gebhart/patrepeval huggingface dataset:
Direct amplification of a single dissected chromosomal segment by polymerase chain reaction: a human brain sodium channel gene is on chromosome 2q22-q23. (1991)

We have devised a general strategy for gene mapping based upon the direct amplification of a target sequence within a single microdissected Giemsa-banded chromosomal segment using the polymerase chain reaction. The usefulness of this approach was demonstrated by mapping a cloned human brain sodium channel (alpha subunit) gene sequence to chromosome 2q22-q23. When DNA from single, dissected chromosome segments 2q21-qter and 2q24-pter were used as templates, a sodium channel-specific 172-base-pair polymerase chain reaction product was obtained. This product was not synthesized when segments 2q21-pter and 2q24-qter were used. Chromosome microdissection-polymerase chain reaction is not only a simple, fast, and accurate method for gene mapping but also may offer significant advantages for other applications, such as cancer cytogenetics and linkage analysis.
Cooperative interaction of factor B and other complement components with mononuclear cells in the antibody-independent lysis of xenogeneic erythrocytes. (1982)

Synergistic cytotoxicity is a term used to describe a cytotoxic system in which xenogeneic erythrocyte target cells are lysed in the presence of nonimmune human mononuclear effector cells and antibody-depleted normal human serum. Neither the mononuclear cells nor the serum alone are cytolytic to the target erythrocytes. Previous studies have shown that the serum activity is not immunoglobulin and is heat-labile, suggesting a similarity to serum complement. In this report, sera deficient in various complement components as well as highly purified single complement components were tested with whole mononuclear cell populations and purified monocytes and lymphocytes to further characterize this cytotoxicity system. Whole mononuclear cell populations failed to mediate target cell lysis in sera deficient in C5 or factor B. However, C3-deficient serum, even in the presence of anti-C3 antibody, supported synergistic cytotoxicity normally. Purified lymphocytes were also normally cytotoxic in C3-deficient serum but failed to lyse targets in sera deficient in C5, C7, C8, or depleted of factor B. Purified monocytes failed to lyse the target cells only in factor B-depleted serum and could lyse the target cells in serum-free medium when purified factor B alone was added. Monocyte-mediated cytotoxicity induced by factor B was inhibited 73-100% by adding lymphocytes back to the purified monocytes. Thus, both lymphocytes and monocytes can serve as effector cells in this form of cytotoxicity but require cooperative interaction with different sets of complement components. In addition, lymphocytes can modulate the monocyte-mediated form of target cell lysis associated with factor B.
DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples (2015)

DMSO improves HRM mutation scanning sensitivity with saturating dyes. When full-COLD-PCR is used, followed by DMSO-HRM, the overall improvement is about 20-fold compared with conventional PCR-HRM.
Recombination and chimeragenesis by in vitro heteroduplex formation and in vivo repair (1999)

We describe a simple method for creating libraries of chimeric DNA sequences derived from homologous parental sequences.A heteroduplex formed in vitro is used to transform bacterial cells where repair of regions of non-identity in the heteroduplex creates a library of new, recombined sequences composed of elements from each parent.Heteroduplex recombination provides a convenient addition to existing DNA recombination methods ('DNA shuffling') and should be particularly useful for recombining large genes or entire operons.This method can be used to create libraries of chimeric polynucleotides and proteins for directed evolution to improve their properties or to study structure-function relationships.We also describe a simple test system for evaluating the performance of DNA recombination methods in which recombination of genes encoding truncated green fluorescent protein (GFP) reconstructs the full-length gene and restores its characteristic fluorescence.Comprising seven truncated GFP constructs, this system can be used to evaluate the efficiency of recombination between mismatches separated by as few as 24 bp and as many as 463 bp.The optimized heteroduplex recombination protocol is quite efficient, generating nearly 30% fluorescent colonies for recombination between two genes containing stop codons 463 bp apart (compared to a theoretical limit of 50%).
RGD-conjugated gold nanorods induce radiosensitization in melanoma cancer cells by downregulating &alpha;v&beta;3 expression (2012)

Our study indicated that RGD-GNRs could sensitize melanoma A375 cells to irradiation. It was hypothesized that this was mainly through downregulation of radiation-induced α(v)β₃, in addition to induction of a higher proportion of cells within the G2/M phase. The combination of RGD-GNRs and radiation needs further investigation.
Analysis of Envelope-Tracking Power Amplifier Using Mathematical Modeling (2014)

This paper describes analysis of an envelope-tracking power amplifier (ET PA) to show its operational behavior. The RF PA is modeled by sweeping the input power and supply voltage. The RF PA model is composed of three 2-D lookup tables including the amplitude-to-amplitude modulation, amplitude-to-phase modulation, and amplitude-to-efficiency modulation. The hybrid switching supply modulator is also modeled using an ideal op-amp, ideal switches, and other assisting blocks. Based on the mathematical models of the RF PA and supply modulator, the ET PA can be analyzed with a fast calculation speed and a good accuracy to find the optimum ET operation point. A power control strategy is presented for the optimal ET operation over a broad output power range. The effect of the delay mismatch on the characteristics of the ET PA is also described to assist the time alignment algorithm. For a 10-MHz long-term evolution signal with a 7.44-dB PAPR, the implemented ET PA at 1.71 GHz delivers a PAE of 44.3%, a gain of 29 dB, an evolved universal terrestrial radio access adjacent channel leakage ratio of -35.1 dBc, and an error vector magnitude of 2.91% at an average output power of 28 dBm.
Low on-resistance GaN pin rectifiers grown on 6H-SiC substrates (2007)

Low on-resistance gallium nitride pin rectifiers grown by metal organic chemical vapour deposition on n-type 6H-SiC substrates are reported. The diode structures consist of an n+-GaN layer grown on the substrate, followed by a 2.5 µm unintentionally doped i-GaN layer, and a p-type GaN layer capped with a p++-GaN contact layer. The mesa-structure pin diodes exhibited a blocking voltage as large as Vr ∼−500 V, at a reverse current density of Ir ∼1 A/cm2. The on-resistance is 2.3 mΩ · cm2 for an 80 µm mesa diameter circular device. This yields a power figure of merit value of 108.69 MW/cm2. The on-resistance and the figure of merit values are believed to be the best reported for vertical mesa-geometry GaN pin rectifiers grown on 6H-SiC substrates with comparable i-layer thickness.
Non-enzymatic roles of human RAD51 at stalled replication forks (2018)

ABSTRACT The central recombination enzyme RAD51 has been implicated in replication fork processing and restart in response to replication stress. Here, we use a separation-of-function allele of RAD51 that retains DNA binding, but not strand exchange activity, to reveal mechanistic aspects of RAD51’s roles in the response to replication stress. We find that cells lacking RAD51 strand exchange activity protect replication forks from MRE11-dependent degradation, as expected from previous studies. Unexpectedly we find that RAD51’s strand exchange activity is not required to convert stalled forks to a form that can be degraded by DNA2. Such conversion was shown previously to require replication fork reversal, supporting a model in which fork reversal depends on a non-enzymatic function of RAD51. We also show RAD51 promotes replication restart by both strand exchange-dependent and strand exchange-independent mechanisms.
Elemental and Molecular Heritage: An Internet-based Display (1998)

The background to a Web page describing elemental and molecular heritage at Imperial College chemistry department is described. Photographs are shown of the original samples of elemental bromine and crystalline silicon, and molecular ferrocene and mauveine. 3D "Hyperactive" models of these systems are shown, together with a recently discovered heterocyclic systems scorpionine, which like mauveine is made by a deceptively simple chemical synthesis.
A new OFDM standard for high rate wireless LAN in the 5 GHz band (1999)

An overview is given of the new OFDM based wireless LAN standard which is being developed by IEEE 802.11, ETSI and MMAC. Signal processing issues are described and some simulations are shown to demonstrate the achievable performance in multipath fading channels.
Transcription of a novel mouse semaphorin gene, M-semaH, correlates with the metastatic ability of mouse tumor cell lines. (1998)

In the attempt to identify genes associated with metastasis, we have compared gene expressions of two metastatic cell lines, 4T1 and 66cl4, and one noninvasive, nonmetastatic cell line, 67NR, which originate from the same mouse mammary adenocarcinoma. Using the technique of differential display, we identified a novel member of the semaphorin/collapsin family in the two metastatic cell lines. We have named it M-semaH. Northern hybridization to a panel of tumor cell lines revealed transcripts in 12 of 12 metastatic cell lines but in only 2 of 6 nonmetastatic cells and none in immortalized mouse fibroblasts. To our knowledge, this is the first time that the expression of a semaphorin gene has been shown to correlate positively with tumor progression. We have characterized two transcripts present in the tumor cells. One transcript, M-semaH-v, is a putative splice variant, which is less abundant in normal tissue and lacks 478 bp in the 3' untranslated region. Both transcripts encode the same 775 amino acids with the features of a secreted glycoprotein. Northern analysis suggests that the M-semaH gene is involved in embryonic development and in situ hybridization locates the M-semaH expression to the developing lungs, to developing skeletal elements, and to the ventral horns of the developing neural tube.
Oligonucleotide sequence signaling transcriptional termination of vaccinia virus early genes. (1987)

In an in vitro system containing enzymes extracted from vaccinia virions, transcription of the vaccinia growth factor gene terminated approximately 50 base pairs downstream of a thymidine-rich sequence. Deletion mutagenesis suggested the presence of two tandem termination signals. The signal was identified by replacing the 3' end of the gene with the oligonucleotide AATTTTTAT that induced downstream termination. Further analysis of the transcripts formed with a series of templates containing 16 related synthetic oligonucleotides established the minimum functional termination signal as TTTTTNT, in which N represents any nucleotide. Termination efficiency may be increased, however, by the presence of an adenosine preceding the thymidine cluster. The general use of this signal at early times in infection but not at late times is supported by a survey of vaccinia virus gene sequences.
Differential space-time coding for frequency-selective channels (2002)

We introduce two space-time transmission schemes which allow full-rate and full-diversity noncoherent communications using two transmit antennas over fading frequency-selective channels. The first scheme operates in the frequency domain where it combines differential Alamouti (seeIEEE J. Select. Areas Commun., vol.16, p.1451-58, Nov. 1998) space-time block-coding (STBC) with OFDM. The second scheme operates in the time domain and employs differential time-reversal STBC to guarantee blind channel identifiability without the need for temporal oversampling or multiple receive antennas.
Comparison of Graphene Growth on Single-Crystalline and Polycrystalline Ni by Chemical Vapor Deposition (2010)

We report a comparative study and Raman characterization of the formation of graphene on single crystal Ni (111) and polycrystalline Ni substrates using chemical vapor deposition (CVD). Preferential formation of monolayer/bilayer graphene on the single crystal surface is attributed to its atomically smooth surface and the absence of grain boundaries. In contrast, CVD graphene formed on polycrystalline Ni leads to a higher percentage of multilayer graphene (≥3 layers), which is attributed to the presence of grain boundaries in Ni that can serve as nucleation sites for multilayer growth. Micro-Raman surface mapping reveals that the area percentages of monolayer/bilayer graphene are 91.4% for the Ni (111) substrate and 72.8% for the polycrystalline Ni substrate under comparable CVD conditions. The use of single crystal substrates for graphene growth may open ways for uniform high-quality graphene over large areas.
Prevalence and Clinical Correlates of YMDD Variants during Lamivudine Therapy for Patients with Chronic Hepatitis B (2003)

YMDD variants of hepatitis B virus (HBV) emerge in some patients with chronic hepatitis B who receive lamivudine. YMDD variants were examined in 794 patients in 4 controlled studies of 1 year's duration. The long-term effects of YMDD variants were examined in a subset of patients treated up to 4 years. YMDD variants were detected by polymerase chain reaction (PCR) and restriction fragment-length polymorphism assays. After 1 year, YMDD variants were detected in 81 (24%) of 335 patients. In these patients, the median serum HBV DNA concentration at 1 year was <20% of the baseline level, and serum alanine transaminase (ALT) levels and liver histologic findings had significantly improved. In patients with YMDD variants who were treated for up to 4 years, median HBV DNA and ALT levels showed improvements. Sex, baseline body mass index, and HBV DNA level were associated with emergence of YMDD variants. Patients with YMDD variants losing clinical response with a significant increase in the HBV DNA and ALT levels may require additional therapy.
Recruitment of the p97 ATPase and ubiquitin ligases to the site of retrotranslocation at the endoplasmic reticulum membrane (2005)

Misfolded proteins are eliminated from the endoplasmic reticulum (ER) by retrotranslocation into the cytosol, a pathway hijacked by certain viruses to destroy MHC class I heavy chains. The translocation of polypeptides across the ER membrane requires their polyubiquitination and subsequent extraction from the membrane by the p97 ATPase [also called valosin-containing protein (VCP) or, in yeast, Cdc48]. In higher eukaryotes, p97 is bound to the ER membrane by a membrane protein complex containing Derlin-1 and VCP-interacting membrane protein (VIMP). How the ubiquitination machinery is recruited to the p97/Derlin/VIMP complex is unclear. Here, we report that p97 interacts directly with several ubiquitin ligases and facilitates their recruitment to Derlin-1. During retrotranslocation, a substrate first interacts with Derlin-1 before p97 and other factors join the complex. These data, together with the fact that Derlin-1 is a multispanning membrane protein forming homo-oligomers, support the idea that Derlin-1 is part of a retrotranslocation channel that is associated with both the polyubiquitination and p97-ATPase machineries.
Multiscale texture synthesis (2008)

Example-based texture synthesis algorithms have gained widespread popularity for their ability to take a single input image and create a perceptually similar non-periodic texture. However, previous methods rely on single input exemplars that can capture only a limited band of spatial scales. For example, synthesizing a continent-like appearance at a variety of zoom levels would require an impractically high input resolution. In this paper, we develop a multiscale texture synthesis algorithm. We propose a novel example-based representation, which we call an exemplar graph, that simply requires a few low-resolution input exemplars at different scales. Moreover, by allowing loops in the graph, we can create infinite zooms and infinitely detailed textures that are impossible with current example-based methods. We also introduce a technique that ameliorates inconsistencies in the user's input, and show that the application of this method yields improved interscale coherence and higher visual quality. We demonstrate optimizations for both CPU and GPU implementations of our method, and use them to produce animations with zooming and panning at multiple scales, as well as static gigapixel-sized images with features spanning many spatial scales.
Survival, Persistence, and Isolation of the Emerging Multidrug-Resistant Pathogenic Yeast Candida auris on a Plastic Health Care Surface (2017)

The emerging multidrug-resistant pathogenic yeast <i>Candida auris</i> represents a serious threat to global health. Unlike most other <i>Candida</i> species, this organism appears to be commonly transmitted within health care facilities and causes health care-associated outbreaks. To better understand the epidemiology of this emerging pathogen, we investigated the ability of <i>C. auris</i> to persist on plastic surfaces common in health care settings compared with that of <i>Candida parapsilosis</i>, a species known to colonize the skin and plastics. Specifically, we compiled comparative and quantitative data essential to understanding the vehicles of spread and the ability of both species to survive and persist on plastic surfaces under controlled conditions (25°C and 57% relative humidity), such as those found in health care settings. When a test suspension of 10<sup>4</sup> cells was applied and dried on plastic surfaces, <i>C. auris</i> remained viable for at least 14 days and <i>C. parapsilosis</i> for at least 28 days, as measured by CFU. However, survival measured by esterase activity was higher for <i>C. auris</i> than <i>C. parapsilosis</i> throughout the 28-day study. Given the notable length of time <i>Candida</i> species survive and persist outside their host, we developed methods to more effectively culture <i>C. auris</i> from patients and their environment. Using our enrichment protocol, public health laboratories and researchers can now readily isolate <i>C. auris</i> from complex microbial communities (such as patient skin, nasopharynx, and stool) as well as environmental biofilms, in order to better understand and prevent <i>C. auris</i> colonization and transmission.
Hepatotoxicity Associated with Chronic Acetaminophen Administration in Patients without Risk Factors (2002)

Acetaminophen should be used cautiously on a chronic basis because several case reports show that it may be hepatotoxic at therapeutic doses.
Regulation of Cellular Cholesterol Efflux by Lecithin:Cholesterol Acyltransferase Reaction through Nonspecific Lipid Exchange (1996)

Erythrocyte was found lacking in reactivity to lipid-free apolipoproteins to generate pre-beta-high density lipoprotein (HDL) with the cellular lipid and, therefore, was used to study cellular cholesterol efflux to plasma lipoproteins exclusively by a nonspecific exchange mechanism. Over the range of hematocrit from 1-20% (cellular cholesterol pool of 2.5 micrograms per 250 microliters), the fractional rate of cellular cholesterol efflux to lipoprotein was constant, and, therefore, absolute efflux rate was a linear function of the hematocrit of this range. In the absence of lecithin:cholesterol acyltransferase (LCAT), the cholesterol influx rate from lipoproteins was equal to the efflux rate from erythrocyte resulting in no net transfer of cholesterol, with either HDL or low density lipoprotein. In the presence of LCAT in the mixture of HDL and erythrocyte, cholesterol was esterified exclusively in HDL regardless of the origin. When the hematocrit was low and efflux of cellular cholesterol was slower than cholesterol esterification, the esterification of cell-originating cholesterol did not directly enhance the efflux. With high hematocrit that gives faster cholesterol efflux, the efflux was increased directly by the cholesterol esterification. On the other hand, the LCAT reaction significantly reduced HDL-cholesterol influx. The LCAT reaction thus induces substantial net cholesterol efflux from erythrocytes through a nonspecific cholesterol exchange mechanism.
Autonomous driving in urban environments: Boss and the Urban Challenge (2008)

Abstract Boss is an autonomous vehicle that uses on‐board sensors (global positioning system, lasers, radars, and cameras) to track other vehicles, detect static obstacles, and localize itself relative to a road model. A three‐layer planning system combines mission, behavioral, and motion planning to drive in urban environments. The mission planning layer considers which street to take to achieve a mission goal. The behavioral layer determines when to change lanes and precedence at intersections and performs error recovery maneuvers. The motion planning layer selects actions to avoid obstacles while making progress toward local goals. The system was developed from the ground up to address the requirements of the DARPA Urban Challenge using a spiral system development process with a heavy emphasis on regular, regressive system testing. During the National Qualification Event and the 85‐km Urban Challenge Final Event, Boss demonstrated some of its capabilities, qualifying first and winning the challenge. © 2008 Wiley Periodicals, Inc.
Engineered Enzymes (2005)

Abstract The term ‘engineered enzymes’ encompasses the process of creating new proteins through manipulation of the DNA of the gene encoding the protein. The engineered gene is translated into protein through expression in a suitable cellular system.
Association between Early-Onset Parkinson's Disease and Mutations in theParkinGene (2000)

Mutations in the parkin gene are a major cause of early-onset autosomal recessive familial Parkinson's disease and isolated juvenile-onset Parkinson's disease (at or before the age of 20 years). Accurate diagnosis of these cases cannot be based only on the clinical manifestations of the disease.
Analysis of Growth and Interaction of Multiple Hydraulic Fractures (1983)

Abstract A general-purpose numerical formulation is presented for the incremental quasistatic stable lateral growth and interaction of fluid driven fractures in reservoir structures. Multiple fractures emanating from multiple wellbores are allowed to evolve on arbitrarily curved trajectories, dictated by non-uniform stress fields arising from interaction of fractures with one another and with material/stress variations. The model simulates fracture growth by simultaneously solving for stresses, displacements and pressure distributions associated with the fracturing configuration at each timestep. The elastostatic computation employs a surface integral method, while the coupled fluid flow and crack opening modelling involves a weak starting assumption of (instantaneous) self-similarity in the opening displacement profile. A search scheme is used to determine the directions and amounts of growth at the end of each timestep. Several sample fracture growth patterns are presented to illustrate the generality and applicability of the simulator, which is verified by comparison with many of our laboratory experiments. The overall scheme provides an efficient, direct and convenient tool for design of multiple fracturing treatments, whenever these begin to be used for creation of suitable underground fracture networks (e.g., for enhanced petroleum recovery or solution mining).