gebhart/patrepeval huggingface dataset:
Cloning of chicken embryo tRNA genes using single stranded nucleosomal DNA highly enriched for tRNA complementary sequences (1979)

DNA from chicken embryo nucleosome tetramers (about 760 base pairs in size) was enriched for tRNA genes by RPC-5 chromatography. The enriched DNA was hybridized with chicken embryo total tRNA and the hybridized DNA isolated utilizing a) avidinbiotin interaction, b) diazobenzyloxymethyl paper, and c) high temperature RPC-5 chromatography. The obtained single stranded DNA highly enriched for tRNA complementary sequences was hybridized with total DNA from nucleosome monomers (140--190 base pairs in size) and the excess of non hybridized monomer nucleosome DNA removed by Sepharose 4B chromatography. The hybrid molecules obtained were made fully double stranded by incubation with E. coli DNA polymerase I, DNA ligase, and exonuclease III. DNA was inserted into plasmid pBR322 by G-C joining procedure and the recombinant DNA used to transform the E. coli strain chi 1776. More than 70% of the transformants obtained hybridize to chicken embryo total tRNA.
Cloud-Based Software Platform for Big Data Analytics in Smart Grids (2013)

This article focuses on a scalable software platform for the Smart Grid cyber-physical system using cloud technologies. Dynamic Demand Response (D <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> R) is a challenge-application to perform intelligent demand-side management and relieve peak load in Smart Power Grids. The platform offers an adaptive information integration pipeline for ingesting dynamic data; a secure repository for researchers to share knowledge; scalable machine-learning models trained over massive datasets for agile demand forecasting; and a portal for visualizing consumption patterns, and validated at the University of Southern California's campus microgrid. The article examines the role of clouds and their tradeoffs for use in the Smart Grid Cyber-Physical Sagileystem.
Catalytic Electrophilic Halogenations and Haloalkoxylations by Non‐Heme Iron Halides (2014)

Abstract Synthetic non‐heme iron halides promote sub‐stoichiometric aliphatic halogenation reactions via a radical mechanism. Complementary to such activity, we have developed an electrophilic halogenation of arenes employing non‐heme iron halides. A catalytic version of these reactions has also been developed using potassium halide as the source of halogen atom for arenes at room temperature. Efforts towards understanding the mechanism of these catalytic halogenation reactions led to the discovery of the haloalkoxylation of olefins by a non‐heme iron complex. Implications of these findings with respect to natural transformations are also discussed. magnified image
VOCL: An optimized environment for transparent virtualization of graphics processing units (2012)

Graphics processing units (GPUs) have been widely used for general-purpose computation acceleration. However, current programming models such as CUDA and OpenCL can support GPUs only on the local computing node, where the application execution is tightly coupled to the physical GPU hardware. In this work, we propose a virtual OpenCL (VOCL) framework to support the transparent utilization of local or remote GPUs. This framework, based on the OpenCL programming model, exposes physical GPUs as decoupled virtual resources that can be transparently managed independent of the application execution. The proposed framework requires no source code modifications. We also propose various strategies for reducing the overhead caused by data communication and kernel launching and demonstrate about 85% of the data write bandwidth and 90% of the data read bandwidth compared to data write and read, respectively, in a native nonvirtualized environment. We evaluate the performance of VOCL using four real-world applications with various computation and memory access intensities and demonstrate that compute-intensive applications can execute with negligible overhead in the VOCL environment.
Nitric oxide metabolites and interleukin‐6 in cerebrospinal fluid from multiple sclerosis patients (2002)

Interleukin-6 (IL-6) and nitric oxide (NO) are implicated in the pathology of multiple sclerosis (MS). We have investigated the levels of these mediators in the cerebrospinal fluid (CSF) from 50 patients with MS and 23 control subjects. Mean CSF IL-6 level was higher in the total MS group in comparison with controls, but not significantly, whilst the difference between patients with stable MS and controls reached the level of statistical significance. Mean CSF nitrite/nitrate level was significantly higher in the total MS group compared with the control group, as well as in active MS patients versus controls. There was significant difference neither in the mean CSF IL-6 nor in nitrite/nitrate levels between active and stable MS patients. Interestingly, we observed a significant negative correlation between IL-6 and nitrite/nitrate levels in the CSF in the total MS group. Such a trend existed in both subgroups with active and stable MS, but without reaching the level of statistical significance. Our data further support the involvement of IL-6 and NO in ongoing pathological processes in MS, suggesting their potential interplay within the central nervous system in this disease.
Synthesis and conformational investigation of cyclic dipeptides: 7‐membered rings containing α‐ and β‐amino acids (2003)

The synthesis of heterocyclic compounds containing the 7-membered ring system [1,4]diazepane-2,5-dione is described. The aim of this study was to elaborate the solid phase and solution synthesis of eight representatives of the cyclic scaffold and to investigate their chemical stability and their conformational properties. The solid phase synthesis was performed on aminomethyl polystyrene resin using 5-(4-formyl-3,5-dimethoxyphenoxy)valeric acid as a backbone linker system (BAL-linker). After attachment of the alpha- and beta-amino acid and deprotection of the amino function, the dipeptide ester was obtained. The molecule was cyclized on the solid support by treatment with NaOMe in MeOH/NMP. The product was cleaved from the resin by TFA. For the solution pathway the linear dipeptides were synthesized by coupling of the BOC-protected L-alpha-amino acid with the beta2-amino acid ester (EDC/HOBT). After N- and C-terminal deprotection of the dipeptide, the linear species was cyclized with EDC/HOBT at a concentration of 3 mM in DMF. The products showed high chemical stability after storage in DMSO at room temperature for weeks. The x-ray and two dimensional NMR investigations were performed to investigate the conformation of the molecules. Three types of configuration could be distinguished by NMR, depending on the substitution pattern of the cyclic compounds. The x-ray results confirmed the NMR observations. In general the 7-membered rings showed rigidity, thus they could represent optimal scaffolds for new receptor ligands.
Automated polarimeter–macroscope for optical mapping of birefringence, azimuths, and transmission in large area wafers. Part II. Measurement setup and results (1995)

In the first part of this work (see preceding paper) the theory of the method lying upon a novel concept of birefringence, azimuths, and transmission mapping in large area (up to 6 in. diameter) wafers has been presented. The arrangement consisting of two HR-type linear polarizers rotated simultaneously by a stepper motor versus an immobile wafer and using a video frame grabber (VFG)/TV camera detecting system is capable of collecting data and plotting the three maps within a fraction of a minute. A detailed error analysis presented in the preceding paper has shown that in usual circumstances the VFG with 256 grey levels enables determination of birefringence with an error not greater than approximately 5×10−7, whereas errors of the azimuths and transmission are fractions of a degree and of a percent, respectively. In this part of the work the arrangement constructed is fully described and a set of polariscopic images and measured maps are presented for an exemplary 4 in. GaAs wafer.
MULTIPLICATIVE GROUP IN A FINITE RING (1993)

In this paper, we will show that the multiplicative group G in a finite ring R with identity 1 has a (B, N)-pair satisfying the following conditions; (1) G=BNB where B and N are subgroups of G. (2) B.cap.N is a normal subgroup of N and W = N/(B.cap.N), is generated by a set S = { , , .., } where .mem.N/(B.cap.N), .iden.1 and .neq.1. (3) For any s.mem.S and w.mem.W, we have sBw.contnd.BwB.cup.BswB. (4) We have sBs not .subeq. B for any s.mem.S. When G, B, N and S satisfy the above conditions, we say that the quadruple (G, B, N, S) is a Tits system. The group W is called the Weyl gorup of the Tits system.ystem.m.
Unified multi-camera detection and tracking using region-matching (2002)

We describe an algorithm for detecting and tracking multiple people in a cluttered scene using multiple synchronized cameras located far away from each other. This camera arrangement results in multiple wide-baseline camera systems. We segment each image, and then, for each pair we compare regions across the views along epipolar lines. The centers of the matching segments are then back-projected to identify 3D points in the scene potentially corresponding to people. These 3D points are then projected onto the ground plane. The results from these wide-baseline camera systems are then combined using a scheme that rejects outliers and gives very robust estimates of the 2D locations of the people. These estimates are then used to track people across time. We have found that the algorithm works quite well in practice in scenes containing multiple people even when they occlude each other in every camera view.
Potential turbine fuels from western Kentucky tar sand bitumen (1987)

The declining quality of petroleum is a particular problem for aviation turbine fuels. Since these fuels are required to meet stringent corrosion, thermal stability and purity specification, very little in the way of contaminants or heteroatoms can be tolerated. However, heavier and more sour crude supplied result in lower straight-run turbine fuel yields, higher sulfur contents, and higher aromatic contents. While all turbine fuels were originally prepared from high quality stocks by distillation, many commercial and military fuels now require hydrotreatment to meet specifications. The work described in this program extrapolates these present trends to very heavy feedstocks. Tar sands bitumen and heavy crude oils are low API gravity, high viscosity hydrocarbonaceous materials commonly exhibiting high levels of heteroatomic species, high metals content and high levels of asphaltenes, plus water and solids not readily separated by conventional technology without dilution. Tar sands bitumen is highly cyclic with many polycyclic rings and naphthenic constituents. Sulfur is primarily in thiophenic structures, with nitrogen included in the ring structure. Asphaltenes are in high proportion, with a large amount of sulfur, nitrogen and metallic inclusions. Each of these characteristics represent specific concerns to refiners.
Arrhythmogenesis in Catecholaminergic Polymorphic Ventricular Tachycardia (2006)

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited disease characterized by life threatening arrhythmias and mutations in the gene encoding the ryanodine receptor (RyR2). Disagreement exists on whether (1) RyR2 mutations induce abnormal calcium transients in the absence of adrenergic stimulation; (2) decreased affinity of mutant RyR2 for FKBP12.6 causes CPVT; (3) K201 prevent arrhythmias by normalizing the FKBP12.6-RyR2 binding. We studied ventricular myocytes isolated from wild-type (WT) and knock-in mice harboring the R4496C mutation (RyR2(R4496C+/-)). Pacing protocols did not elicit delayed afterdepolarizations (DADs) (n=20) in WT but induced DADs in 21 of 33 (63%) RyR2(R4496C+/-) myocytes (P=0.001). Superfusion with isoproterenol (30 nmol/L) induced small DADs (45%) and no triggered activity in WT myocytes, whereas it elicited DADs in 87% and triggered activity in 60% of RyR2(R4496C+/-) myocytes (P=0.001). DADs and triggered activity were abolished by ryanodine (10 micromol/L) but not by K201 (1 micromol/L or 10 micromol/L). In vivo administration of K201 failed to prevent induction of polymorphic ventricular tachycardia (VT) in RyR2(R4496C+/-) mice. Measurement of the FKBP12.6/RyR2 ratio in the heavy sarcoplasmic reticulum membrane showed normal RyR2-FKBP12.6 interaction both in WT and RyR2(R4496C+/-) either before and after treatment with caffeine and epinephrine. We suggest that (1) triggered activity is the likely arrhythmogenic mechanism of CPVT; (2) K201 fails to prevent DADs in RyR2(R4496C+/-) myocytes and ventricular arrhythmias in RyR2(R4496C+/-) mice; and (3) RyR2-FKBP12.6 interaction in RyR2(R4496C+/-) is identical to that of WT both before and after epinephrine and caffeine, thus suggesting that it is unlikely that the R4496C mutation interferes with the RyR2/FKBP12.6 complex.
Development and Validation of a Ureteral Anastomosis Simulation Model for Surgical Training (2013)

Superior performance on the model by more experienced surgeons demonstrates evidence of construct validity. This authentic and useful model allows surgeons to learn and practice the ureteral anastomosis portion of the ureteral reimplantation surgeries before operating on a live patient.
IL-1ra delivered from poly(lactic-co-glycolic acid) microspheres attenuates IL-1β-mediated degradation of nucleus pulposus in vitro (2012)

In this study, we successfully demonstrated that IL-1ra microspheres can attenuate the degradative effects of IL-1β on the NP for extended periods. This therapeutic strategy may be appropriate for treating early-stage, cytokine-mediated disc degeneration. Ongoing studies are focusing on testing IL-1ra microspheres in an in vivo model of disc degeneration, as a prelude to clinical translation.
Membrane‐bound tetramer and trimer Aβ oligomeric species correlate with toxicity towards cultured neurons (2015)

Amyloid beta (Aβ) peptide is the major constituent of the extracellular amyloid plaques deposited in the brains of Alzheimer's disease patients and is central to the pathogenic pathway causing this disease. The identity of the neurotoxic Aβ species remains elusive. We previously reported that Aβ toxicity correlates strongly with its neuronal cell binding leading us to hypothesize that neuronal cell death is caused by the binding of a specific oligomeric Aβ species. To identify the specific oligomeric Aβ species that is associated with cell death, we treated mouse cortical neuronal cultures with synthetic Aβ40 and Aβ42 peptides and identified that the cellular Aβ binding and neurotoxicity were time and concentration dependent. We found a significant correlation between the amount of trimer and tetramer species bound to neurons with increasing neurotoxicity. We prepared Aβ40 oligomers (up to tetramers) using photo-induced cross-linking of unmodified peptides to confirm this oligomer-specific neurotoxic activity. Our results identify the Aβ tetramer, followed by the trimer, as the most toxic low-order oligomers Aβ species. Our findings suggested that binding of amyloid-β (Aβ) tetramer and trimer, not monomer or dimer, to neurons is critical to induce neuronal cell death associated with Alzheimer's Disease. We proposed that Aβ trimer and tetramer are the potential neurotoxic Aβ species. This would provide more specific therapeutic target for Alzheimer's Disease.
A Simple and Efficient Separation of the Curcumins, the Antiprotozoal Constituents of <i>Curcuma longa</i> (2000)

A simple and efficient method for the separation of the three phenolic diketones, curcumin 1, demethoxycurcumin 2, and bis-demethoxycurcumin 3, isolated from the rhizomes of Curcuma longa has been developed. The method is of general applicability for the separation of compounds containing acidic and chelating groups and is amenable to large scale separations. The curcumins 1-3 show moderate activity against Plasmodium falciparum (IC50: 3.5, 4.2 and 3.0 micrograms/ml) and Leishmania major (IC50: 7.8, 14.1 and 21.5 micrograms/ml) respectively.
HATRIC-based identification of receptors for orphan ligands (2018)

Cellular responses depend on the interactions of extracellular ligands, such as nutrients, growth factors, or drugs, with specific cell-surface receptors. The sensitivity of these interactions to non-physiological conditions, however, makes them challenging to study using in vitro assays. Here we present HATRIC-based ligand receptor capture (HATRIC-LRC), a chemoproteomic technology that successfully identifies target receptors for orphan ligands on living cells ranging from small molecules to intact viruses. HATRIC-LRC combines a click chemistry-based, protein-centric workflow with a water-soluble catalyst to capture ligand-receptor interactions at physiological pH from as few as 1 million cells. We show HATRIC-LRC utility for general antibody target validation within the native nanoscale organization of the surfaceome, as well as receptor identification for a small molecule ligand. HATRIC-LRC further enables the identification of complex extracellular interactomes, such as the host receptor panel for influenza A virus (IAV), the causative agent of the common flu.
R<scp>ESISTANCE</scp>G<scp>ENE</scp>C<scp>OMPLEXES</scp>: Evolution and Utilization (2001)

More than 30 genes have been characterized from different plant species that provide resistance to a variety of different pathogen and pest species. The structures of most are consistent with a role in pathogen recognition and defense response signaling. Resistance genes are very abundant in plant genomes and most belong to tightly linked gene families. Evolution of R genes is driven by selection on allelic variation created by mutation and re-assorted by recombination between alleles and sometimes between different gene family members. Selection favors genes that can recognize pathogen avr gene products that are present in pathogen populations. Selection at linked gene families favors haplotypes with useful combinations of genes but a limited physiological cost to the plant. Future utilization of R genes will include transfer between related genera and identification or construction of genes that condition durable resistance to variable pathogens. Genes with durable resistance may interact with conserved pathogen elicitors or condition resistance responses that are independent of specific Avr gene interactions.
Faraday Rotation in the Absorption Edge of Amorphous Selenium (1971)

The Faraday rotation in amorphous Se has been measured with an ac technique between 1.1 and 0.64 \ensuremath{\mu} (1.127 - 1.94eV). The results are compared with a theoretical dispersion formula based on the Tauc model of optical absorption in an amorphous semiconductor. A key feature of the model is a description of the violation of the $k$-conservation rule, induced by the disorder of the amorphous state, with a single parameter $z$. For $z=0$ the dispersion formula reduces to the standard one for direct transitions, and for $z>1$ it reduces to the form for indirect transitions. A satisfactory fit is obtained with $z=0.2$, which indicates a range of local order about half that in amorphous Ge. The gap energy obtained in the fit is ${E}_{g}=2.13$ eV. This value is interpreted as further evidence for a two mechanism absorption in the absorption edge in amorphous Se. One is due to localized-molecular states and the other to delocalized bandlike states. The present experiments have allowed an optical resolution of these two absorption mechanisms, because of the different magneto-optical properties of the associated states.
Comparison of Colony Stimulation Factors on in vitro Rat and Human Neutrophil Function (1994)

The effects of rhCSFs on in vitro polymorphonuclear leukocyte (PMN) function were studied in Sprague-Dawley neonatal and adult rats and adult and umbilical cord derived human PMN to compare species response. Following in vitro exposure to buffer or rhCSFs (50-100 micrograms/ml), PMN oxidative burst, chemotactic activity and adherence protein expression were measured. RhG-CSF increased the oxidative burst of adult rat PMN as measured by chemiluminescence and altered CD11b/CD18 in resting neonatal rat but not adult rat cells. RhGM-CSF had no effect on adult rat PMN function in vitro, but led to modest changes in adult rat PMN diapedesis across rat peritoneum. No responses were noted to rhM-CSF. Human PMN responded best to GM-CSF (particularly in the neonate), intermediately to G-CSF and none to M-CSF. These experiments show that the profile of cytokine effects is not similar in adult and neonatal rat PMN when compared to human cells. The diversity of actions in other species must be considered when using rhCSFs in animal models.
Antiangiogenesis Targeting Tumor Microenvironment Synergizes Glucuronide Prodrug Antitumor Activity (2009)

Our study provides in vivo evidence that 9ACG has potential for prodrug monotherapy or in combination with antiangiognesis treatment for tumors with infiltration of macrophage or neutrophil inflammatory cells.
ExpressEther - Ethernet-Based Virtualization Technology for Reconfigurable Hardware Platform (2006)

We propose ExpressEther as Ethernet-based virtualization technology for a reconfigurable hardware platform. It groups modularized hardware resources interconnected by an Ethernet, and transports a PCI express (PCIe) packet between the grouped modules by encapsulating it into an Ethernet frame. The configuration of the group is dynamically reconfigured by an Ethernet connection, followed by standardized PCIe hot-plug event. Such reconfigurability enables sharing of a physical resource among computer entities. We demonstrate that an I/O device is shared by servers, using our developed prototype consisted of an interface card and I/O concentrator. A commercially available server and serial ATA card are used for the demonstration, without any change for an operating system, device driver, PCIe interface, and Ethernet switch. The benchmark of I/O performance shows at most 16% degradation, which is caused by the implementation matters of our prototype. No degradation is measured when data flow from an I/O to a server
Molecular cloning of avian sarcoma virus closed circular DNA: structural and biological characterization of three recombinant clones (1980)

Unintegrated, circular viral DNA, isolated from Prague A avian sarcoma virus (PrA-ASV)-infected quail cells (QT6), was cloned in the lambda vector lambda gtWES x lambda B. Three independent lambda-ASV recombinants were identified, and each contained a complete copy of the PrA-ASV genome. The arrangement of the ASV sequences within the recombinants was determined by restriction enzyme analysis and hybridization with labeled ASV-specific complementary DNA. One of the recombinants (lambda RPA101) resulted from cloning at the EcoRI site located within the terminally repeated sequence and therefore was virtually co-linear with PrA-ASV virion RNA. The other two recombinants (lambda RPA102 and 103) resulted from cloning at the EcoRI site located within the viral env gene. By restriction enzyme analysis and by measurement of R-loops formed between lambda RPA101 and PrA-ASV virion 35S RNA, the viral genome was estimated to be 9,100 bases in length. Genome length viral DNA purified from clones lambda RPA102 and 103 was biologically active. Transfection of chicken embryo cells with viral DNA, in the form of either circles or linear dimers, produced foci of transformed cells within 8 to 10 days. Linear DNA was much less efficient at inducing transformation. Viral DNA from the clone lambda RPA101 was unable to cause transformation; the basis for this defect is unknown.