gebhart/patrepeval huggingface dataset:
The SWISS-MODEL Repository and associated resources (2008)

SWISS-MODEL Repository (http://swissmodel.expasy.org/repository/) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for all sequences in Swiss-Prot and for relevant models organisms. Regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline are fully utilised. As of September 2008, the database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. SWISS-MODEL Repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via SWISS-MODEL Workspace (http://swissmodel.expasy.org/workspace/). Annotation of models with functional information and cross-linking with other databases such as the Protein Model Portal (http://www.proteinmodelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources.
The effects of tegaserod, a 5‐HT4 receptor agonist, on gastric emptying in a murine model of diabetes mellitus (2005)

Gastric emptying was impaired in db/db mice. Low dose tegaserod improved gastric emptying rates in this model of gastroparesis through the activation of 5-HT(4) receptors. These findings suggest that 5-HT(4) receptor agonists may prove useful for improving delayed gastric emptying in gastroparesis.
Association of heparan sulfate proteoglycan with the neurofibrillary tangles of Alzheimer's disease (1991)

The major intracytoplasmic lesion of Alzheimer's disease is the neurofibrillary tangle (NFT), which is primarily composed of paired helical filaments (PHFs). The mechanism responsible for the formation of PHFs, as well as their insolubility and apparent heterogeneity, is unknown. We found that basic fibroblast growth factor (bFGF) binds to heparinase-sensitive sites in NFTs. bFGF binding is due to a heparan sulfate proteoglycan (HSPG) immunocytochemically identified in NFTs. In the presence of polycations (e.g., Ca2+), HSPG will bind to free carboxyl groups in NFT proteins. HSPG binding may play a role in transforming normal soluble proteins into insoluble PHFs.
Real-Time Detection of Virus Particles and Viral Protein Expression with Two-Color Nanoparticle Probes (2005)

Respiratory syncytial virus (RSV) mediates serious lower respiratory tract illness in infants and young children and is a significant pathogen of the elderly and immune compromised. Rapid and sensitive RSV diagnosis is important to infection control and efforts to develop antiviral drugs. Current RSV detection methods are limited by sensitivity and/or time required for detection. In this study, we show that antibody-conjugated nanoparticles rapidly and sensitively detect RSV and estimate relative levels of surface protein expression. A major development is use of dual-color quantum dots or fluorescence energy transfer nanobeads that can be simultaneously excited with a single light source.
Effective hole extraction using MoOx-Al contact in perovskite CH3NH3PbI3 solar cells (2014)

We report an 11.4%-efficient perovskite CH3NH3PbI3 solar cell using low-cost molybdenum oxide/aluminum (i.e., MoOx/Al) as an alternative top contact to replace noble/precious metals (e.g., Au or Ag) for extracting photogenerated holes. The device performance of perovskite solar cells using a MoOx/Al top contact is comparable to that of cells using the standard Ag top contact. Analysis of impedance spectroscopy measurements suggests that using 10-nm-thick MoOx and Al does not affect charge-recombination properties of perovskite solar cells. Using a thicker (20-nm) MoOx layer leads to a lower cell performance caused mainly by a reduced fill factor. Our results suggest that MoOx/Al is promising as a low-cost and effective hole-extraction contact for perovskite solar cells.
A fast method for high-quality genomic DNA extraction from whole human blood. (1991)

A simple and fast protocol is described for the purification of genomic DNA from 0.3 ml of whole human blood. The recovery of DNA is quantitative and reproducible; the quality is such that it can be used for all relevant molecular biology techniques.
Directed self‐immobilization of alkaline phosphatase on micro‐patterned substrates via genetically fused metal‐binding peptide (2009)

Current biotechnological applications such as biosensors, protein arrays, and microchips require oriented immobilization of enzymes. The characteristics of recognition, self-assembly and ease of genetic manipulation make inorganic binding peptides an ideal molecular tool for site-specific enzyme immobilization. Herein, we demonstrate the utilization of gold binding peptide (GBP1) as a molecular linker genetically fused to alkaline phosphatase (AP) and immobilized on gold substrate. Multiple tandem repeats (n = 5, 6, 7, 9) of gold binding peptide were fused to N-terminus of AP (nGBP1-AP) and the enzymes were expressed in E. coli cells. The binding and enzymatic activities of the bi-functional fusion constructs were analyzed using quartz crystal microbalance spectroscopy and biochemical assays. Among the multiple-repeat constructs, 5GBP1-AP displayed the best bi-functional activity and, therefore, was chosen for self-immobilization studies. Adsorption and assembly properties of the fusion enzyme, 5GBP1-AP, were studied via surface plasmon resonance spectroscopy and atomic force microscopy. We demonstrated self-immobilization of the bi-functional enzyme on micro-patterned substrates where genetically linked 5GBP1-AP displayed higher enzymatic activity per area compared to that of AP. Our results demonstrate the promising use of inorganic binding peptides as site-specific molecular linkers for oriented enzyme immobilization with retained activity. Directed assembly of proteins on solids using genetically fused specific inorganic-binding peptides has a potential utility in a wide range of biosensing and bioconversion processes.
Reactions of transient C-nitrosocarbonyl compounds with dienes, mono-olefins, and nucleophiles (1985)

Nitrosocarbonylbenzene and nitrosocarbonylmethane, formed as transient intermediates by oxidation of benzo- and aceto-hydroxamic acid, respectively, with tetraethylammonium periodate, are trapped by cyclopentadiene to give the corresponding cycloadducts (5). The adduct (5; R = Ph) dissociates in solution at 80 °C to reform nitrosocarbonylbenzene, which reacts with thebaine (1) to give (4; R = Ph) and with triphenylphosphine to give phenyl isocyanate. Cycloadducts of nitrosocarbonylbenzene with cyclohexa-1,3-diene (6) and with cycle-octatetraene (7) have also been prepared. The adduct (3; R = Ph) of nitrosocarbonylbenzene and 9,10-dimethylanthracene, when heated with 1-allyl-3,4-methylenedioxybenzene, oct-1-ene, or 2,5-dimethylhexa-2,4-diene, gives the corresponding [ene] reaction products of the olefins and nitrosocarbonylbenzene. When heated alone, the adduct (3; R = Ph) gives 9,10-dimethylanthracene, benzoic anhydride, and nitrous oxide. Oxidation of 2,4,6-trimethylbenzohydroxamic acid in the presence of thebaine gives the adduct (4; R = 2,4,6-trimethylphenyl). However, 2,4,6-trimethylnitrosocarbonylbenzene is insufficiently stable to be isolated; in the absence of a diene it decomposes to give 2,4,6-trimethylbenzoic anhydride as the major product.
Multivalency in the recognition and antagonism of a HIV TAR RNA–TAT assembly using an aminoglycoside benzimidazole scaffold (2016)

Recognition of RNA by high-affinity binding small molecules is crucial for expanding existing approaches in RNA recognition, and for the development of novel RNA binding drugs.
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing (2012)

SAAP-RRBS is freely available to non-commercial users at the web site http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.
Vascular endothelial cell lineage-specific promoter in transgenic mice (1995)

Vascular endothelial cells play essential roles in the function and development of the cardiovascular system. However, due to the lack of lineage-specific markers suitable for molecular and biochemical analyses, very little is known about the molecular mechanisms that regulate endothelial cell differentiation. We report the first vascular endothelial cell lineage-specific (including angioblastic precursor cells) 1.2 kb promoter in transgenic mice. Moreover, deletion analysis of this promoter region in transgenic embryos revealed multiple elements that are required for the maximum endothelial cell lineage-specific expression. This is a powerful molecular tool that will enable us to identify factors and cellular signals essential for the establishment of vascular endothelial cell lineage. It will also allow us to deliver genes specifically into this cell type in vivo to test specifically molecules that have been implicated in cardiovascular development. Furthermore, we have established embryonic stem (ES) cells from the blastocysts of the transgenic mouse that carry the 1.2 kb promoter-LacZ reporter transgene. These ES cells were able to differentiate in vitro to form cystic embryoid bodies (CEB) that contain endothelial cells determined by PECAM immunohistochemistry. However, these in vitro differentiated endothelial cells did not express the LacZ reporter gene. This indicates the lack of factors and/or cellular interactions which are required to induce the expression of the reporter gene mediated by this 1.2 kb promoter in this in vitro differentiation system. Thus this system will allow us to screen for the putative inducers that exist in vivo but not in vitro. These putative inducers are presumably important for in vivo differentiation of vascular endothelial cells.
Complete Genome Sequences of Lactobacillus johnsonii Strain N6.2 and Lactobacillus reuteri Strain TD1 (2014)

We report here the complete genome sequences of Lactobacillus johnsonii strain N6.2, a homofermentative lactic acid intestinal bacterium, and Lactobacillus reuteri strain TD1, a heterofermentative lactic acid intestinal bacterium, both isolated from a type 1 diabetes-resistant rat model.
Pulsatile flow and atherosclerosis in the human carotid bifurcation. Positive correlation between plaque location and low oscillating shear stress. (1985)

Fluid velocities were measured by laser Doppler velocimetry under conditions of pulsatile flow in a scale model of the human carotid bifurcation. Flow velocity and wall shear stress at five axial and four circumferential positions were compared with intimal plaque thickness at corresponding locations in carotid bifurcations obtained from cadavers. Velocities and wall shear stresses during diastole were similar to those found previously under steady flow conditions, but these quantities oscillated in both magnitude and direction during the systolic phase. At the inner wall of the internal carotid sinus, in the region of the flow divider, wall shear stress was highest (systole = 41 dynes/cm2, diastole = 10 dynes/cm2, mean = 17 dynes/cm2) and remained unidirectional during systole. Intimal thickening in this location was minimal. At the outer wall of the carotid sinus where intimal plaques were thickest, mean shear stress was low (-0.5 dynes/cm2) but the instantaneous shear stress oscillated between -7 and +4 dynes/cm2. Along the side walls of the sinus, intimal plaque thickness was greater than in the region of the flow divider and circumferential oscillations of shear stress were prominent. With all 20 axial and circumferential measurement locations considered, strong correlations were found between intimal thickness and the reciprocal of maximum shear stress (r = 0.90, p less than 0.0005) or the reciprocal of mean shear stress (r = 0.82, p less than 0.001). An index which takes into account oscillations of wall shear also correlated strongly with intimal thickness (r = 0.82, p less than 0.001). When only the inner wall and outer wall positions were taken into account, correlations of lesion thickness with the inverse of maximum wall shear and mean wall shear were 0.94 (p less than 0.001) and 0.95 (p less than 0.001), respectively, and with the oscillatory shear index, 0.93 (p less than 0.001). These studies confirm earlier findings under steady flow conditions that plaques tend to form in areas of low, rather than high, shear stress, but indicate in addition that marked oscillations in the direction of wall shear may enhance atherogenesis.
Photonic integrated circuits for access and transport networks (2014)

In this talk, we will review recent advances in the semiconductor photonic components, photonic integrated circuits and the integration methodologies implemented on the traditional compound semiconductor as well as the emerging CMOS-compatible silicon platform. The proliferations of smart phones and multimedia network of things have escalated the traffic of speedily delivery of multimedia contents from the remote data centers to the end users through the vast broadband optic fiber access network and high capacity optic transport infrastructures. To deliver these content-rich data from the remote data centers to the end users, the capacity and speed of the optic fiber infrastructure and access nodes have seen 100x increases over the past decade, which is expected to continue growing by another 10- to 100-fold in the next decade, as illustrated in Figure 1. Traditional optoelectronics transceivers in the optical terminals are made with discrete optical components. With the increasing popularity and deployment of compact pluggable modules to achieve higher operating speed and packing density on the precious real estate in optical terminals, many photonic integration technologies are utilized to achieve the economic scale to match the fast expansion of the optic fiber networks, as shown in Figure 2. Table 1 lists several examples of high speed optoelectronic devices which constitute the building blocks of the photonic integration technologies. It is clear that these components are able to generate and detect optical signals at a channel data rate of 100 Gb/s and beyond with advanced modulation formats. Many performance trade-offs by the integration can be mitigated by the accompanied CMOS electronic processors to offer enhanced stability with new functionalities. In this talk, we will review recent advances in the high speed semiconductor optoelectronic devices and photonic integrated circuits implemented on traditional III-V compound semiconductors, the CMOS-compatible silicon photonics and the emerging hybrid III-V/SOI integration platforms.
Targeting of human immunodeficiency virus-infected cells by CD8+ T lymphocytes armed with universal T-cell receptors (1994)

We have developed an immunotherapeutic approach with potential application in the treatment of viral and malignant disease. We show that primary CD8+ T cells isolated from peripheral blood can be genetically modified by retroviral transduction to express high levels of universal (major histocompatibility complex-unrestricted) chimeric T-cell receptors specific for human immunodeficiency virus (HIV) antigens. Two classes of HIV-specific URs in which the antigen-binding domain is comprised of either CD4 or a single-chain antibody are capable of activating a number of T-cell effector functions in response to target cells, including cytolysis, in a highly sensitive and specific manner. Importantly, we have addressed a number of issues which, although particularly relevant to the clinical application of this approach in the treatment of HIV infection, may also impact on the potential of UR immunotherapy for other disease targets. The UR immunotherapeutic system is particularly suited for evaluation in the clinical setting.
Deep packet inspection using parallel Bloom filters (2004)

Recent advances in network packet processing focus on payload inspection for applications that include content-based billing, layer-7 switching and Internet security. Most of the applications in this family need to search for predefined signatures in the packet payload. Hence an important building block of these processors is string matching infrastructure. Since conventional software-based algorithms for string matching have not kept pace with high network speeds, specialized high-speed, hardware-based solutions are needed. We describe a technique based on Bloom filters for detecting predefined signatures (a string of bytes) in the packet payload. A Bloom filter is a data structure for representing a set of strings in order to support membership queries. We use hardware Bloom filters to isolate all packets that potentially contain predefined signatures. Another independent process eliminates false positives produced by Bloom filters. We outline our approach for string matching at line speeds and present a performance analysis. Finally, we report the results for a prototype implementation of this system on the FPX platform. Our analysis shows that with the state-of-the-art FPGAs, a set of 10,000 strings can be scanned in the network data at the line speed of OC-48 (2.4 Gbps).
Moesin Functions as a Lipopolysaccharide Receptor on Human Monocytes (1999)

Bacterial endotoxin (lipopolysaccharide [LPS]), a glycolipid found in the outer membranes of gram-negative bacteria, induces the secretion of proinflammatory cytokines such as tumor necrosis factor alpha (TNF-alpha), interleukin-1 (IL-1), and IL-6 by monocytes/macrophages. The secretion of these biologically active compounds leads to multiple pathological conditions, such as septic shock. There is substantial evidence that chronic exposure to LPS mediates, at least in part, the tissue destruction associated with gram-negative infection. CD14, a 55-kDa protein, has been identified as an LPS receptor. In conjunction with a serum protein, LPS binding protein (LBP), LPS-CD14 interactions mediate many LPS functions in the inflammatory response. However, CD14 lacks a cytoplasmic domain, or any known signal transduction sequence motif, suggesting the existence of another cell surface domain capable of transducing signals. In this paper, we report a second, CD14-independent LPS binding site, which, based on biological activity, appears to be a functional LPS receptor. Cross-linking experiments were performed to identify LPS binding sites. Two molecules were identified: a 55-kDa protein (CD14) and a second, 78-kDa band. Sequencing of the 78-kDa protein by mass spectroscopic analysis revealed 100% homology with moesin (membrane-organizing extension spike protein). Antibody to CD14 induced partial blocking of the LPS response. However, antimoesin monoclonal antibody completely blocked the LPS-induced TNF-alpha response in human monocytes, without blocking CD14 binding of LPS. Irrelevant isotype controls had no effect. Additional experiments were performed to evaluate the specificity of the antimoesin blocking. Separate experiments evaluated antimoesin effects on monocyte chemotaxis, IL-1 production in response to IL-1 stimulation, and TNF-alpha secretion in response to Staphylococcus aureus stimulation. Antimoesin blocked only LPS-mediated events. The data suggest that moesin functions as an independent LPS receptor on human monocytes. The role of moesin in transduction of CD14-mediated signals is discussed.
<title>Color indexing with weak spatial constraints</title> (1996)

To improve the discrimination power of color indexing techniques we encode a minimal amount of spatial information in the index. We propose an approach that lies between uniformly tesselating the images with rectangular regions and relying on fully segmented images. For each image we define 5 partially overlapping, fuzzy regions. From each region in the image we extract the first three moments of the color distribution and store them in the index. The feature vectors in the index are relatively insensitive to small translations and small rotations of an image because they are extracted from fuzzy regions. To retrieve images we define a function which measures the similarity of two color feature vectors. Invariance of retrieval results with respect to the typical image rotations of 90 degrees around the center of the image is guaranteed because our feature similarity function exploits the spatial arrangement of the 5 image regions. We present experimental results using an image database which contains more than 11,000 color images. Our experiments demonstrate clearly that our weak encoding of spatial information significantly increases the discrimination power of the index compared to plain color indexing techniques.
General, Room-Temperature Method for the Synthesis of Isolated as Well as Arrays of Single-Crystalline ABO4-Type Nanorods (2004)

Single-crystalline BaWO(4) and BaCrO(4) nanorods of reproducible shape and of varying sizes have been controllably prepared using a simple, room-temperature approach, based on the use of porous alumina template membranes. Aligned BaWO(4) and BaCrO(4) nanorod arrays can be obtained by dissolving the template. Our facile technique, which is analogous to biomineralization, offers a promising and generalized methodology to prepare other types of free-standing ABO(4) nanorods and their corresponding nanorod arrays. Extensive characterization of these samples has been performed using scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), energy-dispersive X-ray spectroscopy (EDS), selected area electron diffraction (SAED), Raman spectroscopy, FT-infrared spectroscopy (FT-IR), and X-ray diffraction (XRD).
A Filtration System That Greatly Reduces Aluminum in Calcium Gluconate Injection, USP Used to Prepare Parenteral Nutrition Solutions (2014)

A point-of-use, self-contained, single-use, disposable, Al-complexing filter has been created. It was calculated to reduce Al delivered in PN solutions by 72%, resulting in daily Al delivery below the level that results in Al accumulation associated with central nervous system and bone toxicity to all but the smallest (<1 kg) infants.
Poly(dimethylsiloxane)-Based Microchip for Two-Dimensional Solid-Phase Extraction-Capillary Electrophoresis with an Integrated Electrospray Emitter Tip (2005)

A microchip in poly(dimethylsiloxane) (PDMS) for in-line solid-phase extraction-capillary electrophoresis-electrospray ionization-time-of-flight mass spectrometry (SPE-CE-ESI-TOF-MS) has been developed and evaluated. The chip was fabricated in a novel one-step procedure where mixed PDMS was cast over steel wires in a mold. The removed wires defined 50-microm cylindrical channels. Fused-silica capillaries were inserted into the structure in a tight fit connection. The inner walls of the inserted fused-silica capillaries and the PDMS microchip channels were modified with a positively charged polymer, PolyE-323. The chip was fabricated in a two-level cross design. The channel at the lower level was packed with 5-microm hyper-cross-linked polystyrene beads acting as a SPE medium used for desalting. The upper level channel acted as a CE channel and ended in an integrated emitter tip coated with conducting graphite powder to facilitate the electrical contact for sheathless ESI. An overpressure continuously provided fresh CE electrolyte independently of the flows in the different levels. Further studies were carried out in order to investigate the electrophoretic and flow rate properties of the chip. Finally, six-peptide mixtures, in different concentrations, dissolved in physiological salt solution was injected, desalted, separated, and sprayed into the mass spectrometer for analysis with a limit of detection in femtomole levels.