bluuebunny/crossref_metadata_2025_split huggingface dataset:
An optimized approach to study sub-sarcomere structure utilizing super-resolution microscopy with secondary VHH nanobodies
Authors: Douglas CM , Bird JE , Kopinke D , Esser KA 
Published: September 2022

AbstractThe sarcomere is the fundamental contractile unit in skeletal muscle, and the maintenance of its structure is critical for its function. While alterations in sarcomere structure are implicated in many clinical conditions of muscle weakness this area has made limited progress due, in part, to limitations in the ability to robustly detect and measure at sub-sarcomere resolution. Classically the field has relied on approaches including confocal and electron microscopy, but there are technique-specific limitations with respect to resolution, tissue morphology, and protein specific labeling. In this study, our goal was to establish a robust and reproducible method to probe sub-sarcomere protein localization in longitudinal muscle sections. We optimized several steps from tissue preparation to antibody selection and imaging to provide the ability to quantitatively assess spatial distribution of proteins within a single sarcomere. This includes 1) in situ fixation for structural integrity, 2) use of multiple same host-species primary antibodies with Fab fragment antibody blocking to maintain specificity, and 3) the use of super-resolution structured illumination microscopy (SIM) to improve from confocal, along with use of emergent VHH secondary nanobodies to double the resolution. The combination of these methods provides a unique approach to improve visualization of sarcomere structure while simultaneously providing the ability to rigorously probe protein localization. While this study focused on assessment of skeletal muscle structure and provides an important set of tools for analysis of skeletal muscle health in disease and aging, we suggest the methods herein may prove advantageous for research outside of skeletal muscle.
Musleblind-1 regulates microtubule cytoskeleton in C. elegans mechanosensory neuron through tubulin mRNAs
Authors: Puri Dharmendra , Samaddar Sarbani , Banerjee Sourav , Ghosh-Roy Anindya 
Published: September 2022

AbstractRegulation of microtubule cytoskeleton is fundamental for the development and maintenance of neuronal architecture. Recent studies have shown that regulated RNA processing is also critical for the establishment and maintenance of neural circuits. In a genetic screen using mechanosensory neurons of C. elegans, we identified a mutation in muscleblind-1 as a suppressor of loss of kinesin-13 family microtubule destabilizing factor klp-7. Muscleblind-1(MBL-1) is an RNA-binding protein that regulates the splicing, localization, and stability of RNA. We found that mbl-1 is required cell-autonomously for axon growth and synapse formation in the posterior lateral microtubule (PLM) neuron. Loss of mbl-1 affects stability and plus-end-out organization of microtubules in the anterior process of PLM. These defects are also accompanied by abnormal axonal transport of the synaptic protein RAB-3 and loss of gentle touch sensation in mbl-1 mutant. Our data showed that mbl-1 is genetically epistatic to mec-7 (β tubulin) and mec-12 (a tubulin) for axon growth. The immunoprecipitation of MBL-1 pulls down the mec-7, mec-12, and sad-1 mRNAs. Additionally, the mbl-1 mutants show a reduction in the level and stability of mec-7 and mec-12 transcripts. Independently, mbl-1 is epistatic to sad-1 for synapse formation. Our work elucidated a previously unknown link between RNA binding protein and cytoskeletal machinery for the development and maintenance of the nervous system.
On the performance of multi-compartment relaxometry for myelin water imaging – Intra-subject and inter-protocol reproducibility
Authors: Chan Kwok-Shing , Chamberland Maxime , Marques José P. 
Published: September 2022

AbstractWe evaluate the test-retest repeatability and study the tissue properties of multicompartment relaxometry-based myelin water imaging (MCR-MWI) derived from different gradient echo (GRE) acquisition settings. Additionally, the variable flip angle acquisition scheme is optimised based on numerical simulations to reduce the acquisition time of MCR-MWI in a clinically practical range without using advanced image acquisition methods. For the test-retest analysis, in vivo imaging was performed to collect data from three healthy volunteers in two identical sessions. Three GRE sequence settings with different echo times and repetition times imitating various scanner setups were evaluated. The in vivo data was also used to validate the optimal variable flip angle combination derived from simulations. Bundle-specific profiles of MCR-MWI derived microstructural parameters were investigated, as well as the cross-correlations of those parameters. Good cross-session repeatability is observed for MCR-MWI. While good correlations can also be found in myelin water fraction (MWF) across protocols, systematic differences, particularly for protocols with different repetition times, are observed. Numerical simulations indicate that MCR-MWI can be performed with a minimum of three flip angles covering a wide range of T1 weighting without adding significant measurement bias and the result is supported by the in vivo experiment allowing whole brain 1.5mm isotropic MWF maps to be acquired in 9 minutes. Bundles-specific MWF analysis reveals that certain white matter bundles are similar in all three participants. We also found that microstructure relaxation parameters have low correlations with MWF. MCR-MWI is a reproducible measure of myelin. However, attention should be paid to considering the protocol related MWF differences for comparison studies, especially when different repetition times are used as this can introduce biases up to 0.5% of MWF in our tested protocols. The optimised flip angle acquisition scheme can reduce the total scan time to 40% of the original implementation without significant quality degradation.Highlights-Multi-compartment relaxometry based myelin water imaging (MCR-MWI) can be performed with data comprising as few as 3 flip angles without introducing substantial bias or instability in the fitting procedure;-MCR-MWI is a reproducible measure of myelin water fraction (MWF) and incorporating DWI can further improve the measurement reproducibility;-MCR-MWI allows the acquisition of whole brain 1.5mm isotropic MWF maps in 9 minutes, even without the use of advanced model-based reconstructions;-Small MWF bias can present in cross-protocol comparison if the MT effect is not constant across GRE protocols (e.g., different TRs or flip angle combinations);-Compartmental relaxation parameters derived from MCR-MWI possess complimentary information beyond myelin water concentration.
A clinical stage LMW-DS drug inhibits cell infection by coronaviruses and modulates reactive cytokine release from microglia
Authors: Logan Ann , Mazzon Michela , Bruce Lars , Barnes Nicholas M. 
Published: September 2022

AbstractMost coronaviruses infect animals including bats, birds and mammals, which act as hosts and reservoirs for the viruses, but the viruses can sometimes move host species and infect humans. Coronoviruses were first identified as human pathogens in the 1960s and now there are seven types known to infect humans. Whilst four of these types cause mild-to-moderate respiratory disease, the other three may cause more severe and possibly even fatal disease in vulnerable individuals particularly, with the most recent SARS-CoV-2 pandemic being associated with severe acute respiratory syndrome (SARS) in many infected people. The aim of the present study was to evaluate the potential of a unique low molecular weight dextran sulphate (LMW-DS) clinical stage drug, ILB®, to inhibit infection of human cells by the NL63 coronavirus assessed by immunofluorescence of viral particles, and also to see if the drug directly blocked the interaction of the SARS-CoV-2 viral spike protein with the ACE2 receptor. Furthermore, we evaluated if ILB® could modulate the downstream consequences of viral infection including the reactive cytokine release from human microglia induced by various SARS-CoV-2 variant spike proteins. We demonstrated that ILB® blocked ACE2:spike protein interaction and inhibited coronaviral infection. ILB® also attenuated the omicron-induced release of pro-inflammatory cytokines, including TNFα, from human microglia, indicating control of post-viral neuroinflammation. In conclusion, given the safety profile of ILB® established in a number of Phase I and Phase II clinical trials, these results highlight the potential of ILB® to treat patients infected with coronaviruses to both limit infectivity and attenuate the progression to severe disease. There is now an opportunity to translate these findings quickly by the clinical investigation of drug efficacy.
PAMR1 negatively impacts cell proliferation and migration of Human Colon Cancer HT29 Cell Line
Authors: Haymour Layla , Chaunavel Alain , Assaf Mona Diab , Maftah Abderrahman , Legardinier Sébastien 
Published: September 2022

ABSTRACTColorectal cancer (CRC) is becoming one of the most prevalent cancers worldwide. Among cancers, it ranks the third place in terms of incidence and the second in terms of mortality. Even though immunological test allows fast and easy diagnostic method, there is no specific and reliable methods for early detection of CRC. Despite different treatments, high risk of re-occurrence is associated with advanced and metastatic CRC stages. An exhaustive knowledge on specific biomarkers or molecular actors involved in CRC could help to eradicate tumors or limit cancer recurrence. In this study, we focused on PAMR1 (Peptidase Domain Containing Associated with Muscle Regeneration 1), which is already considered as a tumor suppressor in breast and cervical cancers.In silicoanalysis of RNASeq data showed that PAMR1 was significantly downregulated in CRC tissues compared to their adjacent normal ones, as well as in cervical cancer. Our analysis showed that this downregulation, probably due to promoter hypermethylation, such as in breast cancer tissues, appeared in the four cancer stages as early as the first stage. In consistency within silicoanalyses, the expression of PAMR1 was found to be lower at the transcript and protein levels in CRC tissue samples compared to normal ones, as well as in different CRC cell lines (HCT116, HT29, and SW620) compared to normal colon cell line (CCD841CoN). To understand the role of PAMR1 in CRC cancer, recombinant purified PAMR1 or concentrated secretome from CHO overexpressing PAMR1 were used to exogenously treat CRC cell lines with a focus on HT-29 cells as well as Hela cervical cancer cell line known to be sensitive to PAMR1. Transient or stable transfections were also performed to determine the impact of PAMR1 overexpression in HT29 and/or HeLa cells. In this study, we finally showed that presence of PAMR1 could reduce both cell proliferation and cell migration with a positive correlation between these biological effects and PAMR1’s quantity. This implies that PAMR1 expresses anti-proliferative and anti-migrative effects in CRC. Further studies to be done in order to confirm the tumor suppressive role of PAMR1 in CRC.
Statistical Learning of Distractor Suppression Down-regulates Pre-Stimulus Neural Excitability in Early Visual Cortex
Authors: Ferrante Oscar , Zhigalov Alexander , Hickey Clayton , Jensen Ole 
Published: September 2022

AbstractVisual attention is highly influenced by past experiences. Recent behavioral research has shown that expectations about the spatial location of distractors within a search array are implicitly learned, with expected distractors becoming less interfering. Little is known about the neural mechanism supporting this form of statistical learning. Here we used magnetoencephalography (MEG) to measure human brain activity to test whether proactive mechanisms are involved in the statistical learning of distractor locations. Specifically, we used a new technique called rapid invisible frequency tagging (RIFT) to assess neural excitability in early visual cortex during statistical learning of distractor suppression, while concurrently investigating the modulation of posterior alpha-band activity (8-12 Hz). Male and female human participants performed a visual search task in which a target was occasionally presented alongside a color-singleton distractor. Unbeknown to the participants, the distracting stimuli were presented with different probabilities across the two hemifields. RIFT analysis showed that early visual cortex exhibited reduced neural excitability in the pre-stimulus interval at retinotopic locations associated with higher distractor probabilities. In contrast, we did not find any evidence of expectation-driven distractor suppression in alpha-band activity. These findings indicate that proactive mechanisms of attention are involved in predictive distractor suppression and that these mechanisms are associated with altered neural excitability in early visual cortex. Moreover, our findings indicate that RIFT and alpha-band activity might subtend different and possibly independent attentional mechanisms.
DELLA proteins regulate spore germination and reproductive development inPhyscomitrium patens
Authors: Phokas Alexandros , Meyberg Rabea , Briones-Moreno Asier , Hernandez-Garcia Jorge , Wadsworth Panida T. , Vesty Eleanor F. , Blazquez Miguel A. , Rensing Stefan A. , Coates Juliet C. 
Published: September 2022

SummaryProteins of the DELLA family integrate environmental signals to regulate growth and development throughout the plant kingdom. Plants expressing non-degradable DELLA proteins underpinned the development of high-yielding ‘Green Revolution’ dwarf crop varieties in the 1960s. In vascular plants, DELLAs are regulated by gibberellins, diterpenoid plant hormones. How DELLA protein function has changed during land plant evolution is not fully understood.We have examined the function and interactions of DELLA proteins in the mossPhyscomitrium(Physcomitrella)patens, in the sister group of vascular plants (Bryophytes).PpDELLAs do not undergo the same regulation as flowering plant DELLAs.PpDELLAs are not degraded by diterpenes, do not interact with GID1 gibberellin receptor proteins and do not participate in responses to abiotic stress.PpDELLAs do share a function with vascular plant DELLAs during reproductive development.PpDELLAs also regulate spore germination.PpDELLAs interact with moss-specific photoreceptors although a function forPpDELLAs in light responses was not detected.PpDELLAs likely act as ‘hubs’ for transcriptional regulation similarly to their homologues across the plant kingdom.Taken together, these data demonstrate thatPpDELLA proteins share some biological functions with DELLAs in flowering plants, but other DELLA functions and regulation evolved independently in both plant lineages.
Shifts in isoform usage underlie transcriptional differences in regulatory T cells in type 1 diabetes
Authors: Newman Jeremy R. B. , Long S. Alice , Speake Cate , Greenbaum Carla J. , Cerosaletti Karen , Rich Stephen S. , Onengut-Gumuscu Suna , McIntyre Lauren M. , Buckner Jane H. , Concannon Patrick 
Published: September 2022

AbstractGenome-wide association studies have identified numerous loci with allelic associations to Type 1 Diabetes (T1D) risk. Most disease-associated variants are enriched in regulatory sequences active in lymphoid cell types, suggesting that lymphocyte gene expression is altered in T1D. We assayed gene expression between T1D cases and healthy controls in two autoimmunity-relevant lymphocyte cell types, memory CD4+/CD25+ T-regulatory cells (Treg) and memory CD4+/CD25- T-cells, using a splicing event-based approach to characterize tissue-specific transcriptomes. Limited differences in isoform usage between T1D cases and controls were observed in memory CD4+/CD25- T-cells. In Tregs, 553 genes demonstrated differences in isoform usage between cases and controls, particularly RNA recognition and splicing factor genes. Many of these genes are regulated by the variable inclusion of exons that can trigger nonsense mediated decay. Our results suggest that dysregulation of gene expression, through shifts in alternative splicing in Tregs, contributes to T1D etiology.
Spectrin forms a periodic cytoskeleton within the epidermis to preserve axonal integrity
Authors: Coakley Sean , Bonacossa-Pereira Igor , Hilliard Massimo A. 
Published: September 2022

AbstractSpectrins are highly conserved molecules that form a distinct membrane associated periodic scaffold within axons thought to provide mechanical resilience. In C. elegans, UNC-70/ß-Spectrin also functions outside the nervous system, within the epidermis, to maintain the integrity of sensory neurons. The precise molecular organization and cellular mechanisms that mediate this protection are unknown. Here, using 3D-structured illumination microscopy, we show that within the epidermis spectrins form a crescent-shaped scaffold with a periodicity of ∼ 200 nm that embraces adjacent axons. This epidermal spectrin scaffold is induced by developing axons and reformed during axonal regeneration, and creates a “molecular imprint” of the adjacent nervous system. Disruption of this epidermal scaffold causes widespread axonal damage in sensory and motor neurons. These findings reveal the existence of a distinct and periodic spectrin framework within the epidermis that is molded by the developing nervous system and is necessary to protect it from mechanical damage.TeaserSpectrin forms a periodic scaffold in the epidermis that protects axons from damage.
Optimal Stimulation Sites and Networks for Deep Brain Stimulation of the Fornix in Alzheimer’s Disease
Authors: Ríos Ana Sofía , Oxenford Simón , Neudorfer Clemens , Butenko Konstantin , Li Ningfei , Rajamani Nanditha , Boutet Alexandre , Elias Gavin J.B. , Germann Jurgen , Loh Aaron , Deeb Wissam , Wang Fuyixue , Setsompop Kawin , Salvato Bryan , Almeida Leonardo , Foote Kelly D. , Amaral Robert , Rosenberg Paul B. , Tang-Wai David F. , Wolk David A. , Burke Anna D. , Salloway Stephen , Sabbagh Marwan N. , Chakravarty M. Mallar , Smith Gwenn S. , Lyketsos Constantine G. , Okun Michael S. , Anderson William S. , Mari Zoltan , Ponce Francisco A. , Lozano Andres M. , Horn Andreas 
Published: September 2022

AbstractDeep brain stimulation (DBS) to the fornix is an investigational treatment option for patients with mild Alzheimer’s Disease. Outcomes from randomized clinical trials have shown that cognitive function improved in some patients but deteriorated in others. One reason could be variance in electrode placement leading to differential engagement of neural circuits. To investigate this, we analyzed a multi-center cohort of 46 patients with DBS to the fornix. Using normative structural and functional connectivity data, we demonstrate that stimulation of the circuit of Papez and stria terminalis robustly associated with cognitive improvement (R = 0.45, p = 0.031). On a local level, the optimal stimulation site resided at the direct interface between these structures (R = 0.33, p = 0.016). Finally, modulating specific distributed brain networks related to memory accounted for optimal outcomes (R = 0.38, p = 0.006). Findings were robust to multiple cross-validation designs and may now define an optimal network target which could subsequently guide refinement of DBS surgery and programming.
The risk of myocardial ischemia in patients with Kawasaki Disease: Insights from patient-specific simulations of coronary hemodynamics
Authors: Menon Karthik , Seo Jongmin , Kahn Andrew M. , Burns Jane C. , Marsden Alison L. 
Published: September 2022

BackgroundPediatric patients with aneurysms due to Kawasaki disease require life-long and uninterrupted cardiology follow-up. Current AHA guidelines for risk stratification and long-term management are based primarily on maximal coronary artery luminal dimensions, normalized as Z-scores. Hemodynamic and functional significance of coronary arteries aneurysms on myocardial ischemic risk is not well studied.MethodsWe retrospectively studied a cohort of 15 patients who underwent coronary CT angiography imaging. We constructed patient-specific anatomic models from CT images and performed computational hemodynamic simulations incorporating pulsatile flow and deformable arterial walls. Simulation parameters were tuned to match patient-specific arterial pressure, ejection fraction, and cardiac output. From simulation results, we evaluated hemodynamic iscmemic risk metrics, including fractional flow reserve, wall shear stress, and residence time, in 153 coronary arteries.ResultsFractional flow reserve (FFR) showed a weak correlation with aneurysm Z-scores. The slope of FFR significantly increased distal to the lumen narrowing at the end of aneurysms. Ischemic risk does not correlate well with aneurysm diameter measured by Z-score, but correlates much better with the ratio of maximum lumen diameter within aneurysms to minimum lumen diameter distal to aneurysms. Wall shear stress also correlates better with this diameter ratio, while residence can be stratified via Z-score.ConclusionsZ-score alone is not a good indicator of abnormal FFR. Although FFR immediately distal to aneurysms is not critical, it starts to drop more rapidly distal to aneurysms and can therefore present an elevated risk of myocardial ischemia. Maximum-to-minimum lumen diameter is a good proxy for ischemic risk.
Comparison of Peripheral Blood Oxygen Saturation Measurements Using Pulse Oximetry at Three Anatomical Sites on Sleep Patients
Authors: Strickland Kellie R. , Brown Chris J. , Wilks Leigh , Dunn Peter K. , Holmes Mark A. 
Published: September 2022

ABSTRACTBackground and ObjectiveAccurate measurements of peripheral blood oxygen saturation (SpO2) are important in evaluating sleep patients with frequent desaturations due to pathological breathing events. This project compared synchronised SpO2measurements at the finger, forehead and toe of patients undergoing Type 1 polysomnography (PSG) to evaluate potential SpO2variability across the sites.MethodsPulse oximetry SpO2measurements were simultaneously and continuously recorded for 41 sleep patients at the finger, forehead and toe, and synchronised with PSG data. Recordings were scored for desaturations of ≤ 3% (peak to trough, lasting ≤10 seconds), signal dropouts, and artefact occurrences. Forehead and toe SpO2measurements were compared against the finger as the standard PSG oximetry site.ResultsDifferences between anatomical sites for mean SpO2, mean number of SpO2desaturations per hour, and time spent below an SpO2level of 95% during total sleep time were significant (P< 0.01). The forehead pulse oximeter had the highest mean SpO2, least number of SpO2desaturations per hour, and experienced the least number of artefact occurrences. Dropouts were lowest for the forehead and toe pulse oximeters.ConclusionDifferences between SpO2measurements, dropouts and artefact occurrences at the finger, forehead and toe may have diagnostic and prognostic implications for sleep patients. The differences in SpO2 measurements may be attributed to variability in perfusion of the extremities and core during sudden oscillating blood pressure changes associated with breathing events. Further research is required to determine which anatomical site correlates closest to arterial oxygenation for pulse oximetry in sleep patients.BRIEF SUMMARYStudy rationaleAn absence of research investigating anatomical site location for pulse oximetry during overnight polysomnography exists. Our study was performed to fill this gap, as accurate pulse oximetry measurements are key for the diagnosis, treatment and monitoring of sleep patients; a patient cohort where SpO2desaturations are recurrent.Study impactOur findings demonstrate there are significant differences between finger, forehead and toe pulse oximetry measurements, particularly SpO2desaturations per hour, which may have diagnostic and clinical implications. This research is applicable and important to not only sleep physicians and scientists, but also other disciplines where continuous SpO2monitoring is required.