gebhart/patrepeval huggingface dataset:
The SH2-like Akt homology (AH) domain of c-akt is present in multiple copies in the genome of vertebrate and invertebrate eucaryotes. Cloning and characterization of the Drosophila melanogaster c-akt homolog Dakt1. (1994)

The Akt proto-oncogene encodes a serine-threonine protein kinase whose carboxyterminal catalytic domain is closely related to the catalytic domains of all the known members of the protein kinase C (PKC) family. Akt, however, differs from PKC in its N-terminal region which contains a domain related distantly to the SH2 domain of cytoplasmic tyrosine kinases and other signalling proteins, which we have named Akt homology (AH) domain. Low stringency hybridization of a c-akt AH probe to a panel of genomic DNAs from vertebrate and invertebrate eucaryotes detected multiple DNA bands (perhaps multiple genes) in all tested species. Drosophila DNA contains at least three hybridizing DNA bands. One of them was cloned, and found by sequence analysis, to define an Akt related gene (Dakt1). Comparison between the coding regions of c-akt and Dakt1 revealed 64.6% identity at the nucleotide level and 76.5% similarity at the amino acid level. The highest degree of homology was detected in the AH domain (68.3% similarity at the amino acid level) and the catalytic domain (83.3% similarity). Additional sequence comparisons revealed that the amino acid similarity between the catalytic domains of Dkt1 and the three known members of the Drosophila protein kinase C (PKC) family, Dpkc1, Dpkc2 and Dpkc3, is 68%, 63.6% and 67.1%, respectively. Dakt1 was mapped to Drosophila chromosome 3R 89BC. Its expression is subject to developmental regulation with the highest levels detected within the fourth hour of embryonic development. These results confirm that the AH domain of Akt defines new protein families in both vertebrate and invertebrate eucaryotes. The high degree of homology between the catalytic domains of Dkt1 and the three known members of the Drosophila PKC family suggests an evolutionarily conserved functional relationship between the members of the two families.
Primary stentriever versus combined stentriever plus aspiration thrombectomy approaches: in vitro stroke model comparison (2014)

The combined stentriever-aspiration approach to thrombectomy leads to better angiographic recanalization rates than use of the stentriever alone. Further experiments are needed to test the value of balloon-guide catheters and aspiration performed using other types of catheters and modes of aspiration.
Analysis of the Deubiquitinating Enzymes of the Yeast Saccharomyces cerevisiae (2000)

Attachment of proteins to ubiquitin is reversed by specialized proteases called deubiquitinating enzymes (Dubs), which are also essential for ubiquitin precursor processing. In the genome of Saccharomyces cerevisiae, 17 potential DUB genes can be discerned. We have now constructed strains deleted for each of these genes. Surprisingly, given the essential nature of the ubiquitin system, none of the mutants is lethal or strongly growth defective under standard conditions, although a number have detectable abnormalities. Including results from this study, 14 of the 17 Dubs have now been shown to have ubiquitin-cleaving activity. The most extensively characterized yeast Dub is Doa4, which is required for both ubiquitin homeostasis and proteasome-dependent proteolysis. To help determine what distinguishes Doa4 functionally from other Dubs, we have cloned a DOA4 ortholog from the yeast Kluyveromyces lactis. The K. lactis protein is 42% identical to Doa4, but unexpectedly the K. lactis gene is slightly closer in nucleotide sequence to UBP5, which cannot substitute for DOA4 even in high dosage. The data suggest that the DOA4 locus underwent a duplication after the divergence of K. lactis and S. cerevisiae. This information will facilitate fine-structure analysis of the Doa4 protein to help delineate its key functional elements.
Real-time spatial–spectral interference measurements of ultrashort optical pulses (1997)

Real-time linear spectral interference measurements of ultrashort pulses are shown experimentally. The technique involves measurements of the two-dimensional interference pattern of the spectral interference between a reference and a signal pulse propagating at an angle with respect to each other. No postprocessing is needed to extract the spectral phase difference between the two pulses. Quadratic spectral phase distortions as well as spectral phase discontinuities are measured. The method is applicable to single-shot measurements of ultraweak pulses and is useful for identification of the critical adjustments of ultrashort pulse shapers and compressors.
A dual-layer estimator architecture for long-term localization (2008)

In this paper, we present a localization algorithm for estimating the 3D position and orientation (pose) of a moving vehicle based on visual and inertial measurements. The main advantage of the proposed method is that it provides precise pose estimates at low computational cost. This is achieved by introducing a two-layer estimation architecture that processes measurements based on their information content. Inertial measurements and feature tracks between consecutive images are processed locally in the first layer (multi-state-constraint Kalman filter) providing estimates for the motion of the vehicle at a high rate. The second layer comprises a bundle adjustment iterative estimator that operates intermittently so as to (i) reduce the effect of the linearization errors, and (ii) update the state estimates every time an area is re-visited and features are re-detected (loop closure). Through this process reliable state estimates are available continuously, while the estimation errors remain bounded during long-term operation. The performance of the developed system is demonstrated in large-scale experiments, involving a vehicle localizing within an urban area.
Theoretische Vorüberlegungen (2009)

Begriffsbestimmungen und Definitionen sind ein notwendiger aber mühseliger Teil der Wissenschaft. Notwendig, da sie eine gemeinsame Verständnisgrundlage für die in der Arbeit zentralen Begriffe und Konzepte bereitstellen. Mühselig, da Phänomene (egal ob dinglich oder abstrakt) niemals allumfassend, sondern immer nur aus einer bestimmten Perspektive beschrieben werden können, unter Vernachlässigung anderer Aspekte und möglichen Erklärungsansätzen. Grundsätzlich lassen sich Phänomene in ihrer Entstehung, in ihrem Wesen und in ihrer Funktion beschreiben. In dem Bewusstsein, dass jede Definition eine Entscheidung für eine bestimmte Perspektive (unter Ausklammerung anderer Aspekte) beinhaltet, werden in Folge die Begriffe Kommunikation, Kultur und Globalisierung sowie im folgenden Kapitel Public Relations (PR) bestimmt.
Tunable gain equalization using a Mach-Zehnder optical filter in multistage fiber amplifiers (1991)

Tunable signal gain equalization is demonstrated in three-stage Er/sup 3+/-doped fiber amplifiers using a waveguide type Mach-Zehnder (MZ) optical fiber. A 29-channel multiplexed system is examined where signal wavelengths are positioned from 1.548 to 1.555 mu m. By adjusting the MZ transmittance with the external control current, tunable gain equalization is achieved at the output of each amplifier.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Carbon Nanotube Applications in Microelectronics (2004)

The extraordinary characteristics of carbon nanotubes make them a promising candidate for applications in microelectronics. Catalyst-mediated chemical vapor deposition growth is very well suited for selective in-situ growth of nanotubes compatible with the requirements of microelectronics technology. This deposition method can be exploited for carbon nanotube vias. Semiconducting single-walled tubes can be successfully operated as carbon nanotube field effect transistors (CNTFET). A simulation of an ideal CNTFET is presented and compared with the requirements of the ITRS roadmap. Finally, we compare an upgraded CNTFET with the most advanced silicon metal oxide semiconductor field effect transistors and discuss integration issues.
Synthesis, Material Properties, and Biocompatibility of a Novel Self-Cross-Linkable Poly(caprolactone fumarate) as an Injectable Tissue Engineering Scaffold (2005)

A novel self-cross-linkable and biodegradable macromer, poly(caprolactone fumarate) (PCLF), has been developed for guided bone regeneration. This macromer is a copolymer of fumaryl chloride, which contains double bonds for in-situ cross-linking, and poly(epsilon-caprolactone), which has a flexible chain to facilitate self-cross-linkability. PCLF was characterized with Fourier transform infrared spectroscopy, 1H and 13C nuclear magnetic resonance spectroscopy, and gel permeation chromatography. Porous scaffolds were fabricated with sodium chloride particles as the porogen and a chemical initiation system. The PCLF scaffolds were characterized with scanning electron microscopy and micro-computed-tomography. The cytotoxicity and in vivo biocompatibility of PCLF were also assessed. Our results suggest that this novel copolymer, PCLF, is an injectable, self-cross-linkable, and biocompatible macromer that may be potentially used as a scaffold for tissue engineering applications.
Evaluation of Nine Automated High-Sensitivity C-Reactive Protein Methods: Implications for Clinical and Epidemiological Applications. Part 2 (2001)

Abstract Background: C-Reactive protein (CRP) can provide prognostic information about risk of future coronary events in apparently healthy subjects. This application requires higher sensitivity assays than have traditionally been available in the clinical laboratory. Methods: Nine high-sensitivity CRP (hs-CRP) methods from Dade Behring, Daiichi, Denka Seiken, Diagnostic Products Corporation, Iatron, Kamiya, Olympus, Roche, and Wako were evaluated for limit of detection, linearity, precision, prozone effect, and comparability with samples from 388 apparently healthy individuals. Results: All methods had limits of detection that were lower than the manufacturers’ claimed limit of quantification except for the Kamiya, Roche, and Wako methods. All methods were linear at 0.3–10 mg/L. The Diagnostic Products Corporation, Kamiya, Olympus, and Wako methods had imprecision (CVs) &amp;gt;10% at 0.15 mg/L. The Iatron, Olympus, and Wako methods demonstrated prozone effects at hs-CRP concentrations of 12, 206, and 117 mg/L, respectively. hs-CRP concentrations demarcating each quartile in a healthy population were method-dependent. Ninety-two to 95% of subjects were classified into the same quartile of hs-CRP established by the Dade Behring method by the Denka Seiken, Diagnostic Products Corporation, Iatron, and Wako methods. In contrast, 68–77% of subjects were classified into the same quartile by the Daiichi, Kamiya, Olympus, and Roche methods. No subject varied by more than one quartile by any method. Conclusions: Four of the nine examined hs-CRP methods classified apparently healthy subjects into quartiles of hs-CRP similar to the classifications assigned by the comparison method. Additional standardization efforts are required because an individual patient’s results will be interpreted using population-based cutpoints.
Expedient Synthesis of α-Heteroaryl Piperidines Using a Pd-Catalyzed Suzuki Cross-Coupling–Reduction Sequence (2014)

A method for the modular synthesis of α-heteroaryl piperidines is reported. The two-step procedure consists of an initial Pd-catalyzed Suzuki cross-coupling of the heteroaryl bromide with a boronate ester derived from N-Boc piperidone, followed by subsequent tetrahydropyridine reduction. Using this method, α-heteroaryl piperidine products featuring a broad range of pharmaceutically relevant azine and diazine substitutions have been prepared.
Single-Chain Soluble BG505.SOSIP gp140 Trimers as Structural and Antigenic Mimics of Mature Closed HIV-1 Env (2015)

The trimeric HIV-1 envelope glycoprotein (Env) is the sole target of virus-directed neutralizing antibody responses and a primary focus of vaccine design. Soluble mimics of Env have proven challenging to obtain and have been thought to require proteolytic cleavage into two-component subunits, gp120 and gp41, to achieve structural and antigenic mimicry of mature Env spikes on virions. Here we show that replacement of the cleavage site between gp120 and gp41 in a lead soluble gp140 construct, BG505.SOSIP, with flexible linkers can result in molecules that do not require cleavage to fold efficiently into the mature closed state. Our results provide insights into the impact of cleavage on HIV-1 Env folding. In some contexts such as genetic immunization, optimized cleavage-independent soluble gp140 constructs may have utility over the parental BG505.SOSIP, as they would not require furin cleavage to achieve mimicry of mature Env spikes on virions.
Absolute configuration of the diastereomers of adenosine 5'-O-(1-thiotriphosphate): consequences for the stereochemistry of polymerization by DNA-dependent RNA polymerase from Escherichia coli. (1978)

The diastereomers of uridyl-(3'-5')adenyl-O,O-phosphorothioate [Up(S)A] have been separated by high-performance liquid chromatography. Their identification as RP and SP follows from the RNase A digestion of these products. It was then shown, by the same method, that the R isomer is hydrolyzed by snake venom phosphodiesterase (PDEase) approximately 500 times faster than the S isomer. Similarly, the stereoisomer of adenosine 5'-O-(1-thiotriphosphate) (ATPalphaS), until now arbitrarily designated as isomer B, is hydrolyzed ca 400 times faster by PDEase than is isomer A. From these results it is concluded that the R isomers of Up(S)A and ATPalphaS, isomers B, have the same absolute configuration. It then follows that isomer A of ATPalphaS, the preferred of the two isomers as substrate for DNA-dependent RNA polymerase, has the S configuration. The implications for the stereochemistry of action of the latter enzyme are discussed.
Novel thermal curing of cycloaliphatic resins by thiol–epoxy click process with several multifunctional thiols (2017)

Abstract Novel thermosets were prepared by the base‐catalysed reaction between a cycloaliphatic resin ( ECC ) and various thiol crosslinkers. 4‐( N , N ‐Dimethylaminopyridine) ( DMAP ) was used as base catalyst for the thiol–epoxy reaction. A commercial tetrathiol ( PETMP ) and three different thiols synthesized by us, 6SH‐SQ , 3SH‐EU and 3SH‐ISO , were tested. 6SH‐SQ and 3SH‐EU were prepared from vinyl or allyl compounds from renewable resources such as squalene and eugenol, respectively. Thiol 3SH‐ISO was prepared starting from commercially available triallyl isocyanurate. A kinetic study of the mixtures was performed using differential scanning calorimetry. Stoichiometric ECC /thiol/ DMAP formulations were cured at 120 °C for 1 h, at 150 °C for 1 h and post‐cured for 30 min at 200 °C. The materials were characterized using Fourier transform infrared spectroscopy, thermogravimetric analysis and dynamic mechanical thermal analysis. The results revealed that the materials obtained from the synthesized thiols had higher thermal stability and glass transition temperatures than those obtained from the commercial PETMP . In addition, all the materials obtained exhibited very good transparency. This study proves the ability of multifunctional thiols to crosslink cycloaliphatic epoxy resins, leading to more flexible materials than those obtained by cationic homopolymerization of ECC or base‐catalysed ECC –anhydride copolymerization. © 2017 Society of Chemical Industry
Representation of freeform surfaces suitable for optimization (2012)

To represent the freeform surface shape, the axially asymmetric quadric and a new set of the orthogonal polynomials are introduced. In this representation, surface tilt, paraxial properties, and higher order surface shape are clearly separated. With this representation, the optimization process can be simple and efficient.
Atomic Coherence: Leveraging nanophotonics to build race-free cache coherence protocols (2011)

This paper advocates Atomic Coherence, a framework that simplifies cache coherence protocol specification, design, and verification by decoupling races from the protocol's operation. Atomic Coherence requires conflicting coherence requests to the same addresses be serialized with a mutex before they are issued. Once issued, requests follow a predictable race-free path. Because requests are guaranteed not to race, coherence protocols are simpler and protocol extensions are straightforward. Our implementation of Atomic Coherence uses optical mutexes because optics provides very low latency. We begin with a state-of-the-art non-atomic MOEFSI protocol and demonstrate that an atomic implementation is much simpler while imposing less than a 2% performance penalty. We then show how, in the absence of races, it is easy to add support for speculative coherence and improve performance by up to 70%. Similar performance gains may be possible in a non-atomic protocol, but not without considerable effort in race management.
Effect of Insulinase-Inhibitor on Hypoglycemic Action of Insulin (1955)

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Moving shadow and object detection in traffic scenes (2002)

We present an algorithm for segmentation of traffic scenes that distinguishes moving objects from their moving cast shadows. A fading memory estimator calculates mean and variance of all three color components for each background pixel. Given the statistics for a background pixel, simple rules for calculating its statistics when covered by a shadow are used. Then, MAP classification decisions are made for each pixel. In addition to the color features, we examine the use of neighborhood information to produce smoother classification. We also propose the use of temporal information by modifying class a priori probabilities based on predictions from the previous frame.
Conotoxin TVIIA, a novel peptide from the venom of Conus tulipa (2000)

A novel conotoxin belonging to the 'four-loop' structural class has been isolated from the venom of the piscivorous cone snail Conus tulipa. It was identified using a chemical-directed strategy based largely on mass spectrometric techniques. The new toxin, conotoxin TVIIA, consists of 30 amino-acid residues and contains three disulfide bonds. The amino-acid sequence was determined by Edman analysis as SCSGRDSRCOOVCCMGLMCSRGKCVSIYGE where O = 4-transL-hydroxyproline. Two under-hydroxylated analogues, [Pro10]TVIIA and [Pro10,11]TVIIA, were also identified in the venom of C. tulipa. The sequences of TVIIA and [Pro10]TVIIA were further verified by chemical synthesis and coelution studies with native material. Conotoxin TVIIA has a six cysteine/four-loop structural framework common to many peptides from Conus venoms including the omega-, delta- and kappa-conotoxins. However, TVIIA displays little sequence homology with these well-characterized pharmacological classes of peptides, but displays striking sequence homology with conotoxin GS, a peptide from Conus geographus that blocks skeletal muscle sodium channels. These new toxins and GS share several biochemical features and represent a distinct subgroup of the four-loop conotoxins.
A phase I, open label, perioperative study of AG-120 and AG-881 in recurrent IDH1 mutant, low-grade glioma: Results from cohort 1. (2019)

2003 Background: AG-120 (ivosidenib [IVO]) is a first-in-class oral inhibitor of mutant isocitrate dehydrogenase 1 (mIDH1) evaluated in 66 glioma patients (pts) in an ongoing phase 1 study. AG-881 (vorasidenib [VOR]) is an oral, potent, brain-penetrant inhibitor of mIDH1/2 evaluated in 52 glioma pts in an ongoing phase 1 study. In an orthotopic glioma model, IVO and VOR reduced 2-hydroxyglutarate (2-HG) by 85% and 98%, respectively, despite different brain:plasma ratios (&lt;0.04 vs 1.33). Methods: Primary endpoint: brain tumor 2-HG concentration with IVO or VOR treatment in mIDH1 low-grade glioma. Pts with recurrent non-enhancing WHO-2016 Grade (Gr) 2 or 3 mIDH1-R132H oligodendroglioma or astrocytoma undergoing craniotomy were randomized 2:2:1 to IVO 500mg QD, VOR 50mg QD, or no treatment for 4 wks preoperatively in Cohort 1. Post-operatively, pts continued to receive IVO or VOR and control pts were randomized 1:1 to IVO or VOR. Tumors were assessed for mIDH1 status, cellularity, 2-HG, and drug concentration. Treated samples were compared to control pts and mIDH1 and wild type (WT) banked reference (ref) samples. Plasma and CSF 2-HG were assessed. Pts with non-evaluable tissue were replaced. Results: As of 29 Nov 2018, 26 pts (17M, 9F; 25 Gr 2, 1 Gr 3) were randomized preoperatively (IVO 10, VOR 11, control 5), 25 received drug (IVO 12, VOR 13). At the data cut, 19 tumors were analyzed with 16 evaluable. Common (&gt;10%) TEAEs (all grade 1/2): diarrhea (36%), hypocalcemia and constipation (each 20%), anemia, hyperglycemia, pruritus, headache and nausea (each 16%), and hypokalemia and fatigue (each 12%). Mean brain:plasma ratio: 0.16 for IVO, 2.4 for VOR. Tumor 2-HG results are shown in Table. Updated data from Cohort 1 will be presented. Conclusions: In Cohort 1 of this phase 1 perioperative study, IVO and VOR were CNS penetrant and lowered 2-HG compared to untreated samples. Cohort 2 is open and will evaluate IVO 250mg BID and VOR 10mg QD. Brain tumor 2-HG concentration. Clinical trial information: NCT03343197. [Table: see text]
Crystallization of bacteriorhodopsin from bicelle formulations at room temperature (2005)

We showed previously that high-quality crystals of bacteriorhodopsin (bR) from Halobacterium salinarum can be obtained from bicelle-forming DMPC/CHAPSO mixtures at 37 degrees C. As many membrane proteins are not sufficiently stable for crystallization at this high temperature, we tested whether the bicelle method could be applied at a lower temperature. Here we show that bR can be crystallized at room temperature using two different bicelle-forming compositions: DMPC/CHAPSO and DTPC/CHAPSO. The DTPC/CHAPSO crystals grown at room temperature are essentially identical to the previous, twinned crystals: space group P21 with unit cell dimensions of a = 44.7 A, b = 108.7 A, c = 55.8 A, beta = 113.6 degrees . The room-temperature DMPC/CHAPSO crystals are untwinned, however, and belong to space group C222(1) with the following unit cell dimensions: a = 44.7 A, b = 102.5 A, c = 128.2 A. The bR protein packs into almost identical layers in the two crystal forms, but the layers stack differently. The new untwinned crystal form yielded clear density for a previously unresolved CHAPSO molecule inserted between protein subunits within the layers. The ability to grow crystals at room temperature significantly expands the applicability of bicelle crystallization.