gebhart/patrepeval huggingface dataset:
Evaluation of SARS-CoV-2 3C-like protease inhibitors using self-assembled monolayer desorption ionization mass spectrometry (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic that began in 2019. The coronavirus 3-chymotrypsin-like cysteine protease (3CLpro) controls replication and is therefore considered a major target for antiviral discovery. This study describes the evaluation of SARS-CoV-2 3CLpro inhibitors in a novel self-assembled monolayer desorption ionization mass spectrometry (SAMDI-MS) enzymatic assay. Compared with a traditional FRET readout, the label-free SAMDI-MS assay offers greater sensitivity and eliminates false positive inhibition from compound interference with the optical signal. The SAMDI-MS assay was optimized and validated with known inhibitors of coronavirus 3CLpro such as GC376 (IC<sub>50</sub> = 0.060 μM), calpain inhibitors II and XII (IC<sub>50</sub> ~20-25 μM). The FDA-approved drugs shikonin, disulfiram, and ebselen did not inhibit SARS-CoV-2 3CLpro activity in the SAMDI-MS assay under physiologically relevant reducing conditions. The three drugs did not directly inhibit human β-coronavirus OC-43 or SARS-CoV-2 in vitro, but instead induced cell death. In conclusion, the SAMDI-MS 3CLpro assay, combined with antiviral and cytotoxic assessment, provides a robust platform to evaluate antiviral agents directed against SARS-CoV-2.
Immune regulatory cells: circulating biomarker factories in cardiovascular disease (2008)

TLRs (Toll-like receptors) are the first line of defence of the innate immune system. These receptors recognize not only exogenous but also endogenous ligands that are expressed following arterial injury and atherosclerotic disease. Expression of TLR2 and TLR4 is observed in macrophages and different vascular cells and is increased in atherosclerotic disease. It is suggested that TLR expression and functional responsiveness following ligation could serve as biomarkers for atherosclerotic disease progression. Recently published research papers support the concept that the TLRs are fast responders upon arterial injury. In the present issue of Clinical Science, Ishikawa and co-workers provide new evidence emerges that points to the potential prognostic properties of the TLRs.
Ethanol from cellulose: a general review. (2002)

INTRODUCTION The use of ethanol as an alternative motor fuel has been steadily increasing around the world for a number of reasons. Domestic production and use of ethanol for fuel can decrease dependence on foreign oil, reduce trade deficits, create jobs in rural areas, reduce air pollution, and reduce global climate change carbon dioxide buildup. Ethanol, unlike gasoline, is an oxygenated fuel that contains 35% oxygen, which reduces particulate and NOx emissions from combustion. Ethanol can be made synthetically from petroleum or by microbial conversion of biomass materials through fermentation. In 1995, about 93% of the ethanol in the world was produced by the fermentation method and about 7% by the synthetic method. The fermentation method generally uses three steps: (1) the formation of a solution of fermentable sugars, (2) the fermentation of these sugars to ethanol, and (3) the separation and purification of the ethanol, usually by distillation.
Altered Immune Phenotype in Peripheral Blood Cells of Patients with Scleroderma‐Associated Pulmonary Hypertension (2010)

Pulmonary arterial hypertension is a common and fatal complication of scleroderma that may involve inflammatory and autoimmune mechanisms. Alterations in the gene expression of peripheral blood mononuclear cells have been previously described in patients with pulmonary arterial hypertension. Our goal is to identify differentially expressed genes in peripheral blood mononuclear cells in scleroderma patients with and without pulmonary hypertension as biomarkers of disease. Gene expression analysis was performed on a Microarray Cohort of scleroderma patients with (n = 10) and without (n = 10) pulmonary hypertension. Differentially expressed genes were confirmed in the Microarray Cohort and validated in a Validation Cohort of scleroderma patients with (n = 15) and without (n = 19) pulmonary hypertension by RT-qPCR. We identified inflammatory and immune-related genes including interleukin-7 receptor (IL-7R) and chemokine receptor 7 as differentially expressed in patients with scleroderma-associated pulmonary hypertension. Flow cytometry confirmed decreased expression of IL-7R on circulating CD4+ T-cells from scleroderma patients with pulmonary hypertension. Differences exist in the expression of inflammatory and immune-related genes in peripheral blood cells from patients with scleroderma-related pulmonary hypertension compared to those with normal pulmonary artery pressures. These findings may have implications as biomarkers to screen at-risk populations for early diagnosis and provide insight into mechanisms of scleroderma-related pulmonary hypertension.
Treatment of moderate to severe inflammatory acne vulgaris: photodynamic therapy with 5-aminolevulinic acid and a novel advanced fluorescence technology pulsed light source. (2007)

The use of photodynamic therapy (PDT) with 20% 5-aminolevulinic acid (ALA) for the treatment of acne vulgaris has been explored. This study evaluates the safety and efficacy of a new Advanced Fluorescence Technology (AFT) pulsed light source (420-950 nm) for photoactivation in ALA PDT for the treatment of moderate to severe inflammatory facial acne vulgaris. Nineteen subjects received 4 ALA PDT treatments with the AFT pulsed light source. Treatments were spaced 2 weeks apart. ALA was incubated for 15 to 30 minutes. At the end of the fourth treatment, the total reductions in inflammatory and noninflammatory lesion counts were 54.5% and 37.5%, respectively. Median Global Severity Scores suggest a trend toward reduction after several treatments. Investigator and subject assessments show moderate to marked improvement in most patients. The new AFT pulsed light source with ALA PDT appears to be a safe and effective modality for the treatment of moderate to severe inflammatory acne vulgaris.
Structural interactions of fibroblast growth factor receptor with its ligands (2000)

Fibroblast growth factors (FGFs) effect cellular responses by binding to FGF receptors (FGFRs). FGF bound to extracellular domains on the FGFR in the presence of heparin activates the cytoplasmic receptor tyrosine kinase through autophosphorylation. We have crystallized a complex between human FGF1 and a two-domain extracellular fragment of human FGFR2. The crystal structure, determined by multiwavelength anomalous diffraction analysis of the selenomethionyl protein, is a dimeric assemblage of 1:1 ligand:receptor complexes. FGF is bound at the junction between the two domains of one FGFR, and two such units are associated through receptor:receptor and secondary ligand:receptor interfaces. Sulfate ion positions appear to mark the course of heparin binding between FGF molecules through a basic region on receptor D2 domains. This dimeric assemblage provides a structural mechanism for FGF signal transduction.
Cell-specific aptamers and their conjugation with nanomaterials for targeted drug delivery (2014)

Advances in nanotechnology have led to new and improved nanomaterials for biomedical applications. Conjugation of nanoparticles (NPs) with aptamers exploits both technologies, making aptamer-NP conjugates ideal agents for drug delivery with proven therapeutic effects and the reduction of toxicity to normal tissue. The use of multivalent aptamer-conjugated nanomaterials represents one of the new directions for drug development in the future; as such, continuing studies of these multivalent aptamers and bioconjugates should result in important clinical applications in targeted drug delivery.
Growing Poxviruses and Determining Virus Titer (2004)

Poxviruses are cell-associated viruses that can be grown in adherent- or suspension-cell cultures or chorioallantoic membranes of embryonated hen's eggs. The main principle of isolating the virus is to mechanically lyse infected cells. The virus can then be semipurified by centrifugation through a sucrose cushion. Further purification can be achieved with a sucrose gradient. This chapter describes methods for the preparation of large-scale growth and purification of the virus.
Flexible fabrication of long-period in-fiber gratings (1998)

Summary form only given. We have demonstrated a novel, simple, low-cost and all-fiber interrogation technique for a strain/temperature fiber Bragg sensor using a long-period grating. We show the schematic diagram of the demodulation scheme. The amount of light transmitted by the long-period grating is determined by its wavelength and is therefore proportional to the wavelength of the backreflected light from the fiber Bragg sensor acting as a spectral filter.
Effects of Bradykinin on Permeability and Diameter of Pial VesselsIn vivo (1984)

The effect of bradykinin on the permeability and vasomotor response of pial vessels has been studied to enhance our understanding of the pathophysiological role of the kallikrein-kinin system in cerebral tissue. Intravital fluorescence microscopy of the pia arachnoidea was conducted using Na+-fluorescein, FITC-dextran, and FITC-albumin as low and high molecular weight blood-brain barrier indicators. Massive arterial dilatation evolved immediately upon administration of bradykinin by superfusion of the exposed cerebral surface. An increase of the arterial diameter by 40% was the maximal response found at bradykinin concentrations of 4 x 10(-5) M. Arterial dilatation became attenuated with continuous superfusion of the preparation with bradykinin. In pial veins, a moderate reduction of the vessel diameter was observed, however, only after prolonged superfusion of the preparation. Bradykinin led to selective opening of the blood-brain barrier for Na+-fluorescein at superfusate concentrations of greater than or equal to 4 x 10(-7) M, but not for FITC-dextran or FITC-albumin. Topical administration of l-isoproterenol (10(-4) M) was found to prevent extravasation of Na+-fluorescein in the presence of bradykinin concentrations of 4 x 10(-6) M. Protection of the blood-brain barrier by isoproterenol was not observed when higher concentrations of bradykinin were employed. Intracarotid infusion of bradykinin were employed. Intracarotid infusion of bradykinin led also to a selective opening of the blood-brain barrier for Na+-fluorescein, but not for FITC-dextran or FITC-albumin. In contrast to superfusion, this route of administration did not induce changes of the vasomotor behavior of the arteries or veins. Additional experiments with B1-agonists and -antagonists suggest that bradykinin causes the openings of the blood-brain barrier th rough an interaction with B2-receptors on endothelial cells, and arterial dilatation via interaction with B2-receptors on vascular smooth muscle cells. Our findings support the concept that the release of kinins in the brain during an acute cerebral lesion mediates secondary damaging processes by the enhancement of blood-brain barrier dysfunction.
Preliminary observations of bone ingrowth into porous materials (1976)

A preliminary investigation has been performed (a) to determine the kinetics of bone ingrowth into porous materials and to determine if this ingrowth could be catalyzed by the presence of a foreign substrate; and (b) to measure the bonding capability of bone with a porous-surfaced metallic implant. Tests on porous-surfaced implants corroborate the work of other investigators in showing that bony tissue will grow into a porous substance that has pores large enough to support tissue nourishment. The shear strength of the bone-implant interface appears to increase with pore size and time of healing. Furthermore, it may be possible to catalyze this tissue ingrowth by the introduction into the fracture site of a foreign substance; in this experiment, glass beads 200-290mu in diameter were used.
PPG embedded system for blood pressure monitoring (2014)

In this work, we have designed and implemented a microcontroller-based embedded system for blood pressure monitoring through a PhotoPlethysmoGraphic (PPG) technique. In our system, it is possible to perform PPG measurements via reflectance mode. Hardware novelty of our system consists in the adoption of Silicon PhotoMultiplier detectors. The signal received from the photodetector is used to calculate the instantaneous heart rate and therefore the heart rate variability. The obtained results show that, by using our system, it is possible to easily extract both the PPG and the breath signal. These signals can be used to monitor the patients during the convalescence both in hospital and at home.
Two-Stage Melting of Au−Pd Nanoparticles (2006)

Several series of molecular dynamics runs were performed to simulate the melting transition of bimetallic cuboctahedral nanoparticles of gold-palladium at different relative concentrations to study their structural properties before, in, and after the transition. The simulations were made in the canonical ensemble, each series covering a range of temperatures from 300 to 980 K, using the Rafii-Tabar version of the Sutton and Chen interatomic potential for metallic alloys. We found that the melting transition temperature has a strong dependence on the relative concentrations of the atomic species. We also found that, previous to the melting transition, the outer layer of the nanoparticle gets disordered in what can be thought as a premelting stage, where Au atoms near the surface migrate to the surface and remain there after the particle melts as a whole. The melting of the surface below Tm is consistent with studies of the interaction of a TEM electron beam with Au and Au-Pd nanoparticles.
Leech Thrombin Inhibitors (2002)

Serine proteases (SP), such as thrombin, factor Xa, elastase, trypsin are implicated in many clinical disorders such as emphysema, arthritis and cardiovascular diseases. These enzymes, in normal physiological conditions, are regulated by naturally occurring serine protease inhibitors, such as anti-thrombin III involved in thromb in inhibition. Primitive parasitic invertebrates have co-evolved highly specific mechanisms to communicate with their hosts for survival purposes, by blocking host processes such as blood coagulation. Thus a battery of new powerful molecules from blood-sucker animals acting at different points of the coagulation cascade such like factor Xa, thrombin, platelets aggregation inhibitors have been isolated and are now at a clinical level. In this review, we focus our attention on thrombin inhitors.
MCP-1 and CCR2 in HIV infection: regulation of agonist and receptor expression (1997)

Monocyte chemotactic protein-1 (MCP-1) interacts with the chemokine receptor CCR2. Two CCR2 cDNAs have been described. Sequence analysis as well as Northern blotting and RNase protection with different probes revealed that the CCR2 gene is expressed in activated natural killer (NK) cells and mononuclear phagocytes as a predominant long transcript (3.4 kb) consisting of CCR2B followed by a novel sequence (X), corresponding to an intron in the genome, and by a CCR2A specific portion. The predominant long transcript is polyadenylated and present in the cytoplasm. We found that bacterial products and cytokines affect CCR2 expression. Interleukin-2 (IL-2) augmented CCR2 mRNA in monocytes and NK cells. The augmented migratory capacity of IL-2-activated versus resting NK cells was associated with increased CCR2 transcript levels. Lipopolysaccharide (LPS) and other microbial agents caused a rapid and drastic reduction of CCR2 mRNA levels. The rate of nuclear transcription of CCR2 was not affected by LPS, whereas the mRNA half life was reduced. These results suggest that regulation of receptor expression, in addition to agonist production, is probably a crucial point in the regulation of the chemokine system. Down-regulation of chemokine receptor expression may play a role in the modulation of HIV infection in macrophages by LPS. Levels of MCP-1 were markedly elevated in the cerebrospinal fluid (CSF) but not in blood of HIV-infected patients with cytomegalovirus (CMV) encephalitis. The CSF levels of MCP-1 in CMV encephalitis were markedly higher than those found in the CSF of HIV-infected patients with or without unrelated neurological diseases. IL-8, the prototype of C-X-C chemokines and RANTES and macrophage inflammatory protein-1 alpha (C-C chemokines) were not substantially increased in the liquor of CMV encephalitis patients. High levels of MCP-1 may underlie monocyte recruitment and tissue damage in CMV encephalitis and may represent a rapid and useful tool in the diagnostic armamentarium for neurological disorders associated with HIV.
Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila (2014)

The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas.
Quantitative Comparison of Five SERS Substrates: Sensitivity and Limit of Detection (1997)

Five surface-enhanced Raman scattering (SERS) substrates were quantitatively compared for ease of preparation, sensitivity, limit of detection (LOD), reproducibility, and stability. Specifically, vapor-deposited Ag films, electrochemically roughened Ag electrodes, nitric acid-etched Ag foil, Tollens-produced Ag films, and photore-duced Ag films on TiO 2 were examined. Of these substrates, post-deposition-annealed Ag films exhibited the greatest sensitivity and lowest LOD, with 152 ± 1 counts per femtomole and an LOD of 0.36 ± 0.02 femtomoles of trans-1,2-bis(4-pyridyl)ethene (BPE). The substrate demonstrating the poorest sensitivity and highest LOD was Ag deposited from the Tollens reaction, with 0.38 ± 0.01 counts per femtomole and an LOD of 270 ± 20 femtomoles of BPE. The easiest substrate to prepare, nitric acid-etched Ag foils, exhibited a sensitivity of 0.485 ± 0.008 counts per femtomole and an LOD of 200 ± 10 femtomoles of BPE.
Two Sets of Paralogous Genes Encode the Enzymes Involved in the Early Stages of Clavulanic Acid and Clavam Metabolite Biosynthesis in Streptomyces clavuligerus (2004)

Recently, a second copy of a gene encoding proclavaminate amidinohydrolase (pah1), an enzyme involved in the early stages of clavulanic acid and clavam metabolite biosynthesis in Streptomyces clavuligerus, was identified and isolated. Using Southern analysis, we have now isolated second copies of the genes encoding the carboxyethylarginine synthase (ceaS) and beta-lactam synthetase (bls) enzymes. These new paralogues are given the gene designations ceaS1 and bls1 and are located immediately upstream of pah1 on the chromosome. Furthermore, sequence analysis of the region downstream of pah1 revealed a second copy of a gene encoding ornithine acetyltransferase (oat1), thus indicating the presence of a cluster of paralogue genes. ceaS1, bls1, and oat1 display 73, 60, and 63% identities, respectively, at the nucleotide level to the original ceaS2, bls2, and oat2 genes from the clavulanic acid gene cluster. Single mutants defective in ceaS1, bls1, or oat1 were prepared and characterized and were found to be affected to variable degrees in their ability to produce clavulanic acid and clavam metabolites. Double mutants defective in both copies of the genes were also prepared and tested. The ceaS1/ceaS2 and the bls1/bls2 mutant strains were completely blocked in clavulanic acid and clavam metabolite biosynthesis. On the other hand, oat1/oat2 double mutants still produced some clavulanic acid and clavam metabolites. This may be attributed to the presence of the argJ gene in S. clavuligerus, which encodes yet another ornithine acetyltransferase enzyme that may be able to compensate for the lack of OAT1 and -2 in the double mutants.
Vascular Endothelial Growth Factor and Microvascular Permeability (1999)

Vascular Endothelial Growth Factors (VEGFs) are endogenously produced vascular cytokines which result in angiogenesis, vasodilatation, and increased microvascular permeability in vivo. They are endothelial specific and result in mitosis, migration, stress fiber formation and increased permeability of endothelial cells in culture. They have been critically implicated in a host of pathological conditions including solid tumor growth and diabetes, and been proposed as a therapy for coronary and peripheral ischemic disease. However, the potent permeability-enhancing properties of VEGFs are very poorly understood. The pharmacology, signal transduction pathways, intracellular signaling mechanisms, and ultrastructural changes which result in increased permeability are still not clear. This review discusses the available evidence for how VEGFs increase permeability in vivo, and some of the pitfalls in interpreting experiments which do not take into account the vasoactive properties of VEGFs. It also discusses the clinical implications of the permeability enhancing effect of VEGFs, and the relevance of these studies to development of new therapies.
Neutrophil Granulocytes Are Required for EffectiveBacillus Calmette-GuerinImmunotherapy of Bladder Cancer and Orchestrate Local Immune Responses (2006)

The role of polymorphonuclear neutrophil granulocytes (PMN) in antitumoral immune responses displays a striking dichotomy. Under inflammatory conditions, PMN may promote tumor growth and progression. In contrast, especially in the context of therapeutic interventions, PMN can exert important antitumor functions. However, until now, the mechanisms of PMN-mediated activation of tumor immunity are poorly defined. Based on a murine model of Bacillus Calmette-Guérin (BCG) immunotherapy of bladder cancer, we provide evidence for a novel immunoregulatory role of this leukocyte subset. PMN immigrate into the bladder after intravesical BCG instillation and depletion of PMN from tumor-bearing mice completely abrogated antitumor efficacy of BCG. PMN stimulated with BCG in vitro as well as PMN isolated from the urine of BCG-treated patients were a major source of the chemokines interleukin-8, growth-related oncogene-alpha, macrophage inflammatory protein-1 alpha and of the inflammatory cytokine migration inhibitory factor. In vitro, BCG-stimulated PMN indirectly induced T-cell chemotaxis via the accessory function of activated monocytes. In vivo, depletion of PMN from BCG-treated mice significantly impaired CD4(+) T-cell trafficking to the bladder. These data show that PMN direct the migration of effector cells to the bladder and by this means are indispensable for effective tumor immunotherapy. Thus, our findings provide evidence for a novel early immunoregulatory role of these innate immune cells in local antitumor immunity.