bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Sox17 downstream geneRasip1is involved in the hematopoietic activity of intra-aortic hematopoietic clusters in the midgestation mouse embryo
Authors: Melig Gerel , Nobuhisa Ikuo , Saito Kiyoka , Tsukahara Ryota , Itabashi Ayumi , Kanai Yoshiakira , Kanai-Azuma Masami , Osawa Mitsujiro , Oshima Motohiko , Iwama Atsushi , Taga Tetsuya 
Published: November 2022

AbstractBackgroundDuring mouse embryonic development, definitive hematopoiesis is first detected around embryonic day (E) 10.5 in the aorta-gonad-mesonephros (AGM) region. Hematopoietic stem cells (HSCs) arise in the dorsal aorta’s intra-aortic hematopoietic cell clusters (IAHCs). We have previously reported that a transcription factor Sox17, is expressed in IAHCs, and that, among them, CD45lowc-Kithighcells have high hematopoietic activity. Furthermore, forced expression of Sox17 in this population of cells can maintain the formation of hematopoietic cell clusters. However, how Sox17 does so, particularly downstream signaling involved, remains poorly understood. The purpose of this study is to search for new Sox17 targets which contribute to cluster formation with hematopoietic activity.MethodsRNA-sequencing (RNA-seq) analysis was done to identify genes that are up- regulated in Sox17-expressing IAHCs as compared with Sox17-negative ones. Among the top 7 highly expressed genes, Rasip1 which had been reported to be a vascular-specific regulator was focused on in this study and firstly the whole-mount immunostaining was done. We conducted a luciferase reporter assay to identify the Sox17 binding site for Rasip1 gene induction. We also analyzed the cluster formation and the multi-lineage colony forming ability of Rasip1-transduced cells and Rasip1-knockdown Sox17-transduced cells.ResultsThe increase of theRasip1expression level was observed in Sox17-positive CD45lowc-Kithighcells as compared with the Sox17-nonexpressing control. Also, the expression level of theRasip1gene was increased by the Sox17-nuclear translocation. Rasip1 was expressed on the membrane of IAHCs, overlapping with the endothelial cell marker, CD31, and hematopoietic stem/progenitor marker (HSPC), c-Kit. Overexpression of Rasip1 in CD45lowc-Kithighcells led to a significant but transient increase in hematopoietic activity, while Rasip1 knock-down in Sox17-transduced cells decreased the cluster formation and diminished the colony-forming ability.ConclusionsRasip1 knockdown in Sox17-transduced CD45lowc-Kithighcells displayed a significant decrease in the multi-lineage colony forming ability and the cluster size. Rasip1 overexpression in Sox17-untransduced CD45lowc-Kithighcells led to a significant but transient increase in the multi-lineage colony forming ability, suggesting the presence of a cooperating factor for sustained hematopoietic activity.
END-TO-END CLASSIFICATION OF CELL-CYCLE STAGES WITH CENTER-CELL FOCUS TRACKER USING RECURRENT NEURAL NETWORKS
Authors: Jose Abin , Roy Rijo , Eschweiler Dennis , Laube Ina , Azad Reza , Moreno-Andrés Daniel , Stegmaier Johannes 
Published: November 2022

ABSTRACTCell division, or mitosis, guarantees the accurate inheritance of the genomic information kept in the cell nucleus. Malfunctions in this process cause a threat to the health and life of the organism, including cancer and other manifold diseases. It is therefore crucial to study in detail the cell-cycle in general and mitosis in particular. Consequently, a large number of manual and semi-automated time-lapse microscopy image analyses of mitosis have been carried out in recent years. In this paper, we propose a method for automatic detection of cell-cycle stages using a recurrent neural network (RNN). An end-to-end model with center-cell focus tracker loss, and classification loss is trained. The evaluation was conducted on two time-series datasets, with 6-stages and 3-stages of cell splitting labeled. The frame-to-frame accuracy was calculated and precision, recall, and F1-Score were measured for each cell-cycle stage. We also visualized the learned feature space. Image reconstruction from the center-cell focus module was performed which shows that the network was able to focus on the center-cell and classify it simultaneously. Our experiments validate the superior performance of the proposed network compared to a classifier baseline.
A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis
Authors: Wang Ming , Zhong Zhenhui , Gallego-Bartolomé Javier , Li Zheng , Feng Suhua , Kuo Peggy Hsuanyu , Kan Ryan L. , Lam Hoiyan , Richey John , Jami-Alahmadi Yasaman , Wohlschlegel James , Jacobsen Steven E. 
Published: November 2022

AbstractDNA methylation has been utilized for target gene silencing in plants, however it’s not well-understood whether other silencing pathways can be also used to manipulate gene expression. Here we performed a gain of function screen for proteins that could silence a target gene when fused to an artificial zinc finger. We uncovered many proteins that suppressed gene expression either through the establishment of DNA methylation, or via DNA methylation-independent processes including histone H3K27me3 deposition, H3K4me3 demethylation, H3K9, H3K14, H3K27, and H4K16 deacetylation, inhibition of RNA Polymerase II transcription elongation or Ser-5 dephosphorylation. The silencing fusion proteins also silenced many other genes with different efficacy, and a machine learning model could accurately predict the efficacy of each silencer based on various chromatin features of the target loci. These results provide a more comprehensive understanding of epigenetic regulatory pathways and provide an armament of tools for targeted manipulation of gene expression.
Hippocampal collagen as a potential target for post-surgical treatment; effects of whole-body vibration and exercise
Authors: Keijzer Noa , Oberman Klaske , Oroszi Tamás , Nyakas Csaba , van der Zee Eddy A , Schoemaker Regien G 
Published: November 2022

AbstractPeripheral surgery may evoke neuroinflammation, associated with neuronal damage and consequently mental health problems. However, anti-inflammatory treatment showed limited therapeutic efficacy. Preservation of neuron integrity during neuroinflammation, by targeting their protective collagen sheet, may provide an alternative strategy. Whole-body vibration (WBV) and exercise combine anti-inflammatory and collagen-increasing effects in the periphery. The present study aimed to explore the therapeutic efficacy of postoperative WBV and exercise on hippocampal neuroinflammation and collagen expression.Three months old male Wistar rats underwent abdominal surgery. Starting from one day after surgery, rats were submitted to WBV (10 min, once or twice daily, 30 Hz), running exercise (30 min, daily), or pseudo WBV/exercise, for two weeks. Rats were sacrificed and brain tissue was collected and processed for (immuno)histochemistry. Hippocampal microglia activity, total collagen content, and expression of fibrous and non-fibrous collagen subtypes were analysed.Surgery was associated with increased microglia activity in the CA1 area, which was only partly reversed by the interventions. Surgery specifically reduced total collagen expression in the CA1 area, which was restored by both WBV and exercise. Collagen I was absent in the hippocampal granular layers. The surgery-induced decrease in collagen III expression in the CA1 area was not affected by either WBV or exercise. However, surgery increased collagen III in the CA2 (ns), CA3 and DG. Exercise, and to a lower extent WBV, seemed to (partly) reverse this effect. Collagen IV expression was not altered by surgery, but increased by WBV. No significant effects were observed on collagen VI expression.WBV as well as exercise restored the surgery-induced declined collagen expression, while partly reversing microglia activation in the CA1 area. Moreover, effects on collagen appeared to be subtype- and region-specific, with overall similar effects of WBV and exercise. Nevertheless, the neuroprotective potential of postoperatively altered brain collagen needs further investigation.
Pharmacological Modulation of Autophagy Prevents Mutant SOD1G93AInduced Neurotoxicity in Experimental Models of Amyotrophic Lateral Sclerosis (ALS)
Authors: Bi Yue , Yan Xin , Yacipi Nazmiye , Duan Weisong , Li Chunyan , Thompson Martin , Shan Zhiying , Bi Lanrong 
Published: November 2022

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder resulting from the progressive loss of both upper and lower motor neurons in the cerebral cortex, brainstem, and spinal cord. Currently, there are only two drugs, Riluzole (Rilutek) and Edaravone (Radicava), approved by FDA for ALS treatment. These two drugs are very expensive with only a few months of life extension. So far, there is no cure for ALS. Aberrant protein aggregation in motor neurons is an intracellular hallmark of ALS. The disturbance in protein homeostasis may contribute to the onset and progression of ALS. Autophagy plays an important role in degrading misfolded proteins, thereby preventing their aggregation. Pharmacological manipulation of autophagy has been proposed as a new therapeutic approach for treating ALS. IADB, a novel indole alkaloid derivative, has been reported to exert mitochondrial protection and cardioprotection through its autophagy-modulating potential. Our present study attempted to examine whether IADB has therapeutic potential in SOD1G93A-associated experimental models of ALS. We found that IADB could promote the clearance of SOD1G93Aaggregates and reduce the overproduction of mitochondrial reactive oxygen species (mtROS) in motor neuron-like NSC-34 cells transfected with SOD1G93A. We further examined the IADB in a SOD1-G93A mouse model of ALS. Administration of IADB started at the age of 55 days until the end stage of the disease. IADB treatment significantly increased LC3-II levels and decreased human SOD1 levels and p62 expression in the spinal cords of SOD1G93Amice, suggesting that IADB treatment could induce autophagy activation and promote clearance of mutant SOD1 aggregates in this mouse model of ALS. Moreover, IADB treatment could alleviate the activation of microglia and astrocytes and reduce mitochondrial oxidative damage in the spinal cord of SOD1G93Amice. Finally, we demonstrated that IADB treatment could improve motor performance and delay the onset and progression of the disease in a mouse model of ALS. The neuroprotective effects of IADB may mainly originate from its autophagy-promoting property.
Modification of blood-based (IgG) to salivary-based (IgA) ELISA for Inflammatory Bowel Disease Diagnostic: Tumor necrosis factor (TNF) alpha quantification
Authors: Kim Doeun , Ganesh Anjana , Riedel Timothy E. 
Published: November 2022

AbstractApproximately 1.6 million people in the United States are struggling with Inflammatory bowel disease. Even though there are a number of diagnostic tools present, including MRI, CT scan, and laboratory tests, the public still lacks access to diagnostic tools due to their expensive costs and needs for the labor of trained phlebotomists. In response, this study focused on modification from blood based enzyme-linked immunoassay (ELISA) to salivary based ELISA in order to expand its accessibility. A 1mL saliva sample was spiked with 1 ± 0.01 μg/mL lyophilized IgG TNFα proteins, and the unspiked saliva was used as a control to test the modified diagnostic. Saliva samples were processed through centrifugation and syringe filtration steps. The change in color between a serum and salivary ELISA kit using either centrifugation or syringe filtration steps was measured by a Color Analysis app that compared red, green and blue values and a microtiter plate reader. The new protocol of salivary-based ELISA lost sensitivity from 31.5pg/mL to 15.6pg/mL of TNFα protein concentration. The best centrifugation method was when a combination of stock saliva and buffer was used before spiking the sample. This means that we can modify the current serum based diagnostic tool to a salivary diagnostic using centrifugation to filter the sample and implement it in developing countries due to its lower cost.
SUMOylation regulates Lem2 function in centromere clustering and silencing
Authors: Strachan Joanna , Leidecker Orsolya , Spanos Christos , Coz Clementine Le , Chapman Elliott , Arsenijevic Ana , Zhang Haidao , Zhao Ning , Bayne Elizabeth H. 
Published: November 2022

AbstractRegulation by the small modifier SUMO is heavily dependent on spatial control of enzymes that mediate the attachment and removal of SUMO on substrate proteins. Here we show that in fission yeast, delocalisation of the SUMO protease Ulp1 from the nuclear envelope results in centromeric defects that can be attributed to hyper-SUMOylation at the nuclear periphery. Unexpectedly, we find that while this localised hyper-SUMOylation impairs centromeric silencing, it can also enhance centromere clustering. Moreover, both effects are at least partially dependent on SUMOylation of the inner nuclear membrane protein Lem2. Lem2 has previously been implicated in diverse biological processes, including the promotion of both centromere clustering and silencing, but how these distinct activities are coordinated was unclear; our observations suggest a model whereby SUMOylation may serve as a regulatory switch, modulating Lem2 interactions with competing partner proteins to balance its roles in alternative pathways. Our findings also reveal a previously unappreciated role for SUMOylation in promoting centromere clustering.
The dissociative role of bursting and non-bursting neural activity in the oscillatory nature of functional brain networks
Authors: Cordier Alix , Mary Alison , Vander Ghinst Marc , Goldman Serge , De Tiège Xavier , Wens Vincent 
Published: November 2022

AbstractThe oscillatory nature of intrinsic brain networks is largely taken for granted in the systems neuroscience community. However, the hypothesis that brain rhythms—and by extension transient bursting oscillations—underlie functional networks has not been demonstratedper se. Electrophysiological measures of functional connectivity are indeed affected by the power bias, which may lead to artefactual observations of spectrally specific network couplings not genuinely driven by neural oscillations, bursting or not. We investigate this crucial question by introducing a unique combination of a rigorous mathematical analysis of the power bias in frequency-dependent amplitude connectivity with a neurobiologically informed model of cerebral background noise based on hidden Markov modeling of resting-state magnetoencephalography (MEG). We demonstrate that the power bias may be corrected by a suitable renormalization depending nonlinearly on the signal-to-noise ratio, with noise identified as non-bursting oscillations. Applying this correction preserves the spectral content of amplitude connectivity, definitely proving the importance of brain rhythms in intrinsic functional networks. Our demonstration highlights a dichotomy between spontaneous oscillatory bursts underlying network couplings and non-bursting oscillations acting as background noise but whose function remains unsettled.Significance statementBrain rhythms are paramount electrophysiological correlates of human cerebral activity as they coordinate neurons across distinct brain areas and establish neural synchronization. Spontaneous cortical oscillations, and particularly transient “bursts” of oscillations, also appear as the main electrophysiological subtrate of intrinsic functional brain networks. However, we argue that this oscillatory theory of brain networks, despite being widely accepted, should be requestioned due to a critical bias in electrophysiological measures of network connectivity. Here, we combined mathematical and neurobiological modeling techniques with magnetoencephalography recordings to set this theory on firm and rigorous grounds. Key to our analysis are scarcely studied non-bursting cortical oscillations. Although their precise function remains elusive, our results reveal that dissociating bursting and non-bursting oscillations is fundamental to the rigorous interpretation of electrophysiological network connectivity.
CineFinch: An animated female zebra finch for studying courtship interactions
Authors: Phaniraj Nikhil , Joshi Sanjana , Trimbake Pradeepkumar , Pujari Aditya , Ramadurai Samyuktha , Kalra Shikha , Ratnaparkhi Nikhil , Rajan Raghav 
Published: November 2022

ABSTRACTDummies, videos and computer animations have been used extensively in animal behaviour to study simple social interactions. These methods allow complete control of one interacting animal, making it possible to test hypotheses about the significance and relevance of different elements of animal displays. Recent studies have demonstrated the potential of videos and interactive displays for studying more complex courtship interactions in the zebra finch, a well-studied songbird. Here, we extended these techniques by developing an animated female zebra finch and showed that ~40% of male zebra finches (n=5/12) sing to this animation. To study real-time social interactions, we developed two possible methods for closed loop control of animations; (1) an arduino based system to initiate videos/animations based on perch hops and (2) a video game engine based system to change animations. Overall, our results provide an important tool for understanding the dynamics of complex social interactions during courtship.SUMMARY STATEMENTWe develop and test an animation of a female zebra finch to study song and courtship interactions in the male zebra finch.
Alterations in intestinal Proteobacteria and antimicrobial resistance gene burden in individuals administered microbial ecosystem therapeutic (MET-2) for recurrentClostridioides difficileinfection
Authors: Rooney Ashley M. , Cochrane Kyla , Fedsin Stephanie , Yao Samantha , Anwer Shaista , Dehmiwal Satyender , Hota Susy , Poutanen Susan , Allen-Vercoe Emma , Coburn Bryan ,   the MTOP Investigators
Published: November 2022

AbstractIntestinal colonisation with pathogens and antimicrobial resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrentClostridioides difficileinfection (rCDI) and to decolonise intestinal AROs. However, FMT has significant practical barriers to implementation. A microbial consortium, microbial ecosystem therapeutic (MET)-2, is an alternative to FMT for the treatment of rCDI. It is unknown whether MET-2 is associated with decreases in pathogens and antimicrobial resistance genes (ARGs). We conducted a post-hoc metagenomic analysis of stool collected from two interventional studies of MET-2 (published) and FMT (unpublished) for rCDI treatment to understand if MET-2 had similar effects to FMT for decreasing pathogens and ARGs as well as increasing anaerobes. Patients were included in the current study if baseline stool had Proteobacteria relative abundance ≥10% by metagenomic sequencing. We assessed pre- and post-treatment Proteobacteria, obligate anaerobe and butyrate-producer relative abundances and total ARGs. MET-2 and FMT were associated with decreases in Proteobacteria relative abundance as well as increases in obligate anaerobe and butyrate-producer relative abundances. The microbiota response remained stable over 4 or 6 months for MET-2 and FMT, respectively. MET-2, but not FMT, was associated with a decrease in the total number of ARGs. MET-2 is a potential therapeutic strategy for ARO/ARG decolonisation and anaerobe repletion.
Effect of chloride concentration on the properties of passive film formed on Q235 steel in simulated concrete pore solutions
Authors: Liu Lupeng , Li Senlin , Gao Zhiming , Jia Hang , Hu Wenbin 
Published: November 2022

PurposeThis paper aims to study the effect of chloride concentration on the properties of passive film formed on Q235 steel in simulated concrete pore solutions.Design/methodology/approachMott–Schottky analysis and electrochemical impedance spectroscopy were used to study the passive film of Q235 steel in simulated concrete pore solution. X-ray photoelectron spectroscopy was used to analyze the composition of passive film on Q235 steel.FindingsWhen the chloride concentration is below the chloride threshold value, open circuit potential (OCP) and Rct gradually increases and donor concentration (ND) remains unchanged with the increasing immersion time. When the chloride concentration exceeds chloride threshold value, OCP and Rct decreases after a temporary increase andNDincreases. The linear region of the Mott–Schottky curve lost its linearity. The electrochemical process control step is changed from charge transfer control to oxygen diffusion control. As the chloride concentration increases, the FeO content in the passive film increases and the Fe2O3content decreases. Chloride can destroy the outer layer of passive film and introduce impurities.Originality/valueThe effects of chloride and immersion time on the change process of passive films on Q235 steel in simulated concrete pore solution were studied using electrochemical methods. The mechanism of chloride destroying passive film was analyzed.
Multi-objective optimization of high torque density spoke-type PM machine for special vehicle drive system
Authors: Xu Hongli , Wang Chen 
Published: November 2022

Purpose
This paper proposes a spoke-type fractional-slot concentrated windings (FSCW) permanent magnet (PM) machine for special vehicle driving systems to obtain higher torque and power density, high efficiency and wide field-weakening range. To enhance the efficiencies of multi-objective optimization processes, the respond surface (RS) method and black-hole (BH) algorithm are used.

Design/methodology/approach
The spoke-type FSCW PM machine is optimized to meet the requirements of the special vehicle driving system. The combination of the RS and BH algorithm is used to obtain high torque, low torque ripple and high efficiency.

Findings
The optimal spoke-type PM machine is obtained, and it has higher torque density, lower torque ripple, cogging torque and wider magnetic field weakening range. Finally, a 15-kW prototype machine is fabricated and tested to verify the results of the optimization method and finite-element analysis.

Originality/value
This paper designs a high torque density and efficiency spoke-type FSCW PM machine, which is superior for special vehicle driving systems. Meanwhile, the RS model combined with BH algorithm is applied to the field of electrical machine multi-objective optimal design.