gebhart/patrepeval huggingface dataset:
Mutants of <i>Discosoma</i> red fluorescent protein with a GFP‐like chromophore (2001)

The green fluorescent protein (GFP)-homologous red fluorescent protein (RFP) from Discosoma (drFP583) which emits bright red fluorescence peaking at 583 nm is an interesting novel genetic marker. We show here that RFP maturation involves a GFP-like fluorophore which can be stabilized by point mutations selected from a randomly mutated expression library. By homology modeling, these point mutations cluster near the imidazolidinone ring of the chromophore. Exciting the GFP-like absorption band in the mutant proteins produces both green and red fluorescence. Upon unfolding and heating, the absorption spectrum of the RFP chromophore slowly becomes similar to that of the GFP chromophore. This can be interpreted as a covalent modification of the GFP chromophore in RFP that appears to occur in the final maturation step.
Several endoplasmic reticulum stress proteins, including ERp72, interact with thyroglobulin during its maturation. (1994)

We have previously demonstrated that several endoplasmic reticulum (ER) proteins, including BiP, ERp72, grp94, and protein disulfide isomerase, bind to a denatured thyroglobulin (Tg) affinity column and can be specifically eluted by ATP (Nigam, S.K., Goldberg, A.L., Ho, S., Rohde, M.F., Bush, K.T., and Sherman, M.Y. (1994) J. Biol. Chem. 269, 1744-1749). Using chemical cross-linking, we now demonstrate that BiP, ERp72, and grp94 associate with Tg in two types of cultured thyroid cells, FRTL-5 and PCC13. Whereas BiP could be coimmunoprecipitated with anti-Tg antibodies in the absence of cross-linking, only trace amounts of ERp72 and grp94 were coimmunoprecipitated. Likewise, in both cell types, anti-BiP antibodies were able to coimmunoprecipitate Tg in the absence of cross-linking, though ERp72 and grp94 were only minimally present. Coprecipitation of BiP and Tg was abolished when ATP and Mg2+ were added to cell lysates. In contrast, after cross-linking, there was a large increase in the amount of ERp72 and grp94 that coimmunoprecipitated with anti-Tg antibodies, although there was only a slight increase in BiP. Similarly, in cross-linked lysates, grp94 and ERp72 were also coimmunoprecipitated with anti-BiP antibodies. An apparently novel 200-kDa protein was also consistently immunoprecipitated by anti-BiP antibodies in both cell types. In addition, anti-ERp72 antibodies coimmunoprecipitated Tg, BiP, and grp94 only after cross-linking. Analysis of uncross-linked and cross-linked samples by sucrose density gradient centrifugation confirmed that Tg, BiP, grp94, and ERp72 are present together in high molecular weight complexes only after treatment of cells with cross-linking reagent. These results suggest that ERp72, as well as BiP and grp94, function as molecular chaperones in the maturation of Tg, potentially as part of a macromolecular complex.
Mitigation of residual film stress deformation in multilayer microelectromechanical systems cantilever devices (2003)

An approach to compensate for the residual thin film stress deformation of multilayer microelectromechanical systems (MEMS) devices is presented based upon analytical and numerical modeling and in-process thin film characterization. Thermal and intrinsic deposition stresses can lead to the warping of released MEMS structures. This detrimental phenomenon in many cases can prevent proper device operation. Ellispsometric and laser wafer bow measurements yield thickness and film stress values that are used to update the deflection model during device fabrication, allowing for the compensation of the fabrication process variability. The derivations of linear and nonlinear residual film stress induced deflection models are presented. These models are based upon Bernoulli–Euler beam theory and are thus restricted to the associated geometric constraints. The models are initially validated by comparison with surface micro-machined sol–gel lead–zirconate–titanate cantilever structures; with initial experimental results agreeing well with both.
THE USE OF A LOW DOSE OF ATRAZINE ALONE AND IN MIXTURES WITH OTHER HERBICIDES IN THE MAIZE CROP (1973)

Summary. Linuron, 2,4‐D‐aniine, propachlor, pyriclor and cypromid, singly and mixture with atrazine, were compared with atrazine and fluromidine alone for effectiveness of weed control in maize on Oxford clay soil. Pre‐emergence applications were made under wet conditions and atrazine, even at 0·28 kg/ha a.i. gave an excellent control of three main weeds, Stellaria media, Veronica spp. and Polygonum aviculare , and at 0·56 kg/ha also killed Aethusa cynapium. Fluromidine was comparable with atrazine, but linuron,2,4‐D‐amine, propachlor and pyriclor were less effective. Post‐emergence treatments were less satisfactory. High doses of atrazine were needed for good weed control. Acynapium was resistant to pyriclor and cypromid and P. aviculare to fluromidine. 2,4‐Daminewas ineffective, but atrazine/2,4‐D‐amine mixtures were more effective than the individual components for the control of P. aviculare. Pyriclor, at 0·56 kg/ha pre‐emergenceand cypromid at 2·24 kg/ha post‐emergence directly reduced the yield of the crop. Utilisation de I'atrazine à faible dose, seule et en mélange avec d'autres herbicides, dans les culturesde maïs
Schedulability analysis of heterogeneous systems for performance message sequence chart (1998)

Telecommunication systems are often specified in the standardized languages SDL and MSC. These languages allow only the specification of pure functional aspects. To remedy this problem we have combined the language MSC and performance aspects in Performance MSC (PMSC). From a PMSC specification a task model can be derived that includes beside computation times, periods and deadlines of tasks, also absolute start times of tasks and dependencies between tasks. This allows us to apply an extended schedulability analysis of asynchronous tasks on heterogeneous target architectures. We present the analysis technique and demonstrate with a small example, how the algorithm can be used for the real-time analysis of a cordless telephone.
Accurate, fast, and robust vessel contour segmentation of CTA using an adaptive self-learning edge model (2009)

We present an efficient algorithm for the robust segmentation of vessel contours in Computed Tomography Angiography (CTA) images. The algorithm performs its task within several steps based on a 3D Active Contour Model (ACM) with refinements on Multi-Planar Reconstructions (MPRs) using 2D ACMs. To be able to distinguish true vessel edges from spurious, an adaptive self-learning edge model is applied. We present details of the algorithm together with an evaluation on n=150 CTA data sets and compare the results of the automatic segmentation with manually outlined contours resulting in a median dice similarity coefficient (DSC) of 92.2%. The algorithm is able to render 100 contours within 1.1s on a Pentium®4 CPU 3.20 GHz, 2 GByte of RAM.
Content and buffer aware scheduling for video delivery over LTE (2013)

We propose a content and buffer aware Long Term Evolution (LTE) downlink scheduler for allocating radio resources to multiple users requesting Scalable Video Coding (SVC) encoded videos from a server. The scheduler adaptively controls the video quality by assigning physical resource blocks (PRBs) to the users based on the requested video type, device capability, channel quality, and buffer state in the user equipment (UE). The scheduler maximizes the average video quality across all users for a limited number of PRBs, and can be installed in existing LTE systems without additional equipment and very limited signaling overhead.
A Twin Study of Autism in Denmark, Finland, Iceland, Norway and Sweden (1989)

The Nordic countries were screened for the occurrence of cases of autism with a same-sexed twin under age 25 years. Twenty-one pairs (11 monozygotic and 10 dizygotic) of twins and one set of identical triplets were found and extensively examined. The concordance for autism by pair was 91% in the monoygotic and 0% in the dizygotic pairs. The corresponding concordances for cognitive disorder were 91% and 30%, respectively. In most of the pairs discordant for autism, the autistic twin had more perinatal stress. The results lend support for the notion that autism sometimes has a hereditary component and that perinatal stress is involved in some cases.
Construction of replication-competent Herpesvirus saimiri deletion mutants (1984)

DNA fragments derived from the left end of Herpesvirus saimiri 11 L-DNA were cloned in Escherichia coli by using vector pBR322. Deletions were introduced within a cloned 7.4-kilobase-pair sequence by using restriction endonucleases that cut once or twice within this sequence. Permissive owl monkey kidney-cultured cells were transfected with parental strain 11 viral DNA plus cloned DNA with specific sequences deleted. By screening the progeny of these transfections with a limiting-dilution spot hybridization assay, we isolated recombinant viruses containing deletions in this region. A contiguous 4.5-kilobase-pair sequence representing 4.1% of the coding capacity of the virus was found to be unnecessary for virus replication in cultured cells. These deletion mutants will allow us to test whether sequences in this region are required for the lymphoma-inducing capacity of H. saimiri. These same procedures should also allow us to introduce foreign DNA sequences into this region for studying their expression.
Noninvasive quantitative fluorodeoxyglucose PET studies with an estimated input function derived from a population-based arterial blood curve. (1993)

The authors have developed a technique to estimate input functions from a population-based arterial blood curve in positron emission tomography (PET) studies with fluorine-18 fluorodeoxyglucose (FDG). A standardized pump injection was used in 34 subjects. A population-based blood curve was generated based on the first 10 subjects. In the remaining 24 subjects, an estimated input function (EIFa) was obtained by scaling the population-based curve with two arterial blood samples, one obtained at 10 minutes and the other at 45. Time integrals for EIFa and the real arterial input function (RIF) were in excellent agreement (r = .998, P < .0001). Cerebral metabolic rates for glucose calculated with EIFa and RIF and the autoradiographic method also correlated excellently (r = .992, P < .0001). Analogous correlations were achieved with arterialized venous samples as scaling factors. These results suggest that individually scaled, population-derived input functions may serve as an adequate alternative to continuous arterial blood sampling in quantitative FDG-PET imaging.
LEAFY COTYLEDON 2 activation is sufficient to trigger the accumulation of oil and seed specific mRNAs in <i>Arabidopsis</i> leaves (2005)

LEAFY COTYLEDON 2 (LEC2) is a key regulator of seed maturation in Arabidopsis. To unravel some of its complex pleiotropic functions, analyses were performed with transgenic plants expressing an inducible LEC2:GR protein. The chimeric protein is functional and can complement lec2 mutation. Interestingly, the induction of LEC2 leads to the accumulation of storage oil in leaves. In addition, short-term induction and use of translation inhibitors allowed to demonstrate that LEC2 can directly trigger the accumulation of seed specific mRNAs. Consistent with these results, the expression of three other major seed regulators namely, LEC1, FUS3, and ABI3 were also induced by LEC2 activation.
Animating suspended particle explosions (2003)

This paper describes a method for animating suspended particle explosions. Rather than modeling the numerically troublesome, and largely invisible blast wave, the method uses a relatively stable incompressible fluid model to account for the motion of air and hot gases. The fluid's divergence field is adjusted directly to account for detonations and the generation and expansion of gaseous combustion products. Particles immersed in the fluid track the motion of particulate fuel and soot as they are advected by the fluid. Combustion is modeled using a simple but effective process governed by the particle and fluid systems. The method has enough flexibility to also approximate sprays of burning liquids. This paper includes several demonstrative examples showing air bursts, explosions near obstacles, confined explosions, and burning sprays. Because the method is based on components that allow large time integration steps, it only requires a few seconds of computation per frame for the examples shown.
From spiking neurons to rate models: A cascade model as an approximation to spiking neuron models with refractoriness (2006)

A neuron that is stimulated repeatedly by the same time-dependent stimulus exhibits slightly different spike timing at each trial. We compared the exact solution of the time-dependent firing rate for a stochastically spiking neuron model with refractoriness (spike response model) with that of an inhomogeneous Poisson process subject to the same stimulus. To arrive at a mapping between the two models we used alternatively (i) a systematic parameter-free Volterra expansion of the exact solution or (ii) a linear filter combined with nonlinear Poisson rate model (linear-nonlinear Poisson cascade model) with a single free parameter. Both the cascade model and the second-order Volterra model showed excellent agreement with the exact rate dynamics of the spiking neuron model with refractoriness even for strong and rapidly changing input. Cascade rate models are widely used in systems neuroscience. Our method could help to connect experimental rate measurements to the theory of spiking neurons.
Hierarchical Cascade Controller for Assistance Modulation in a Soft Wearable Arm Exoskeleton (2017)

In recent years soft wearable exoskeletons, commonly referred to as exosuits, have been widely exploited in human assistance. Hence, a shared approach for a systematic and exhaustive control architecture is extremely important. Most of the exosuits developed so far employ a bowden cable transmission to conveniently place the actuator away from the end-effector. While having many advantages this actuation strategy presents some intrinsic limitations caused by the presence of nonlinearities, such as friction and backlash of the cables, which make it difficult to predict and control the dynamics between the device and the user. In this letter, we propose a novel hierarchical control paradigm for a cable-driven upper limb exosuits that aims at evaluating and consequently deliver the appropriate assistive torque to the user's elbow joint. The proposed control method comprises three main layers: an active impedance control which estimates the user's arm motion intention and guarantees an intuitive response of the suit to the wearer's motion; a mid-level controller which compensates for the backlash in the transmission and converts the reference arm motion to the desired position of the actuator; a low-level controller which is responsible for driving the actuation stage by compensating for the nonlinear dynamics occurring in the bowden cable to provide the desired assistive torque at the joint. Tests on healthy subjects show that wearing the exosuit reduces by 48.3% the muscular effort required to lift 1 kg and that the controller is able to modulate its level of assistance to the wearer's motor ability.
The National Film Board of Canada's Computerised Film Booking System: A Strategy for the Future (1977)

The National Film Board is an agency of the Canadian Government which was created in 1939 to initiate and promote the production and distribution of films in the national interest, and in particular, films designed to interpret Canada to Canadians and to other countries.
The persistence of cognitive deficits in remitted and unremitted <scp>ADHD</scp> : a case for the state‐independence of response inhibition (2013)

Results demonstrate that response inhibition not only distinguishes ADHD children from their unaffected peers but is also state-independent, such that deficits remain present irrespective of changes in the disease phenotype. In other words, inhibitory deficits measured in childhood persist into adolescence even when the ADHD phenotype remits. These findings provide further evidence that the ability to stop prepotent actions is an endophenotype of ADHD.
Qualitative Analysis of Precipitates by Graphite Filter Methods (1970)

In many chemical processes there is a need to quickly identify unexpected precipitates in a solution. If x-ray fluorescence equipment is available, the precipitates can be collected by a Millipore filter and easily analyzed qualitatively. When an x-ray fluorescence spectrometer is not available, or the suspected elements are not amenable to the technique, the methods described here are helpful.
High voltage GaN Schottky rectifiers (2000)

Mesa and planar GaN Schottky diode rectifiers with reverse breakdown voltages (V/sub RB/) up to 550 and >2000 V, respectively, have been fabricated. The on-state resistance, R/sub ON/, was 6 m/spl Omega//spl middot/cm/sup 2/ and 0.8 /spl Omega/ cm/sup 2/, respectively, producing figure-of-merit values for (V/sub RB/)/sup 2//R/sub ON/ in the range 5-48 MW/spl middot/cm/sup -2/. At low biases the reverse leakage current was proportional to the size of the rectifying contact perimeter, while at high biases the current was proportional to the area of this contact. These results suggest that at low reverse biases, the leakage is dominated by the surface component, while at higher biases the bulk component dominates. On-state voltages were 3.5 V for the 550 V diodes and /spl ges/15 for the 2 kV diodes. Reverse recovery times were <0.2 /spl mu/s for devices switched from a forward current density of /spl sim/500 A/spl middot/cm/sup -2/ to a reverse bias of 100 V.
Detection of Explosives in Hair Using Ion Mobility Spectrometry (2008)

Conventional explosives 2,4,6-trinitrotoluene (TNT), nitroglycerin (NG), and ethylene glycol dinitrate (EGDN) sorbed to hair can be directly detected by an ion mobility spectrometer (IMS) in E-mode (for explosives). Terrorist explosive, triacetone triperoxide (TATP), difficult to detect by IMS in E-mode, was detected in N-mode (for narcotics). Three modes of sample introduction to IMS vapor desorption unit were used: (i) placement of hair directly into the unit, (ii) swabbing of hair and placement of swabs (i.e., paper GE-IMS sample traps) into the unit, and (iii) acetonitrile extracts of hair positioned on sample traps and placed into the unit. TNT, NG, and EGDN were detected in E-mode by all three sample introduction methods. TATP could only be detected by the acetonitrile extraction method after exposure of the hair to vapor for 16 days because of lower sensitivity. With standard solutions, TATP detection in E-mode required about 10 times as much sample as EGDN (3.9 mug compared with 0.3 mug). IMS in N-mode detected TATP from hair by all three modes of sample introduction.
An embedded energy monitoring circuit for a 128kbit SRAM with body-biased sense-amplifiers (2012)

Embedded energy monitoring of critical system components can be used to enable better power management by capturing run time system conditions such as temperature and application load. In this work, an energy sensing circuit that provides digitally represented absolute energy per operation of a 128kbit SRAM is presented. Designed in a 65nm low-power CMOS process, SRAMs can operate down to 370 mV. Energy sensing circuit consumes 16.7μW during sensing at 1.2V (only 0.28% of SRAM active power at the same voltage). For improved performance, SRAMs utilize body-biased PMOS input strong-arm type sense amplifiers that can achieve 45% tighter input offset distribution for only ~3.5% of total SRAM area overhead.
Analysis of EGFR, HER2, and TOP2A gene status and chromosomal polysomy in gastric adenocarcinoma from Chinese patients (2008)

The data from our study suggest that chromosome 7 polysomy may be responsible for increased EGFR gene copy number in gastric carcinomas, and that HER2 gene amplification may be the major reason for HER2 protein overexpression. A combined investigation of the gene status of EGFR, HER2, and TOP2A should facilitate the identification of a target therapeutic regimen for gastric carcinoma patients.
Gene expression profiling of single circulating tumor cells in ovarian cancer – Establishment of a multi‐marker gene panel (2016)

The presence of circulating tumor cells (CTCs) in the blood of ovarian cancer patients was shown to correlate with decreased overall survival, whereby CTCs with epithelial-mesenchymal-transition (EMT) or stem-like traits are supposed to be involved in metastatic progression and recurrence. Thus, investigating the transcriptional profiles of CTCs might help to identify therapy resistant tumor cells and to overcome treatment failure. For this purpose, we established a multi-marker panel for the molecular characterization of single CTCs, detecting epithelial (EpCAM, Muc-1, CK5/7), EMT (N-cadherin, Vimentin, Snai1/2, CD117, CD146, CD49f) and stem cell (CD44, ALDH1A1, Nanog, SOX2, Notch1/4, Oct4, Lin28) associated transcripts. First primer specificity and PCR-performance of the multiplex-RT-PCRs were successfully validated on genomic DNA and cDNA isolated from OvCar3 cells. The assay sensitivity of the epithelial panel was evaluated by adding defined numbers of tumor cells into the blood of healthy donors and performing a subsequent immunomagnetic tumor cell enrichment (AdnaTest OvarianCancerSelect), resulting in a 100% concordance for the epithelial markers EpCAM and Muc-1 to the AdnaTest OvarianCancerDetect. Additionally, by processing blood from ovarian cancer patients, high assay sensitivity could be verified. In blood of healthy donors no signals for epithelial markers were detected, for EMT and stem cell markers, however, signals were obtained mainly originating from leukocytes which calls for single cell analysis. To that aim by using the ovarian cancer cell line OvCar3, we successfully established a workflow enabling the characterization of single CTCs. It consists of a density gradient-dependent enrichment for nucleated cells, a depletion of CD45-positive cells of hematopoietic origin followed by immunofluorescent labeling of CTCs by EpCAM and Muc-1. Single CTCs are then isolated by micromanipulation and processed for panel gene expression profiling. Finally, fifteen single CTCs from three ovarian cancer patients were analyzed and found to be positive for stem cell (CD44, ALDH1A1, Nanog, Oct4) and EMT markers (N-cadherin, Vimentin, Snai2, CD117, CD146). Albeit, inter-cellular and intra/inter-patient heterogeneity and co-expression of epithelial, mesenchymal and stem cell transcripts on the same CTC was observed. We have established a robust workflow to perform sensitive single cell panel gene expression analysis without the need of pre-amplification steps. Our data point towards a heterogeneous expression of stem cell and EMT associated transcripts in ovarian cancer CTCs.