bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissociating experience-dependent and maturational changes in fine motor function during adolescence
Authors: Berencsi Andrea , Gombos Ferenc , Gerván Patrícia , Tróznai Zsófia , Utczás Katinka , Oláh Gyöngyi , Kovács Ilona 
Published: November 2021

ABSTRACTAdolescence is a sensitive period in motor development but little is known about how long-term learning dependent processes shape hand function in tasks of different complexity. We mapped two fundamental aspects of hand function: simple repetitive and complex sequential finger movements, as a function of the length of musical instrumental training. We controlled maturational factors such as chronological and biological age of adolescent female participants (11 to 15 years of age, n=114). We demonstrated that experience improves performance as a function of task complexity, the more complex task being more susceptible for experience driven performance changes. Overall, these results suggest that fine motor skills involving cognitive control and relying on long-range functional brain networks are substantially shaped by experience. On the other hand, performance in a simple repetitive task that explains fine motor speed is primarily shaped by white matter development driven by maturational factors.
A dual voltage clamp technique to study gap junction hemichannels in astrocytes cultured from neonatal rodent spinal cords
Authors: Garré Juan Mauricio , Bukauskas Feliksas F. , Bennett Michael V.L. 
Published: November 2021

AbstractAstrocytes express surface channels involved in purinergic signaling, and among these channels, pannexin-1 (Px1) and connexin-43 (Cx43) hemichannels (HCs) mediate ATP release that acts directly, or through its derivatives, on neurons and glia via purinergic receptors. Although HCs are functional, i.e., open and close, under physiological and pathological conditions, single channel conductance of Px1 HCs is not well defined. Here, we developed a dual voltage clamp technique in HeLa cells overexpressing human Px1-YFP, and then applied this system to rodent spinal astrocytes. Single channels were recorded in cell attached patches and evoked with ramp cycles of 2 s duration and -/+ 80-100 mV amplitude through another pipette in whole cell clamp. Conductance of Px1 HC openings recorded during ramp stimuli ranged 25-110 pS. Based on their single channel conductances, Px1 HCs could be distinguished from Cx43 HCs and P2X7 receptors (P2X7Rs) in spinal astrocytes during dual voltage clamp experiments. Furthermore, we found that single channel activity of Cx43 HCs and P2X7Rs was increased, and that of Px1 HCs was decreased, in spinal astrocytes treated for 7 h with FGF-1, a growth factor implicated in neurodevelopment, repair and inflammation.
Robust and Efficient Assessment of Potency (REAP): A Quantitative Tool for Dose-response Curve Estimation
Authors: Zhou Shouhao , Liu Xinyi , Fang Xinying , Chinchilli Vernon M. , Wang Michael , Wang Hong-Gang , Dokholyan Nikolay V , Shen Chan , Lee J Jack 
Published: November 2021

AbstractThe median-effect equation has been widely used to describe the dose-response relationship and identify compounds that activate or inhibit specific disease targets in contemporary drug discovery. However, the experimental data often contain extreme responses, which may significantly impair the estimation accuracy and impede valid quantitative assessment in the standard estimation procedure. To improve the quantitative estimation of the dose-response relationship, we introduce a novel approach based on robust beta regression. Substantive simulation studies under various scenarios demonstrate solid evidence that the proposed approach consistently provides robust estimation for the median-effect equation, particularly when there are extreme outcome observations. Moreover, simulation studies illustrate that the proposed approach also provides a narrower confidence interval, suggesting a higher power in statistical testing. Finally, to efficiently and conveniently perform common lab data analyses, we develop a freely accessible web-based analytic tool to facilitate the quantitative implementation of the proposed approach for the scientific community.
A fast variational algorithm to detect the clonal copy number substructure of tumors from single-cell data
Authors: De Falco Antonio , Caruso Francesca , Su Xiao-Dong , Iavarone Antonio , Ceccarelli Michele 
Published: November 2021

ABSTRACTHere we report Single CEll Variational ANeuploidy analysis (SCEVAN), a fast variational algorithm for the deconvolution of the clonal substructure of tumors from single cell data. It uses a multichannel segmentation algorithm exploiting the assumption that all the cells in a given copy number clone share the same breakpoints. Thus, the smoothed expression profile of every individual cell constitutes part of the evidence of the copy number profile in each subclone. SCEVAN can automatically and accurately discriminate between malignant and non-malignant cells, resulting in a practical framework to analyze tumors and their microenvironment. We apply SCEVAN to several datasets encompassing 106 samples and 93,322 cells from different tumors types and technologies. We demonstrate its application to characterize the intratumor heterogeneity and geographic evolution of malignant brain tumors.
Characterization of Reactive Oxygen Species Signaling changes in a cell culture model of skeletal muscle ageing, and its application to screening pharmacokinetically-relevant exposures of dietary polyphenols for bioactivity
Authors: Hayes N. , Fogarty M. , Sadofsky L. , Jones H.S. 
Published: November 2021

AbstractAge-related frailty is a significant health and social care burden, however treatment options are limited. There is currently a lack of suitable cell culture model for screening large numbers of test compounds to identifying those which can potentially promote healthy skeletal muscle function. This paper describes the characterization of reactive oxygen and nitrogen species (RONS) signalling changes in young and aged myoblasts and myotubes using the C2C12cell line, and the application of aged myoblast and myotube cultures to assess the effect of dietary polyphenols on RONS signalling. Aged myoblasts and myotubes were observed to have significantly increased reactive oxygen species levels (p<0.01 and p<0.001 respectively), increases in nitric oxide levels (p<0.05 for myoblasts and myotubes), and lipid peroxidation markers (p<0.05 for myoblasts and myotubes). A panel of nine polyphenols were assessed in aged myoblasts and myotubes using concentrations and incubation times consistent with known pharmacokinetic parameters for these compounds. Of these, although several polyphenols were seen to reduce single markers of RONS signalling, only kaempferol and resveratrol consistently reduced multiple markers of RONS signalling with statistical significance in both cell models. Modulation of cellular enzymatic antioxidant activities (superoxide and catalase) was assessed as a possible mechanism of action for these polyphenols, and although both superoxide and catalase activities were significantly reduced in aged (versus young) myotubes (p<0.01 and p<0.05 respectively), no effect of polyphenol treatment on these enzyme activities were observed. Overall, this research has shown the utility of the C2C12model, as both myoblasts and myotubes, as a suitable cell model for screening compounds for modulating RONS signalling in aged muscle, and that resveratrol and kaempferol (using pharmacokinetically-informed exposures) can modulate RONS signalling in skeletal muscle cells after an acute exposure.
Antitumor Effects Of Phytochemicals Of Hot Three Plants On Gastric Adenocarcinoma
Authors: Ragchaasuren Narankhuu , Tumurkhuu Munkhtuya , Byambaa Tserentsoo , Bold Uranbileg , Dagvadorj Enkhmaa , Gendaram Odontuya , Dalkh Tserendagva 
Published: November 2021

ABSTRACTBACKGROUNDThymoquinone (TQ) and beta-sitosterol (BS), the bioactive constituents derived from the medicinal plant Atragene sibirica L, Ranunculus repens L, Pulsatilla Bungeana have been used for anti-cancer treatment in Traditional Mongolian Medicine. Recent studies reported that TQ, BS exhibited anti-proliferative effects on several cancer cell lines. This study was performed to investigate the antitumor effects of phytochemicals on gastric adenocarcinoma in vitro.METHODSTo this aim, we performed a cell apoptosis assay WST1 and several cancer-related gene expressions (Bcl, BIRC5, p53, BAX). NCI-N87, MKN74 cells were seeded at a density of 5×104 cells per well in 96-well culture plates. After overnight incubation, the fresh medium containing different concentrations of TQ (20, 40, 60, 80, and 100 mM/ml) and beta-sitosterol (10, 1, 0.1, 0.001, 0.001 mM/ml) were applied. Following a 24-h incubation, the cell viability was determined by WST-1 assay. We also quantified the expression levels of mRNAs of these genes through qRT-PCR experiments.RESULTSOur results showed that TQ induced a higher percentage of cell apoptosis in the human gastric adenocarcinoma cell lines compared to that of control. We observed a significant 4.8-fold change in BAX/BCL2 ratio. These increases were highly correlated with a concentration-dependent manner (p=0.00178). Moreover, the expression of p53 and BIRC5 was downregulated in MKN74 cells after treatment with TQ.CONCLUSIONSOur results demonstrate that TQ effectively inhibits cell proliferation through several gene expressions in vitro. Moreover, inhibition of the downstream molecule of these genes would explain the underlying mechanism of the antitumor activity in cancer cell lines.
Stress deceleration theory – chronic adolescent stress exposure results in decelerated neurobehavioral maturation
Authors: Jadhav Kshitij S. , Hoffman Alexander F. , Burgisser Morgane , Rosetti Clara , Aeschlimann Léa , Lupica Carl R. , Boutrel Benjamin 
Published: November 2021

AbstractNormative development in adolescence indicates that the prefrontal cortex is still under development thereby unable to exert efficient top-down inhibitory control on subcortical regions such as the basolateral amygdala and the nucleus accumbens. This imbalance in the developmental trajectory between cortical and subcortical regions is implicated in expression of the prototypical impulsive, compulsive, reward seeking and risk-taking adolescent behavior. Here we demonstrate that a chronic mild unpredictable stress procedure during adolescence in male Wistar rats arrests the normal behavioral maturation such that they continue to express adolescent-like impulsive, hyperactive, and compulsive behaviors into late adulthood. This arrest in behavioral maturation is associated with the hypoexcitability of prelimbic cortex (PLC) pyramidal neurons and reduced PLC-mediated synaptic glutamatergic control of BLA and nucleus accumbens core (NAcC) neurons that lasts late into adulthood. At the same time stress exposure in adolescence results in the hyperexcitability of the BLA pyramidal neurons sending stronger glutamatergic projections to the NAcC. Chemogenetic reversal of the PLC hypoexcitability decreased compulsivity and improved the expression of goal-directed behavior in rats exposed to stress during adolescence, suggesting a causal role for PLC hypoexcitability in this stress-induced arrested behavioral development.
Miniscope-LFOV: A large field of view, single cell resolution, miniature microscope for wired and wire-free imaging of neural dynamics in freely behaving animals
Authors: Guo Changliang , Blair Garrett J. , Sehgal Megha , Sangiuliano Jimka Federico N. , Bellafard Arash , Silva Alcino J. , Golshani Peyman , Basso Michele A. , Blair H. Tad , Aharoni Daniel 
Published: November 2021

AbstractImaging large-population, single-cell fluorescent dynamics in freely behaving animals larger than mice remains a key endeavor of neuroscience. We present a large field of view open-source miniature microscope (MiniLFOV) designed for large-scale (3.6 × 2.7 mm), single cell resolution neural imaging in freely behaving rats. It has an electrically adjustable working distance of up to 3.5 mm±100 μm, incorporates an absolute head-orientation sensor, and weighs only 13.9 grams. The MiniLFOV is capable of both deep brain and cortical imaging and has been validated in freely behaving rats by simultaneously imaging >1000 GCaMP7s expressing neurons in the hippocampal CA1 layer and in head-fixed mice by simultaneously imaging ~2000 neurons in the dorsal cortex through a cranial window. The MiniLFOV also supports optional wire-free operation using a novel, wire-free data acquisition expansion board. We expect this new open-source implementation of the UCLA Miniscope platform will enable researchers to address novel hypotheses concerning brain function in freely behaving animals.
Unravelling the regulation pathway of photosynthetic AB-GAPDH
Authors: Marotta Roberto , Del Giudice Alessandra , Gurrieri Libero , Fanti Silvia , Swuec Paolo , Galantini Luciano , Falini Giuseppe , Trost Paolo , Fermani Simona , Sparla Francesca 
Published: November 2021

AbstractOxygenic phototrophs perform carbon fixation through the Calvin–Benson cycle. Different mechanisms adjust the cycle and the light-harvesting reactions to rapid environmental changes. Photosynthetic glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a key enzyme of the cycle. In land plants, different photosynthetic GAPDHs exist: the most abundant formed by hetero-tetramers of A and B-subunits, and the homo-tetramer A4. Regardless of the subunit composition, GAPDH is the major consumer of photosynthetic NADPH and for this reason is strictly regulated. While A4-GAPDH is regulated by CP12, AB-GAPDH is autonomously regulated through the C-terminal extension (CTE) of B-subunits. Reversible inactivation of AB-GAPDH occurs via oxidation of a cysteine pair located in the CTE, and substitution of NADP(H) with NAD(H) in the cofactor binding domain. These combined conditions lead to a change in the oligomerization state and enzyme inactivation. SEC-SAXS and single-particle cryoEM analysis disclosed the structural basis of this regulatory mechanism. Both approaches revealed that (A2B2)n-GAPDH oligomers with n=1, 2, 4 and 5 co-exist in a dynamic system. B-subunits mediate the contacts between adjacent A2B2 tetramers in A4B4 and A8B8 oligomers. The CTE of each B-subunit penetrates into the active site of a B-subunit of the adjacent tetramer, while the CTE of this subunit moves in the opposite direction, effectively preventing the binding of the substrate 1,3-bisphosphoglycerate in the B-subunits. The whole mechanism is made possible, and eventually controlled, by pyridine nucleotides. In fact, NAD(H) by removing NADP(H) from A-subunits allows the entrance of the CTE in B-subunits active sites and hence inactive oligomer stabilization.Significance StatementIn land plants, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) unique sink of reducing power of the entire Calvin-Benson cycle, is finely regulated. Based on the redox state and substrates concentration, its heteromeric form AB-GAPDH oscillates between a fully active heterotetramer (A2B2) and inactive oligomers. Experimental evidence demonstrates that GAPDH inactivation depends on the formation of dimers, tetramers or pentamers of A2B2-modules, linked together by C-terminal extensions (CTE) of B-subunits that extrude from one modular tetramer and occupy two active sites of the adjacent one. This molecular mechanism along with the unexpected observed dynamism of the system, shed light on how the Calvin-Benson cycle is modulated in function of the light environmental changes.
Transient inhibition to light explains stronger V1 responses to dark stimuli
Authors: St-Amand David , Baker Curtis L. 
Published: November 2021

AbstractNeurons in the primary visual cortex (V1) receive excitation and inhibition from distinct parallel pathways processing lightness (ON) and darkness (OFF). V1 neurons overall respond more strongly to dark than light stimuli, consistent with a preponderance of darker regions in natural images, as well as human psychophysics. However, it has been unclear whether this “dark-dominance” is due to more excitation from the OFF pathway or more inhibition from the ON pathway. To understand the mechanisms behind dark-dominance, we record electrophysiological responses of individual simple-type V1 neurons to natural image stimuli and then train biologically inspired convolutional neural networks to predict the neurons’ responses. Analyzing a sample of 74 neurons (in anesthetized, paralyzed cats) has revealed their responses to be more driven by dark than light stimuli, consistent with previous investigations. We show that this asymmetry is predominantly due to slower inhibition to dark stimuli rather than to stronger excitation from the thalamocortical OFF pathway. Consistent with dark-dominant neurons having faster responses than light-dominant neurons, we find dark-dominance to solely occur in the early latencies of neurons’ responses. Neurons that are strongly dark-dominated also tend to be less orientation selective. This novel approach gives us new insight into the dark-dominance phenomenon and provides an avenue to address new questions about excitatory and inhibitory integration in cortical neurons.SignificanceNeurons in the early visual cortex respond on average more strongly to dark than to light stimuli, but the mechanisms behind this bias have been unclear. Here we address this issue by combining single-unit electrophysiology with a novel machine learning model to analyze neurons’ responses to natural image stimuli in primary visual cortex. Using these techniques, we find slower inhibition to light than to dark stimuli to be the leading mechanism behind stronger dark responses. This slower inhibition to light might help explain other empirical findings, such as why orientation selectivity is weaker at earlier response latencies. These results demonstrate how imbalances in excitation vs. inhibition can give rise to response asymmetries in cortical neuron responses.
Motor plans under uncertainty reflect a trade-off between maximizing reward and success
Authors: Wong Aaron L. , Green Audrey L. , Isaacs Mitchell W. 
Published: November 2021

ABSTRACTWhen faced with multiple potential movement options, individuals either reach directly to one of the options, or initiate a reach intermediate between the options. It remains unclear why people generate these two types of behaviors. Using the go-before-you-know task (commonly used to study behavior under choice uncertainty), we examined two key questions. First, do these two types of responses reflect distinct movement strategies, or are they simply examples of a more general response to choice uncertainty? If the former, the relative desirability (i.e., weighing the likelihood of successfully hitting the target versus the attainable reward) of the two target options might be computed differently for direct versus intermediate reaches. We showed that indeed, when exogenous reward and success likelihood (i.e., endogenous reward) differ between the two options, direct reaches were more strongly biased by likelihood whereas intermediate movements were more strongly biased by reward. Second, what drives individual differences in how people respond under uncertainty? We found that risk/reward-seeking individuals generated a larger proportion of intermediate reaches and were more sensitive to trial-to-trial changes in reward, suggesting these movements reflect a strategy to maximize reward. In contrast, risk-adverse individuals tended to generate more direct reaches in an attempt to maximize success. Together, these findings suggest that when faced with choice uncertainty, individuals adopt movement strategies consistent with their risk/reward-seeking tendency, preferentially biasing behavior toward exogenous rewards or endogenous success and consequently modulating the relative desirability of the available options.
Theoretical Guarantees for Phylogeny Inference from Single-Cell Lineage Tracing
Authors: Wang Robert , Zhang Richard , Khodaverdian Alex , Yosef Nir 
Published: November 2021

AbstractCRISPR-Cas9 lineage tracing technologies have emerged as a powerful tool for investigating development in single-cell contexts, but exact reconstruction of the underlying clonal relationships in experiment is plagued by data-related complications. These complications are functions of the experimental parameters in these systems, such as the Cas9 cutting rate, the diversity of indel outcomes, and the rate of missing data. In this paper, we develop two theoretically grounded algorithms for reconstruction of the underlying phylogenetic tree, as well as asymptotic bounds for the number of recording sites necessary for exact recapitulation of the ground truth phylogeny at high probability. In doing so, we explore the relationship between the problem difficulty and the experimental parameters, with implications for experimental design. Lastly, we provide simulations validating these bounds and showing the empirical performance of these algorithms. Overall, this work provides a first theoretical analysis of phylogenetic reconstruction in the CRISPR-Cas9 lineage tracing technology.
Reconstructing essential active zone functions within a synapse
Authors: Tan Chao , Wang Shan Shan H. , de Nola Giovanni , Kaeser Pascal S. 
Published: November 2021

AbstractActive zones are molecular machines that control neurotransmitter release through synaptic vesicle docking and priming, and through coupling of these vesicles to Ca2+ entry. The complexity of active zone machinery has made it challenging to determine which mechanisms drive these roles in release. Here, we induce RIM+ELKS knockout to eliminate active zone scaffolding networks, and then reconstruct each active zone function. Re-expression of RIM1-Zn fingers positioned Munc13 on undocked vesicles and rendered them release-competent. Reconstitution of release-triggering required docking of these vesicles to Ca2+ channels. Fusing RIM1-Zn to CaVβ4-subunits sufficed to restore docking, priming and release-triggering without reinstating active zone scaffolds. Hence, exocytotic activities of the 80 kDa CaVβ4-Zn fusion protein bypassed the need for megadalton-sized secretory machines. These data define key mechanisms of active zone function, establish that fusion competence and docking are mechanistically separable, and reveal that active zone scaffolding networks are not required for release.
Human Biopsies in Nanofibrillar Cellulose Hydrogel – A Novel Method for Long-term Tissue Culture
Authors: Niklander Johanna , Koivuniemi Raili , Stallinger Alexander , Kleinegger Florian , Paasonen Lauri , Schrom Silke , Liegl-Atzwanger Bernadette , Zalaudek Iris , von Campe Gord , Singer Georg , Haybaeck Johannes , Yliperttula Marjo , Rinner Beate 
Published: November 2021

AbstractAdvanced 3D in vitro models are laborious to prepare and susceptible to unintentional design errors due to culture adaptations, cell immaturity, xenofactors or yet incomplete knowledge of the dynamics within tissues or materials. In order to acquire cost-efficient research material with intact in vivo composition, we developed novel tissue culture method with plant-derived scaffolding.Human skin-, foreskin- and glioblastoma multiforme biopsies were dissected mechanically and cultivated for 28 days in plant-derived nanofibrillar cellulose hydrogel. Comparative cultures were done using mouse sarcoma tumor –derived Matrigel™. Long-term preservation of cultivated tissues was evaluated against typical immunohistochemical biomarkers for each tissue type: skin tissues for cytokeratins 5/6, E-cadherin and vimentin for sustained tissue structures, and brain neoplasia for Olig2, S100, Nestin, NOTCH1, MAP2 and GFAP for preserved disease profile.Histological analysis from both culture conditions showed that until day 28, all cultivated biopsy types were able to sustain their characteristic protein expressions without signs of necrosis. We here conclude a novel tissue culture model in xeno-free 3D scaffolding, that can enable long-term sample storage in vitro, studies of human tumor tissues and their non-neoplastic microenvironment, and innovations in personalized medicine research.