bluuebunny/crossref_metadata_2025_split huggingface dataset:
A kinase-deficient NTRK2 splice variant predominates in glioma and amplifies several oncogenic signaling pathways
Authors: Pattwell Siobhan S. , Arora Sonali , Cimino Patrick J. , Ozawa Tatsuya , Szulzewsky Frank , Hoellerbauer Pia , Bonifert Tobias , Hoffstrom Benjamin G. , Boiani Norman E. , Bolouri Hamid , Correnti Colin E. , Oldrini Barbara , Silber John R. , Squatrito Massimo , Paddison Patrick J. , Holland Eric C. 
Published: June 2020

AbstractIndependent scientific achievements have led to the discovery of aberrant splicing patterns in oncogenesis, while more recent advances have uncovered novel gene fusions involving neurotrophic tyrosine receptor kinases (NTRKs) in gliomas. The exploration of NTRK splice variants in normal and neoplastic brain provides an intersection of these two rapidly evolving fields. Tropomyosin receptor kinase B (TrkB), encoded NTRK2, is known for critical roles in neuronal survival, differentiation, molecular properties associated with memory, and exhibits intricate splicing patterns and post-translational modifications. Here, we show a role for a truncated NTRK2 splice variant, TrkB.T1, in human glioma. TrkB.T1 enhances PDGF-driven gliomas in vivo, augments PDGF-induced Akt and STAT3 signaling in vitro, while next generation sequencing broadly implicates TrkB.T1 in the PI3K signaling cascades in a ligand-independent fashion. These TrkB.T1 findings highlight the importance of expanding upon whole gene and gene fusion analyses to include splice variants in basic and translational neuro-oncology research.
Autophagy-mediated apoptosis eliminates aneuploid cells in a mouse model of chromosome mosaicism
Authors: Singla Shruti , Iwamoto-Stohl Lisa K. , Zhu Meng , Zernicka-Goetz Magdalena 
Published: June 2020

AbstractThe high incidence of aneuploidy in the embryo is considered the principal cause for low human fecundity. However, the prevalence of aneuploidy dramatically declines as pregnancy progresses, with the steepest drop occurring as the embryo completes implantation. Despite the fact that the plasticity of the embryo in dealing with aneuploidy is fundamental to normal development, the mechanisms responsible for eliminating aneuploid cells are unclear. Here, using a mouse model of chromosome mosaicism, we show that aneuploid cells are preferentially eliminated from the embryonic lineage in a p53-dependent process involving both autophagy and apoptosis before, during and after implantation. Moreover, we show that diploid cells in mosaic embryos undertake compensatory proliferation during the implantation stages to confer embryonic viability. Together, our results indicate a close link between aneuploidy, autophagy, and apoptosis to refine the embryonic cell population and ensure only chromosomally fit cells proceed through development of the fetus.
Dynamic and scalable DNA-based information storage
Authors: Lin Kevin N. , Volkel Kevin , Tuck James M. , Keung Albert J. 
Published: June 2020

AbstractThe physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. Here we show that a simple architecture comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA), can unlock dynamic DNA-based information storage with powerful capabilities and advantages. The overhang provides a physical address for accessing specific DNA strands as well as implementing a range of in-storage file operations. It increases theoretical storage densities and capacities by expanding the encodable sequence space and simplifies the computational burden in designing sets of orthogonal file addresses. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it. Furthermore, saturation mutagenesis around the T7 promoter and systematic analyses of environmental conditions reveal design criteria that can be used to optimize information access. This simple but powerful ss-dsDNA architecture lays the foundation for information storage with versatile capabilities.
Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots
Authors: Jalili Pégah , Bowen Danae , Langenbucher Adam , Park Shinho , Aguirre Kevin , Corcoran Ryan B. , Fleischman Angela G. , Lawrence Michael S. , Zou Lee , Buisson Rémi 
Published: June 2020

AbstractAPOBEC3A is a cytidine deaminase driving mutagenesis, DNA replication stress and DNA damage in cancer cells. While the APOBEC3A-induced vulnerability of cancers offers an opportunity for therapy, APOBEC3A protein and mRNA are difficult to quantify in tumors due to their low abundance. Here, we describe a quantitative and sensitive assay to measure the ongoing activity of APOBEC3A in tumors. Using hotspot RNA mutations identified from APOBEC3A-positive tumors and droplet digital PCR, we develop an assay to quantify the RNA-editing activity of APOBEC3A. This assay is superior to APOBEC3A protein- and mRNA-based assays in predicting the activity of APOBEC3A on DNA. Importantly, we demonstrate that the RNA mutation-based APOBEC3A assay is applicable to clinical samples from cancer patients. Our study presents a strategy to follow the dysregulation of APOBEC3A in tumors, providing opportunities to investigate the role of APOBEC3A in tumor evolution and to target the APOBEC3A-induced vulnerability in therapy.
Measurement-device-independent quantification of irreducible high-dimensional entanglement
Authors: Guo Yu , Yu Bai-Chu , Hu Xiao-Min , Liu Bi-Heng , Wu Yu-Chun , Huang Yun-Feng , Li Chuan-Feng , Guo Guang-Can 
Published: June 2020

AbstractThe certification of entanglement dimensionality is of great importance in characterizing quantum systems. Recently, it was pointed out that quantum correlation of high-dimensional states can be simulated with a sequence of lower-dimensional states. Such a problem may render existing characterization protocols unreliable—the observed entanglement may not be a truly high-dimensional one. Here, we introduce the notion of irreducible entanglement to capture its dimensionality that is indecomposable in terms of a sequence of lower-dimensional entangled systems. We prove this new feature can be detected in a measurement-device-independent manner with an entanglement witness protocol. To demonstrate the practicability of this technique, we experimentally apply it on a 3-dimensional bipartite state, and the result certifies the existence of irreducible (at least) 3-dimensional entanglement.
The role of nicotinic cholinergic neurotransmission in delusional thinking
Authors: Caton Michael , Ochoa Enrique L. M. , Barrantes Francisco J. 
Published: June 2020

AbstractDelusions are a difficult-to-treat and intellectually fascinating aspect of many psychiatric illnesses. Although scientific progress on this complex topic has been challenging, some recent advances focus on dysfunction in neural circuits, specifically in those involving dopaminergic and glutamatergic neurotransmission. Here we review the role of cholinergic neurotransmission in delusions, with a focus on nicotinic receptors, which are known to play a part in some illnesses where these symptoms appear, including delirium, schizophrenia spectrum disorders, bipolar disorder, Parkinson, Huntington, and Alzheimer diseases. Beginning with what we know about the emergence of delusions in these illnesses, we advance a hypothesis of cholinergic disturbance in the dorsal striatum where nicotinic receptors are operative. Striosomes are proposed to play a central role in the formation of delusions. This hypothesis is consistent with our current knowledge about the mechanism of action of cholinergic drugs and with our abstract models of basic cognitive mechanisms at the molecular and circuit levels. We conclude by pointing out the need for further research both at the clinical and translational levels.
Unit policies regarding tocolysis after preterm premature rupture of membranes: association with latency, neonatal and 2-year outcomes (EPICE cohort)
Authors: Lorthe Elsa , Moreira Carla , Weber Tom , Huusom Lene D. , Schmidt Stephan , Maier Rolf F. , Jarreau Pierre-Henri , Cuttini Marina , Draper Elizabeth S. , Zeitlin Jennifer , Barros Henrique ,   The EPICE research group, Martens E. , Martens G. , Van Reempts P. , Boerch K. , Hasselager A. , Huusom L. , Pryds O. , Weber T. , Toome L. , Varendi H. , Ancel P.-Y. , Blondel B. , Burguet A. , Jarreau P.-H. , Truffert P. , Maier R. F. , Misselwitz B. , Schmidt S. , Gortner L. , Baronciani D. , Gargano G. , Agostino R. , Croci I. , Franco F. , Carnielli V. , Cuttini M. , DiLallo D. , Koopman-Esseboom C. , Van Heijst A. , Nijman J. , Gadzinowski J. , Mazela J. , Graça L.-M. , Machado M.-C. , Rodrigues C. , Rodrigues T. , Barros H. , Bonamy A-K. , Norman M. , Wilson E. , Boyle E. , Draper E. S. , Manktelow B. N. , Fenton A. C. , Milligan D. W. A. , Zeitlin J. , Bonet M. , Piedvache A. 
Published: June 2020

AbstractAfter preterm premature rupture of membranes (PPROM), antibiotics and antenatal steroids are effective evidence-based interventions, but the use of tocolysis is controversial. We investigated whether a unit policy of tocolysis use after PPROM is associated with prolonged gestation and improved outcomes for very preterm infants in units that systematically use these other evidence-based treatments. From the prospective, observational, population-based EPICE cohort study (all very preterm births in 19 regions from 11 European countries, 2011–2012), we included 607 women with a singleton pregnancy and PPROM at 24–29 weeks’ gestation, of whom 101, 195 and 311 were respectively managed in 17, 32 and 45 units with no-use, restricted and liberal tocolysis policies for PPROM. The association between unit policies and outcomes (early-onset sepsis, survival at discharge, survival at discharge without severe morbidity and survival at two years without gross motor impairment) was investigated using three-level random-intercept logistic regression models, showing no differences in neonatal or two-year outcomes by unit policy. Moreover, there was no association between unit policies and prolongation of gestation in a multilevel survival analysis. Compared to a unit policy of no-use of tocolysis after PPROM, a liberal or restricted policy is not associated with improved obstetric, neonatal or two-year outcomes.
Visualising spatio-temporal distributions of assimilated carbon translocation and release in root systems of leguminous plants
Authors: Yin Yong-Gen , Suzui Nobuo , Kurita Keisuke , Miyoshi Yuta , Unno Yusuke , Fujimaki Shu , Nakamura Takuji , Shinano Takuro , Kawachi Naoki 
Published: June 2020

AbstractThe release of rhizodeposits differs depending on the root position and is closely related to the assimilated carbon (C) supply. Therefore, quantifying the C partitioning over a short period may provide crucial information for clarifying root–soil carbon metabolism. A non-invasive method for visualising the translocation of recently assimilated C into the root system inside the rhizobox was established using 11CO2 labelling and the positron-emitting tracer imaging system. The spatial distribution of recent 11C-photoassimilates translocated and released in the root system and soil were visualised for white lupin (Lupinus albus) and soybean (Glycine max). The inputs of the recently assimilated C in the entire root that were released into the soil were approximately 0.3%–2.9% for white lupin within 90 min and 0.9%–2.3% for soybean within 65 min, with no significant differences between the two plant species; however, the recently assimilated C of lupin was released at high concentrations in specific areas (hotspots), whereas that of soybean was released uniformly in the soil. Our method enabled the quantification of the spatial C allocations in roots and soil, which may help to elucidate the relationship between C metabolism and nutrient cycling at specific locations of the root–soil system in response to environmental conditions over relatively short periods.
Statistical modeling-approach for optimization of Cu2+ biosorption by Azotobacter nigricans NEWG-1; characterization and application of immobilized cells for metal removal
Authors: Ghoniem Abeer Abdulkhalek , El-Naggar Noura El-Ahmady , Saber WesamEldin I. A. , El-Hersh Mohammed S. , El-khateeb Ayman Y. 
Published: June 2020

AbstractHeavy metals are environmental pollutants affect the integrity and distribution of living organisms in the ecosystem and also humans across the food chain. The study targeted the removal of copper (Cu2+) from aqueous solutions, depending on the biosorption process. The bacterial candidate was identified using 16S rRNA sequencing and phylogenetic analysis, in addition to morphological and cultural properties as Azotobacter nigricans NEWG-1. The Box-Behnken design was applied to optimize copper removal by Azotobacter nigricans NEWG-1 and to study possible interactive effects between incubation periods, pH and initial CuSO4 concentration. The data obtained showed that the maximum copper removal percentage of 80.56% was reached at run no. 12, under the conditions of 200 mg/L CuSO4, 4 days’ incubation period, pH, 8.5. Whereas, the lowest Cu2+ removal (12.12%) was obtained at run no.1. Cells of Azotobacter nigricans NEWG-1 before and after copper biosorption were analyzed using FTIR, EDS and SEM. FTIR analysis indicates that several functional groups have participated in the biosorption of metal ions including hydroxyl, methylene, carbonyl, carboxylate groups. Moreover, the immobilized bacterial cells in sodium alginate-beads removed 82.35 ± 2.81% of copper from the aqueous solution, containing an initial concentration of 200 mg/L after 6 h. Azotobacter nigricans NEWG-1 proved to be an efficient biosorbent in the elimination of copper ions from environmental effluents, with advantages of feasibility, reliability and eco-friendly.
Mutations in virus-derived small RNAs
Authors: Nigam Deepti , LaTourrette Katherine , Garcia-Ruiz Hernan 
Published: June 2020

AbstractRNA viruses exist as populations of genome variants. Virus-infected plants accumulate 21–24 nucleotide small interfering RNAs (siRNAs) derived from viral RNA (virus-derived siRNAs) through gene silencing. This paper describes the profile of mutations in virus-derived siRNAs for three members of the family Potyviridae: Turnip mosaic virus (TuMV), Papaya ringspot virus (PRSV) and Wheat streak mosaic virus (WSMV). For TuMV in Arabidopsis thaliana, profiles were obtained for mechanically inoculated rosette leaves and systemically infected cauline leaves and inflorescence. Results are consistent with selection pressure on the viral genome imposed by local and systemic movement. By genetically removing gene silencing in the plant and silencing suppression in the virus, our results showed that antiviral gene silencing imposes selection in viral populations. Mutations in siRNAs derived from a PRSV coat protein transgene in the absence of virus replication showed the contribution of cellular RNA-dependent RNA polymerases to the generation of mutations in virus-derived siRNAs. Collectively, results are consistent with two sources of mutations in virus-derived siRNAs: viral RNA-dependent RNA polymerases responsible for virus replication and cellular RNA-dependent RNA polymerases responsible for gene silencing amplification.
RXR Expression in Marine Gastropods with Different Sensitivity to Imposex Development
Authors: Giulianelli Sebastián , Primost Mónica A. , Lanari Claudia , Bigatti Gregorio 
Published: June 2020

AbstractThe superposition of male sexual characteristics in female marine gastropods (imposex) represents one of the clearest ecological examples of organotin-mediated endocrine disruption. Recent evidences suggest that signaling pathways mediated by members of the nuclear receptor superfamily, RXR and PPARγ, are involved in the development of this pseudohermaphroditic condition. Here, we identified significant differences in RXR expression in two caenogastropod species from Nuevo Gulf, Argentina, Buccinanops globulosus and Trophon geversianus, which present clear contrast in imposex incidence. In addition, B. globulosus males from a polluted and an unpolluted area showed differences in RXR expression. Conversely, PPARγ levels were similar between both analyzed species. These findings indicate specie-specific RXR and PPARγ expression, suggesting a major role of RXR in the induction of imposex.
NeuroMem: Analog Graphene-Based Resistive Memory for Artificial Neural Networks
Authors: Abunahla Heba , Halawani Yasmin , Alazzam Anas , Mohammad Baker 
Published: June 2020

AbstractArtificial Intelligence (AI) at the edge has become a hot subject of the recent technology-minded publications. The challenges related to IoT nodes gave rise to research on efficient hardware-based accelerators. In this context, analog memristor devices are crucial elements to efficiently perform the multiply-and-add (MAD) operations found in many AI algorithms. This is due to the ability of memristor devices to perform in-memory-computing (IMC) in a way that mimics the synapses in human brain. Here, we present a novel planar analog memristor, namely NeuroMem, that includes a partially reduced Graphene Oxide (prGO) thin film. The analog and non-volatile resistance switching of NeuroMem enable tuning it to any value within the RON and ROFF range. These two features make NeuroMem a potential candidate for emerging IMC applications such as inference engine for AI systems. Moreover, the prGO thin film of the memristor is patterned on a flexible substrate of Cyclic Olefin Copolymer (COC) using standard microfabrication techniques. This provides new opportunities for simple, flexible, and cost-effective fabrication of solution-based Graphene-based memristors. In addition to providing detailed electrical characterization of the device, a crossbar of the technology has been fabricated to demonstrate its ability to implement IMC for MAD operations targeting fully connected layer of Artificial Neural Network. This work is the first to report on the great potential of this technology for AI inference application especially for edge devices.
Multivariate analysis applied in dataset of Poison Control Center of São Paulo, Brazil
Authors: Eller Sarah , Zucoloto Alexandre Dias , de Oliveira Carolina Dizioli Rodrigues , Hernandez Edna Maria Miello , Fruchtengarten Ligia Veras Gimenez , de Oliveira Flávia Neri Meira , de Oliveira Tiago Franco , Yonamine Mauricio 
Published: June 2020

AbstractMultivariate analysis techniques could be used to identify possible intercorrelations in intoxications cases. The statistical analyses used were a multiple logistic regression, multiple correspondence analysis, principal component and hierarchical cluster analysis. Of the 320 samples analysed, 192 samples were positive for some of the investigated toxic agents, of which 100 were positive for ethanol and 131 were positive for other substances. It was possible to group the patients into 3 clusters, which appears 66.5% of this information in the three first factorial axes. On the first axis, the male patients were separated from the female patients. Patients exposed to drugs, between 30 and 39 years old were grouped in the same cluster. On the second factorial axis, patients who were intoxicated with ethanol and who became intoxicated with diazepam were grouped. This work contributed to the mapping of intoxication cases at the Poison Control Centre of the São Paulo city, Brazil (CCI-SP) and serves as an initial study for the creation of a database that could be updated constantly and thus could provide a toxicovigilance system for educational policies.
Artocarpus altilis extracts as a food-borne pathogen and oxidation inhibitors: RSM, COSMO RS, and molecular docking approaches
Authors: Ahmad Mohammad Norazmi , Karim Nazatul Umira , Normaya Erna , Mat Piah Bijarimi , Iqbal Anwar , Ku Bulat Ku Halim 
Published: June 2020

AbstractLipid oxidation and microbial contamination are the major factors contributing to food deterioration. Food additives like antioxidants and antibacterials can prevent food spoilage by delaying oxidation and preventing the growth of bacteria. Artocarpus altilis leaves exhibited biological properties that suggested its use as a new source of natural antioxidant and antimicrobial. Supercritical fluid extraction (SFE) was used to optimize the extraction of bioactive compounds from the leaves using response surface methodology (yield and antioxidant activity). The optimum SFE conditions were 50.5 °C temperature, 3784 psi pressure and 52 min extraction time. Verification test results (Tukey’s test) showed that no significant difference between the expected and experimental DPPH activity and yield value (99%) were found. Gas-chromatography –mass spectrometry (GC-MS) analysis revealed three major bioactive compounds existed in A. altilis extract. The extract demonstrated antioxidant and antibacterial properties with 2,3-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, ferric reducing ability of plasma (FRAP), hydroxyl radical scavenging activity, tyrosinase mushrrom inhibition of 41.5%, 8.15 ± 1.31 (µg of ascorbic acid equivalents), 32%, 37% and inhibition zone diameter of 0.766 ± 0.06 cm (B. cereus) and 1.27 ± 0.12 cm (E. coli). Conductor like screening model for real solvents (COSMO RS) was performed to explain the extraction mechanism of the major bioactive compounds during SFE. Molecular electrostatic potential (MEP) shows the probability site of nucleophilic and electrophilic attack during bacterial inhibition. Based on molecular docking study, non-covalent interactions are the main interaction occurring between the major bioactive compounds and bacteria (antibacterial inhibition).
Sound source localization by Ormia ochracea inspired low–noise piezoelectric MEMS directional microphone
Authors: Rahaman Ashiqur , Kim Byungki 
Published: June 2020

AbstractThe single-tone sound source localization (SSL) by majority of fly Ormia ochracea’s ears–inspired directional microphones leaves a limited choice when an application like hearing aid (HA) demands broadband SSL. Here, a piezoelectric MEMS directional microphone using a modified mechanical model of fly’s ear has been presented with primary focus to achieve SSL in most sensitive audio bands to mitigate the constraints of traditional SSL works. In the modified model, two optimized rectangular diaphragms have been pivoted by four optimized torsional beams; while the backside of the whole structure has been etched. As a result, the SSL relative to angular rotation of the incoming sound depicts the cosine dependency as an ideal pressure–gradient sensor. At the same time, the mechanical coupling leads the magnitude difference between two diaphragms which has been accounted as SSL in frequency domain. The idea behind this work has been analytical simulated first, and with the convincing mechanical results, the designed bio–inspired directional microphone (BDM) has been fabricated using commercially available MEMSCAP based on PiezoMUMPS processes. In an anechoic chamber, the fabricated device has been excited in free-field sound, and the SSL at 1 kHz frequency, rocking frequency, bending frequency, and in-between rocking and bending frequencies has been found in full compliance with the given angle of incidence of sound. With the measured inter-aural sensitivity difference (mISD) and directionality, the developed BDM has been demonstrated as a practical SSL device, and the results have been found in a perfect match with the given angle of incidence of sound. Furthermore, to facilitate the SSL in noisy environment, the noise has been optimized in all scopes, like the geometry of the diaphragm, supportive torsional beam, and sensing. As a result, the A-weighted noise of this work has been found less than 23 dBA across the audio bands, and the equivalent-input noise (EIN) has been found to be 25.52 dB SPL at 1 kHz frequency which are the lowest ever reported by a similar device. With the developed SSL in broadband–in addition to the lowest noise–the developed device can be extended in some audio applications like an HA device.