gebhart/patrepeval huggingface dataset:
Molecular mechanisms of pH‐driven conformational transitions of proteins: Insights from continuum electrostatics calculations of acid unfolding (2006)

The acid unfolding of staphylococcal nuclease (SNase) is very cooperative (Whitten and García-Moreno, Biochemistry 2000;39:14292-14304). As many as seven hydrogen ions (H+) are bound preferentially by the acid-unfolded state relative to the native (N) state in the pH range 3.2-3.9. To investigate the mechanism of acid unfolding, structure-based pKa calculations were performed with a variety of continuum electrostatic methods. The calculations reproduced successfully the H+ binding properties of the N state between pH 5 and 9, but they systematically overestimated the number of H+ bound upon acid unfolding. The calculated pKa values of all carboxylic residues in the N state were more depressed than they should be. The discrepancy between the observed and the calculated H+ uptake upon acid unfolding was not improved by using high protein dielectric constants, structures relaxed with molecular dynamics, or other empirical modifications implemented previously by others to maximize agreement between measured and calculated pKa values. This suggests an important role for conformational fluctuations of the backbone as important determinants of pKa values of carboxylic groups. Because no global or subglobal conformational changes have been observed previously for SNase under acidic conditions above the acid-unfolding region, these fluctuations must be local. The acid unfolding of SNase does not seem to involve the disruption of the N state by accruement of intramolecular repulsive interactions, nor the protonation of key ion paired carboxylic residues. It is more consistent with modest contributions from many H+ binding groups, with an important role for local conformational fluctuations in the coupling between H+ binding and the global structural transition.
Demodex mites in acne rosacea: reflectance confocal microscopic study (2016)

Demodex mite density was markedly increased in both ETR and PPR patients. It is believed that the presence of demodex mites plays an important role in rosacea aetiopathogenesis. Demodex mite treatment may reduce the severity of the disease and slow its progressive nature.
N‐acetylcysteine reduces lipopolysaccharide‐sensitized hypoxic‐ischemic brain injury (2007)

NAC provides substantial neuroprotection against brain injury in a model that combines infection/inflammation and HI. Protection by NAC was associated with improvement of the redox state and inhibition of apoptosis, suggesting that these events play critical roles in the development of lipopolysaccharide-sensitized HI brain injury.
Fast 100-nm resolution three-dimensional microscope reveals structural plasticity of mitochondria in live yeast (2002)

By introducing beam-scanning multifocal multiphoton 4Pi-confocal microscopy, we have attained fast fluorescence imaging of live cells with axial super resolution. Rapid scanning of up to 64 pairs of interfering high-angle fields and subsequent confocal detection enabled us to perform three to five times finer optical sectioning than confocal microscopy. In conjunction with nonlinear image restoration, we demonstrate, to our knowledge for the first time, three-dimensional imaging of live eukaryotic cells at an equilateral resolution of approximately 100 nm. This imaging mode allowed us to reveal the morphology and size of the green fluorescent protein-labeled mitochondrial compartment of live Saccharomyces cerevisiae (bakers' yeast) growing on different carbon sources. Our studies show that mitochondria of cells grown on medium containing glycerol as the only carbon source, as opposed to glucose-grown cells, exhibit a strongly branched tubular reticulum. We determine the average tubular diameter and find that it increases from 339 +/- 5 nm to 360 +/- 4 nm when changing from glucose to glycerol, that is, from a fermentable to a nonfermentable carbon source. Moreover, this change is associated with a 2.8-fold increase of the surface of the reticulum, resulting in an average increase in volume of the mitochondrial compartment by a factor of 3.0 +/- 0.2.
Flow Cytometric Techniques for Studying Plasmacytoid Dendritic Cells in Mixed Populations (2005)

Plasmacytoid dendritic cells (PDCs) are the natural interferon (IFN-alpha)-producing cells in human peripheral blood that produce vast quantities of IFN-alpha in response to viral infection and other stimuli. PDCs are a rare cell type, making up less than 0.5% of peripheral blood mononuclear cells. To date, these cells have not been successfully cultured in vitro and are very sensitive to selection via magnetic bead labeling, making them very difficult to study as a purified population. Therefore, our laboratory has developed techniques to study PDCs in mixed populations. Using flow cytometry to label specific cell-surface markers, PDCs can be easily identified from other peripheral blood mononuclear cells or in mononuclear cell suspensions of lymphoid tissue. PDCs can also be permeabilized and stained for intracellular proteins or cytokines. Using surface and intracellular flow cytometry, phenotypic and functional aspects can be combined to accurately study PDCs in a mixed population of cells.
Lipid-coated nanoscale coordination polymers for targeted cisplatin delivery (2013)

Nanoscale coordination polymers (NCPs) containing a Pt(IV) cisplatin prodrug, disuccinatocisplatin, were formed by a surfactant-templated synthesis and were shown to have a prodrug loading of 8.2 wt% and a diameter of ~133 nm by dynamic light scattering. These NCPs were stabilized by coating with a DOPC/cholesterol/DSPE-Peg<sub>2K</sub> lipid layer; a release profile in phosphate buffered saline showed an initial drug release of ~25% within the first hour and no more release observed up to 192 h. The NCP was rendered target-specific for sigma receptors by addition of an AA-DSPE-Peg<sub>2K</sub> conjugate (AA = anisamide) in the lipid formulation. The AA-containing NCP showed a statistically significant decrease in IC<sub>50</sub> (inhibitory concentration, 50%) compared to the non-targeted NCP. Enhanced uptake of the AA-containing NCP was further supported by confocal microscopy and competitive binding assays.
Proposal for the recognition of two species in the genus Chlamydia Jones, Rake, and Stearns, 1945 (1968)

The bacteria which cause the psittacosis-trachoma group of diseases and which are assigned to the genus Chlamydia Jones, Rake, and Stearns, 1945, can be separated conveniently and logically into two species. This separation is based on relatively stable morphological and chemical characteristics of the organisms rather than on their presumed host or tissue preferences or on the specific serology of their cell wall antigens. The type species Chlamydia trachomatis (Busacca) Rake 1957 is differentiated from the second species Chlamydia psittaci (Lillie 1930) comb. nov., by a simple key using tests that can be performed readily in the laboratory. Each species is defined, and the laboratory tests are described.
Transgenic Approaches to Combat Fusarium Head Blight in Wheat and Barley (2001)

Fusarium head blight (FHB) and contamination with deoxynivalenol (DON) produced by the primary pathogen Fusarium graminearum Schwabe [teleomorph Gibberella zeae (Schwein.)] have caused devastating losses to wheat ( Triticum aestivum L.), durum ( Triticum turgidum L. ssp. durum Desf.Husr.), and barley ( Hordeum vulgare L.) growers across the USA since the early 1990s. Evaluation of barley, wheat, and related germplasm yielded only a few accessions with partial resistance. This resistance appears, in most cases, to be under polygenic control, making the development of resistant cultivars with suitable agronomic and quality traits a challenge. The insertion of individual antifungal and antitoxin genes via genetic transformation has the potential to aid in development of resistant wheat and barley cultivars. Although wheat and barley transformation has been achieved in several laboratories, the development of a high throughput wheat and barley transformation systems has been slowed by genotype effects on plant regeneration, low transformation efficiencies, somaclonal variation, and problems with transgene inheritance and stability of expression. Among the antifungal genes targeted to combat FHB are coding sequences for proteins that degrade fungal cell walls, disorganize fungal membranes, bolster the host defense response systems, and interfere with fungal protein synthesis, pathogenesis, and/or accumulation of DON. Promoter sequences have been selected that confer high levels of expression to the antifungal constructs, particularly in the spike tissues which are susceptible to FHB. As more antifungal genes are inserted into wheat and barley, field and greenhouse evaluation will show whether transgenes achieve their potential in the fight against FHB.
TheLy‐6A(Sca‐1)GFPTransgene is Expressed in all Adult Mouse Hematopoietic Stem Cells (2002)

The Sca-1 cell surface glycoprotein is used routinely as a marker of adult hematopoietic stem cells (HSCs), allowing a >100-fold enrichment of these rare cells from the bone marrow of the adult mouse. The Sca-1 protein is encoded by the Ly-6A/E gene, a small 4-exon gene that is tightly controlled in its expression in HSCs and several hematopoietic cell types. For the ability to sort and localize HSCs directly from the mouse, we initiated a transgenic approach in which we created Ly-6A (Sca-1) green fluorescent protein (GFP) transgenic mice. We show here that a 14-kb Ly-6A expression cassette directs the transcription of the GFP marker gene in all functional repopulating HSCs in the adult bone marrow. A >100-fold enrichment of HSCs occurred by sorting for the GFP-expressing cells. Furthermore, as shown by fluorescence-activated cell sorting and histologic analysis of several hematopoietic tissues, the GFP transgene expression pattern generally corresponded to that of Sca-1. Thus, the Ly-6A GFP transgene facilitates the enrichment of HSCs and presents the likelihood of identifying HSCs in situ.
A novel adhesive biosensor system for detecting respiration, cardiac, and limb movement signals during sleep: validation with polysomnography (2018)

The results demonstrate that BiostampRC<sup>®</sup> is a tolerable and accurate method for capturing respiration, ECG, and AT EMG time series signals during overnight sleep when compared with simultaneous PSG recordings. The signal quality sufficiently supports analytics of clinical relevance. Larger longitudinal in-home studies are required to support the role of BiostampRC<sup>®</sup> in clinical management of sleep disorders involving the autonomic nervous system and limb movements.
Patterning of high density magnetic nanodot arrays by nanoimprint lithography (2007)

In this work the authors present results from thermal nanoimprint lithography patterning of high density arrays of circular holes with 100nm diameters at 300nm pitch, or with 50nm diameters at 100nm pitch, throughout an area of 1cm2. They demonstrate the fabrication of dense gigabit magnetic nanodot arrays using polymethyl methacrylate and polymethyl glutarimide resist bilayers and a lift-off process. The magnetic properties of these nanodot arrays are shown to be readily characterized by alternating gradient magnetometry. Several issues are addressed which arise during patterning and characterization, such as template damage induced by Au metallization, metal residue control, and nanodot diameter tuning by oxygen plasma etching.
Rheolytic thrombectomy with the Possis AngioJet: technical considerations and initial clinical experience. (1999)

Percutaneous revascularization of thrombus-containing lesions has an increased incidence of adverse events such as abrupt vessel closure, periprocedural myocardial infarction and death. Various pharmacologic and mechanical approaches have demonstrated modest angiographic success with significant periprocedural complications. The AngioJet (Possis Medical, Inc., Minneapolis, Minnesota) is a dual lumen catheter that uses the principle of rheolytic thrombectomy to remove unorganized thrombus. A previously unreported scoring system based on clinical and angiographic data may help to select patients most likely to benefit from AngioJet treatment. When compared with urokinase in the randomized VeGAS 2 Trial, AngioJet therapy yields greater angiographic success with a lower incidence of 30-day major adverse events. Technical considerations and complications are reviewed in detail.
Design Options for Molecular Epidemiology Research within Cohort Studies (2005)

Past discussions of the relative strengths of nested case-control and case-cohort designs have not fully considered cohorts with stored biological samples in which biomarker analyses are planned. Issues related to biomarker analyses can affect an investigator's choice of design and the conduct of these two designs. The key issues identified are effects of analytic batch, long-term storage, and freeze-thaw cycles on biomarkers. In comparison with the nested case-control design, the case-cohort design is less able to handle these challenges. Problems arise because most implementations of the case-cohort design do not allow for simultaneous evaluation of biomarkers in cases and reference group members, and there is no matching. By design, the nested case-control study controls for storage duration and the batching of biological samples from cases and controls is logistically simple. The allowance for matching also means that subjects can be matched on the number of freeze-thaw cycles experienced by the biological sample. However, the matching generates complex data sets that can be more difficult to analyze, and the costly biomarker data generated from the controls has few uses outside of testing the specific hypotheses of the study. In addition, because the same subject can serve as a control and a case, or multiple times as a control, biomarker analyses and sample batching can be more complex than initially anticipated. However, in total, of the two designs, the nested case-control study is better suited for studying biomarkers that can be influenced by analytic batch, long-term storage, and freeze-thaw cycles.
Some General Properties of Nonlinear Elements-Part I. General Energy Relations (1956)

Two independent equations relating the average powers at the different frequencies in nonlinear inductors and capacitors are derived. These equations are a consequence only of the assumption of a single-valued characteristic for the nonlinear element. They are independent of the particular shape of this characteristic, of the power levels at the various frequencies, and of the external circuit in which the nonlinear reactor is connected. These general energy relations give information regarding the gain and stability of nonlinear reactor modulators and demodulators, and consequently of magnetic and dielectric amplifiers, without requirng detailed information about these devices. The utility of these equations is illustrated by discussing the gain and stability of the simplest types of nonlinear reactor modulators and demodulators and harmonic generators. This analysis for nonlinear inductors and capacitors is extended to include the effects of hysteresis in the nonlinear characteristic in the special case where the operating hysteresis loop is no more than double-valued. A similar analysis applied to nonlinear resistors yields two equations relating the reactive powers at the different frequencies, rather than the real powers as above. The interpretation of reactive power under these conditions is not clear.
Pharmacodynamics of taxol in human head and neck tumors. (1996)

The pharmacodynamics of taxol in human head and neck squamous cell carcinoma were studied using histocultures of surgical specimens from patients (n = 22). Tumors were treated with taxol for 24 h. The inhibition of DNA synthesis was determined by 48 h cumulative bromodexyuridine (BrdUrd) incorporation. The induction of apoptosis was measured by morphological changes, in situ DNA end labeling, post-exonuclease III BrdUrd labeling, and DNA fragmentation. Inhibition of the BrdUrd labeling index (LI) by taxol was incomplete, with 11 tumors showing maximal inhibition (Emax) of 30-50% and the remaining 11 tumors showing and Emax of 50-80%. For both groups, the inhibition approached maximum values at 1 microM taxol concentration; an additional 10-fold increase in drug concentrations did not significantly enhance the inhibition. The taxol concentrations required for a 30% inhibition (IC30) were 4.2 and 0.3 microM for the first and second groups, respectively. The IC30 correlated with the Emax (r2 = 0.39; P < 0.001). Taxol induced apoptosis in all tumors, 11 tumors showed a maximal fraction of apoptotic tumor cells between 3 and 10% and 11 tumors between 13 and 28%, whereas untreated controls showed a maximal apoptotic index of < 1%. For individual tumors, the maximal apoptotic index occurred between 0.1 and 3 microM, and correlated with the BrdUrd LI for the untreated control (r2 = 0.37; P < 0.01). It is interesting that > 95% of apoptotic cells were BrdUrd labeled, whereas not all BrdUrd-labeled cells were apoptotic. To investigate the basis of the variable tumor response to taxol, we determined the expression of multidrug resistance P-glycoprotein (Pgp), p53, and bcl-2 proteins, using immunohistochemical staining and Western blot analysis. Eleven (50%), 10 (45%), and 7 (32%) tumors expressed Pgp, p53, and bcl-2, respectively. Patients with Pgp-positive tumors showed a higher number of affected lymph nodes than those with Pgp-negative tumors (P < 0.05). Compared with moderately and well differentiated tumors, the poorly differentiated tumors expressed p53 and Pgp more frequently and showed a lower maximum inhibition of DNA synthesis and a higher apoptotic fraction after taxol treatment (P < 0.05 in both cases). Pgp expression correlated differently with taxol-induced inhibition of DNA synthesis than with apoptosis; Pgp-positive tumors showed a significantly higher Emax (63%) and IC30 (4.2 microM) but also a higher apoptotic index (17%) than Pgp-negative tumors (Emax 36%; IC30, 0.3 microM; and apoptotic index; 6%; P < 0.05 for all cases). p53 and bcl-2 expression did not correlated with taxol-induced inhibition of DNA synthesis or apoptosis. The data indicate that taxol acts through apoptosis and inhibition of proliferation in human head and neck cancer. Pgp overexpression appears to protect cells from the antiproliferative effect of taxol but correlated with a higher apoptosis.
β2-Glycoprotein I/HLA class II complexes are novel autoantigens in antiphospholipid syndrome (2015)

Antiphospholipid syndrome (APS) is an autoimmune disorder characterized by thrombosis and/or pregnancy complications. β2-glycoprotein I (β2GPI) complexed with phospholipid is recognized as a major target for autoantibodies in APS; however, less than half the patients with clinical manifestations of APS possess autoantibodies against the complexes. Therefore, the range of autoantigens involved in APS remains unclear. Recently, we found that human leukocyte antigen (HLA) class II molecules transport misfolded cellular proteins to the cell surface via association with their peptide-binding grooves. Furthermore, immunoglobulin G heavy chain/HLA class II complexes were specific targets for autoantibodies in rheumatoid arthritis. Here, we demonstrate that intact β2GPI, not peptide, forms a complex with HLA class II molecules. Strikingly, 100 (83.3%) of the 120 APS patients analyzed, including those whose antiphospholipid antibody titers were within normal range, possessed autoantibodies that recognize β2GPI/HLA class II complexes in the absence of phospholipids. In situ association between β2GPI and HLA class II was observed in placental tissues of APS patients but not in healthy controls. Furthermore, autoantibodies against β2GPI/HLA class II complexes mediated complement-dependent cytotoxicity against cells expressing the complexes. These data suggest that β2GPI/HLA class II complexes are a target in APS that might be involved in the pathogenesis.
Mitochondrial dysfunction in a cell culture model of familial amyotrophic lateral sclerosis (2002)

The molecular mechanisms by which mutations in the gene for Cu/Zn superoxide dismutase (SOD1) lead to the selective death of motor neurones in familial amyotrophic lateral sclerosis (FALS) remain incompletely understood. Previous evidence has indicated that mitochondrial abnormalities may develop during motor neurone injury, but several important questions remain unanswered. We have developed a cell culture model of FALS in which a motor neurone cell line (NSC34) has been stably transfected to express normal or mutant human SOD1 at levels approximating to those seen in the human disease. The aims of the study were to: (i) investigate whether morphological mitochondrial abnormalities occur at expression levels of mutant SOD1 close to physiological levels; and (ii) determine whether the presence of mutant SOD1 causes abnormalities of mitochondrial respiratory chain function and changes in cellular bioenergetic parameters in motor neuronal cells. Using this cellular model, we demonstrate that the presence of mutant SOD1 results in the development of abnormally swollen and pale staining mitochondria. These morphological changes are accompanied by biochemical abnormalities with specific decreases in the activities of complexes II and IV of the mitochondrial electron transfer chain. These same complexes are inhibited when control NSC34 cells are subjected to oxidative stress induced by serum withdrawal. The decrease in respiratory chain complex activity in the presence of mutant SOD1 was not accompanied by decreased expression of representative proteins present in these complexes. Motor neuronal cells expressing mutant SOD1 showed increased cell death when exposed to oxidative stress by serum withdrawal, whereas the presence of normal human SOD1 exerted a protective effect. Under basal, unstressed culture conditions, no change in the ATP : ADP ratio was observed in the presence of mutant SOD1. However, the mitochondrial changes associated with the presence of mutant SOD1 clearly had adverse cellular bioenergetic consequences as shown by increased cell death in the presence of pharmacological inhibition of the glycolytic pathway. We conclude that one important mechanism by which mutant SOD1 causes motor neurone injury involves inhibition of specific components of the mitochondrial electron transfer chain. Therapeutic measures aimed at protecting mitochondrial respiratory chain function may be useful in SOD1 related familial and possibly other forms of amyotrophic lateral sclerosis.
Melanoma localization in nude mice with monoclonal Fab against p97. (1985)

The tumor targeting capacity of monoclonal antibody Fab fragments was explored in nude mice bearing human melanoma xenografts. Radioiodinated Fab 8.2 and 96.5, specific for melanoma-associated antigen p97, were tested in vitro for immunoreactivity and in vivo for tumor localization relative to a co-administered control, Fab 1.4. Fab was cleared rapidly from the blood with a T1/2 of 3-3.5 hr and greater than 90% of the injected radioactivity was excreted by 16 hr. The mean specific Fab in tumor reached a maximum of 3.5% injected dose/g at 4 hr and decreased to 1.5% at 16 hr. Over the same period, the ratio of specific/control Fab in tumor normalized to blood, the localization index, rose from 3 to 25 compared with ratios near unity for all other tissues. The concentration of specific Fab in tumor could be correlated to the amount of Fab protein administered as well as its immunoreactivity.