gebhart/patrepeval huggingface dataset:
iKernel: Isolating Buggy and Malicious Device Drivers Using Hardware Virtualization Support (2007)

The users of today's operating systems demand high reliability and security. However, faults introduced outside of the core operating system by buggy and malicious device drivers can significantly impact these dependability attributes. To help improve driver isolation, we propose an approach that utilizes the latest hardware virtualization support to efficiently sandbox each device driver in its own minimal virtual machine (VM) so that the kernel is protected from faults in these drivers. We present our implementation of a low-overhead virtual-machine based framework which allows reuse of existing drivers. We have constructed a prototype to demonstrate that it is feasible to utilize existing hardware virtualization techniques to allow device drivers in a VM to communicate with devices directly without frequent hardware traps into the virtual machine monitor (VMM). We have implemented a prototype parallel port driver which interacts through iKernel to communicate with a physical LED device.
TWO-DIMENSIONAL INFRARED SPECTROSCOPY: REVEALING MOLECULAR STRUCTURE AND DYNAMICS IN SOLUTION (2002)

Author Institution: Department of Chemistry, Massachusetts Institute of Technology
Lipids, lipid-protein interactions and the quality of baked cereal products (1998)

chap. 6
Future options for the management of hepatitis C. (1999)

Current therapy for hepatitis C virus (HCV) infection is believed to be based in part on the ability of interferons to directly inhibit intracellular HCV replication and prevent infection of uninfected hepatocytes, although the exact mechanisms by which this therapy exerts its effect remain unknown. There are several potential avenues open to development of new antiviral treatment strategies for HCV infection. These include extracellular neutralization of virus to prevent new infection, inhibition of viral entry and uncoating, impairment of intracellular replication by either inhibition of host or viral enzymes or by destruction of the viral genome, enhancement of the host immune response to HCV, or control of the hepatic inflammation that results in progressive liver injury. Although the potential of these therapeutic approaches have been demonstrated in vitro or have been used for the treatment of other infections, their use in man, and so their future and potential efficacy, require further investigation.
Conversion technology, an assessment (1981)

article Conversion technology, an assessment Share on Author: James P. Fry University of Michigan (DL) LOGICAL DATA BASE DESIGN University of Michigan (DL) LOGICAL DATA BASE DESIGNView Profile Authors Info & Claims ACM SIGMIS Database: the DATABASE for Advances in Information SystemsVolume 12,13Issue 4,1Summer-Fall 1981 pp 39–61https://doi.org/10.1145/982996.983034Online:01 July 1981Publication History 0citation332DownloadsMetricsTotal Citations0Total Downloads332Last 12 Months1Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Increasing Intestinal Absorption of Drugs by Formulation (1986)

Abstract The biological potency of steroid hormones was increased by formulation with cholesterol, or its esters, in proportions at which the drugs form a solid solution. Improved intestinal absorption was most likely achieved by increasing the contransport of the drugs with the lipid into the lymphatic system. Increases in blood concentrations were highest for hormones possessing a short biological half‐life.
A Handwriting-Based Equation Editor (1999)

Current equation editing systems rely on either text-based equation description languages or on interactive construction by means of structure templates and menus. These systems are often tedious to use, even for experts, because the user is forced to ''parse'' the expressions mentally before they are entered. This step is not normally part of the process of writing equations on paper or on a whiteboard. We describe a prototype equation editor that is based on handwriting recognition and automatic equation parsing. It is coupled with a user interface that incorporates a set of simple procedures for correcting errors made by the automatic interpretation. Although some correction by the user is typically necessary before the formula is recognized, we have found that the system is simpler and more natural to use than systems based on specialized languages or template-based interaction.
Water hardness control by detergent builders (1984)

Abstract Commercial detergent additives to control water hardness are of three main types, sequestrant, precipitant or ion‐exchange builders. These builders lower the free hardness ion (Ca +2 , Mg +2 ) concentration in a wash system by different mechanisms. An electrometric experimental method was used to evaluate the relative water hardness control performances of different builder‐types under conditions closely simulating those of detergent's end‐use. Experimental data for the following builders are presented: EDTA, NTA, STPP, PAA, CMOS, Na‐Citrate, Na 2 CO 3 and type A zeolite. It is shown that the relative rankings of the various builders in water hardness control differ significantly with differences in use level concentration of the builder (0.005–0.100 gm per 100 ml). The application of the method to the selection of optimum molecular weight range of the newly emerging class of organic polymeric detergent builders like sodium polyacrylates (Na‐PAA) (M w =2000−220,000) also is discussed.
Complete Stereochemistry of Tetrafibricin (2002)

With use of the NMR databases in achiral and chiral solvents, the complete stereochemistry of tetrafibricin (1) has been elucidated without degradation of the carbon framework. [structure--see text]
Chemical Modification of Self-Assembled Monolayers by Exposure to Soft X-rays in Air (2000)

Methyl-, vinyl-, and trifluoroacetoxy-terminated self-assembled monolayers (SAMs) of alkylsiloxanes on SiOx/Si substrates were exposed to soft X-rays (0−4000 mJ/cm2) at air pressures from 2 × 10-2 to 2 Torr. The exposed and unexposed monolayers were characterized by using advancing-contact-angle measurements of water, ellipsometry, and X-ray photoelectron spectroscopy (XPS). No significant differences in the thicknesses of the monolayers were observed under any exposure conditions. Advancing-contact angles of water (θa) on all of the monolayers did not change with increasing dose up to 2000 mJ/cm2 for exposures performed at 2 × 10-2 Torr. A 15% loss of fluorine was observed from the CF3COO-terminated SAMs at this pressure at a dose of 4000 mJ/cm2. The θa decreased monotonically with dose for all monolayers exposed at 0.5, 1, and 2 Torr of air pressure. The rate of decrease of θa increased with increasing air pressure. A simple kinetic model based on competing oxidation and cross-linking reactions of reactive surface species fit the data well. The model adequately described the asymptotic value of the contact angle at high doses for the three exposure pressures and was insightful for the analysis of the role of oxygen in surface-modification reactions. Loss of fluorine from the CF3COO-terminated SAMs followed the same trends as the contact-angle data. XPS data showed that hydroxyl (C−OH) and aldehyde (CHO) groups were incorporated onto the surface of the SAMs upon irradiation at 0.5, 1, and 2 Torr of air pressure, irrespective of the initial terminal groups of the SAMs. The hydroxyl groups were shown to be reactive for the formation of bilayer structures. These results are relevant for the optimization of chemical contrast and sensitivity in imaging layers based on SAMs for nanolithographic techniques using ionizing radiation.
Generation control circuit for photovoltaic modules (2001)

Photovoltaic modules must generally be connected in series in order to produce the voltage required to efficiently drive an inverter. However, if even a very small part of photovoltaic module (PV module) is prevented from receiving light, the generation power of the PV module is decreased disproportionately. This greater than expected decrease occurs because PV modules which do not receive adequate light cannot operate on the normal operating point, but rather operate as loads. As a result, the total power from the PV modules is decreased if even only a small part of the PV modules are shaded. In the present paper, a novel circuit, referred to as the generation control circuit (GCC), which enables maximum power to be obtained from all of the PV modules even if some of the modules are prevented from receiving light. The proposed circuit enables the individual PV modules to operate effectively at the maximum power point tracking, irrespective of the series connected PV module system. In addition, the total generated power is shown experimentally to increase for the experimental set-up used in the present study.
The Cardiac Microvasculature in Hypertension, Cardiac Hypertrophy and Diastolic Heart Failure (2008)

Recent studies revealed an exceedingly high mortality with diastolic heart failure that was previously regarded as relatively benign compared to systolic heart failure. Prominent risk factors for diastolic heart failure are increasing age, hypertension and diabetes. These risk factors are associated with coronary microvascular rarefaction and resultant decreased coronary flow reserve, thereby rendering the myocardium vulnerable to ischemia. We discuss the importance of angiogenic gene programming in preserving the coronary microvasculature, preserving cardiac function and altering disease course. Further, we discuss the possible utility of therapies that activate hypoxia inducible factor-1 in preventing rarefaction of the coronary microvasculature and maintaining cardiac diastolic function.
Photothermally Assisted Thinning of Silicon Nitride Membranes for Ultrathin Asymmetric Nanopores (2018)

Sculpting solid-state materials at the nanoscale is an important step in the manufacturing of numerous types of sensor devices, in particular solid-state nanopore sensors. Here we present mechanistic insight into laser-induced thinning of low-stress silicon nitride (SiN <sub>x</sub>) membranes and films. In a recent study, we observed that focusing a visible wavelength laser beam on a SiN <sub>x</sub> membrane results in efficient localized heating, and we used this effect to control temperature at a solid-state nanopore sensor. A side-effect of the observed heating was that the pores expand/degrade under prolonged high-power illumination, prompting us to study the mechanism of this etching process. We find that SiN <sub>x</sub> can be etched under exposure to light of ∼10<sup>7</sup> W/cm<sup>2</sup> average intensity, with etch rates that are influenced by the supporting electrolyte. Combining this controlled etching with dielectric breakdown, an electrokinetic process for making pores, nanopores of arbitrary dimensions as small as 1-2 nm in diameter and thickness can easily be fabricated. Evidence gathered from biomolecule-pore interactions suggests that the pore geometries obtained using this method are more funnel-like, rather than hourglass-shaped. Refined control over pore dimensions can expand the range of applications of solid-state nanopores, for example, biopolymer sequencing and detection of specific biomarkers.
Activation of heat shock gene transcription by heat shock factor 1 involves oligomerization, acquisition of DNA-binding activity, and nuclear localization and can occur in the absence of stress. (1993)

The existence of multiple heat shock factor (HSF) genes in higher eukaryotes has promoted questions regarding the functions of these HSF family members, especially with respect to the stress response. To address these questions, we have used polyclonal antisera raised against mouse HSF1 and HSF2 to examine the biochemical, physical, and functional properties of these two factors in unstressed and heat-shocked mouse and human cells. We have identified HSF1 as the mediator of stress-induced heat shock gene transcription. HSF1 displays stress-induced DNA-binding activity, oligomerization, and nuclear localization, while HSF2 does not. Also, HSF1 undergoes phosphorylation in cells exposed to heat or cadmium sulfate but not in cells treated with the amino acid analog L-azetidine-2-carboxylic acid, indicating that phosphorylation of HSF1 is not essential for its activation. Interestingly, HSF1 and HSF2 overexpressed in transfected 3T3 cells both display constitutive DNA-binding activity, oligomerization, and transcriptional activity. These results demonstrate that HSF1 can be activated in the absence of physiological stress and also provide support for a model of regulation of HSF1 and HSF2 activity by a titratable negative regulatory factor.
Tunable acoustophoretic band-pass particle sorter (2010)

Acoustophoretic separation in microchannels offers a promising avenue for high-throughput, label-free, cell and particle separation for many applications. However, previous acoustophoretic separation approaches have been limited to a single size separation threshold, analogous to a binary filter, (i.e., high-pass or low-pass). Here, we describe a tunable acoustophoretic separation architecture capable of sorting cells and particles based on a range of sizes, analogous to a band-pass filter. The device is capable of sorting an arbitrary range of particle sizes between 3 and 10 mum in diameter with high efficiency (transfer fraction=0.98+/-0.02) at a throughput of approximately 10(8) particleshmicrochannel.
Rapid construction and characterization of synthetic antibody libraries without DNA amplification (2010)

We report on a simple method to rapidly generate very large libraries of genes encoding mutant proteins without the use of DNA amplification, and the application of this methodology in the construction of synthetic immunoglobulin variable heavy (V(H)) and light (V(kappa)) libraries. Four high quality, chemically synthesized polynucleotides (90-140 bases) were annealed and extended using T4 DNA polymerase. Following electroporation, >10(9) transformants could be synthesized within 1 day. Fusion to beta-lactamase and selection on ampicillin resulted in 3.7 x 10(8) V(H) and 6.9 x 10(8) V(kappa) clones highly enriched for full-length, in-frame genes. High-throughput 454 DNA sequencing of >250,000 V(H) and V(kappa) genes from the pre- and post-selection libraries revealed that, in addition to the expected reduction in reading-frame shifts and stop codons, selection for functional expression also resulted in a statistical decrease in the cysteine content. Apart from these differences, there was a good agreement between the expected and actual diversity, indicating that neither oligonucleotide synthesis nor biological constrains due to protein synthesis of V(H)/V(kappa)-beta-lactamase fusions introduce biases in the amino acid composition of the randomized regions. This methodology can be employed for the rapid construction of highly diverse libraries with the near elimination of PCR errors in invariant regions.
Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. (1993)

The efficiency of fluorescence resonance energy transfer (FRET) between fluorescein and rhodamine covalently attached to both 5' termini of a series of double-stranded DNA species (ranging from 8 to 20 bp) was measured. FRET efficiency varied with a dependence compatible with dye-to-dye distances (R) calculated on the basis of double-stranded B-DNA structure; the helical geometry of double-stranded DNA in solution is clearly evident. The experimental data were consistent with a 1/[1 + (R/R0)6] dependence of FRET efficiency characteristic for the Förster dipole-dipole mechanism. The thermal dissociation of the strands of the duplex DNA species can be followed by using FRET, and from these data we have been able to obtain enthalpies of duplex formation in good agreement with earlier measurements using alternative techniques. FRET measurements at very different salt concentrations can be accurately compared. We conclude that FRET is a reliable and valuable method for studying structure and conformational transitions in nucleic acids.
Nanostructured Ceramics for Biomedical Implants (2002)

Recent progress in the synthesis, characterization, and biological compatibility of nanostructured ceramics for biomedical implants is reviewed. A major goal is to develop ceramic coating technology that can reduce the friction and wear in mating total joint replacement components, thus contributing to their significantly improved function and longer life span. Particular attention is focused on the enhancement of mechanical properties such as hardness, toughness, and friction coefficient and on the bioactivity as they pertain to the nanostructure of the material. The development of three nanostructured implant coatings is discussed: diamond, hydroxyapatite, and functionally graded metalloceramics based on the Cr-Ti-N ternary system. Nanostructured diamond produced by chemical vapor deposition (CVD) techniques and composed of nano-size diamond grains have particular promise because of the combination of ultrahigh hardness, improved toughness over conventional microcrystalline diamond, low friction, and good adhesion to titanium alloys. Nanostructured processing applied to hydroxyapatite coatings is used to achieve the desired mechanical characteristics and enhanced surface reactivity and has been found to increase osteoblast adhesion, proliferation, and mineralization. Finally, nanostructured metalloceramic coatings provide continuous variation from a nanocrystalline metallic bond at the interface to the hard ceramic bond on the surface and have the ability to overcome adhesion problems associated with ceramic hard coatings on metallic substrates.
13C NMR chemical shifts of the carbon atoms of the methoxymethyl group of di‐ortho‐substituted aromatic methoxymethyl ethers (1989)

Abstract Complete 13 C spectral assignments of 28 aromatic methoxymethyl ethers bearing different substituents and substitution patterns were made. While meta ‐, para ‐ or mono‐ ortho ‐substitution did not significantly affect the 13 C resonances of the carbon atoms of the methoxymethyl group, di‐ ortho ‐substitution produced the deshielding of both carbons. This effect was more pronounced on the methylene carbon atom.
The association of herpes simplex virus and Alzheimer's disease: a potential synthesis of genetic and environmental factors. (2001)

The chronic and sporadic nature of Alzheimer's disease (AD), in which the majority of presenting cases are over 65 years of age, suggests that compounded injury or long-term exposure to environmental factors is involved in the aetiology, rather than inherited genetic alterations. Great hope has been placed on identifying a causative infectious agent that would present the potential for therapeutic or preventative vaccines or drugs. Although not the sole causative agent, herpes simplex virus type 1 has been the most clearly established pathogen to be associated with AD development to date. Recent advances have begun to suggest mechanisms by which this ubiquitous, neurotropic pathogen may predispose an individual to the development of AD. Such progress should ultimately lead to therapeutic strategies that limit predisposing neurological damage and potentially reverse the process, increasing the quality and quantity of life in this patient population.
The role of telomeres in ageing and cancer. (1998)

Telomeres are regions of DNA that cap the ends of linear chromosomes. In somatic cells the telomeres shorten progressively with every cell division, reducing the number of tandem repeat sequences. Eventually the chromosomes become unstable and the cell is no longer able to replicate. This represents an inherent biological clock in which the somatic cell has only a finite capacity for division. In contrast, germ cells do not undergo telomeric shortening and have relatively unlimited capacities for cell division. The difference is that germ cells retain the enzyme telomerase which is able to restore the telomere ends that are lost during cell division. Although telomerase activity is absent in most somatic cells, cancer cells acquire the ability to activate the enzyme, ensuring their immortal growth characteristics and selective advantage over normal somatic cells.
The Role of Salt Bridge Formation in Glucagon: An Experimental and Theoretical Study of Glucagon Analogs and Peptide Fragments of Glucagon (2002)

Glucagon is a 29-residue peptide produced in the a cells of the pancreas that interacts with hepatic receptors to stimulate glucose production and release, via a cAMP-mediated pathway. Type 2 diabetes patients may have an excess of glucagon and, as such, glucagon antagonists might serve as diabetes drugs. The antagonists that bind to the glucagon receptor but do not exhibit activity could be analogs of glucagon. The presence of salt bridges between some residues of glucagons (such as aspartic acid) and others (such as lysine) might influence both the binding to the receptor and the activity. Experimental—The solid phase method with 4-methylbenzilhydrilamine resin (p-MBHA resin) was used for the synthesis of glucagon analogs. Rat liver membranes were prepared from male Sprague-Dawley rats by the Neville procedure. The receptor binding essay was performed in 1% BSA, 1 mM dithiothreitol, 25 mM Tris-HCl buffer, pH 7.2. Adenyl cyclase activity was measured in an assay medium containing 1% serum albumin, 25 mM MgCl2, 2 mM dithiothreitol, 0.025 mM GTP, 5 mM ATP, 0.9 mM theophylline, 17.2 mM creatine phosphate, and 1 mg/ml creatine phosphokinase. Theoretical—Quantum chemical calculations using the Titan program with the 6–31G* basis set were performed to calculate the binding energies of salt bridges between aspartic or glutamic acids and lysine. The relative stability of cyclic conformations of glucagon segments versus the extended segments was determined. It was found that the cyclic Glu9-Lys12 amide compound displayed a 20-fold decrease in binding affinity. DesHis1 cyclic compounds Glu20-Lys24 amide and DesHis1Glu9 Glu20-Lys24 amide behave as glucagon antagonists. The calculations show that cyclic conformations of tetrapeptidic and pentapeptidic segments of glucagon are more stable than the extended species. The biological data and the theoretical calculations show that an intramolecular salt bridge might impart stability to some glucagon antagonists and, when situated at the C-terminus of glucagon, might facilitate induction of an α-helix upon initial hormone association with the membrane bilayer. These findings might be a useful tool for the design of new glucagon antagonists.