gebhart/patrepeval huggingface dataset:
Roles of the TGACT repeat sequence in the yeast TRP5 promoter. (1987)

Yeast genes under general amino acid control contain multiple copies of a sequence known as the TGACT repeat in the 5'-flanking DNA. The yeast TRP5 gene contains two copies of the TGACT repeat sequence in its 5'-flanking region. The upstream TGACT repeat of TRP5 is required for normal basal expression as well as derepression by general control. Synthetic oligonucleotides containing a TGACT sequence were inserted into previously constructed TRP5 control region deletion mutants. A synthetic 17-base pairs (bp) oligonucleotide containing a TGACT copy along with flanking nucleotides from HIS3 was able to restore derepression in all deletion mutants tested. The 17-bp oligonucleotide also functioned bidirectionally. Replacements in the upstream control region by synthetic oligonucleotides indicated that sequences other than the TGACT repeat are required for high basal expression. Replacements of the downstream repeat sequence by the 17-bp oligonucleotide suggest its main role in this position is for derepressed expression. High level derepressed expression was found to correlate with the presence of two repeats.
Antigenicity and immunogenicity of PvRALP1, a novel Plasmodium vivax rhoptry neck protein (2015)

This study analysed the antigenicity and immunogenicity of PvRALP1 and suggested that PvRALP1 may be immunogenic in humans during parasite infection and might play an important role during invasion of P. vivax parasites.
Revealing the internal heavy chalcogen atom effect on the photophysics of the dibenzo[ a,j ]phenazine-cored donor–acceptor–donor triad (2021)

Donor–acceptor–donor molecules containing heavy chalcogen atoms, which feature multi-color polymorphism, external-stimuli responsive luminochromism, thermally-activated delayed fluorescence, and room-temperature phosphorescence, have been developed.
Novel Therapeutic Strategy for Stroke in Rats by Bone Marrow Stromal Cells and ex vivo HGF Gene Transfer with HSV-1 Vector (2006)

Occlusive cerebrovascular disease leads to brain ischemia that causes neurological deficits. Here we introduce a new strategy combining mesenchymal stromal cells (MSCs) and ex vivo hepatocyte growth factor (HGF) gene transferring with a multimutated herpes simplex virus type-1 vector in a rat transient middle cerebral artery occlusion (MCAO) model. Gene-transferred MSCs were intracerebrally transplanted into the rats' ischemic brains at 2 h (superacute) or 24 h (acute) after MCAO. Behavioral tests showed significant improvement of neurological deficits in the HGF-transferred MSCs (MSC-HGF)-treated group compared with the phosphate-buffered saline (PBS)-treated and MSCs-only-treated group. The significant difference of infarction areas on day 3 was detected only between the MSC-HGF group and the PBS group with the superacute treatment, but was detected among each group on day 14 with both transplantations. After the superacute transplantation, we detected abundant expression of HGF protein in the ischemic brain of the MSC-HGF group compared with others on day 1 after treatment, and it was maintained for at least 2 weeks. Furthermore, we determined that the increased expression of HGF was derived from the transferred HGF gene in gene-modified MSCs. The percentage of apoptosis-positive cells in the ischemic boundary zone (IBZ) was significantly decreased, while that of remaining neurons in the cortex of the IBZ was significantly increased in the MSC-HGF group compared with others. The present study shows that combined therapy is more therapeutically efficient than MSC cell therapy alone, and it may extend the therapeutic time window from superacute to acute phase.
The kinematics of legged locomotion over uneven terrain (1986)

This paper describes a complete motion-planning algorithm for uneven-terrain locomotion for a multilegged vehicle. The algorithm has been developed based on the vehicle/terrain kinematic relationships. The vehicle model is chosen from a hexapod vehicle, named the Adaptive Suspension Vehicle (ASV), which has been constructed at OSU and is currently being tested. A simple body regulation plan has been designed based on the local slope of the terrain and should increase the safety and adaptability of the vehicle. The local terrain is estimated by using the support points of the supporting legs and proximity information from the transfer legs. The algorithm has been implemented in simulation on the PDP-11/70 minicomputer and test results are given.
A Fast and High-Precision VCO Frequency Calibration Technique for Wideband $\Delta \Sigma $ Fractional-N Frequency Synthesizers (2010)

A VCO frequency calibration technique suitable for a wideband fractional-N PLL is presented. It provides a fast and high-precision search for an optimal discrete tuning curve of an LC VCO during the coarse tuning process in a fractional-N PLL. A high-speed frequency error detector (FED) converts the VCO frequency to a digital value and computes the exact frequency difference from a target frequency. A minimum error code finder finds an optimal code that is closest to the target frequency. Due to the pure digital domain operation, a ΔΣ modulator in PLL can be deactivated during the calibration process, which makes this technique fast and accurate especially for a ΔΣ fractional-N PLL. We achieve a single-bit calibration time of only kT <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">REF</sub> for obtaining a frequency resolution of f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">REF</sub> /k, and compared to the conventional techniques, which is the best performance in terms of the calibration time versus resolution. Such fast VCO frequency calibration can greatly reduce the total lock time in a PLL. A 2.3-3.9 GHz fractional-N PLL employing the proposed calibration technique is implemented in 0.13 μm CMOS. Successful operation is verified through experimental results. The measured calibration time for a 6-bit capbank is 1.09 and 2.03 μs for a frequency resolution of 19.2 and 4.8 MHz, respectively.
Golgi retention of a trans-Golgi membrane protein, galactosyltransferase, requires cysteine and histidine residues within the membrane-anchoring domain. (1992)

Galactosyltransferase (GT; UDPgalactose:beta-D-N-acetylglucosaminide beta-1,4-galactosyltransferase, EC 2.4.1.22) is a type II membrane-anchored protein composed of a short N-terminal cytoplasmic tail, a signal/membrane-anchoring domain, and a stem region followed by a large catalytic domain including the C terminus. To identify the peptide segment and key amino acid residues that are critical for Golgi localization of GT, the expression vector pGT-hCG was designed to encode the entire GT molecule fused to the C-terminal region of human chorionic gonadotropin alpha subunit (hCG alpha) as a reporter. COS-1 cells transfected with pGT-hCG expressed the chimera in the Golgi region, as detected by immunofluorescence microscopy using anti-hCG antibodies. Two deletion mutants, delta tail and delta stem, which are lacking most of the N-terminal cytoplasmic tail or 10 amino acids immediately after the membrane-anchoring domain, were localized in the Golgi. Replacement mutations of the membrane-anchoring domain of GT showed that the second quarter of the transmembrane domain or Cys29-Ala30-Leu31-His32-Leu33 is necessary for GT to be retained in the Golgi. Furthermore, the point mutants Cys29----Ser29 and His32----Leu32 were partially transported to the plasma membrane, whereas an Ala30-Leu31----Phe30-Gly31 mutant was localized in the Golgi. Finally, a double mutant, Cys29/His32----Ser29/Leu32, was found to be transported efficiently to the plasma membrane. The signal-anchoring domain of the transferrin receptor, a type II plasma membrane protein, was then replaced by portions of the GT transmembrane domain. Although the Cys-Xaa-Xaa-His sequence by itself cannot retain the transferrin receptor in the Golgi, the cytoplasmic half of the transmembrane domain of GT was partially capable of retaining the transferrin receptor in the Golgi. These results suggest that the cytoplasmic (or N-terminal) half of the transmembrane domain of GT contributes to the Golgi retention signal and that particularly Cys29 and His32 in this region are critical for GT to be retained in the Golgi.
Distinct descending motor cortex pathways and their roles in movement (2017)

ABSTRACT Activity in motor cortex predicts specific movements, seconds before they are initiated. This preparatory activity has been observed in L5 descending ‘pyramidal tract’ (PT) neurons. A key question is how preparatory activity can be maintained without causing movement, and how preparatory activity is eventually converted to a motor command to trigger appropriate movements. We used single cell transcriptional profiling and axonal reconstructions to identify two types of PT neuron. Both types share projections to multiple targets in the basal ganglia and brainstem. One type projects to thalamic regions that connect back to motor cortex. In a delayed-response task, these neurons produced early preparatory activity that persisted until the movement. The second type projects to motor centers in the medulla and produced late preparatory activity and motor commands. These results indicate that two motor cortex output neurons are specialized for distinct roles in motor control.
Synthesis of Novel Tetracarboxylato Dirhenium(III) Compounds and Crystal Structure of [Re2(1-Adamantylcarboxylate)4Cl2] · 4 CHCl3 (2001)

Abstract The coordination compounds o f the general formula Re 2 (L) 4 X 2 (X = Cl, Br; L = 1 -adamantyl-carboxylate and 1 -adamantylacetate) have been prepared and characterized by means of UV-VIS spectroscopy (20000 cm -1 , δ → δ*). The crystal and molecular structure of Re 2 (AdCOO) 4 Cl 2 · 4 CHCl 3 solvate was determined by X-ray diffraction. The units Re 2 (AdCOO) 4 Cl 2 adopt a centrosymmetric dinuclear array with each metal atom coordinated in a distorted octahedron comprising one rhenium and one chlorine atoms (Re-Cl 2.505(2) Å) and four carboxylate oxygen atoms in the equatorial plane. The rhenium-rhenium separation of 2.2300(5) Å corresponds to quadruple bond between the metal atoms. All R e-0 bonds have an almost uniform length (2.017(4) -2.032(4) Å) and do not differ essentially from the parameters reported for related compounds. The closest environment of the Re 2 (AdCOO) 4 Cl 2 molecules in the crystal comprises weak Cl---HC hydrogen bonds with the chloroform molecules and significantly shortened van der Waals contacts Cl---Cl, 3.46 Å.
Design of fiber optical high temperature sensors for gas turbine monitoring (2009)

Their small size, the multiplexing capability, and the high elasticity of glass fiber can provide reasons to use optical fiber temperature sensors instead of approved conventional thermo couples for temperature monitoring of hot gas turbine components.
Skew-Tolerant Key Distribution for Load Balancing in MapReduce (2012)

MapReduce is a parallel processing framework for large scale data. In the reduce phase, MapReduce employs the hash scheme in order to distribute data sharing the same key across cluster nodes. However, this approach is not robust for the skewed data distribution. In this paper, we propose a skew-tolerant key distribution method for MapReduce. The proposed method assigns keys to cluster nodes balancing their workloads. We implemented our proposed method on Hadoop. Through experiments, we evaluate the performance of the proposed method in comparison with the conventional method.
Deletion of the SARS-CoV-2 Spike Cytoplasmic Tail Increases Infectivity in Pseudovirus Neutralization Assays (2021)

Pseudotyped viruses are valuable tools for studying virulent or lethal viral pathogens that need to be handled in biosafety level 3 (BSL-3) or higher facilities. With the explosive spread of the coronavirus disease 2019 (COVID-19) pandemic, the establishment of a BSL-2 adapted SARS-CoV-2 pseudovirus neutralization assay is needed to facilitate the development of countermeasures. Here we describe an approach to generate a single-round lentiviral vector-based SARS-CoV-2 pseudovirus, which produced a signal more than 2 logs above background. Specifically, a SARS-CoV-2 spike variant with a cytoplasmic tail deletion of 13 amino acids, termed SΔCT13, conferred enhanced spike incorporation into pseudovirions and increased viral entry into cells as compared with full-length spike (S). We further compared S and SΔCT13 in terms of their sensitivity to vaccine sera, purified convalescent IgG, hACE2-mIgG, and the virus entry inhibitor BafA1. We developed a SΔCT13-based pseudovirus neutralization assay and defined key assay characteristics, including linearity, limit of detection, and intra- and intermediate-assay precision. Our data demonstrate that the SΔCT13-based pseudovirus shows enhanced infectivity in target cells, which will facilitate the assessment of humoral immunity to SARS-CoV-2 infection, antibody therapeutics, and vaccination. This pseudovirus neutralization assay can also be readily adapted to SARS-CoV-2 variants that emerge. IMPORTANCE SARS-CoV-2 is the etiologic agent of the COVID-19 pandemic. The development of a high throughput pseudovirus neutralization assay is critical for the development of vaccines and immune-based therapeutics. In this study, we show that deletion of the cytoplasmic tail of the SARS-CoV-2 spike leads to pseudoviruses with enhanced infectivity. This SΔCT13-based pseudovirus neutralization assay should be broadly useful for the field.
Mustard carbonate analogues: influence of the leaving group (2016)

The substitution of a chlorine atom with a carbonate moiety in mustard compounds has led to a new class of molecules, namely mustard carbonates that retain the reactivity of the well-know toxic iprites, but are safe for the operator and the environment [1].&#13;\nHerein we report the influence of the leaving group on the neighboring effect of sulfur half mustard carbonates (HMCs) usually less reactive than nitrogen ones [2]. Several new 2-(methylthio)ethyl alkyl carbonates have been synthesized and their reactivity has been investigated in both autoclave and neat conditions. The results reactions between the HMCs and phenol performed in autoclave (180 °C, no base, in acetonitrile media) showed that the efficiency of the anchimeric effect is directly dependent on the steric hindrance of the HMC leaving group. The least steric hindered 2-(methylthio)ethyl methyl carbonate gave the methyl (2-phenoxyethyl)sulfane in higher yield, whereas the most steric hindered 2-(methylthio)ethyl t-butyl carbonate did not reacted at all. The influence of the leaving group on the anchimeric effect has been also investigated in neat conditions at 150 °C in the presence of catalytic amount of K2CO3. In this case, due to the absence of the solvent and the presence of the base the reaction is more complicated by transesterification reactions and formation of unwanted products. Interestingly 2-(methylthio)ethyl ethyl carbonate showed to be the most efficient carbonate among the ones studied. This resulted might be ascribed to its ability to free the cyclic intermediate from its molecular cage as intimate ion pair more readily than the other HMCs. Finally, several nucleophiles have been then tested in neat reaction conditions using 2-(methylthio)ethyl ethyl carbonate and a catalytic amount of base. In all cases studied it was observed an almost quantitative anchimeric aided alkylation over SN2 reaction, i.e., formation of ethyl aryl ethers. The best results achieved have led to an enhanced product selectivity, more accessible reaction conditions and a better insight on the reaction mechanism of mustard carbonates.
Simultaneous Inverse Identification of Transient Thermal Properties and Heat Sources Using Sparse Sensor Information (2007)

A study is presented herein on the simultaneous inverse identification of transient internal heat generation, transient thermal diffusivity, and constant convection coefficients. The formulations of the direct and inverse problems are presented in the context of finite-element analysis and nonlinear optimization, respectively. A real-coded genetic algorithm was used to solve the inverse problem because of the global convergence properties of this optimization technique. It was found through numerical studies that heat generation and thermal conductivity as functions of time can be simultaneously and consistently estimated from sparse sensor information, as long as convection coefficients are known. However, treating convection coefficients as unknown may significantly affect the accuracy of the estimated thermal diffusivity function and to a lesser extent, the accuracy of the heat generation function. The numerical experiments showed, however, that the Biot number can be accurately estimated when the convection coefficients are not well known. These results can have wide and important implications in problems related to monitoring and quality control of structures.
Bilateral cingulumotomy in the treatment of reflex sympathetic dystrophy (1990)

Bilateral anterior cingulumotomy has been used to treat psychiatric diseases and chronic pain. We report an interesting case involving a young woman who underwent cingulumotomy for the treatment of intractable total body pain secondary to generalized reflex sympathetic dystrophy. Her initial response after two procedures was excellent though 1 year later her pain recurred and was resistant to a subsequent cingulumotomy.
La flexiguridad: una aproximación al estado actual de una política comunitaria de empleo (2009)

La flexiguridad es parte de la politica de empleo comunitaria, tal y como se aprecia en el Libro Verde y en la Comunicacion, asi como en el Informe de 2008. La experiencia danesa exige especial atencion
Quadrature Mismatch Shaping with a Complex, Data Directed Swapper (2006)

Quadrature bandpass (QBP) ΣΔ ADCs require a feedback path for both the I and the Q part of the complex feedback signal. A complex DAC could give this feedback with near-perfect I/Q balance. Still, the mismatch between the unit elements of the complex DAC introduces mismatch noise that should be shaped out of the signal band with dynamic element-matching (DEM) techniques. To select the unit DAC elements of the complex multibit DAC, the well-known data directed swapper is generalized towards a complex structure and the necessary constraints for its correct functioning are derived. Additionally, a hardware efficient structure is presented: the reduced butterfly shuffler. Here, some of the QBP swapper cells are replaced by bandpass (BP) swapper cells. Also, great attention is paid to the interconnection pattern of the data directed swapper to prevent instability.
Neratinib augments the lethality of [regorafenib + sildenafil] (2018)

Regorafenib is approved for the treatment of colorectal cancer and hepatocellular carcinoma. In the trial NCT02466802, we have discovered that regorafenib can be safely combined with the phosphodiesterase 5 inhibitor sildenafil in advanced solid tumor patients. The present studies determined whether the approved ERBB1/2/4 and RAS downregulating drug neratinib, could enhance the lethality of [regorafenib + sildenafil]. Neratinib enhanced [regorafenib + sildenafil] lethality in a greater than additive fashion in colon cancer cells. The drug combination reduced the expression of mutant K-RAS and of multiple histone deacetylase (HDAC) proteins that required autophagosome formation. It caused green fluorescent protein or red fluorescent protein-tagged forms of K-RAS V12 to localize into large intracellular vesicles. Compared with [regorafenib + sildenafil], the three-drug combination caused greater and more prolonged activation of the ATM-AMPK-ULK-1 pathway and caused a greater suppression and prolonged inactivation of mammalian target of rapamycin, AKT, and p70 S6K. Approximately 70% of enhanced lethality caused by neratinib required ataxia-telangiectasia-mutated (ATM)-AMP-dependent protein kinase (AMPK) signaling whereas knockdown of Beclin1, ATG5, FADD, and CD95 completely prevented the elevated killing effect. Exposure of cells to [regorafenib + sildenafil] reduced the expression of the checkpoint immunotherapy biomarkers programmed death-ligand 1, ornithine decarboxylase, and indoleamine 2,3-dioxygenase-1 and increased the expression of major histocompatibility complex A (MHCA), which also required autophagosome formation. Knockdown of specific HDAC proteins recapitulated the effects observed using chemical agents. In vivo, using mouse cancer models, neratinib significantly enhanced the antitumor efficacy of [regorafenib + sildenafil]. Our data support performing a new three drug Phase I trial combining regorafenib, sildenafil, and neratinib.
Eve Was Right to Eat the "Apple": The Importance of Narrative in the Art of Lawyering (1995)

Every litigator uses narratives in his or her work. Yet many may not recognize the extent of their use of narrative or the creative ways in which they can deploy narratives. Without an examination of how people tell and understand stories, lawyers may be missing opportunities to convince others of their clients' positions. One way to demonstrate how stories change depending on the facts a lawyer emphasizes and a lawyer's theory of the case would be to take a story known to all and to "retell" it as a criminal defense lawyer might.
Synthesis of 1-(2,6-Dihydroxyphenyl)-1-alkanones and Benzophenone by Aromatization of 2-Acyl-3-hydroxy-2-cyclohexene-1-ones with Mercuric Acetate (1990)

1-(2,6-Dihydroxyphenyl)-1-alkanones, natural products identified from insects and from medicinal plants, are readily prepared from 1,3-cyclohexanedione and appropriate carboxylic acids. The final step involves aromatization using mercuric acetate.
The Role of Mass Transport Limitation and Surface Heterogeneity in the Biophysical Characterization of Macromolecular Binding Processes by SPR Biosensing (2010)

This chapter presents an introduction to the kinetic analysis of SPR biosensor data for the determination of affinity and kinetic rate constants of biomolecular interactions between an immobilized and a soluble binding partner. The need to be aware of and critically test the assumptions underlying the analysis models is emphasized and the consequences for the experimental design are discussed. The two most common sources of deviation in SPR surface binding kinetics from the ideal pseudo-first-order binding kinetics of bimolecular reactions are mass transport limitations and the heterogeneity of the surface sites. These problems are intrinsic to the use of a biosensor surface for characterizing interactions. The effect of these factors on the observed binding kinetics, and strategies to account for them are reviewed, both in the context of mathematical data analysis, as well as the design of the experiments and controls.