gebhart/patrepeval huggingface dataset:
Synthesis of Maleimide-End-Functionalized Star Polymers and Multimeric Protein−Polymer Conjugates (2009)

Protein-polymer conjugates exhibit superior properties to unmodified proteins, generating a high demand for these materials in the fields of medicine, biotechnology, and nanotechnology. Multimeric conjugates are predicted to surpass the activity of monomeric conjugates. Herein, we report a straightforward method to synthesize multimeric polymer-conjugates. Four armed poly(N-isopropylacrylamide) (pNIPAAm) was synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization in the presence of a tetra-functionalized trithiocarbonate chain transfer agent (CTA). The polymer molecular weight, architecture and polydispersity index (PDI) were verified by gel permeation chromatography (GPC), dynamic light scattering gel permeation chromatography (DLS-GPC), and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. This approach afforded well-defined polymers (PDI's < 1.06) and the ability to target various molecular weights. Maleimide functional groups were introduced at the chain ends by heating the polymers in the presence of a furan-protected azo-initiator. This allowed for site-specific conjugation of V131C T4 lysozyme to the polymers to generate multimeric protein-polymer conjugates. MALDI-TOF mass spectrometry, electrospray ionization gas-phase electrophoretic-mobility macromolecule analysis (ESI-GEMMA), gel electrophoresis, and liquid chromatography tandem mass spectrometry (LC-MS/MS) of the trypsin digests demonstrated that multimeric protein-polymer conjugates had formed. This simple strategy provides ready access to star protein-polymer conjugates for application in the fields of drug discovery, drug delivery, and nanotechnology.
Seminal plasma cytokine levels in the diagnosis of chronic pelvic pain syndrome (2001)

Although there are individual variables between the discrimination of inflammatory and non-inflammatory CPPS, cytokines are frequently present and elevated in the expressed prostatic secretions from men with CPPS. Our results indicate that several soluble cytokines can be used to identify this chronic and long-term disease.
Improved RNase protection assay for quantifying LDL-receptor mRNA; estimation of analytical imprecision and biological variance in peripheral blood mononuclear cells (1995)

We have improved the protocol for RNA quantification by using RNase protection. Instead of precipitation and extraction with phenol and chloroform, we use a faster and more reliable precipitation based on guanidinium thiocyanate (GdSCN). The internal standard is produced by in vitro transcription of a DNA template constructed so as to allow simultaneous detection of the in vitro transcript and the low-density lipoprotein receptor (LDLR) mRNA by use of the same probe and hybridization. Addition of this internal standard at the step for RNA isolation reduced the analytical imprecision from 40.8% to 19.3%. Estimates of the within- and between-subject biological variations of the LDLR mRNA content in peripheral blood mononuclear cells (PBMCs) isolated from healthy volunteers were 21.5% and 13.6%, respectively, and the analytical imprecision was 22.6%. The mean content of LDLR mRNA in PBMCs from healthy individuals was 0.78 copies per cell.
Deep Convolutional Neural Networks for Breast Image Analysis on Holographic Microwave Imaging (2018)

This paper presents the development of a deep convolutional neural network (CNN) method namely super-solution CNN to produce a high-resolution microwave breast image from a low-resolution model, which helps to improve the accuracy and efficiency of breast lesion detection within microwave image. Various experiments are conducted to validate the proposed method. Experimental results show that the proposed approach has the potential to produce a high-resolution breast image with high-accuracy.
Regular FFT-related transform kernels for DCT/DST-based polyphase filter banks (1991)

A realization for the discrete cosine and sine transforms (DCT and DST) is proposed which is based on an FFT (fast Fourier transform) optimized for DSP (digital signal processor) use. Besides its regular structure, even the theoretically interesting total number of required operations is about the same as needed by the most regular direct approach and only slightly higher than the minimum number yet published. Compared to a similar approach published recently by N. Ramamurthy and M.N.S. Swamy (1990), it is even more efficient.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electron Transfer through Organic Molecules (1999)

Electron transfer through molecular frameworks is central to a wide range of chemical, physical, and biological processes. We demonstrate a means to measure electronically and to quantify electron transfer through organic molecules and films. We show quantitative agreement with universal values of electron transfer inferred from biological, electrochemical, photochemical, and related systems. Scanning tunneling microscopy was used to image adjacent chains and molecular terraces of different length alkanethiolates in an ordered self-assembled monolayer lattice on Au{111}. In electron transfer measurements using a scanning tunneling microscope, both the driving force and the electrode separation can be continuously varied. This allows independent electronic measurement of the molecular bridges through which electron transfer takes place. The differences between the measured topography in scanning tunneling microscopy and the physical heights of these molecules can be understood in terms of the transconductance through individual chains using a two-layer tunnel junction model.
Useful daylight illuminance: a new paradigm for assessing daylight in buildings (2005)

This paper introduces a new paradigm to assess daylight in buildings called ‘useful daylight illuminance’, or UDI. The UDI paradigm preserves much of the interpretive simplicity of the conventional daylight factor approach. In contrast to daylight factors however, UDI is founded on an annual time-series of absolute values for illuminance predicted under realistic skies generated from standard meteorological datasets. Achieved UDI is defined as the annual occurrence of illuminances across the work plane where all the illuminances are within the range 100-2000 lux. These limits are based on reports of occupant preferences and behaviour in daylit offices with user-operated shading devices. The degree to which UDI is not achieved because illuminances exceed the upper limit is indicative of the potential for occupant discomfort. The relation between achieved UDI and annual energy consumption for lighting is examined.
Nd:YAG laser-induced hematoporphyrin visible fluorescence and two-photon-excited photochemical effect on malignant tumor cells (1985)

A new and promising method for localization and treatment of certain forms of cancer is based on the joint action of laser irradiation and a fluorescent photosensitizer. This technique, which is customarily referred to as photoradiation therapy, is currently under development in various institutions and hospitals throughout the world. A nontoxic, photosensitizing dye with fluorescent properties, hematoporphyrin derivative, is first injected systematically. After 2–3 days this dye exhibits a higher retention in the cancerous region than in the surrounding normal tissue. Subsequent irradiation with a proper optical wavelength, mainly red light around 630 nm, results in rapid necrosis of the neoplastic tissue. However, the absorption by skin pigments for this visible light is usually larger, to a greater extent, than that of a Nd:YAG laser output at 1.064 μ m. Hence spectroscopic studies including absorption and fluorescence were performed using hematoporphyrin dihydrochloride (Hp.2HCI) dissolved in PBS and ethanol solutions excited by Q -switched Nd:YAG laser output and its second harmonic beam at 532 nm. The visible fluorescence thus observed by Nd:YAG laser irradiation was attributed to the two-photon absorption, although its intensity was ∼10 −4 weaker than that for second harmonic excitation. Survival rate of cultured esophagus cancer cells uptaken Hp.2HCI exhibited a linear decrease with the Nd:YAG laser irradiation time, and this two-photon excited photochemical effect was formed more appreciably for higher dye concentration.
Unsupervised Learning of Spatiotemporally Coherent Metrics (2015)

Current state-of-the-art classification and detection algorithms train deep convolutional networks using labeled data. In this work we study unsupervised feature learning with convolutional networks in the context of temporally coherent unlabeled data. We focus on feature learning from unlabeled video data, using the assumption that adjacent video frames contain semantically similar information. This assumption is exploited to train a convolutional pooling auto-encoder regularized by slowness and sparsity priors. We establish a connection between slow feature learning and metric learning. Using this connection we define "temporal coherence" -- a criterion which can be used to set hyper-parameters in a principled and automated manner. In a transfer learning experiment, we show that the resulting encoder can be used to define a more semantically coherent metric without the use of labels.
Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus (1990)

Phylogenetic analysis of 20 influenza A virus PB2 genes showed that PB2 genes have evolved into the following four major lineages: (i) equine/Prague/56 (EQPR56); (ii and iii) two distinct avian PB2 lineages, one containing FPV/34 and H13 gull virus strains and the other containing North American avian and recent equine strains; and (iv) human virus strains joined with classic swine virus strains (i.e., H1N1 swine virus strains related to swine/Iowa/15/30). The human virus lineage showed the greatest divergence from its root relative to other lineages. The estimated nucleotide evolutionary rate for the human PB2 lineage was 1.82 x 10(-3) changes per nucleotide per year, which is within the range of published estimates for NP and NS genes of human influenza A viruses. At the amino acid level, PB2s of human viruses have accumulated 34 amino acid changes over the past 55 years. In contrast, the avian PB2 lineages showed much less evolution, e.g., recent avian PB2s showed as few as three amino acid changes relative to the avian root. The completion of evolutionary analyses of the PB1, PB2, PA and NP genes of the ribonucleoprotein (RNP) complex permits comparison of evolutionary pathways. Different patterns of evolution among the RNP genes indicate that the genes of the complex are not coevolving as a unit. Evolution of the PB1 and PB2 genes is less correlated with host-specific factors, and their proteins appear to be evolving more slowly than NP and PA. This suggests that protein functional constraints are limiting the evolutionary divergence of PB1 and PB2 genes. The parallel host-specific evolutionary pathways of the NP and PA genes suggest that these proteins are coevolving in response to host-specific factors. PB2s of human influenza A viruses share a common ancestor with classic swine virus PB2s, and the pattern of evolution suggests that the ancestor was an avian virus PB2. This same pattern of evolution appears in the other genes of the RNP complex. Antigenic studies of HA and NA proteins and sequence comparisons of NS and M genes also suggest a close ancestry for these genes in human and classic swine viruses. From our review of the evolutionary patterns of influenza A virus genes, we propose the following hypothesis: the common ancestor to current strains of human and classic swine influenza viruses predated the 1918 human pandemic virus and was recently derived from the avian host reservoir.
Retention in Plaque and Remineralization of Enamel Lesions by Various Forms of Calcium in a Mouthrinse or Sugar-free Chewing Gum (2003)

Casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) nanocomplexes incorporated into sugar-free chewing gum have been shown to remineralize enamel subsurface lesions in situ. The aim of this study was to compare the ability of CPP-ACP, with that of other forms of calcium, to be retained in supragingival plaque and remineralize enamel subsurface lesions in situ when delivered in a mouthrinse or sugar-free gum in randomized, double-blind trials. In the mouthrinse study, only the CPP-ACP-containing mouthrinse significantly increased plaque calcium and inorganic phosphate levels, and the CPP were immunolocalized to the surfaces of bacterial cells as well as the intercellular matrix. In the chewing gum studies, the gum containing the CPP-ACP, although not containing the most calcium per piece of gum, produced the highest level of enamel remineralization independent of gum-chewing frequency and duration. The CPP could be detected in plaque extracts 3 hrs after subjects chewed the CPP-ACP-containing gum. The results showed that CPP-ACP were superior to other forms of calcium in remineralizing enamel subsurface lesions.
[Role of CDX2 immunostaining in diagnosis of gastrointestinal adenocarcinoma]. (2006)

CDX2 is expressed mainly in normal epithelium of intestinal tract and small pancreatic ducts, as well as in primary adenocarcinoma of gastrointestinal tract. CDX2 may thus play an important role in distinguishing primary non-intestinal adenocarcinoma from metastatic adenocarcinoma of gastric or colorectal primary.
Ultrafast Photoinduced Electron Transfer and Charge Stabilization in Donor–Acceptor Dyads Capable of Harvesting Near‐Infrared Light (2015)

To harvest energy from the near-infrared (near-IR) and infrared (IR) regions of the electromagnetic spectrum, which constitutes nearly 70 % of the solar radiation, there is a great demand for near-IR and IR light-absorbing sensitizers that are capable of undergoing ultrafast photoinduced electron transfer when connected to a suitable electron acceptor. Towards achieving this goal, in the present study, we report multistep syntheses of dyads derived from structurally modified BF2-chelated azadipyrromethene (ADP; to extend absorption and emission into the near-IR region) and fullerene as electron-donor and electron-acceptor entities, respectively. The newly synthesized dyads were fully characterized based on optical absorbance, fluorescence, geometry optimization, and electrochemical studies. The established energy level diagram revealed the possibility of electron transfer either from the singlet excited near-IR sensitizer or singlet excited fullerene. Femtosecond and nanosecond transient absorption studies were performed to gather evidence of excited state electron transfer and to evaluate the kinetics of charge separation and charge recombination processes. These studies revealed the occurrence of ultrafast photoinduced electron transfer leading to charge stabilization in the dyads, and populating the triplet states of ADP, benzanulated-ADP and benzanulated thiophene-ADP in the respective dyads, and triplet state of C60 in the case of BF2 -chelated dipyrromethene derived dyad during charge recombination. The present findings reveal that these sensitizers are suitable for harvesting light energy from the near-IR region of the solar spectrum and for building fast-responding optoelectronic devices operating under near-IR radiation input.
Coarse-Grained Model Of Entropic Allostery (2004)

Many signaling functions in molecular biology require proteins to bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit information via a conformational change in response to the ligand binding. An alternative entropic mechanism of "allostery" suggests that the inducer ligand changes the intramolecular vibrational entropy, not just the mean static structure. We present a quantitative, coarse-grained model of entropic allostery, which suggests design rules for internal cohesive potentials in proteins employing this effect. It also addresses the issue of how the signal information to bind or unbind is transmitted through the protein. The model may be applicable to a wide range of repressors and also to signaling in trans-membrane proteins.
Conserved domains of glycosyltransferases (1999)

Glycosyltransferases catalyze the synthesis of glycoconjugates by transferring a properly activated sugar residue to an appropriate acceptor molecule or aglycone for chain initiation and elongation. The acceptor can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. A catalytic reaction is believed to involve the recognition of both the donor and acceptor by suitable domains, as well as the catalytic site of the enzyme. To elucidate the structural requirements for substrate recognition and catalytic reactions of glycosyltransferases, we have searched the databases for homologous sequences, identified conserved amino acid residues, and proposed potential domain motifs for these enzymes. Depending on the configuration of the anomeric functional group of the glycosyl donor molecule and of the resulting glycoconjugate, all known glycosyltransferases can be divided into two major types: retaining glycosyltransferases, which transfer sugar residue with the retention of anomeric configuration, and inverting glycosyltransferases, which transfer sugar residue with the inversion of anomeric configuration. One conserved domain of the inverting glycosyltransferases identified in the database is responsible for the recognition of a pyrimidine nucleotide, which is either the UDP or the TDP portion of a donor sugar-nucleotide molecule. This domain is termed "Nucleotide Recognition Domain 1 beta," or NRD1 beta, since the type of nucleotide is the only common structure among the sugar donors and acceptors. NRD1 beta is present in 140 glycosyltransferases. The central portion of the NRD1 beta domain is very similar to the domain that is present in one family of retaining glycosyltransferases. This family is termed NRD1 alpha to designate the similarity and stereochemistry of sugar transfer, and it consists of 77 glycosyltransferases identified thus far. In the central portion there is a homologous region for these two families and this region probably has a catalytic function. A third conserved domain is found exclusively in membrane-bound glycosyltransferases and is termed NRD2; this domain is present in 98 glycosyltransferases. All three identified NRDs are present in archaebacterial, eubacterial, viral, and eukaryotic glycosyltransferases. The present article presents the alignment of conserved NRD domains and also presents a brief overview of the analyzed glycosyltransferases which comprise about 65% of all known sugar-nucleotide dependent (Leloir-type) and putative glycosyltransferases in different databases. A potential mechanism for the catalytic reaction is also proposed. This proposed mechanism should facilitate the design of experiments to elucidate the regulatory mechanisms of glycosylation reactions. Amino acid sequence information within the conserved domain may be utilized to design degenerate primers for identifying DNA encoding new glycosyltransferases.
Automated site-directed drug design : the formation of molecular templates in primary structure generation (1989)

In this paper the spacer skeleton concept is used to produce molecular graphs of putative ligands for binding sites. The skeletons are transformed into molecular templates within the constraints of the accessible surface of the ligand-binding site. A distance-matrix method is used to compare ligand points with vertices of the spacer skeleton through a permutation of all possible correspondences. A tolerance parameter is used to screen for poor matches. As a result, a small number of matched vertices and ligand points are produced. These are fitted into the site by a constrained optimization routine using an analytical function. Ligand points fall within the site and are optimally positioned adjacent to the corresponding site points; other vertices of the spacer skeleton lying beneath the accessible surface of the site are clipped off. A molecular template is thereby formed with its vertices linked to the ligand points. The final step is to verify that the bonding integrity of the skeleton remains. The computational methods outlined in this paper have been tested at two binding sites: the pteridine binding site in dihydrofolate reductase and the amidinophenylpyruvate site of trypsin. Molecular graphs for both sites were generated automatically; they showed strong similarity to those of the natural ligands.
The status of surgery for cardiac arrhythmias. (1985)

Successful surgical treatment of all forms of supraventricular tachyarrhythmias is dependent on accurate electrophysiologic guidance. Surgery for WPW syndrome is no longer experimental and should be offered to (1) patients with medically refractory reciprocating tachycardia associated with the syndrome, (2) patients with spontaneous atrial fibrillation who are at risk for sudden death, (3) patients with drug intolerance, and (4) young, otherwise healthy patients with symptoms that warrant more than minimal medical therapy. The current results of surgery for WPW syndrome would seem to lessen the likelihood that a major new method of superior nonpharmacologic treatment will emerge in the near future. Surgery for most other types of supraventricular tachyarrhythmias remains experimental and should be applied only under the most controlled circumstances and after satisfying the most rigid criteria for surgical intervention, the main indication being absolute medical refractoriness. The single exception at the present time is surgery for AV node reentry tachycardia, which appears to be easily cured by the new technique of discrete cryosurgery of the peri-AV nodal region of the lower right atrial septum. In a majority of patients, ventricular tachycardia can be successfully ablated surgically without the use of electrophysiologic mapping to guide the surgeon. If such an approach is taken, however, the surgical treatment of these complex arrhythmias becomes a completely service-oriented exercise. Although delivery of such a service is of undeniable importance, the potential for learning more about these complex and lethal arrhythmias is lost unless each patient is studied as comprehensively as possible.(ABSTRACT TRUNCATED AT 250 WORDS)