gebhart/patrepeval huggingface dataset:
ABYSS: ATrusted Architecture for Software Protection (1987)

ABYSS (A Basic Yorktown Security System) is an architecture for the trusted execution of application software. It supports a uniform security service across the. range of computing systems. The use of ABYSS discussed in this paper is oriented towards solving the software protection problem, especially in the lower end of the market. Both current and planned software distribution channels are supportable by the architecture, and the system is nearly transparent to legitimate users. A novel use-once authorization mechanism, called a token, is introduced as a solution to the problem of providing authorizations without direct communication. Software vendors may use the system to obtain technical enforcement of virtually any terms and conditions of the sale of their software, including such things as rental software. Software may be transferred between systems, and backed up to guard against loss in case of failure. We discuss the problem of protecting software on these systems, and offer guidelines to its solution. ABYSS is shown to be a general security base, in which many security applications may execute.
Clinical Use of Respiratory Changes in Arterial Pulse Pressure to Monitor the Hemodynamic Effects of PEEP (1999)

In ventilated patients with acute lung injury (ALI) we investigated whether respiratory changes in arterial pulse pressure (DeltaPP) could be related to the effects of PEEP and fluid loading (FL) on cardiac index (CI). Measurements were performed before and after application of a PEEP (10 cm H2O) in 14 patients. When the PEEP-induced decrease in CI was > 10% (six patients), measurements were also performed after FL. Maximal (PPmax) and minimal (PPmin) values of pulse pressure were determined over one respiratory cycle and DeltaPP was calculated: DeltaPP (%) = 100 x ((PPmax - PPmin)/ ([PPmax + PPmin]/2)). PEEP decreased CI from 4.2 +/- 1.1 to 3.8 +/- 1.3 L/min/m2 (p < 0.01) and increased DeltaPP from 9 +/- 7 to 16 +/- 13% (p < 0.01). The PEEP-induced changes in CI correlated with DeltaPP on ZEEP (r = -0.91, p < 0.001) and with the PEEP-induced increase in DeltaPP (r = -0.79, p < 0.001). FL increased CI from 3.5 +/- 1.1 to 4.2 +/- 0.9 L/min/m2 (p < 0.05) and decreased DeltaPP from 27 +/- 13 to 14 +/- 9% (p < 0.05). The FL-induced changes in CI correlated with DeltaPP before FL (r = 0.97, p < 0.01) and with the FL-induced decrease in DeltaPP (r = -0.85, p < 0.05). In ventilated patients with ALI, DeltaPP may be useful in predicting and assessing the hemodynamic effects of PEEP and FL.
Expression of the genes (, , , , and ) in (2003)

The luxA, B, C, D, and E genes from Photorhabdus luminescens were cloned and functionally expressed in Saccharomyces cerevisiae to construct a bacterial lux-based yeast bioreporter capable of autonomous bioluminescence emission. The bioreporter was engineered using a series of pBEVY yeast expression vectors that allowed for bi-directional constitutive or inducible expression of the individual luxA, B, C, and E genes. The luxD gene, encoding the acyl-ACP transferase that ultimately supplies the requisite aldehyde substrate for the bioluminescent reaction, was fused to a yeast internal ribosomal entry site (IRES) sequence to ensure high bi-cistronic expression. Although self-generation of bioluminescence was achieved by the bioreporter, the signal was relatively weak and decayed rapidly. To overcome this instability, a flavin oxidoreductase gene (frp) from Vibrio harveyi was co-expressed to provide sufficient concentrations of the FMNH(2) co-factor required for the bioluminescent reaction. Expression of frp with the lux genes not only stabilized but also enhanced bioluminescence to levels approaching 9.0x10(5) times above background.
Activated transcription factor nuclear factor-kappa B is present in the atherosclerotic lesion. (1996)

Nuclear factor-kappa B (NF-kappaB)/Rel transcription factors play an important role in the inducible regulation of a variety of genes involved in the inflammatory and proliferative responses of cells. The present study was designed to elucidate the implication of NF-kappaB/Rel in the pathogenesis of atherosclerosis. Activation of the dimeric NF-kappaB complex is regulated at a posttranslational level and requires the release of the inhibitor protein IkappaB. The newly developed mAb alpha-p65mAb recognizes the IkappaB binding region on the p65 (RelA) DNA binding subunit and therefore selectively reacts with p65 in activated NF-kappaB. Using immunofluorescence and immunohistochemical techniques, activated NF-kappaB was detected in the fibrotic-thickened intima/media and atheromatous areas of the atherosclerotic lesion. Activation of NF-kappaB was identified in smooth muscle cells, macrophages, and endothelial cells. Little or no activated NF-kappaB was detected in vessels lacking atherosclerosis. Electrophoretic mobility shift assays and colocalization of activated NF-kappaB with NF-kappaB target gene expression suggest functional implications for this transcription factor in the atherosclerotic lesion. This study demonstrates the presence of activated NF-kappaB in human atherosclerotic tissue for the first time. Atherosclerosis, characterized by features of chronic inflammation and proliferative processes, may be a paradigm for the involvement of NF-kappaB/Rel in chronic inflammatory disease.
Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination (2007)

The bacterial chromosome and plasmids can be engineered in vivo by homologous recombination using PCR products and synthetic oligonucleotides as substrates. This is possible because bacteriophage-encoded recombination functions efficiently to recombine sequences with homologies as short as 35 to 40 bases. This recombineering allows DNA sequences to be inserted or deleted without regard to location of restriction sites. This unit first describes preparation of electrocompetent cells expressing the recombineering functions and their transformation with dsDNA or ssDNA. Support protocols describe a two-step method of making genetic alterations without leaving any unwanted changes, and a method for retrieving a genetic marker (cloning) from the E. coli chromosome or a co-electroporated DNA fragment and moving it onto a plasmid. A method is also given to screen for unselected mutations. Additional protocols describe removal of defective prophage, methods for recombineering.
A classification of compression methods and their usefulness for a large data processing center (1975)

The compression techniques surveyed in this paper all work to reduce storage space for data files at the price of increased CPU activity needed for compression and decompression. As CPU time becomes cheaper relative to the cost of external storage devices, compression appears as an increasingly attractive option for dealing with large files.
Intrinsic secondary structure propensities of the amino acids, using statistical ϕ–ψ matrices: Comparison with experimental scales (1994)

Today there are several different experimental scales for the intrinsic alpha-helix as well as beta-strand propensities of the 20 amino acids obtained from the thermodynamic analysis of various model systems. These scales do not compare well with those extracted from statistical analysis of three-dimensional structure databases. Possible explanations for this could be the limited size of the databases used, the definitions of intrinsic propensities, or the theoretical approach. Here we report a statistical determination of alpha-helix and beta-strand propensities derived from the analysis of a database of 279 three-dimensional structures. Contrary to what has been generally done, we have considered a particular residue as in alpha-helix or beta-strand conformation by looking only at its dihedral angles (phi-psi matrices). Neither the identity nor the conformation of the surrounding residues in the amino acid sequence has been taken into consideration. Pseudoenergy empirical scales have been calculated from the statistical propensities. These scales agree very well with the experimental ones in relative and absolute terms. Moreover, its correlation with the average of the experimental scales for alpha-helix or beta-strand is as good as the correlations of the individual experimental scales with the average. These results show that by using a large enough database and a proper definition for the secondary structure propensities, it is possible to obtain a scale as good as any of experimental origin. Interestingly the phi-psi analysis of the Ramachandran plot suggests that the amino acids could have different beta-strand propensities in different subregions of the beta-strand area.
RESPAID: computer aided decision support for respiratory data in ICU (2003)

A prototype developed to support interpretation of respiratory data for ventilated patients is described. Data are taken from standard respirators and/or monitors used in intensive care units (ICUs). An initial knowledge base was built from data given by four specialists in intensive care. Both quantitative and qualitative aspects were taken into account. Major attention was paid to different aspects of the system: monitor interface to produce valid data, user interface and time representation. The prototype, called RESPAID, runs in real-time on an IBM PC AT3 with first class shell. This shell uses the concept of learning from examples. RESPAID is currently undergoing clinical validation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Current trends in quantitative proteomics (2009)

It was inevitable that as soon as mass spectrometrists were able to tell biologists which proteins were in their samples, the next question would be how much of these proteins were present. This has turned out to be a much more challenging question. In this review, we describe the multiple ways that mass spectrometry has attempted to address this issue, both for relative quantitation and for absolute quantitation of proteins. There is no single method that will work for every problem or for every sample. What we present here is a variety of techniques, with guidelines that we hope will assist the researcher in selecting the most appropriate technique for the particular biological problem that needs to be addressed. We need to emphasize that this is a very active area of proteomics research-new quantitative methods are continuously being introduced and some 'pitfalls' of older methods are just being discovered. However, even though there is no perfect technique--and a better technique may be developed tomorrow--valuable information on biomarkers and pathways can be obtained using these currently available methods.
Architecture and applications of the Connection Machine (1988)

The concept of data-parallel computers is explained, and their architecture of the Connection Machine (CM), which implements this approach, is described. It provides 64 K physical processing elements, millions of virtual processing elements with its virtual processor mechanism, and general-purpose, reconfigurable communications networks. The evolution of the CM architecture is examined, and the software environment, engineering and physical characteristics, and performance of the current embodiment (the CM-2) are discussed. Applications of the CM to molecular dynamics, VLSI design and circuit simulation, and computer vision are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing (2014)

Noninvasive prenatal testing using fetal DNA in maternal plasma is an actively researched area. The current generation of tests using massively parallel sequencing is based on counting plasma DNA sequences originating from different genomic regions. In this study, we explored a different approach that is based on the use of DNA fragment size as a diagnostic parameter. This approach is dependent on the fact that circulating fetal DNA molecules are generally shorter than the corresponding maternal DNA molecules. First, we performed plasma DNA size analysis using paired-end massively parallel sequencing and microchip-based capillary electrophoresis. We demonstrated that the fetal DNA fraction in maternal plasma could be deduced from the overall size distribution of maternal plasma DNA. The fetal DNA fraction is a critical parameter affecting the accuracy of noninvasive prenatal testing using maternal plasma DNA. Second, we showed that fetal chromosomal aneuploidy could be detected by observing an aberrant proportion of short fragments from an aneuploid chromosome in the paired-end sequencing data. Using this approach, we detected fetal trisomy 21 and trisomy 18 with 100% sensitivity (T21: 36/36; T18: 27/27) and 100% specificity (non-T21: 88/88; non-T18: 97/97). For trisomy 13, the sensitivity and specificity were 95.2% (20/21) and 99% (102/103), respectively. For monosomy X, the sensitivity and specificity were both 100% (10/10 and 8/8). Thus, this study establishes the principle of size-based molecular diagnostics using plasma DNA. This approach has potential applications beyond noninvasive prenatal testing to areas such as oncology and transplantation monitoring.
Designed drug-release systems having various breathable polyurethane film-backed hydrocolloid acrylated adhesive layers for moisture healing (2014)

A series of designed drug-release systems were prepared and established for clear moisture healing. These systems were designed to have an interpenetrating polymer network (IPN) structure, which contained a breathable polyurethane film, hydrocolloidlayer, and polyacrylate adhesive layer. Breathable polyurethane film (2000 g/m(2)/24 hr) with high moisture permeability was employed as a base for new drug-release systems or wound dressings. All drug-release systems having a polyurethane film-backed hydrocolloid acrylated adhesive layer showed an increase of water uptakes with increasing time. After 114 hours, high water uptakes of drug-release systems with 20% hydrocolloid components were observed in the values of 160, 1100, and 1870% for different additional hydrocolloid components of carboxymethylcellulose, sodium alginate, and carbomer U10, respectively. New drug-release systems of polyurethane film-backed hydrocolloid/adhesive layers could be designed and established for wound care managements.
Nature's Nanotechnologists: Unveiling the Secrets of Diatoms (2004)

Diatoms are unicellular algae with ornate silica shells. Their dazzling ability to build tiny structures could inspire applications in the semiconductor industry, drug delivery, and engineering
A DFM Methodology to Evaluate the Impact of Lithography Conditions on the Speed of Critical Paths in a VLSI Circuit (2006)

This paper presents a new methodology to analyze the impact of lithography conditions on a VLSI circuit. Previous methods require a flow that is partially manual, but in this work full automation is demonstrated for the first time. OPC is run on a group of NAND gates with different dummy gates and then the gate lengths are extracted using calibrated lithography models across focus and exposure. An updated netlist is extracted, and the speed and delay are measured using SPICE. The results show over a 30% speed difference over focus for the same NAND gate. Because of the differences in the surrounding layout, the relative delay between NAND gates can differ by over 25% for the same focus and exposure conditions. Simple SPICE corner models will not capture the impact of focus and exposure for deep submicron designs and more detailed analysis is required in the future.
Utilization of Site-Directed Spin Labeling and High-Resolution Heteronuclear Nuclear Magnetic Resonance for Global Fold Determination of Large Proteins with Limited Nuclear Overhauser Effect Data (2000)

To test whether distances derived from paramagnetic broadening of (15)N heteronuclear single quantum coherence (HSQC) resonances could be used to determine the global fold of a large, perdeuterated protein, we used site-directed spin-labeling of 5 amino acids on the surface of (15)N-labeled eukaryotic translation initiation factor 4E (eIF4E). eIF4E is a 25 kDa translation initiation protein, whose solution structure was previously solved in a 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate hydrate (CHAPS) micelle of total molecular mass approximately 45-50 kDa. Distance-dependent line broadening consistent with the three-dimensional structure of eIF4E was observed for all spin-label substitutions. The paramagnetic broadening effects (PBEs) were converted into distances for modeling by a simple method comparing peak heights in (15)N-HSQC spectra before and after reduction of the nitroxide spin label with ascorbic acid. The PBEs, in combination with HN-HN nuclear Overhauser effects (NOEs) and chemical shift index (CSI) angle restraints, correctly determined the global fold of eIF4E with a backbone precision of 2.3 A (1.7 A for secondary structure elements). The global fold was not correctly determined with the HN-HN NOEs and CSI angles alone. The combination of PBEs with simulated restraints from another nuclear magnetic resonance (NMR) method for global fold determination of large proteins (methyl-protonated, highly deuterated samples) improved the quality of calculated structures. In addition, the combination of the two methods simulated from a crystal structure of an all alpha-helical protein (40 kDa farnesyl diphoshphate synthase) correctly determined the global fold where neither method individually was successful. These results show the potential feasibility of obtaining medium-resolution structures for proteins in the 40-100 kDa range via NMR.
Number of ganglion cells in glaucoma eyes compared with threshold visual field tests in the same persons. (2000)

At least 25% to 35% RGC loss is associated with statistical abnormalities in automated visual field testing. In addition, these data corroborate previous findings that RGCs with larger diameter axons preferentially die in glaucoma.
Sensor-Based Abnormal Human-Activity Detection (2008)

With the availability of affordable sensors and sensor networks, sensor-based human activity recognition has attracted much attention in artificial intelligence and ubiquitous computing. In this paper, we present a novel two-phase approach for detecting abnormal activities based on wireless sensors attached to a human body. Detecting abnormal activities is a particular important task in security monitoring and healthcare applications of sensor networks, among many others. Traditional approaches to this problem suffer from a high false positive rate, particularly when the collected sensor data are biased towards normal data while the abnormal events are rare. Therefore, there is a lack of training data for many traditional data mining methods to be applied. To solve this problem, our approach first employs a one-class support vector machine (SVM) that is trained on commonly available normal activities, which filters out the activities that have a very high probability of being normal. We then derive abnormal activity models from a general normal model via a kernel nonlinear regression (KNLR) to reduce false positive rate in an unsupervised manner. We show that our approach provides a good tradeoff between abnormality detection rate and false alarm rate, and allows abnormal activity models to be automatically derived without the need to explicitly label the abnormal training data, which are scarce. We demonstrate the effectiveness of our approach using real data collected from a sensor network that is deployed in a realistic setting.
Shape memory alloy servo actuator system with electric resistance feedback and application for active endoscope (2003)

A control system for a shape memory alloy (SMA) servo actuator, and its application to a unique medical tool, are considered. It is thought that the electric resistance value of an SMA can be utilized to monitor the transformation of the SMA directly. Therefore, an antagonistic transformation control scheme using electric resistance feedback is proposed and is verified by several experiments. This control scheme reduces the open-loop hysteresis of an SMA actuator and improves greatly its robustness against heat disturbance due to changes in the cooling condition. Research into the application of the method in an active endoscope is reported. It consists of five segments of 13 mm diameter, 40 mm length each. The bending angle of each segment can be controlled individually from outside by using antagonistic electric resistance feedback without any motion sensors. A model for smooth insertion to the colon is verified.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
BBF RFC 108: Synthetic Biology Open Language (SBOL) Version 2.0.0 (2015)

The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards.
Early Life Stage Toxicity of 2,3,7,8-Tetrachlorodibenzo-p-dioxin in Zebrafish (Danio rerio) (1997)

Toxicity and histopathology of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in zebrafish (Danio rerio) early life stages was characterized from 12 to 240 hr postfertilization (hpf) following water-borne exposure of newly fertilized eggs. TCDD did not increase egg mortality (0-48 hpf), nor did it affect time to hatching (48-96 hpf). Egg doses of 1.5 ng [3H]TCDD/g or greater elicited toxic responses in zebrafish larvae. Pericardial edema and craniofacial malformations were first observed at 72 hpf, followed by the onset of yolk sac edema (96 hpf) and mortality (132 hpf). At 240 hpf the ED50s for pericardial edema, yolk sac edema, and craniofacial malformations were 2.2, 2.1, and 1.9 ng [3H]TCDD/g egg, respectively. The LD50, determined at 240 hpf, was 2.5 ng [3H]TCDD/g egg. Severe hemodynamic changes, observed as slowed blood flow in vascular beds of the trunk, head, and gills and slowed heart rate, occurred in TCDD-treated zebrafish prior to or coincident with the onset of gross signs of toxicity. Histological examination of TCDD-treated zebrafish revealed a variety of epithelial tissue lesions including arrested gill development and ballooning degeneration and/or necrosis of the renal tubules, hepatocytes, pancreas, and all major brain regions. Mesenchymal tissue lesions included subcutaneous edema in the head, trunk, and yolk sac, edema of the pericardium and skeletal muscle, and underdevelopment of the swim bladder. This demonstration of zebrafish responsiveness to TCDD early life stage toxicity coupled with the considerable information on developmental biology and genetics of zebrafish provides a foundation for future investigations into the mechanism of TCDD developmental toxicity.