Miracle-dz/UniFAR-FTUs huggingface dataset:
M-Current Inhibition in Hippocampal Excitatory Neurons Triggers Intrinsic and Synaptic Homeostatic Responses at Different Temporal Scales

Persistent alterations in neuronal activity elicit homeostatic plastic changes in synaptic transmission and/or intrinsic excitability. However, it is unknown whether these homeostatic processes operate in concert or at different temporal scales to maintain network activity around a set-point value. Here we show that chronic neuronal hyperactivity, induced by M-channel inhibition, triggered intrinsic and synaptic homeostatic plasticity at different timescales in cultured hippocampal pyramidal neurons from mice of either sex. Homeostatic changes of intrinsic excitability occurred at a fast timescale (1–4 h) and depended on ongoing spiking activity. This fast intrinsic adaptation included plastic changes in the threshold current and a distal relocation of FGF14, a protein physically bridging Nav1.6 and Kv7.2 channels along the axon initial segment. In contrast, synaptic adaptations occurred at a slower timescale (∼2 d) and involved decreases in miniature EPSC amplitude. To examine how these temporally distinct homeostatic responses influenced hippocampal network activity, we quantified the rate of spontaneous spiking measured by multielectrode arrays at extended timescales. M-Channel blockade triggered slow homeostatic renormalization of the mean firing rate (MFR), concomitantly accompanied by a slow synaptic adaptation. Thus, the fast intrinsic adaptation of excitatory neurons is not sufficient to account for the homeostatic normalization of the MFR. In striking contrast, homeostatic adaptations of intrinsic excitability and spontaneous MFR failed in hippocampal GABAergic inhibitory neurons, which remained hyperexcitable following chronic M-channel blockage. Our results indicate that a single perturbation such as M-channel inhibition triggers multiple homeostatic mechanisms that operate at different timescales to maintain network mean firing rate. SIGNIFICANCE STATEMENT Persistent alterations in synaptic input elicit homeostatic plastic changes in neuronal activity. Here we show that chronic neuronal hyperexcitability, induced by M-type potassium channel inhibition, triggered intrinsic and synaptic homeostatic plasticity at different timescales in hippocampal excitatory neurons. The data indicate that the fast adaptation of intrinsic excitability depends on ongoing spiking activity but is not sufficient to provide homeostasis of the mean firing rate. Our results show that a single perturbation such as M-channel inhibition can trigger multiple homeostatic processes that operate at different timescales to maintain network mean firing rate.
Antitumor effects of flavokawain-B flavonoid in gemcitabine-resistant lung cancer cells are mediated via mitochondrial-mediated apoptosis, ROS production, cell migration and cell invasion inhibition and blocking of PI3K/AKT Signaling pathway.

PURPOSE Drug resistance in lung cancer is a growing and challenging problem affecting the overall treatment and quality of the patient's life. The main purpose of the current study was to investigate the anticancer effects of flavokawain-B in gemcitabine-resistant non-small lung cancer cells (NSCLC) along with evaluating its mode of action by studying its effects on programmed cell death, ROS production, cell migration and invasion and PI3K/AKT signalling pathway. METHODS Cell proliferation rate was studied using MTS cell viability assay while apoptosis induction by flavokawain-B was studied by fluorescence microscopy using DAPI staining as well as flow cytometry using Annexin V-FITC/propidium iodide (PI). Effects on mitochondrial membrane potential (MMP) and reactive oxygen species (ROS) were studied by flow cytometry using Rh-123 and DCH-DA dyes respectively. Effects on cell migration and cell invasion were examined by in vitro wound healing assay and transwell assay respectively. Changes in PI3K/AKT protein expressions were evaluated by western blot. RESULTS Flavokawain-B selectively inhibited the viability of the human NSCLC cell line A549, indicating lower toxicity compared with normal lung cancer (NLC) CCL-151 cells and both showed dose-dependent inhibition. DAPI and annexin V-FITC/PI staining showed that flavokawain-B led to a dose-dependent onset of apoptosis in lung cancer cells characterized by shrunken cells, fragmented nuclei and chromatin condensation. Western blot showed that flavokawain-B resulted in downregulation of Bcl-2 and upregulation of Bax in a dose dependent manner. Flavokawain-B treatment led to increase of intracellular ROS concentration and decrease of mitochondrial membrane potential (MMP) both showing dose-dependence. It also led to suppression of cell migration and invasion along with blocking PI3K/AKT signalling pathway. CONCLUSIONS Flavokawain-B targets gemcitabine-resistant NSCLC cells selectively without inducing any significant toxicity in normal cells and these effects are mediated via apoptosis induction, ROS production, loss of MMP, suppression of cell migration and invasion and blocking PI3K/AKT signalling pathway.
Nipple-Sparing Mastectomy Long-Term Outcomes: Early and Late Complications

Background and Objectives: The surgical choice treatment of the breast cancer mostly depends on the stage of the disease. In the last years, breast cancer surgery has moved from being destructive to being more respectful of the anatomical and physiological integrity of the gland. The aim of the breast surgery should be finalized to obtain the best aesthetic and functional results, respecting the principles of oncologic radicality. The present study is a retrospective analysis aimed to evaluate the long-term outcomes of a conservative technique like the nipple-sparing mastectomy. Materials and Methods: We observed 894 patients with a median age of 47.5 years old, underwent nipple-sparing mastectomy between 2002–2017. The data acquired include population and tumor characteristics, patient reconstructive outcomes, including locoregional, regional, and distant metastases; other variables, among nipple–areola complex necrosis and infection were collected. Results: The complications detected were considered as “early” within 1 month later the nipple-sparing mastectomy or “late” after this time. The overall complications rate (early and late) and the overall survival and the relapses detected by this study were comparable with those reported in the literature. In order to identify factors that correlate with complications, either early or later, it has been processed an evaluation of the univariate analysis showing adjuvant chemotherapy as the only predictive factor for late complications, while we encountered no predictors for early complications. Conclusions: The present study adds to the data already present in literature, demonstrating that the nipple-sparing mastectomy is a safe procedure, providing good oncological and aesthetic results in patients carefully selected.
MicroRNA-22 regulates the proliferation, drug sensitivity and metastasis of human glioma cells by targeting SNAIL1.

PURPOSE Gliomas are aggressive brain tumors accounting for significant mortality across the globe. Biomarkers for early detection and therapeutic targets for efficient treatment are lacking for glioma. This study was undertaken to investigate the role and therapeutic implications of miR-22 in glioma. METHODS U-87 glioma cell line was used in this study. qRT-PCR was employed for expression analysis. MTT assay was used for determination of cell viability. Lipofectamine 2000 was used for transfection. Flow cytometry was used for cell analysis. Wound healing assay and transwell assay were used for monitoring cell migration and invasion. Western blot analysis was used for estimation of protein expression. RESULTS The miR-22 expression was found decreased in glioma cells. Overexpression of miR-22 resulted in arrest of the U-87 glioma cells at G2/M checkpoint of the cell cycle. The percentage of apoptotic U-87 cells in G2/M phase were 13.05% in negative control (NC) and 29.06% in miR-22 mimics transfected cells. The cell cycle arrest promoted by miR-22 overexpression was also associated with depletion of cyclin B1 expression in U-87 cells. Furthermore, miR-22 could also significantly increase the sensitivity of glioma U-87 cells to cisplatin. The TargetScan analysis and dual luciferase assay showed SNAIL1 to be the target of miR-22. The expression of SNAIL1 was also enhanced in all the glioma cells and miR-22 overexpression could cause suppression of the SNAIL1 expression in U-87 cells. Furthermore, SNAIL1 silencing could also cause decline in the viability of the U-87 cells. The wound healing assay showed that miR-5 overexpression caused decrease in the migration of U-87 cells, while the transwell assay showed decline in the invasion of miR-22 mimics transfected U-87 cells. CONCLUSION Taken together, miR-22 may exhibit therapeutic implications in glioma and may prove useful in glioma treatment.
RNase T1 Refolding Assay for Determining Mitochondrial Cyclophilin D Activity - A Novel in vitro Method Applicable in Drug Research and Discovery.

Human cyclophilin D is a mitochondrial peptidyl-prolyl isomerase that plays a role in regulating the opening of the mitochondrial permeability transition pore. It is considered a viable and promising molecular target for the treatment of diseases for which disease development is associated with pore opening, e.g., Alzheimer's disease or ischemia/reperfusion injury. Currently available and widely used in vitro methods based on Kofron's assay for determining cyclophilin D activity suffer from serious drawbacks and limitations. In this study, a completely novel approach for an in vitro assay of cyclophilin D activity using RNase T1 refolding was introduced. The method is simple and is more in line with the presumed physiological role of cyclophilin D in protein folding than Kofron's assay, which relies on a peptide substrate. The method is applicable for identifying novel inhibitors of cyclophilin D as potential drugs for the treatment of the abovementioned diseases. Moreover, the description of CypD activity in the in vitro RNAse T1 refolding assay reveals new possibilities for investigating the role of cyclophilin D in protein folding in cells and may lead to better understanding of its patho/physiological roles.
Mechanobiology of antigen‐induced T cell arrest

To mount an immune response, T cells must first find rare antigens present at the surface of antigen‐presenting cells (APCs). They achieve this by migrating rapidly through the crowded space of tissues and constantly sampling the surface of APCs. Upon antigen recognition, T cells decelerate and polarise towards the APC, ultimately forming a specialised interface known as the immunological synapse. These conjugates form as the result of the interaction between pairs of receptors/ligands that are under mechanical stress due to the continuously reorganising cell cytoskeleton. In this review, we discuss the involvement of mechanical forces during antigen recognition by migrating T cells. We will explore this question from a conceptual and technical perspective, with the aim of providing new insights into the emerging field of mechanobiology.
Robust Functional Manifold Clustering

In machine learning, it is common to interpret each data sample as a multivariate vector disregarding the correlations among covariates. However, the data may actually be functional, i.e., each data point is a function of some variable, such as time, and the function is discretely sampled. The naive treatment of functional data as traditional multivariate data can lead to poor performance due to the correlations. In this article, we focus on subspace clustering for functional data or curves and propose a new method robust to shift and rotation. The idea is to define a function or curve and all its versions generated by shift and rotation as an equivalent class and then to find the subspace structure among all equivalent classes as the surrogate for all curves. Experimental evaluation on synthetic and real data reveals that this method massively outperforms prior clustering methods in both speed and accuracy when clustering functional data.
The prognostic value of neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio in nasopharyngeal cancer.

PURPOSE To investigate the prognostic value of pre-treatment neutrophil/lymphocyte ratio (NLR), platelet/lymphocyte ratio (PLR) and hemoglobin level in patients treated with definitive chemoradiotherapy (CRT) for nasopharyngeal carcinoma. METHODS We retrospectively analyzed 97 patients who received definitive CRT for nasopharyngeal cancer. An NLR cut-off value of 4.42 was identified using receiver operating characteristic curve (ROC) analysis, an PLR cut-off value of 128.6 was identified using ROC analysis and a hemoglobin cut-off value of 13g/dl was identified using ROC analysis with overall survival (OS) as an endpoint. RESULTS The 5-year progression-free survival (PFS) and overall survival (OS) for all patients were 67.1% and 72.6%, respectively. The patients with a high NLR (20.6%) had a significantly lower 5-year OS than those with a low NLR (79.4%) (OS: 46.9% vs. 79.7%, p<0.001). The patients with a high PLR (66.3%) had a borderline significant lower 5-year OS than those with a low PLR (32.7%) (OS: 66.1% vs. 87.9%, p=0.055). The patients with a low hemoglobin (18.4%) had a significantly lower 5-year OS than those with a high hemoglobin (80.6%) (OS: 46.6% vs. 78.9%, p<0.001). In univariate analysis, older age, IMRT technique, low hemoglobin and high NLR were prognostic factors. In multivariate analysis, high NLR, low hemoglobin and older age remained independent prognostic factors for OS. CONCLUSIONS Nasopharyngeal cancer tends to be more aggressive in patients with a high NLR and low hemoglobin. These patients should be treated more aggressively, given their unfavorable prognosis.
Gut dysbacteriosis and intestinal disease: mechanism and treatment

The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) inflammatory bowel disease, primary sclerosing cholangitis‐IBD, irritable bowel syndrome, chronic constipation, osmotic diarrhoea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota–derived signalling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, faecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.
Keratoacanthoma centrifugum marginatum associated with mechanical trauma: Response to acitretin—A case report and review of the literature

Keratoacanthoma centrifugum marginatum (KCM) is a very rare variant of keratoacanthoma, characterized with progressive centrifugal growth, central healing, and atrophy. Due to its rarity and lack of distinctive histopathological features, KCM often raises diagnostic and therapeutic challenge. We present a case of a 76‐year‐old Caucasian woman with a single large tumor on her right shin that responded to oral retinoids. The patient presented history of local trauma. The tumor developed over the course of 20 months from a scar. To the best of our knowledge, this is the fifth case of KCM associated with mechanical trauma as a possible triggering factor.
Early onset demyelinating Charcot‐Marie‐Tooth disease caused by a novel in‐frame isoleucine deletion in peripheral myelin protein 2

Peripheral myelin protein 2 (PMP2) is a small protein located on the cytoplasmic side of compact myelin, involved in the lipids transport and in the myelination process. In the last years few families affected with demyelinating Charcot‐Marie‐Tooth neuropathy (CMT1), caused by PMP2 mutations, have been identified. In this study we describe the first case of a PMP2 in‐frame deletion. PMP2 was analyzed by direct sequencing after exclusion of the most frequent CMT‐associated genes by using a next generation sequencing (NGS) genes panel. Sanger sequencing was used for family's segregation analysis. Molecular modeling analysis was used to evaluate the mutation impact on the protein structure. A novel PMP2: p.I50del has been identified in a child with early onset CMT1 and in three affected family members. All family members show an early onset demyelinating neuropathy without other distinguish features. Molecular modeling analysis and in silico evaluations do not suggest a strong impact on the overall protein structure, but a most likely altered protein function. This study suggests the importance to add PMP2 in CMT NGS genes panels or, at most, to test it after major CMT1 genes exclusion, due to the lack of diagnostic‐addressing additional features.
Monitoring Winter Stress Vulnerability of High-Latitude Understory Vegetation Using Intraspecific Trait Variability and Remote Sensing Approaches

In this study, we focused on three species that have proven to be vulnerable to winter stress: Empetrum nigrum, Vaccinium vitis-idaea and Hylocomium splendens. Our objective was to determine plant traits suitable for monitoring plant stress as well as trait shifts during spring. To this end, we used a combination of active and passive handheld normalized difference vegetation index (NDVI) sensors, RGB indices derived from ordinary cameras, an optical chlorophyll and flavonol sensor (Dualex), and common plant traits that are sensitive to winter stress, i.e. height, specific leaf area (SLA). Our results indicate that NDVI is a good predictor for plant stress, as it correlates well with height (r = 0.70, p < 0.001) and chlorophyll content (r = 0.63, p < 0.001). NDVI is also related to soil depth (r = 0.45, p < 0.001) as well as to plant stress levels based on observations in the field (r = −0.60, p < 0.001). Flavonol content and SLA remained relatively stable during spring. Our results confirm a multi-method approach using NDVI data from the Sentinel-2 satellite and active near-remote sensing devices to determine the contribution of understory vegetation to the total ecosystem greenness. We identified low soil depth to be the major stressor for understory vegetation in the studied plots. The RGB indices were good proxies to detect plant stress (e.g. Channel G%: r = −0.77, p < 0.001) and showed high correlation with NDVI (r = 0.75, p < 0.001). Ordinary cameras and modified cameras with the infrared filter removed were found to perform equally well.
Structural and kinetic basis for the regulation and potentiation of Hsp104 function

Significance Cryo-electron microscopy now shows what many massive protein molecular machines look like. What is needed is a methodology that can probe into the machinery under working conditions. This work demonstrates the ability of hydrogen exchange mass spectrometry to provide detailed structural, biophysical, and functional information on the hexameric 0.6-MDa AAA+ Hsp104 protein in its various static nucleotide-bound states and during functional cycling at near amino acid resolution. Hsp104 provides a valuable model for the many essential proteostatic functions performed by the AAA+ superfamily of protein molecular machines. We developed and used a powerful hydrogen exchange mass spectrometry (HX MS) analysis that can provide positionally resolved information on structure, dynamics, and energetics of the Hsp104 molecular machinery, even during functional cycling. HX MS reveals that the ATPase cycle is rate-limited by ADP release from nucleotide-binding domain 1 (NBD1). The middle domain (MD) serves to regulate Hsp104 activity by slowing ADP release. Mutational potentiation accelerates ADP release, thereby increasing ATPase activity. It reduces time in the open state, thereby decreasing substrate protein loss. During active cycling, Hsp104 transits repeatedly between whole hexamer closed and open states. Under diverse conditions, the shift of open/closed balance can lead to premature substrate loss, normal processing, or the generation of a strong pulling force. HX MS exposes the mechanisms of these functions at near-residue resolution.
Pitfalls in Cancer Biomarker Discovery and Validation with Emphasis on Circulating Tumor DNA

Despite significant investment of funds and resources, few new cancer biomarkers have been introduced to the clinic in the last few decades. Although many candidates produce promising results in the laboratory, deficiencies in sensitivity, specificity, and predictive value make them less than desirable in a patient setting. This review will analyze these challenges in detail as well as discuss false discovery, problems with reproducibility, and tumor heterogeneity. Circulating tumor DNA (ctDNA), an emerging cancer biomarker, is also analyzed, particularly in the contexts of assay specificity, sensitivity, fragmentation, lead time, mutant allele fraction, and clinical relevance. Emerging artificial intelligence technologies will likely be valuable tools in maximizing the clinical utility of ctDNA which is often found in very small quantities in patients with early-stage tumors. Finally, the implications of challenging false discoveries are examined and some insights about improving cancer biomarker discovery are provided. See all articles in this CEBP Focus section, “NCI Early Detection Research Network: Making Cancer Detection Possible. ”