bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of a novel device for cryoprevention of oral mucositis: a randomized, blinded, multicenter, parallel group, phase 3 trial
Authors: Walladbegi Java , Henriksson Roger , Tavelin Björn , Svanberg Anncarin , Larfors Gunnar , Jädersten Martin , Schjesvold Fredrik , Mahdi Aram , Garming Legert Karin , Peterson Douglas E. , Jontell Mats 
Published: November 2021

AbstractCryoprevention (CP) using ice (IC) is an effective strategy to prevent chemotherapy-induced oral mucositis (OM). However, the use of IC may cause adverse reactions and requires water of safe quality to minimize risk of serious infections. This randomized, blinded, parallel group, phase 3 trial was conducted in five Scandinavian centers. Eligible patients were diagnosed with multiple myeloma or lymphoma, scheduled to receive conditioning with high-dose chemotherapy prior to autologous hematopoietic stem cell transplantation (ASCT). Patients were assigned to cooling with IC or a novel intraoral cooling device (ICD). The primary outcome was the highest OM score during the study period, expressed as peak value on the Oral Mucositis Assessment Scale (OMAS–total). When the entire study population (n = 172) was analyzed for peak OMAS–total, the two cooling methods were equally effective. However, when the lymphoma group was analyzed separately, the ICD significantly reduced the peak OMAS–total score to a greater extent compared to IC (x̄ ± SD; 1.77 ± 1.59 vs. 3.08 ± 1.50; p = 0.047). Combined with existing evidence, the results of the present trial confirm that CP is an effective method to prevent OM. ClinicalTrials.gov. NCT03203733.
Band-based similarity indices for gene expression classification and clustering
Authors: Torrente Aurora 
Published: November 2021

AbstractThe concept of depth induces an ordering from centre outwards in multivariate data. Most depth definitions are unfeasible for dimensions larger than three or four, but the Modified Band Depth (MBD) is a notable exception that has proven to be a valuable tool in the analysis of high-dimensional gene expression data. This depth definition relates the centrality of each individual to its (partial) inclusion in all possible bands formed by elements of the data set. We assess (dis)similarity between pairs of observations by accounting for such bands and constructing binary matrices associated to each pair. From these, contingency tables are calculated and used to derive standard similarity indices. Our approach is computationally efficient and can be applied to bands formed by any number of observations from the data set. We have evaluated the performance of several band-based similarity indices with respect to that of other classical distances in standard classification and clustering tasks in a variety of simulated and real data sets. However, the use of the method is not restricted to these, the extension to other similarity coefficients being straightforward. Our experiments show the benefits of our technique, with some of the selected indices outperforming, among others, the Euclidean distance.
Estimating DNA methylation potential energy landscapes from nanopore sequencing data
Authors: Abante Jordi , Kambhampati Sandeep , Feinberg Andrew P. , Goutsias John 
Published: November 2021

AbstractHigh-throughput third-generation nanopore sequencing devices have enormous potential for simultaneously observing epigenetic modifications in human cells over large regions of the genome. However, signals generated by these devices are subject to considerable noise that can lead to unsatisfactory detection performance and hamper downstream analysis. Here we develop a statistical method, CpelNano, for the quantification and analysis of 5mC methylation landscapes using nanopore data. CpelNano takes into account nanopore noise by means of a hidden Markov model (HMM) in which the true but unknown (“hidden”) methylation state is modeled through an Ising probability distribution that is consistent with methylation means and pairwise correlations, whereas nanopore current signals constitute the observed state. It then estimates the associated methylation potential energy function by employing the expectation-maximization (EM) algorithm and performs differential methylation analysis via permutation-based hypothesis testing. Using simulations and analysis of published data obtained from three human cell lines (GM12878, MCF-10A, and MDA-MB-231), we show that CpelNano can faithfully estimate DNA methylation potential energy landscapes, substantially improving current methods and leading to a powerful tool for the modeling and analysis of epigenetic landscapes using nanopore sequencing data.
Abnormal nodal and global network organization in resting state functional MRI from subjects with the 22q11 deletion syndrome
Authors: Pelgrim Teuntje A. D. , Bossong Matthijs G. , Cuiza Analía , Alliende Luz María , Mena Carlos , Tepper Angeles , Ramirez-Mahaluf Juan Pablo , Iruretagoyena Barbara , Ornstein Claudia , Fritsch Rosemarie , Cruz Juan Pablo , Tejos Cristian , Repetto Gabriela , Crossley Nicolas 
Published: November 2021

AbstractThe 22q11 deletion syndrome is a genetic disorder associated with a high risk of developing psychosis, and is therefore considered a neurodevelopmental model for studying the pathogenesis of schizophrenia. Studies have shown that localized abnormal functional brain connectivity is present in 22q11 deletion syndrome like in schizophrenia. However, it is less clear whether these abnormal cortical interactions lead to global or regional network disorganization as seen in schizophrenia. We analyzed from a graph-theory perspective fMRI data from 40 22q11 deletion syndrome patients and 67 healthy controls, and reconstructed functional networks from 105 brain regions. Between-group differences were examined by evaluating edge-wise strength and graph theoretical metrics of local (weighted degree, nodal efficiency, nodal local efficiency) and global topological properties (modularity, local and global efficiency). Connectivity strength was globally reduced in patients, driven by a large network comprising 147 reduced connections. The 22q11 deletion syndrome network presented with abnormal local topological properties, with decreased local efficiency and reductions in weighted degree particularly in hub nodes. We found evidence for abnormal integration but intact segregation of the 22q11 deletion syndrome network. Results suggest that 22q11 deletion syndrome patients present with similar aberrant local network organization as seen in schizophrenia, and this network configuration might represent a vulnerability factor to psychosis.
Developmental defects and impaired network excitability in a cerebral organoid model of KCNJ11 p.V59M-related neonatal diabetes
Authors: Dalgin Gokhan , Tryba Andrew K. , Cohen Ashley P. , Park Soo-Young , Philipson Louis H. , Greeley Siri Atma W. , Garcia Alfredo J. 
Published: November 2021

AbstractThe gene KCNJ11 encodes Kir6.2 a major subunit of the ATP-sensitive potassium channel (KATP) expressed in both the pancreas and brain. Heterozygous gain of function mutations in KCNJ11 can cause neonatal diabetes mellitus (NDM). In addition, many patients exhibit neurological defects ranging from modest learning disorders to severe cognitive dysfunction and seizures. However, it remains unclear to what extent these neurological deficits are due to direct brain-specific activity of mutant KATP. We have generated cerebral organoids derived from human induced pluripotent stem cells (hiPSCs) possessing the KCNJ11 mutation p.Val59Met (V59M) and from non-pathogenic/normal hiPSCs (i.e., control/WT). Control cerebral organoids developed neural networks that could generate stable synchronized bursting neuronal activity whereas those derived from V59M cerebral organoids showed reduced synchronization. Histocytochemical studies revealed a marked reduction in neurons localized to upper cortical layer-like structures in V59M cerebral organoids suggesting dysfunction in the development of cortical neuronal network. Examination of temporal transcriptional profiles of neural stem cell markers revealed an extended window of SOX2 expression in V59M cerebral organoids. Continuous treatment of V59M cerebral organoids with the KATP blocker tolbutamide partially rescued the neurodevelopmental differences. Our study demonstrates the utility of human cerebral organoids as an investigative platform for studying the effects of KCNJ11 mutations on neurophysiological outcome.
The proximity of a highway increases CO2 respiration in forest soil and decreases the stability of soil organic matter
Authors: Kupka Dawid , Kania Mateusz , Gruba Piotr 
Published: November 2021

AbstractRoadways traverse many forest areas and they often have harmful effects on forest soils, including the modified stability of soil organic matter (SOM). Soil CO2 respiration is an important indicator of SOM biological stability. The aim of this study was to test the hypotheses that a roadway will (1) modify the composition of the cation exchange capacity of adjacent forest soils, and (2) significantly decrease the stability of SOM. Two study sites were established in Scots pine and Silver fir stands, located close to the S7 highway in central Poland, which was opened to traffic in 1984. From each site, samples were taken at 2, 12 and 22 m from the forest edge. Soil CO2 respiration was determined using closed chamber incubation with an alkali trap. We also conducted a comprehensive analysis of soil chemical properties. The stoichiometric ratios of chosen chemical parameters to total carbon (Ct) were calculated. In both sites, we observed increased soil pH and CO2 respiration in the vicinity of the highway, as well as increased ratios of exchangeable calcium (Ca), magnesium (Mg) and sodium (Na) to Ct. In the fir site, the humic and fulvic acids, the dissolved organic carbon (DOC) content and aluminum (Al) to Ct ratio were depleted in close proximity to the highway. We suggest that the combined effect of Ca and Na ions, originating from winter de-icing, caused the depletion of Al and hydrogen (H) in the soil close to the forest edge and, therefore, resulted in lower SOM stability expressed as the decreased DOC and pyrophosphate-extractable carbon content, as well as the release of CO2. We conclude that the changes of SOM stability with distance were the effect of modification of ion-exchange relationships (particularly base cations versus Al3+ with H+) rather than forest stand species or intrinsic SOM properties (like functional groups, the recalcitrance of bindings etc.). Our work supports earlier studies, confirming the significant impact of Al and H on SOM stability.
The role of guanidine hydrochloride in graphitic carbon nitride synthesis
Authors: Smýkalová Aneta , Foniok Kryštof , Cvejn Daniel , Górecki Kamil Maciej , Praus Petr 
Published: November 2021

AbstractGraphitic carbon nitride (CN) was synthesized from guanidine hydrochloride (G), melamine (M) and dicyandiamide (DCDA). The CN materials synthetized from the pure precursors and their mixtures were characterized by common methods, including thermal analysis, and their photocatalytic activities were tested by the degradation of selected organic pollutants, such as amoxicillin, phenol, Rhodamine B (RhB). Remarkable changes in their texture properties in terms of particle sizes, specific surface areas (SSA) and consequently their photocatalytic activity were explained by the role of guanidine hydrochloride in their synthesis. The SSA increased due to the release of NH3 and HCl and its complex reactions with melamine and DCDA forming structure imperfections and disruptions. The photocatalytic activity of the CN materials was found to be dependent on their SSA.
The relationship of smoking to cg05575921 methylation in blood and saliva DNA samples from several studies
Authors: Dawes Kelsey , Andersen Allan , Reimer Rachel , Mills James A. , Hoffman Eric , Long Jeffrey D. , Miller Shelly , Philibert Robert 
Published: November 2021

AbstractNumerous studies have shown that cg05575921 methylation decreases in response to smoking. However, secondary to methodological issues, the magnitude and dose dependency of that response is as of yet unclear. This lack of certainty is a barrier to the use of DNA methylation clinically to assess and monitor smoking status. To better define this relationship, we conducted a joint analysis of methylation sensitive PCR digital (MSdPCR) assessments of cg05575921 methylation in whole blood and/or saliva DNA to smoking using samples from 421 smokers and 423 biochemically confirmed non-smokers from 4 previously published studies. We found that cg05575921 methylation manifested a curvilinear dose dependent decrease in response to increasing cigarette consumption. In whole blood DNA, the Receiver Operating Characteristic (ROC) Area Under the Curve (AUC) of cg05575921 methylation for predicting daily smoking status was 0.98. In saliva DNA, the gross AUC was 0.91 with correction for cellular heterogeneity improving the AUC to 0.94. Methylation status was significantly associated with the Fagerstrom Test for Nicotine Dependence score, but with significant sampling heterogeneity. We conclude that MSdPCR assessments of cg05575921 methylation are a potentially powerful, clinically implementable tool for the assessment and management of smoking.
Classifying migraine subtypes and their characteristics by latent class analysis using data of a nation-wide population-based study
Authors: Lee Wonwoo , Min In Kyung , Yang Kwang Ik , Kim Daeyoung , Yun Chang-Ho , Chu Min Kyung 
Published: November 2021

AbstractMigraine neither presents with a definitive single symptom nor has a distinct biomarker; thus, its diagnosis is based on combinations of typical symptoms. We aimed to identify natural subgroups of migraine based on symptoms listed in the diagnostic criteria of the third edition of the International Classification of Headache Disorders. Latent class analysis (LCA) was applied to the data of the Korean Sleep-Headache Study, a nationwide population-based survey. We selected a three-class model based on Akaike and Bayesian information criteria and characterized the three identified classes as “mild and low frequency,” “photophobia and phonophobia,” and “severe and high frequency.” In total, 52.0% (65/125) of the participants were classified as “mild and low frequency,” showing the highest frequency of mild headache intensity but the lowest overall headache frequency. Meanwhile, “photophobia and phonophobia” involved 33.6% (42/125) of the participants, who showed the highest frequency of photophobia and phonophobia. Finally, “severe and high frequency” included 14.4% (18/125) of the participants, and they presented the highest frequency of severe headache intensity and highest headache frequency. In conclusion, LCA is useful for analyzing the heterogeneity of migraine symptoms and identifying migraine subtypes. This approach may improve our understanding of the clinical characterization of migraine.
Preparation of ZnNiAl-LDHs microspheres and their adsorption behavior and mechanism on U(VI)
Authors: Ouyang Yanquan , Xu Yuanxin , Zhao Limei , Deng Mingzhan , Yang Pengfei , Peng Guowen , Ke Guojun 
Published: November 2021

AbstractTernary zinc-nickel-aluminum hydrotalcites (ZnNiAl-LDHs) were prepared by hydrothermal synthesis. The structure and morphology of the materials were characterized using X-ray diffraction (XRD), fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), nitrogen adsorption–desorption (BET) and other test techniques. ZnNiAl-LDHs was applied in the treatment of uranium-containing wastewater, the effects of initial pH of the solution, adsorption temperature and contact time on its adsorption performance were systematically investigated, and the adsorption performance of ZnNiAl-LDHs and ZnAl-LDHs on uranyl ions were compared. The result showed that ZnNiAl-LDHs were 3D microspheres self-assembled from flakes, with a specific surface area of 102.02 m2/g, which was much larger than that of flake ZnAl-LDHs (18.49 m2/g), and the saturation adsorption capacity of ZnNiAl-LDHs for uranyl ions (278.26 mg/g) was much higher than that of ZnAl-LDHs for uranyl ions (189.16 mg/g), so the ternary ZnNiAl-LDHs had a more excellent adsorption capacity. In addition, kinetic and thermodynamic studies showed that the adsorption process of ZnNiAl-LDHs on uranyl ions conformed to the pseudo-second-order kinetic model and Langmuir isotherm model. The positive value of ΔH and the negative value of ΔG indicated that the adsorption process was endothermic and spontaneous. The adsorption mechanism was analyzed by X-ray energy spectroscopy (EDS), fourier transform infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS). The results showed that the adsorption of uranyl ions by ZnNiAl-LDHs mainly consisted of complexation and ion substitution. The research results prove that ZnNiAl-LDHs is an adsorbent with low cost and excellent performance, and it has a good application prospect in the field of uranium-containing wastewater treatment.
miRNA-200c-3p targets talin-1 to regulate integrin-mediated cell adhesion
Authors: Obeng Gideon , Park Eun Jeong , Appiah Michael G. , Kawamoto Eiji , Gaowa Arong , Shimaoka Motomu 
Published: November 2021

AbstractThe ability of integrins on the cell surface to mediate cell adhesion to the extracellular matrix ligands is regulated by intracellular signaling cascades. During this signaling process, the talin (TLN) recruited to integrin cytoplasmic tails plays the critical role of the major adaptor protein to trigger integrin activation. Thus, intracellular levels of TLN are thought to determine integrin-mediated cellular functions. However, the epigenetic regulation of TLN expression and consequent modulation of integrin activation remain to be elucidated. Bioinformatics analysis led us to consider miR-200c-3p as a TLN1-targeting miRNA. To test this, we have generated miR-200c-3p-overexpressing and miR-200c-3p-underexpressing cell lines, including HEK293T, HCT116, and LNCaP cells. Overexpression of miR-200c-3p resulted in a remarkable decrease in the expression of TLN1, which was associated with the suppression of integrin-mediated cell adhesion to fibronectin. In contrast, the reduction in endogenous miR-200c-3p levels led to increased expression of TLN1 and enhanced cell adhesion to fibronectin and focal adhesion plaques formation. Moreover, miR-200c-3p was found to target TLN1 by binding to its 3′-untranslated region (UTR). Taken together, our data indicate that miR-200c-3p contributes to the regulation of integrin activation and cell adhesion via the targeting of TLN1.
Sea ice presence is linked to higher carbon export and vertical microbial connectivity in the Eurasian Arctic Ocean
Authors: Fadeev Eduard , Rogge Andreas , Ramondenc Simon , Nöthig Eva-Maria , Wekerle Claudia , Bienhold Christina , Salter Ian , Waite Anya M. , Hehemann Laura , Boetius Antje , Iversen Morten H. 
Published: November 2021

AbstractArctic Ocean sea ice cover is shrinking due to warming. Long-term sediment trap data shows higher export efficiency of particulate organic carbon in regions with seasonal sea ice compared to regions without sea ice. To investigate this sea-ice enhanced export, we compared how different early summer phytoplankton communities in seasonally ice-free and ice-covered regions of the Fram Strait affect carbon export and vertical dispersal of microbes. In situ collected aggregates revealed two-fold higher carbon export of diatom-rich aggregates in ice-covered regions, compared toPhaeocystisaggregates in the ice-free region. Using microbial source tracking, we found that ice-covered regions were also associated with more surface-born microbial clades exported to the deep sea. Taken together, our results showed that ice-covered regions are responsible for high export efficiency and provide strong vertical microbial connectivity. Therefore, continuous sea-ice loss may decrease the vertical export efficiency, and thus the pelagic-benthic coupling, with potential repercussions for Arctic deep-sea ecosystems.
Dual function of HPF1 in the modulation of PARP1 and PARP2 activities
Authors: Kurgina Tatyana A. , Moor Nina A. , Kutuzov Mikhail M. , Naumenko Konstantin N. , Ukraintsev Alexander A. , Lavrik Olga I. 
Published: November 2021

AbstractPoly(ADP-ribosyl)ation catalyzed by poly(ADP-ribose) polymerases (PARPs) is one of the immediate cellular responses to DNA damage. The histone PARylation factor 1 (HPF1) discovered recently to form a joint active site with PARP1 and PARP2 was shown to limit the PARylation activity of PARPs and stimulate their NAD+-hydrolase activity. Here we demonstrate that HPF1 can stimulate the DNA-dependent and DNA-independent autoPARylation of PARP1 and PARP2 as well as the heteroPARylation of histones in the complex with nucleosome. The stimulatory action is detected in a defined range of HPF1 and NAD+ concentrations at which no HPF1-dependent enhancement in the hydrolytic NAD+ consumption occurs. PARP2, comparing with PARP1, is more efficiently stimulated by HPF1 in the autoPARylation reaction and is more active in the heteroPARylation of histones than in the automodification, suggesting a specific role of PARP2 in the ADP-ribosylation-dependent modulation of chromatin structure. Possible role of the dual function of HPF1 in the maintaining PARP activity is discussed.
Helicobacter pylori-induced REDD1 modulates Th17 cell responses that contribute to gastritis
Authors: Yan Zong-Bao , Zhang Jin-Yu , Lv Yi-Pin , Tian Wen-Qing , Shan Zhi-Guo , Mao Fang-Yuan , Liu Yu-Gang , Chen Wan-Yan , Wang Pan , Yang Yun , Cheng Ping , Peng Liu-Sheng , Liao Ya-Ling , Yue Geng-Yu , Xu Xiao-Lin , Zhao Yong-Liang , Lü Mu-Han , Zhuang Yuan 
Published: November 2021

Abstract
Objective: Regulated in development and DNA damage responses-1 (REDD1) is a conserved and ubiquitous protein, which is induced in response to multiple stimuli. However, the regulation, function and clinical relevance of REDD1 in Helicobacter pylori-associated gastritis are presently unknown.
Approach: Immunohistochemistry, real-time PCR and Western blot analyses were performed to examine the levels of REDD1 in gastric samples from H. pylori-infected patients and mice. Gastric tissues from Redd1−/− and wildtype (WT, control) mice were examined for inflammation. Gastric epithelial cells (GECs), monocytes and T cells were isolated, stimulated and/or cultured for REDD1 regulation and functional assays.
Results: REDD1 was increased in gastric mucosa of H. pylori-infected patients and mice. H. pylori induced GECs to express REDD1 via the phosphorylated cytotoxin associated gene A (cagA) that activated MAPKp38 pathway to mediate NF-κB directly binding to REDD1 promoter. Human gastric REDD1 increased with the severity of gastritis, and mouse REDD1 from non-marrow chimera-derived cells promoted gastric inflammation that was characterized by the influx of MHCII+ monocytes. Importantly, gastric inflammation, MHCII+ monocyte infiltration, IL-23 and IL-17A were attenuated in Redd1−/− mice. Mechanistically, REDD1 in GECs regulated CXCL1 production, which attracted MHCII+ monocytes migration by CXCL1-CXCR2 axis. Then H. pylori induced MHCII+ monocytes to secrete IL-23, which favored IL-17A-producing CD4+ cell (Th17 cell) polarization, thereby contributing to the development of H. pylori-associated gastritis.
Conclusions: The present study identifies a novel regulatory network involving REDD1, which collectively exert a pro-inflammatory effect within gastric microenvironment. Efforts to inhibit this REDD1-dependent pathway may prove valuable strategies in treating of H. pylori-associated gastritis.