gebhart/patrepeval huggingface dataset:
Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding (2003)

We recently reported statistical analysis of structural data on glycosidic linkages. Here we extend this analysis to the glycan-protein linkage, and the peptide primary, secondary, and tertiary structures around N-glycosylation sites. We surveyed 506 glycoproteins in the Protein Data Bank crystallographic database, giving 2592 glycosylation sequons (1683 occupied) and generated a database of 626 nonredundant sequons with 386 occupied. Deviations in the expected amino acid composition were seen around occupied asparagines, particularly an increased occurrence of aromatic residues before the asparagine and threonine at position +2. Glycosylation alters the asparagine side chain torsion angle distribution and reduces its flexibility. There is an elevated probability of finding glycosylation sites in which secondary structure changes. An 11-class taxonomy was developed to describe protein surface geometry around glycosylation sites. Thirty-three percent of the occupied sites are on exposed convex surfaces, 10% in deep recesses and 20% on the edge of grooves with the glycan filling the cleft. A surprisingly large number of glycosylated asparagine residues have a low accessibility. The incidence of aromatic amino acids brought into close contact with the glycan by the folding process is higher than their normal levels on the surface or in the protein core. These data have significant implications for control of sequon occupancy and evolutionary selection of glycosylation sites and are discussed in relation to mechanisms of protein fold stabilization and regional quality control of protein folding. Hydrophobic protein-glycan interactions and the low accessibility of glycosylation sites in folded proteins are common features and may be critical in mediating these functions.
Sidedness of interfacial arginine residues and anti-atherogenicity of apolipoprotein A-I mimetic peptides (2012)

To test the hypothesis that sidedness of interfacial arginine (Arg) in apoA-I mimetic peptides, similar to that observed in apoA-I (Bashtovyy, D. et al. 2011. Sequence conservation of apolipoprotein A-I affords novel insights into HDL structure-function. J. Lipid Res. 52: 435-450.), may be important for biological activity, we compared properties of 4F and analogs, [K⁴,¹⁵>R]4F and [K⁹,¹³>R]4F, with Lys>Arg substitutions on the right and left side, respectively, of the 4F amphipathic helix. Intraperitoneal administration of these peptides into female apoE null mice (n = 13 in each group) reduced en face lesions significantly compared with controls; 4F and [K⁴,¹⁵>R]4F were equally effective whereas [K⁹,¹³>R]4F was less effective. Turnover experiments indicated that [K⁴,¹⁵>R]4F reached the highest, whereas [K⁹,¹³>R]4F had the lowest, plasma peak levels with a similar half life as the [K⁴,¹⁵>R]4F analog. The half life of 4F was two times longer than the other two peptides. The order in their abilities to associate with HDL in human plasma, generation of apoA-I particles with pre-β mobility from isolated HDL, lipid associating ability, and sensitivity of lipid complexes to trypsin digestion was: 4F>[K⁴,¹⁵,>R]4F>[K⁹,¹³>R]4F. These studies support our hypothesis that the sidedness of interfacial Arg residues in the polar face of apoA-I mimetics results in differential biological properties.
Deep Learning-Based Image Segmentation on Multimodal Medical Imaging (2019)

Multi-modality medical imaging techniques have been increasingly applied in clinical practice and research studies. Corresponding multi-modal image analysis and ensemble learning schemes have seen rapid growth and bring unique value to medical applications. Motivated by the recent success of applying deep learning methods to medical image processing, we first propose an algorithmic architecture for supervised multi-modal image analysis with cross-modality fusion at the feature learning level, classifier level, and decision-making level. We then design and implement an image segmentation system based on deep Convolutional Neural Networks (CNN) to contour the lesions of soft tissue sarcomas using multi-modal images, including those from Magnetic Resonance Imaging (MRI), Computed Tomography (CT) and Positron Emission Tomography (PET). The network trained with multi-modal images shows superior performance compared to networks trained with single-modal images. For the task of tumor segmentation, performing image fusion within the network (i.e. fusing at convolutional or fully connected layers) is generally better than fusing images at the network output (i.e. voting). This study provides empirical guidance for the design and application of multi-modal image analysis.
Effect of papaverine treatment on replication of measles virus in human neural and nonneural cells (1984)

The replication of measles virus in human neural and nonneural cell lines in terms of growth and cytopathic effect was affected by treatment of the cells with papaverine, which increases endogenous cyclic AMP. Suppression of virus growth was most prominent in neuroblastoma cells, followed by that in epidermoid carcinoma and glioblastoma cells, whereas the suppressive effect was relatively weak in oligodendroglioma cells. The papaverine-induced suppression of virus growth in neuroblastoma cells was studied in detail. The suppression that occurred was dependent on the dose of papaverine and was reversible. By treatment with 10 microM papaverine, virus-cell interactions were modified as follows: (i) early replication steps such as adsorption, penetration, and uncoating of the virus were not affected; (ii) synthesis of viral RNAs, including genomic RNA and mRNA, was inhibited; (iii) translation of viral proteins from mRNA was not blocked; and (iv) glycosylation and transport of viral glycoproteins to the cell membrane were not inhibited, but phosphorylation was blocked. The significance of suppressed virus replication in neural cells is discussed in relation to the persistence mechanisms of measles virus in the central nervous system.
Design of a computer vision based tree ring dating system (2002)

The purpose of this paper is to describe the design and implementation of a computer vision based analysis system for dendrochronology. The issues involved in the detection and analysis of tree rings are not unique to the application, but are likely of interest to anyone developing automated image analysis systems.
Hydrogel Formation via Cell Crosslinking (2003)

It is demonstrated that cells can be utilized as a crosslinker to form network structures from polymers. The properties of these systems can be interpreted with classical network theory. This approach can be useful to determine various parameters related to cell receptor–ligand binding (see Figure), such as the number of bonds, as well as to suggest a unique means to the delivery of cells for therapeutic purposes.
Analysis of Drosophila Glucuronyl C5-Epimerase (2013)

During the biosynthesis of heparan sulfate (HS), glucuronyl C5-epimerase (Hsepi) catalyzes C5-epimerization of glucuronic acid (GlcA), converting it to iduronic acid (IdoA). Because HS 2-O-sulfotransferase (Hs2st) shows a strong substrate preference for IdoA over GlcA, C5-epimerization is required for normal HS sulfation. However, the physiological significance of C5-epimerization remains elusive. To understand the role of Hsepi in development, we isolated Drosophila Hsepi mutants. Homozygous mutants are viable and fertile with only minor morphological defects, including the formation of an ectopic crossvein in the wing, but they have a short lifespan. We propose that two mechanisms contribute to the mild phenotypes of Hsepi mutants: HS sulfation compensation and possible developmental roles of 2-O-sulfated GlcA (GlcA2S). HS disaccharide analysis showed that loss of Hsepi resulted in a significant impairment of 2-O-sulfation and induced compensatory increases in N- and 6-O-sulfation. Simultaneous block of Hsepi and HS 6-O-sulfotransferase (Hs6st) activity disrupted tracheoblast formation, a well established FGF-dependent process. This result suggests that the increase in 6-O-sulfation in Hsepi mutants is critical for the rescue of FGF signaling. We also found that the ectopic crossvein phenotype can be induced by expression of a mutant form of Hs2st with a strong substrate preference for GlcA-containing units, suggesting that this phenotype is associated with abnormal GlcA 2-O-sulfation. Finally, we show that Hsepi formed a complex with Hs2st and Hs6st in S2 cells, raising the possibility that this complex formation contributes to the close functional relationships between these enzymes.
Computer-derived microstructures by 3D Printing: Sio- and Structural Materials (2018)

3D Plinting is a rapid prototyping technique to manufacture functional components&#13;\ndirectly from computer models. The process involves spreading the powder in thin layers&#13;\nand then selective binding of the powder using a technology similar to ink-jet ptinting.&#13;\nLayers are added sequentially until a part is completed. 3DP has been used to make&#13;\ncomplex-shaped components from several monolithic matetials, including cOlnponents for&#13;\nuse in structural applications. This paper focuses, however, on the ability to control&#13;\nmicrostlucture and local composition by 3DP. We envision cases where cOlnputer&#13;\ndelived-microstructlu'es can be created by approptiate control of the ptinting paralneters.&#13;\nThus, one can build components with the desired microstlucture independent of the&#13;\ncomplexity of the desired shape. Examples for both structural matetials and biomedical&#13;\ndevices are discussed.
Targets for Gene Therapy of Parkinson's Disease: Growth Factors, Signal Transduction, and Promoters (1997)

Parkinson's disease gene therapy is in its infancy. All studies to date have been in experimental animals and there are no clinical protocols currently approved. Several non-human primate studies however, have been completed and preliminary data appear promising. When dealing with a complex acquired disorder of unknown etiology, gene therapy is likely to provide symptomatic and palliative relief at best and will not be curative. However, if the gene therapy approach has advantages in terms of the risk/benefit ratio, cost and efficacy over current treatments, then it should be brought to clinical trial. This article discusses some future directions and areas of intense investigation at present. The advances in the field over the past five years have been tremendous and it appears possible that before the year 2000, clinical gene therapy trials in Parkinson's disease will be ongoing.
A Composite Element Binding the Vitamin D Receptor, Retinoid X Receptor α, and a Member of the CTF/NF-1 Family of Transcription Factors Mediates the Vitamin D Responsiveness of the c -fos Promoter (1996)

The hormonal form of vitamin D, 1 alpha,25-dihydroxyvitamin D3 [1,25- (OH)2D3], transiently stimulates the transcription of the c-fos proto-oncogene in osteoblastic cells. We have identified and characterized a vitamin D response element (VDRE) in the promoter of c-fos. The 1,25-(OH)2D3-responsive region was delineated between residues -178 and -144 upstream of the c-fos transcription start site. A mutation that inhibited binding to the sequence concomitantly abolished 1,25-(OH)2D3-induced transcriptional responsiveness; similarly, cloning to the site upstream of a heterologous promoter conferred copy-number-dependent vitamin D responsiveness to a reporter gene, demonstrating that we have identified a functional response element. The structure of the c-fos VDRE was found to be unusual. Mutational analysis revealed that the c-fos VDRE does not conform to the direct repeat configuration in which hexameric core-binding sites are spaced by a few nucleotide residues. In contrast, the entire 36-bp sequence was essential for binding. We identified the vitamin D receptor and the retinoid X receptor alpha as components of the complex that bound the c-fos VDRE. However, our results also show that a putative CCAAT-binding transcription factor/nuclear factor 1 (CTF/NF-1) family member bound the response element in conjunction with the nuclear hormone receptors. The expression of this CTF/NF-1 family member appeared restricted to bone cells. These data hint at new molecular mechanisms of action for vitamin D.
Composition of lignin in outer cell-wall layers (2006)

The composition of lignin in the outer cell-wall layers of spruce and poplar has been studied and the data obtained have been compared with those of the mature reference wood in which the secondary cell wall predominates. Materials with exclusively or predominantly outer cell-wall layers were examined. Accurate data relating to the lignin monomer composition and the number of β-O-4´ bonds were obtained from pure middle lamella/primary cell wall lignin. Firstly, a 10 000 year old white spruce material, with most of the secondary cell wall missing, was studied. The aged lignin was composed of guaiacyl units only, and was slightly more condensed but otherwise similar to the reference lignin. Secondly, the developing xylem of a Norway spruce clone was analyzed during a growth season. In spring and early summer, growth is very rapid and the intention was to sample tissues in which the secondary cell-wall layers had not yet lignified, but where the outer layers at least had started to lignify. Microscopy, Klason lignin and carbohydrate analyses showed that the lignin in the developing xylem of samples from mid-June was located exclusively in the middle lamella. The lignin was more condensed, was composed of guaiacyl units only and contained more end-groups than the reference Norway spruce wood. Thirdly, the cambial tissues of a Balsam poplar clone were surveyed during a growth season. Both the phloem side and the xylem side of the cambial region were examined. The Klason lignin content and carbohydrate monomer distribution showed that in June and August the tissues on the phloem side contained material with mainly middle lamella/primary walls. In June, the xylem side in the cambial region contained mainly middle lamella/primary walls, and in August the secondary cell wall carbohydrates were being deposited. Both tissues contained lignin that was more condensed and had more end-groups than the reference lignin. In mid-June, the developing xylem had a ratio of syringyl to guaiacyl units of 0.6, whereas the ratio for the reference wood was 1.3. In the final study, lignin from the primary cell walls from a hybrid aspen cell suspension culture was investigated. The lignin contained only guaiacyl units which were more condensed than those observed in the reference poplar wood.
On lattices, learning with errors, random linear codes, and cryptography (2005)

Our main result is a reduction from worst-case lattice problems such as SVP and SIVP to a certain learning problem. This learning problem is a natural extension of the 'learning from parity with error' problem to higher moduli. It can also be viewed as the problem of decoding from a random linear code. This, we believe, gives a strong indication that these problems are hard. Our reduction, however, is quantum. Hence, an efficient solution to the learning problem implies a quantum algorithm for SVP and SIVP. A main open question is whether this reduction can be made classical.Using the main result, we obtain a public-key cryptosystem whose hardness is based on the worst-case quantum hardness of SVP and SIVP. Previous lattice-based public-key cryptosystems such as the one by Ajtai and Dwork were only based on unique-SVP, a special case of SVP. The new cryptosystem is much more efficient than previous cryptosystems: the public key is of size Õ(n2) and encrypting a message increases its size by Õ(n)(in previous cryptosystems these values are Õ(n4) and Õ(n2), respectively). In fact, under the assumption that all parties share a random bit string of length Õ(n2), the size of the public key can be reduced to Õ(n).
Network Single-Walled Carbon Nanotube-Field Effect Transistors (SWNT-FETs) with Increased Schottky Contact Area for Highly Sensitive Biosensor Applications (2006)

Highly sensitive single-walled carbon nanotube-field effect transistor (SWNT-FET) devices, which detect protein adsorptions and specific protein-protein interactions at 1 pM concentrations, have been achieved. The detection limit has been improved 104-fold compared to the devices fabricated by photolithography. The substantially increased sensitivity is mainly due to the increased Schottky contact area which accommodates relatively more numbers of proteins even at very low concentration. The augmented number of proteins adsorbed on a device induces instant modulation of the work function of metal contact electrodes, which eventually changes the conductance of the device. Such devices have been attained by addressing metal electrodes on network-type SWNTs using a shadow mask on a tilted angle sample stage. The shadow mask allows metals to penetrate underneath the mask efficiently, therefore forming a thin and wide Schottky contact area on SWNT channels.
Molecular comparison of bacterial isolates from blood with strains colonizing pharynx and intestine in immunocompromised patients with sepsis (2003)

Most causative organisms of sepsis in immunocompromised patients are the same species as those that colonize their own nasopharynx or intestinal tract. To determine whether the strains recovered from blood originate mainly from patients’ own flora, isolates from blood and throat and/or stool were investigated by genomic analyses. Surveillance cultures of throat and stool were taken prospectively from cancer patients being treated with intensive chemotherapy followed by haematopoietic stem-cell transplantation. In those cases of sepsis in which the isolate from blood was the same species as that from the throat and/or stool, the genomic profiles of the isolates were compared by PFGE. Ten cases of blood culture-positive sepsis were documented in six of 14 subjects during a 2 year period; isolates of Pseudomonas aeruginosa , Staphylococcus epidermidis , Enterococcus sp., viridans streptococci and Fusobacterium sp. were recovered from blood. In five of seven cases in which the blood isolate was the same species as that from the throat or stool, the genotypes of the isolates from both sites were identical. In the majority of immunocompromised patients, the causative organisms of bloodstream infections originated mainly from their own flora.
Generation of mucosal cytotoxic T cells against soluble protein by tissue-specific environmental and costimulatory signals (1998)

We compared peripheral and mucosal primary CD8 T cell responses to inflammatory and noninflammatory forms of antigen in a T cell-adoptive transfer system. Immunization with the soluble antigen, ovalbumin (ova), administered i.p. or orally without adjuvant, activated nonmucosal CD8 T cells but did not induce cytotoxic activity. However, after activation, the transferred cells entered the intestinal mucosa and became potent antigen-specific killers. Thus, exogenous intact soluble protein entered the major histocompatibility complex class I antigen presentation pathway and induced mucosal cytotoxic T lymphocytes. Moreover, distinct costimulatory requirements for activation of peripheral versus mucosal T cells were noted in that the CD28 ligand, B7-1, was critical for activated mucosal T cell generation but not for activation of peripheral CD8 T cells. The costimulator, B7-2, was required for optimum activation of both populations. Infection with a new recombinant vesicular stomatitis virus encoding ovalbumin induced lytic activity in mucosal as well as peripheral sites, demonstrating an adjuvant effect of inflammatory mediators produced during virus infection. Generation of antiviral cytotoxic T lymphocytes was also costimulation-dependent. The results indicated that induction of peripheral tolerance via antigen administration may not extend to mucosal sites because of distinct costimulatory and inflammatory signals in the mucosa.
Determination of Phage Antibody Affinities to Antigen by a Microbalance Sensor System (1999)

Over the past decade, phage display has maturated to be a frequently used method for the generation of monoclonal antibodies of human origin. The essential step of this method is the "biopanning" of phage carrying functional antibody fragments on their surface on an immobilized antigen. The screening of large combinatorial gene libraries with this method usually leads to a set of diverse clones specifically binding to the antigen that need to be characterized further. Beside its specificity, the key parameter to be determined is the affinity of the recombinant antibody fragment to its antigen. Here, we present a mass sensitive microsensor method that allows the estimation of antibody affinity directly from the phage supernatant. Binding of phage antibodies to the antigen immobilized on a quartz crystal microbalance (QCM) induced a mass dependent decrease in frequency. This principle was used to determine the apparent affinity of a single-chain (sc)Fv antibody against the RNA polymerase of Drosophila melanogaster presented on the surface of a filamentous phage (M13) from its association and dissociation rates. The apparent affinity obtained is in accordance with the affinity of the scFv fragment as determined by conventional equilibrium enzyme-linked immunosorbent assay (ELISA) and plasmon resonance methods.
Evidence for Subclinical Influenza A(H1N1)pdm09 Virus Infection among Dogs in Guangdong Province, China (2014)

During 2012, we identified sampled dogs with elevated levels of antibodies (≥1:40) against A(H1N1)pdm09 virus by using a hemagglutination inhibition (HI) assay (seroprevalence, 24.7%) and a microneutralization (MN) assay (seroprevalence, 10.8%). These high seroprevalences of A(H1N1)pdm09 among dogs without clinical signs of influenza support the premise that dogs may play a role in the human influenza ecology in China.