potential resolution and limitation of all optical microscopy. This principle opens the door to study unexplored theoretical questions and lead to new applications.
Evolutionary analysis of the Moringa oleifera genome reveals a recent burst of plastid to nucleus gene duplications
Authors: Ojeda-López José , Marczuk-Rojas Juan Pablo , Polushkina Oliver Aleksandrei , Purucker Darius , Salinas María , Carretero-Paulet Lorenzo 
Published: October 2020

AbstractIt is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population. The genome of Moringa oleifera, a fast-growing drought-tolerant orphan crop with highly valuable agronomical, nutritional and pharmaceutical properties, has recently been reported. We model here gene family evolution in Moringa as compared with ten other flowering plant species. Despite the reduced number of genes in the compact Moringa genome, 101 gene families, grouping 957 genes, were found as significantly expanded. Expanded families were highly enriched for chloroplastidic and photosynthetic functions. Indeed, almost half of the genes belonging to Moringa expanded families grouped with their Arabidopsis thaliana plastid encoded orthologs. Microsynteny analysis together with modeling the distribution of synonymous substitutions rates, supported most plastid duplicated genes originated recently through a burst of simultaneous insertions of large regions of plastid DNA into the nuclear genome. These, together with abundant short insertions of plastid DNA, contributed to the occurrence of massive amounts of plastid DNA in the Moringa nuclear genome, representing 4.71%, the largest reported so far. Our study provides key genetic resources for future breeding programs and highlights the potential of plastid DNA to impact the structure and function of nuclear genes and genomes.
Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors
Authors: Kim Jieun , Cho Youna , Seo Mi-Ran , Bae Mi Hyun , Kim Bongyoung , Rho Mina , Pai Hyunjoo 
Published: October 2020

AbstractObjective was to analyse bacterial composition and abundance of Clostridioides difficile in gut microbiome of patients with C. difficile infection (CDI) in association with clinical characteristics. Whole metagenome sequencing of gut microbiome of 26 CDI patients was performed, and the relative abundance of C. difficile and its toxin genes was measured. Clinical characteristics of the patients were obtained through medical records. A strong correlation between the abundance of C. difficile and tcdB genes in CDI patients was found. The relative abundance of C. difficile in the gut microbiome ranged from undetectable to 2.8% (median 0.089). Patients with fever exhibited low abundance of C. difficile in their gut, and patients with fewer C. difficile organisms required long-term anti-CDI treatment. Abundance of Bifidobacterium and Bacteroides negatively correlated with that of C. difficile at the genus level. CDI patients were clustered using the bacterial composition of the gut: one with high population of Enterococcus (cluster 1, n = 12) and another of Bacteroides or Lactobacillus (cluster 2, n = 14). Cluster1 showed significantly lower bacterial diversity and clinical cure at the end of treatment. Additionally, patients with CDI exhibited increased ARGs; notably, blaTEM, blaSHV and blaCTX-M were enriched. C. difficile existed in variable proportion of the gut microbiome in CDI patients. CDI patients with Enterococcus-rich microbiome in the gut had lower bacterial diversity and poorer clinical cure.
A multilevel analysis of financial institutions’ systemic exposure from local and system-wide information
Authors: Gandica Yérali , Béreau Sophie , Gnabo Jean-Yves 
Published: October 2020

AbstractIn the aftermath of the financial crisis of 2007–2009, the growing body of literature on financial networks has widely documented the predictive power of topological characteristics (e.g., degree centrality measures) to explain the systemic impact or systemic exposure of financial institutions. This study shows that considering alternative topological measures based on local sub-network environment improves our ability to identify systemic institutions. To provide empirical evidence, we apply a two-step procedure. First, we recover network communities (i.e., close-peer environment) on a spillover network of financial institutions. Second, we regress alternative measures of vulnerability (i.e. firm’s losses)on three levels of topological measures: the global level (i.e., firm topological characteristics computed over the whole system), local level (i.e., firm topological characteristics computed over the community to which it belongs), and aggregated level by averaging individual characteristics over the community. The sample includes 46 financial institutions (banks, broker-dealers, and insurance and real-estate companies) listed in the Standard & Poor’s 500 index. Our results confirm the informational content of topological metrics based on a close-peer environment. Such information is different from that embedded in traditional system-wide topological metrics and can help predict distress of financial institutions in times of crisis.
Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples
Authors: Newton Yulia , Sedgewick Andrew J. , Cisneros Luis , Golovato Justin , Johnson Mark , Szeto Christopher W. , Rabizadeh Shahrooz , Sanborn J. Zachary , Benz Stephen Charles , Vaske Charles 
Published: October 2020

AbstractTranscriptome profiling can provide information of great value in clinical decision-making, yet RNA from readily available formalin-fixed paraffin-embedded (FFPE) tissue is often too degraded for quality sequencing. To assess the clinical utility of FFPE-derived RNA, we performed ribo-deplete RNA extractions on > 3200 FFPE slide samples; 25 of these had direct FFPE vs. fresh frozen (FF) replicates, 57 were sequenced in 2 different labs, 87 underwent multiple library analyses, and 16 had direct microdissected vs. macrodissected replicates. Poly-A versus ribo-depletion RNA extraction methods were compared using transcriptomes of TCGA cohort and 3116 FFPE samples. Compared to FF, FFPE transcripts coding for nuclear/cytoplasmic proteins involved in DNA packaging, replication, and protein synthesis were detected at lower rates and zinc finger family transcripts were of poorer quality. The greatest difference in extraction methods was in histone transcripts which typically lack poly-A tails. Encouragingly, the overall sequencing success rate was 81%. Exome coverage was highly concordant in direct FFPE and FF replicates, with 98% agreement in coding exon coverage and a median correlation of whole transcriptome profiles of 0.95. We provide strong rationale for clinical use of FFPE-derived RNA based on the robustness, reproducibility, and consistency of whole transcriptome profiling.
Forebrain delta opioid receptors regulate the response of delta agonist in models of migraine and opioid-induced hyperalgesia
Authors: Dripps Isaac J. , Bertels Zachariah , Moye Laura S. , Tipton Alycia F. , Siegersma Kendra , Baca Serapio M. , Kieffer Brigitte L. , Pradhan Amynah A. 
Published: October 2020

AbstractDelta opioid receptor (DOR) agonists have been identified as a promising novel therapy for headache disorders. DORs are broadly expressed in several peripheral and central regions important for pain processing and mood regulation; and it is unclear which receptors regulate headache associated symptoms. In a model of chronic migraine-associated pain using the human migraine trigger, nitroglycerin, we observed increased expression of DOR in cortex, hippocampus, and striatum; suggesting a role for these forebrain regions in the regulation of migraine. To test this hypothesis, we used conditional knockout mice with DORs deleted from forebrain GABAergic neurons (Dlx-DOR), and investigated the outcome of this knockout on the effectiveness of the DOR agonist SNC80 in multiple headache models. In DOR loxP controls SNC80 blocked the development of acute and chronic cephalic allodynia in the chronic nitroglycerin model, an effect that was lost in Dlx-DOR mice. In addition, the anti-allodynic effects of SNC80 were lost in a model of opioid induced hyperalgesia/medication overuse headache in Dlx-DOR conditional knockouts. In a model reflecting negative affect associated with migraine, SNC80 was only effective in loxP controls and not Dlx-DOR mice. Similarly, SNC80 was ineffective in the cortical spreading depression model of migraine aura in conditional knockout mice. Taken together, these data indicate that forebrain DORs are necessary for the action of DOR agonists in relieving headache-related symptoms and suggest that forebrain regions may play an important role in migraine modulation.
Association of advanced glycation end products with sarcopenia and frailty in chronic kidney disease
Authors: Yabuuchi Junko , Ueda Seiji , Yamagishi Sho-ichi , Nohara Nao , Nagasawa Hajime , Wakabayashi Keiichi , Matsui Takanori , Yuichiro Higashimoto , Kadoguchi Tomoyasu , Otsuka Tomoyuki , Gohda Tomohito , Suzuki Yusuke 
Published: October 2020

AbstractPrevalence of sarcopenia is high in patients with chronic kidney disease (CKD), especially in those with dialysis. Various pathological conditions related to CKD, such as chronic inflammation, insulin resistance, and endothelial dysfunction, are thought to be associated with the development and progression of sarcopenia. Advanced glycation end products (AGE), one of the representative uremic toxins, have been shown to contribute to various CKD-associated complications. This study investigated the role of AGE in frailty and sarcopenia in patients and animals with CKD, respectively. In patients undergoing dialysis, serum AGE levels were significantly increased according to the frailty status and inversely associated with physical performance and activity. AGE accumulated in the gastrocnemius muscle of 5/6 nephrectomy mice in association with morphological abnormalities, capillary rarefaction, and mitochondrial dysfunction, all of which were completely inhibited by DNA-aptamer raised against AGE. Our present findings may suggest the pathological role of AGE in sarcopenia and frailty in CKD.
Defective liver glycogen autophagy related to hyperinsulinemia in intrauterine growth-restricted newborn wistar rats
Authors: de Toro-Martín Juan , Fernández-Marcelo Tamara , González-Rodríguez Águeda , Escrivá Fernando , Valverde Ángela M. , Álvarez Carmen , Fernández-Millán Elisa 
Published: October 2020

AbstractMaternal malnutrition plays a critical role in the developmental programming of later metabolic diseases susceptibility in the offspring, such as obesity and type 2 diabetes. Because the liver is the major organ that produces and supplies blood glucose, we aimed at defining the potential role of liver glycogen autophagy in the programming of glucose metabolism disturbances. To this end, newborns were obtained from pregnant Wistar rats fed ad libitum with a standard diet or 65% food-restricted during the last week of gestation. We found that newborns from undernourished mothers showed markedly high basal insulin levels whereas those of glucagon were decreased. This unbalance led to activation of the mTORC1 pathway and inhibition of hepatic autophagy compromising the adequate handling of glycogen in the very early hours of extrauterine life. Restoration of autophagy with rapamycin but not with glucagon, indicated no defect in autophagy machinery per se, but in signals triggered by glucagon. Taken together, these results support the notion that hyperinsulinemia is an important mechanism by which mobilization of liver glycogen by autophagy is defective in food-restricted animals. This early alteration in the hormonal control of liver glycogen autophagy may influence the risk of developing metabolic diseases later in life.
Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method
Authors: Lucchetta Marta , Pellegrini Marco 
Published: October 2020

AbstractGenes are organized in functional modules (or pathways), thus their action and their dysregulation in diseases may be better understood by the identification of the modules most affected by the disease (aka disease modules, or active subnetworks). We describe how an algorithm based on the Core&Peel method is used to detect disease modules in co-expression networks of genes. We first validate Core&Peel for the general task of functional module detection by comparison with 42 methods participating in the Disease Module Identification DREAM challenge. Next, we use four specific disease test cases (colorectal cancer, prostate cancer, asthma, and rheumatoid arthritis), four state-of-the-art algorithms (ModuleDiscoverer, Degas, KeyPathwayMiner, and ClustEx), and several pathway databases to validate the proposed algorithm. Core&Peel is the only method able to find significant associations of the predicted disease module with known validated relevant pathways for all four diseases. Moreover, for the two cancer datasets, Core&Peel detects further eight relevant pathways not discovered by the other methods used in the comparative analysis. Finally, we apply Core&Peel and other methods to explore the transcriptional response of human cells to SARS-CoV-2 infection, finding supporting evidence for drug repositioning efforts at a pre-clinical level.
Establishment of fast-growing serum-free immortalised cells from Chinese hamster lung tissues for biopharmaceutical production
Authors: Yamano-Adachi Noriko , Arishima Rintaro , Puriwat Sukwattananipaat , Omasa Takeshi 
Published: October 2020

AbstractChinese hamster (Cricetulus griseus) ovary-derived Chinese hamster ovary (CHO) cells are the most commonly used mammalian hosts for the industrial production of recombinant therapeutics because of their ability to fold, assemble, and perform post-translational modifications, such as glycosylation, on proteins. They are also valuable for their ability to grow in serum-free suspension cultures. In this study, we established a cell line derived from lung tissue of Chinese hamsters, named Chinese hamster lung (CHL)-YN cells. The biosafety of CHL-YN cells was confirmed by in vitro sterility testing, mycoplasma detection, and reverse transcriptase assays. One of the key characteristics of CHL-YN cells was their doubling time of 8.1 h in chemically defined culture medium; thus, they proliferate much faster than conventional CHO cells and general mammalian cells. Transgenes could be introduced into CHL-YN cells with high efficiency. Finally, between 50% to > 100% of the amount of glycosylated immunoglobulin G (IgG)1 produced by CHO-K1 cells was produced by CHL-YN cells over a shorter period of time. In summary, fast-growing CHL-YN cells are a unique cell line for producing recombinant proteins.
Altered amygdala-based functional connectivity in individuals with attenuated psychosis syndrome and first-episode schizophrenia
Authors: Kim Woo-Sung , Shen Guangfan , Liu Congcong , Kang Nam-In , Lee Keon-Hak , Sui Jing , Chung Young-Chul 
Published: October 2020

AbstractAltered resting-state functional connectivity (FC) of the amygdala (AMY) has been demonstrated to be implicated in schizophrenia (SZ) and attenuated psychosis syndrome (APS). Specifically, no prior work has investigated FC in individuals with APS using subregions of the AMY as seed regions of interest. The present study examined AMY subregion-based FC in individuals with APS and first-episode schizophrenia (FES) and healthy controls (HCs). The resting state FC maps of the three AMY subregions were computed and compared across the three groups. Correlation analysis was also performed to examine the relationship between the Z-values of regions showing significant group differences and symptom rating scores. Individuals with APS showed hyperconnectivity between the right centromedial AMY (CMA) and left frontal pole cortex (FPC) and between the laterobasal AMY and brain stem and right inferior lateral occipital cortex compared to HCs. Patients with FES showed hyperconnectivity between the right superficial AMY and left occipital pole cortex and between the left CMA and left thalamus compared to the APS and HCs respectively. A negative relationship was observed between the connectivity strength of the CMA with the FPC and negative-others score of the Brief Core Schema Scales in the APS group. We observed different altered FC with subregions of the AMY in individuals with APS and FES compared to HCs. These results shed light on the pathogenetic mechanisms underpinning the development of APS and SZ.
Impact of heat generation/absorption of magnetohydrodynamics Oldroyd-B fluid impinging on an inclined stretching sheet with radiation
Authors: Mabood Fazle , Bognár Gabriella , Shafiq Anum 
Published: October 2020

AbstractIn this paper, we have investigated thermally stratified MHD flow of an Oldroyd-B fluid over an inclined stretching surface in the presence of heat generation/absorption. Similarity solutions for the transformed governing equations are obtained. The reduced equations are solved numerically using the Runge–Kutta Fehlberg method with shooting technique. The influences of various involved parameters on velocity profiles, temperature profiles, local skin friction, and local Nusselt number are discussed. Numerical values of local skin friction and local Nusselt number are computed. The significant outcomes of the study are that the velocity decreases when the radiation parameter $$R_{d}$$

R
d

is increased while the temperature profile is increased for higher values of radiation parameter $$R_{d}$$

R
d

in case of opposing flow, moreover, growth in Deborah number $$\beta_{2}$$

β
2

enhance the velocity and momentum boundary layer. The heat transfer rate is decrease due to magnetic strength but increase with the increased values of Prandtl and Deborah numbers. The results of this model are closely matched with the outputs available in the literature.
EEG microstate complexity for aiding early diagnosis of Alzheimer’s disease
Authors: Tait Luke , Tamagnini Francesco , Stothart George , Barvas Edoardo , Monaldini Chiara , Frusciante Roberto , Volpini Mirco , Guttmann Susanna , Coulthard Elizabeth , Brown Jon T. , Kazanina Nina , Goodfellow Marc 
Published: October 2020

AbstractThe dynamics of the resting brain exhibit transitions between a small number of discrete networks, each remaining stable for tens to hundreds of milliseconds. These functional microstates are thought to be the building blocks of spontaneous consciousness. The electroencephalogram (EEG) is a useful tool for imaging microstates, and EEG microstate analysis can potentially give insight into altered brain dynamics underpinning cognitive impairment in disorders such as Alzheimer’s disease (AD). Since EEG is non-invasive and relatively inexpensive, EEG microstates have the potential to be useful clinical tools for aiding early diagnosis of AD. In this study, EEG was collected from two independent cohorts of probable AD and cognitively healthy control participants, and a cohort of mild cognitive impairment (MCI) patients with four-year clinical follow-up. The microstate associated with the frontoparietal working-memory/attention network was altered in AD due to parietal inactivation. Using a novel measure of complexity, we found microstate transitioning was slower and less complex in AD. When combined with a spectral EEG measure, microstate complexity could classify AD with sensitivity and specificity > 80%, which was tested on an independent cohort, and could predict progression from MCI to AD in a small preliminary test cohort of 11 participants. EEG microstates therefore have potential to be a non-invasive functional biomarker of AD.