gebhart/patrepeval huggingface dataset:
The Ibd1 Locus for Susceptibility To Crohnʼs Disease Has A Greater Impact in Ashkenazi Jews With Early Onset Disease (2001)

The IBD1 gene plays a greater role in conferring susceptibility to CD in Jews with early onset disease than in Jews with late onset disease.
Poxviruses and Immune Evasion (2003)

Large DNA viruses defend against hostile assault executed by the host immune system by producing an array of gene products that systematically sabotage key components of the inflammatory response. Poxviruses target many of the primary mediators of innate immunity including interferons, tumor necrosis factors, interleukins, complement, and chemokines. Poxviruses also manipulate a variety of intracellular signal transduction pathways such as the apoptotic response. Many of the poxvirus genes that disrupt these pathways have been hijacked directly from the host immune system, while others have demonstrated no clear resemblance to any known host genes. Nonetheless, the immunological targets and the diversity of strategies used by poxviruses to disrupt these host pathways have provided important insights into diverse aspects of immunology, virology, and inflammation. Furthermore, because of their anti-inflammatory nature, many of these poxvirus proteins hold promise as potential therapeutic agents for acute or chronic inflammatory conditions.
Nucleoside syntheses, XXV1) A new simplified nucleoside synthesis (1981)

Abstract The several steps of the Friedel‐Crafts catalyzed silyl‐Hilbert‐Johnson nucleoside synthesis ‐ silylation of the heterocyclic base, silylation of the perfluorosulfonic acids or its salts (if SnCl 4 is not used as catalyst) and finally the nucleoside synthesis itself ‐ can be combined to a simple one‐step/one‐pot reaction which generally affords nucleosides in high yields.
A Wide-Band Parallel-Connected Balun (1970)

It is pointed out that parallel-connected baluns (4:1 impedance transformation) have approximately four times the operating bandwidth of series-connected baluns (1:1 impedance transformation). The simple theory of uncompensated resonant baluns is discussed, and design curves are presented which may be used to design any balun of this type. Experimental results are given on one type of parallel-connected balun showing it capable of a 25:1 operating bandwidth as predicted by theory. Operating over this bandwidth, the balun is only /spl lambda/ / 25 in length at the lower band-edge frequency. Because of its 4:1 impedance transformation, the balun should be very useful in the feeding of frequency-independent antennas with high impedance, such as the conical spiral.
Retinoids and related compounds. Part 26. Synthesis of (11Z)-8,18-propano- and methano-retinals and conformational study of the rhodopsin chromophore† (2001)

In order to clarify the conformation of the chromophore in rhodopsin, especially the effect of the torsional angle around the C6–C7 single bond on the CD spectrum, 8,18-propano- and methano-retinal 4 and 5 were prepared via the palladium-catalyzed coupling reaction of vinyl triflates derived from bicyclic ketones 10 and 27 with methyl (E)-3-(trimethylstannyl)but-2-enoate. In a binding experiment with bovine opsin, retinal analogs 4 and 5 afforded the new rhodopsin analogs. Although the opsin shifts of these pigments were similar to that of the native rhodopsin, CD spectra exhibited the characteristic feature owing to the locked structures of retinal analogs. This fact strongly indicates that the CD spectra were significantly influenced by the torsional angles around the 6–7 and 8–9 single bonds of the chromophore in the protein.
A 100 Mb/s BiCMOS adaptive pulse-shaping filter (1995)

With the growing demand for high-speed transmission of digital data, there is a challenge for utilizing the existing copper plant as the transmission medium, especially for short-hop links. This medium offers a lower cost to a fiber medium, but requires more sophisticated electronics to account for electromagnetic emissions, cross-talk, and cable loss. These include pulse shaping filters, cross-talk cancelers, and equalizers. To maintain system cost at a minimum, analog solutions are preferred. A continuous-time tunable biquad implemented in a 0.8 /spl mu/m BiCMOS process and configured as an adaptive pulse-shaping filter is described. The biquad is tunable over the range 10-230 MHz with variable Q factors. It is composed of five transconductance-C integrators each dissipating a static power of 10 mW at 5 V. A method for adapting the filter's pole-frequency and Q-factor while servicing 100 Mb/s NRZ data is presented together with experimental results.
Carbon nanotubes – becoming clean (2006)

Carbon nanotubes (CNTs) are now well into their teenage years. Early on, theoretical predictions and experimental data showed that CNTs possess chemical and mechanical properties that exceed those of many other materials. This has triggered intense research into CNTs. A variety of production methods for CNTs have been developed; chemical modification, functionalization, filling, and doping have been achieved; and manipulation, separation, and characterization of individual CNTs is now possible. Today, products containing CNTs range from tennis rackets and golf clubs to vehicle fenders, X-ray tubes, and Li ion batteries. Breakthroughs for CNT-based technologies are anticipated in the areas of nanoelectronics, biotechnology, and materials science. In this article, I review the current situation in CNT production and highlight the importance of clean CNT material for the success of future applications.
c-MYC Generates Repair Errors via Increased Transcription of Alternative-NHEJ Factors, LIG3 and PARP1, in Tyrosine Kinase–Activated Leukemias (2015)

In the context of TK-activated leukemias, c-MYC contributes to aberrant DNA repair through downstream targets LIG3 and PARP1, which represent viable and attractive therapeutic targets.
HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time (1996)

A new mathematical model was used to analyze a detailed set of human immunodeficiency virus-type 1 (HIV-1) viral load data collected from five infected individuals after the administration of a potent inhibitor of HIV-1 protease. Productively infected cells were estimated to have, on average, a life-span of 2.2 days (half-life t 1/2 = 1.6 days), and plasma virions were estimated to have a mean life-span of 0.3 days (t 1/2 = 0.24 days). The estimated average total HIV-1 production was 10.3 x 10(9) virions per day, which is substantially greater than previous minimum estimates. The results also suggest that the minimum duration of the HIV-1 life cycle in vivo is 1.2 days on average, and that the average HIV-1 generation time--defined as the time from release of a virion until it infects another cell and causes the release of a new generation of viral particles--is 2.6 days. These findings on viral dynamics provide not only a kinetic picture of HIV-1 pathogenesis, but also theoretical principles to guide the development of treatment strategies.
A novel method to prepare L-Arabinose from xylose mother liquor by yeast-mediated biopurification (2011)

Yeast-mediated biopurification provides a dynamic method to prepare high purity of L-arabinose from the feedstock solution xylose mother liquor, with cost-effective and high-performance properties.
Substituent effects on the kinetics of reductively-initiated fragmentation of nitrobenzyl carbamates designed as triggers for bioreductive prodrugs (1999)

4-Nitrobenzyl carbamates are of interest as triggers for bioreductive drugs, particularly in conjunction with the E. coli B nitroreductase, which efficiently reduces them to the corresponding hydroxylamines. These then fragment to release highly toxic amine-based toxins. While many 4-nitrobenzyl carbamate derivatives have been evaluated as bioreductive drugs, there has been no systematic study of substituent effects on the rate of this fragmentation (which should be as fast as possible following reduction). We therefore prepared a series of 2-, 3- and α-substituted 4-[N-methyl-N-(4-nitrobenzyloxycarbonyl)amino]phenylacetamides as model compounds to study these effects. The majority of the carbamates were prepared by in situ formation of the chloroformate of the appropriate 4-nitrobenzyl alcohol and reaction with methyl 4-(methylamino)phenylacetate, followed by ester hydrolysis and 1,1′-carbonyldiimidazole (CDI) mediated coupling with N,N-dimethylaminoethylamine. The hydroxylamines were generated by 60Co γ-ray irradiation of the nitro compounds in aqueous phosphate-buffered-propan-2-ol. The reactions were analysed by reverse-phase HPLC to determine the maximum half-life (Mt1/2) of the hydroxylamines generated, and the extent of release of amine from these after 10 half-lives (t∞). The parent (unsubstituted) hydroxylaminobenzyl carbamate had a Mt1/2 of 16 min under these conditions, while that of the corresponding α-methyl analogue was 9.5 min. Electron-donating substituents on the benzyl ring also accelerated fragmentation, with the data being fitted to the equation log(Mt1/2) = 0.57σ + 1.30, where σ represents σpfor 2-substituents and σm for 3-substituents. The acceleration of fragmentation of the hydroxylamines with increasing substituent electron-donation is consistent with the proposed mechanism, and is presumably due to stabilisation of the developing positive charge on the benzylic carbon. The extent of release of amine (t∞) also increased with increasing substituent electron-donation. These data suggest that the standard 4-nitrobenzyl carbamate trigger for nitroreductase enzyme (NTR) prodrugs can likely be improved on, by increasing the rate of fragmentation by the use of α-methyl and/or electron-donating benzyl substituents.
Antiangiogenic agents increase breast cancer stem cells via the generation of tumor hypoxia (2012)

Antiangiogenic therapy has been thought to hold significant potential for the treatment of cancer. However, the efficacy of such treatments, especially in breast cancer patients, has been called into question, as recent clinical trials reveal only limited effectiveness of antiangiogenic agents in prolonging patient survival. New research using preclinical models further suggests that antiangiogenic agents actually increase invasive and metastatic properties of breast cancer cells. We demonstrate that by generating intratumoral hypoxia in human breast cancer xenografts, the antiangiogenic agents sunitinib and bevacizumab increase the population of cancer stem cells. In vitro studies revealed that hypoxia-driven stem/progenitor cell enrichment is primarily mediated by hypoxia-inducible factor 1α. We further show that the Akt/β-catenin cancer stem cell regulatory pathway is activated in breast cancer cells under hypoxic conditions in vitro and in sunitinib-treated mouse xenografts. These studies demonstrate that hypoxia-driven cancer stem cell stimulation limits the effectiveness of antiangiogenic agents, and suggest that to improve patient outcome, these agents might have to be combined with cancer stem cell-targeting drugs.
Terpenoids as potential chemopreventive and therapeutic agents in liver cancer (2011)

Despite significant advances in medicine, liver cancer, predominantly hepatocellular carcinoma remains a major cause of death in the United States as well as the rest of the world. As limited treatment options are currently available to patients with liver cancer, novel preventive control and effective therapeutic approaches are considered to be reasonable and decisive measures to combat this disease. Several naturally occurring dietary and non-dietary phytochemicals have shown enormous potential in the prevention and treatment of several cancers, especially those of the gastrointestinal tract. Terpenoids, the largest group of phytochemicals, traditionally used for medicinal purposes in India and China, are currently being explored as anticancer agents in clinical trials. Terpenoids (also called "isoprenoids") are secondary metabolites occurring in most organisms, particularly plants. More than 40 000 individual terpenoids are known to exist in nature with new compounds being discovered every year. A large number of terpenoids exhibit cytotoxicity against a variety of tumor cells and cancer preventive as well as anticancer efficacy in preclinical animal models. This review critically examines the potential role of naturally occurring terpenoids, from diverse origins, in the chemoprevention and treatment of liver tumors. Both in vitro and in vivo effects of these agents and related cellular and molecular mechanisms are highlighted. Potential challenges and future directions involved in the advancement of these promising natural compounds in the chemoprevention and therapy of human liver cancer are also discussed.
Inhibition of bone resorption in vitro and prevention of ovariectomy-induced bone loss in vivo by flurbiprofen nitroxybutylester (HCT1026) (2001)

These data indicate that HCT1026 is a potent inhibitor of bone resorption in vitro and protects against ovariectomy-induced bone loss in vivo by a novel mechanism that appears to be distinct from its NO donor properties and from its inhibitory effects on COX activity. We conclude that HCT1026 may be of clinical value in the prevention and treatment of inflammatory diseases such as rheumatoid arthritis, which are characterized by joint inflammation as well as periarticular and systemic bone loss.
The Role of Aquaporins and Membrane Damage in Chilling and Hydrogen Peroxide Induced Changes in the Hydraulic Conductance of Maize Roots (2004)

When chilling-sensitive plants are chilled, root hydraulic conductance (L(o)) declines precipitously; L(o) also declines in chilling-tolerant plants, but it subsequently recovers, whereas in chilling-sensitive plants it does not. As a result, the chilling-sensitive plants dry out and may die. Using a chilling-sensitive and a chilling-tolerant maize genotype we investigated the effect of chilling on L(o), and its relationship to osmotic water permeability of isolated root cortex protoplasts, aquaporin gene expression, aquaporin abundance, and aquaporin phosphorylation, hydrogen peroxide (H(2)O(2)) accumulation in the roots and electrolyte leakage from the roots. Because chilling can cause H(2)O(2) accumulation we also determined the effects of a short H(2)O(2) treatment of the roots and examined the same parameters. We conclude from these studies that the recovery of L(o) during chilling in the chilling-tolerant genotype is made possible by avoiding or repairing membrane damage and by a greater abundance and/or activity of aquaporins. The same changes in aquaporins take place in the chilling-sensitive genotype, but we postulate that membrane damage prevents the L(o) recovery. It appears that the aquaporin response is necessary but not sufficient to respond to chilling injury. The plant must also be able to avoid the oxidative damage that accompanies chilling.
Fused polycationic peptide mediates delivery of diphtheria toxin A chain to the cytosol in the presence of anthrax protective antigen. (1996)

The lethal factor (LF) and edema factor (EF) of anthrax toxin bind by means of their amino-terminal domains to protective antigen (PA) on the surface of toxin-sensitive cells and are translocated to the cytosol, where they act on intracellular targets. Genetically fusing the amino-terminal domain of LF (LFN; residues 1-255) to certain heterologous proteins has been shown to potentiate these proteins for PA-dependent delivery to the cytosol. We report here that short tracts of lysine, arginine, or histidine residues can also potentiate a protein for such PA-dependent delivery. Fusion of these polycationic tracts to the amino terminus of the enzymic A chain of diphtheria toxin (DTA; residues 1-193) enabled it to be translocated to the cytosol by PA and inhibit protein synthesis. The efficiency of translocation was dependent on tract length: (LFN > Lys8 > Lys6 > Lys3). Lys6 was approximately 100-fold more active than Arg6 or His6, whereas Glu6 and (SerSerGly)2 were inactive. Arg6DTA was partially degraded in cell culture, which may explain its low activity relative to that of Lys6DTA. The polycationic tracts may bind to anionic sites at the cell surface (possibly on PA), allowing the fusion proteins to be coendocytosed with PA and delivered to the endosome, where translocation to the cytosol occurs. Excess free LFN blocked the action of LFNDTA, but not of Lys6DTA. This implies that binding to the LF/EF site is not an obligatory step in translocation and suggests that the polycationic tag binds to a different site. Besides elucidating the process of translocation in anthrax toxin, these findings may aid in developing systems to deliver heterologous proteins and peptides to the cytoplasm of mammalian cells.
Current Perspectives and Future Directions (1985)

BURWELL, R. GEOFFREY M.D., F.R.C.S.; FRIEDLAENDER, GARY E. M.D.; MANKIN, HENRY J. M.D.Editor(s): MALININ, THEODORE I. M.D.; GROSS, ALLAN E. M.D. Author Information
Identification of Individual Proteins in Complex Protein Mixtures by High-Resolution, High-Mass-Accuracy MALDI TOF-Mass Spectrometry Analysis of In-Solution Thermal Denaturation/Enzymatic Digestion (2001)

Identification of individual proteins in complex protein mixtures by high-resolution (HR), high-mass-accuracy matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) is demonstrated for synthetic protein mixtures. Instead of chemical denaturation, thermal denaturation followed by in-solution trypsin digestion is used to achieve uniform digestion of the constituents of the protein mixture. Protein identification is carried out using protein database searches with search scoring systems, which seems more effective than conventional peptide mass mapping without using a scoring system. Identification of individual proteins by MALDI HR-TOF-MS peptide mass mapping dramatically reduces data acquisition/analysis time and does not require special equipment for sample preparation/transfer prior to mass spectral analysis.
MPEG-4 rate control for multiple video objects (1999)

This paper describes an algorithm which can achieve a constant bit rate when coding multiple video objects. The implementation is a nontrivial extension of the MPEG-4 rate control algorithm for single video objects which employs a quadratic rate quantizer model. The algorithm is organized into two stages: a pre- and a post-encoding stage. In the pre-encoding stage, an initial target estimate is made for each object. Based on the buffer fullness, the total target is adjusted and then distributed proportional to the relative size, motion, and variance of each object. Based on the new individual targets and rate-quantizer relation for texture, appropriate quantization parameters are calculated. After each object is encoded, the model parameters for each object are updated, and if necessary, frames are skipped to ensure that the buffer does not overflow. A preframeskip control is exercised to avoid buffer overflow when the motion and shape information occupies a significant portion of the bit budget. The rate control algorithm switches between two operation modes so that the coder can reduce the spatial coding accuracy for an improved temporal resolution. A shape-coding control mechanism is also proposed, which provides a tradeoff between texture and shape coding accuracy. Overall, the algorithm is able to successfully achieve the target bit rate, effectively code arbitrarily shaped objects, and maintain a stable buffer level. These techniques have been adopted by the MPEG committee in July 1997 as part of the video verification model (VM8).
The Graphics PARCUM* System: A 3D Memory Based Computer Architecture for Processing and Display of Solid Models (1985)

Abstract The concept of a computer architecture for processing and display of spatially ordered data is presented in this paper. The central part of the architecture is a memory cube in which the objects can be processed in their real shape as a three‐dimensional data array. The development has been rendered possible at reasonable costs through the rapid progress in the realm of VLSI‐memory technology.
CCF-LRU: a new buffer replacement algorithm for flash memory (2009)

NAND flash memory has been widely used for storage in embedded systems and recently in enterprise computing environment, owing to its shock-resistance, nonvolatile, low energy consumption, and high I/O speed. In addition, flash memory has the characteristics of not-in-place update and asymmetric I/O costs among read, write, and erase operations, in which the cost of write/erase operations is much higher than that of read operation. Hence, the buffer replacement algorithms in flash-based systems should take the asymmetric I/O costs into account. Previous solutions to this issue, such as CFLRU and LRU-WSR, used a clean-first scheme to first evict clean pages from the buffer. Although they outperform the traditional LRU policy in performance, they do not consider the access frequency of clean page, which will consequently result in poor I/O performance. In order to solve this problem, we present a new buffering algorithm in this paper, called CCF-LRU, which enhances the previous CFLRU and LRU-WSR methods by differentiating clean pages into cold and hot ones, and evicting cold clean pages first and delaying the eviction of hot clean pages. We conduct a trace-driven experiment on a flash memory simulation environment, and use six types of synthesized traces as well as a real OLTP trace. The results show that the CCF-LRU algorithm outperforms LRU, CFLRU and LRUWSR in write count and runtime in all experiments. In particular, it provides more than 20% improvement over its competitors both in write count and runtime, when running the real OLTP trace.