gebhart/patrepeval huggingface dataset:
Structure of synaptogyrin (p29) defines novel synaptic vesicle protein. (1995)

Synaptogyrin (p29) is a synaptic vesicle protein that is uniformly distributed in the nervous system (Baumert et al., 1990). We have cloned and sequenced the cDNA encoding synaptogyrin, and the sequence predicts a protein with a molecular mass of 25,900 D with four membrane-spanning domains. The topology of the protein was confirmed by limited proteolysis using domain-specific antibodies. Database searches revealed several cDNA sequences coding polypeptides with sequence identities ranging from 32 to 46%, suggesting that synaptogyrin is a member of a multigene family. When the synaptogyrin cDNA is expressed in COS cells, the generated protein is indistinguishable from native synaptogyrin. To study intracellular sorting, synaptogyrin was expressed in CHO cells that revealed a punctate staining that was very similar to that of synaptophysin and endogenously expressed cellubrevin. Significant overlap with transferrin staining was also observed, suggesting that synaptogyrin is targeted to a recycling compartment involved in membrane traffic to and from the plasma membrane.
Convergence and Energy Landscape for Cheeger Cut Clustering (2014)

This paper provides both theoretical and algorithmic results for the 1 -relaxation of the Cheeger cut problem. The 2 -relaxation, known as spectral clustering, only loosely relates to the Cheeger cut; however, it is convex and leads to a simple optimization problem. The 1 -relaxation, in contrast, is non-convex but is provably equivalent to the original problem. The 1 -relaxation therefore trades convexity for exactness, yielding improved clustering results at the cost of a more challenging optimization. The first challenge is understanding convergence of algorithms. This paper provides the first complete proof of convergence for algorithms that minimize the 1 -relaxation. The second challenge entails comprehending the 1energy landscape, i.e. the set of possible points to which an algorithm might converge. We show that 1 -algorithms can get trapped in local minima that are not globally optimal and we provide a classification theorem to interpret these local minima. This classification gives meaning to these suboptimal solutions and helps to explain, in terms of graph structure, when the 1 -relaxation provides the solution of the original Cheeger cut problem.
High-Selectivity, High-Flux Silica Membranes for Gas Separation (1998)

Process improvements in silica membrane fabrication, especially the use of clean-room techniques, resulted in silica membranes without detectable mesoscopic defects, resulting in significantly improved transport properties. Supported membranes calcined at 400 degreesC were 30 nanometers in thickness, showed a H2 permeance at 200 degreesC of 2 x 10(-6) moles per square meter per second per Pascal (mol m-2 s-1 Pa-1), and had a CH4 permeance more than 500 times smaller. Molecules larger than CH4 were completely blocked. Silica membranes calcined at 600 degreesC showed no detectable CH4 flux, with a H2 permeance of 5 x 10(-7) (mol m-2 s-1 Pa-1) at 200 degreesC. These results signify an important step toward the industrial application of these membranes such as purification of H2 and natural gas as well as the selective removal of CO2.
Novel Vascular Molecule Involved in Monocyte Adhesion to Aortic Endothelium in Models of Atherogenesis (1997)

Adhesion of monocytes to the endothelium in lesion-prone areas is one of the earliest events in fatty streak formation leading to atherogenesis. The molecular basis of increased monocyte adhesion is not fully characterized. We have identified a novel vascular monocyte adhesion-associated protein, VMAP-1, that plays a role in adhesion of monocytes to activated endothelium. Originally selected for its ability to block binding of a mouse monocyte-like cell line (WEHI78/24) to cytokine- or LPS-stimulated cultured mouse endothelial cells in vitro, antiVMAP-1 mAb LM151 cross-reacts with rabbit endothelium and blocks binding of human monocytes to cultured rabbit aortic endothelial cells stimulated with minimally modified low density lipoprotein, thought to be a physiologically relevant atherogenic stimulus. Most importantly, LM151 prevents adhesion of normal monocytes and monocytoid cells to intact aortic endothelium from cholesterol-fed rabbits in an ex vivo assay. VMAP-1 is a 50-kD protein. Immunohistology of vessels reveals focal constitutive expression in aorta and other large vessels. VMAP-1 is thus a novel vascular adhesion-associated protein that appears to play a critical role in monocyte adhesion to aortic endothelial cells in atherogenesis in vivo.
Nanotechnology‐Based Therapies for Skin Wound Regeneration (2012)

The cutting‐edge combination of nanotechnology with medicine offers the unprecedented opportunity to create materials and devices at a nanoscale level, holding the potential to revolutionize currently available macroscale therapeutics. Nanotechnology already provides a plethora of advantages to medical care, and the success of nanoparticulate systems suggests that a progressive increase in the exploration of their potential will take place in the near future. An overview on the current applications of nanotechnology to wound healing and wound care is presented.
Potential Application of Tregitopes as Immunomodulating Agents in Multiple Sclerosis (2011)

The induction of immunologic tolerance is an important clinical goal in autoimmunity. CD4(+) regulatory T (Treg) cells, defined by the expression of the transcription factor forkhead box P3 (FoxP3), play a central role in the control of autoimmune responses. Quantitative and qualitative defects of Tregs have been postulated to contribute to failed immune regulation in multiple sclerosis (MS) and other autoimmune diseases. This paper highlights the potential uses of T regulatory cell epitopes (Tregitopes), natural Treg epitopes found to be contained in human immunoglobulins, as immunomodulating agents in MS. Tregitopes expand Treg cells and induce "adaptive Tregs" resulting in immunosuppression and, therefore, are being considered as a potential therapy for autoimmune diseases. We will compare Tregitopes versus intravenous immunoglobulin (IVIg) in the treatment of EAE with emphasis on the potential applications of Tregitope for the treatment of MS.
A multi-resolution video segmentation scheme for wipe transition identification (2002)

This paper presents a new methodology for wipe transition identification. Shot transition detection is an important technique for making videos easier to handle. Due to the wide variety, wipe transition appears to be the most difficult one to be detected among all types of shot transitions. We propose an approach that takes advantage of the production aspect of video. Each video frame is first decomposed into low-resolution and high-resolution components which are analyzed respectively and further recombined together to form a wipe transition detector. In our system, wavelet transformation is used for multi-resolution decomposition.
Identifying coronary stenosis using an image-recognition neural network (1997)

The present study represents an attempt to improve the separation of specific high-risk coronary stenosis from lower-risk conditions by employing an image-recognition neural network. The system mimics the visual reading of scintigraphs from raw digitized data, with the added benefit of a computerized classification system. It models the human retina as the sensing organ that processes the image signals and forwards them to the brain, where the outputs from each visual segment are processed to produce a recognition code. In the application described here, the recognition code classifies a scintigraphic image as demonstrating normal myocardial perfusion, or a perfusion pattern consistent with single-vessel, multiple-vessel, or left-anterior descending coronary artery stenosis. The input images are from clinically performed postexercise planar myocardial perfusion scintigraphs as produced in many clinical laboratories.
A human amphotropic retrovirus receptor is a second member of the gibbon ape leukemia virus receptor family. (1994)

Retrovirus infection is initiated by binding of the viral envelope glycoprotein to a cell-surface receptor. The envelope proteins of type C retroviruses of mammals demonstrate similarities in structural organization and protein sequence. These similarities suggest the possibility that retroviruses from different interference groups might use related proteins as receptors, despite the absence of any relationship between retrovirus receptors isolated to date. To investigate this possibility, we have identified a human cDNA clone encoding a protein closely related to the receptor for gibbon ape leukemia virus and have found that it functions as the receptor for the amphotropic group of murine retroviruses. Expression of this protein (GLVR-2) is likely to be a requirement for infection of human cells by amphotropic retroviral vectors for purposes of gene therapy.
The packer filter: an efficient mechanism for user-level network code (1987)

Code to implement network protocols can be either inside the kernel of an operating system or in user-level processes. Kernel-resident code is hard to develop, debug, and maintain, but user-level implementations typically incur significant overhead and perform poorly. The performance of user-level network code depends on the mechanism used to demultiplex received packets. Demultiplexing in a user-level process increases the rate of context switches and system calls, resulting in poor performance. Demultiplexing in the kernel eliminates unnecessary overhead. This paper describes the packet filter , a kernel-resident, protocol-independent packet demultiplexer. Individual user processes have great flexibility in selecting which packets they will receive. Protocol implementations using the packet filter perform quite well, and have been in production use for several years.
Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites (2015)

Asthma is prevalent in Western countries, and recent explanations have evoked the actions of the gut microbiota. Here we show that feeding mice a high-fibre diet yields a distinctive gut microbiota, which increases the levels of the short-chain fatty acid, acetate. High-fibre or acetate-feeding led to marked suppression of allergic airways disease (AAD, a model for human asthma), by enhancing T-regulatory cell numbers and function. Acetate increases acetylation at the Foxp3 promoter, likely through HDAC9 inhibition. Epigenetic effects of fibre/acetate in adult mice led us to examine the influence of maternal intake of fibre/acetate. High-fibre/acetate feeding of pregnant mice imparts on their adult offspring an inability to develop robust AAD. High fibre/acetate suppresses expression of certain genes in the mouse fetal lung linked to both human asthma and mouse AAD. Thus, diet acting on the gut microbiota profoundly influences airway responses, and may represent an approach to prevent asthma, including during pregnancy.
Treatment of Sleep Apnea in Heart Failure (2006)

Obstructive and central sleep apnea are common in heart failure, and may participate in its progression by exposing the heart to intermittent hypoxia, increased preload and afterload, sympathetic activation, and vascular endothelial dysfunction. Treatment of sleep apnea in patients with heart failure may reverse these detrimental effects, in addition to alleviating symptoms of sleep apnea. In patients with heart failure and obstructive sleep apnea, short-term randomized trials have demonstrated that continuous positive airway pressure (CPAP) improves cardiac function, and lowers sympathetic activity and blood pressure. However, there are no data on whether treating obstructive sleep apnea in patients with heart failure improves morbidity and mortality. Various treatments have been tested in heart failure patients with central sleep apnea, particularly oxygen and CPAP. Both reduce the frequency of central respiratory events, and lower sympathetic activity. In addition, CPAP improves cardiac function. However, the largest randomized trial did not demonstrate any beneficial effect of CPAP on the rate of mortality and cardiac transplantation (32 vs. 32 events in the control and treatment groups, respectively; p=0.54), but ultimately lacked power to conclude with certainty whether CPAP has an effect on morbidity and mortality in such patients. Thus, although there are data to indicate that treating both obstructive and central sleep apnea in patients with heart failure improves cardiovascular function, larger randomized trials involving interventions such as oxygen, CPAP, or other forms of positive airway pressure will be required to determine whether treating these sleep-related breathing disorders reduces clinically important outcomes such as morbidity and mortality.
Separation of PP2A Core Enzyme and Holoenzyme with Monoclonal Antibodies against the Regulatory A Subunit: Abundant Expression of Both Forms in Cells (1997)

Protein phosphatase 2A (PP2A) holoenzyme is composed of a catalytic subunit, C, and two regulatory subunits, A and B. The A subunit is rod shaped and consists of 15 nonidentical repeats. According to our previous model, the B subunit binds to repeats 1 through 10 and the C subunit binds to repeats 11 through 15 of the A subunit. Another form of PP2A, core enzyme, is composed only of subunits A and C. It is generally believed that core enzyme does not exist in cells but is an artifact of enzyme purification. To study the structure and relative abundance of different forms of PP2A, we generated monoclonal antibodies against the native A subunit. Two antibodies, 5H4 and 1A12, recognized epitopes in repeat 1 near the N terminus and immunoprecipitated free A subunit and core enzyme but not holoenzyme. Another antibody, 6G3, recognized an epitope in repeat 15 at the C terminus and precipitated only the free A subunit. Monoclonal antibodies against a peptide corresponding to the N-terminal 11 amino acids of the A alpha subunit (designated 6F9) precipitated free A subunit, core enzyme, and holoenzyme. 6F9, but not 5H4, recognized holoenzymes containing either B, B', or B" subunits. These results demonstrate that B subunits from three unrelated gene families all bind to repeat 1 of the A subunit, and the results confirm and extend our model of the holoenzyme. By sequential immunoprecipitations with 5H4 or 1A12 followed by 6F9, core enzyme and holoenzyme in cytoplasmic extracts from 10T1/2 cells were completely separated and they exhibited the expected specificities towards phosphorylase a and retinoblastoma peptide as substrates. Quantitative analysis showed that under conditions which minimized proteolysis and dissociation of holoenzyme, core enzyme represented at least one-third of the total PP2A. We conclude that core enzyme is an abundant form in cells rather than an artifact of isolation. The biological implications of this finding are discussed.
Measurement of voltage phase for the French future defence plan against losses of synchronism (1992)

A sure way of detecting loss of synchronism is to measure the rotation of the voltage vector at various points on the grid. Electricite de France plans to use this method to detect loss of synchronism on the French EHV network. The authors describe some of the work which has been undertaken in order to perform local measurements of voltage characteristics such as phase. Particular attention is given to the hypotheses adopted concerning signal modeling, definition of magnitudes and parameter variation; a review of existing calculation methods (zero-crossing algorithm, FFT, etc); the search for a new type of algorithm; the implementation of this algorithm using 16-bit signal processors; and experimentation on the future defense plan. The first stage of the plan, covering the South-East and Alps region of the French network, is to come into service in 1994.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Multiple Applications of Alamar Blue as an Indicator of Metabolic Function and Cellular Health in Cell Viability Bioassays (2012)

Accurate prediction of the adverse effects of test compounds on living systems, detection of toxic thresholds, and expansion of experimental data sets to include multiple toxicity end-point analysis are required for any robust screening regime. Alamar Blue is an important redox indicator that is used to evaluate metabolic function and cellular health. The Alamar Blue bioassay has been utilized over the past 50 years to assess cell viability and cytotoxicity in a range of biological and environmental systems and in a number of cell types including bacteria, yeast, fungi, protozoa and cultured mammalian and piscine cells. It offers several advantages over other metabolic indicators and other cytotoxicity assays. However, as with any bioassay, suitability must be determined for each application and cell model. This review seeks to highlight many of the important considerations involved in assay use and design in addition to the potential pitfalls.
Dendrimer-Modified Silicon Oxide Surfaces as Platforms for the Deposition of Gold and Silver Colloid Monolayers:  Preparation Method, Characterization, and Correlation between Microstructure and Optical Properties (1996)

We describe a novel approach for Au and Ag colloid monolayer formation on different silicon oxide surfaces such as glass, silicon, and ITO. The preparation method is simple and yields monolayers with easily controlled spacing within the monolayer without aggregation of metal particles. The colloid monolayers are prepared in two steps: (1) modification of the substrates with starburst dendrimers and (2) noble metal colloid deposition onto the dendrimer layer. Different Au and Ag colloids, ranging from 15 to 80 nm in particle diameter, have been deposited onto the dendrimer-modified surfaces. The structure and properties of the resulting particle arrays have been studied by atomic force microscopy (AFM), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), UV−vis spectroscopy, and surface-enhanced Raman scattering (SERS). XPS data show that the dendrimers spontaneously adsorb to various silicon oxide surfaces. The thickness of the dendrimer overlayer has been calculated and lies in the d = 14−25 Å range. SEM and AFM data show that the colloids spontaneously form continuous films on the dendrimer-modified surfaces. The noble metal particles are well isolated and confined to a single layer, and aggregation does not occur on the surface. The interparticle spacing (74−829 nm) and surface coverage can be controlled over a wide range by colloid size, colloid concentration, and immersion time. UV−vis spectroscopic data show that the microstructure directly controls the optical properties of the layer. Finally, we demonstrate that the prepared substrates provide a useful platform for SERS studies of materials adsorbed on the metal particles.
Treatment of HIV infection in the older patient (2004)

The number of HIV patients over the age of 50 years is increasing due to increased longevity in patients treated with highly active antiretroviral therapy (HAART), in addition to new primary infections in older patients. Numerous studies have demonstrated worse HIV disease progression and mortality in older HIV patients compared with younger patients. While HAART therapy has been shown to be effective at reducing HIV-1 RNA, the immunologic benefits in older patients may be reduced compared to younger patients. Older patients are more likely to suffer comorbidities requiring concomitant medications than younger patients. Toxicities from HAART, particularly dyslipdemia, insulin resistance, and pancreatitis may also be worse in older HIV patients. Controlled trials on epidemiology, pathogenesis, and therapeutic and clinical outcomes in the elderly are needed. As the HIV-infected population ages, there is a growing need to better determine the efficacy of HAART in older patients, and to investigate factors associated with a more rapid course of HIV infection in patients over the age of 50 years.
Predictive Factors of Response to Biological Disease Modifying Antirheumatic Drugs: Towards Personalized Medicine (2014)

Many therapies are now available for patients with rheumatoid arthritis (RA) who have an inadequate response to methotrexate including tumor necrosis factor inhibitors, abatacept, tocilizumab, and rituximab. Clinical response to drugs varies widely between individuals. A part of this variability is due to the characteristics of the patient such as age, gender, concomitant therapies, body mass index, or smoking status. Clinical response also depends on disease characteristics including disease activity and severity and presence of autoantibodies. Genetic background, cytokine levels, and immune cell phenotypes could also influence biological therapy response. This review summarizes the impact of all those parameters on response to biological therapies.
How we treat higher-risk myelodysplastic syndromes (2013)

Higher-risk myelodysplastic syndromes (MDS) are defined by patients who fall into higher-risk group categories in the original or revised International Prognostic Scoring System. Survival for these patients is dismal, and treatment should be initiated rapidly. Standard therapies include the hypomethylating agents azacitidine and decitabine, which should be administered for a minimum of 6 cycles, and continued for as long as a patient is responding. Once a drug fails in one of these patients, further treatment options are limited, median survival is <6 months, and consideration should be given to clinical trials. Higher-risk eligible patients should be offered consultation to discuss hematopoietic stem cell transplantation close to the time of diagnosis, depending on patient goals of therapy, with consideration given to proceeding to transplantation soon after an optimal donor is located. In the interim period before transplantation, hypomethylating agent therapy, induction chemotherapy, or enrollment in a clinical trial should be considered to prevent disease progression, although the optimal pretransplantation therapy is unknown.
Developmental stage specificity of the lymphoid V(D)J recombination activity. (1987)

We have examined the level of immunoglobulin gene V(D)J recombination activity in a number of cell lines derived from lymphoid or nonlymphoid lineages. The assay we employed uses extrachromosomal DNA as substrate and thereby avoids difficulties associated with the use of chromosomally integrated substrates. The recombination activity decreases during B-lymphoid development. It is highest at the earliest stages of committed B-cell differentiation and then falls progressively, reaching undetectable levels at the mature B-cell stage. The activity is also present in multipotential progenitors of myeloid cells and in pre-T cells but not mature T cells. No activity was found in several nonhematopoietic cell lines. Recombination was seen only among substrate molecules which had replicated in the eukaryotic cells. Several possible interpretations of this result are discussed.