gebhart/patrepeval huggingface dataset:
Three-state analysis of sperm whale apomyoglobin folding (1993)

We give a quantitative description of the urea- and acid-induced transitions of apomyoglobin at 0 degree C and 2 mM sodium citrate. Our data consist of two series of unfolding curves: (1) acid-induced unfolding carried out in the presence of various concentrations of urea and (2) urea-induced unfolding at various pH values. A three-state equation is derived which relates the stability of three different conformations of apomyoglobin (native [N], unfolded [U], and intermediate [I]) as a function of urea and of pH. This equation fits our data reasonably well. The parameters which give the best fit have both thermodynamic and structural implications for N, I, and U. Specifically, I is closer in Gibbs energy to U than to N, indicating that side-chain packing results in much of the stability of native protein structure. The equilibria between N and I and between I and U are equally sensitive to urea, suggesting that much of the surface of I is inaccessible to solvent. The acid-induced transition in which N unfolds can be described as the result of titration of approximately two histidines with low pKaS in N. Under physiological conditions (neutral pH, no urea) I is the most stable non-native conformation.
Effects of In-vivo Application of Cold Atmospheric Plasma on Corneal Wound Healing in New Zealand White Rabbits (2013)

Cold Atmospheric Plasma (CAP) has been shown to influence tissue wound healing but little is known about the impact of CAP on healthy corneal tissues and their ability to respond to injuries. The objective of this study is to examine the effect of CAP on wound healing after corneal epithelial and basement membrane ablation in New Zealand white rabbits. The rabbits were assigned into three groups. Ten Rabbits from two groups underwent a 6 mm corneal ablation to the right eyes. After ablation, five rabbits in group (A) received 2 minutes of CAP whereas the other five rabbits (B) were not treated with CAP. A third group (C) included two rabbits and received CAP without ablation. Eyes monitored for corneal haze, epithelial healing, lens clarity and any signs of inflammation. At 24 hours, two rabbits from group A and two from group B were sacrificed to harvest the corneas. Twenty days, all remaining rabbits in groups A, B, and C were sacrificed and corneas were harvested. Corneas were fixed in formalin and stained with H&E or used for immunofluorescence microscopy to assess scar formation using antibodies against fibronectin and a-smooth muscle actin. At 24 hours, corneas from group A had average epithelial defect of 9.25 mm2 on day 1 whereas those from group B had average defect of 12.05 mm2, a difference of 2.8 mm2 (P=0.57). H & E stained corneal sections didn’t show abnormal responses to injury at 24 hours and 20 days. Epithelial thickness and stromal cell counts 20 days after injury showed no significant differences. Analysis of immunofluorescence microscopy images showed no differences between all groups. In conclusion, CAP application to cornea doesn’t appear to have obvious adverse effects. CAP does not interfere with rate of wound closure or induce increased inflammation. CAP did not have an effect on corneal wound healing or lead to scar formation.
Molecular markers in blood as surrogate prognostic indicators of melanoma recurrence. (2000)

Improvement is needed in the ability to evaluate the prognosis of melanoma patients who are clinically disease-free but likely to develop recurrent metastatic disease. The detection of circulating melanoma cells in blood is a potential surrogate marker of subclinical residual disease. We assessed the prognostic clinical utility of a multimarker melanoma reverse transcriptase-PCR (RT-PCR) assay using blood of 46 patients who were clinically disease-free. All patients were followed up for more than 4 years for disease recurrence. There was a significant correlation between number of RT-PCR markers present in blood and American Joint Committee on Cancer stage (P = 0.009). The number of RT-PCR markers detected in blood was an independent prediction factor of disease recurrence in a Cox proportional hazard model (P = 0.02). A risk factor model using American Joint Committee on Cancer stage and number of positive RT-PCR markers significantly predicted disease recurrence in 2, 3, and 4 years of follow-up. These studies demonstrate that molecular detection of circulating melanoma cells may be of significant prognostic value in determining early disease recurrence and may be useful for stratifying patients for adjuvant therapy.
Human Interferon-Beta: Effects of Deglycosylation (1982)

Human fibroblast-derived interferon-beta (IFN-beta) labeled in vivo with 35S-methionine and purified to greater than 90% radiochemical purity has been used to study the effect of glycosidases on its biological activity and its molecular weight. Incubation of the radioactive interferon with the glycosidases causes a reduction in the estimated molecular weight from 23,000 to 18,000 as determined by electrophoresis on SDS-gels. There are intermediate transient sizes that are generated prior to 18,000, but not proteins are observed that are smaller than 18,000 even after prolonged incubation. The deglycosylated IFN-beta (18,000) induces the antiviral state in cells in culture and inhibits the growth of cells in culture. We conclude that the carbohydrate of IFN-beta is not essential for its biological activity on cells in culture.
Map-likelihood phasing (2001)

The recently developed technique of maximum-likelihood density modification [Terwilliger (2000), Acta Cryst. D56, 965-972] allows a calculation of phase probabilities based on the likelihood of the electron-density map to be carried out separately from the calculation of any prior phase probabilities. Here, it is shown that phase-probability distributions calculated from the map-likelihood function alone can be highly accurate and that they show minimal bias towards the phases used to initiate the calculation. Map-likelihood phase probabilities depend upon expected characteristics of the electron-density map, such as a defined solvent region and expected electron-density distributions within the solvent region and the region occupied by a macromolecule. In the simplest case, map-likelihood phase-probability distributions are largely based on the flatness of the solvent region. Though map-likelihood phases can be calculated without prior phase information, they are greatly enhanced by high-quality starting phases. This leads to the technique of prime-and-switch phasing for removing model bias. In prime-and-switch phasing, biased phases such as those from a model are used to prime or initiate map-likelihood phasing, then final phases are obtained from map-likelihood phasing alone. Map-likelihood phasing can be applied in cases with solvent content as low as 30%. Potential applications of map-likelihood phasing include unbiased phase calculation from molecular-replacement models, iterative model building, unbiased electron-density maps for cases where 2F(o) - F(c) or sigma(A)-weighted maps would currently be used, structure validation and ab initio phase determination from solvent masks, non-crystallographic symmetry or other knowledge about expected electron density.
Genetically Engineered (Chimeric) Antibodies (1989)

The diversity, specificity, and biologic activity of antibodies make them potentially ideal reagents in the clinic and the laboratory, but conventional antibodies do not always fill the bill. Naturally occurring antibodies are heterogeneous, and human hybridoma antibodies are hard to produce. Genetic engineering techniques offer antibodies with just the properties desired.
Sulfation of 25-hydroxycholesterol regulates lipid metabolism, inflammatory responses, and cell proliferation (2013)

Intracellular lipid accumulation, inflammatory responses, and subsequent apoptosis are the major pathogenic events of metabolic disorders, including atherosclerosis and nonalcoholic fatty liver diseases. Recently, a novel regulatory oxysterol, 5-cholesten-3b, 25-diol 3-sulfate (25HC3S), has been identified, and hydroxysterol sulfotransferase 2B1b (SULT2B1b) has been elucidated as the key enzyme for its biosynthesis from 25-hydroxycholesterol (25HC) via oxysterol sulfation. The product 25HC3S and the substrate 25HC have been shown to coordinately regulate lipid metabolism, inflammatory responses, and cell proliferation in vitro and in vivo. 25HC3S decreases levels of the nuclear liver oxysterol receptor (LXR) and sterol regulatory element-binding proteins (SREBPs), inhibits SREBP processing, subsequently downregulates key enzymes in lipid biosynthesis, decreases intracellular lipid levels in hepatocytes and THP-1-derived macrophages, prevents apoptosis, and promotes cell proliferation in liver tissues. Furthermore, 25HC3S increases nuclear PPARγ and cytosolic IκBα and decreases nuclear NF-κB levels and proinflammatory cytokine expression and secretion when cells are challenged with LPS and TNFα. In contrast to 25HC3S, 25HC, a known LXR ligand, increases nuclear LXR and decreases nuclear PPARs and cytosol IκBα levels. In this review, we summarize our recent findings, including the discovery of the regulatory oxysterol sulfate, its biosynthetic pathway, and its functional mechanism. We also propose that oxysterol sulfation functions as a regulatory signaling pathway.
Transformation of a Simple Plastic into a Superhydrophobic Surface (2003)

Superhydrophobic surfaces are generally made by controlling the surface chemistry and surface roughness of various expensive materials, which are then applied by means of complex time-consuming processes. We describe a simple and inexpensive method for forming a superhydrophobic coating using polypropylene (a simple polymer) and a suitable selection of solvents and temperature to control the surface roughness. The resulting gel-like porous coating has a water contact angle of 160 degrees. The method can be applied to a variety of surfaces as long as the solvent mixture does not dissolve the underlying material.
Quantitative Detection of Protein Using a Top-gate Carbon Nanotube Field Effect Transistor (2007)

High-stability sensing of proteins of pig serum albumin (PSA) was achieved using an insulator-covered carbon-nanotube field-effect transistor (CNT-FET) with a top-gate structure. The sensitivity limit of this CNT-FET PSA sensor is at least 5 nmol/L PSA solution. A layer of silicon nitride deposited on the top-gate structure provides an n-type characteristic and a highly stable CNT-FET. Since the CNT is covered with a silicon nitride layer, it is isolated from oxygen, water, and other contaminants. The equilibrium constant of the PSA/anti-PSA reaction, which indicates the strength of the binding energy between PSA and anti-PSA fixed on the Au top-gate electrode, was calculated to be 1.2 × 107 L/mol using the Langmuir equation fitting.
Antigenic specificities of human monoclonal and polyclonal IgM rheumatoid factors. The C gamma 2-C gamma 3 interface region contains the major determinants. (1988)

The binding site specificity of 12 monoclonal and 11 polyclonal IgM rheumatoid factors (RF) isolated from human plasma or serum has been studied. All IgM RF bound best to sites on IgG and intact Fc. The monoclonal IgM RF did not bind at all to fragments lacking the C gamma 2 or C gamma 3 domains. In contrast, low level binding to the pFc' fragment, composed of the C gamma 3 domain, was seen with seven IgM RF, mainly from patients with rheumatoid arthritis (RA). IgG1 binding appeared to be a requisite specificity of all human IgM RF. IgM RF binding to IgG3 subclass was common among the monoclonal IgM RF. Most RA polyclonal IgM RF but only 2 of the monoclonal IgM RF possessed the IgG1, 2 and 4 binding pattern. Monoclonal IgM RF which bound best to histidine-modified IgG also bound well to IgG3. The 7-kDa fragment D of staphylococcal protein A inhibited the IgG binding of most monoclonal and to a lesser degree polyclonal IgM RF. Thus, the results indicate that the C gamma 2-C gamma 3 interface region of IgG contains the predominant determinants for monoclonal and polyclonal IgM RF. For some monoclonal IgM RF the binding site, even though at the interface of the C gamma 2 and C gamma 3 domains, is not the staphylococcal protein A site. Furthermore, polyclonal IgM RF possess specificities not encountered among the monoclonal IgM RF. These specificities may have special
Measurement of Cardiac Natriuretic Hormones (Atrial Natriuretic Peptide, Brain Natriuretic Peptide, and Related Peptides) in Clinical Practice: The Need for a New Generation of Immunoassay Methods (2000)

To date, there is no consensus on the best assay procedure of cardiac natriuretic peptides. To facilitate widespread propagation of determination of these hormones in routine clinical practice, it will be necessary to study the new generation of noncompetitive immunometric methods that are less time-consuming and more sensitive and specific. Although several studies suggest that BNP exhibits better clinical utility than the other CNHs, more studies examining multiple CNHs in the same cohorts of patients will be necessary.
TLR agonists: our best frenemy in cancer immunotherapy (2013)

Various TLR agonists are currently under investigation in clinical trials for their ability to orchestrate antitumor immunity. The antitumor responses are largely attributed to their aptitude to stimulate APCs such as DCs which in turn, activate tumor-specific T cell responses. However, there is a potential for TLR signaling to occur on cells other than professional APCs that could negate antitumor responses or even worse, promote tumor growth. The impetus for this review is twofold. First, there is accumulating data demonstrating that the engagement of TLRs on different T cell subsets and different cancer types could promote tumor growth or conversely, contribute to antitumor responses. Second, the efficacy of TLR agonists as monotherapies to treat cancer patients has been limited. In this review, we discuss how TLR signaling within different T cell subsets and cancer cells can potentially impact the generation of antitumor responses. Based on evidence from preclinical models and clinical trials, we draw attention to several criteria that we believe must be considered when selecting TLR agonists for developing effective immunotherapeutic strategies against cancer.
Potential clinical implications of recent matrix metalloproteinase inhibitor design strategies (2015)

Analysis of matrix metalloproteinases (MMPs) expression profiles in various pathologies correlated with their presence in promoting disease progression. Drugs were designed to inhibit MMPs in an extreme manner by chelating the active site zinc ion. This approach did not distinguish between the 24 members of the MMP family and had devastating consequences during clinical trials. Subsequent knockout mouse studies showed that some MMPs are beneficial in regulating tumor growth, metastasis and indirectly stimulating the immune system. The broad-spectrum inhibitor approach was rethought and modified in order to increase specificity by taking into account the non-conserved secondary binding sites or differences in structures within MMPs and also generating antibodies. These showed interesting results in vitro and in vivo. The recent technological advances that allow us to better understand the function and structure of MMPs are aiding in the development of selective inhibitors.
Trehalose Enhances Transgene Expression Mediated by DNA‐PEI Complexes (2007)

Using enhancers to improve the transfection efficiency of polyethylenimine (PEI) can circumvent the needs of chemical modifications as well as subsequent purification and characterization of the modified PEI. In this study, we found that incorporating trehalose into the transfection reagent could improve the transgene expression mediated by DNA-PEI complexes. Such enhancements were not observed when trehalose was replaced by other disaccharides. In an effort to explore the mechanisms, we examined how the timing of trehalose treatments and the durations of trehalose affected the percentages of cells expressing green fluorescent protein and the levels of intracellular ethidium monoazide labeled plasmid. Treatments with trehalose for 5-120 min prior to transfection could cause drops in transfection efficiency by 30-50%; such treatments, however, hardly affected the amounts of intracellular plasmid, indicating that the preexistence of intracellular trehalose could reduce transfection efficiency without lowering the endocytic activity. The transfection efficiency remained almost unchanged when the transfected cells were treated with trehalose after the removal of transfection reagents, indicating that trehalose had minimal effects on the machinery of protein synthesis. Despite the enhanced transgene expression, the presence of trehalose during transfection showed inhibitory effects on the internalization of DNA-PEI complexes. Additionally, the extent of enhancement in transgene expression strongly depended on the duration of trehalose. As the above observations suggested, only during the transfection process when complexes and trehalose coexisted, trehalose became an effective enhancer of transgene expression mediated by DNA-PEI complexes possibly by affecting the mechanisms of intracellular trafficking.
Expression of the Wilms' tumor gene WT1 in the murine urogenital system. (1991)

The Wilms' tumor gene WT1 is a recessive oncogene that encodes a putative transcription factor implicated in nephrogenesis during kidney development. In this report we analyze expression of WT1 in the murine urogenital system. WT1 is expressed in non-germ-cell components of the testis and ovaries in both young and adult mice. In situ mRNA hybridization studies demonstrate that WT1 is expressed in the granulosa and epithelial cells of ovaries, the Sertoli cells of the testis, and in the uterine wall. In addition to the 3.1-kb WT1 transcript detected by Northern blotting of RNA from kidney, uterus, and gonads, there is an approximately 2.5-kb WT1-related mRNA species in testis. The levels of WT1 mRNA in the gonads are among the highest observed, surpassing amounts detected in the embryonic kidney. During development, these levels are differentially regulated, depending on the sexual differentiation of the gonad. Expression of WT1 mRNA in the female reproductive system does not fluctuate significantly from days 4 to 40 postpartum. In contrast, WT1 mRNA levels in the tesis increase steadily after birth, reaching their highest expression levels at day 8 postpartum and decreasing slightly as the animal matures. Expression of WT1 in the gonads is detectable as early as 12.5 days postcoitum (p.c.). As an initial step toward exploring the tissue-specific expression of WT1, DNA elements upstream of WT1 were cloned and sequenced. Three putative transcription initiation sites, utilized in testis, ovaries, and uterus, were mapped by S1 nuclease protection assays. The sequences surrounding these sites have a high G + C content, and typical upstream CCAAT and TATAA boxes are not present. These studies allowed us to identify the translation initiation site for WT1 protein synthesis. We have also used an epitope-tagging protocol to demonstrate that WT1 is a nuclear protein, consistent with its role as a transcription factor. Our results demonstrate regulation of WT1 expression during development of the gonads, implicate WT1 in genitourinary development, and provide a molecular framework toward understanding genitourinary defects observed among hereditary cases of Wilms' tumor.
CHARACTERISTICS OF FACE SEAL LEAKAGE IN FILTERING FACEPIECES (1992)

Several studies have found that aerosol size, testing method, leak size, leak position, sampling probe location, and the mixing condition inside the respirator affect the results of fit factor measurements. This study focuses on the effect of leak shape and filter resistance because leaks have been reported to vary in shape from circular to slit-like. Four leaks of different shape but the same cross-sectional area were used to study their effect on aerosol penetration. Dust-mist and high-efficiency particulate air filtering facepieces provided different filter resistances. An aerodynamic particle sizer and a laser aerosol spectrometer were used to measure the particle size-dependent aerosol concentrations inside and outside the respirators. The filtering facepieces were sealed to a mannequin and artificial leaks were inserted near the right cheek. Aerosol penetration was measured for five flow rates ranging from 5 to 100 L/min. The pressure drop across the mask was monitored with an inclined manometer. At a given pressure differential, a slit-like leak and multiple circular leaks have been found to pass less aerosols than a single circular leak of equal cross-sectional area because the leak flow decreases with an increase in leak shape complexity. If there is substantial lack of face seal fit and the breathing rate is low, a HEPA respirator may provide less protection than a dust-mist respirator because the pressure drop is considerably higher for a HEPA respirator, resulting in more aerosol flow through the leak.
A role of secreted glycosaminoglycans in cell-substratum adhesion. (1980)

An adhesion-deficient variant, designated M3A, was derived from the anchorage-dependent L6 skeletal muscle myoblast line (Schubert, D., and La Corbiere, M. (1980) J. Biol. Chem. 255, 11557-11563). To investigate the defect in the M3A variant, adhesion to various substrata was studied. M3A adhered rapidly to substrate-attached material (SAM) prepared from L6 cultures and serum, but adhered slowly to SAM derived from M3A itself. The role of collagen and fibronectin in the adhesion of M3A cells to L6- and M3A-derived SAMs was ruled out, but several experiments suggested that glycosaminoglycans play a rate-limiting role in the adhesion process. The adhesive interaction of the M3A cells with the different substrata is specific with respect to the glycosaminoglycans involved, since the type and concentration of purified glycosaminoglycans required to inhibit the interaction is unique to each surface. An alteration in glycosaminoglycan synthesis by M3A cells may account for the difference in the adhesive properties of SAM derived from L6 and from the M3A variant.
Sequence-specific fluorescent labeling of double-stranded DNA observed at the single molecule level (2003)

Fluorescent labeling of a short sequence of double-stranded DNA (dsDNA) was achieved by ligating a labeled dsDNA fragment to a stem-loop triplex forming oligonucleotide (TFO). After the TFO has wound around the target sequence by ligand-induced triple helix formation, its extremities hybridize to each other, leaving a dangling single-stranded sequence, which is then ligated to a fluorescent dsDNA fragment using T4 DNA ligase. A non-repeated 15 bp sequence present on lambda DNA was labeled and visualized by fluorescence microscopy after DNA combing. The label was found to be attached at a specific position located at 4.2 +/- 0.5 kb from one end of the molecule, in agreement with the location of the target sequence for triple helix formation (4.4 kb from one end). In addition, an alternative combing process was noticed in which a DNA molecule becomes attached to the combing slide from the label rather than from one of its ends. The method described herein provides a new tool for the detection of very short sequences of dsDNA and offers various perspectives in the micromanipulation of single DNA molecules.