bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomic structures and orbital energies of 61,489 crystal-forming organic molecules
Authors: Stuke Annika , Kunkel Christian , Golze Dorothea , Todorović Milica , Margraf Johannes T. , Reuter Karsten , Rinke Patrick , Oberhofer Harald 
Published: February 2020

AbstractData science and machine learning in materials science require large datasets of technologically relevant molecules or materials. Currently, publicly available molecular datasets with realistic molecular geometries and spectral properties are rare. We here supply a diverse benchmark spectroscopy dataset of 61,489 molecules extracted from organic crystals in the Cambridge Structural Database (CSD), denoted OE62. Molecular equilibrium geometries are reported at the Perdew-Burke-Ernzerhof (PBE) level of density functional theory (DFT) including van der Waals corrections for all 62 k molecules. For these geometries, OE62 supplies total energies and orbital eigenvalues at the PBE and the PBE hybrid (PBE0) functional level of DFT for all 62 k molecules in vacuum as well as at the PBE0 level for a subset of 30,876 molecules in (implicit) water. For 5,239 molecules in vacuum, the dataset provides quasiparticle energies computed with many-body perturbation theory in the G0W0 approximation with a PBE0 starting point (denoted GW5000 in analogy to the GW100 benchmark set (M. van Setten et al. J. Chem. Theory Comput. 12, 5076 (2016))).
On brain atlas choice and automatic segmentation methods: a comparison of MAPER & FreeSurfer using three atlas databases
Authors: Yaakub Siti Nurbaya , Heckemann Rolf A. , Keller Simon S. , McGinnity Colm J. , Weber Bernd , Hammers Alexander 
Published: February 2020

AbstractSeveral automatic image segmentation methods and few atlas databases exist for analysing structural T1-weighted magnetic resonance brain images. The impact of choosing a combination has not hitherto been described but may bias comparisons across studies. We evaluated two segmentation methods (MAPER and FreeSurfer), using three publicly available atlas databases (Hammers_mith, Desikan-Killiany-Tourville, and MICCAI 2012 Grand Challenge). For each combination of atlas and method, we conducted a leave-one-out cross-comparison to estimate the segmentation accuracy of FreeSurfer and MAPER. We also used each possible combination to segment two datasets of patients with known structural abnormalities (Alzheimer’s disease (AD) and mesial temporal lobe epilepsy with hippocampal sclerosis (HS)) and their matched healthy controls. MAPER was better than FreeSurfer at modelling manual segmentations in the healthy control leave-one-out analyses in two of the three atlas databases, and the Hammers_mith atlas database transferred to new datasets best regardless of segmentation method. Both segmentation methods reliably identified known abnormalities in each patient group. Better separation was seen for FreeSurfer in the AD and left-HS datasets, and for MAPER in the right-HS dataset. We provide detailed quantitative comparisons for multiple anatomical regions, thus enabling researchers to make evidence-based decisions on their choice of atlas and segmentation method.
Tracing multi-isotopically labelled CdSe/ZnS quantum dots in biological media
Authors: Supiandi N. Izyan , Charron G. , Tharaud M. , Benedetti M. F. , Sivry Y. 
Published: February 2020

AbstractThe strengths and limits of isotopically labelled Engineered Nanoparticles (spiked ENPs) spread in biological media have been assessed. Multi-spiked CdSe/ZnS quantum dots (QDs), measuring 7 nm and coated with thioglycolic acid (TGA), were synthesized and enriched in 68Zn, 77Se and 111Cd. These QDs were dispersed at very low concentrations (0.1 to 5000 ppt) in diverse biological matrices (synthetic saliva, synthetic urine, plasma and Dulbecco’s phosphate buffered saline - DPBS growth medium) and the isotopic compositions were determined by HR-ICP-MS. The initial QDs concentrations were calculated to assess the limit of quantification (QD-LOQ) according to the matrix and the isotopically enriched element. The obtained results demonstrated the advantages of the isotopic labelling method in order to work at very low concentrations: the QD-LOQ values for the spiked Zn, Cd and Se originated from the QDs were 10, 0.3 and 6 ppt, respectively, which is below the conventional LOQ of the HR-ICP-MS used (30, 3 and 60 ppt for Zn, Cd and Se, respectively). Conversely, in complex matrices such as saliva, urine, plasma and DPBS growth medium, the QD-LOQ values increased significantly, with values ranging from 16 to 32 ppt for Cd, 446 to 10598 ppt for Zn and 1618 to 8317 ppt for Se. These QD-LOQs are dependent on factors as the elemental background concentration already present in the matrices, and the dilution factor. In this study, the QD-LOQs are expressed for the first time with respect to the background concentration in biological media (QD-RLOQ), which can be used to better assess and then predict the efficiency of the spiking method.
Overlapping connectivity patterns during semantic processing of abstract and concrete words revealed with multivariate Granger Causality analysis
Authors: Fahimi Hnazaee Mansoureh , Khachatryan Elvira , Chehrazad Sahar , Kotarcic Ana , De Letter Miet , Van Hulle Marc M. 
Published: February 2020

AbstractAbstract, unlike concrete, nouns refer to notions beyond our perception. Even though there is no consensus among linguists as to what exactly constitutes a concrete or abstract word, neuroscientists found clear evidence of a “concreteness” effect. This can, for instance, be seen in patients with language impairments due to brain injury or developmental disorder who are capable of perceiving one category better than another. Even though the results are inconclusive, neuroimaging studies on healthy subjects also provide a spatial and temporal account of differences in the processing of abstract versus concrete words. A description of the neural pathways during abstract word reading, the manner in which the connectivity patterns develop over the different stages of lexical and semantic processing compared to that of concrete word processing are still debated. We conducted a high-density EEG study on 24 healthy young volunteers using an implicit categorization task. From this, we obtained high spatio-temporal resolution data and, by means of source reconstruction, reduced the effect of signal mixing observed on scalp level. A multivariate, time-varying and directional method of analyzing connectivity based on the concept of Granger Causality (Partial Directed Coherence) revealed a dynamic network that transfers information from the right superior occipital lobe along the ventral and dorsal streams towards the anterior temporal and orbitofrontal lobes of both hemispheres. Some regions along these pathways appear to be primarily involved in either receiving or sending information. A clear difference in information transfer of abstract and concrete words was observed during the time window of semantic processing, specifically for information transferred towards the left anterior temporal lobe. Further exploratory analysis confirmed a generally stronger connectivity pattern for processing concrete words. We believe our study could guide future research towards a more refined theory of abstract word processing in the brain.
Spatial distribution of oncocerid cephalopods on a Middle Devonian bedding plane suggests semelparous life cycle
Authors: Pohle Alexander , Fuchs Dirk , Korn Dieter , Klug Christian 
Published: February 2020

AbstractReproductive strategies of extinct organisms can only be recognised indirectly and hence, they are exceedingly rarely reported and tend to be speculative. Here, we present a mass-occurrence with common preservation of pairs of late Givetian (Middle Devonian) oncocerid cephalopods from Hamar Laghdad in the Tafilalt (eastern Anti-Atlas, Morocco). We analysed their spatial occurrences with spatial point pattern analysis techniques and Monte Carlo simulations; our results shows that the pairwise clustering is significant, while ammonoids on the same bedding plane reveal a more random distribution. It is possible that processes such as catastrophic mass mortality or post-mortem transport could have produced the pattern. However, we suggest that it is more likely that the oncocerids were semelparous and died shortly after mating. These findings shed new light on the variation and evolution of reproductive strategies in fossil cephalopods and emphasise that they cannot be based on comparisons with extant taxa without question.
A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations
Authors: Caniglia Romolo , Galaverni Marco , Velli Edoardo , Mattucci Federica , Canu Antonio , Apollonio Marco , Mucci Nadia , Scandura Massimo , Fabbri Elena 
Published: February 2020

AbstractAnthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.
RNA cargos in extracellular vesicles derived from blood serum in pancreas associated conditions
Authors: Kumar Senthil R. , Kimchi Eric T. , Manjunath Yariswamy , Gajagowni Saivaroon , Stuckel Alexei J. , Kaifi Jussuf T. 
Published: February 2020

AbstractExosomes are extracellular vesicles which are released from healthy and tumor cells into blood circulation. Unique biomolecular cargos such as RNA and protein are loaded in these vesicles. These molecules may have biological functions such as signaling, cell communications and have the potential to be analyzed as biomarkers. In this initial study, we describe the analysis of exosomes in the serum of healthy subjects, intraductal papillary mucosal neoplasms and pancreatic ductal adenocarcinoma including the characterization of their RNA cargos by next generation sequencing (EXO-NGS). Results indicate the presence of a wide variety of RNAs including mRNA, miRNA, lincRNA, tRNA and piRNA in these vesicles. Based on the differential mRNA expression observed upon EXO-NGS analysis, we independently evaluated two protein coding genes, matrix metalloproteinase-8 (MMP-8) and transcription factor T-Box 3 (TBX3) by qRT-PCR for selective expression in the serum samples. Results indicate a variable expression pattern of these genes across serum samples between different study groups. Further, qRT-PCR analysis with the same serum exosomes processed for EXO-NGS, we observed two long non-coding RNAs,malat-1andCRNDEto be variably expressed. Overall, our observations emphasize the potential value of different exosome components in distinguishing between healthy, premalignant and malignant conditions related to the pancreas.
Colorectal cancer diagnostic model utilizing metagenomic and metabolomic data of stool microbial extracellular vesicles
Authors: Kim Da Jung , Yang Jinho , Seo Hochan , Lee Won Hee , Ho Lee Dong , Kym Sungmin , Park Young Soo , Kim Jae Gyu , Jang In-Jin , Kim Yoon-Keun , Cho Joo-Youn 
Published: February 2020

AbstractColorectal cancer (CRC) is the most common type cancers in the world. CRC occurs sporadically in the majority of cases, indicating the predominant cause of the disease are environmental factors. Diet-induced changes in gut-microbiome are recently supposed to contribute on epidemics of CRC. This study was aimed to investigate the association of metagenomics and metabolomics in gut extracellular vesicles (EVs) of CRC and healthy subjects. A total of 40 healthy volunteers and 32 patients with CRC were enrolled in this study. Metagenomic profiling by sequencing 16 S rDNA was performed for assessing microbial codiversity. We explored the small molecule metabolites using gas chromatography-time-of-flight mass spectrometry. In total, stool EVs were prepared from 40 healthy volunteers and 32 patients with CRC. Metagenomic profiling demonstrated that bacterial phyla, particularly of Firmicutes and Proteobacteria, were significantly altered in patients with colorectal cancer. Through metabolomics profiling, we determined seven amino acids, four carboxylic acids, and four fatty acids; including short-chain to long chain fatty acids that altered in the disease group. Binary logistic regression was further tested to evaluate the diagnostic performance. In summary, the present findings suggest that gut flora dysbiosis may result in alternation of amino acid metabolism, which may be correlated with the pathogenesis of CRC.
Thalidomide Inhibits Human iPSC Mesendoderm Differentiation by Modulating CRBN-dependent Degradation of SALL4
Authors: Belair David G. , Lu Gang , Waller Laura E. , Gustin Jason A. , Collins Nathaniel D. , Kolaja Kyle L. 
Published: February 2020

AbstractExposure to thalidomide during a critical window of development results in limb defects in humans and non-human primates while mice and rats are refractory to these effects. Thalidomide-induced teratogenicity is dependent on its binding to cereblon (CRBN), the substrate receptor of the Cul4A-DDB1-CRBN-RBX1 E3 ubiquitin ligase complex. Thalidomide binding to CRBN elicits subsequent ubiquitination and proteasomal degradation of CRBN neosubstrates including SALL4, a transcription factor of which polymorphisms phenocopy thalidomide-induced limb defects in humans. Herein, thalidomide-induced degradation of SALL4 was examined in human induced pluripotent stem cells (hiPSCs) that were differentiated either to lateral plate mesoderm (LPM)-like cells, the developmental ontology of the limb bud, or definitive endoderm. Thalidomide and its immunomodulatory drug (IMiD) analogs, lenalidomide, and pomalidomide, dose-dependently inhibited hiPSC mesendoderm differentiation. Thalidomide- and IMiD-induced SALL4 degradation can be abrogated by CRBN V388I mutation or SALL4 G416A mutation in hiPSCs. Genetically modified hiPSCs expressing CRBN E377V/V388I mutant or SALL4 G416A mutant were insensitive to the inhibitory effects of thalidomide, lenalidomide, and pomalidomide on LPM differentiation while retaining sensitivity to another known limb teratogen, all-trans retinoic acid (atRA). Finally, disruption of LPM differentiation by atRA or thalidomide perturbed subsequent chondrogenic differentiation in vitro. The data here show that thalidomide, lenalidomide, and pomalidomide affect stem cell mesendoderm differentiation through CRBN-mediated degradation of SALL4 and highlight the utility of the LPM differentiation model for studying the teratogenicity of new CRBN modulating agents.
A Novel Passive Method for the Assessment of Skin-Electrode Contact Impedance in Intraoperative Neurophysiological Monitoring Systems
Authors: Alonso Eduardo , Giannetti Romano , Rodríguez-Morcillo Carlos , Matanza Javier , Muñoz-Frías José Daniel 
Published: February 2020

AbstractIntraoperative Neurophysiological Monitoring is a set of monitoring techniques consisting of reading electrical activity generated by the nervous system structures during surgeries. In order to guarantee signal quality, contact impedance between the sensing electrodes and the patient’s skin needs to be as low as possible. Hence, monitoring this impedance while signals are measured is an important feature of current medical devices. The most commonly used technique involves injection of a known current and measurement of the voltage drop in the contact interface. This method poses several problems, such as power consumption (critical in battery-powered systems), frequency dependency and regulation issues, which are overcome by using a passive method. The fundamentals of the method proposed in this paper are based on the utilization of the variation suffered by the input random signal when a known resistance is connected in parallel to the input terminals of the low-noise amplifier (LNA) of the analog front-end of the acquisition system. Controlling the connection of the resistors and computing the root mean square of the LNA output voltage has been proved to be a useful tool to assess that the contact impedance is suitably low, allowing the user to know if the neural measurements obtained are valid.
Genome-Wide Association Study of VKORC1 and CYP2C9 on acenocoumarol dose, stroke recurrence and intracranial haemorrhage in Spain
Authors: Cullell Natalia , Carrera Caty , Muiño Elena , Torres-Aguila Nuria-Paz , Cárcel-Márquez Jara , González-Sánchez Jonathan , Gallego-Fabrega Cristina , Molina Jessica , Besora Sarah , Sotoca Javier , Buongiorno Maria-Teresa , Jiménez-Conde Jordi , Giralt-Steinhauer Eva , de Torres-Chacón Reyes , Montaner Joan , Mancha Fernando , Cabezas Juan A , Martí-Fàbregas Joan , Prats-Sánchez Luis , Camps-Renom Pol , Purroy Francisco , Cambray Serafi , Freijo María del Mar , Vives-Bauzá Cristòfol , Tur Silvia , Font Maria-Àngels , López-Cancio Elena , Hernandez-Perez Maria , Obach Victor , Calleja Ana , Arenillas Juan , Rodríguez-Yáñez Manuel , Castillo José , Sobrino Tomas , Fernández-Cádenas Israel , Krupinski Jerzy 
Published: February 2020

AbstractAcenocoumarol is an oral anticoagulant with significant interindividual dose variations. Variants in CYP2C9 and VKORC1 have been associated with acenocoumarol maintenance dose. We analysed whether any of the 49 polymorphisms in CYP2C9 and VKORC1 previously associated with acenocoumarol maintenance dose in a Genome-Wide Association study (GWAs) in Dutch population are associated with stroke recurrence, intracranial haemorrhage (ICH) and acenocoumarol maintenance dose in a Spanish population. We performed a GWAs using Human Core Exome-chip (Illumina) in 78 patients stroke patients treated with acenocoumarol for secondary prevention enrolled as part of the prospective investigator-initiated study (IIS) SEDMAN Study. Patients were followed-up a median of 12.8 months. Three and eight patients had recurrent stroke and ICH events, respectively. We found 14 of the 49 published variants associated with acenocoumarol maintenance dose (p < 0.05). Six polymorphisms were associated with stroke recurrence and four variants with ICH (p < 0.05). In conclusion, variants in VKORC1 and CYP2C9 are associated with acenocoumarol maintenance dose, stroke recurrence and ICH in a Spanish cohort. These results highlight the relevance of studying pharmacogenetics associated with efficacy and safety of anticoagulant drugs and justify studies with larger sample size and different ethnic populations.
Upregulation of SMYD3 and SMYD3 VNTR 3/3 polymorphism increase the risk of hepatocellular carcinoma
Authors: Binh Mai Thanh , Hoan Nghiem Xuan , Giang Dao Phuong , Tong Hoang Van , Bock C.-Thomas , Wedemeyer Heiner , Toan Nguyen Linh , Bang Mai Hong , Kremsner Peter G. , Meyer Christian G. , Song Le Huu , Velavan Thirumalaisamy P. 
Published: February 2020

AbstractSMYD3 (SET and MYND domain-containing protein 3) is involved in histone modification, which initiates oncogenesis by activating transcription of multiple downstream genes. To investigate associations of variable numbers of tandem repeats (VNTR) variants in the SMYD3 gene promoter, SMYD3 serum levels and SMYD3 mRNA expression in hepatitis B virus (HBV) infection and clinical progression of related liver disease. SMYD3 VNTRs were genotyped in 756 HBV patients and 297 healthy controls. SMYD3 serum levels were measured in 293 patients and SMYD3 mRNA expression was quantified in 48 pairs of hepatocellular tumor and adjacent non-tumor liver tissues. Genotype SYMD3 VNTR 3/3 was more frequent among HCC patients than in controls (Padjusted = 0.037). SMYD3 serum levels increased according to clinical progression of liver diseases (P = 0.01); HCC patients had higher levels than non-HCC patients (P = 0.04). Among patients with SMYD3 VNTR 3/3, HCC patients had higher SMYD3 levels than others (P < 0.05). SMYD3 mRNA expression was up-regulated in HCC tumor tissues compared to other tissues (P = 0.008). In conclusion, upregulation of SMYD3 correlates with the occurrence of HCC and SMYD3 VNTR 3/3 appears to increase the risk of HCC through increasing SMYD3 levels. SMYD3 may be an indicator for HCC development in HBV patients.
Seroprevalences of autoantibodies and anti-infectious antibodies among Ghana’s healthy population
Authors: Katz Itai , De Luca F. , Dzudzor Bartholomew , Sarpong Baffour Kyei , Osei-Appiah Beatrice , Azoulay Danielle , Katz Daphna , Dey Dzifa , Gilburd Boris , Amital Howard , Vento Sandro , Shoenfeld Yehuda , Shovman Ora 
Published: February 2020

AbstractAutoantibodies, which are antibodies that target self-epitopes, have considerable diagnostic, prognostic and predictive value in specific autoimmune diseases. Various infectious agents have been linked via numerous mechanisms to the formation of different autoantibodies. Therefore, estimating the prevalence of autoantibodies and anti-infectious antibodies in different populations is of high importance. Different genetic and environmental pressures, such as these found in Ghana’s different geographical provinces, may affect the prevalence of autoantibodies. In this study, we assessed the seroprevalence of a diverse panel of autoantibodies and anti-infectious antibodies among the healthy Ghanaian population and investigated possible environmental and genetic predispositions for autoantibodies and autoimmunity. The sera of 406 healthy individuals were obtained from Greater Accra, Upper West, Eastern and Volta regions. Multiplexed assay and chemiluminescent immunoassay techniques were utilized to assess the presence of a panel of autoantibodies and anti-infectious antibodies. We found a high prevalence of anti-HSV-1 IgG (91–100%), anti-EBNA IgG (81–93%) and anti-EBV-VCA IgG (97–100%) antibodies. The prevalence of ANA (at least one of: anti-dsDNA; anti-chromatin; anti-ribosomal-P; anti-Ro/SSA; anti-La/SSB; anti-centromere B; anti-Sm; anti-Sm/RNP; anti-Scl-70; anti-Jo1; anti-DFS70) was estimated at 14%. An inverse association between anti-HSV-2 antibodies and ANA (p = 0.044; adjusted OR = 0.398; CI [0.162–0.975]) was found, after adjusting for differences in gender, age, and familial history of autoimmune diseases. A trend towards reduced seroprevalence of anti-dsDNA antibodies among subjects who were positive for anti-HSV-2 antibodies was also noted (p = 0.1). In conclusion, the inverse association between anti-HSV-2 antibodies and ANA positivity suggests a possible protective role of HSV-2 infection against autoimmunity.