gebhart/patrepeval huggingface dataset:
<b>Self‐processing 2A‐polyproteins – a system for co‐ordinate expression of multiple proteins in transgenic plants</b> (1999)

Achieving co-ordinate, high-level and stable expression of multiple transgenes in plants is currently difficult. Expression levels are notoriously variable and influenced by factors that act independently on transgenes at different genetic loci. Instability of expression due to loss, re-arrangement or silencing of transgenes may occur, and is exacerbated by increasing numbers of transgenic loci and repeated use of homologous sequences. Even linking two or more genes within a T-DNA does not necessarily result in co-ordinate expression. Linking proteins in a single open reading frame--a polyprotein--is a strategy for co-ordinate expression used by many viruses. After translation, polyproteins are processed into constituent polypeptides, usually by proteinases encoded within the polyprotein itself. However, in foot-and-mouth disease virus (FMDV), a sequence (2A) of just 16-20 amino acids appears to have the unique capability to mediate cleavage at its own C-terminus by an apparently enzyme-independent, novel type of reaction. This sequence can also mediate cleavage in a heterologous protein context in a range of eukaryotic expression systems. We have constructed a plasmid in which the 2A sequence is inserted between the reporter genes chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS), maintaining a single open reading frame. Here we report that expression of this construct in wheatgerm lysate and transgenic plants results in efficient cleavage of the polyprotein and co-ordinate expression of active CAT and GUS. Self-processing polyproteins using the FMDV 2A sequence could therefore provide a system for ensuring co-ordinated, stable expression of multiple introduced proteins in plant cells.
Temperature and excitation density dependence of the photoluminescence from annealed InAs/GaAs quantum dots (2003)

Using rapid thermal annealing, we fabricated a series of InAs/GaAs quantum dot samples with ground-state emission ranging from 1.05 eV to 1.35 eV. This set of annealed samples, all having the same density, allows us to study the influence of the barrier height on the temperature dependence of the photoluminescence (PL). The integrated PL follows an Arrhenius-type behavior, with activation energies matching the barrier heights. However, the quenching occurs at lower temperatures as the barrier height decreases. The modeling of these data enables us to understand the important mechanisms determining the critical temperature where the quenching occurs. We also present a detailed investigation into the excitation density dependence of the photoluminescence at different temperatures. Under relatively low excitation, this dependence is linear at 10 K, and becomes increasingly superlinear and eventually quadratic as the temperature is increased and carriers escape from the dots. However, under high excitation, the dependence remains linear even at high temperatures and the activation energy for quenching is different. We show that all these results can be understood by considering the independent capture and escape of electrons and holes in the dots.
Pyrrolo[1,2-a]thieno[3,2-f][1,4]diazepines: New 4H and 4H-5,6-Dihydro Derivatives (1994)

Synthesis of 4H and 4H-5.6-dihydro pyrrolo[l,2-ulthieno-[3,2-fl[l,4]diazepines from 3-[2-(I-pyrrolyl)thienyl]benzylamine is described.In the course of our work on the synthesis of pyrrolothienodiazepines (E'TD).' we have recently published a three step synthesis of 4-phenyl-6-hydroxy-6H-FKI derivatives (2) ' from 2-aminothienyl-3-carbonimle via 2-(I-pyrmlyl) thien-3-ylphenyhethylenimine (1).qw , , L .
Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay (2005)

DNA methylation in CpG islands is associated with transcriptional silencing. Accurate determination of cytosine methylation status in promoter CpG dinucleotides may provide diagnostic and prognostic value for human cancers. We have developed a quantitative PCR/LDR/Universal Array assay that allows parallel evaluation of methylation status of 75 CpG dinucleotides in the promoter regions of 15 tumor suppressor genes (CDKN2B, CDKN2A, CDKN2D, CDKN1A, CDKN1B, TP53, BRCA1, TIMP3, APC, RASSF1, CDH1, MGMT, DAPK1, GSTP1, and RARB). When compared with an independent pyrosequencing method at a single promoter, the two approaches gave good correlation. In a study using 15 promoter regions and seven blinded tumor cell lines, our technology was capable of distinguishing methylation profiles that identified cancer cell lines derived from the same origins. Preliminary studies using 96 colorectal tumor samples and 73 matched normal tissues indicated CpG methylation is a gene-specific and nonrandom event in colon cancer. This new approach is suitable for clinical applications where sample quantity and purity can be limiting factors.
Mechanism of Antiviral Drug Resistance of Vaccinia Virus: Identification of Residues in the Viral DNA Polymerase Conferring Differential Resistance to Antipoxvirus Drugs (2008)

The acyclic nucleoside phosphonate (ANP) family of drugs shows promise as therapeutics for treating poxvirus infections. However, it has been questioned whether the utility of these compounds could be compromised through the intentional genetic modification of viral sequences by bioterrorists or the selection of drug resistance viruses during the course of antiviral therapy. To address these concerns, vaccinia virus (strain Lederle) was passaged 40 times in medium containing an escalating dose of (S)-1-[3-hydroxy-2-(phosphonomethoxypropyl)-2,6-diaminopurine [(S)-HPMPDAP], which selected for mutant viruses exhibiting a approximately 15-fold-increased resistance to the drug. (S)-HPMPDAP-resistant viruses were generated because this compound was shown to be one of the most highly selective and effective ANPs for the treatment of poxvirus infections. DNA sequence analysis revealed that these viruses encoded mutations in the E9L (DNA polymerase) gene, and marker rescue studies showed that the phenotype was produced by a combination of two (A684V and S851Y) substitution mutations. The effects of these mutations on drug resistance were tested against various ANPs, both separately and collectively, and compared with E9L A314T and A684V mutations previously isolated using selection for resistance to cidofovir, i.e., (S)-1-[3-hydroxy-2-(phosphonomethoxypropyl)cytosine]. These studies demonstrated a complex pattern of resistance, although as a general rule, the double-mutant viruses exhibited greater resistance to the deoxyadenosine than to deoxycytidine nucleotide analogs. The S851Y mutant virus exhibited a low level of resistance to dCMP analogues but high-level resistance to dAMP analogues and to 6-[3-hydroxy-2-(phosphonomethoxy)propoxy]-2,4-diaminopyrimidine, which is considered to mimic the purine ring system. Notably, (S)-9-[3-hydroxy-2-(phosphonomethoxy)propyl]-3-deazaadenine retained marked activity against most of these mutant viruses. In vitro studies showed that the A684V mutation partially suppressed a virus growth defect and mutator phenotype created by the S851Y mutation, but all of the mutant viruses still exhibited a variable degree of reduced virulence in a mouse intranasal challenge model. Infections caused by these drug-resistant viruses in mice were still treatable with higher concentrations of the ANPs. These studies have identified a novel mechanism for the development of mutator DNA polymerases and provide further evidence that antipoxviral therapeutic strategies would not readily be undermined by selection for resistance to ANP drugs.
Retention of viral infectivity after extensive mutation of the highly conserved immunodominant domain of the feline immunodeficiency virus envelope (1997)

In lentiviruses, including human immunodeficiency virus and feline immunodeficiency virus (FIV), the principal immunodominant domain (PID) of the transmembrane glycoprotein elicits a strong humoral response in infected hosts. The PID is marked by the presence of two cysteines that delimit a sequence, composed of five to seven amino acids in different lentiviruses, which is highly conserved among isolates of the same lentiviral species. While the conservation of the sequence suggests the presence of functional constraints, the conservation of the immunodominance among divergent lentiviruses raises the hypothesis of a selective advantage for the infecting virus conferred by the host humoral response against this domain. We and others have previously shown that an appropriate structure of the PID is required for the production of a functional envelope. In the present work, we analyzed virological functions and immune reactivity of the envelope after random mutagenesis of the PID of FIV. We obtained nine mutant envelopes which were correctly processed and retained fusogenic ability. Mutation of the two C-terminal residues of the PID sequence between the cysteines in a molecular clone of FIV abolished infectivity. In contrast, three molecular clones containing extensive mutations in the four N-terminal amino acids were infectious. However, the mutations affected PID reactivity with sera from infected cats. Our results suggest that functional constraints, although existent, are not sufficient to account for PID sequence conservation. Such conservation may also result from positive selection by anti-PID antibodies which enhance infection.
From CT Scan to Ceramic Bone Graft (2003)

An indirect fused deposition process was used to fabricate controlled‐porosity alumina bone grafts using a computer‐aided‐design file created from computed tomography (CT) scans of a horse's short pastern bone. Structures with both uniform and gradient porosity were fabricated to show the effectiveness of this process for the fabrication of custom orthopedic implants. Cytotoxicity and cell proliferation studies were conducted with different cell lines to show that these bone grafts are biocompatible. Uniaxial compression tests were also conducted to understand the influence of porosity on the mechanical properties of these structures.
Optimized chirp compensation for ultrashort transform-limited pulse generation by a gain-switched DFB laser (1994)

The gain-switching approach to ultrashort pulse generation consists in the direct modulation of a DFB laser with current pulses having a suitable width to excite only the first peak of the relaxation oscillations. 1,3 The optical pulses at the laser output exhibit a short duration and a strong chirp which distorts and broadens the corresponding spectrum. A further reduction of the pulsewidth can be obtained by passive compression, coupling the laser beam into a fibre with negative dispersion.
P2‐008: A curcumin analogue as a “smart” fluorescent probe with potential capacity for <i>in vivo</i> imaging the full course of amyloidosis of Alzheimer's disease (2011)

The full course of the amyloidosis of Alzheimer's disease (AD) probably starts from over-accumulation of amyloid ß (Aß) monomers caused by imbalanced clearance of Aß, and then the accumulated monomers gradually aggregate/polymerize/cross-link into neurotoxic soluble dimers and oligomers, the likely early stage biomarkers, and insoluble fibrils and plaques, the likely biomarkers of symptomatic stage. Most of the advances in the imaging of AD lesion have focused on the detection of insoluble fibrils and plaques. Imaging probes capable of detecting all the Aß species formed in the full course of amyloidosis are highly desirable. Our approach focuses on developing imaging probes for the detection of both insoluble species and the soluble Aß species. A curcumin derivative, CRANAD-3, was tested with various Aß species, ranging from insoluble plaques to soluble monomers and even the core fragment (KLVFF) of Aß40/42, and with transgenic APP/PS1 mice for in vivo imaging. CRANAD-3, is able to detect a variety of Aß species, ranging from insoluble plaques to soluble monomers and even the core fragment (KLVFF) of Aß40/42. We also show that amino acid K16 of the Aß peptide is the hot spot for CRANAD-3 binding. Two-photon in vivo imaging results demonstrate that CRANAD-3 is specific to Aß plaques. Remarkably, we demonstrated that CRANAD-3 has capacity to differentiate between transgenic AD and wild-type animals at the early stages of the disease by in vivo optical imaging. Our data show the potential for CRANAD-3 to monitor the full course of amyloidosis in AD. We believe that CRANAD-3, along with its analogues will be valuable tools for full course diagnosis of AD and the assessment of AD therapies.
Defect-based compact model for circuit reliability simulation in advanced CMOS technologies (2013)

A defect-based compact modeling approach for circuit reliability simulation based on surface potential calculations is presented. The modeling approach captures the bias-dependence of stress-induced defects such as (bulk) oxide-trapped charge and interface traps that cannot be described by typical fixed voltage shift models (i.e., threshold voltage, V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> -based models). The defect dynamic charge contribution is modeled under non-equilibrium conditions and for all regions of operation (i.e. from weak to strong inversion) and not just at the threshold (as in Vth-based models). The modeled is verified with 2-D TCAD simulations that incorporate oxide trapped charge and interface trap densities. Spice-level simulations of ring oscillators and SRAM cells reveal inaccuracies in describing aging effects when utilizing typical fixed voltage shift models as compared to the presented defect-based compact modeling approach.
A Postural Assessment Utilizing Machine Learning Prospectively Identifies Older Adults at a High Risk of Falling (2020)

<b>Introduction:</b> Falls are the leading cause of accidental death in older adults. Each year, 28.7% of US adults over 65 years experience a fall resulting in over 300,000 hip fractures and $50 billion in medical costs. Annual fall risk assessments have become part of the standard care plan for older adults. However, the effectiveness of these assessments in identifying at-risk individuals remains limited. This study characterizes the performance of a commercially available, automated method, for assessing fall risk using machine learning. <b>Methods:</b> Participants (<i>N</i> = 209) were recruited from eight senior living facilities and from adults living in the community (five local community centers in Houston, TX) to participate in a 12-month retrospective and a 12-month prospective cohort study. Upon enrollment, each participant stood for 60 s, with eyes open, on a commercial balance measurement platform which uses force-plate technology to capture center-of-pressure (60 Hz frequency). Linear and non-linear components of the center-of-pressure were analyzed using a machine-learning algorithm resulting in a postural stability (PS) score (range 1-10). A higher PS score indicated greater stability. Participants were contacted monthly for a year to track fall events and determine fall circumstances. Reliability among repeated trials, past and future fall prediction, as well as survival analyses, were assessed. <b>Results:</b> Measurement reliability was found to be high (ICC(2,1) [95% CI]=0.78 [0.76-0.81]). Individuals in the high-risk range (1-3) were three times more likely to fall within a year than those in low-risk (7-10). They were also an order of magnitude more likely (12/104 vs. 1/105) to suffer a spontaneous fall i.e., a fall where no cause was self-reported. Survival analyses suggests a fall event within 9 months (median) for high risk individuals. <b>Conclusions:</b> We demonstrate that an easy-to-use, automated method for assessing fall risk can reliably predict falls a year in advance. Objective identification of at-risk patients will aid clinicians in providing individualized fall prevention care.
Porous silica pellicle frame (2003)

Two main issues with current pellicle frames are: (1) thermal expansion mismatch between the anodized aluminum frame and the photomask, and (2) the lack of porosity for purging and contamination control. Both issues can be addressed by using a sol-gel-derived porous silica frame. The silica frame has essentially the same thermal expansion coefficient as the fused silica photomask substrate. The porous nature of the silica frame provides contamination control by N<sub>2</sub> purging and scavenging capability. The porosity characteristics and mechanical properties of the frame material were determined. Porous silica frame was successfully mounted onto quartz plate by a commercial process, suggesting the suitability of using porous silica as pellicle frame material. The sol-gel derived porous silica represents the first proof-of-concept for an alternative frame material with a potentially significant impact on the photomask industry.
Influence of Aerogel Morphology and Reinforcement Architecture on Gas Convection in Aerogel Composites (2016)

A variety of thermal protection applications require lightweight insulation capable of withstanding temperatures well above 900 C. Aerogels offer extremely low-density thermal insulation due to their mesoporous structure, which inhibits both gas convection and solid conduction. Silica aerogel systems are limited to use temperatures of 600-700 C, above which they sinter. Alumina aerogels maintain a porous structure to higher temperatures than silica, before transforming to -alumina and densifying. We have synthesized aluminosilicate aerogels capable of maintaining higher surface areas at temperatures above 1100 C than an all-alumina aerogel using -Boehmite as the aluminum source and tetraethoxysilane (TEOS) as the silicon source. The pore structure of these aerogels varies with thermal exposure temperature and time, as the aluminosilicate undergoes a variety of phase changes to form transition aluminas. Transformation to -alumina is inhibited by incorporation of silica into the alumina lattice. The aerogels are fragile, but can be reinforced using a large variety of ceramic papers, felts or fabrics. The objective of the current study is to characterize the influence of choice of reinforcement and architecture on gas permeability of the aerogel composites in both the as fabricated condition and following thermal exposure, as well as understand the effects of incorporating hydrophobic treatments in the composites.
Bragg grating based nested fibre interferometers (1996)

An approach to configuring multiple nested interferometric sensor elements, based on Michelson and Fabry-Perot interferometers in common fibres using Bragg gratings, is described. These configurations can be used to provide adaptive interferometric sensors which provide unique spatial sampling capabilities.
Effect of plasma treatment on the triboelectric properties of polymer powders (1993)

Surfaces of fine polystyrene (PS) and polymethyl methacrylate (PMMA) powders were modified by exposure to the downstream products of a nitrogen or oxygen microwave plasma. The effects of nitrogen and oxygen incorporation in the powder surface were studied with emphasis on variations in the triboelectric properties of the powder. X-ray photoelectron spectroscopy was utilized to determine the changes in surface elemental composition. After nitrogen plasma treatment, the C 1s peak shapes suggested the formation of amines in the case of PS, and the formation of imines and amides in the case of PMMA. Oxygen plasma treatment appears to result in the formation of hydroxyl and carbonyl groups on the surfaces of both PS and PMMA. After treatment with a nitrogen or oxygen plasma, the charge-to-mass ratio (Q/M) of PS and PMMA powders in contact with carrier particles was measured using the cage blowoff method. The surface charge density (Q/A) was calculated from Q/M. The Q/A of nitrogen plasma-treated PS powder was seen to shift towards positive charge with small increases in the nitrogen concentration. The Q/A of oxygen plasma-treated PS powder initially shifted toward negative charge, but changed towards positive charge with higher oxygen concentrations. Plasma-treated PMMA powder showed a different behavior and the variation of Q/A on PMMA was much less than that of PS. Results suggest that triboelectrification of the polymer powder may be related to changes in the electrical surface states, and that nitrogen may act as a group V modifier within the PS surface.
ChemInform Abstract: Novel Heterocycles as Selective α<sub>1</sub>‐Adrenergic Receptor Antagonists. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Specific-sized Hyaluronan Fragments Promote Expression of Human β-Defensin 2 in Intestinal Epithelium (2012)

Hyaluronan (HA) is a glycosaminoglycan polymer found in the extracellular matrix of virtually all mammalian tissues. Recent work has suggested a role for small, fragmented HA polymers in initiating innate defense responses in immune cells, endothelium, and epidermis through interaction with innate molecular pattern recognition receptors, such as TLR4. Despite these advances, little is known regarding the effect of fragmented HA at the intestinal epithelium, where numerous pattern recognition receptors act as sentinels of an innate defense response that maintains epithelial barrier integrity in the presence of abundant and diverse microbial challenges. Here we report that HA fragments promote expression of the innate antimicrobial peptide human β-defensin 2 (HβD2) in intestinal epithelial cells. Treatment of HT-29 colonic epithelial cells with HA fragment preparations resulted in time- and dose-dependent up-regulated expression of HβD2 protein in a fragment size-specific manner, with 35-kDa HA fragment preparations emerging as the most potent inducers of intracellular HβD2. Furthermore, oral administration of specific-sized HA fragments promotes the expression of an HβD2 ortholog in the colonic epithelium of both wild-type and CD44-deficient mice but not in TLR4-deficient mice. Together, our observations suggest that a highly size-specific, TLR4-dependent, innate defense response to fragmented HA contributes to intestinal epithelium barrier defense through the induction of intracellular HβD2 protein.
RECOMBINANT ALPHAVIRUSES ARE SAFE AND USEFUL SEROLOGICAL DIAGNOSTIC TOOLS (2007)

Serological assays for diagnosis of Venezuelan equine encephalitis virus (VEEV) currently require bio-safety level 3 facilities and select agent certification to produce antigens, reference sera, or viral stocks. Rapid identification of VEEV infection is required to respond to human and equine outbreaks of encephalitis caused by that virus and can be useful for epidemiologic surveillance. Alphavirus (Sindbis)-based recombinant viruses that express VEEV structural proteins are attenuated in animal models, thus representing an alternative to the handling of virulent infectious virus. Virus and viral antigens from recombinant Sindbis/VEE constructs engineered to express structural proteins from multiple VEEV subtypes were evaluated as diagnostic reagents in VEEV-specific serological assays, e.g., plaque reduction neutralization test (PRNT), hemagglutination inhibition (HI) assay, and complement fixation (CF) test. Chimeric viruses were produced efficiently in cell culture and were as effective as the parental virus for identifying infection of humans, horses, and rodents in these serological assays.