bluuebunny/crossref_metadata_2025_split huggingface dataset:
The integrative knowledge base for miRNA-mRNA expression in colorectal cancer
Authors: Jevšinek Skok Daša , Hauptman Nina , Boštjančič Emanuela , Zidar Nina 
Published: December 2019

Abstract“miRNA colorectal cancer” (https://mirna-coadread.omics.si/) is a freely available web application for studying microRNA and mRNA expression and their correlation in colorectal cancer. To the best of our knowledge, “miRNA colorectal cancer” has the largest knowledge base of miRNA-target gene expressions and correlations in colorectal cancer, based on the largest available sample size from the same source of data. Data from high-throughput molecular profiling of 295 colon and rectum adenocarcinoma samples from The Cancer Genome Atlas was analyzed and integrated into our knowledge base. The objective of developing this web application was to help researchers to discover the behavior and role of miRNA-target gene interactions in colorectal cancer. For this purpose, results of differential expression and correlation analyses of miRNA and mRNA data collected in our knowledge base are available through web forms. To validate our knowledge base experimentally, we selected genesFN1,TGFB2,RND3,ZEB1andZEB2and miRNAshsa-miR-200a/b/c-3p,hsa-miR-141-3pandhsa-miR-429. Both approaches revealed a negative correlation between miRNAhsa-miR-200b/c-3pand its target geneFN1and betweenhsa-miR-200a-3pand its targetTGFB2, thus supporting the usefulness of the developed knowledge base.
Crude Oil Sensing using Carbon Nano Structures Synthetized from Phoenix Dactylifera L. Cellulose
Authors: Fethiza Tedjani Chouaib , Ben Mya Omar , Rebiai Abdelkrim , Khachkhouche Abdelhamid , Dehbi Abdelhakim , Méchara Nacer Eddine 
Published: November 2019

AbstractThis study reports on the crude oil-sensing using carbon nano structures (CNSs). A mixture of CNSs was obtained by a simple method of preparation using palm cellulose ash and nitric acid as precursors, the powder was characterized by x-ray diffraction and infrared spectroscopy. The optical density of crude oil from Rhoud El-Baguel area (Southeast of Algeria) studied using UV-Vis spectroscopy, before and after adding an amount of CNSs powder to view the CNSs crude oil sensing and therefore a new method to determine the quality of crude oils and the comparison between them. Results show that CNSs prepared from palm cellulose ash have a good crystallinity and it is formed mainly from carbon nano dots (CNDs) with 4.32 Å in layers spacing and 7.4 Å in crystallite size, indicate that CNSs can be used as an excellent crude oil sensor.
Integrative analysis of the gut microbiota and metabolome in rats treated with rice straw biochar by 16S rRNA gene sequencing and LC/MS-based metabolomics
Authors: Han Jie , Meng Jun , Chen Shuya , Li Chuang 
Published: November 2019

AbstractThe intestinal microbiota contributes to host metabolism and health. This study aimed to assess the effects of biochar on cecal microbiome-related metabolic changes in rats. Rats were orally administered rice straw biochar (RSB) at 1120 mg/kg body weight for 5 weeks. Cecal samples were analyzed to perform metabolic and microbial profiling via a combination of 16S rRNA gene sequencing and LC/MS techniques. We observed a significant influence of RSB in shaping the cecal bacterial community, including some potentially beneficial members of phylum Firmicutes belonging to unclassified Lachnospiraceae, Oscillibacter, and Clostridium XlVa and IV, as well as the depletion of some opportunistic pathogens belonging to Prevotella, Bacteroides and Paraprevotella. The metabolomic analysis revealed distinct changes in the cecal metabolic phenotype, including lower levels of L-isoleucine, indole-3-acetic acid, benzoic acid, and tetradecanoic acid as well as higher levels of L-phenylalanine, L-glutamate, 3-phenylpropanoic acid, chenodeoxycholic acid, cholic acid, 7-dehydrocholesterol, (5Z, 8Z, 11Z, 14Z, 17Z)-eicosapentaenoic acid, 11-deoxycorticosterone and retinol, which are mainly involved in the metabolic pathways of linoleic acid, amino acid and steroid hormone biosynthesis. Correlation analysis revealed a positive association of unclassified Lachnospiraceae, Oscillibacter and Clostridium IV with 3-phenylpropanoic acid, L-phenylalanine, L-glutamate, 11-deoxycorticosterone and 7-dehydrocholesterol. These results confirm that the gut microbiome is altered and may be critical for good performance under RSB application by interacting with metabolism.
Aging, sex and cognitive Theory of Mind: a transcranial direct current stimulation study
Authors: Adenzato Mauro , Manenti Rosa , Gobbi Elena , Enrici Ivan , Rusich Danila , Cotelli Maria 
Published: December 2019

AbstractAging is accompanied by changes in cognitive abilities and a great interest is spreading among researchers about aging impact on social cognition skills, such as the Theory of Mind (ToM). Transcranial direct current stimulation (tDCS) has been used in social cognition studies founding evidence of sex-related different effects on cognitive ToM task in a young people sample. In this randomized, double-blind, sham-controlled study, we applied one active and one sham tDCS session on the medial prefrontal cortex (mPFC) during a cognitive ToM task, including both social (i.e., communicative) and nonsocial (i.e., private) intention attribution conditions, in sixty healthy aging individuals (30 males and 30 females). In half of the participants the anode was positioned over the mPFC, whereas in the other half the cathode was positioned over the mPFC. The results showed that: (i) anodal tDCS over the mPFC led to significant slower reaction times (vs. sham) for social intention attribution task only in female participants; (ii) No effects were found in both females and males during cathodal stimulation. We show for the first time sex-related differences in cognitive ToM abilities in healthy aging, extending previous findings concerning young participants.
Gate-tunable graphene-based Hall sensors on flexible substrates with increased sensitivity
Authors: Uzlu Burkay , Wang Zhenxing , Lukas Sebastian , Otto Martin , Lemme Max C. , Neumaier Daniel 
Published: December 2019

AbstractWe demonstrate a novel concept for operating graphene-based Hall sensors using an alternating current (AC) modulated gate voltage, which provides three important advantages compared to Hall sensors under static operation: (1) The sensor sensitivity can be doubled by utilizing both n- and p-type conductance. (2) A static magnetic field can be read out at frequencies in the kHz range, where the 1/f noise is lower compared to the static case. (3) The off-set voltage in the Hall signal can be reduced. This significantly increases the signal-to-noise ratio compared to Hall sensors without a gate electrode. A minimal detectable magnetic field Bmin down to $$290\,{\rm{nT}}/\surd {\rm{Hz}}$$290nT/√Hz and sensitivity up to 0.55 V/VT was found for Hall sensors working on flexible polyimide (PI) substrates. This clearly outperforms state-of-the-art flexible Hall sensors and is comparable to the values obtained by the best rigid III/V semiconductor Hall sensors.
Predicting the spatial abundance of Ixodes ricinus ticks in southern Scandinavia using environmental and climatic data
Authors: Jung Kjær Lene , Soleng Arnulf , Edgar Kristin Skarsfjord , Lindstedt Heidi Elisabeth H. , Paulsen Katrine Mørk , Andreassen Åshild Kristine , Korslund Lars , Kjelland Vivian , Slettan Audun , Stuen Snorre , Kjellander Petter , Christensson Madeleine , Teräväinen Malin , Baum Andreas , Klitgaard Kirstine , Bødker René 
Published: December 2019

AbstractRecently, focus on tick-borne diseases has increased as ticks and their pathogens have become widespread and represent a health problem in Europe. Understanding the epidemiology of tick-borne infections requires the ability to predict and map tick abundance. We measured Ixodes ricinus abundance at 159 sites in southern Scandinavia from August-September, 2016. We used field data and environmental variables to develop predictive abundance models using machine learning algorithms, and also tested these models on 2017 data. Larva and nymph abundance models had relatively high predictive power (normalized RMSE from 0.65–0.69, R2 from 0.52–0.58) whereas adult tick models performed poorly (normalized RMSE from 0.94–0.96, R2 from 0.04–0.10). Testing the models on 2017 data produced good results with normalized RMSE values from 0.59–1.13 and R2 from 0.18–0.69. The resulting 2016 maps corresponded well with known tick abundance and distribution in Scandinavia. The models were highly influenced by temperature and vegetation, indicating that climate may be an important driver of I. ricinus distribution and abundance in Scandinavia. Despite varying results, the models predicted abundance in 2017 with high accuracy. The models are a first step towards environmentally driven tick abundance models that can assist in determining risk areas and interpreting human incidence data.
Role of the I16-D194 ionic interaction in the trypsin fold
Authors: Stojanovski Bosko M. , Chen Zhiwei , Koester Sarah K. , Pelc Leslie A. , Di Cera Enrico 
Published: December 2019

AbstractActivity in trypsin-like proteases is the result of proteolytic cleavage at R15 followed by an ionic interaction that ensues between the new N terminus of I16 and the side chain of the highly conserved D194. This mechanism of activation, first proposed by Huber and Bode, organizes the oxyanion hole and primary specificity pocket for substrate binding and catalysis. Using the clotting protease thrombin as a relevant model, we unravel contributions of the I16-D194 ionic interaction to Na+ binding, stability of the transition state and the allosteric E*-E equilibrium of the trypsin fold. The I16T mutation abolishes the I16-D194 interaction and compromises the architecture of the oxyanion hole. The D194A mutation also abrogates the I16-D194 interaction but, surprisingly, has no effect on the architecture of the oxyanion hole that remains intact through a new H-bond established between G43 and G193. In both mutants, loss of the I16-D194 ionic interaction compromises Na+ binding, reduces stability of the transition state, collapses the 215–217 segment into the primary specific pocket and abrogates the allosteric E*-E equilibrium in favor of a rigid conformation that binds ligand at the active site according to a simple lock-and-key mechanism. These findings refine the structural role of the I16-D194 ionic interaction in the Huber-Bode mechanism of activation and reveal a functional linkage with the allosteric properties of the trypsin fold like Na+ binding and the E*-E equilibrium.
Upregulation of vitamin D-binding protein is associated with changes in insulin production in pancreatic beta-cells exposed to p,p′-DDT and p,p′-DDE
Authors: Pavlíková Nela , Daniel Petr , Šrámek Jan , Jelínek Michael , Šrámková Veronika , Němcová Vlasta , Balušíková Kamila , Halada Petr , Kovář Jan 
Published: December 2019

AbstractPersistent organochlorine pollutants (POPs) gradually accumulate in the human organism due to their presence in the environment. Some studies have described a correlation between the level of POPs in the human body and the incidence of diabetes, but we know little about the direct effect of POPs on pancreatic beta-cells. We exposed pancreatic beta-cells INS1E to non-lethal concentrations of p,p′-DDT (1,1′-(2,2,2-Trichloroethane-1,1-diyl)bis(4-chlorobenzene)) and p,p′-DDE (1,1′-(2,2-dichloroethene-1,1-diyl)bis(4-chlorobenzene)) for 1 month, and assessed changes in protein expression and the intracellular insulin level. 2-D electrophoresis revealed 6 proteins with changed expression in cells exposed to p,p′-DDT or p,p′-DDE. One of the detected proteins – vitamin D-binding protein (VDBP) – was upregulated in both cells exposed to p,p′-DDT, and cells exposed to p,p′-DDE. Both exposures to pollutants reduced the intracellular level of insulin mRNA, proinsulin, and insulin monomer; p,p′-DDT also slightly reduced the level of hexameric insulin. Overexpression of VDBP caused by the stable transfection of beta-cells with the gene for VDBP decreased both the proinsulin and hexameric insulin level in beta-cells similarly to the reduction detected in cells exposed to p,p′-DDT. Our data suggest that in the cells exposed to p,p′-DDT and p,p′-DDE, the increased VDBP protein level decreased the proinsulin expression in an unknown mechanism.
Acyl ethanolamides in Diabetes and Diabetic Nephropathy: Novel targets from untargeted plasma metabolomic profiles of South Asian Indian men
Authors: Devi Sarita , Nongkhlaw Bajanai , Limesh M. , Pasanna Roshni M. , Thomas Tinku , Kuriyan Rebecca , Kurpad Anura V. , Mukhopadhyay Arpita 
Published: December 2019

AbstractThe pathophysiology of diabetic nephropathy (DN) in type 2 diabetes (T2D) patients is minimally understood. We compared untargeted high-resolution accurate mass (HRAM) orbitrap-based plasma metabolomic profiles of 31 T2D-DN (with estimated glomerular filtration rate ≤80 mL/min/1.73 m2), 29 T2D and 30 normal glucose tolerance (NGT) Indian men. Of the 939 plasma metabolites that were differentially abundant amongst the NGT, T2D and T2D-DN (ANOVA, False Discovery Rate – FDR adjusted p-value < 0.05), 48 were associated with T2D irrespective of the renal function of the subjects. Acyl ethanolamides and acetylcholine were decreased while monoacylglycerols (MAGs) and cortisol were elevated in both T2D and T2D-DN. Sixteen metabolites, including amino acid metabolites Imidazolelactate and N-Acetylornithine, changed significantly between NGT, T2D and T2D-DN. 192 metabolites were specifically dysregulated in T2D-DN (ratio ≥2 or ≤0.5 between T2D-DN and T2D, similar abundance in NGT and T2D). These included increased levels of multiple acylcarnitine and amino acid metabolites. We observed a significant dysregulation of amino acid and fatty acid metabolism in South Asian Indian male T2D-DN subjects. Unique to this study, we report a reduction in acyl ethanolamide levels in both T2D and T2D-DN males. Those with dysregulation in acyl ethanolamides, which are endogenous agonists of GPR119, are likely to exhibit improved glycemic control with GPR119 agonists.
Short-term depression shapes information transmission in a constitutively active GABAergic synapse
Authors: Lavian Hagar , Korngreen Alon 
Published: December 2019

AbstractShort-term depression is a low-pass filter of synaptic information, reducing synaptic information transfer at high presynaptic firing frequencies. Consequently, during elevated presynaptic firing, little information passes to the postsynaptic neuron. However, many neurons fire at relatively high frequencies all the time. Does depression silence their synapses? We tested this apparent contradiction in the indirect pathway of the basal ganglia. Using numerical modeling and whole-cell recordings from single entopeduncular nucleus (EP) neurons in rat brain slices, we investigated how different firing rates of globus pallidus (GP) neurons affect information transmission to the EP. Whole-cell recordings showed significant variability in steady-state depression, which decreased as stimulation frequency increased. Modeling predicted that this variability would translate into different postsynaptic noise levels during constitutive presynaptic activity. Our simulations further predicted that individual GP-EP synapses mediate gain control. However, when we consider the integration of multiple inputs, the broad range of GP firing rates would enable different modes of information transmission. Finally, we predict that changes in dopamine levels can shift the action of GP neurons from rate coding to gain modulation. Our results thus demonstrate how short-term depression shapes information transmission in the basal ganglia in particular and via GABAergic synapses in general.
Imaging of intermittent lipid-receptor interactions reflects changes in live cell membranes upon agonist-receptor binding
Authors: Tornmalm Johan , Piguet Joachim , Chmyrov Volodymyr , Widengren Jerker 
Published: December 2019

AbstractProtein-lipid interactions in cellular membranes modulate central cellular functions, are often transient in character, but occur too intermittently to be readily observable. We introduce transient state imaging (TRAST), combining sensitive fluorescence detection of fluorophore markers with monitoring of their dark triplet state transitions, allowing imaging of such protein-lipid interactions. We first determined the dark state kinetics of the biomembrane fluorophore 7-nitrobenz-2-oxa-1,3-diazole-4-yl (NBD) in lipid vesicles, and how its triplet state is quenched by spin-labels in the same membranes. We then monitored collisional quenching of NBD-lipid derivatives by spin-labelled stearic acids in live cell plasma membranes, and of NBD-lipid derivatives by spin-labelled G-Protein Coupled Receptors (GPCRs). We could then resolve transient interactions between the GPCRs and different lipids, how these interactions changed upon GPCR activation, thereby demonstrating a widely applicable means to image and characterize transient molecular interactions in live cell membranes in general, not within reach via traditional fluorescence readouts.
Incidence and risk factors of acute kidney injury in critically ill patients from a single centre in Brazil: a retrospective cohort analysis
Authors: dos Santos Reginaldo Passoni , Carvalho Ariana Rodrigues da Silva , Peres Luis Alberto Batista 
Published: December 2019

AbstractStudies with a comprehensive analysis of the epidemiology of acute kidney injury (AKI) in intensive care units (ICUs) are still limited in developing countries. The aim of this study is to identify the incidence and risk factors of AKI in critically ill patients from a Brazilian ICU. We performed a retrospective analysis of the records of patients admitted to a single-centre adult ICU in Brazil between 1 January 2011 and 31 December 2016. The KDIGO criteria were used to define AKI. Univariate and multivariate data analyses were carried out. We included 1,500 patients. The incidence of AKI was 40.5%, and the AKI dialysis rate was 13%. The predictors of AKI at ICU admission included hypertension [odds ratio (OR) = 1.44, p 0.017], high serum creatinine concentration [OR = 3.54; p < 0.001], low serum albumin concentration [OR = 1.42, p 0.015], high APACHE II score [OR = 2.10; p < 0.001] and high SAPS 3 [OR = 1.75; p < 0.001]. The incidence of AKI was high, and we identified the predictors of AKI among critically ill Brazilian patients. The results of this study may contribute to the implementation of targeted therapies.
CXCR7 promotes migration and invasion in head and neck squamous cell carcinoma by upregulating TGF-β1/Smad2/3 signaling
Authors: Kim Nayoung , Ryu Hyewon , Kim Solbi , Joo Mina , Jeon Heung Jin , Lee Myung-Won , Song Ik-Chan , Kim Mi-Na , Kim Jin-Man , Lee Hyo Jin 
Published: December 2019

AbstractThe chemokine receptor CXCR7 has been suggested to play important roles in the progression of several types of cancers. However, few studies have investigated the biological roles of CXCR7 in head and neck squamous cell carcinoma (HNSCC). CXCR7 expression and its clinical implications were examined in 103 HNSCC tissues using immunohistochemistry (IHC). The biological roles and mechanisms of CXCR7-mediated signaling pathways were investigated in HNSCC cells through CXCR7 overexpression in vitro and in vivo. High expression of CXCR7 was significantly associated with tumor size (P = 0.007), lymph node metastasis (P = 0.004), and stage (P = 0.020) in HNSCC. Overexpression of CXCR7 in HNSCC cells enhanced cell migration and invasion in vitro and promoted lymph node metastasis in vivo. CXCR7 also induced epithelial–mesenchymal transition through PI3K/AKT. CXCR7 increased secretion of transforming growth factor-β1 (TGF-β1) and promoted EMT through phosphorylated Smad2/3. Taken together, our results provide functional and mechanistic roles of CXCR7 as a master regulator of oncogenic TGF-β1/Smad2/3 signaling in HNSCC, suggesting that CXCR7 might be a therapeutic target for the treatment of HNSCC.
Bridging population genetics and the metacommunity perspective to unravel the biogeographic processes shaping genetic differentiation of Myriophyllum alterniflorum DC.
Authors: García-Girón Jorge , García Pedro , Fernández-Aláez Margarita , Bécares Eloy , Fernández-Aláez Camino 
Published: December 2019

AbstractThe degree to which dispersal limitation interacts with environmental filtering has intrigued metacommunity ecologists and molecular biogeographers since the beginning of both research disciplines. Since genetic methods are superior to coarse proxies of dispersal, understanding how environmental and geographic factors influence population genetic structure is becoming a fundamental issue for population genetics and also one of the most challenging avenues for metacommunity ecology. In this study of the aquatic macrophyte Myriophyllum alterniflorum DC., we explored the spatial genetic variation of eleven populations from the Iberian Plateau by means of microsatellite loci, and examined if the results obtained through genetic methods match modern perspectives of metacommunity theory. To do this, we applied a combination of robust statistical routines including network analysis, causal modelling and multiple matrix regression with randomization. Our findings revealed that macrophyte populations clustered into genetic groups that mirrored their geographic distributions. Importantly, we found a significant correlation between genetic variation and geographic distance at the regional scale. By using effective (genetic) dispersal estimates, our results are broadly in line with recent findings from metacommunity theory and re-emphasize the need to go beyond the historically predominant paradigm of understanding environmental heterogeneity as the main force driving macrophyte diversity patterns.
Standalone smartphone apps for mental health—a systematic review and meta-analysis
Authors: Weisel Kiona K. , Fuhrmann Lukas M. , Berking Matthias , Baumeister Harald , Cuijpers Pim , Ebert David D. 
Published: December 2019

AbstractWhile smartphone usage is ubiquitous, and the app market for smartphone apps targeted at mental health is growing rapidly, the evidence of standalone apps for treating mental health symptoms is still unclear. This meta-analysis investigated the efficacy of standalone smartphone apps for mental health. A comprehensive literature search was conducted in February 2018 on randomized controlled trials investigating the effects of standalone apps for mental health in adults with heightened symptom severity, compared to a control group. A random-effects model was employed. When insufficient comparisons were available, data was presented in a narrative synthesis. Outcomes included assessments of mental health disorder symptom severity specifically targeted at by the app. In total, 5945 records were identified and 165 full-text articles were screened for inclusion by two independent researchers. Nineteen trials with 3681 participants were included in the analysis: depression (k = 6), anxiety (k = 4), substance use (k = 5), self-injurious thoughts and behaviors (k = 4), PTSD (k = 2), and sleep problems (k = 2). Effects on depression (Hedges’ g = 0.33, 95%CI 0.10–0.57, P = 0.005, NNT = 5.43, I2 = 59%) and on smoking behavior (g = 0.39, 95%CI 0.21–0.57, NNT = 4.59, P ≤ 0.001, I2 = 0%) were significant. No significant pooled effects were found for anxiety, suicidal ideation, self-injury, or alcohol use (g = −0.14 to 0.18). Effect sizes for single trials ranged from g = −0.05 to 0.14 for PTSD and g = 0.72 to 0.84 for insomnia. Although some trials showed potential of apps targeting mental health symptoms, using smartphone apps as standalone psychological interventions cannot be recommended based on the current level of evidence.