gebhart/patrepeval huggingface dataset:
Rational design and characterization of platelet factor 4 antagonists for the study of heparin-induced thrombocytopenia (2012)

Patients with heparin-induced thrombocytopenia (HIT) remain at risk for recurrent thromboembolic complications despite improvements in management. HIT is caused by antibodies that preferentially recognize ultralarge complexes (ULCs) of heparin and platelet factor 4 (PF4) tetramers. We demonstrated previously that a variant PF4(K50E) forms dimers but does not tetramerize or form ULCs. Here, we identified small molecules predicted to bind PF4 near the dimer-dimer interface and that interfere with PF4 tetramerization. Screening a library of small molecules in silico for binding at this site, we identified 4 compounds that inhibited tetramerization at micromolar concentrations, designated PF4 antagonists (PF4As). PF4As also inhibited formation of pathogenic ULCs, and 3 of these PF4As promoted the breakdown of preformed ULCs. To characterize the ability of PF4As to inhibit cellular activation, we developed a robust and reproducible assay that measures cellular activation by HIT antibodies via FcγRIIA using DT40 cells. PF4As inhibit FcγRIIA-dependent activation of DT40 cells by HIT antibodies as well as platelet activation, as measured by serotonin release. PF4As provide new tools to probe the pathophysiology of HIT. They also may provide insight into the development of novel, disease-specific therapeutics for the treatment of thromboembolic complications in HIT.
Identification of CD4−CD8− Double-Negative Natural Killer T Cell Precursors in the Thymus (2008)

Together, these results demonstrate that thymic DN4 fraction contains NKT cell precursors. Our findings provide new insights into the early development of NKT cells prior to surface expression of the invariant Valpha14 antigen receptor and suggest the possible alternative developmental pathway of NKT cells.
RNA-Pt Adducts Following Cisplatin Treatment ofSaccharomyces cerevisiae (2011)

The numerous regulatory roles of cellular RNAs suggest novel potential drug targets, but establishing intracellular drug-RNA interactions is challenging. Cisplatin (cis-diamminedichloridoplatinum(II)) is a leading anticancer drug that forms exchange-inert complexes with nucleic acids, allowing its distribution on cellular RNAs to be followed ex vivo. Although Pt adduct formation on DNA is well-known, a complete characterization of cellular RNA-Pt adducts has not been performed. In this study, the action of cisplatin on S. cerevisiae in minimal media was established with growth curves, clonogenic assays, and tests for apoptotic markers. Despite high toxicity, cisplatin-induced apoptosis in S. cerevisiae was not observed under these conditions. In-cell Pt concentrations and Pt accumulation on poly(A)-mRNA, rRNA, total RNA, and DNA quantified via ICP-MS indicate ∼4- to 20-fold more Pt accumulation in total cellular RNA than in DNA. Interestingly, similar Pt accumulation is observed on rRNA and total RNA, corresponding to one Pt per (14,600 ± 1,500) and (5760 ± 580) nucleotides on total RNA following 100 and 200 μM cisplatin treatments, respectively. Specific Pt adducts mapped by primer extension analysis of a solvent-accessible 18S rRNA helix occur at terminal and internal loop regions and appear as soon as 1 h post-treatment. Pt per nucleotide accumulation on poly(A)-mRNA is 4- to 6-fold lower than on rRNA but could have consequences for low copy-number or highly regulated transcripts. Taken together, these data demonstrate significant accumulation of Pt adducts on cellular RNA species following in cellulo cisplatin treatment. These and other small molecule-RNA interactions could disrupt processes regulated by RNA.
Cell-Type-Specific Repression of Internal Ribosome Entry Site Activity by Double-Stranded RNA-Binding Protein 76 (2006)

Translation of picornavirus plus-strand RNA genomes occurs via internal ribosomal entry at highly structured 5' untranslated regions. In addition to canonical translation factors, translation rate is likely influenced by supplementary host and viral trans-acting factors. We previously reported that insertion of a heterologous human rhinovirus type 2 internal ribosomal entry site (IRES) into the poliovirus (PV) genome, generating the chimeric virus PV-RIPO, selectively abrogates viral translation and propagation in neurons, which eliminate poliovirus's signature neuropathogenicity. While severely deficient in cells of neuronal lineage, the rhinovirus IRES promotes efficient propagation of PV-RIPO in cancer cells. Tumor-specific IRES function can be therapeutically exploited to direct viral cytotoxicity to cancer cells. Neuron-glioma heterokaryon analysis implicates neuronal trans-dominant inhibition in this effect, suggesting that host trans-acting factors repress IRES function in a cell-type-specific manner. We identified a set of proteins from neuronal cells with affinity for the rhinovirus IRES, including double-stranded RNA-binding protein 76 (DRBP76). DRBP76 associates with the IRES in neuronal but not in malignant glioma cells. Moreover, DRBP76 depletion in neuronal cells enhances rhinovirus IRES-driven translation and virus propagation. Our observations suggest that cell-type-specific association of DRBP76 with the rhinovirus IRES represses PV-RIPO translation and propagation in neuronal cells.
Random Mutagenesis by Error-Prone PCR (2010)

In vitro selection coupled with directed evolution represents a powerful method for generating nucleic acids and proteins with desired functional properties. Creating high-quality libraries of random sequences is an important step in this process as it allows variants of individual molecules to be generated from a single-parent sequence. These libraries are then screened for individual molecules with interesting, and sometimes very rare, phenotypes. Here, we describe a general method to introduce random nucleotide mutations into a parent sequence that takes advantage of the polymerase chain reaction (PCR). This protocol reduces mutational bias often associated with error-prone PCR methods and allows the experimenter to control the degree of mutagenesis by controlling the number of gene-doubling events that occur in the PCR reaction. The error-prone PCR method described here was used to optimize a de novo evolved protein for improved folding stability, solubility, and ligand-binding affinity.
Detection of Human Cytomegalovirus in Peripheral Blood Lymphocytes in a Natural Infection (1985)

In situ hybridization was used to detect human cytomegalovirus (HCMV) in the peripheral blood mononuclear cells of some naturally infected (seropositive) individuals. A subpopulation of cells hybridized specifically to a portion of the HCMV genome that is heavily transcribed during the immediate-early period of infection. The hybridization signal was markedly reduced by base hydrolysis and ribonuclease, and therefore the probe appears to be detecting viral RNA. A fluorescence-activated cell sorter was used to select lymphocytes bearing the OKT4 and OKT8 markers. Hybridization with the HCMV probe revealed a higher proportion of positive cells in the OKT4 than in the OKT8 subset. This observation specifically identifies lymphocytes as a cell population involved in natural HCMV infection and suggests that lymphocytes may be a reservoir for maintaining infection and may also serve as a vehicle for its spread by blood transfusion.
Synthesis of Protein-Loaded Hydrogel Particles in an Aqueous Two-Phase System for Coincident Antigen and CpG Oligonucleotide Delivery to Antigen-Presenting Cells (2005)

Materials that effectively deliver protein antigens together with activating ligands to antigen-presenting cells are sought for improved nonviral vaccines. To this end, we synthesized protein-loaded poly(ethylene glycol) (PEG)-based hydrogel particles by cross-linking PEG within the polymer-rich phase of an emulsion formed by a poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) triblock copolymer in saturated aqueous salt solution. These particles (500-nm diameter) contained high levels of encapsulated protein (approximately 75% of dry mass), which was selectively released by proteolytic enzymes normally present in the phagosomal/endosomal compartments of dendritic cells (DCs). For co-delivery of cellular activation signals, gel particles were surface-modified by sequential adsorption of poly(l-arginine) and CpG oligonucleotides. DCs pulsed with protein-loaded particles activated naïve T cells in vitro approximately 10-fold more efficiently than DCs incubated with soluble protein. This organic solvent-free strategy for protein encapsulation within submicron-sized hydrophilic particles is attractive for macromolecule delivery to a variety of phagocytic and nonphagocytic cells.
Caches and Merkle Trees for Efficient Memory Authentication (1996)

We describe a hardware scheme to authenticate all or a part of untrusted external memory using trusted on-chip storage. Our scheme uses Merkle trees and caches to efficiently authenticate memory. Proper placement of Merkle tree checking and generation is critical to ensure good performance. Naïve schemes where the Merkle tree machinery is placed between caches can result in a large increase in memory bandwidth usage. We integrate the Merkle tree machinery with one of the cache levels to significantly reduce memory bandwidth requirements. We present an evaluation of the area and performance costs of various schemes using simulation. For most benchmarks, the performance overhead of authentication using our integrated Merkle tree/caching scheme is less than 25%, whereas the overhead of authentication for a naïve scheme can be as large as 10×. We explore tradeoffs between external memory overhead and processor performance.
Hydration of Lysozyme Studied by Raman Spectroscopy (2013)

Hydration plays a fundamental role in maintaining the three-dimensional structure and function of proteins. In this study, Raman spectroscopy was used to probe the hydration induced structural changes at various sites of lysozyme under isothermal conditions in the range of water contents from 0 to 44 wt %. Raman hydration curves were constructed from detailed analysis of marker bands. Transition inflection points (w(m)) and onsets determined from the hydration curves have shown that structural changes start at 7-10 and end at about 35 wt % water. The onset of structural changes coincides with the onset of the broad glass transition earlier observed in this system. The increase of α-helix content starts at very low concentrations of water with w(m) = 12 wt %. Monitoring the development of importance for enzymatic action hydrophobic clusters has revealed wm = 15 wt % and completion of the process at 25 wt %. The parameters of 621 cm(-1) (Phe) and 1448 cm(-1) (CH2 bending) modes were found to be sensitive to hydration, suggesting changes in organization of water molecules near the protein surface. The native structure of lysozyme was achieved at 35 wt % water where its content is high enough for filling the space between lysozyme molecules.
Immuno-PCR with a Commercially Available Avidin System (1993)

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Electrohydrodynamic Jet Processing: An Advanced Electric‐Field‐Driven Jetting Phenomenon for Processing Living Cells (2005)

Spraying live cells in suspension: The electrohydrodynamic jet, driven by high-intensity electric fields, can be exploited for processing living cells (see setup in the Figure). No adverse effects on the living cells have been observed when they are processed with this technique. This technology is not hampered by the disadvantages encountered with inkjets and can process concentrated biological suspensions containing living cells.
Quantitative Microwave Imaging of Realistic Numerical Breast Phantoms Using an Enclosed Array of Multiband, Miniaturized Patch Antennas (2012)

We present a 3-D microwave breast imaging study in which we reconstruct the dielectric profiles of MRI-derived numerical breast phantoms from simulated array measurements using an enclosed array of multiband, miniaturized patch antennas. The array is designed to overcome challenges relating to the ill-posed nature of the inverse scattering system. We use a multifrequency formulation of the distorted Born iterative method to image four normal-tissue breast phantoms, each corresponding to a different density class. The reconstructed fibroglandular distributions are very faithful to the true distributions in location and basic shape. These results establish the feasibility of using an enclosed array of miniaturized, multiband patch antennas for quantitative microwave breast imaging.
New human chromosomal safe harbor sites for genome engineering with CRISPR/Cas9, TAL effector and homing endonucleases (2018)

Abstract Safe Harbor Sites (SHS) are genomic locations where new genes or genetic elements can be introduced without disrupting the expression or regulation of adjacent genes. We have identified 35 potential new human SHS in order to substantially expand SHS options beyond the three widely used canonical human SHS, AAVS1, CCR5 and hROSA26 . All 35 potential new human SHS and the three canonical sites were assessed for SHS potential using 9 different criteria weighted to emphasize safety that were broader and more genomics-based than previous efforts to assess SHS potential. We then systematically compared and rank-ordered our 35 new sites and the widely used human AAVS1, hROSA26 and CCR5 sites, then experimentally validated a subset of the highly ranked new SHS together versus the canonical AAVS1 site. These characterizations included in vitro and in vivo cleavage-sensitivity tests; the assessment of population-level sequence variants that might confound SHS targeting or use for genome engineering; homology–dependent and –independent, SHS-targeted transgene integration in different human cell lines; and comparative transgene integration efficiencies at two new SHS versus the canonical AAVS1 site. Stable expression and function of new SHS-integrated transgenes were demonstrated for transgene-encoded fluorescent proteins, selection cassettes and Cas9 variants including a transcription transactivator protein that were shown to drive large deletions in a PAX3/FOXO1 fusion oncogene and induce expression of the MYF5 gene that is normally silent in human rhabdomyosarcoma cells. We also developed a SHS genome engineering ‘toolkit’ to enable facile use of the most extensively characterized of our new human SHS located on chromosome 4p. We anticipate our newly identified human SHS, located on 16 chromosomes including both arms of the human X chromosome, will be useful in enabling a wide range of basic and more clinically-oriented human gene editing and engineering.
Arthroscopic Fixation Devices (2006)

Abstract Arthroscopic fixation devices enable surgeons to repair ligament and tendon damage at the joints of the body without creating larger incisions or tissue retractions for access to the repair site. Until recently, surgical procedures, such as anterior cruciate ligament (ACL) and meniscal repair in the knee and rotator cuff repair in the shoulder, were done exclusively through large incisions, which was necessary to allow a surgeon's fingers to reach the repair site. Visualization instruments such as the arthroscope provide a window into the joint for diagnostic and visual guidance purposes. Small suture anchors and tissue anchors and their associated insertion and access instruments used under arthroscopic visualization now make it possible for the same procedures to be done through 10‐mm diameter and smaller access portals. The development of novel materials such as absorbable copolymers along with continued innovation in design will continue to provide the surgeon and the patient with better and better solutions, expanding the number of procedures and their efficacy in the challenging area of arthroscopic surgery.
Woodchuck hepatitis virus surface antigen induces nitric oxide synthesis in hepatocytes: possible role in hepatocarcinogenesis (1994)

Woodchuck hepatitis virus surface antigen (WHsAg) stimulated hepatocytes in culture to produce nitric oxide (NO.), as evidenced by the accumulation of nitrite in the medium. NO. synthesis by hepatocytes was positively correlated with WHsAg concentration. WHsAg-induced NO. synthesis was inhibited by NG-monomethyl-L-arginine and anti-WHsAg antibody. To our knowledge, this is the first demonstration of an increase in NO. formation by a viral antigen. These data, when considered in the light of the known genotoxicity of NO., raise the possibility that viral hepatitis increases the risk of liver cancer by increasing the production of NO.. Long-term elevated production of NO. free radicals due to stimulation by WHsAg in chronic hepatitis may directly cause reactions with cellular DNA leading to mutagenesis, as well as the formation of hepatocarcinogenic N-nitroso compounds. This provides a new mechanism by which hepatitis B virus infection might hypothetically increase the risk of liver cancer.
Therapeutic Nanomedicine for Brain Cancer (2013)

Malignant brain cancer treatment is limited by a number of barriers, including the blood-brain barrier, transport within the brain interstitium, difficulties in delivering therapeutics specifically to tumor cells, the highly invasive quality of gliomas and drug resistance. As a result, the prognosis for patients with high-grade gliomas is poor and has improved little in recent years. Nanomedicine approaches have been developed in the laboratory, with some technologies being translated to the clinic, in order to address these needs. This review discusses the obstacles to effective treatment that are currently faced in the field, as well as various nanomedicine techniques that have been used or are being explored to overcome them, with a focus on liposomal and polymeric nanoparticles.
Reversible inhibition by retinoids of 3-methylcholanthrene-induced neoplastic transformation in C3H/10T1/2 clone 8 cells. (1979)

Abstract Several investigators have recently shown that retinoids inhibit chemically induced carcinomas in vivo and may be important in the prevention of the development of cancer. Studies were initiated using cultured C3H/10T½ clone 8 cells to study the effects of retinoids on 3-methylcholanthrene (MCA)-induced neoplastic transformation. At concentrations that did not affect cell survival (0.005 to 0.5 µg/ml), retinyl acetate was found to inhibit MCA-induced transformation. Complete inhibition of transformation was observed when MCA-treated cells were continuously treated with retinyl acetate (0.1 µg/ml) starting 7 days after MCA exposure (2.5 µg/ml; 24 hr). A brief exposure to retinyl acetate (0.5 µg/ml) on Days 7 to 14 after MCA caused a 70% inhibition in transformation, while delaying treatment with retinyl acetate up to 3 weeks after MCA still decreased transformation by 80%. Nontoxic concentrations of retinol and retinal were found to be approximately equal in potency to retinyl acetate. The inhibition of neoplastic transformation by retinoids was found to be fully reversible on maintaining initiated cultures for 3 to 5 weeks in drug-free medium. Growth of three established transformed C3H/10T½ clone 8 cell lines in the presence of normal cells was not inhibited by 1 µg/ml doses of retinyl acetate or retinol. Thus, in extension of the in vivo studies, we have shown that retinoids inhibit chemically induced neoplastic transformation in cultured mouse fibroblasts and, furthermore, that this inhibition is not related to toxicity. The results of this study indicate that retinoids are acting to delay the progression of preneoplastic cells to fully neoplastic cells.
ChemInform Abstract: NOVEL DIURETIC AGENTS, SYNTHESES OF SUBSTITUTED ISATYLIDENES AND 3‐ALKYL OR 3‐ARYLALKYL‐2‐OXINDOLES (1975)

Abstract Die Benzylhalogenide (I) werden über die Derivate (II) und (III) in die Nitroester (IV) übergeführt, die mit Na‐dithionit zu den Oxindolen (V) cyclisiert werden.
Characteristics of CMOS device isolation for the ULSI age (2002)

Scaling requirements for abrupt active-isolation transitions, isolation depth, and isolation planarity are discussed quantitatively. We review how LOCOS and STI isolation are being improved to meet these requirements. Independent of fabrication techniques, we see that a necessary consequence of achieving the desired narrow isolation and abrupt transitions is a discrete edge parasitic. We show that the edge parasitic can be distinguished from the planar channel and can be characterized separately. Edge device sensitivities are investigated with experiment and simulation to show that design and process control of the discrete edge parasitic will be a significant thrust of device engineering for future isolation technologies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Speaker identification based text to audio alignment for an audio retrieval system (2002)

We report on an audio retrieval system which lets Internet users efficiently access a large audio database containing recordings of the proceedings of the United States House of Representatives. The audio has been temporally aligned to text transcripts of the proceedings (which are manually generated by the US Government) using a novel method based on speaker identification. Speaker sequence and approximate timing information is extracted from the text transcript and used to constrain a Viterbi alignment of speaker models to the observed audio. Speakers are modeled by computing Gaussian statistics of cepstral coefficients extracted from samples of each person's speech. The speaker identification is used to locate speaker transition points in the audio which are then linked to corresponding speaker transitions in the text transcript. The alignment system has been successfully integrated into a World Wide Web based search and browse system as an experimental service on the Internet.
Iterative decoding of binary block and convolutional codes (1996)

Iterative decoding of two-dimensional systematic convolutional codes has been termed "turbo" (de)coding. Using log-likelihood algebra, we show that any decoder can be used which accepts soft inputs-including a priori values-and delivers soft outputs that can be split into three terms: the soft channel and a priori inputs, and the extrinsic value. The extrinsic value is used as an a priori value for the next iteration. Decoding algorithms in the log-likelihood domain are given not only for convolutional codes but also for any linear binary systematic block code. The iteration is controlled by a stop criterion derived from cross entropy, which results in a minimal number of iterations. Optimal and suboptimal decoders with reduced complexity are presented. Simulation results show that very simple component codes are sufficient, block codes are appropriate for high rates and convolutional codes for lower rates less than 2/3. Any combination of block and convolutional component codes is possible. Several interleaving techniques are described. At a bit error rate (BER) of 10/sup -4/ the performance is slightly above or around the bounds given by the cutoff rate for reasonably simple block/convolutional component codes, interleaver sizes less than 1000 and for three to six iterations.