gebhart/patrepeval huggingface dataset:
Molecular Size Analysis of<i>Haemophilus Influenzae</i>Type B Capsular Polysaccharide (1993)

Abstract The molar mass and molar mass distribution of polyribosyl ribitol phosphate (PRP) was determined using high performance size-exclusion chromatography with light scattering, viscometric, and refractive index detection. Light scattering data showed the PRP preparations to have an Mw of ca. 75,000, and a polydispersity (Mw/Mn) of about 1.46. Based on integration of the molar mass and intrinsic viscosity data, the Mark-Houwink-Sakurada coefficients for PRP were determined to be a = 1.45, and K = 3.57×10−6 cm3/g for 0.2 M ammonium acetate, pH 7.0, and a = 1.54 and K= 0.6×10−6 cm3/g for 0.1 M sodium phosphate, pH 7.2. The values of a indicate that PRP is a rigid, rod-like molecule. The rigidity of the PRP molecules is characterized by unperturbed dimensions (<Ro>/M1/2) of 0.24 nm in ammonium acetate buffer and 0.22 nm in sodium phosphate buffer. These results suggest that PRP likely has a highly ordered secondary structure.
Silencing of Keratinocyte Growth Factor Receptor Restores 5-Fluorouracil and Tamoxifen Efficacy on Responsive Cancer Cells (2008)

These findings suggest that selective inhibition of the KGF/KGFR pathway may provide a useful tool to ameliorate the efficacy of the therapeutic strategies for certain epithelial tumors.
Enzymatische Synthese von Peptiden und <i>Ras</i>‐Lipopeptiden unter Verwendung des Cholinesters als löslichkeitsvermittelnder Schutz‐ und Aktivierungsgruppe (1996)

Unter mildesten Bedingungen und vollkommen selektiv kann mit Hilfe von Cholinesterase die löslichkeitsvermittelnde Cholinester‐Schutzgruppe abgespalten werden, so daß Peptide und Lipopeptide in hohen Ausbeuten hergestellt werden können. Mit dieser enzymlabilen Schutzgruppe gelang die Synthese des S‐palmitoylierten und S‐farnesylierten C‐terminalen Lipohexapeptids des menschlichen N‐ Ras ‐Proteins.
Use of acoustic temperature measurements in the cement manufacturing pyroprocess (2005)

Acoustic pyrometry enables accurate, reliable gas temperature measurements for use in combustion and emission control systems. This paper reviews traditional temperature measurement techniques, then focuses on two practical applications in the cement manufacturing pyroprocess that have utilized acoustic pyrometry for monitoring of gas temperatures. Progress in acoustic pyrometer technology has enabled the reliable measurement of gas temperatures, providing instantaneous temperature data, which can be used on a real-time basis for controlling operations, minimizing forced outages, and avoiding excessive NOx generation. This information can support process tuning and optimization programs to improve plant operation. The method also provides a valuable tool for obtaining empirical data to help guide design modifications, and characterize process performance.
Capacity and Efficiency in Variable Speed, Vapor Injection and Multi-Compressor Systems (2004)

Air conditioning and refrigeration systems are designed to meet the load at some particular design\nconditions. At off-design conditions, the compressor is either cycled or a variable speed drive enables the\ncompressor to run at a speed that matches the load. However, cycling can incur efficiency losses as large as 10-20%\nof total compressor power. Similarly, the variable speed compressors suffer from an efficiency penalty as a result of\nthe losses in the inverter drive (4-6%).\nPart 1 of this report focuses on the use of tandem compressors, that is, a combination of two or more\ncompressors running in parallel with each other, to more closely match the load at different conditions. Simulation\nmodels were run for various operating conditions and the results from the tandem simulations were compared with\nthe single speed and the variable speed compressor results, showing a significant COP over the single speed case\nand a smaller improvement over the variable speed case. Temperature data from Pittsburgh and Dallas was then\nincorporated, and the optimum compressor sizing and operating strategies were compared. Results again showed a\nCOP gain of 7.5% and 6.2% for the two cities, respectively, over the case of a single-speed compressor, and 2.2%\nand 2.0% compared to a variable-speed compressor.\nPart 2 focuses on vapor injection in case of scroll compressors used in air-conditioning and refrigeration\napplications. Vapor injection alters the normal refrigeration cycle by adding an injection port to the scroll\ncompressor. After partial expansion upstream of the evaporator, refrigerant vapor is injected into the compressor. It\nsaves compressor energy because that fraction of the flow needs only partial compression, and saves compressor\nvolume because less vapor enters the suction port and the refrigerating effect increases due to the lower inlet quality.\nSimulation models were run for different operating conditions and it was discovered that for systems sized to meet\nthe same design load, the VI systems had a higher COP of around 8-10%, for air-conditioning applications.\nSimilarly for the refrigeration case, the VI system registered a COP increase of as much 16%. VI systems also\nhelped in reducing the compressor displacement by around 25% in the air-conditioning and 30% in the refrigeration\ncase respectively.
Chaperone activation by unfolding (2013)

Conditionally disordered proteins can alternate between highly ordered and less ordered configurations under physiological conditions. Whereas protein function is often associated with the ordered conformation, for some of these conditionally unstructured proteins, the opposite applies: Their activation is associated with their unfolding. An example is the small periplasmic chaperone HdeA, which is critical for the ability of enteric bacterial pathogens like Escherichia coli to survive passage through extremely acidic environments, such as the human stomach. At neutral pH, HdeA is a chaperone-inactive dimer. On a shift to low pH, however, HdeA monomerizes, partially unfolds, and becomes rapidly active in preventing the aggregation of substrate proteins. By mutating two aspartic acid residues predicted to be responsible for the pH-dependent monomerization of HdeA, we have succeeded in isolating an HdeA mutant that is active at neutral pH. We find this HdeA mutant to be substantially destabilized, partially unfolded, and mainly monomeric at near-neutral pH at a concentration at which it prevents aggregation of a substrate protein. These results provide convincing evidence for direct activation of a protein by partial unfolding.
Isolation and site-directed mutagenesis of DNA methyltransferase SssI (2007)

Prokaryotic DNA methyltransferase SssI (M.SssI) methylates cytosines at C5 in CpG sequences. Bacterial strains that produced M.SssI and its mutants as His6-tagged proteins were constructed. To verify the role of Ser300 in recognizing the CpG sequence by the enzyme, Ser300 was replaced by Gly or Pro. The substitutions had virtually no effect on DNA binding and methylation by M.SssI apart from a slight decrease in binding in the case of S300P. It was assumed that no contact with DNA is formed by the side chain of Ser300 and the carbonyl oxygen and amide nitrogen of its peptide bonds. In addition, Ala was substituted for highly conserved Val188, presumably involved in stabilization of the flipped-out cytosine during the reaction. The substitution decreased fivefold the dissociation constant of the enzyme-substrate complex and halved the initial rate of DNA methylation. Despite the lack of a considerable effect of V188A, it was assumed that Val188 does form a contact with the target cytosine, but such a contact is formed with Ala in the case of the V188A mutant.
Tire Pressure Monitoring System encryption to improve vehicular security (2016)

Vehicles are increasingly wirelessly connected and each wireless connection is a potential cyber threat surface. Many of these wireless communications are related to the infotainment systems and are optional, some are not. Since 2008, when the U.S. government mandated the need for real-time tire pressure diagnostics, automotive manufacturers have inserted Tire Pressure Monitoring System (TPMS)-based devices in all vehicles sold domestically. These sensors are divided into “direct” and “indirect” TPMS based on the mechanisms used to observe the tire pressure, temperature, and other characteristics; while marginally more expensive, most such systems are directly embedded in the tire to achieve the diagnostics requirements stated in National Highway Traffic Safety Administration [1], [2], necessitating a wireless communications link back to a car's Controller Area Network (CAN) bus and engine control unit (ECU). In this paper, we seek to evaluate the cyber-security of that TPMS wireless communications interface, proposing and evaluating the viability of incorporating a more secure TPMS protocol that takes advantage of simple linear feedback shift register (LFSR)-based message encryption. The proposed models were designed and implemented in both a Universal Serial Radio Peripheral (USRP) N210 software defined radio (SDR) testbed that replicates each side of the TPMS link; the resulting capabilities were also simulated on an inexpensive Arduino platform to demonstrate cost realism in the threat to the TPMS system.
Photochemistry of 3-Substituted Bicyclo[3.1.0]hex-3-en-2-ones. Regioselective Synthesis of <i>O</i><i>rtho</i>-Substituted Phenols by Pauson−Khand Reaction (2001)

[reaction: see text] 3-Substituted bicyclo[3.1.0]hex-3-en-2-ones 3, easily obtained by Pauson-Khand reaction between terminal alkynes and cyclopropene, have been quantitatively converted into ortho-substituted phenols 4 by irradiation with UV light (350 nm). The kinetics and mechanism of this photochemical process have been studied by means of FT-IR and semiempirical (AM1 3x3 CI) calculations.
Protein Tertiary Structure Prediction (2000)

Abstract This unit addresses how to predict the tertiary structure of a protein from its amino acid sequence using computational methods. Three types of prediction methods‐‐homology modeling, fold recognition, and ab initio prediction‐‐are introduced.
Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance (2014)

Both pipelines, GATK multi-sample calling and Illumina CASAVA single sample calling, have highly similar performance in SNP calling at the level of putatively causative variants.
Semi-supervised deep learning for object tracking and classification (2014)

A semi-supervised deep learning paradigm is proposed for object classification/tracking. The method addresses the main difficulties of deep learning, by allowing unsupervised data to initially configure the network and then a gradient descent optimization scheme is triggered to fine tune the data. Unsupervised learning transforms the input data into smaller and more abstract forms of representations and therefore improves the stability, convergence and performance of the model. Additionally, an adaptive approach is presented in a way to allow dynamic modification of the model to the current visual conditions. Adaptation is performed by exploiting both unsupervised and supervised samples, coming by the application of a combined motion/deep learning tracker activating only at frames a decision mechanisms ascertains retraining.
Repeated, noninvasive, high resolution spectral domain optical coherence tomography imaging of zebrafish embryos. (2008)

SD-OCT allowed noninvasive, in vivo, ultra-high resolution, high-speed imaging of zebrafish embryos in their native state. The ability to measure structural and functional features repeatedly on the same specimen, without the need to sacrifice, promises to be a powerful tool in small animal developmental imaging.
Performance Analysis of Arithmetic Operations in Homomorphic Encryption (2010)

Homomorphic encryption allows computation on encrypted data and may protect privacy in cloud computing. Is homomorphic encryption ready for deployment? This paper is an attempt to answer the question.
Assessment of spatial inhomogeneities in intima media thickness along an arterial segment using its dynamic behavior (2003)

To assess locally deviating structural and mechanical properties of arterial walls, the spatial variance in end-diastolic intima media thickness (IMT) and the change in IMT during the cardiac cycle (DeltaIMT) were determined along a short segment of the common carotid artery (15.86 mm), at 16 positions simultaneously. Intrasubject spatial inhomogeneities along the artery were revealed by a spatial variance significantly larger than the temporal variance over several beats. If differences between positions were confirmed, the extent of the inhomogeneity was obtained by comparison of IMT and DeltaIMT at each position with their spatial medians +/- the least-significant difference. Because no intersubject comparisons were necessary, a single session of several measurements was sufficient to assess inhomogeneities in the arterial wall properties of a subject, making the method independent of biological variability between subjects. The method was evaluated on 47 presumed healthy subjects (age range 21-75 yr). In 22 subjects, spatial inhomogeneities in DeltaIMT occurred (P < 0.05). In young subjects, DeltaIMT was locally decreased, i.e., in systole inhomogeneities were less compressed than their surrounding tissue. In older subjects, DeltaIMT was locally increased, i.e., the inhomogeneity was locally more compressed than its surrounding wall tissue.
Temporal Trends in the Utilization of Diagnostic Testing and Treatments for Cardiovascular Disease in the United States, 1993–2001 (2006)

Temporal increases in the use of noninvasive and invasive cardiac services are not explained by changes in disease prevalence and have not succeeded in narrowing preexisting treatment differences by gender and race. Such increases, although conferring benefit for some, may expose others to risk and cost without benefit.
Risk for Myopathy With Statin Therapy in High-Risk Patients (2003)

Emerging data suggest that the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors (statins) offer important benefits for the large population of individuals at high risk for coronary heart disease. This population encompasses a sizable portion of individuals who are also at high risk for drug-drug interactions due to their need for multiple medications. In general, statins are associated with a very small risk for myopathy (which may progress to fatal or nonfatal rhabdomyolysis); however, the potential for drug-drug interactions is known to increase this risk in specific high-risk groups. The incidence of myopathy associated with statin therapy is dose related and is increased when statins are used in combination with agents that share common metabolic pathways. Of particular concern is the potential for interactions with other lipid-lowering agents such as fibrates and niacin (nicotinic acid), which may be used in patients with mixed lipidemia, and with immunosuppressive agents, such as cyclosporine, which are commonly used in patients after transplantation. Clinicians should be alert to the potential for drug-drug interactions to minimize the risk of myopathy during long-term statin therapy in patients at high risk for coronary heart disease.
Effect of Gender on Atrial Electrophysiologic Changes Induced by Rapid Atrial Pacing and Elevation of Atrial Pressure (2001)

The results of this study demonstrate a significant gender difference in atrial electrophysiologic changes in response to rapid atrial pacing and an increase in atrial pressure. The effect of menopause on the observed changes suggests that the gender differences may be mediated by the effects of estrogen on atrial electrophysiologic properties.
Structural properties of a low Earth orbit satellite constellation - the Walker delta network (2002)

The Walker (1984) delta satellite constellation appears to be practical to serve as a low Earth orbit satellite network to provide world-wide networking. The structural properties of the Walker delta network, including diameter, mean message traversal, traffic density, and network saturation conditions are investigated and presented. Three different traffic patterns are used in this study. It has been found that for a fixed number of satellites, the Walker delta network can provide minimum mean message traversal, minimum traffic density and maximum traffic injection rate provided that the number of orbital planes is equal to the number of satellites in each orbital plane. Regarding the injection of messages from ground stations to the satellite network, the network with a smaller size can accept more messages than a network with a larger size before the network saturates. Furthermore, an adaptive routing algorithm, which always routes the message to its destination through one of several available minimal paths, is also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Cell Migration from Baby to Mother (2007)

Fetal cells migrate into the mother during pregnancy. Fetomaternal transfer probably occurs in all pregnancies and in humans the fetal cells can persist for decades. Microchimeric fetal cells are found in various maternal tissues and organs including blood, bone marrow, skin and liver. In mice, fetal cells have also been found in the brain. The fetal cells also appear to target sites of injury. Fetomaternal microchimerism may have important implications for the immune status of women, influencing autoimmunity and tolerance to transplants. Further understanding of the ability of fetal cells to cross both the placental and blood-brain barriers, to migrate into diverse tissues, and to differentiate into multiple cell types may also advance strategies for intravenous transplantation of stem cells for cytotherapeutic repair. Here we discuss hypotheses for how fetal cells cross the placental and blood-brain barriers and the persistence and distribution of fetal cells in the mother.
Omegalib: A multi-view application framework for hybrid reality display environments (2014)

In the domain of large-scale visualization instruments, hybrid reality environments (HREs) are a recent innovation that combines the best-in-class capabilities of immersive environments, with the best-in-class capabilities of ultra-high-resolution display walls. HREs create a seamless 2D/3D environment that supports both information-rich analysis as well as virtual reality simulation exploration at a resolution matching human visual acuity. Co-located research groups in HREs tend to work on a variety of tasks during a research session (sometimes in parallel), and these tasks require 2D data views, 3D views, linking between them and the ability to bring in (or hide) data quickly as needed. In this paper we present Omegalib, a software framework that facilitates application development on HREs. Omegalib is designed to support dynamic reconfigurability of the display environment, so that areas of the display can be interactively allocated to 2D or 3D workspaces as needed. Compared to existing frameworks and toolkits, Omegalib makes it possible to have multiple immersive applications running on a cluster-controlled display system, have different input sources dynamically routed to applications, and have rendering results optionally redirected to a distributed compositing manager. Omegalib supports pluggable front-ends, to simplify the integration of third-party libraries like OpenGL, OpenSceneGraph, and the Visualization Toolkit (VTK). We present examples of applications developed with Omegalib for the 74-megapixel, 72-tile CAVE2™ system, and show how a Hybrid Reality Environment proved effective in supporting work for a co-located research group in the environmental sciences.
Phencyclidine-induced psychosis (1978)

During a 13-month period, 9 patients with phencyclidine-induced psychosis were admitted to Darnall Army Hospital. They exhibited hostility agitation, and tangentiality and had delusions of influence and religious grandiosity. Six subjects reported auditory hallucinations, and 4 were disoriented in at least 1 sphere. Despite treatment with antipsychotic medication, the psychotic episodes often persisted for more than 30 days. Our clinical finding of prolonged psychotic reactions, together with previous reports of the effects of phencyclidine, suggests that phenycyclidine provides an intriguing drug model for schizophrenia.
Coupling Reaction of Grignard Reagents with α,ω-Dibromoalkanes in the Presence of Copper(I) Bromide-HMPA:Preparation of α,ω-Bis(vinylaryl)alkanes (1986)

Abstract The coupling reaction of Grignard reagents with α,β-dibromoalkanes took place smoothly in THF/ HMPA (12:1) in the presence of a catalytic amount of copper(I) bromide and gave the products in 60–100% yields. Several α,ω-bis(vinylaryl)alkanes were prepared in reasonable yields by the application of this reaction.
Identification of higher-order functional domains in the human ENCODE regions (2007)

It has long been posited that human and other large genomes are organized into higher-order (i.e., greater than gene-sized) functional domains. We hypothesized that diverse experimental data types generated by The ENCODE Project Consortium could be combined to delineate active and quiescent or repressed functional domains and thereby illuminate the higher-order functional architecture of the genome. To address this, we coupled wavelet analysis with hidden Markov models for unbiased discovery of "domain-level" behavior in high-resolution functional genomic data, including activating and repressive histone modifications, RNA output, and DNA replication timing. We find that higher-order patterns in these data types are largely concordant and may be analyzed collectively in the context of HeLa cells to delineate 53 active and 62 repressed functional domains within the ENCODE regions. Active domains comprise approximately 44% of the ENCODE regions but contain approximately 75%-80% of annotated genes, transcripts, and CpG islands. Repressed domains are enriched in certain classes of repetitive elements and, surprisingly, in evolutionarily conserved nonexonic sequences. The functional domain structure of the ENCODE regions appears to be largely stable across different cell types. Taken together, our results suggest that higher-order functional domains represent a fundamental organizing principle of human genome architecture.
Preparation of a DNA matrix via an electrqchemically directed copolymerization of pyrrole and oligonucleotides bearing a pyrrole group (1994)

A new methodology for the preparation of addressed DNA matrices is described. The process includes an electrochemically directed copolymerization of pyrrole and oligonucleotides bearing on their 5' end a pyrrole moiety introduced by phosphoramidite chemistry. The electro-controlled synthesis of the copolymer (poly-pyrrole) gives, in one step, a solid conducting film deposited on the surface of an electrode. The resulting polymer consists of pyrrole chains bearing covalently linked oligonucleotide. The polymer growth is limited to the electrode surface, so that it is possible to prepare a DNA matrix on a multiple electrode device by successive copolymerizations. A support bearing four oligonucleotides was used to detect three ras mutations on a synthetic DNA fragment.