gebhart/patrepeval huggingface dataset:
Identification of proteins that interact with the UL24 protein of herpes simplex virus 1 (2011)

Infection with herpes simplex virus 1 (HSV-1) typically results in the formation of cold sores; however, in individuals with a compromised immune system the infection can be severe. The virus life cycle is characterized by two distinct phases: a lytic replication phase occurring in mucous membranes, and a latent state that is established in neurons of the trigeminal ganglia.

The UL24 protein of HSV-1 is implicated in both the lytic and latent phases of infection. Infection with a UL24-deficient virus in vitro results in reduced viral yields and the formation of syncytial plaques, where the plasma membranes of infected cells fuse together. In vivo, the absence of UL24 results in reduced viral titers and a drastic reduction in viral reactivation ex vivo. Previously, we showed that UL24 is both necessary and sufficient to induce the redistribution of the nucleolar protein nucleolin. The UL24 protein contains 269 amino acids and is expressed late in the virus life cycle. A bioinformatics study identified an endonuclease motif within the conserved N-terminal portion of the protein; however, its function remains to be demonstrated. Although several roles have been attributed to UL24, the mechanisms involved are unknown.

We hypothesized that UL24 functions, at least in part, through protein-protein interactions. To investigate this possibility, we used a virus that expresses UL24 with a hemagglutinin (HA) tag fused to its N-terminus, vHA-UL24. Lysates from infected cells were harvested, and fractionated on glycerol gradients. We found that UL24 was present in fractions corresponding to a much higher molecular mass than would be expected for UL24 alone, suggesting an association of UL24 with cellular or viral proteins during infection. To isolate potential UL24-binding proteins, we performed immunoprecipitations on fractions containing HA-UL24, using antibodies directed against the HA epitope. Immunoprecipitated proteins were resolved by denaturing polyacrylamide gel electrophoresis. Silver staining of the gel enabled the detection of proteins that appeared to specifically co-precipitate with HA-UL24. Candidate binding proteins will be identified by mass spectrometry. The identification of UL24-interacting partners will contribute to a better understanding of the roles of UL24 in different steps of the virus life cycle.
Preparation of highly purified Inter-alpha inhibitor proteins from human plasma and their analysis by use of SELDI-TOF technology. (2004)

Inter-alpha inhibitor proteins (IaIp) are a family of structurally related serine protease inhibitors (serpins) found in relatively high concentrations in human plasma. The major forms found in human plasma are inter-alpha inhibitor (IaI), which consists of two heavy chains (H1 & H1) and a single light chain (bikunin), and pre alpha inhibitor (PaI), which consists of one heavy (H3) and one light chain. Recently, the involvement of IaIp in sepsis has become an area of intensive investigation. We found markedly decreased plasma levels of IaIp in septic patients compared to healthy controls. Furthermore, the concomitant increase of IaIp-related fragments in uine suggest that these proteins are “ consumed” and rapidly cleared from the systemic circulation during sepsis. This offers a therapeutic rationale for replacement of IaIp during sepsis. Using a combination of several chromatographic methods, both members of IaIp family (IaIp and PaI) were isolated from human plasma in highly purity and biologically active forms. The highly purified IaIp preparation was effective in reducing mortality in the experimental animal model. For characterization of the isolated proteins and identification of the main contaminant during purification we used SELDI-TOF technique. After separation by SDS-PAGE, polypeptide bands with apparent molecular weights of 80 kDa, 125 kDa, and 25 kDa were cut out from the gel, reduced, akylated, and digested by trypsin. After extraction, the peptides were spotted to a hydrophobic and SEDN-ID chip and analyzed by mass spectrometry. To our surprise, the 80 kDa band was identified as heavy chain H3 precursor. Another plasma protein, clotting factor X, which was identified in this band by Western blot and measurement of clotting activity seems to be only a minor component in the fraction. In the 125 kDa band containing PaI not only heavy chain H3, but also heavy chains H1, H2 and recently described heavy chain H4 together with bikunin were detected. The 250 kDa band contains only two heavy chains H1 and H2 together with the light chain, bikunin. Heavy chains H3 and H4 were not detected in this band. Current efforts are focused on further biochemical and clinical investigation of these preparation as an effective strategy for reducing the severe complications of sepsis in humans.
Abstract 3251: Characterization of a novel Rac inhibitor as an anti cancer metastasis compound (2011)

Abstract The objective of this project is to design novel therapeutics targeting cancer metastasis, the most deadly aspect of epithelial cancers. Our previous studies have shown that Rac, a key signaling intermediate that regulates actin cytoskeletal changes during cell migration/invasion and cancer metastasis, is associated with high cancer metastatic efficiency. Since Rac proteins are activated by GDP/GTP exchange, inhibition of the interaction of Rac with its guanine nucleotide exchange factors (GEF) is expected to inhibit Rac activity. Since the known Rac inhibitor NSC-23766 is not effective at therapeutically useful concentrations, we synthesized novel NSC-23766 derivatives. Results show that the new inhibitor EHop-016 is 100-fold more efficient than the parent compound at inhibiting Rac activity of metastatic cancer cells without affecting the activity of the related GTPase, Rho. EHop-016 inhibited Rac activity of metastatic cancer cells with an IC50 of 0.78 microM. Cell viability assays, performed to test for the toxicity of this compound, demonstrated that at concentrations below 5 microM, EHop-016 did not affect mammary epithelial cell (MCF-10A) viability and decreased proliferation of metastatic cancer cells (MDA-MB-435) by only 20%. We conclude that EHop-16 is a potent Rac inhibitor with promise of further development as a small molecule inhibitor of cancer cell invasion, and thus, metastasis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3251. doi:10.1158/1538-7445.AM2011-3251
Stage-Specific Action of Matrix Metalloproteinases Influences Progressive Hereditary Kidney Disease (2006)

These results suggest that preserving GBM/extracellular matrix integrity before the onset of proteinuria leads to significant disease protection, but if this window of opportunity is lost, MMP-inhibition at the later stages of Alport disease leads to accelerated glomerular and interstitial fibrosis. Our findings identify a crucial dual role for MMPs in the progression of Alport disease in alpha3(IV)-/- mice, with an early pathogenic function and a later protective action. Hence, we propose possible use of MMP-inhibitors as disease-preventive drugs for patients with Alport syndrome with identified genetic defects, before the onset of proteinuria.
A Second-Generation Synthesis of Polypyrrolinone Nonpeptidomimetics:  Prelude to the Synthesis of Polypyrrolinones on Solid Support (2000)

[reaction: see text] A second-generation asymmetric synthesis of polypyrrolinones (3) has been achieved exploiting scalemic alpha-aminolactones (1) as building blocks. Imine formation between an appropriate lactone (1) and aldehyde (2), followed in turn by pyrrolinone ring construction promoted by KHMDS in the presence of 18-crown-6 and modified Swern oxidation furnished pyrrolinone aldehyde 3. This iterative, efficient three-step protocol paves the way for the synthesis of polypyrrolinones on solid support.
[Studies on bonding interfaces of two dentin adhesives by scanning electron microscopy]. (2003)

PBNT and P-One provided good resin infiltration, producing a three-dimensional interlocking micro-network of resin tags in the dentin tubules with multiple lateral branches that penetrate the intertubular dentin, which positively influenced the adhesion between dentin and the two bond systems.
A highly conserved region present in transcripts encoding heterologous M proteins of group A streptococci (1987)

In group A streptococcal strains of 10 different serotypes, the sequence previously identified as homologous to the structural gene for type 6 M protein (emm6) was found to be transcribed. The conserved sequence, which shows greater than 95% homology among heterologous M proteins, was identified as the 3' third of the gene.
Development of targeted therapy for a broad spectrum of cancers (pancreatic cancer, ovarian cancer, glioblastoma and HCC) mediated by a double promoter plasmid expressing diphtheria toxin under the control of H19 and IGF2-P4 regulatory sequences. (2012)

Our findings show that administration of H19-DTA-P4-DTA has the potential to reach tumor cells, deliver its intracellular toxin without targeting normal tissues, and thus may help reduce tumor burden, improve the quality of life of the patient; and prolong their life span. As H19 and IGF2 were expressed in a broad spectrum of different cancers, therefore we propose a double promoter expression approach for treating a variety of tumors expressing H19, IGF2, or both. According to this approach patients may be treated with a single double promoter expression toxin vector which is under the control of the IGF2 and H19 regulatory sequences, differentially expressed in those cancers. As majority of the tumor cells express H19, IGF2, or both, therefore the use of prerequisite diagnostic test will be unnecessary.
Heterocyclic Compounds That Inhibit Rev-RRE Function and Human Immunodeficiency Virus Type 1 Replication (2008)

A cell-based screening assay was performed to identify compounds that inhibited the postintegration stage of the human immunodeficiency virus (HIV) life cycle. This assay utilized a cell line that contains the HIV gag and pol genes expressed in a Rev-dependent fashion. The cell line produces about 10 to 15 ng of p24 per milliliter of medium over a 24-h period in the form of viruslike particles. Any compound that inhibits a postintegration step in the HIV life cycle scores in this assay by decreasing particle production. Forty thousand compounds were screened, and 192 compounds were selected from the original screen because they showed more than 50% inhibition at a 10 muM concentration. The cumulative evidence presented in this study strongly suggests that 2 of the 192 compounds work as inhibitors of HIV Rev function. This was determined by a variety of cell-based assays, although the compounds do not interfere with Rev-RRE (Rev response element) binding in vitro. Both compounds inhibit replication of the lab isolate NL4-3 as well as an HIV primary isolate from Brazil (93BR021) and thus are promising leads as therapeutic candidates that target HIV replication through inhibition of Rev function.
Reaction Kinetics of the Formation of Poly(oxymethylene) Dimethyl Ethers from Formaldehyde and Methanol in Aqueous Solutions (2015)

Poly(oxymethylene) dimethyl ethers (OME) are attractive oxygenated fuel additives and physical solvents for the absorption of carbon dioxide. This works studies the synthesis of OME from formaldehyde and methanol in aqueous solutions. The reaction kinetics of OME formation is studied experimentally in a stirred batch reactor on a laboratory scale using the heterogeneous catalyst Amberlyst 46. The influences of the ratio of formaldehyde to methanol, the amount of water, and the temperature (303.15–363.15 K) are investigated. A model of the reaction kinetics is developed that differentiates two competing reaction mechanisms. The model explicitly accounts for the intermediates poly(oxymethylene) hemiformals and poly(oxymethylene) glycols.
Production and characterization of eggs from hens with ovomucoid gene mutation (2020)

Ovomucoid is a major egg white protein which is considered as the most dominant allergen in chicken eggs. Owing to the difficulty of separating ovomucoid from egg whites, researchers have adopted genetic deletion for development of hypoallergenic eggs. Previously, we used CRISPR/Cas9 to establish chickens with ovomucoid gene (OVM) mutations, but it remained unknown whether such hens could produce eggs at maturity. Here, we have reported on eggs laid by OVM-targeted hens. Except for watery egg whites, the eggs had no evident abnormalities. Real-time PCR revealed alternative splicing of OVM mRNA in hens, but their expression was limited. Immunoblotting detected neither mature ovomucoid nor ovomucoid-truncated splicing variants in egg whites. Sixteen chicks hatched from 28 fertilized eggs laid by OVM-targeted hens, and fourteen of the sixteen chicks demonstrated healthy growth. Taken together, our results demonstrated that OVM knockout could almost completely eliminate ovomucoid from eggs, without abolishing fertility. Thus, the eggs developed in this study have potential as a hypoallergenic food source for most patients with egg allergies.
Surface drawing (1999)

We present Surface Drawing, a medium which provides direct control over the creation of a wide range of intricate shapes. Surface Drawing addresses several key issues in creative expression and perceptual thinking by providing a direct link between the motions of the hand and the forging of shapes. Surfaces are created by moving a hand, instrumented with a special glove, through space in a semi-immersive 3D display and interaction environment (the Responsive Workbench). This technique allows both novices and experts to create intricate forms without the perceptual constraints of a rigid mathematical structure, large toolset, or a reduction of modeling to editing. In Surface Drawing the design space can be freely explored during the modeling process without the need to plan the construction of the final shape. In particular it supports unconstrained erasing and buildup of new geometry. This is achieved through the use of a novel incremental construction method for triangulated meshes, the Cookie Cutter algorithm. It allows the user to freely grow, join, and erase surfaces based on hand motions. We report on our experiences with the system and present results created by artists and designers exploring problems in industrial design, character design, and fine art.
Joint Power Optimization for Device-to-Device Communication in Cellular Networks With Interference Control (2017)

For device-to-device (D2D) communication under laid in a cellular network with uplink resource sharing, both cellular and D2D pairs may cause significant inter-cell interference (ICI) at a neighboring base station (BS). In this paper, under optimal BS receive beamforming, we jointly optimize the power of a cellular user (CU) and a D2D pair for their sum rate maximization, while satisfying minimum SINR requirements and worst-case ICI limit in multiple neighboring cells. We solve this non-convex joint optimization problem in two steps. First, the necessary and sufficient condition for the D2D admissibility under given constraints is obtained. Finally, we consider joint power control of the CU and D2D transmitters. We propose a power control algorithm to maximize the sum rate. Depending on the severity of ICI that D2D and CU may cause, we categorize the feasible solution region into five cases, each of which may further include several scenarios based on minimum SINR requirements. The proposed algorithm is optimal when ICI to a single neighboring cell is considered. For multiple neighboring cells, we provide an upper bound on the performance loss by the proposed algorithm and conditions for its optimality. We further extend our consideration to the scenario of multiple CUs and D2D pairs, and formulate the joint power control and CU-D2D matching problem. We show how our proposed solution for one CU and one D2D pair can be utilized to solve this general joint optimization problem. Simulation demonstrates the effectiveness of our power control algorithm and the nearly optimal performance of the proposed approach in the setting of multiple CUs and D2D pairs.
A cost-effective synthesis of heteroatom-doped porous carbons as efficient CO<sub>2</sub> sorbents (2016)

Heteroatom-doped porous carbons are generated through a one-step synthesis (including salt formation, carbonization and activation) using an organic monomer as the precursor.
Analysis of segmented-cladding fiber by the radial-effective-index method (2004)

A segmented-cladding fiber consists of a uniform core of high refractive index and a cladding with regions of high and low refractive index alternating angularly. This type of fiber provides an effective approach for achieving widely extended single-mode operation with a large core size. We analyze the fiber in detail by the radial-effective-index method, which replaces the fiber with an effective circular fiber. The accuracy of the method is confirmed by comparison with results obtained from the finite-element method. By applying the transverse-matrix method to the effective fiber, the leakage losses of the first two modes of the fiber are calculated. These then form the basis for discussion of the single-mode operation of the fiber. The analysis elucidates not only the physics of the fiber, but also the dependence of the performance of the fiber on various fiber parameters. With illustrations, we demonstrate the possibility of designing an ultralarge-core, segmented-cladding fiber that is single moded over the entire S+C+L band. The fiber should be able to suppress nonlinear optical effects and therefore prove useful for broadband optical communication employing dense-wavelength-division multiplexing.
Molecular Recognition of Methyl α-<scp>d</scp>-Mannopyranoside by Antifreeze (Glyco)Proteins (2014)

Antifreeze proteins and glycoproteins [AF(G)Ps] have been well-known for more than three decades for their ability to inhibit the growth and recrystallization of ice through binding to specific ice crystal faces, and they show remarkable structural compatibility with specific ice crystal faces. Here, we show that the crystal growth faces of methyl α-D-mannopyranoside (MDM), a representative pyranose sugar, also show noteworthy structural compatibility with the known periodicities of AF(G)Ps. We selected fish AFGPs (AFGP8, AFGP1-5), and a beetle AFP (DAFP1) with increasing antifreeze activity as potential additives for controlling MDM crystal growth. Similar to their effects on ice growth, the AF(G)Ps can inhibit MDM crystal growth and recrystallization, and more significantly, the effectiveness for the AF(G)Ps are well correlated with their antifreeze activity. MDM crystals grown in the presence of AF(G)Ps are smaller and have better defined shapes and are of higher quality as indicated by single crystal X-ray diffraction and polarized microscopy than control crystals, but no new polymorphs of MDM were identified by single crystal X-ray diffraction, solid-state NMR, and attenuated total reflectance infrared spectroscopy. The observed changes in the average sizes of the MDM crystals can be related to the changes in the number of the MDM nuclei in the presence of the AF(G)Ps. The critical free energy change differences of the MDM nucleation in the absence and presence of the additives were calculated. These values are close to those of the ice nucleation in the presence of AF(G)Ps suggesting similar interactions are involved in the molecular recognition of MDM by the AF(G)Ps. To our knowledge this is the first report where AF(G)Ps have been used to control crystal growth of carbohydrates and on AFGPs controlling non-ice-like crystals. Our finding suggests MDM might be a possible alternative to ice for studying the detailed mechanism of AF(G)P-crystal interactions. The relationships between AF(G)Ps and carbohydrate binding proteins are also discussed. The structural compatibility between AF(G)Ps and growing crystal faces demonstrated herein adds to the repertoire of molecular recognition by AF(G)Ps, which may have potential applications in the sugar, food, pharmaceutical, and materials industries.
Potential Serological Biomarkers of Cerebral Malaria (2011)

Biomarkers have been used to diagnose and prognosticate the progress and outcome of many chronic diseases such as neoplastic and non communicable diseases. However, only recently did the field of malaria research move in the direction of actively identifying biomarkers that can accurately discriminate the severe forms of malaria. Malaria continues to be a deadly disease, killing close to a million people (mostly children) every year. One life-threatening complication of malaria is cerebral malaria (CM). Studies carried out in Africa have demonstrated that even with the best treatment, as high as 15–30% of CM patients die and about 10–24% of CM survivors suffer short-or long-term neurological impairment. The transition from mild malaria to CM can be sudden and requires immediate intervention. Currently, there is no biological test available to confirm the diagnosis of CM and its complications. It is hoped that development of biomarkers to identify CM patients and potential risk for adverse outcomes would greatly enhance better intervention and clinical management to improve the outcomes. We review here what is currently known regarding biomarkers for CM outcomes. A Pub Med literature search was performed using the following search terms: “malaria,” “cerebral malaria,” “biomarkers,” “mortality” and “neurological sequelae.” This search revealed a paucity of usable biomarkers for CM management. We propose three main areas in which researchers can attempt to identify CM biomarkers: 1) early biomarkers, 2) diagnostic biomarkers and 3) prognostic biomarkers.
<title>Fabrication of square spiral photonic crystals by glancing angle deposition</title> (2002)

Using Glancing Angle Deposition, a novel thin film deposition technique, it is possible to fabricate complex, periodic structures suited for applications in photonic band gap crystals. In comparison to complex lithography processes used to produce conventional structures on the scale of several nanometers, GLAD is ideally suited to a virtual single step deposition, producing a novel tetragonal square spiral crystal structure and having a large predicted band gap of up to 15%.
Predicting Lexical Answer Types in Open Domain QA (2012)

Automatic open-domain Question Answering has been a long standing research challenge in the AI community. IBM Research undertook this challenge with the design of the DeepQA architecture and the implementation of Watson. This paper addresses a specific subtask of Deep QA, consisting of predicting the Lexical Answer Type (LAT) of a question. Our approach is completely unsupervised and is based on PRISMATIC, a large-scale lexical knowledge base automatically extracted from a Web corpus. Experiments on the Jeopardy! data shows that it is possible to correctly predict the LAT in a substantial number of questions. This approach can be used for general purpose knowledge acquisition tasks such as frame induction from text.