bluuebunny/crossref_metadata_2025_split huggingface dataset:
The degree of context un/familiarity impacts the emotional feeling and preaware cardiac-brain activity: a study with emotionally salient naturalistic paradigm using DENS Dataset
Authors: Mishra Sudhakar , Tiwary U.S. 
Published: August 2021

ABSTRACTEmotion experiments with naturalistic paradigms are emerging and giving new insights into dynamic brain activity. Context familiarity is considered as an important dimensions of emotion processing by appraisal theorists. However, how the context un/familiarity of the naturalistic stimuli influences the central and autonomic activity is not probed yet [check it]. Hence, we tried to address this issue in this work by breaking it down into three questions. 1) What is the relation between context un/familiarity with the neural correlates of self-assessment affective dimensions viz. valence and arousal; 2) the influence of context un/familiarity in cardiac-brain mutual interaction during emotion processing; 3.) brain network reorganization to accommodate the degree of context familiarity. We found that the less-context familiarity is primarily attributed to negative emotion feeling mediated by lack of predictability of sensory experience. Whereas, with high-context familiarity, both positive and negative emotions are felt. For less-context familiarity, the arousal activity is negatively correlated with EEG power. In addition, the cardiac activity for both high and less context familiarity is modulated before the reported self-awareness of emotional feeling. The correlation of cortical regions with cardiac activity and connectivity patterns reveals that ECG is modulated by salient feature during pre-awareness and correlates with AIC and conceptual hub in high-familiarity. Whereas, for the low familiarity, the cardiac activity is correlated with the exteroceptive sensory regions. In addition, we found that OFC and dmPFC have high connectivity with less-context familiarity, whereas AIC has high connectivity with high-context familiarity. To the best of our knowledge, the context familiarity and its influence on cardiac and brain activity have never been reported with a naturalistic paradigm. Hence, this study significantly contributes to understanding automatic processing of emotions by analyzing the effect of context un/familiarity on affective feelings, the dynamics of cardiac-brain mutual interaction, and the brain’s effective connectivity during pre-awareness.
The looping lullaby: closed-loop neurostimulation decreases sleepers’ sensitivity to environmental noise
Authors: Pathak Vidushi , Juan Elsa , van der Goot Reina , Talamini Lucia M. 
Published: August 2021

AbstractStudy ObjectiveSleep is critical for physical and mental health. However, sleep disruption due to noise is a growing problem, causing long-lasting distress and fragilizing entire populations mentally and physically. Here for the first time, we tested an innovative and non-invasive potential countermeasure for sleep disruptions due to noise.MethodsWe developed a new, modeling-based, closed-loop acoustic neurostimulation procedure (CLNS) to precisely phase-lock stimuli to slow oscillations (SO). We used CLNS to align, soft sound pulses to the start of the SO positive deflection to boost SO and sleep spindles during non-rapid eye movement (NREM) sleep. Participants underwent three overnight EEG recordings. The first night served to determine each participant’s individual noise arousal threshold. The remaining two nights occurred in counterbalanced order: in the “Disturbing night”, loud, real-life noises were repeatedly presented; in the “Intervention night”, similar loud noises were played while using the CLNS to boost SO. All experimental manipulations were performed in the first three hours of sleep; participants slept undisturbed for the rest of the night.ResultsIn contrast to the Disturbing night, the probability of arousals caused by noise was significantly decreased in the Intervention night. Moreover, the CLNS intervention increased NREM duration and sleep spindle power across the night.ConclusionsThese results show that our CLNS procedure can effectively protect sleep from disruptions caused by noise. Remarkably, even in the presence of loud environmental noise, CLNS’ soft and precisely timed sound pulses played a beneficial role in protecting sleep continuity. This represents the first successful attempt at using CLNS in a noisy environment.Statement of SignificanceExposure to noise during sleep impairs sleep quality, leading to impaired biological functioning, decreased day-time performance and higher occurrence of accidents. Slow wave sleep is hallmarked by slow oscillations (SO) and sleep spindles, both of which are markers of sleep stability. In previous experiments, acoustic stimulation has shown potential in enhancing SO and sleep spindles. Whether these manipulations also work to stabilize sleep against the disrupting effects of environmental noise remains unclear. Here we use a new closed-loop approach to precisely align subtle acoustic stimuli with SO phase. We show that this method effectively stabilizes sleep in the presence of noise. Our results bear crucial relevance for improving sleep in the general public and in many high-risk professions.
The initial response of females towards congeneric males matches the propensity to hybridise in Ophthalmotilapia
Authors: Van Steenberge Maarten , Jublier Noémie , Kéver Loïc , Gresham Sophie , Derycke Sofie , Snoeks Jos , Parmentier Eric , Poncin Pascal , Verheyen Erik 
Published: August 2021

AbstractCichlid radiations often harbour closely related species with overlapping niches and distribution ranges. Such species sometimes hybridise in nature, which raises the question how can they coexist. This also holds for the Tanganyika mouthbrooders Ophthalmotilapia ventralis and O. nasuta. Earlier studies found indications of asymmetrical hybridisation with females of O. ventralis accepting males of O. nasuta, but not the other way around. We hypothesised that this was due to differences in the capacity for species recognition. Given the higher propensity of O. ventralis females towards hybridisation, we expect a reduced ability for species recognition in O. ventralis females, compared to O. nasuta females. We staged two experiments, one focusing on 22 female O. nasuta and one on 21 female O. ventralis. These fish were placed in one half of a tank and briefly exposed to a conspecific or a heterospecific male, a conspecific female, or nothing (control). Female response was evaluated by scoring six tracking parameters and by noting the occurrence of ten discrete behaviours before and during the encounter. Females always responded to the presence of another fish by approaching it. Remarkably, for both O. nasuta and O. ventralis, we did not find a different response between encounters with conspecific males and females. However, in agreement with our hypothesis, O. nasuta females behaved differently towards conspecific or heterospecific males, whereas O. ventralis females did not. When presented with a heterospecific male, O. nasuta females performed a lower number of ‘ram’ behaviours. Additionally, they never displayed the ‘flee’ behaviour, a component of the species’ mating repertoire that was seen in all but one of the presentations with a conspecific male. Our findings show that differences in species recognition at first encounter predict to a large degree the outcome of the mating process, even in the absence of mating behaviour.
Continuous sensing of nutrients and growth factors by the mTORC1-TFEB axis
Authors: Sparta Breanne , Pargett Michael , Kosaisawe Nont , Albeck John G. 
Published: August 2021

AbstractmTORC1 senses nutrient and growth factor status and phosphorylates downstream targets, including the transcription factor TFEB, to coordinate metabolic supply and demand. The molecular mechanisms of mTORC1 activation are thought to enforce a strict requirement for simultaneous amino acid and growth factor stimuli, but this model has not been evaluated with quantitative or single-cell methods. Here, we develop a series of fluorescent protein-TFEB fusions and investigate how combinations of stimuli jointly regulate signaling from mTORC1 to TFEB at the single-cell level. Live-cell imaging of individual cells revealed that mTORC1-TFEB signaling responds with graded changes to individual amino acid and growth factor inputs, rather than behaving as a logical “AND” gate. We find that mTORC1 inputs can be sequentially sensed, with responses that vary between mTORC1 substrates and are amplified by input from other kinases, including GSK3β. In physiologically relevant concentrations of amino acids, we observe fluctuations in mTORC1-TFEB signaling that indicate continuous responsiveness to nutrient availability. Our results clarify how the molecular regulation of mTORC1 enables homeostatic processes at the cellular level and provide a more precise understanding of its behavior as an integrator of multiple inputs.
Augmenting Neutralization breadth against Diverse HIV-1 by increasing the Ab-Ag interface on V2
Authors: Gao Nan , Gai Yanxin , Meng Lina , Wang Chu , Wang Wei , Li Xiaojun , Gu Tiejun , Louder Mark K. , Doria-Rose Nicole A. , Wiehe Kevin , Nazzari Alexandra F. , Olia Adam S. , Gorman Jason , Rawi Reda , Wu Wenmin , Smith Clayton , Khant Htet , de Val Natalia , Yu Bin , Luo Junhong , Niu Haitao , Tsybovsky Yaroslav , Liao Huaxin , Kepler Thomas B. , Kwong Peter D. , Mascola John R. , Qin Chuan , Zhou Tongqing , Yu Xianghui , Gao Feng 
Published: August 2021

SUMMARYUnderstanding maturation pathways of broadly neutralizing antibodies (bnAbs) against HIV-1 in non-human primates can be highly informative for HIV-1 vaccine development. We now obtained a lineage of J038 from Chinese rhesus macaques after 7-years of SHIV infection. J038 has short complementary determining loops and neutralizes 54% of global circulating HIV-1 strains. Its binding induces a unique “up” conformation for one of the V2 loops in the trimeric envelope glycoprotein (Env) and is heavily dependent on glycan, which provides nearly half of the binding surface. The unmutated common ancestor of the J038 lineage antibodies binds monomeric gp120 and neutralizes the autologous virus. Continuous maturation enhances neutralization potency and breadth of J038 lineage antibodies via expanding antibody-Env contact areas surrounding the core region contacted by germline-encoded residues. Developmental details and recognition features of J038 lineage antibodies revealed here provide a new pathway for maturation elicitation of V2-targeting bnAbs.Highlights•Long-term infected NHPs develop antibodies neutralizing up to 54% of HIV-1 strains•Antibody J038 binds one V2 loop on HIV-1 Env trimer in a unique “up” position•UCA of the J038 lineage effectively neutralizes the autologous virus•J038 lineage antibodies mature through gradually increased contact to glycans
DAAM mediates the assembly of long-lived, treadmilling stress fibers in collectively migrating epithelial cells in Drosophila
Authors: Sherrard Kristin M , Cetera Maureen , Horne-Badovinac Sally 
Published: August 2021

ABSTRACTStress fibers (SFs) are actomyosin bundles commonly found in individually migrating cells in culture. However, whether and how cells use SFs to migrate in vivo or collectively is largely unknown. Studying the collective migration of the follicular epithelial cells in Drosophila, we found that the SFs in these cells show a novel treadmilling behavior that allows them to persist as the cells migrate over multiple cell lengths. Treadmilling SFs grow at their fronts by adding new integrin-based adhesions and actomyosin segments over time. This causes the SFs to have many internal adhesions along their lengths, instead of adhesions only at the ends. The front-forming adhesions remain stationary relative to the substrate and typically disassemble as the cell rear approaches. By contrast, a different type of adhesion forms at the SF’s terminus that slides with the cell’s trailing edge as the actomyosin ahead of it shortens. We further show that SF treadmilling depends on cell movement and identify a developmental switch in the formins that mediate SF assembly, with DAAM acting during migratory stages and Diaphanous acting during post-migratory stages. We propose that treadmilling SFs keep each cell on a linear trajectory, thereby promoting the collective motility required for epithelial migration.
Regeneration of the larval sea star nervous system by wounding induced respecification to the sox2 lineage
Authors: Zheng Minyan , Zueva Olga , Hinman Veronica F. 
Published: August 2021

AbstractThe ability to restore lost body parts following traumatic injury is a fascinating area of biology that challenges current understanding of the ontogeny of differentiation. The origin of new cells needed to regenerate lost tissue, and whether they are pluripotent stem cells, tissue-specific stem cells or have de- or trans- differentiated, remains one of the most important open questions in regeneration. Additionally, it is not clearly known whether developmental gene regulatory networks (GRNs) are reused to direct specification in these cells or whether regeneration specific networks are deployed. Echinoderms, including sea stars, have extensive ability for regeneration and have therefore been the subject of many thorough studies on the ultrastructural and molecular properties of cells needed for regeneration. However, the technologies for obtaining transgenic echinoderms are limited and tracking cells involved in regeneration, and thus identifying the cellular sources and potencies has proven challenging. In this study we develop new transgenic tools for cell tracking in the regenerating bipinnaria larva of the sea star Patira minaita. We show that the larval serotonergic nervous system can regenerate following decapitation. Using a BAC-transgenesis approach with photoconvertible fluorescent proteins, we show that expression of the pan ectodermal marker, sox2, is induced in previously sox2 minus cells at the wound site, even when cell division is inhibited. sox2+ cells give rise to new sox4+ neural precursors that then proceed along an embryonic neurogenesis pathway to reform the anterior nervous systems. sox2+ cells contribute to only neural and ectoderm lineages, indicating that these progenitors maintain their normal, embryonic lineage restriction. This indicates that sea star larval regeneration uses a combination of existing lineage restricted stem cells, as well as respecification of cells into neural lineages, and at least partial reuse of developmental GRNs to regenerate their nervous system.
A method for simultaneously monitoring phloem and xylem reconnections in grafted watermelon seedlings
Authors: Xu Jianuo , Wei Xiaoyang , Xiong Mu , Zhang Ting , Liu Changjin , Bie Zhilong , Huang Yuan 
Published: August 2021

AbstractGrafting is an effective way to increase watermelon tolerance to biotic and abiotic stresses. However, the survival of grafted seedlings largely depends on successful graft formation. Therefore, understanding the graft formation process, particularly the vascular reconnection process is of critical importance. This study found that lignin in watermelon stem shows strong auto-fluorescence under blue-light excitation which makes blue-light excited fluorescent tracers (FTs) such as 5(6)-carboxy fluorescein diacetate (CFDA) become unsuitable for assaying vascular connectivity in watermelon. In contrast, UV-light excited esculin and red-light excited acid fuchsin were proved to be efficient FTs for monitoring the phloem and xylem connectivity, respectively, in self-grafted watermelon. Furthermore, a combined application of esculin to the scion cotyledon and acid fuchsin to the rootstock root enabled simultaneous monitoring of the phloem and xylem connectivity in individual self-grafted watermelon seedlings. In addition, this method is also applicable in investigating the phloem and xylem reconnections in self-grafted melon and cucumber, and heterograft of watermelon, melon and cucumber onto pumpkin rootstock. Based on this established method, we found that phloem and xylem reconnections are not timely separated in self-grafted watermelon. Furthermore, low temperature and removal of the rootstock cotyledons both delayed the vascular reconnection process in watermelon. In conclusion, this new method provides a convenient, accurate and rapid way to analyze the vascular connectivity not only in watermelon, but also in other cucurbit crops.
Ccr4-Not complex reduces transcription efficiency in heterochromatin
Authors: Monteagudo Pablo , Brönner Cornelia , Kohvaei Parastou , Amedi Haris , Canzar Stefan , Halic Mario 
Published: August 2021

AbstractHeterochromatic silencing is thought to occur through a combination of transcriptional silencing and RNA degradation, but the relative contribution of each pathway is not known. In this study we analyzed RNA Polymerase II (RNA Pol II) occupancy and levels of nascent and steady-state RNA in different strains of fission yeast, in order to quantify the contribution of each pathway to heterochromatic silencing. We found that transcriptional silencing consists of two components, reduced RNA Pol II accessibility and, unexpectedly, reduced transcriptional efficiency. Heterochromatic loci showed lower transcriptional output compared to euchromatic loci, despite the presence of comparable amounts of RNA Pol II in both types of regions. We determined that the Ccr4-Not complex and H3K9 methylation are required for reduced transcriptional efficiency in heterochromatin and that a subset of heterochromatic RNA is degraded more rapidly than euchromatic RNA. Finally, we quantified the contribution of different chromatin modifiers, RNAi and RNA degradation to each silencing pathway. Our data show that several pathways contribute to heterochromatic silencing in a locus-specific manner and reveal transcriptional efficiency as a new mechanism of silencing.
BioPhi: A platform for antibody design, humanization and humanness evaluation based on natural antibody repertoires and deep learning
Authors: Prihoda David , Maamary Jad , Waight Andrew , Juan Veronica , Fayadat-Dilman Laurence , Svozil Daniel , Bitton Danny A. 
Published: August 2021

AbstractDespite recent advances in transgenic animal models and display technologies, humanization of mouse sequences remains the primary route for therapeutic antibody development. Traditionally, humanization is manual, laborious, and requires expert knowledge. Although automation efforts are advancing, existing methods are either demonstrated on a small scale or are entirely proprietary. To predict the immunogenicity risk, the human-likeness of sequences can be evaluated using existing humanness scores, but these lack diversity, granularity or interpretability. Meanwhile, immune repertoire sequencing has generated rich antibody libraries such as the Observed Antibody Space (OAS) that offer augmented diversity not yet exploited for antibody engineering. Here we present BioPhi, an open-source platform featuring novel methods for humanization (Sapiens) and humanness evaluation (OASis). Sapiens is a deep learning humanization method trained on the OAS database using language modeling. Based on anin silicohumanization benchmark of 177 antibodies, Sapiens produced sequences at scale while achieving results comparable to that of human experts. OASis is a granular, interpretable and diverse humanness score based on 9-mer peptide search in the OAS. OASis separated human and non-human sequences with high accuracy, and correlated with clinical immunogenicity. Together, BioPhi offers an antibody design interface with automated methods that capture the richness of natural antibody repertoires to produce therapeutics with desired properties and accelerate antibody discovery campaigns.BioPhi is accessible athttps://biophi.dichlab.organdhttps://github.com/Merck/BioPhi.
Charting Brain Growth and Aging at High Spatial Precision
Authors: Rutherford Saige , Fraza Charlotte , Dinga Richard , Kia Seyed Mostafa , Wolfers Thomas , Zabihi Mariam , Berthet Pierre , Worker Amanda , Verdi Serena , Andrews Derek , Han Laura , Bayer Johanna , Dazzan Paola , McGuire Phillip , Mocking Roel T. , Schene Aaart , Pennix Brenda W. , Sripada Chandra , Tso Ivy F. , Duval Elizabeth R. , Chang Soo-Eun , Heitzeg Mary , Burt S. Alexandra , Hyde Luke , Amaral David , Nordahl Christine Wu , Andreasssen Ole A. , Westlye Lars T. , Zahn Roland , Ruhe Henricus G. , Beckmann Christian , Marquand Andre F. 
Published: August 2021

AbstractDefining reference models for population variation, and the ability to study individual deviations is essential for understanding inter-individual variability and its relation to the onset and progression of medical conditions. In this work, we assembled a reference cohort of neuroimaging data from 82 sites (N=58,836; ages 2-100) and use normative modeling to characterize lifespan trajectories of cortical thickness and subcortical volume. Models are validated against a manually quality checked subset (N=24,354) and we provide an interface for transferring to new data sources. We showcase the clinical value by applying the models to a transdiagnostic psychiatric sample (N=1,985), showing they can be used to quantify variability underlying multiple disorders whilst also refining case-control inferences. These models will be augmented with additional samples and imaging modalities as they become available. This provides a common reference platform to bind results from different studies and ultimately paves the way for personalized clinical decision making.
Overexpression of SHORT-ROOT2 transcription factor enhanced the outgrowth of mature axillary buds in poplar trees
Authors: Yi Minglei , Yang Heyu , Yang Shaohui , Wang Jiehua 
Published: August 2021

AbstractPlant branching is usually prevented by an actively proliferating apex. In poplars, one GRAS family member, SHORT-ROOT2 (PtSHR2), was preferentially expressed in axillary buds (AXBs) and was inducible during bud maturation and activation. Overexpression of PtSHR2 (PtSHR2OE) in hybrid poplar impaired the apical dominance and simultaneously promoted the outgrowth of axillary branches below the maturation point (BMP), accompanied by regulated expression of genes critical for axillary meristem initiation and bud formation.Following a detained phenotypic characterization, we compared the IAA and trans-zeatin levels in apical shoots and AXBs of wild-type and PtSHR2OE trees, together with gene expression analyses and defoliation, decapitation, and hormone reapplication assays.PtSHR2OE AXBs contained a significantly lower ratio of auxin to cytokinin than wild-type AXBs, particularly in those below the BMP. Decapitation induced a faster bud burst in PtSHR2OE trees than in wild-type plants, and it could be strongly inhibited by exogenously applied auxin and cytokinin biosynthesis inhibitor, but only partially inhibited by N-1-naphthylphthalamic acid (NPA).An impaired basipetal auxin transport, rather than an insufficient auxin biosynthesis or auxin insensitivity, disturbed the local hormonal homeostasis in PtSHR2OE AXBs, which in turn enhanced the axillary bud initiation and promoted the bud release.HighlightOverexpression of PtSHR2 in poplar impaired the apical dominance and promoted axillary bud outgrowth below the maturation point through disturbing the basipetal auxin transport and auxin and cytokinin homeostasis.