gebhart/patrepeval huggingface dataset:
Postprandial Lipoprotein Metabolism in Normal and Obese Subjects: Comparison after the Vitamin A Fat-Loading Test* (1990)

Abnormalities in fasting lipid and lipoprotein levels are known to occur in obesity and other hyperinsulinemic states. However, postprandial lipoprotein metabolism has not been studied systematically in obese subjects using sensitive techniques to distinguish between triglyceride-rich lipoprotein particles derived from the intestine and the liver. In the present study the vitamin A fat-loading test was used to label intestinally derived triglyceride-rich lipoprotein particles in the postprandial state. Lipid parameters in seven normolipidemic obese subjects [body mass index, 43.7 +/- 2.81 kg/m2 (mean +/- SEM)] were compared to those in eight matched normal weight controls (body mass index, 23.6 +/- 0.72 kg/m2) during the 24-h period following ingestion of a mixed meal with a high fat content to which vitamin A had been added. Although subjects were selected for normal fasting lipid levels, in the obese group fasting triglycerides were significantly higher (1.35 +/- 0.12 vs. 0.68 +/- 0.08 mmol/L; P less than 0.0005) and high density lipoprotein (HDL) cholesterol was lower (0.94 +/- 0.08 vs. 1.35 +/- 0.11 mmol/L; P less than 0.01). The obese subjects had a greater postprandial triglyceride response to the test meal (P less than 0.05). The cumulative increment in total plasma triglycerides was 3.35-fold greater in obese than control subjects, while that of retinyl ester was only 1.63-fold greater, suggesting that a significant portion of the postprandial triglyceride response is due to endogenous hepatic lipoproteins. Postprandial plasma triglyceride and retinyl ester increment correlated with basal triglycerides (r = 0.72; P less than 0.005 and r = 0.57; P less than 0.03, respectively) and negatively with fasting HDL (r = -0.51; P less than 0.05 and r = -0.60; P less than 0.02, respectively). In the obese, the HDL triglyceride content increased maximally 4 h postprandially (4.1% to 6.1%; P less than 0.005) and phospholipid at 12 h (25.8% to 28.7%; P less than 0.05), with lower cholesteryl ester (21.1% to 17.5%; P less than 0.002) at 8 h, reflecting exchange of surface and core lipids with triglyceride-rich particles after the meal. In obese and control subjects the magnitude of HDL triglyceride enrichment after the meal correlated positively with the postprandial triglyceride increment (r = 0.74; P less than 0.007) and negatively with the fasting HDL cholesterol concentration (r = -0.80; P = 0.002). We conclude that even normolipidemic obese subjects have greater postprandial lipemia and triglyceride enrichment of HDL after ingestion of a high fat meal.(ABSTRACT TRUNCATED AT 400 WORDS)
Protein ranking: From local to global structure in the protein similarity network (2004)

Biologists regularly search databases of DNA or protein sequences for evolutionary or functional relationships to a given query sequence. We describe a ranking algorithm that exploits the entire network structure of similarity relationships among proteins in a sequence database by performing a diffusion operation on a precomputed, weighted network. The resulting ranking algorithm, evaluated by using a human-curated database of protein structures, is efficient and provides significantly better rankings than a local network search algorithm such as psi-blast.
Symmetric convolution and the discrete sine and cosine transforms (1994)

This paper discusses the use of symmetric convolution and the discrete sine and cosine transforms (DSTs and DCTs) for general digital signal processing. The operation of symmetric convolution is a formalized approach to convolving symmetrically extended sequences. The result is the same as that obtained by taking an inverse discrete trigonometric transform (DTT) of the product of the forward DTTs of those two sequences. There are 16 members in the family of DTTs. Each provides a representation for a corresponding distinct type of symmetric-periodic sequence. The author defines symmetric convolution, relates the DSTs and DCTs to symmetric-periodic sequences, and then use these principles to develop simple but powerful convolution-multiplication properties for the entire family of DSTs and DCTs. Symmetric convolution can be used for discrete linear filtering when the filter is symmetric or antisymmetric. The filtering will be efficient because fast algorithms exist for all versions of the DTTs. Conventional linear convolution is possible if one first zero-pad the input data. Symmetric convolution and its fast implementation using DTTs are now an alternative to circular convolution and the DFT.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improved Material Constants for LiNb03 and LiTaO3 (1990)

Piezoelectric substrates used for SAW devices are characterized by their linear elastic, piezo- electric and dielectric material constants. These data can be computed from precise SAW velocity measure- ments by a non-linear least squares algorithm, if the measured crystal cut is sensitive to all those material constants. For LiNb03 such a cut is the 128' rot Y- cut. New measurements on the entire surface of that cut are presented. Results for free and metallized sur- face - including mechanical loading influence - are given as trigonometric expansions. These recent measurements as well as our previous re- sults on Y-cut are the basis for the calculation of an improved dataset of LiNbOa. The same algorithm was also applied to LiTa03, for which we used our measure- ments on X-cut, published last year. Here we present datasets for both materials. Further we include er- ror bounds for each individual constant derived from its influence on the SAW velocities and from the mea- surement accuracy.
Learning Video Object Segmentation from Static Images (2017)

Inspired by recent advances of deep learning in instance segmentation and object tracking, we introduce the concept of convnet-based guidance applied to video object segmentation. Our model proceeds on a per-frame basis, guided by the output of the previous frame towards the object of interest in the next frame. We demonstrate that highly accurate object segmentation in videos can be enabled by using a convolutional neural network (convnet) trained with static images only. The key component of our approach is a combination of offline and online learning strategies, where the former produces a refined mask from the previous frame estimate and the latter allows to capture the appearance of the specific object instance. Our method can handle different types of input annotations such as bounding boxes and segments while leveraging an arbitrary amount of annotated frames. Therefore our system is suitable for diverse applications with different requirements in terms of accuracy and efficiency. In our extensive evaluation, we obtain competitive results on three different datasets, independently from the type of input annotation.
Nanomaterials: A Membrane-Based Synthetic Approach (1994)

Materials with nanoscopic dimensions not only have potential technological applications in areas such as device technology and drug delivery but also are of fundamental interest in that the properties of a material can change in this regime of transition between the bulk and molecular scales. In this article, a relatively new method for preparing nanomaterials, membrane-based synthesis, is reviewed. This method entails synthesis of the desired material within the pores of a nanoporous membrane. Because the membranes used contain cylindrical pores of uniform diameter, monodisperse nanocylinders of the desired material, whose dimensions can be carefully controlled, are obtained. This "template" method has been used to prepare polymers, metals, semiconductors, and other materials on a nanoscopic scale.
RNAMotif, an RNA secondary structure definition and search algorithm (2001)

RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures are assembled from a collection of RNA structural motifs. These basic building blocks are used repeatedly, and in various combinations, to form different RNA types and define their unique structural and functional properties. Identification of recurring RNA structural motifs will therefore enhance our understanding of RNA structure and help associate elements of RNA structure with functional and regulatory elements. Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif search algorithm, RNAMotif, and demonstrate its utility with some motif search examples. RNAMotif differs from other motif search tools in two important aspects: first, the structure definition language is more flexible and can specify any type of base-base interaction; second, RNAMotif provides a user controlled scoring section that can be used to add capabilities that patterns alone cannot provide.
Why Is HIV Rarely Transmitted by Oral Secretions? (1999)

Hypotonic disruption may be a major mechanism by which saliva kills infected mononuclear leukocytes and prevents their attachment to mucosal epithelial cells and production of infectious HIV, thereby preventing transmission. Implications for the known oral HIV transmission by milk and seminal fluid, as well as potential oral transmission to contacts and health care workers, are considered. This effective salivary defense may be applicable medically to interdict vaginal, rectal, and oral transmission of HIV by infected cells in seminal fluid or milk by the use of anticellular substances.
Lipooligosaccharides (LOS) of Neisseria gonorrhoeae and Neisseria meningitidis have components that are immunochemically similar to precursors of human blood group antigens. Carbohydrate sequence specificity of the mouse monoclonal antibodies that recognize crossreacting antigens on LOS and human erythrocytes. (1988)

We have used mouse mAbs, 3F11 and 06B4, that are specific for highly conserved epitopes of Neisseria gonorrhoeae lipooligosaccharides (LOS) to identify immunochemically similar structures on human erythrocytes. mAb 3F11 agglutinated erythrocytes from all randomly selected adult humans, while mAb 06B4 agglutinated only 80% of the same specimens. The antibodies had an activity with erythrocytes similar to human cold agglutinins in that agglutination occurred at 4 degrees C and decreased with increasing incubation temperature. Human infant erythrocytes were agglutinated less well, but enzymatic treatment of either infant or adult cells resulted in an increase in expression of the 3F11- and 06B4-defined epitopes. Both antibodies bound to a series of neutral glycosphingolipids from human erythrocytes and neutrophils that have a type 2 (Gal beta 1----4GlcNAc) or N-acetyllactosamine structure. Neither antibody bound to glycosphingolipids from human meconium, which have a type 1 (Gal beta 1----3GlcNAc) structure. The antibodies were unable to bind to N-acetyl-lactosamine glycosphingolipids with a nonreducing terminal sialic acid or a Gala1----3Gal disaccharide. Antibody binding also was blocked by the presence of fucose linked to the penultimate glucosamine residue of N-acetyllactosamine glycosphingolipids. Although both antibodies bound to linear and branched-chain N-acetyllactosamine glycosphingolipids, 3F11 had a higher affinity for branched structures than did 06B4. The activity of 3F11 with human adult and infant treated and untreated erythrocytes with N-acetyllactosamine glycosphingolipids, and with LOS was very similar, if not identical, in specificity to 1B2, an mAb prepared from mice inoculated with a linear N-acetyllactosamine glycosphingolipid.
A Phase I Clinical Trial of the hu14.18-IL2 (EMD 273063) as a Treatment for Children with Refractory or Recurrent Neuroblastoma and Melanoma: a Study of the Children's Oncology Group (2006)

Hu14.18-IL2 (EMD 273063) can be administered safely with reversible toxicities in pediatric patients at doses that induce immune activation. A phase II clinical trial of hu14.18-IL2, administered at a dose of 12 mg/m2/d x 3 days repeated every 28 days, will be done in pediatric patients with recurrent/refractory neuroblastoma.
Prioritizing genes associated with prostate cancer development (2010)

By using this large 3-level meta-analysis of the gene-expression data to identify candidate genes associated with prostate cancer development, we have generated a list of candidate genes that may be a useful resource for researchers studying the molecular mechanisms underlying prostate cancer development.
Molecular Mechanism for Antibody-Dependent Enhancement of Coronavirus Entry (2019)

Antibody-dependent enhancement (ADE) of viral entry has been a major concern for epidemiology, vaccine development, and antibody-based drug therapy. However, the molecular mechanism behind ADE is still elusive. Coronavirus spike protein mediates viral entry into cells by first binding to a receptor on the host cell surface and then fusing viral and host membranes. In this study, we investigated how a neutralizing monoclonal antibody (MAb), which targets the receptor-binding domain (RBD) of Middle East respiratory syndrome (MERS) coronavirus spike, mediates viral entry using pseudovirus entry and biochemical assays. Our results showed that MAb binds to the virus surface spike, allowing it to undergo conformational changes and become prone to proteolytic activation. Meanwhile, MAb binds to cell surface IgG Fc receptor, guiding viral entry through canonical viral-receptor-dependent pathways. Our data suggest that the antibody/Fc-receptor complex functionally mimics viral receptor in mediating viral entry. Moreover, we characterized MAb dosages in viral-receptor-dependent, Fc-receptor-dependent, and both-receptors-dependent viral entry pathways, delineating guidelines on MAb usages in treating viral infections. Our study reveals a novel molecular mechanism for antibody-enhanced viral entry and can guide future vaccination and antiviral strategies.<b>IMPORTANCE</b> Antibody-dependent enhancement (ADE) of viral entry has been observed for many viruses. It was shown that antibodies target one serotype of viruses but only subneutralize another, leading to ADE of the latter viruses. Here we identify a novel mechanism for ADE: a neutralizing antibody binds to the surface spike protein of coronaviruses like a viral receptor, triggers a conformational change of the spike, and mediates viral entry into IgG Fc receptor-expressing cells through canonical viral-receptor-dependent pathways. We further evaluated how antibody dosages impacted viral entry into cells expressing viral receptor, Fc receptor, or both receptors. This study reveals complex roles of antibodies in viral entry and can guide future vaccine design and antibody-based drug therapy.
ProtEx™: A Novel Technology to Display Exogenous Proteins on the Cell Surface for Immunomodulation (2005)

Gene therapy as an immunomodulatory approach has the potential to treat various inherited and acquired immune-based human diseases. However, its clinical application has several challenges, varying from the efficiency of gene transfer, control of gene expression, cell and tissue targeting, and safety concerns associated with the introduction of exogenous DNA into cells/tissues. Gene therapy is also a time- and labor-intensive procedure. As an alternative, we recently developed a novel technology, ProtEx, that allows for rapid, efficient, and durable display of exogenous proteins on the surface of cells, tissues, and organs without detectable toxicity. This technology exploits the strong binding affinity (Kd = 10(-15) M) of streptavidin with biotin and involves generation of chimeric molecules composed of the extracellular portions of immunological proteins of interest and a modified form of streptavidin, biotinylation of biological surfaces, and decoration of the modified surface with chimeric proteins. Biotin persists on the cell surface for weeks both in vitro and in vivo, thereby providing a platform to display exogenous proteins with extended cell surface kinetics. Two chimeric proteins, rat FasL (SA-FasL) and human CD80 (CD80-SA), were generated and tested for cell surface display and immunomodulatory functions. SA-FasL and CD80-SA molecules persisted on the surface of various cell types for extended periods, varying from days to weeks in vitro and in vivo. The cell surface kinetics, however, were protein and cell type dependent. SA-FasL showed potent apoptotic activity against Fas+ cells as a soluble protein or displayed on the cell surface and effectively blocked alloreactive responses. The display of CD80-SA on the surface of tumor cells, however, converted them into antigen-presenting cells for effective stimulation of autologous and allogeneic T-cell responses. ProtEx technology, therefore, represents a practical and effective alternative to DNA-based gene therapy for immunomodulation.
Risk and resilience: Genetic and environmental influences on development of the stress response (2009)

Exposure to stressful events during development has consistently been shown to produce long-lasting alterations in the hypothalamic-pituitary-adrenal (HPA) axis, which may increase vulnerability to disease, including posttraumatic stress disorder and other mood and anxiety disorders. Recently reported genetic association studies indicate that these effects may be mediated, in part, by genexenvironment interactions involving polymorphisms within two key genes, CRHR1 and FKBP5. Data suggest that these genes regulate HPA axis function in conjunction with exposure to child maltreatment or abuse. In addition, a large and growing body of preclinical research suggests that increased activity of the amygdala-HPA axis induced by experimental manipulation of the amygdala mimics several of the physiological and behavioral symptoms of stress-related psychiatric illness in humans. Notably, interactions between the developing amygdala and HPA axis underlie critical periods for emotional learning, which are modulated by developmental support and maternal care. These translational findings lead to an integrated hypothesis: high levels of early life trauma lead to disease through the developmental interaction of genetic variants with neural circuits that regulate emotion, together mediating risk and resilience in adults.
The neuroscience of emotion in music (2008)

Abstract Music moves us. Its rhythms can make our bodies dance and its tones and melodies can stir emotions. It brings life to solitary thoughts and memories, can comfort and relieve loneliness, promote private or shared happiness, and engender feelings of deep sadness and loss. The sounds of music communicate emotions vividly in ways beyond the ability of words and most other forms of art. It can draw us together in affectionate intimacy, as in the first prosodic song-like conversations between mothers and infants. It can carry the volatile emotions of human attachments and disputes in folk songs and grand opera, and excite the passions of crowds on great social occasions.
Therapeutic approaches in trauma-induced coagulopathy. (2005)

Coagulopathy is a phenomenon which is a life threatening complication in the trauma patient who has sustained significant injuries and blood loss. With our increasing understanding of the mechanisms which drive the coagulopathy and the availability of new treatment options, most notably recombinant factor VIIa (rFVIIa), we are now able to treat those patients who have had a massive traumatic haemorrhage with greater efficacy. This paper reviews the current considerations in dealing with patients with trauma-induced coagulopathy and offers a strategy for their management.
Requirement of endogenous interferon-gamma production for resolution of Listeria monocytogenes infection. (1985)

Peritoneal exudate cells and splenic cells of mice infected with Listeria monocytogenes show increased production of interferon-gamma (IFN-gamma) after antigen or mitogen stimulation. When an IFN-gamma-specific enzyme-linked immunosorbent assay was used, increased production was first observed 2 days after infection in peritoneal cells and 4 to 6 days after infection in splenic cells. The increased production of IFN-gamma correlated with the clearance of Listeria from the peritoneal cavity and spleen. Macrophages derived from mice at these times were activated as evidenced by expression of nonspecific tumoricidal activity against 111In-labeled P815 mastocytoma cells. Injection of neutralizing monoclonal anti-IFN-gamma into 1-day-infected mice completely inhibited the generation of activated macrophages. Normal hamster IgG had no effect. In vivo, the monoclonal antibody also abrogated clearance of bacteria from the spleen and peritoneal cavity. Six days after injection of a sublethal dose of Listeria, the peritoneal cavity of control mice treated with normal hamster IgG was devoid of bacteria and the spleen contained less than 10(3) colony-forming units. However, mice treated with anti-IFN-gamma carried more than 8 X 10(6) colony-forming units in either anatomical site at day 6 and exhibited a higher mortality rate. These results indicate that IFN-gamma production is required for the in vivo generation of activated macrophages and the clearance of bacteria during Listeria infection.
Altered expression of muscle glucose transporter GLUT-4 in diabetic fatty Zucker rats (ZDF/Drt-fa) (1991)

We examined GLUT-4 glucose transporter protein and mRNA in muscle tissue from a new rodent model of non-insulin-dependent diabetes mellitus (NIDDM), the male obese Zucker diabetic fatty (ZDF) rat [ZDF/Drt-fa(F10)]. We also determined whether prevention of hyperglycemia might affect GLUT-4 expression by feeding the intestinal alpha-glucosidase inhibitor acarbose (40 mg/100 g diet) in the diet of male ZDF rats for 19 wk, starting at least 1 wk before the onset of diabetes. Fasting glucose was four- to sixfold greater in diabetic ZDF rats (24.1 +/- 6.7 mM) compared with lean or obese nondiabetic rats. Fasting insulin in diabetic ZDF rats (0.5 +/- 0.1 ng/ml) was similar to lean rats (0.4 +/- 0.1) but greatly reduced compared with obese nondiabetic rats (18.7 +/- 4.0 ng/ml). Acarbose treatment significantly reduced fasting glucose levels to 13.4 +/- 1.4 mM, while insulin levels increased to 1.6 +/- 0.3 ng/ml. GLUT-4 protein levels in diabetic ZDF rats were reduced approximately 40% in red quadriceps and mixed gastrocnemius muscles but were unchanged in white quadriceps muscle. Acarbose treatment was associated with a twofold increase in GLUT-4 protein and mRNA in mixed gastrocnemius muscle. These data indicate that, in this obese model of NIDDM without hyperinsulinemia, there is reduced muscle GLUT-4 protein in red but not white muscle fiber types. The decrease in muscle GLUT-4 expression in this model of NIDDM can be prevented by acarbose treatment, which reduces hyperglycemia and increases beta-cell responsiveness.