Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic identification of autophagy-related proteins in Aedes albopictus

Autophagy is a conserved cellular process playing a role in maintenance of cellular homeostasis and response to changing nutrient conditions via degradation and recirculation of cellular redundant components. Autophagy-related proteins (Atg) play important function in autophagy pathway. Aedes albopictus mosquito is an effective vector transmitting multiple viruses which cause serious human diseases. Moreover, Aedes albopictus mosquito is becoming a serious threat to human health due to its widening distribution in recent years and thus worth of more research attention. It was reported that autophagy might play a role in viral infection in Aedes mosquito. To better understand the interaction between autophagy and arbovirus infection in mosquito system, it is necessary to identify autophagy pathway in the system. However, autophagy in Aedes albopictus mosquito is still poorly understood so far. We recently identified AaAtg8, the first Atg protein reported in Aedes albopictus mosquito. This work further identified twelve atg genes in Aedes albopictus mosquito. Sequence and phylogenetic analysis of the twelve atg genes were performed. Expression profiles of all the twelve Aaatg genes in different developmental stages and genders of Aedes albopictus mosquito were conducted. Effects of chemicals inhibiting or inducing autophagy on the levels of eight identified AaAtg proteins were examined. The function of two identified AaAtg proteins AaAtg6 and AaAtg16 and their response to arbovirus SINV infection were studied preliminarily. Taken together, this work systematically identified Aedes albopictus atg genes and provided basic information which might help to elucidate the autophagy pathway and the role of autophagy in arbovirus infection in Aedes mosquito system.
Murine Intrarectal Instillation of Purified Recombinant Clostridioides difficile Toxins Enables Mechanistic Studies of Pathogenesis

Clostridioides difficile is linked to nearly 225,000 antibiotic-associated diarrheal infections and almost 13,000 deaths per year in the United States. Pathogenic strains of C. difficile produce toxin A (TcdA) and toxin B (TcdB), which can directly kill cells and induce an inflammatory response in the colonic mucosa. ABSTRACT Clostridioides difficile is linked to nearly 225,000 antibiotic-associated diarrheal infections and almost 13,000 deaths per year in the United States. Pathogenic strains of C. difficile produce toxin A (TcdA) and toxin B (TcdB), which can directly kill cells and induce an inflammatory response in the colonic mucosa. Hirota et al. (S. A. Hirota et al., Infect Immun 80:4474–4484, 2012) first introduced the intrarectal instillation model of intoxication using TcdA and TcdB purified from VPI 10463 (VPI 10463 reference strain [ATCC 43255]) and 630 C. difficile strains. Here, we expand this technique by instilling purified, recombinant TcdA and TcdB, which allows for the interrogation of how specifically mutated toxins affect tissue. Mouse colons were processed and stained with hematoxylin and eosin for blinded evaluation and scoring by a board-certified gastrointestinal pathologist. The amount of TcdA or TcdB needed to produce damage was lower than previously reported in vivo and ex vivo. Furthermore, TcdB mutants lacking either endosomal pore formation or glucosyltransferase activity resemble sham negative controls. Immunofluorescent staining revealed how TcdB initially damages colonic tissue by altering the epithelial architecture closest to the lumen. Tissue sections were also immunostained for markers of acute inflammatory infiltration. These staining patterns were compared to slides from a human C. difficile infection (CDI). The intrarectal instillation mouse model with purified recombinant TcdA and/or TcdB provides the flexibility needed to better understand structure/function relationships across different stages of CDI pathogenesis.
Maedi–visna virus Vif protein uses motifs distinct from HIV-1 Vif to bind zinc and the cofactor required for A3 degradation

The mammalian apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 or A3) family of cytidine deaminases restrict viral infections by mutating viral DNA and impeding reverse transcription. To overcome this antiviral activity, most lentiviruses express a viral accessory protein called the virion infectivity factor (Vif), which recruits A3 proteins to cullin–RING E3 ubiquitin ligases such as cullin-5 (Cul5) for ubiquitylation and subsequent proteasomal degradation. Although Vif proteins from primate lentiviruses such as HIV-1 utilize the transcription factor core-binding factor subunit beta as a noncanonical cofactor to stabilize the complex, the maedi–visna virus (MVV) Vif hijacks cyclophilin A (CypA) instead. Because core-binding factor subunit beta and CypA are both highly conserved among mammals, the requirement for two different cellular cofactors suggests that these two A3-targeting Vif proteins have different biochemical and structural properties. To investigate this topic, we used a combination of in vitro biochemical assays and in vivo A3 degradation assays to study motifs required for the MVV Vif to bind zinc ion, Cul5, and the cofactor CypA. Our results demonstrate that although some common motifs between the HIV-1 Vif and MVV Vif are involved in recruiting Cul5, different determinants in the MVV Vif are required for cofactor binding and stabilization of the E3 ligase complex, such as the zinc-binding motif and N- and C-terminal regions of the protein. Results from this study advance our understanding of the mechanism of MVV Vif recruitment of cellular factors and the evolution of lentiviral Vif proteins.
The role of clinical examination of the optic nerve head in glaucoma today

Purpose of review The study was undertaken to assess the current importance of clinical examination of the optic nerve head (ONH) in glaucoma management. Recent findings ONH changes in glaucoma are easily assessed with good specificity on examination, whereas imaging has not been able to identify pallor of the neuroretinal rim (NRR), disc hemorrhages, or vascular signs of acquired cupping. Glaucomatous neuropathy in primary open angle glaucoma (POAG) has extensive databases on imaging machines, however, other glaucomas such as primary angle closure glaucoma (PACG), juvenile open angle glaucoma (JOAG), congenital, and secondary glaucomas have been reported to have a significantly different ONH morphology. Clinical evaluation with knowledge of the underlying cause of glaucoma allows easy diagnosis of any abnormality, whereas the absence of an imaging database in such eyes makes diagnosis difficult on optical coherence tomography (OCT) and so forth. In eyes with congenital anomalies and dysplastic discs, clinical examination and history provide better identification of glaucomatous damage. Staging of glaucoma on ONH examination when perimetry is unreliable provides a means of determining the amount of damage and appropriate reduction of intraocular pressure (IOP). Summary Clinical examination of the ONH is very relevant for screening, diagnosis, staging, and management of all glaucomas, and is irreplaceable in detecting nonglaucomatous causes of ONH cupping and visual field defects similar to those in glaucoma.
Melanoma Cell Resistance to Vemurafenib Modifies Inter-Cellular Communication Signals

The therapeutic success of BRAF inhibitors (BRAFi) and MEK inhibitors (MEKi) in BRAF-mutant melanoma is limited by the emergence of drug resistance, and several lines of evidence suggest that changes in the tumor microenvironment can play a pivotal role in acquired resistance. The present study focused on secretome profiling of melanoma cells sensitive or resistant to the BRAFi vemurafenib. Proteomic and cytokine/chemokine secretion analyses were performed in order to better understand the interplay between vemurafenib-resistant melanoma cells and the tumor microenvironment. We found that vemurafenib-resistant melanoma cells can influence dendritic cell (DC) maturation by modulating their activation and cytokine production. In particular, human DCs exposed to conditioned medium (CM) from vemurafenib-resistant melanoma cells produced higher levels of pro-inflammatory cytokines—that potentially facilitate melanoma growth—than DCs exposed to CM derived from parental drug-sensitive cells. Bioinformatic analysis performed on proteins identified by mass spectrometry in the culture medium from vemurafenib-sensitive and vemurafenib-resistant melanoma cells suggests a possible involvement of the proteasome pathway. Moreover, our data confirm that BRAFi-resistant cells display a more aggressive phenotype compared to parental ones, with a significantly increased production of interferon-γ, interleukin-8, vascular-endothelial growth factor, CD147/basigin, and metalloproteinase 2 (MMP-2). Plasma levels of CD147/basigin and MMP-2 were also measured before the start of therapy and at disease progression in a small group of melanoma patients treated with vemurafenib or vemurafenib plus cobimetinib. A significant increment in CD147/basigin and MMP-2 was observed in all patients at the time of treatment failure, strengthening the hypothesis that CD147/basigin might play a role in BRAFi resistance.
Cultivation of Saccharomyces cerevisiae with Feedback Regulation of Glucose Concentration Controlled by Optical Fiber Glucose Sensor

Glucose belongs among the most important substances in both physiology and industry. Current food and biotechnology praxis emphasizes its on-line continuous monitoring and regulation. These provoke increasing demand for systems, which enable fast detection and regulation of deviations from desired glucose concentration. We demonstrated control of glucose concentration by feedback regulation equipped with in situ optical fiber glucose sensor. The sensitive layer of the sensor comprises oxygen-dependent ruthenium complex and preimmobilized glucose oxidase both entrapped in organic–inorganic polymer ORMOCER®. The sensor was placed in the laboratory bioreactor (volume 5 L) to demonstrate both regulations: the control of low levels of glucose concentrations (0.4 and 0.1 mM) and maintenance of the glucose concentration (between 2 and 3.5 mM) during stationary phase of cultivation of Saccharomyces cerevisiae. Response times did not exceed 6 min (average 4 min) with average deviation of 4%. Due to these regulation characteristics together with durable and long-lasting (≥2 month) sensitive layer, this feedback regulation system might find applications in various biotechnological processes such as production of low glucose content beverages.
MARANGONI CONVECTIONS IN A HORIZONTAL POROUS LAYER SUPERPOSED BY A FLUID LAYER IN THE PRESENCE OF UNIFORM VERTICAL MAGNETIC FIELD AND SOLUTE

A linear stability analysis applied to a system consisting of a horizontal fluid layer overlying a porous layer in the presence of uniform vertical magnetic field and solute on both layers. Flow in porous medium is assumed to be governed by Darcy’s law, where as the flow in the fluid layer is governed by Navier-Stokes equation. The Beavers-Joseph condition is applied at the interface between the two layers. Numerical solutions are obtained for stationary convection case using the method of expansion of Chebyshev polynomials. It is found that the spectral method has a strong ability to solve the multi-layered problem, the depth ratio has a strong effect and that the magnetic field has effect in this model.
Developmental Hazard of Environmentally Persistent Free Radicals and Protective Effect of TEMPOL in Zebrafish Model

Environmentally persistent free radicals (EPFRs) can be detected in ambient PM2.5, cigarette smoke, and soils and are formed through combustion and thermal processing of organic materials. The hazards of EPFRs are largely unknown. In this study, we assess the developmental toxicity of EPFRs and the ability of TEMPOL (4-Hydroxy-2,2,6,6-tetramethylpiperidine 1-oxyl) to protect against such hazards using zebrafish embryos. Particles containing EPFRs were acquired by dosing dichlorobenzene (DCB) vapor on the Cab-o-sil/5% CuO particles at 230 °C in vacuo (referred to as DCB-230). The particles were suspended in ultrapure water to make 1 mg/mL of stock solution from which series dilution was undertaken to obtain 10, 20, 30, 40, 50, 60, 80, and 100 µg/mL final test solutions, which were then placed in individual wells with a 4 h postfertilization (hpf) zebrafish embryo. Plates were run in duplicate to obtain a sample size of 24 animals per concentration; 12 embryos were exposed per concentration per plate. Statistical analysis of the morphology endpoints was performed. We investigated overt toxicity responses to DCB-230 in a 22-endpoint battery that included developing zebrafish from 24–120 hpf. Exposure to concentrations greater than 60 µg/mL of DCB-230 induced high mortality in the developmental zebrafish model. Exposure to EPFRs induced developmental hazards that were closely related to the concentrations of free radicals and EPFRs. The potential protective effects of TEMPOL against EPFRs’ toxicity in zebrafish were investigated. Exposure to EPFRs plus TEMPOL shifted the concentration to an induced 50% adverse effect (EC50), from 23.6 to 30.8 µg/mL, which verifies TEMPOL’s protective effect against EPFRs in the early phase of zebrafish development.
A Workshop on Cognitive Aging and Impairment in the 9/11-Exposed Population

The terrorist attacks on 11 September 2001 potentially exposed more than 400,000 responders, workers, and residents to psychological and physical stressors, and numerous hazardous pollutants. In 2011, the World Trade Center Health Program (WTCHP) was mandated to monitor and treat persons with 9/11-related adverse health conditions and conduct research on physical and mental health conditions related to the attacks. Emerging evidence suggests that persons exposed to 9/11 may be at increased risk of developing mild cognitive impairment. To investigate further, the WTCHP convened a scientific workshop that examined the natural history of cognitive aging and impairment, biomarkers in the pathway of neurodegenerative diseases, the neuropathological changes associated with hazardous exposures, and the evidence of cognitive decline and impairment in the 9/11-exposed population. Invited participants included scientists actively involved in health-effects research of 9/11-exposed persons and other at-risk populations. Attendees shared relevant research results from their respective programs and discussed several options for enhancements to research and surveillance activities, including the development of a multi-institutional collaborative research network. The goal of this report is to outline the meeting’s agenda and provide an overview of the presentation materials and group discussion.
Endocrine-Disrupting Organochlorine Pesticides in Human Breast Milk: Changes during Lactation

The aim of the present study was to assess infant safety associated with the occurrence of endocrine-disrupting organochlorine pesticides (OCP) in breast milk. Moreover, the association between pregnant mothers’ dietary habits and these compounds levels in breast milk was investigated. Breast milk was collected at various stages of lactation. The samples were analyzed by the GC-MS method. The OCP concentrations ranged from < limit of detection (LOD) to 6.81 ng/g lipids. The highest OCP concentrations in breast milk occurred primarily within the first month of lactation, and decreased over the lactation period. It was found that the maternal consumption of certain food products—in particular pork, beef, poultry, eggs, and dairy products—could have affected the content of 1,1’-(2,2,2-Trichloroethane-1,1-diyl)bis(4-chlorobenzene), called DDT and its metabolites in the breast milk. The levels of beta-endosulfan were positively correlated with fish and poultry consumption. The redundancy analysis indicated that the diets of the pregnant women had an important impact on pesticide residues in the breast milk. There is a potential possibility of lowering the content of organochlorine compounds in breast milk by adhering to nutritional recommendations, e.g., avoiding the excessive consumption of fish and other raw food materials of unknown origin.
Hydration Characteristics of Tricalcium Aluminate in the Presence of Nano-Silica

Tricalcium aluminate (C3A) is the most reactive component of the Portland cement and its hydration has an important impact on the workability and early strength of concrete. Recently, nanomaterials such as nano-silica (nano-SiO2) have attracted much attention in cement-based materials because of its pozzolanic reactivity and the pore-filling effect. However, its influence on the hydration of C3A needs to be well understood. In this study, the hydration kinetics of C3A mixed with different percentages of nano-SiO2 were studied and compared with pure C3A. The hydration products were examined by different characterization techniques including XRD, XPS, and NMR spectroscopy and isothermal calorimetry analyses. The XRD results showed that the addition of nano-SiO2 promoted the conversion of the intermediate product C4AH13. The isothermal calorimetry results showed that the addition of nano-SiO2 significantly reduced the hydration exotherm rate of C3A from 0.34 to less than 0.1 mW/g. With the presence of nano-SiO2, the peaks for Q1 were observed in 29Si MAS-NMR measurements, and the content of Q1 increased from 6.74% to 30.6% when the nano-SiO2 content increased from 2 wt. % to 8 wt. %, whereas the proportion of Q4 gradually decreased from 89.1% to 63.6%. These results indicated a pozzolanic reaction provoked by the nano-SiO2 combined with aluminate structures generating C-A-S-H gel.
The Double Life-Saving Approach of Abdominal Radical Trachelectomy during Pregnancy for Early-Stage Cervical Cancer—An Overview of the Literature and Our Institutional Experience

(1) Background: Cervical cancer is the most common type of cancer encountered during pregnancy, with a frequency of 0.8–1.5 cases per 10,000 births. It is a dire condition endangering patients’ lives and pregnancy outcomes, and jeopardizing their fertility. However, there is a lack of current evidence and consensus regarding a standard surgical technique for pregnant patients who suffer from this condition during pregnancy. The study aims to comprehensively update all published data, evaluating the obstetrical and oncological results of pregnant patients who underwent abdominal radical trachelectomy during early stages of cervical cancer. (2) Methods: A literature search on the Medline, PubMed, and Google Scholar databases was performed, including all articles in question up to July 2020. This study presents an overview of the literature and our institutional experience. (3) Results: A total of 25 cases of abdominal radical trachelectomy were performed during pregnancy for early cervical cancer, including the five cases managed by the authors. Of these, 81% (19 patients) gave birth to live newborns through elective C-section, and 19% (6 patients) experienced miscarriage shortly after the procedure. None of the 25 patients (100%) reported disease recurrence. (4) Conclusions: The results of the current study were satisfactory. However, abdominal radical trachelectomy does not represent the current standard of care for cervical cancer during pregnancy, but it could play an important role if more evidence on its effectiveness will be provided.
A Roadmap for Developing Plasma Diagnostic and Prognostic Biomarkers of Cerebral Cavernous Angioma With Symptomatic Hemorrhage (CASH).

BACKGROUND Cerebral cavernous angioma (CA) is a capillary microangiopathy predisposing more than a million Americans to premature risk of brain hemorrhage. CA with recent symptomatic hemorrhage (SH), most likely to re-bleed with serious clinical sequelae, is the primary focus of therapeutic development. Signaling aberrations in CA include proliferative dysangiogenesis, blood-brain barrier hyperpermeability, inflammatory/immune processes, and anticoagulant vascular domain. Plasma levels of molecules reflecting these mechanisms and measures of vascular permeability and iron deposition on magnetic resonance imaging are biomarkers that have been correlated with CA hemorrhage. OBJECTIVE To optimize these biomarkers to accurately diagnose cavernous angioma with symptomatic hemorrhage (CASH), prognosticate the risk of future SH, and monitor cases after a bleed and in response to therapy. METHODS Additional candidate biomarkers, emerging from ongoing mechanistic and differential transcriptome studies, would further enhance the sensitivity and specificity of diagnosis and prediction of CASH. Integrative combinations of levels of plasma proteins and characteristic micro-ribonucleic acids may further strengthen biomarker associations. We will deploy advanced statistical and machine learning approaches for the integration of novel candidate biomarkers, rejecting noncorrelated candidates, and determining the best clustering and weighing of combined biomarker contributions. EXPECTED OUTCOMES With the expertise of leading CA researchers, this project anticipates the development of future blood tests for the diagnosis and prediction of CASH to clinically advance towards precision medicine. DISCUSSION The project tests a novel integrational approach of biomarker development in a mechanistically defined cerebrovascular disease with a relevant context of use, with an approach applicable to other neurological diseases with similar pathobiologic features.
The p.E152K-STIM1 mutation deregulates Ca2+ signaling contributing to chronic pancreatitis

ABSTRACT Since deregulation of intracellular Ca2+ can lead to intracellular trypsin activation, and stromal interaction molecule-1 (STIM1) protein is the main regulator of Ca2+ homeostasis in pancreatic acinar cells, we explored the Ca2+ signaling in 37 STIM1 variants found in three pancreatitis patient cohorts. Extensive functional analysis of one particular variant, p.E152K, identified in three patients, provided a plausible link between dysregulated Ca2+ signaling within pancreatic acinar cells and chronic pancreatitis susceptibility. Specifically, p.E152K, located within the STIM1 EF-hand and sterile α-motif domain, increased the release of Ca2+ from the endoplasmic reticulum in patient-derived fibroblasts and transfected HEK293T cells. This event was mediated by altered STIM1–sarco/endoplasmic reticulum calcium transport ATPase (SERCA) conformational change and enhanced SERCA pump activity leading to increased store-operated Ca2+ entry (SOCE). In pancreatic AR42J cells expressing the p.E152K variant, Ca2+ signaling perturbations correlated with defects in trypsin activation and secretion, and increased cytotoxicity after cholecystokinin stimulation. This article has an associated First Person interview with the first author of the paper. Summary: The p.E152K-STIM1 variant found in pancreatitis patients leads to intracellular changes in Ca2+ homeostasis through SERCA conformational changes, enabling intracellular trypsin activation and pancreatic acinar cell death.