gebhart/patrepeval huggingface dataset:
Quantitative Analysis of MicroRNA in Blood Serum with Protein-Facilitated Affinity Capillary Electrophoresis (2011)

MicroRNAs (miRNAs) are small (∼22 nt) regulatory RNAs that are frequently deregulated in cancer and have shown promise as tissue- and blood-based biomarkers for cancer classification and prognostication. Here we present a protein-facilitated affinity capillary electrophoresis (ProFACE) assay for rapid quantification of miRNA levels in blood serum using single-stranded DNA binding protein (SSB) and double-stranded RNA binding protein (p19) as separation enhancers. The method utilizes either the selective binding of SSB to a single-stranded DNA/RNA probe or the binding of p19 to miRNA-RNA probe duplex. For the detection of ultralow amounts of miRNA without polymerase chain reaction (PCR) amplification in blood samples we apply off-line preconcentration of synthetic miRNA-122 from serum by p19-coated magnetic beads followed by online sample stacking in the ProFACE assay. The detection limit is 0.5 fM or 30 000 miRNA molecules in 1 mL of serum as a potential source of naïve miRNAs.
Rapid Loss of Dendritic Spines after Stress Involves Derangement of Spine Dynamics by Corticotropin-Releasing Hormone (2008)

Chronic stress causes dendritic regression and loss of dendritic spines in hippocampal neurons that is accompanied by deficits in synaptic plasticity and memory. However, the responsible mechanisms remain unresolved. Here, we found that within hours of the onset of stress, the density of dendritic spines declined in vulnerable dendritic domains. This rapid, stress-induced spine loss was abolished by blocking the receptor (CRFR(1)) of corticotropin-releasing hormone (CRH), a hippocampal neuropeptide released during stress. Exposure to CRH provoked spine loss and dendritic regression in hippocampal organotypic cultures, and selective blockade of the CRFR(1) receptor had the opposite effect. Live, time-lapse imaging revealed that CRH reduced spine density by altering dendritic spine dynamics: the peptide selectively and reversibly accelerated spine retraction, and this mechanism involved destabilization of spine F-actin. In addition, mice lacking the CRFR(1) receptor had augmented spine density. These findings support a mechanistic role for CRH-CRFR(1) signaling in stress-evoked spine loss and dendritic remodeling.
Modification of guanine derivatives by reduced 2-nitroimidazoles. (1983)

Misonidazole, after reduction to the hydroxylamine derivative, was found to react with guanosine in aqueous solution at pH 7. The guanosine product was isolated and was assigned a structure having a new 5-membered ring with a -CHOH-CHOH-linkage between the N-1 and N-2 positions of guanine. Removal of the sugar residue from the guanosine product by acid hydrolysis resulted in the corresponding guanine derivative, which was also made by reacting guanine with reduced misonidazole. In aqueous solution at pH 11, the guanine product was quantitatively converted to guanine within 20 min. A number of N-1-substituted 2-nitroimidazoles and 2-nitroimidazole reacted with guanosine in an analogous manner, giving rise to the same product as misonidazole, indicating that the C-4-C-5 fragment from the imidazoles is involved in the modification. Neither misonidazole nor its amine or hydrazo derivatives reacted with guanosine. Reduced misonidazole reacted with N-2-methyl guanosine, whereas with N-1-methyl guanosine a reaction was not detected. The identity of Structure I was confirmed by comparison with an authentic sample of Structure I that was prepared by reacting guanosine with glyoxal. Reactions such as the modification of guanine provide a possible molecular mechanism for the cytotoxic and neurotoxic properties of misonidazole.
THE NEEDS OF PACIFIC WOMEN WHEN THEY ARE VICTIMS OF FAMILY VIOLENCE (2005)

A concern about the dearth of research data on the specific needs of Pacific victims of crime led to a study which explored the needs of Pacific people who have been victims of three types of crime: violence, family violence and property offences. The study was designed to provide qualitative information to complement the quantitative information provided by the second New Zealand National Survey of Crime Victims 2001. Various Pacific theoretical frameworks for research were utilised to inform the design and analysis used in this study. This paper focuses on the women in that sample, and considers the needs of Pacific women who are victims of family violence. The findings indicate that victims of family violence were at different stages of dealing with the impacts of the violence inflicted by other members of their families. The paper concludes by suggesting some implications for social policy.
CTLA-4 Activation of Phosphatidylinositol 3-Kinase (PI 3-K) and Protein Kinase B (PKB/AKT) Sustains T-Cell Anergy without Cell Death (2008)

The balance of T-cell proliferation, anergy and apoptosis is central to immune function. In this regard, co-receptor CTLA-4 is needed for the induction of anergy and tolerance. One central question concerns the mechanism by which CTLA-4 can induce T-cell non-responsiveness without a concurrent induction of antigen induced cell death (AICD). In this study, we show that CTLA-4 activation of the phosphatidylinositol 3-kinase (PI 3-K) and protein kinase B (PKB/AKT) sustains T-cell anergy without cell death. CTLA-4 ligation induced PI 3K activation as evidenced by the phosphorylation of PKB/AKT that in turn inactivated GSK-3. The level of activation was similar to that observed with CD28. CTLA-4 induced PI 3K and AKT activation also led to phosphorylation of the pro-apoptotic factor BAD as well as the up-regulation of BcL-XL. In keeping with this, CD3/CTLA-4 co-ligation prevented apoptosis under the same conditions where T-cell non-responsiveness was induced. This effect was PI 3K and PKB/AKT dependent since inhibition of these enzymes under conditions of anti-CD3/CTLA-4 co-ligation resulted in cell death. Our findings therefore define a mechanism by which CTLA-4 can induce anergy (and possibly peripheral tolerance) by preventing the induction of cell death.
Low-loss photonic wires and compact ring resonators in silicon-on-insulator (2004)

We fabricated single-mode photonic wires, nanophotonic waveguides confining light by total internal reflection. The structures are defined in silicon-on-insulator using 248nm deep UV lithography, a widely adopted technology for CMOS applications. The crystalline silicon core has a thickness of 220nm and a width of up to 600nm. A 1um thick silica layer serves as the lower cladding. We measured the loss of straight waveguides using the Fabry-Perot interference spectrum of the cleaved samples. A 500nm wide waveguide has a loss as low as 2.4dB/cm at 1550nm wavelength. We measured 90 degree bends to have excess losses of about 1dB. Mirror bends perform comparably. We fabricated symmetrically coupled ring and "racetrack" resonators with small radius. Q-factors higher than 3000 are achieved, leading to low add-drop crosstalk, high finesse and low at-resonance insertion loss. By fitting the theoretical model to the experimental results, we extracted parameters such as the coupling ratio, cavity loss and group index. We analyzed the fabrication tolerances allowed for these resonators to be suitable as a building block for WDM filtering components. The allowed deviation on the waveguide widths and gaps for the coupling ratio to be within specification are within the possibilities of the fabrication method. However, a method to tightly control the optical cavity length is needed as the ring's group index is highly dependent on waveguide width.
Mesenchymal Stem Cells in Musculoskeletal Tissue Engineering: A Review of Recent Advances in National University of Singapore (2005)

A key factor in the tissue engineering approach to tissue repair and regeneration is the use of appropriate cells. Mesenchymal stem cells (MSCs) are derived from bone marrow stroma or connective tissues and they have the potential to differentiate into various mesenchymal cell lines in vitro and in vivo. These cells hold great promise for musculoskeletal tissue engineering. This review is based mainly on the work which has been done in the National University of Singapore on the use of MSCs for engineering cartilage, growth plate, bone and tendon/ligament as well as the clinical trail of autologous chondrocyte implantation. It can help to shape future research on musculoskeletal tissue engineering.
Expression of the major human ribonucleoprotein (RNP) autoantigens in Escherichia coli and their use in an EIA for screening sera from patients with autoimmune diseases. (1989)

Journal Article Expression of the major human ribonucleoprotein (RNP) autoantigens in Escherichia coli and their use in an EIA for screening sera from patients with autoimmune diseases. Get access M Renz, M Renz Denagen Lab., Heidelberg, F.R.G Search for other works by this author on: Oxford Academic Google Scholar C Heim, C Heim Denagen Lab., Heidelberg, F.R.G Search for other works by this author on: Oxford Academic Google Scholar O Bräunling, O Bräunling Denagen Lab., Heidelberg, F.R.G Search for other works by this author on: Oxford Academic Google Scholar A Czichos, A Czichos Denagen Lab., Heidelberg, F.R.G Search for other works by this author on: Oxford Academic Google Scholar C Wieland, C Wieland Denagen Lab., Heidelberg, F.R.G Search for other works by this author on: Oxford Academic Google Scholar H P Seelig H P Seelig Denagen Lab., Heidelberg, F.R.G Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 35, Issue 9, 1 September 1989, Pages 1861–1863, https://doi.org/10.1093/clinchem/35.9.1861 Published: 01 September 1989
Clinical Evaluation of Branched DNA Signal Amplification for Quantifying HIV Type 1 in Human Plasma (1995)

Quantification of HIV-1 RNA in human plasma has provided unique insight into AIDS pathogenesis and promises to hasten progress in antiretroviral therapy and vaccine research. However, no generally available HIV-1 RNA assay has yet been subjected to rigorous clinical testing or to comparative evaluation with research-based RNA assays using large numbers of well-characterized clinical specimens. In this study, the Chiron Quantiplex branched DNA (bDNA) signal amplification assay was used to measure viral RNA in the plasma of 152 HIV-1-positive individuals at all stages of infection and in 12 patients before and after initiating zidovudine therapy. Eighty-six percent of patients had bDNA assay results above the 10,000-RNA Eq/ml sensitivity cutoff. Branched DNA values were significantly correlated with plasma viral RNA levels determined by quantitative competitive polymerase chain reaction (QC-PCR) assay (Spearman rank correlation, r = 0.89), infectious plasma virus titers (r = 0.72), p24 antigen levels (r = 0.51), immune complex dissociated p24 antigen levels (r = 0.56), and CD4+ lymphocyte counts (r = -0.72; p < 0.0001 for all comparisons). Plasma viral RNA determinations by bDNA and QC-PCR assays were quantitatively similar in the range of 10(4) to 10(7) RNA molecules/ml [log bDNA = 0.93 + 0.80 (log QC-PCR); R2 = 0.81, p < 0.0001] and declined identically following the institution of zidovudine therapy (68-73% decrease from baseline). The close quantitative correlation between bDNA and QC-PCR results, and their significant association with other viral markers and CD4+ counts, support the use of plasma viral RNA measurement in HIV-1 clinical trials.
Disciplined Convex Programming (2006)

SummaryA new methodology for constructing convex optimization models called disciplined convex programming is introduced. The methodology enforces a set of conventions upon the models constructed, in turn allowing much of the work required to analyze and solve the models to be automated.
Fast Algorithm for HDR Color Conversion (2016)

The paper addresses a problem of perceptual artifacts that appear in Y'CbCr non-linear luminance 4:2:0 HDR video. A computationally inexpensive method is proposed for converting the 4:4:4 HDR video to Y'CbCr 4:2:0 nonconstant luminance format. The method removes artifacts in areas with saturated colors. The approach obtains results in one step, improving the average linear light PSNR by 2.16 dB and tPSNR metric by 1.99 dB on the investigated videos.
Understanding Challenges in Preserving and Reconstructing Computer-Assisted Medical Decision Processes (2007)

This paper addresses the problem of understanding preservation and reconstruction requirements for computer- aided medical decision-making. With an increasing number of computer-aided decisions having a large impact on our society, the motivation for our work is not only to document these decision processes semi-automatically but also to understand the preservation cost and related computational requirements. Our objective is to support computer-assisted creation of medical records, to guarantee authenticity of records, as well as to allow managers of electronic medical records (EMR), archivists and other users to explore and evaluate computational costs (e.g., storage and processing time) depending on several key characteristics of appraised records. Our approach to this problem is based on designing an exploratory simulation framework for investigating preservation tradeoffs and assisting in appraisals of electronic records. We have a prototype simulation framework called image provenance to learn (IP2Learn) to support computer-aided medical decisions based on visual image inspection. The current software enables to explore some of the tradeoffs related to (1) information granularity (category and level of detail), (2) representation of provenance information, (3) compression, (4) encryption, (5) watermarking and steganography, (6) information gathering mechanism, and (7) final medical report content (level of detail) and its format. We illustrate the novelty of IP2Learn by performing example studies and the results of tradeoff analyses for a specific image inspection task.
Use of transduction proteins to target trabecular meshwork cells: outflow modulation by profilin I. (2005)

Protein transduction technology is a valuable tool for targeting trabecular meshwork tissue, not only for performing physiological studies, but also as a potential drug-delivery method. Profilin I action on the actin cytoskeleton further reinforces the importance of this structure in outflow facility regulation.
Charge Transfer on the Nanoscale:  Current Status (2003)

This is the report of a DOE-sponsored workshop organized to discuss the status of our understanding of charge-transfer processes on the nanoscale and to identify research and other needs for progress in nanoscience and nanotechnology. The current status of basic electron-transfer research, both theoretical and experimental, is addressed, with emphasis on the distance-dependent measurements, and we have attempted to integrate terminology and notation of solution electron-transfer kinetics with that of conductance analysis. The interface between molecules or nanoparticles and bulk metals is examined, and new research tools that advance description and understanding of the interface are presented. The present state-of-the-art in molecular electronics efforts is summarized along with future research needs. Finally, novel strategies that exploit nanoscale architectures are presented for enhancing the efficiences of energy conversion based on photochemistry, catalysis, and electrocatalysis principles.
Surface organization and nanopatterning of collagen by dip-pen nanolithography (2001)

Collagen is a key fibrous protein in biological systems, characterized by a complex structural hierarchy as well as the ability to self-assemble into liquid crystalline mesophases. The structural features of collagen influence cellular responses and material properties, with importance for a wide range of biomaterials and tissue architectures. The mechanism by which fibrillar collagen structures form from liquid crystalline mesophases is not well characterized. We report positive printing of collagen and a collagen-like peptide down to 30-50-nm line widths, using the atomic force microscopy technique of dip-pen nanolithography. The method preserved the triple-helical structure and biological activity of collagen and even fostered the formation of characteristic higher levels of structural organization. The "direct-write" capability of biologically relevant molecules, while preserving their structure and functionality, provides tremendous flexibility in future biological device applications and in proteomics arrays, as well as a new strategy to study the important hierarchical assembly processes of biological systems.
Human N-Acetylglucosamine-6-O-Sulfotransferase Involved in the Biosynthesis of 6-Sulfo Sialyl Lewis X: Molecular Cloning, Chromosomal Mapping, and Expression in Various Organs and Tumor Cells (1998)

N-Acetylglucosamine-6-O-sulfotransferase catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to position 6 of a non-reducing N-acetylglucosamine (GlcNAc) residue. We have cloned human GlcNAc-6-O-sulfotransferase cDNA, based on the sequence homology to cloned cDNA of mouse GlcNAc-6-O-sulfotransferase. The predicted protein sequence of the human enzyme was highly homologous to that of the mouse enzyme; in the 363 amino acid stretch of the catalytic region, the two proteins were nearly identical except for conservative changes in 3 amino acid residues. The expressed enzyme transferred sulfate to GlcNAcbeta1-3Galbeta1-4GlcNAcbeta1-3Galbeta1-4Gl cNAc. Co-transfection of the enzyme cDNA and fucosyltransferase VII cDNA into COS-7 cells resulted in cell surface expression of 6-sulfo sialyl Lewis X. Fluorescence in situ hybridization analysis revealed that the GlcNAc-6-O-sulfotransferase gene is located on human chromosome 7q31. mRNA of the human enzyme was strongly expressed in the bone marrow, peripheral blood leukocytes, spleen, brain, spinal cord, ovary, and placenta, and moderate levels of expression were observed in many organs including lymph nodes and thymus. In situ hybridization with the mouse system showed that the transcript was localized in specific regions of the brain, i.e. pyramidal cells in the CA3 subregion of the hippocampus, cerebellar nucleus and Purkinje cells. Among human tumor cells, strong expression of the mRNA was found in MOLT-4 and Jarkat lymphoblastic leukemia cells, Raji lymphoma cells, K-562 chronic myelogeneous leukemia cells, U251 glioma cells, and G361 melanoma cells. Carbohydrate structures synthesized by the sulfotransferase may be involved in various aspects of the differentiation and behavior of blood cells, their progenitor cells, and neurons in the central nervous system.
Antibody-structure-based design of pharmacological agents (1994)

The well-studied antigen-combining sites of antibody molecules hold considerable promise as a model system for the design of bioactive peptides. These small, immunoglobulin-derived peptides can be used in the development of alternative treatments for disease and in diagnostic strategies. The general principles derived from the design of small pharmacological agents based on the structural features of antibodies may also be extended to the design of other bioactive peptides.
Regulators of Angiogenesis (1991)

Proliferation of blood vessels is a process necessary for the nonnal growth and development of tissue (36). In the adult, angiogenesis occurs infrequently. Exceptions are found in the female reproductive system, where angiogenesis occurs in the follicle during its development, in the corpus luteum during ovulation, and in the placenta after pregnancy. These periods of angiogenesis are relatively brief and tightly regulated. Nonnal angiogenesis also occurs as part of the body's repair processes, e.g. in the healing of wounds and fractures. By contrast, uncontrolled angiogenesis can often be pathological. For example, the growth of solid tumors depends on vascularization (37), and in diabetic retinopathy vascularization of the retina often leads to blindness. Given the physiologic and pathological importance of angiogenesis, much effort in the last twenty years has been devoted to the isolation, characteriza­ tion, and purification of factors that can either stimulate or inhibit an­ giogenesis. Several bioassays have been developed to measure angiogenesis. The most common ones are endothelial cell migration (47) and proliferation (38) in vitro, and capillary growth in vivo in the developing chick chorioallantoic membrane (CAM) (4) and the cornea (45). The goal of this review is to describe those stimulators and inhibitors of angiogenesis that have been best-characterized.
Receptor-Mediated Endocytosis: Concepts Emerging from the LDL Receptor System (1985)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Multiple Pathways in Capsid Assembly (2018)

For a three-dimensional structure to spontaneously self-assemble from many identical components, the steps on the pathway must be kinetically accessible. Many virus capsids are icosahedral and assembled from hundreds of identical proteins, but how they navigate the assembly process is poorly understood. Capsid assembly is thought to involve stepwise addition of subunits to a growing capsid fragment. Coarse-grained models suggest that the reaction occurs on a downhill energy landscape, so intermediates are expected to be fleeting. In this work, charge detection mass spectrometry (CDMS) has been used to track assembly of the hepatitis B virus (HBV) capsid in real time. The icosahedral T = 4 capsid of HBV is assembled from 120 capsid protein dimers. Our results indicate that there are multiple pathways for assembly. Under conditions that favor a modest association energy there is no accumulation of large intermediates, which indicates that available pathways include ones on a downhill energy surface. Under higher salt conditions, where subunit interactions are strengthened, around half of the products of the initial assembly reaction have masses close to the T = 4 capsid and the other half are stalled intermediates which emerge abruptly at around 90 dimers, indicating a bifurcation in the ensemble of assembly paths. When incubated at room temperature, the 90-dimer intermediates accumulate dimers and gradually shift to higher mass and merge with the capsid peak. Though free subunits are present in solution, the stalled intermediates indicate the presence of a local minima on the energy landscape. Some intermediates may result from hole closure, where the growing capsid distorts to close the hole due to the missing capsid proteins or from a species where subsequent additions are particularly labile.