bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic modulation of auditory hair cell stereocilia membrane mechanics by the scrambling mechanotransduction complex
Authors: George Shefin S. , Ricci Anthony J. 
Published: September 2024

SummaryInner ear sensory hair cells convert mechanical deflection of their hair bundle into an electrical signal by gating novel mechanoelectrical transduction (MET) channels. Transmembrane channel-like proteins (TMCs) are a component of the MET machinery and part of a superfamily of molecules whose members are ion channels or lipid scramblases. As the stereocilia membrane modulates MET channels properties and the stereocilia membrane has different properties than the soma, we investigated the potential scramblase activity of the MET machinery using a novel viscosity sensor BODIPY 1c. Developmental, genetic, electrophysiological and pharmacological data demonstrate that both TMC1 and TMC2 are mechanosensitive scramblases as activity depends on MET channel being open. Blockage of scramblase activity unmasks a second process that increases effective membrane viscosity independent of MET machinery. Together our data reveal a dynamic regulation of stereocilia membrane that may underlie the speed and sensitivity of the MET process.
Long non-coding RNA UCA1 affects chromatin remodeling via SMARCA2-containing SWI/SNF complex in human colorectal cancer
Authors: Neve Bernadette , Bachir Elsa Hadj , Duchêne Belinda , Souidi Mouloud , Figeac Martin , Meneboo Jean-Pascal , Leteurtre Emmanuelle ,   OrgaRES consortium, Jonckheere Nicolas , Vincent Audrey , Van Seuningen Isabelle 
Published: September 2024

SummaryDifferential lncRNA expression has been correlated to clinical characteristics of colorectal cancers (CRC), which are the second leading cause of cancer-related deaths. LncRNA UCA1 plays a role in epigenetic gene regulation in diverse cancers. We studied CRC cell properties in CRISPR/Cas9 HT29-derived models and, interestingly, UCA1-depleted HT29 cells presented an increased stem-cell phenotype. We show that loss of UCA1 affected SWI/SNF chromatin remodeling complexes, which are previously shown to be involved in maintaining stem-cell properties. Not only was UCA1 permissive for induced SWI/SNF subunit SMARCA2 (BRM) expression upon chemo-drug treatment, but it also affected subunit compositions of SWI/SNF complexes by direct interaction of UCA1 with both ATP helicase BRM and BRG1. UCA1 is known to stimulate proliferation and decrease apoptosis, and we here show that it can restrain cells from a stem cell phenotype. The dual action of UCA1 revealed in this study highlights the complex actions of lncRNAs in cancer.
CPK3-mediated cytosolic-nuclear translocation of bHLH107 recruits HY5 to regulate the Cu2+-triggered upregulation ofACS8
Authors: Yu Yue , Liu Haifeng , Chen Xiangsong , Chu Zhaohui 
Published: September 2024

ABSTRACTCopper serves as a micronutrient for plant growth and development and has been a key component of copper-based antimicrobial compounds (CBACs) for protection against plant diseases for more than 130 years. We previously revealed that nanomolar- to-micromolar concentrations of Cu2+elicit plant immune responses by activating the expression of the ethylene synthesis rate-limiting enzymeACS8, which is dependent on the promoter copper response element (CuRE)cis-element. Here, we genetically confirmed that Cu2+-induced resistance toPseudomonas syringaepv.tomato(Pst) DC3000 is dependent on the CuRE inACS8. Upon screening for CuRE-binding transcription factors, bHLH107, which is required for Cu2+-triggered activation ofACS8expression and resistance toPstDC3000, was identified via DNA-pull-down and mass spectrometry (MS) assays. Calcium-dependent protein kinase 3 (CPK3) interacts with and phosphorylates bHLH107 at Ser62 and Ser72 to mediate bHLH07 translocation from the cytoplasm into the nucleus, where it interacts withArabidopsisELONGATED HYPOCOTYL5 (HY5). HY5 directly binds to the G-box and acts as a coactivator to promote bHLH107 binding to the CuREcis-element and to increase transcription ofACS8upon Cu2+treatment. Overall, we revealed a CPK3-bHLH107-HY5 module that regulates the Cu2+-responsive regulatory network upstream ofACS8that is involved in the cytosolic-nuclear translocation of bHLH107.
Measurement of cellular traction forces during confined migration
Authors: Hockenberry Max A. , Ulmer Andrew J. , Rapp Johann L. , Leibfarth Frank A. , Bear James E. , Legant Wesley R. 
Published: September 2024

AbstractTo migrate efficiently through tissues, cells must transit through small constrictions within the extracellular matrix. However, in vivo environments are geometrically, mechanically, and chemically complex, and it has been difficult to understand how each of these parameters contribute to the propulsive strategy utilized by cells in these diverse settings. To address this, we employed a sacrificial micromolding approach to generate polymer substrates with tunable stiffness, controlled adhesivity, and user-defined microscale geometries. We combined this together with live-cell imaging and three-dimensional traction force microscopy (TFM) to quantify the forces that cells use to transit through constricting channels. Surprisingly, we observe that cells migrating through compliant constrictions take longer to transit and experience greater nuclear deformation than those migrating through more rigid constrictions. TFM reveals that this deformation is generated by inwardly directed contractile forces that decrease the size of the opening and pull the walls closed around the nucleus. These findings show that nuclear deformation during confined migration can be accomplished by internal cytoskeletal machinery rather than by reactive forces from the substrate, and our approach provides a mechanism to test between different models for how cells translocate their nucleus through narrow constrictions. The methods, analysis, and results presented here will be useful to understand how cells choose between propulsive strategies in different physical environments.Significance StatementCell migration is critical for both physiological events like wound healing and pathological events like metastasis. Understanding how cells move through complex environments will assist efforts to enhance or inhibit such processes. We developed a method to quantify the forces that cells use to move through multidimensional environments, including through narrow constrictions like those in tissues. Surprisingly, we find that cells transiting through soft constrictions take longer and deform more than those transiting through rigid constrictions, and we connect this finding to inwardly directed contractile forces generated by migrating cells. Together, this work reveals a key role for substrate rigidity to regulate cell transit through confining geometries and provides a quantitative platform to investigate similar processes in other settings.
Endosomal hyper-acidification via proton-activated chloride channel deletion in neurons impairs AMPA receptor endocytosis and LTD
Authors: Chen Kevin H. , Yang Junhua , Liu Bian , Jiang Chaohua , Koylass Nicholas , Zhang Zhe , Sun Shuying , Huganir Richard , Qiu Zhaozhu 
Published: September 2024

AbstractEndosomal homeostasis is critical for neuronal function, including the post-synaptic trafficking of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs). Dynamic AMPAR trafficking is a major component of synaptic plasticity, such as hippocampal long-term potentiation (LTP) and long-term depression (LTD) and is thought to be required for learning and memory. Dramatic alteration of endosomal pH has been reported to negatively affect synaptic transmission and neural development, but the underlying mechanisms by which pH is involved in AMPAR trafficking are unclear. Here, we show that the proton-activated chloride (PAC) channel localizes to early and recycling endosomes along neuronal dendrites and prevents hyper-acidification of endosomes. To directly measure AMPAR endocytosis, we used a new method to assess LTD using HaloTag-GluA2 and found that the loss of PAC reduces AMPAR internalization during chemical LTD in primary neurons, while AMPAR trafficking in unstimulated cells or during chemical LTP is unaffected. Consistently, pyramidal neuron-specific PAC knockout mice had impaired hippocampal LTD, but not LTP, and performed poorly in the Morris water maze reversal test, exhibiting an inability to adapt to changing environments (also referred to as behavioral flexibility). We conclude that proper maintenance of pH by PAC is important during LTD to regulate AMPAR trafficking in a manner critical for animal physiology and behavior.SummaryThe ability to adapt to changing environments stems from the plasticity of neurons, which can modulate their synaptic strength in response to neural activity. We discovered a novel mechanism by which an endosomal proton-activated chloride channel (PAC) is involved in synaptic weakening, or long-term depression (LTD). To improve tools used to study LTD, we developed a live-cell imaging assay to directly observe α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) endocytosis. PAC-deficient neurons have hyper-acidified endosomes and fail to endocytose AMPARs during LTD. Neuron-specific PAC knockout mice have impaired hippocampal LTD and fail to adapt to changes in their environment. The role of endosomal pH in synaptic function is understudied, and our results provide a novel mechanism whereby PAC can affect synaptic LTD.
Three-fold Quantum Leap in Butterfly Nectar Knowledge: A Comprehensive Study Revolutionizing Conservation Strategies
Authors: Dunlap Susan C. 
Published: September 2024

AbstractThis study addresses a critical gap in butterfly conservation: the lack of comprehensive data on nectar plants preferred by US butterflies. The research presented has dramatically improved our understanding, increasing knowledge of nectar plant genera used by butterflies from representing just 25% of all species to an impressive 90%, a more than three-fold or 260% improvement in species representation. This substantial expansion in data has significant implications for conservation strategies and will shift our approach to butterfly habitat restoration. A seven-year longitudinal study of adult butterfly nectaring behavior resulted in over 12,000 detailed records of nectar plant usage by US butterflies. This curated dataset provides a valuable resource with significant implications for all levels of effort directed at butterfly conservation.Recent recommendations for monarch habitat restoration suggest a balanced mix of host and nectar plants. However, the implementation of this guideline has been hampered by a lack of specific data on monarchs’ preferred nectar plants. New research addresses this gap, providing necessary information to refine plant selection for butterfly habitats. This study also gives cause to modify the current approach of creating generalized pollinator habitats, suggesting that focusing on plants preferred by long-distance migrating butterflies like monarchs may effectively support a broad range of pollinators.
GoldPolish-Target: Targeted long-read genome assembly polishing
Authors: Zhang Emily , Coombe Lauren , Wong Johnathan , Warren René L , Birol Inanç 
Published: September 2024

AbstractBackgroundAdvanced long-read sequencing technologies, such as those from Oxford Nanopore Technologies and Pacific Biosciences, are finding a wide use inde novogenome sequencing projects. However, long reads typically have higher error rates relative to short reads. If left unaddressed, subsequent genome assemblies may exhibit high base error rates that compromise the reliability of downstream analysis. Several specialized error correction tools for genome assemblies have since emerged, employing a range of algorithms and strategies to improve base quality. However, despite these efforts, many genome assembly workflows still produce regions with elevated error rates, such as gaps filled with unpolished or ambiguous bases. To address this, we introduce GoldPolish-Target, a modular targeted sequence polishing pipeline. Coupled with GoldPolish, a linear-time genome assembly algorithm, GoldPolish-Target isolates and polishes user-specified assembly loci, offering a resource-efficient means for polishing targeted regions of draft genomes.ResultsExperiments usingDrosophila melanogasterandHomo sapiensdatasets demonstrate that GoldPolish-Target can reduce insertion/deletion (indel) and mismatch errors by up to 49.2% and 53.4% respectively, achieving base accuracy values upwards of 99.9% (Phred score Q>30). This polishing accuracy is comparable to the current state-of-the-art, Medaka, while exhibiting up to 36-fold shorter run times and consuming 94% less memory, on average.ConclusionGoldPolish-Target, in contrast to most other polishing tools, offers the ability to target specific regions of a genome assembly for polishing, providing a computationally light-weight and highly scalable solution for base error correction.Availabilityhttps://github.com/bcgsc/goldpolish
TRACKing Tandem Repeats: a customizable pipeline for identification and cross-species comparisons
Authors: Adam Carolina L. , Rocha Joana , Sudmant Peter , Rohlfs Rori 
Published: September 2024

AbstractSummaryTRACK is a user-friendly command-line pipeline designed to consolidate the discovery and comparison of tandem repeats (TRs) across species. TRACK facilitates the cataloging and filtering of TRs based on reference genomes or T2T transcripts, and applies reciprocal LiftOver and sequence alignment methods to identify putative homologous TRs between species. For further streamlined analyses, TRACK can be used to genotype TRs and subsequently estimate and plot basic population genetic statistics. By integrating existing tools into one integrated workflow, TRACK enhances TR analysis accessibility and reproducibility, while offering flexibility for the user.AvailabilityThe TRACK toolkit with step-by-step tutorial is freely available athttps://github.com/caroladam/track.
Validity and reliability of the Hypersensitive Narcissism Scale (HSNS) in China
Authors: Li Yuxin , Zou Fan , Cheng Hao 
Published: September 2024

AbstractBackgroundWink distinguishes between explicit and implicit narcissism, the latter being vulnerability-sensitive narcissism, which manifests itself as outward humility and inhibition masking an underlying pompous outlook and sense of entitlement. Early measures of vulnerability-sensitive narcissism used Murray’s Narcissism Scale, which was explored by measuring the narcissism levels of Harvard undergraduates. Hendin and Cheek subsequently developed the Vulnerable Sensitive Narcissism Scale based on this narcissism scale. In addition to this, there are few ways to measure vulnerability-sensitive narcissism, and Chinese measurement tools on narcissism mainly measure explicit narcissism, neglecting to accurately measure vulnerability-sensitive narcissism, and failing to completely respond to an individual’s implicit narcissistic traits.AimThe hypersensitive narcissism scale was applied to college students to explore the factor structure of the scale under the background of Chinese culture, and to test its reliability and validity.Methods1000 questionnaires were distributed to college students, and 912 valid questionnaires were collected. Self-Esteem Scale, Aggression Scale and Narcissism subscale of Dark Triad Scale were used as the criterion. After 3 weeks, 100 college students were randomly selected for retest.ResultsThe exploratory factor analysis showed that one dimension should be extracted. Eigenvalue was 5.352 and 53.518% cumulative variance interpretation rate. The confirmatory factor analysis showed that the scale structure validity was good (χ2/df=3.237,CFI=0.936,TLI=0.931, RMSEA=0.066,SRMR=0.053). Internal consistency reliability of the scale was 0.785; The test-retest reliability was 0.833, and the criterion correlation validity reached a significant level.ConclusionThe Chinese version of hypersensitive narcissism scale has good reliability and validity, which can effectively measure hypersensitive narcissism. The localisation of the scale can better serve the research and development of the university student population on the one hand, and on the other hand, it can help the research in this field to have a more in-depth development in China.
Aspergillus nidulanscell wall integrity kinase, MpkA, impacts cellular phenotypes that alter mycelial-material mechanical properties
Authors: Gray Kelsey , Edwards Harley , Doan Alexander G. , Huso Walker , Lee JungHun , Pan Wanwei , Bolima Nelanne , Morse Meredith E. , Yoda Sarah , Gautam Isha , Harris Steven D. , Zupan Marc , Wang Tuo , deCarvalho Tagide , Marten Mark R. 
Published: September 2024

ABSTRACTMycelial materials are an emerging, natural material made from filamentous fungi that have the potential to replace unsustainable materials used in numerous commercial applications (e.g., packaging, textiles, construction). Efforts to change the mechanical properties of mycelial-materials have typically involved altering growth medium, processing approaches, or fungal species. Although these efforts have shown varying levels of success, all approaches have shown there is a strong correlation between phenotype (of both fungal mycelia and mycelial material’s assembly) and resultant mechanical properties. We hypothesize that genetic means can be used to generate specific fungal phenotypes, leading to mycelial materials with specific mechanical properties. To begin to test this hypothesis, we used a mutant of the model filamentous fungus,Aspergillus nidulans, with a deletion of the last kinase in the cell wall integrity (CWI) signaling pathway, mpkA. We generated one set of mycelial materials from the ΔmpkAdeletion mutant (A1404), and another from its isogenic parent (A1405; control). When subjected to tensile testing, and compared to material generated from the control, ΔmpkAmaterial has similar elastic modulus, but significantly increased ultimate tensile strength, and strain at failure. When subjected to a fragmentation assay (i.e., resistance to shear-stress), the ΔmpkAmaterial also had higher relative mechanical strength. To determine possible causes for this behavior, we carried out a comprehensive set of phenotype assessments focused on: three-dimensional structure, hyphal morphology, hyphal growth behaviors, and conidial development. We find, compared to the control, material generated from the ΔmpkAmutant manifests significantly less development, a modified cell wall composition, larger diameter hyphae, more total biomass, higher water capacity and more densely packed material, which all appear to impact the altered mechanical properties.
Cross-trial prediction of treatment response to transcranial direct current stimulation in patients with major depressive disorder
Authors: Burkhardt Gerrit , Goerigk Stephan , Bulubas Lucia , Dechantsreiter Esther , Keeser Daniel , Vogelmann Ulrike , von Wartensleben Katharina , Wolf Johannes , Plewnia Christian , Fallgatter Andreas , Langguth Berthold , Normann Claus , Frase Lukas , Zwanzger Peter , Kammer Thomas , Schönfeldt-Lecuona Carlos , Kamp Daniel , Bajbouj Malek , Koutsouleris Nikolaos , Brunoni Andre R , Padberg Frank 
Published: September 2024

AbstractMachine-learning (ML) classification may offer a promising approach for treatment response prediction in patients with major depressive disorder (MDD) undergoing non-invasive brain stimulation. This analysis aims to develop and validate such classification models based on easily attainable sociodemographic and clinical information across two randomized controlled trials on transcranial direct-current stimulation (tDCS) in MDD. Using data from 246 patients with MDD from the randomized-controlled DepressionDC and ELECT-TDCS trials, we employed an ensemble machine learning strategy to predict treatment response to either active tDCS or sham tDCS/placebo, defined as ≥ 50% reduction in the Montgomery-Åsberg Depression Rating Scale at 6 weeks. Separate models for active tDCS and sham/placebo were developed in each trial and evaluated for external validity across trials and for treatment specificity across modalities. Additionally, models with above-chance detection rates were associated with long-term outcomes to assess their clinical validity. In the DepressionDC trial, models achieved a balanced accuracy of 63.5% for active tDCS and 62.5% for sham tDCS in predicting treatment responders. The tDCS model significantly predicted MADRS scores at the 18-week follow-up visit (F(1,60)= 4.53, pFDR= .037, R2= 0.069). Baseline self-rated depression was consistently ranked as the most informative feature. However, response prediction in the ELECT-TDCS trial and across trials was not successful. Our findings indicate that ML-based models have the potential to identify responders to active and sham tDCS treatments in patients with MDD. However, to establish their clinical utility, they require further refinement and external validation in larger samples and with more features.
The father’s singing voice may impact premature infants’ brain more than their mother’s: A study protocol and preliminary data on a singing and EEG randomized controlled trial (RCT) based on the fundamental frequency of voice and kinship parameters
Authors: Papatzikis Efthymios , Dimitropoulos Kyriakos , Tataropoulou Kassandra , Kyrtsoudi Maria , Pasoudi Elena , O’Toole John M. , Nika Angeliki 
Published: September 2024

AbstractThis article presents the study protocol for a randomized controlled trial (RCT) investigating the impact of singing on the brain activity of premature infants in the Neonatal Intensive Care Unit (NICU). The study focuses on how the differentiation of voices, as defined by the fundamental frequency (F0) shaped by biological sex and kinship, influences neurophysiological responses when measured by electroencephalography (EEG). Premature infants, who are highly sensitive to auditory stimuli, may benefit from music-based interventions; however, there is limited understanding of how voice variations between male and female caregivers, and whether they are biologically related, affect brain activity. Our protocol outlines a structured intervention where infants are exposed to singing by four facilitators - a male music therapist, a female music therapist, the mother, and the father - and includes two singing stages: a sustained note (A at 440 Hz) and a 90-second lullaby, both interspersed with silent periods to allow for baseline measurements. EEG recordings track brain activity throughout these sessions, followed by quantitative EEG (qEEG) analysis and thorough statistical computations (e.g., mixed-effects models, spectral power analysis, and post-hoc tests) to explore how these auditory stimuli influence brain function. Preliminary data from five infants show that maternal singing elicits the highest delta spectral power in all measured conditions except during the ‘lullaby song’, where paternal singing elicits the highest effects followed by the male music therapist and then the mother. These early findings highlight the potential influence of parental voices, particularly the fathers’ voice, on neonatal brain development, while the detailed study protocol ensures rigor and replicability, providing a robust framework for future research. Additionally, this protocol lays the groundwork for exploring the long-term effects of music-based interventions, with the goal of improving neurodevelopmental outcomes in premature infants through tailored auditory stimulation. (clinincaltrials.govunique identifier:NCT06398912)