gebhart/patrepeval huggingface dataset:
Effects of (-)-2'-deoxy-3'-thiacytidine (3TC) 5'-triphosphate on human immunodeficiency virus reverse transcriptase and mammalian DNA polymerases alpha, beta, and gamma (1992)

(-)-2'-Deoxy-3'-thiacytidine (3TC) is a selective inhibitor of human immunodeficiency virus replication in vitro (J. A. V. Coates, N. Cammack, H. J. Jenkinson, A. J. Jowett, M. I. Jowett, B. A. Pearson, C. R. Penn, P. L. Rouse, K. C. Viner, and J. M. Cameron, Antimicrob. Agents Chemother. 36:733-739, 1992). The effect of 3TC 5'-triphosphate on both the RNA-dependent and DNA-dependent activities of human immunodeficiency virus type 1 reverse transcriptase and DNA polymerases alpha, beta, and gamma from HeLa cells was investigated. 3TC 5'-triphosphate is a competitive inhibitor (with respect to dCTP) of the RNA-dependent DNA polymerase activity (apparent Ki = 10.6 +/- 1.0 to 1.24 +/- 5.1 microM, depending on the template and primer used); the DNA-dependent DNA polymerase activity is 50% inhibited by a 3TC 5'-triphosphate concentration of 23.4 +/- 2.5 microM when dCTP is present at a concentration equal to its Km value. Chain elongation studies show that 3TC 5'-triphosphate is incorporated into newly synthesized DNA and that transcription is terminated in a manner identical to that found for ddCTP. The 50% inhibitory concentrations of 3TC 5'-triphosphate against DNA polymerases alpha, beta, and gamma at concentrations of dCTP equal to the Km were 175 +/- 31, 24.8 +/- 10.9, and 43.8 +/- 16.4 microM, respectively. More detailed kinetic studies with 3TC 5'-triphosphate and DNA polymerases beta and gamma are consistent with the fact that inhibition of these enzymes by 3TC 5'-triphosphate is competitive with respect to dCTP. The values of Ki were determined to be 18.7 microM for DNA polymerase beta and 15.8 +/- 0.8 microM for DNA polymerase gamma.
Optical Resolution and Configuration of <i>cis</i>-β-Phenylglycidic Acid (1974)

Abstract Dl-cis-β-phenylglycidic acid was resolved using (−)-ephedrine. The configurations of α- and β-carbons of the resolved cis-(+)-glycidic acid were determined by oxydative and hydrogenolytic reactions.
Association of the <i>Agrobacterium</i> T-DNA–protein complex with plant nucleosomes (2008)

Agrobacterium represents the only natural example of transkingdom transfer of genetic information, from bacteria to plants. Before the bacterial transferred DNA (T-DNA) can integrate into the plant genome, it should be targeted to and bind the host chromatin. However, the T-DNA association with the host chromatin has not been demonstrated. Here, we study T-DNA binding to plant nucleosomes in vitro and show that it is mediated by bacterial and host proteins associated with the T-DNA. The main factor that determines nucleosomal binding of the T-DNA is the cellular VirE2-interacting protein 1 (VIP1), which functions as a molecular link between the T-DNA-associated bacterial virulence protein VirE2 and core histones. The presence of both VIP1 and VirE2 is required for association of the T-DNA with mononucleosomes in which the DNA molecule exists as a tripartite complex DNA-VirE2-VIP1. Furthermore, this nucleosome-associated ternary complex can bind another bacterial virulence factor, VirF, which is an F-box protein known to target both VirE2 and VIP1 for proteasomal degradation and uncoat the T-DNA.
Showdown at the RXLR motif: Serious differences of opinion in how effector proteins from filamentous eukaryotic pathogens enter plant cells (2011)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Ultimate limits of subcarrier multiplexed lightwave transmission (1991)

An analysis of the fundamental limits in SCM lightwave transmission is presented. The system studied comprises an ideal overmodulated laser transmitter with nonsymmetrical threshold clipping and a shot-noise limited receiver. The power spectral density of the nonlinear distortion noise is evaluated and the optimum modulation index mopt is determined. Results are given for the ultimate requirements for VSB-AM and FM SCM modulation formats.
Super-smooth x-ray reflection grating fabrication (1997)

Blazed, grazing incidence x-ray reflection gratings are an important component of modern high resolution spectrometers and related x-ray optics. These have traditionally been fabricated by diamond scribing in a ruling engine, or more recently by interferometric lithography followed by ion etching. These traditional methods result in gratings which suffer from a number of deficiencies, including high surface roughness and poor control of the groove profile. These deficiencies lead to poor diffraction efficiency and high levels of scattered light. We have developed a novel fabrication method for fabricating blazed x-ray reflection gratings which utilizes silicon wafers that are cut 0.7° off of the (111) plane. In solutions such as potassium hydroxide (KOH), silicon is etched in 〈111〉 directions orders of magnitude slower than in other directions, resulting in extremely smooth {111} facets. The gratings are patterned using interferometric lithography with 351.1 nm wavelength and transferred into the substrate using tri-level resist processing, reactive-ion etching (RIE), and silicon nitride masking during the KOH etch. The narrow (&lt;0.1 μm) ridge of silicon which supports the nitride mask is removed using a chromium lift-off step followed by a CF4 RIE trench etch. The result is a grating with extremely smooth blaze facets which is suitable for x-ray reflection after evaporative coating with thin Cr/Au. Atomic force microscope images confirm that fabricated gratings have less than a 0.4 nm rms roughness—much smoother than conventional gratings which have over ∼1 nm roughness. Theory predicts that reduced blaze facet roughness increases diffraction efficiency. Experiments and simulations performed at the Lawrence Berkeley Laboratory and Columbia University confirm that efficiency is increased; in fact, measured peak efficiencies reach ∼80% of calculated theoretical limits. Peak grating efficiencies were achieved that are ∼35% greater than that of the best available ruled masters of comparable design.
Characteristics and outcomes of COVID-19 in patients with HIV: a multicentre research network study (2020)

Crude COVID-19 mortality is higher in PLH; however, propensity-matched analyses revealed no difference in outcomes, showing that higher mortality is driven by higher burden of comorbidities. Early diagnosis and intensive surveillance are needed to prevent a 'Syndemic' of diseases in this vulnerable cohort.
Music, Cognition, and Computerized Sound (1999)

The first book to provide comprehensive introductory coverage of the multiple topics encompassed under psychoacoustics. How hearing works and how the brain processes sounds entering the ear to provide the listener with useful information are of great interest to psychologists, cognitive scientists, and musicians. However, while a number of books have concentrated on individual aspects of this field, known as psychoacoustics, there has been no comprehensive introductory coverage of the multiple topics encompassed under the term. Music, Cognition, and Computerized Sound is the first book to provide that coverage, and it does so via a unique and useful approach. The book begins with introductory chapters on the basic physiology and functions of the ear and auditory sections of the brain, then proceeds to discuss numerous topics associated with the study of psychoacoustics, including cognitive psychology and the physics of sound. The book has a particular emphasis on music and computerized sound. An accompanying download includes many sound examples to help explicate the text and is available with the code included in the book at http://mitpress.mit.edu/mccs. To download sound samples, you can obtain a unique access code by emailing digitalproducts-cs@mit.edu or calling 617-253-2889 or 800-207-8354 (toll-free in the U.S. and Canada).The contributing authors include John Chowning, Perry R. Cook, Brent Gillespie, Daniel J. Levitin, Max Mathews, John Pierce, and Roger Shepard.
A Subthreshold Baseband Processor Core Design With Custom Modules and Cells for Passive RFID Tags (2017)

Sophisticated subthreshold passive radio frequency identification tag's baseband processor (BBP) core design for ultralow-power Internet of Things end devices is presented in this paper. Custom logic cells and tailored logic architectures are applied to eliminate timing violations when the operating voltage is much lower than nominal level. For the consideration of limited availability of radio frequency power, power-aware scheme is applied to the key modules, including PIE decoding and command receiving. Furthermore, Galois linear feedback shift register and double-edge-triggered techniques help to improve clock efficiency and reduce the impact of frequency variation in data link portions. Importantly, a novel custom ratioed logic style is adopted in key modules to fundamentally speed up signals' propagation at ultralow-voltage. The proposed BBP was fabricated in 90-nm CMOS as well as the regular design with the same function. It was also implemented in the tag chip's fabrication. In measurement the proposed design indicates good robustness and is much more competent for subthreshold operation. It can operate below 0.3 V with power consumption below 130 nW.
Human motor cortical activity recorded with Micro-ECoG electrodes, during individual finger movements (2009)

In this study human motor cortical activity was recorded with a customized micro-ECoG grid during individual finger movements. The quality of the recorded neural signals was characterized in the frequency domain from three different perspectives: (1) coherence between neural signals recorded from different electrodes, (2) modulation of neural signals by finger movement, and (3) accuracy of finger movement decoding. It was found that, for the high frequency band (60-120 Hz), coherence between neighboring micro-ECoG electrodes was 0.3. In addition, the high frequency band showed significant modulation by finger movement both temporally and spatially, and a classification accuracy of 73% (chance level: 20%) was achieved for individual finger movement using neural signals recorded from the micro-ECoG grid. These results suggest that the micro-ECoG grid presented here offers sufficient spatial and temporal resolution for the development of minimally-invasive brain-computer interface applications.
Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks (2016)

DNA double-strand breaks (DSBs) are known to be powerful inducers of homologous recombination (HR), but single-strand breaks (nicks) have also been shown to trigger HR. Both DSB- and nick-induced HR ((nick)HR) are exploited in advanced genome-engineering approaches based on the bacterial RNA-guided nuclease Cas9. However, the mechanisms of (nick)HR are largely unexplored. Here, we applied Cas9 nickases to study (nick)HR in mammalian cells. We find that (nick)HR is unaffected by inhibition of major damage signaling kinases and that it is not suppressed by nonhomologous end-joining (NHEJ) components, arguing that nick processing does not require a DSB intermediate to trigger HR. Relative to a single nick, nicking both strands enhances HR, consistent with a DSB intermediate, even when nicks are induced up to ∼1kb apart. Accordingly, HR and NHEJ compete for repair of these paired nicks, but, surprisingly, only when 5' overhangs or blunt ends can be generated. Our study advances the understanding of molecular mechanisms driving nick and paired-nick repair in mammalian cells and clarify phenomena associated with Cas9-mediated genome editing.
Optical Properties and Microstructure of Nanocrystalline Cubic Zirconia Prepared by High‐Pressure Spark Plasma Sintering (2011)

The optical properties and microstructure are evaluated for a transparent cubic (8 mol% yttria‐stabilized) zirconia ( c ‐YSZ) prepared by high‐pressure spark plasma sintering. Oxygen vacancies and residual pores are primary defects in the present transparent c ‐YSZ, and the combination influence of these two defects determines the optical properties. The as‐sintered transparent zirconia strongly absorbs the incident light due to the formation of high concentration of oxygen vacancies. Annealing treatment in oxidizing atmosphere can improve the transparency by reducing oxygen defects. The existence of fine pores in the present zirconia causes scattering of the incident light.
Extracellular Matrix 2: Role of extracellular matrix molecules and their receptors in the nervous system (1993)

Extracellular matrix molecules help regulate many aspects of neural development, including survival, migration, axon growth, and synapse formation by neurons. These same molecules have been shown to modulate regeneration of neurons after injuries. They also regulate the development and differentiation of other neural cells, such as astroglia and Schwann cells. Significant progress has been made recently in characterizing both ECM constituents and their receptors in the nervous system. Extracellular matrix molecules promote cell adhesion, activate intracellular signaling pathways, and modulate the activities of several growth factors and proteins. Our current understanding of the extracellular matrix, its receptors, and its functions in the nervous system are discussed.
173nA-7.5ppm/&#x00B0;C-771mV-0.03mm<sup>2</sup> CMOS resistorless voltage reference (2011)

A low power voltage reference generator operating with a supply voltage ranging from 1.6V to 3.6V has been implemented in a 90-nm standard CMOS process. The reference is based on MOSFETs biased in the weak inversion region to consume nanowatts of power and uses no resistors. The maximum supply current at 3.6V and at 125°C is 173nA. It provides an 771mV voltage reference. A temperature coefficient of 7.5ppm/°C is achieved at best and 39.5ppm/°C on average, in a range from -40 to 125°C, as the combined effect of a suppression of the temperature dependence of mobility and the compensation of the threshold voltage temperature variation. The total block area is 0.03mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Human Immunodeficiency Virus Type 1 Tat Protein Activates Transcription Factor NF-κB through the Cellular Interferon-Inducible, Double-Stranded RNA-Dependent Protein Kinase, PKR (1999)

The transactivator protein of human immunodeficiency virus type 1 (HIV-1) (Tat) is a powerful activator of nuclear factor-kappaB (NF-kappaB), acting through degradation of the inhibitor IkappaB-alpha (F. Demarchi, F. d'Adda di Fagagna, A. Falaschi, and M. Giacca, J. Virol. 70:4427-4437, 1996). Here, we show that this activity of Tat requires the function of the cellular interferon-inducible protein kinase PKR. Tat-mediated NF-kappaB activation and transcriptional induction of the HIV-1 long terminal repeat were impaired in murine cells in which the PKR gene was knocked out. Both functions were restored by cotransfection of Tat with the cDNA for PKR. Expression of a dominant-negative mutant of PKR specifically reduced the levels of Tat transactivation in different human cell types. Activation of NF-kappaB by Tat required integrity of the basic domain of Tat; previous studies have indicated that this domain is necessary for specific Tat-PKR interaction.
Assembly/Disassembly of DNA‐Au Nanoparticles: A Strategy of Intervention (2008)

This report describes the viability of a strategy for manipulating the assembly/disassembly processes of DNA‐Au nanoparticles by molecular intervention. Using the temperature‐induced assembly and disassembly processes of DNAs and gold nanoparticles as a model system, the introduction of a molecular recognition probe is demonstrated to lead to the intervention of the assembly/disassembly processes depending on its specific biorecognition. This process can be detected by monitoring the change in the optical properties of gold nanoparticles and their DNA assemblies. Implications of the preliminary results to exploration of the resulting nanostructures for fine‐tuning of the interfacial reactivities in DNA‐based bioassays and biomaterial engineering are also discussed.
Lovastatin Inhibits Transforming Growth Factor-β1 Expression in Diabetic Rat Glomeruli and Cultured Rat Mesangial Cells (2000)

Diabetic nephropathy is a leading cause of end-stage renal disease and is characterized by excessive deposition of extracellular matrix (ECM) proteins in the glomeruli. Transforming growth factor-beta (TGF-beta) is the major mediator of excessive accumulation of ECM proteins in diabetic nephropathy through upregulation of genes encoding ECM proteins as well as downregulation of genes for ECM-degrading enzymes. It has been shown that lovastatin, an inhibitor of 3-hydroxy3-methylglutaryl CoA reductase, delays the onset and progression of different models of experimental nephropathy. To evaluate the effect of lovastatin on the development and progression of diabetic nephropathy, streptozotocin-induced diabetic rats were studied for 12 mo. In untreated diabetic rats, there were significant increases in blood glucose, urine albumin excretion, kidney weight, glomerular volume, and TGF-beta1 mRNA expression in the glomeruli compared with normal control rats treated with citrate buffer only. Treatment with lovastatin in diabetic rats significantly suppressed the increase in urine albumin excretion, kidney weight, glomerular volume, and TGF-beta1 mRNA expression despite high blood glucose levels. To elucidate the mechanisms of the renal effects of lovastatin, rat mesangial cells were cultured under control (5.5 mM) or high (30 mM) glucose with lovastatin alone, mevalonate alone, or with both. Under high glucose, TGF-beta1 and fibronectin mRNA and proteins were upregulated. These high glucose-induced changes were suppressed by lovastatin (10 micro/M) and nearly completely restored by mevalonate (100 microM). These results suggest that lovastatin has a direct cellular effect independent of a cholesterol-lowering effect and delays the onset and progression of diabetic nephropathy, at least in part, through suppression of glomerular expression of TGF-beta1.
Toxicological and Environmental Aspects of Anilines (2007)

This chapter contains sections titled: Introduction Cyanosis Analytical Methods for Environmental Detection and Sampling of Anilines Carcinoma Mechanism of Bladder Cancer Specific Aromatic Amines Environmental Fate Regulation and Legislation Aromatic Amines as Dietary Carcinogens Conclusion References
Vasodynamics of pial and penetrating arterioles in relation to arteriolo-arteriolar anastomosis after focal stroke (2015)

Changes in blood perfusion in highly interconnected pial arterioles provide important insights about the vascular response to ischemia within brain. The functional role of arteriolo-arteriolar anastomosis (AAA) in regulating blood perfusion through penetrating arterioles is yet to be discovered. We apply a label-free optical microangiography (OMAG) technique to evaluate the changes in vessel lumen diameter and red blood cell velocity among a large number of pial and penetrating arterioles within AAA abundant region overlaying the penumbra in the parietal cortex after a middle cerebral artery occlusion (MCAO). In comparison with two-photon microscopy, the OMAG technique makes it possible to image a large number of vessels in a short period of time without administering exogenous contrast agents during a time-constrained MCAO experiment. We compare vasodynamics in penetrating arterioles at various locations. The results show that the MCA connected penetrating arterioles close to a strong AAA dilate, while those belonging to a region away from AAAs constrict in various degrees. These results suggest AAAs play a major role in supporting the active dilation of the penetrating arterioles, thus compensating a significant amount of blood to the ischemic region, whereas the poor blood perfusion occurs at the regions away from AAA connections, leading to ischemia.
Optimized Protein Extraction for Quantitative Proteomics of Yeasts (2007)

An improved method for quantitative protein extraction has been developed that removes some of the sources of artefacts in quantitative proteomics experiments, while at the same time allowing novel types of applications.
Accelerated programmed cell death (apoptosis) in erythroid precursors of patients with severe beta-thalassemia (Cooley's anemia) [see comments] (1993)

The profound and life-threatening anemia in patients with Cooley's anemia is ascribed primarily to intramedullary hemolysis (ineffective erythropoiesis), the cause of which is obscure. Based on prior morphologic data showing nuclear abnormalities, we hypothesized that accelerated apoptosis could occur in these erythroid precursors. The highly successful bone marrow (BM) transplantation program for patients with Cooley's anemia provided us with a unique opportunity to test this hypothesis. We obtained pretransplantation BM aspiration samples from patients undergoing BM transplantation in Pesaro, Italy and from their allogeneic donors. The erythroid precursors were isolated using ficoll sedimentation and then panning selecting fro CD45- cells. Cytospin and Giemsa staining showed that the separation provided greater than 90% erythroblasts. Five million of these erythroblasts were lysed and their DNA was isolated. There were obvious ladder patterns of DNA breakdown products in beta-thalassemia major samples, with less occurring in beta-thalassemia trait. Normal individuals showed only a slight smear of breakdown of DNA. These results indicate there is enhanced apoptosis in the erythroblasts in the BMs of Cooley's anemia patients. This finding might partially explain why most of these erythroblasts never survive to become mature erythrocytes.
Interactions of<i>Neisseria gonorrhoeae</i>with Mature Human Macrophage Opacity Proteins Influence Production of Proinflammatory Cytokines (2001)

The pathological features of ascending gonococcal infection suggest that proinflammatory mediators secreted by tissue-resident macrophages are important components of the host response. Challenge of fully differentiated, mature macrophages with variants of Neisseria gonorrhoeae strain P9 or purified bacterial surface components (pili, lipooligosaccharide, and outer membrane vesicles) induced the secretion of interleukin 6 (IL-6), tumor necrosis factor alpha, growth-related protein alpha, macrophage inflammatory protein 1alpha (MIP-1alpha), and RANTES cytokines but had no effect on IL-8 production. No secretion of IL-1beta, epithelial-derived neutrophil attractant 78, granulocyte-macrophage colony-stimulating factor, IL-10, or IL-12 cytokines was observed. Notably, the P9-Opa(b) protein, in comparison to P9-Opa(a), increased the association of gonococci with macrophages and elevated the secretion of cytokines. Thus, variation in Opa protein expression by the gonococcus may be a determining factor in the severity of pelvic inflammatory disease.
Stimulated photon-electron scattering (1968)

Consideration is given to the possibility of using stimulated Compton scattering for obtaining laser action. The advantages of a Compton laser are that it is voltage tunable over a wide frequency range and may provide intense, coherent radiation in portions of the spectrum where other sources are not readily available. It is found that appreciable gain exists at far infrared wavelengths.