bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-myogenic mesenchymal cells contribute to muscle degeneration in facioscapulohumeral muscular dystrophy patients
Authors: Di Pietro Lorena , Giacalone Flavia , Ragozzino Elvira , Saccone Valentina , Tiberio Federica , De Bardi Marco , Picozza Mario , Borsellino Giovanna , Lattanzi Wanda , Guadagni Enrico , Bortolani Sara , Tasca Giorgio , Ricci Enzo , Parolini Ornella 
Published: September 2022

AbstractMuscle-resident non-myogenic mesenchymal cells play key roles that drive successful tissue regeneration within the skeletal muscle stem cell niche. These cells have recently emerged as remarkable therapeutic targets for neuromuscular disorders, although to date they have been poorly investigated in facioscapulohumeral muscular dystrophy (FSHD). In this study, we characterised the non-myogenic mesenchymal stromal cell population in FSHD patients’ muscles with signs of disease activity, identified by muscle magnetic resonance imaging (MRI), and compared them with those obtained from apparently normal muscles of FSHD patients and from muscles of healthy, age-matched controls. Our results showed that patient-derived cells displayed a distinctive expression pattern of mesenchymal markers, along with an impaired capacity to differentiate towards mature adipocytes in vitro, compared with control cells. We also demonstrated a significant expansion of non-myogenic mesenchymal cells (identified as CD201- or PDGFRA-expressing cells) in FSHD muscles with signs of disease activity, which correlated with the extent of intramuscular fibrosis. In addition, the accumulation of non-myogenic mesenchymal cells was higher in FSHD muscles that deteriorate more rapidly. Our results prompt a direct association between an accumulation, as well as an altered differentiation, of non-myogenic mesenchymal cells with muscle degeneration in FSHD patients. Elucidating the mechanisms and cellular interactions that are altered in the affected muscles of FSHD patients could be instrumental to clarify disease pathogenesis and identifying reliable novel therapeutic targets.
Self-heating hotspots in superconducting nanowires cooled by phonon black-body radiation
Authors: Dane Andrew , Allmaras Jason , Zhu Di , Onen Murat , Colangelo Marco , Baghdadi Reza , Tambasco Jean-Luc , Morimoto Yukimi , Forno Ignacio Estay , Charaev Ilya , Zhao Qingyuan , Skvortsov Mikhail , Kozorezov Alexander , Berggren Karl K. 
Published: September 2022

AbstractControlling thermal transport is important for a range of devices and technologies, from phase change memories to next-generation electronics. This is especially true in nano-scale devices where thermal transport is altered by the influence of surfaces and changes in dimensionality. In superconducting nanowire single-photon detectors, the thermal boundary conductance between the nanowire and the substrate it is fabricated on influences all of the performance metrics that make these detectors attractive for applications. This includes the maximum count rate, latency, jitter, and quantum efficiency. Despite its importance, the study of thermal boundary conductance in superconducting nanowire devices has not been done systematically, primarily due to the lack of a straightforward characterization method. Here, we show that simple electrical measurements can be used to estimate the thermal boundary conductance between nanowires and substrates and that these measurements agree with acoustic mismatch theory across a variety of substrates. Numerical simulations allow us to refine our understanding, however, open questions remain. This work should enable thermal engineering in superconducting nanowire electronics and cryogenic detectors for improved device performance.
Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling
Authors: Zeke András , Takács Tamás , Sok Péter , Németh Krisztina , Kirsch Klára , Egri Péter , Póti Ádám Levente , Bento Isabel , Tusnády Gábor E. , Reményi Attila 
Published: September 2022

AbstractSerine/threonine phosphorylation of insulin receptor substrate (IRS) proteins is well known to modulate insulin signaling. However, the molecular details of this process have mostly been elusive. While exploring the role of phosphoserines, we have detected a direct link between Tyr-flanking Ser/Thr phosphorylation sites and regulation of specific phosphotyrosine phosphatases. Here we present a concise structural study on how the activity of SHP2 phosphatase is controlled by an asymmetric, dual phosphorylation of its substrates. The structure of SHP2 has been determined with three different substrate peptides, unveiling the versatile and highly dynamic nature of substrate recruitment. What is more, the relatively stable pre-catalytic state of SHP2 could potentially be useful for inhibitor design. Our findings not only show an unusual dependence of SHP2 catalytic activity on Ser/Thr phosphorylation sites in IRS1 and CD28, but also suggest a negative regulatory mechanism that may also apply to other tyrosine kinase pathways as well.
Structure-based discovery of small molecules that disaggregate Alzheimer’s disease tissue derived tau fibrils in vitro
Authors: Seidler Paul M. , Murray Kevin A. , Boyer David R. , Ge Peng , Sawaya Michael R. , Hu Carolyn J. , Cheng Xinyi , Abskharon Romany , Pan Hope , DeTure Michael A. , Williams Christopher K. , Dickson Dennis W. , Vinters Harry V. , Eisenberg David S. 
Published: September 2022

AbstractAlzheimer’s disease (AD) is the consequence of neuronal death and brain atrophy associated with the aggregation of protein tau into fibrils. Thus disaggregation of tau fibrils could be a therapeutic approach to AD. The small molecule EGCG, abundant in green tea, has long been known to disaggregate tau and other amyloid fibrils, but EGCG has poor drug-like properties, failing to fully penetrate the brain. Here we have cryogenically trapped an intermediate of brain-extracted tau fibrils on the kinetic pathway to EGCG-induced disaggregation and have determined its cryoEM structure. The structure reveals that EGCG molecules stack in polar clefts between the paired helical protofilaments that pathologically define AD. Treating the EGCG binding position as a pharmacophore, we computationally screened thousands of drug-like compounds for compatibility for the pharmacophore, discovering several that experimentally disaggregate brain-derived tau fibrils in vitro. This work suggests the potential of structure-based, small-molecule drug discovery for amyloid diseases.
A temporal sequence of thalamic activity unfolds at transitions in behavioral arousal state
Authors: Setzer Beverly , Fultz Nina E. , Gomez Daniel E. P. , Williams Stephanie D. , Bonmassar Giorgio , Polimeni Jonathan R. , Lewis Laura D. 
Published: September 2022

AbstractAwakening from sleep reflects a profound transformation in neural activity and behavior. The thalamus is a key controller of arousal state, but whether its diverse nuclei exhibit coordinated or distinct activity at transitions in behavioral arousal state is unknown. Using fast fMRI at ultra-high field (7 Tesla), we measured sub-second activity across thalamocortical networks and within nine thalamic nuclei to delineate these dynamics during spontaneous transitions in behavioral arousal state. We discovered a stereotyped sequence of activity across thalamic nuclei and cingulate cortex that preceded behavioral arousal after a period of inactivity, followed by widespread deactivation. These thalamic dynamics were linked to whether participants subsequently fell back into unresponsiveness, with unified thalamic activation reflecting maintenance of behavior. These results provide an outline of the complex interactions across thalamocortical circuits that orchestrate behavioral arousal state transitions, and additionally, demonstrate that fast fMRI can resolve sub-second subcortical dynamics in the human brain.
Water regulates the residence time of Benzamidine in Trypsin
Authors: Ansari Narjes , Rizzi Valerio , Parrinello Michele 
Published: September 2022

AbstractThe process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the binding of Benzamidine to Trypsin which is a much studied and paradigmatic ligand-protein system. We use machine learning methods to determine efficient collective coordinates for the complex non-local network of water. These coordinates are used to perform On-the-fly Probability Enhanced Sampling simulations, which we adapt to calculate also the ligand residence time. Our results, both static and dynamic, are in good agreement with experiments. We find that the presence of a water molecule located at the bottom of the binding pocket allows via a network of hydrogen bonds the ligand to be released into the solution. On a finer scale, even when unbinding is allowed, another water molecule further modulates the exit time.
Tackling realistic Li+ flux for high-energy lithium metal batteries
Authors: Zhang Shuoqing , Li Ruhong , Hu Nan , Deng Tao , Weng Suting , Wu Zunchun , Lu Di , Zhang Haikuo , Zhang Junbo , Wang Xuefeng , Chen Lixin , Fan Liwu , Fan Xiulin 
Published: September 2022

AbstractElectrolyte engineering advances Li metal batteries (LMBs) with high Coulombic efficiency (CE) by constructing LiF-rich solid electrolyte interphase (SEI). However, the low conductivity of LiF disturbs Li+ diffusion across SEI, thus inducing Li+ transfer-driven dendritic deposition. In this work, we establish a mechanistic model to decipher how the SEI affects Li plating in high-fluorine electrolytes. The presented theory depicts a linear correlation between the capacity loss and current density to identify the slope k (determined by Li+ mobility of SEI components) as an indicator for describing the homogeneity of Li+ flux across SEI, while the intercept dictates the maximum CE that electrolytes can achieve. This model inspires the design of an efficient electrolyte that generates dual-halide SEI to homogenize Li+ distribution and Li deposition. The model-driven protocol offers a promising energetic analysis to evaluate the compatibility of electrolytes to Li anode, thus guiding the design of promising electrolytes for LMBs.
Multiclass classification of breast cancer histopathology images using multilevel features of deep convolutional neural network
Authors: Hameed Zabit , Garcia-Zapirain Begonya , Aguirre José Javier , Isaza-Ruget Mario Arturo 
Published: September 2022

AbstractBreast cancer is a common malignancy and a leading cause of cancer-related deaths in women worldwide. Its early diagnosis can significantly reduce the morbidity and mortality rates in women. To this end, histopathological diagnosis is usually followed as the gold standard approach. However, this process is tedious, labor-intensive, and may be subject to inter-reader variability. Accordingly, an automatic diagnostic system can assist to improve the quality of diagnosis. This paper presents a deep learning approach to automatically classify hematoxylin-eosin-stained breast cancer microscopy images into normal tissue, benign lesion, in situ carcinoma, and invasive carcinoma using our collected dataset. Our proposed model exploited six intermediate layers of the Xception (Extreme Inception) network to retrieve robust and abstract features from input images. First, we optimized the proposed model on the original (unnormalized) dataset using 5-fold cross-validation. Then, we investigated its performance on four normalized datasets resulting from Reinhard, Ruifrok, Macenko, and Vahadane stain normalization. For original images, our proposed framework yielded an accuracy of 98% along with a kappa score of 0.969. Also, it achieved an average AUC-ROC score of 0.998 as well as a mean AUC-PR value of 0.995. Specifically, for in situ carcinoma and invasive carcinoma, it offered sensitivity of 96% and 99%, respectively. For normalized images, the proposed architecture performed better for Makenko normalization compared to the other three techniques. In this case, the proposed model achieved an accuracy of 97.79% together with a kappa score of 0.965. Also, it attained an average AUC-ROC score of 0.997 and a mean AUC-PR value of 0.991. Especially, for in situ carcinoma and invasive carcinoma, it offered sensitivity of 96% and 99%, respectively. These results demonstrate that our proposed model outperformed the baseline AlexNet as well as state-of-the-art VGG16, VGG19, Inception-v3, and Xception models with their default settings. Furthermore, it can be inferred that although stain normalization techniques offered competitive performance, they could not surpass the results of the original dataset.
MicroRNA-570 targets the HSP chaperone network, increases proteotoxic stress and inhibits mammary tumor cell migration
Authors: Okusha Yuka , Guerrero-Gimenez Martin E. , Lang Benjamin J. , Borges Thiago J. , Stevenson Mary A. , Truman Andrew W. , Calderwood Stuart K. 
Published: September 2022

AbstractThe dynamic network of chaperone interactions known as the chaperome contributes significantly to the proteotoxic cell response and the malignant phenotype. To bypass the inherent redundancy in the network, we have used a microRNA (mir) approach to target multiple members of the chaperome simultaneously. We identified a potent microRNA, miR-570 that could bind the 3′untranslated regions of multiple HSP mRNAs and inhibit HSP synthesis. Transfection of cells with this miR species reduced expression of multiple HSPs, inhibited the heat shock response and reduced tumor cell growth while acted additively in combination with cytotoxic drugs. As overexpression of miR-570 elicited tumor suppressive effects, we inferred that this miR could play a potential role in inhibiting tumorigenesis and cancer cell growth. In accordance with this hypothesis, we determined a significant role for miR-570 in regulating markers of mammary tumor progression, including cell motility and invasion. Our data provide a proof of the principle that the tumor chaperome can be targeted by microRNAs suggesting a potential therapeutic avenue towards cancer therapy.
Customized strategies for high-yield purification of retinal pigment epithelial cells differentiated from different stem cell sources
Authors: Regha Kakkad , Bhargava Mayuri , Al-Mubaarak Abdurrahmaan , Chai Chou , Parikh Bhav Harshad , Liu Zengping , Wong Claudine See Wei , Hunziker Walter , Lim Kah Leong , Su Xinyi 
Published: September 2022

AbstractRetinal pigment epithelial (RPE) cell dysfunction and death are characteristics of age-related macular degeneration. A promising therapeutic option is RPE cell transplantation. Development of clinical grade stem-cell derived RPE requires efficient in vitro differentiation and purification methods. Enzymatic purification of RPE relies on the relative adherence of RPE and non-RPE cells to the culture plate. However, morphology and adherence of non-RPE cells differ for different stem cell sources. In cases whereby the non-RPE adhered as strongly as RPE cells to the culture plate, enzymatic method of purification is unsuitable. Thus, we hypothesized the need to customize purification strategies for RPE derived from different stem cell sources. We systematically compared five different RPE purification methods, including manual, enzymatic, flow cytometry-based sorting or combinations thereof for parameters including cell throughput, yield, purity and functionality. Flow cytometry-based approach was suitable for RPE isolation from heterogeneous cultures with highly adherent non-RPE cells, albeit with lower yield. Although all five purification methods generated pure and functional RPE, there were significant differences in yield and processing times. Based on the high purity of the resulting RPE and relatively short processing time, we conclude that a combination of enzymatic and manual purification is ideal for clinical applications.
Plasma microRNAs as potential biomarkers in early Alzheimer disease expression
Authors: Peña-Bautista Carmen , Tarazona-Sánchez Adrián , Braza-Boils Aitana , Balaguer Angel , Ferré-González Laura , Cañada-Martínez Antonio J. , Baquero Miguel , Cháfer-Pericás Consuelo 
Published: September 2022

AbstractThe microRNAs (miRNAs) are potential biomarkers for complex pathologies due to their involvement in the regulation of several pathways. Alzheimer Disease (AD) requires new biomarkers in minimally invasive samples that allow an early diagnosis. The aim of this work is to study miRNAS as potential AD biomarkers and their role in the pathology development. In this study, participants (n = 46) were classified into mild cognitive impairment due to AD (MCI-AD, n = 19), preclinical AD (n = 8) and healthy elderly controls (n = 19), according to CSF biomarkers levels (amyloid β42, total tau, phosphorylated tau) and neuropsychological assessment. Then, plasma miRNAomic expression profiles were analysed by Next Generation Sequencing. Finally, the selected miRNAs were validated by quantitative PCR (q-PCR). A panel of 11 miRNAs was selected from omics expression analysis, and 8 of them were validated by q-PCR. Individually, they did not show statistically significant differences among participant groups. However, a multivariate model including these 8 miRNAs revealed a potential association with AD for three of them. Specifically, relatively lower expression levels of miR-92a-3p and miR-486-5p are observed in AD patients, and relatively higher levels of miR-29a-3p are observed in AD patients. These biomarkers could be involved in the regulation of pathways such as synaptic transmission, structural functions, cell signalling and metabolism or transcription regulation. Some plasma miRNAs (miRNA-92a-3p, miRNA-486-5p, miRNA-29a-3p) are slightly dysregulated in AD, being potential biomarkers of the pathology. However, more studies with a large sample size should be carried out to verify these results, as well as to further investigate the mechanisms of action of these miRNAs.
Recapping and mite removal behaviour in Cuba: home to the world’s largest population of Varroa-resistant European honeybees
Authors: Luis Anais Rodríguez , Grindrod Isobel , Webb Georgiana , Piñeiro Adolfo Pérez , Martin Stephen John 
Published: September 2022

AbstractTheVarroa destructorectoparasitic mite has spread globally and in conjunction with Deformed Wing Virus has killed millions of honeybee (Apis mellifera) colonies. This has forced Northern hemisphere beekeepers into using miticides to avoid mass colony losses. However, in many Southern hemisphere countries widespread treatment did not occur since miticides were prohibitively expensive, or a centralised choice was made not to treat, both allowing natural selection to act. The Varroa mite initially caused high losses before mite-resistance appeared in the honeybee populations. Initially, mite-resistance was only associated with African and Africanised honeybees. Although recently, several isolated mite-resistant European honeybee populations have appeared. Here we studied the mite-resistance in Cuba and found high rates of recapping of infested worker cells (77%), high removal of mites (80%) and corresponding low mite fertility (r = 0.77). These are all traits found in all naturally evolved Varroa-resistant populations. We can confirm Cuba has the world’s largest European mite-resistant population with 220,000 colonies that have been treatment-free for over two decades and illustrating the power of natural selection. Cuban honeybees are also highly productive, 40–70 kg of honey produced annually, and are mild mannered. Cuba is an excellent example of what is possible when honeybees are allowed to adapt naturally to Varroa with minimal human interference.
Zinc chelator treatment in crush syndrome model mice attenuates ischemia–reperfusion-induced muscle injury due to suppressing of neutrophil infiltration
Authors: Haruta Yohei , Kobayakawa Kazu , Saiwai Hirokazu , Hata Kazuhiro , Tamaru Tetsuya , Iura Hirotaka , Ono Gentaro , Kitade Kazuki , Kijima Ken , Iida Keiichiro , Kawaguchi Kenichi , Matsumoto Yoshihiro , Kubota Kensuke , Maeda Takeshi , Konno Dai-Jiro , Okada Seiji , Nakashima Yasuharu 
Published: September 2022

AbstractIn crush syndrome, massive muscle breakdown resulting from ischemia–reperfusion muscle injury can be a life-threatening condition that requires urgent treatment. Blood reperfusion into the ischemic muscle triggers an immediate inflammatory response, and neutrophils are the first to infiltrate and exacerbate the muscle damage. Since free zinc ion play a critical role in the immune system and the function of neutrophils is impaired by zinc depletion, we hypothesized that the administration of a zinc chelator would be effective for suppressing the inflammatory reaction at the site of ischemia–reperfusion injury and for improving of the pathology of crush syndrome. A crush syndrome model was created by using a rubber tourniquet to compress the bilateral hind limbs of mice at 8 weeks. A zinc chelator N,N,N′,N′-tetrakis-(2-pyridylmethyl)-ethylenediamine (TPEN) was administered immediately after reperfusion in order to assess the anti-inflammatory effect of the chelator for neutrophils. Histopathological evaluation showed significantly less muscle breakdown and fewer neutrophil infiltration in TPEN administration group compared with control group. In addition, the expression levels of inflammatory cytokine and chemokine such as IL-6, TNFα, CXCL1, CXCL2, CXCR2, CCL2 in ischemia–reperfusion injured muscle were significantly suppressed with TPEN treatment. Less dilatation of renal tubules in histological evaluation in renal tissue and significantly better survival rate were demonstrated in TPEN treatment for ischemia–reperfusion injury in crush syndrome. The findings of our study suggest that zinc chelators contributed to the resolution of exacerbation of the inflammatory response and attenuation of muscle breakdown in the acute phase after crush syndrome. In addition, our strategy of attenuation of the acute inflammatory reaction by zinc chelators may provide a promising therapeutic strategy not only for crush syndrome, but also for other diseases driven by inflammatory reactions.
Association between arterial hypertension and liver outcomes using polygenic risk scores: a population-based study
Authors: Åberg Fredrik , Kantojärvi Katri , Männistö Ville , But Anna , Salomaa Veikko , Niiranen Teemu , Färkkilä Martti , Luukkonen Panu , Männistö Satu , Lundqvist Annamari , Perola Markus , Jula Antti 
Published: September 2022

AbstractArterial hypertension (HTA) is associated with liver disease, but causality remains unclear. We investigated whether genetic predisposition to HTA is associated with liver disease in the population, and if antihypertensive medication modifies this association. Participants of the Finnish health-examination surveys, FINRISK 1992–2012 and Health 2000 (n = 33,770), were linked with national electronic healthcare registers for liver-related outcomes (K70-K77, C22.0) and with the drug reimbursement registry for new initiation of antihypertensive medication during follow-up. Genetic predisposition to HTA was defined by polygenic risk scores (PRSs). During a median 12.9-year follow-up (409,268.9 person-years), 441 liver-related outcomes occurred. In the fully-adjusted Cox-regression models, both measured systolic blood pressure and clinically defined HTA were associated with liver-related outcomes. PRSs for systolic and diastolic blood pressure were significantly associated with liver-related outcomes (HR/SD 1.19, 95% CI 1.01–1.24, and 1.12, 95% CI 1.01–1.25, respectively). In the highest quintile of the systolic blood pressure PRS, new initiation of antihypertensive medication was associated with reduced rates of liver-related outcomes (HR 0.55, 95% CI 0.31–0.97). HTA and a genetic predisposition for HTA are associated with liver-related outcomes in the population. New initiation of antihypertensive medication attenuates this association in persons with high genetic risk for HTA.