bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the epigenomic and transcriptomic interplay during alcohol-induced anxiolysis
Authors: Krishnan Harish R. , Zhang Huaibo , Chen Ying , Bohnsack John Peyton , Shieh Annie W. , Kusumo Handojo , Drnevich Jenny , Liu Chunyu , Grayson Dennis R. , Maienschein-Cline Mark , Pandey Subhash C. 
Published: September 2022

AbstractPositive effects of alcohol drinking such as anxiolysis and euphoria appear to be a crucial factor in the initiation and maintenance of alcohol use disorder (AUD). However, the mechanisms that lead from chromatin reorganization to transcriptomic changes after acute ethanol exposure remain unknown. Here, we used Assay for Transposase-Accessible Chromatin followed by high throughput sequencing (ATAC-seq) and RNA-seq to investigate epigenomic and transcriptomic changes that underlie anxiolytic effects of acute ethanol using an animal model. Analysis of ATAC-seq data revealed an overall open or permissive chromatin state that was associated with transcriptomic changes in the amygdala after acute ethanol exposure. We identified a candidate gene, Hif3a (Hypoxia-inducible factor 3, alpha subunit), that had ‘open’ chromatin regions (ATAC-seq peaks), associated with significantly increased active epigenetic histone acetylation marks and decreased DNA methylation at these regions. The mRNA levels of Hif3a were increased by acute ethanol exposure, but decreased in the amygdala during withdrawal after chronic ethanol exposure. Knockdown of Hif3a expression in the central nucleus of amygdala attenuated acute ethanol-induced increases in Hif3a mRNA levels and blocked anxiolysis in rats. These data indicate that chromatin accessibility and transcriptomic signatures in the amygdala after acute ethanol exposure underlie anxiolysis and possibly prime the chromatin for the development of AUD.
Crosstalk of Synapsin1 palmitoylation and phosphorylation controls the dynamicity of synaptic vesicles in neurons
Authors: Yan Peipei , Liu Huicong , Zhou Tao , Sun Pu , Wang Yilin , Wang Xibin , Zhang Lin , Wang Tian , Dong Jing , Zhu Jiangli , Lv Luxian , Li Wenqiang , Qi Shiqian , Liang Yinming , Kong Eryan 
Published: September 2022

AbstractThe dynamics of synaptic vesicles (SVs) within presynaptic domains are tightly controlled by synapsin1 phosphorylation; however, the mechanism underlying the anchoring of synapsin1 with F-actin or SVs is not yet fully understood. Here, we found that Syn1 is modified with protein palmitoylation, and examining the roles of Syn1 palmitoylation in neurons led us to uncover that Syn1 palmitoylation is negatively regulated by its phosphorylation; together, they manipulate the clustering and redistribution of SVs. Using the combined approaches of electron microscopy and genetics, we revealed that Syn1 palmitoylation is vital for its binding with F-actin but not SVs. Inhibition of Syn1 palmitoylation causes defects in SVs clustering and a reduced number of total SVs in vivo. We propose a model in which SVs redistribution is triggered by upregulated Syn1 phosphorylation and downregulated Syn1 palmitoylation, and they reversibly promote SVs clustering. The crosstalk of Syn1 palmitoylation and phosphorylation thereby bidirectionally manipulates SVs dynamics in neurons.
Improved immunoassay sensitivity and specificity using single-molecule colocalization
Authors: Hariri Amani A. , Newman Sharon S. , Tan Steven , Mamerow Dan , Adams Alexandra M. , Maganzini Nicolò , Zhong Brian L. , Eisenstein Michael , Dunn Alexander R. , Soh H. Tom 
Published: September 2022

AbstractEnzyme-linked immunosorbent assays (ELISAs) are a cornerstone of modern molecular detection, but the technique still faces notable challenges. One of the biggest problems is discriminating true signal generated by target molecules versus non-specific background. Here, we developed a Single-Molecule Colocalization Assay (SiMCA) that overcomes this problem by employing total internal reflection fluorescence microscopy to quantify target proteins based on the colocalization of fluorescent signal from orthogonally labeled capture and detection antibodies. By specifically counting colocalized signals, we can eliminate the effects of background produced by non-specific binding of detection antibodies. Using TNF-α, we show that SiMCA achieves a three-fold lower limit of detection compared to conventional single-color assays and exhibits consistent performance for assays performed in complex specimens such as serum and blood. Our results help define the pernicious effects of non-specific background in immunoassays and demonstrate the diagnostic gains that can be achieved by eliminating those effects.
sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network
Authors: Xu Yang , Begoli Edmon , McCord Rachel Patton 
Published: September 2022

AbstractThe boom in single-cell technologies has brought a surge of high dimensional data that come from different sources and represent cellular systems from different views. With advances in these single-cell technologies, integrating single-cell data across modalities arises as a new computational challenge. Here, we present an adversarial approach, sciCAN, to integrate single-cell chromatin accessibility and gene expression data in an unsupervised manner. We benchmarked sciCAN with 5 existing methods in 5 scATAC-seq/scRNA-seq datasets, and we demonstrated that our method dealt with data integration with consistent performance across datasets and better balance of mutual transferring between modalities than the other 5 existing methods. We further applied sciCAN to 10X Multiome data and confirmed that the integrated representation preserves biological relationships within the hematopoietic hierarchy. Finally, we investigated CRISPR-perturbed single-cell K562 ATAC-seq and RNA-seq data to identify cells with related responses to different perturbations in these different modalities.
Brain-enriched RagB isoforms regulate the dynamics of mTORC1 activity through GATOR1 inhibition
Authors: Figlia Gianluca , Müller Sandra , Hagenston Anna M. , Kleber Susanne , Roiuk Mykola , Quast Jan-Philipp , ten Bosch Nora , Carvajal Ibañez Damian , Mauceri Daniela , Martin-Villalba Ana , Teleman Aurelio A. 
Published: September 2022

AbstractMechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability to appropriately regulate cellular anabolism and catabolism. During nutrient restriction, different organs in an animal do not respond equally, with vital organs being relatively spared. This raises the possibility that mTORC1 is differentially regulated in different cell types, yet little is known about this mechanistically. The Rag GTPases, RagA or RagB bound to RagC or RagD, tether mTORC1 in a nutrient-dependent manner to lysosomes where mTORC1 becomes activated. Although the RagA and B paralogues were assumed to be functionally equivalent, we find here that the RagB isoforms, which are highly expressed in neurons, impart mTORC1 with resistance to nutrient starvation by inhibiting the RagA/B GTPase-activating protein GATOR1. We further show that high expression of RagB isoforms is observed in some tumours, revealing an alternative strategy by which cancer cells can retain elevated mTORC1 upon low nutrient availability.
Effect of temperature on the life cycle of Harmonia axyridis (Pallas), and its predation rate on the Spodoptera litura (Fabricius) eggs
Authors: Islam Yasir , Güncan Ali , Zhou Xingmiao , Naeem Afifa , Shah Farhan Mahmood 
Published: September 2022

AbstractBiological control is one of the strategies of pest control which is determined by the biological fitness and metabolic rates of the predator species used. Temperature and resource are important factors which influence the role of insects as biocontrol agents. Harmonia axyridis is a cosmopolitan and non-specific polyphagous predator. It can survive ecologically diverse environments and exploit multiple preys. This study investigated the effects of temperature on the population parameters of H. axyridis and its predation on the eggs of prey Spodoptera litura. For this purpose, an age–stage, two-sex life table of the predator was constructed at four constant temperatures, i.e. 15, 20, 25 and 30 °C, under laboratory settings of: 70 ± 5% RH, and 16:8 h (L: D) photoperiod. A computer simulation was then used to project the population and predation responses with respect to temperatures tested. We found that the development of larvae and adult (male/female) stages of H. axyridis decreased with colder temperatures (i.e., 15 and 20 °C) but increased with warmer temperatures (25 and 30 °C). The intrinsic rate of increase (r) and mean generation time (T) were 0.0662 d−1 and 79.84 d at 15 °C, 0.0843 d−1 and 64.90 d at 20 °C, 0.1067 d−1 and 48.89 d at 25 °C, and 0.1378 d−1 and 35.55 d at 30 °C, respectively. The mean duration of the total pre-adult stage was 44.26, 32.91, 20.63, and 15.39 d at 15, 20, 25, and 30 °C, respectively. At 30 °C. the finite rate of increase (1.1477 d−1) was the highest and the mean generation time (35.55 d) was the shortest. The net predation rate (C0) was 7935.54, 10,466.28, 10,139.38, and 7126.36 eggs at 15, 20, 25, and 30 °C, respectively. Population and predation projections were proportional to temperature. These findings are important for modelling the population responses of H. axyridis to climate change and tailoring integrated pest management strategies to altered climates.
Fluorochromized tyramide-glucose oxidase as a multiplex fluorescent tyramide signal amplification system for histochemical analysis
Authors: Yamauchi Kenta , Okamoto Shinichiro , Ishida Yoko , Konno Kohtarou , Hoshino Kisara , Furuta Takahiro , Takahashi Megumu , Koike Masato , Isa Kaoru , Watanabe Masahiko , Isa Tadashi , Hioki Hiroyuki 
Published: September 2022

AbstractTyramide signal amplification (TSA) is a highly sensitive method for histochemical analysis. Previously, we reported a TSA system, biotinyl tyramine-glucose oxidase (BT-GO), for bright-filed imaging. Here, we develop fluorochromized tyramide-glucose oxidase (FT-GO) as a multiplex fluorescent TSA system. FT-GO involves peroxidase-catalyzed deposition of fluorochromized tyramide (FT) with hydrogen peroxide produced by enzymatic reaction between glucose and glucose oxidase. We showed that FT-GO enhanced immunofluorescence signals while maintaining low background signals. Compared with indirect immunofluorescence detections, FT-GO demonstrated a more widespread distribution of monoaminergic projection systems in mouse and marmoset brains. For multiplex labeling with FT-GO, we quenched antibody-conjugated peroxidase using sodium azide. We applied FT-GO to multiplex fluorescent in situ hybridization, and succeeded in labeling neocortical interneuron subtypes by coupling with immunofluorescence. FT-GO immunofluorescence further increased the detectability of an adeno-associated virus tracer. Given its simplicity and a staining with a high signal-to-noise ratio, FT-GO would provide a versatile platform for histochemical analysis.
Epitaxial growth of SiGe films by annealing Al–Ge alloyed pastes on Si substrate
Authors: Fukuda Keisuke , Miyamoto Satoru , Nakahara Masahiro , Suzuki Shota , Dhamrin Marwan , Maeda Kensaku , Fujiwara Kozo , Uraoka Yukiharu , Usami Noritaka 
Published: September 2022

AbstractA simple, low-cost, and non-vacuum epitaxial growth method to realize large-area semiconductors on crystalline silicon will become the game-changer for various applications. For example, we can expect the disruptive effect on the cost of large-scale III–V multi-junction solar cells if we could replace the high-cost germanium substrate with silicon–germanium (SiGe) on Si. For SiGe epitaxial growth, we attempted to develop a process using original Al–Ge pastes for screen printing and subsequent annealing. We compare two pastes including Al–Ge alloyed pastes with compositional uniformity in each particle and Al–Ge mixed pastes. We revealed that Al–Ge alloyed paste could form flatter SiGe film with much less residual pastes, supported by in-situ observations. The uniform and sufficient dissolution of the alloyed paste is responsible for these and led to higher average Ge-composition by annealing at 500 °C. The composition in SiGe was vertically graded up to ~ 90% at the topmost surface. These results show that printing and firing of Al–Ge alloyed paste on Si is the desirable, simple, and high-speed process for epitaxial growth of SiGe, which could be potentially used as the lattice-matched virtual substrate with III–V semiconductors.
Quantum Zeno repeaters
Authors: Bayrakci Veysel , Ozaydin Fatih 
Published: September 2022

AbstractQuantum repeaters pave the way for long-distance quantum communications and quantum Internet, and the idea of quantum repeaters is based on entanglement swapping which requires the implementation of controlled quantum gates. Frequently measuring a quantum system affects its dynamics which is known as the quantum Zeno effect (QZE). Beyond slowing down its evolution, QZE can be used to control the dynamics of a quantum system by introducing a carefully designed set of operations between measurements. Here, we propose an entanglement swapping protocol based on QZE, which achieves almost unit fidelity. Implementation of our protocol requires only simple frequent threshold measurements and single particle rotations. We extend the proposed entanglement swapping protocol to a series of repeater stations for constructing quantum Zeno repeaters which also achieve almost unit fidelity regardless of the number of repeaters. Requiring no controlled gates, our proposal reduces the quantum circuit complexity of quantum repeaters. Our work has potential to contribute to long distance quantum communications and quantum computing via quantum Zeno effect.
An in-depth analysis of nucleation and growth mechanism of CdS thin film synthesized by chemical bath deposition (CBD) technique
Authors: Najm A. S. , Naeem Hasanain Salah , Majdi Hasan Sh. , Hasbullah Siti Aishah , Hasan Hiba Ali , Sopian K. , Bais Badariah , Al-Iessa Heidar J. , Dhahad Hayder A. , Ali Jamal M. , Sultan Abbas J. 
Published: September 2022

AbstractThe aim of this study is to acquire a deeper understanding of the response mechanism that is associated with the formation of CdS thin films. We presented an effective and new hybrid sensitisation technique, which involved the 1-step linker between the related chemical bath deposition (CBD) process and the traditional doping method during CBD for synthesising high-quality, CdS thin films. The mechanism for the combined synthesis of the films is also describes. CdS films were electrostatically bonded to soda-lime glass, causing the formation of the intermediate complexes [Cd(NH3)4]2+, which aided in the collision of these complexes with a soda-lime glass slide. In the one-step fabrication technique, 3-Mercaptopropionic Acid (MPA) was employed as a second source of sulphur ions and a linker molecule. Optical studies showed that the bandgap ranged between (2.26–2.52) eV. CdS + MPA films exhibited a uniform distribution of spherical molecules based on their morphological properties. After annealing, this approach significantly altered the electrical characteristics of CdS films. The CdS + MPA films displayed the highest carrier concentration whereas the CdS + Ag + MPA films exhibited the lowest resistivity, with a jump of 3 orders of magnitude.
Structural plasticity driven by task performance leads to criticality signatures in neuromorphic oscillator networks
Authors: Feketa Petro , Meurer Thomas , Kohlstedt Hermann 
Published: September 2022

AbstractOscillator networks rapidly become one of the promising vehicles for energy-efficient computing due to their intrinsic parallelism of execution. The criticality property of the oscillator-based networks is regarded to be essential for performing complex tasks. There are numerous bio-inspired synaptic and structural plasticity mechanisms available, especially for spiking neural networks, which can drive the network towards the criticality. However, there is no solid connection between these self-adaption mechanisms and the task performance, and it is not clear how and why particular self-adaptation mechanisms contribute to the solution of the task, although their relation to criticality is understood. Here we propose an evolutionary approach for the structural plasticity that relies solely on the task performance and does not contain any task-independent adaptation mechanisms, which usually contribute towards the criticality of the network. As a driver for the structural plasticity, we use a direct binary search guided by the performance of the classification task that can be interpreted as an interaction of the network with the environment. Remarkably, such interaction with the environment brings the network to criticality, although this property was not a part of the objectives of the employed structural plasticity mechanism. This observation confirms a duality of criticality and task performance, and legitimizes internal activity-dependent plasticity mechanisms from the viewpoint of evolution as mechanisms contributing to the task performance, but following the dual route. Finally, we analyze the trained network against task-independent information-theoretic measures and identify the interconnection graph’s entropy to be an essential ingredient for the classification task performance and network’s criticality.
Amelioration of prevalence of threatened preterm labor during the COVID-19 pandemic: nationwide database analysis in Japan
Authors: Ohashi Mizuki , Tsuji Shunichiro , Tanaka-Mizuno Sachiko , Kasahara Kyoko , Kasahara Makiko , Miura Katsuyuki , Murakami Takashi 
Published: September 2022

AbstractWe aimed to evaluate the changes in maternal and neonatal complications such as threatened preterm labor (TPL) and preterm birth before and during the coronavirus disease 2019 (COVID-19) pandemic using large-scale real-world data in Japan. We obtained data from the Japan Medical Data Center claims database and evaluated differences in maternal and neonatal complications, such as the prevalence of TPL and preterm birth before the COVID-19 pandemic (in the year 2018 or 2019) and during the COVID-19 pandemic (in 2020). We included 5533, 6257, and 5956 deliveries in the years 2018, 2019, and 2020, respectively. TPL prevalence and preterm birth had significantly decreased in 2020 (41.3%, 2.6%, respectively) compared with those reported in 2018 (45.3%, 3.9%, respectively) and 2019 (44.5%, 3.8%, respectively). Neonatal outcomes such as low-birth-weight infants and retinopathy of prematurity were also improved during the pandemic. There were no clear trends in the prevalence of maternal complications such as hypertensive disorders of pregnancy; hemolysis, elevated liver enzymes, and low platelets (HELLP) syndrome; and preeclampsia. Oral ritodrine hydrochloride usage in all participants had significantly decreased during the COVID-19 pandemic. In conclusion, our results suggest that the COVID-19 pandemic has ameliorated TPL and consequently reduced the number of preterm births.
Bioengineering of CuO porous (nano)particles: role of surface amination in biological, antibacterial, and photocatalytic activity
Authors: Bagherzadeh Mojtaba , Safarkhani Moein , Ghadiri Amir Mohammad , Kiani Mahsa , Fatahi Yousef , Taghavimandi Fahimeh , Daneshgar Hossein , Abbariki Nikzad , Makvandi Pooyan , Varma Rajender S. , Rabiee Navid 
Published: September 2022

AbstractNanotechnology is one of the most impressive sciences in the twenty-first century. Not surprisingly, nanoparticles/nanomaterials have been widely deployed given their multifunctional attributes and ease of preparation via environmentally friendly, cost-effective, and simple methods. Although there are assorted optimized preparative methods for synthesizing the nanoparticles, the main challenge is to find a comprehensive method that has multifaceted properties. The goal of this study has been to synthesize aminated (nano)particles via the Rosmarinus officinalis leaf extract-mediated copper oxide; this modification leads to the preparation of (nano)particles with promising biological and photocatalytic applications. The synthesized NPs have been fully characterized, and biological activity was evaluated in antibacterial assessment against Bacillus cereus as a model Gram-positive and Pseudomonas aeruginosa as a model Gram-negative bacterium. The bio-synthesized copper oxide (nano)particles were screened by MTT assay by applying the HEK-293 cell line. The aminated (nano)particles have shown lower cytotoxicity (~ 21%), higher (~ 50%) antibacterial activity, and a considerable increase in zeta potential value (~ + 13.4 mV). The prepared (nano)particles also revealed considerable photocatalytic activity compared to other studies wherein the dye degradation process attained 97.4% promising efficiency in only 80 min and just 7% degradation after 80 min under dark conditions. The biosynthesized copper oxide (CuO) (nano)particle’s biomedical investigation underscores an eco-friendly synthesis of (nano)particles, their noticeable stability in the green reaction media, and impressive biological activity.
Evaluation of fluorescence-based viability stains in cells dissociated from scleractinian coral Pocillopora damicornis
Authors: Roger Liza M. , Adarkwa Darko Yaa , Bernas Tytus , White Frances , Olaosebikan Monsurat , Cowen Lenore , Klein-Seetharaman Judith , Lewinski Nastassja A. 
Published: September 2022

AbstractThe application of established cell viability assays such as the commonly used trypan blue staining method to coral cells is not straightforward due to different culture parameters and different cellular features specific to mammalian cells compared to marine invertebrates. Using Pocillopora damicornis as a model, we characterized the autofluorescence and tested different fluorescent dye pair combinations to identify alternative viability indicators. The cytotoxicity of different representative molecules, namely small organic molecules, proteins and nanoparticles (NP), was measured after 24 h of exposure using the fluorescent dye pair Hoechst 33342 and SYTOX orange. Our results show that this dye pair can be distinctly measured in the presence of fluorescent proteins plus chlorophyll. P. damicornis cells exposed for 24 h to Triton-X100, insulin or titanium dioxide (TiO2) NPs, respectively, at concentrations ranging from 0.5 to 100 µg/mL, revealed a LC50 of 0.46 µg/mL for Triton-X100, 6.21 µg/mL for TiO2 NPs and 33.9 µg/mL for insulin. This work presents the approach used to customize dye pairs for membrane integrity-based cell viability assays considering the species- and genotype-specific autofluorescence of scleractinian corals, namely: endogenous fluorescence characterization followed by the selection of dyes that do not overlap with endogenous signals.