gebhart/patrepeval huggingface dataset:
Arithmetic coding for data compression (1994)

Arithmetic coding provides an effective mechanism for removing redundancy in the encoding of data. We show how arithmetic coding works and describe an efficient implementation that uses table lookup as a first alternative to arithmetic operations. The reduced-precision arithmetic has a provably negligible effect on the amount of compression achieved. We can speed up the implementation further by use of parallel processing. We discuss the role of probability models and how they provide probability information to the arithmetic coder. We conclude with perspectives on the comparative advantages and disadvantages of arithmetic coding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of Cancer-Associated Mutant Isocitrate Dehydrogenases: Synthesis, Structure–Activity Relationship, and Selective Antitumor Activity (2014)

Mutations of isocitrate dehydrogenase 1 (IDH1) are frequently found in certain cancers such as glioma. Different from the wild-type (WT) IDH1, the mutant enzymes catalyze the reduction of α-ketoglutaric acid to d-2-hydroxyglutaric acid (D2HG), leading to cancer initiation. Several 1-hydroxypyridin-2-one compounds were identified to be inhibitors of IDH1(R132H). A total of 61 derivatives were synthesized, and their structure-activity relationships were investigated. Potent IDH1(R132H) inhibitors were identified with Ki values as low as 140 nM, while they possess weak or no activity against WT IDH1. Activities of selected compounds against IDH1(R132C) were found to be correlated with their inhibitory activities against IDH1(R132H), as well as cellular production of D2HG, with R(2) of 0.83 and 0.73, respectively. Several inhibitors were found to be permeable through the blood-brain barrier in a cell-based model assay and exhibit potent and selective activity (EC50 = 0.26-1.8 μM) against glioma cells with the IDH1 R132H mutation.
A pilot examination of the genome-wide DNA methylation signatures of subjects entering and exiting short-term alcohol dependence treatment programs (2014)

Alcoholism has a profound impact on millions of people throughout the world. However, the ability to determine if a patient needs treatment is hindered by reliance on self-reporting and the clinician's capability to monitor the patient's response to treatment is challenged by the lack of reliable biomarkers. Using a genome-wide approach, we have previously shown that chronic alcohol use is associated with methylation changes in DNA from human cell lines. In this pilot study, we now examine DNA methylation in peripheral mononuclear cell DNA gathered from subjects as they enter and leave short-term alcohol treatment. When compared with abstinent controls, subjects with heavy alcohol use show widespread changes in DNA methylation that have a tendency to reverse with abstinence. Pathway analysis demonstrates that these changes map to gene networks involved in apoptosis. There is no significant overlap of the alcohol signature with the methylation signature previously derived for smoking. We conclude that DNA methylation may have future clinical utility in assessing acute alcohol use status and monitoring treatment response.
A Wireless Brain-Machine Interface for Real-Time Speech Synthesis (2009)

Our results support the feasibility of neural prostheses that may have the potential to provide near-conversational synthetic speech output for individuals with severely impaired speech motor control. They also provide an initial glimpse into the functional properties of neurons in speech motor cortical areas.
Static stretch affects neural stem cell differentiation in an extracellular matrix-dependent manner (2015)

Neural stem and progenitor cell (NSPC) fate is strongly influenced by mechanotransduction as modulation of substrate stiffness affects lineage choice. Other types of mechanical stimuli, such as stretch (tensile strain), occur during CNS development and trauma, but their consequences for NSPC differentiation have not been reported. We delivered a 10% static equibiaxial stretch to NSPCs and examined effects on differentiation. We found static stretch specifically impacts NSPC differentiation into oligodendrocytes, but not neurons or astrocytes, and this effect is dependent on particular extracellular matrix (ECM)-integrin linkages. Generation of oligodendrocytes from NSPCs was reduced on laminin, an outcome likely mediated by the α6 laminin-binding integrin, whereas similar effects were not observed for NSPCs on fibronectin. Our data demonstrate a direct role for tensile strain in dictating the lineage choice of NSPCs and indicate the dependence of this phenomenon on specific substrate materials, which should be taken into account for the design of biomaterials for NSPC transplantation.
Style Transfer from Non-Parallel Text by Cross-Alignment (2017)

This paper focuses on style transfer on the basis of non-parallel text. This is an instance of a broad family of problems including machine translation, decipherment, and sentiment modification. The key challenge is to separate the content from other aspects such as style. We assume a shared latent content distribution across different text corpora, and propose a method that leverages refined alignment of latent representations to perform style transfer. The transferred sentences from one style should match example sentences from the other style as a population. We demonstrate the effectiveness of this cross-alignment method on three tasks: sentiment modification, decipherment of word substitution ciphers, and recovery of word order.
Influence of the acousto-optic effect on laser Doppler anemometry signals (1998)

When laser Doppler anemometry (LDA) is used to measure sound fields in water it is important to take into account the refractive index variations in the water due to the sound wave. These have the effect of creating a phase difference between the two laser beams in the LDA setup so that when they intersect they create moving fringes. In some situations this acousto-optic effect can dominate over the movement of the particles due to the sound wave, thereby influencing the Doppler signal. This article determines in which situations the acousto-optic effect can be ignored and in which situations it has a dominant effect. Theoretical expressions are derived for the magnitude of the acousto-optic effect on the LDA signal in terms of the distance of the laser beam propagation and acoustic wave number. The results show that varying the value of the wave number, the distance the laser beams have traveled in the direction perpendicular to the optical axis, or the angle of the sound wave, has an effect on the amplitude, yamp, of the fringe movement. For low wave number values, an angle of 0, ±π from the optic axis (y direction) corresponds to the situation in which the laser beams have been affected to the same degree by refractive index changes in the water and thus the path difference is zero and the value of yamp is a minimum. A maximum value of yamp is obtained for an angle of ±π/2 from the y direction for low wave number values. It is shown that the ratio of the acousto-optic effect to the amplitude of the particle movement due to the sound wave varies as the square of both the acoustic wave number and the distance of the laser beam propagation for low wave number values. An equation for the apparent motion of the particles in the fringes is determined and is used to show that the acousto-optic effect dominates as the value of the wave number and the distance of propagation of the beams increases. Also, for very low wave numbers and short distances, the acousto-optic effect is negligible. This is because at low wave numbers, corresponding to low sound frequencies, the refractive index gradients, and hence the phase changes along the lengths of the laser beams, are small.
Colloidal Semiconductor Q‐Particles: Chemistry in the Transition Region Between Solid State and Molecules (1993)

Abstract In semiconductor particles of nanometer size, a gradual transition from solid‐state to molecular structure occurs as the particle size decreases. Consequently, a splitting of the energy bands into discrete, quantized levels occurs. Particles that exhibit these quantization effects are often called “Q‐particles” or, generally, quantized material. The optical, electronic and catalytic properties of Q‐particles drastically differ from those of the corresponding macrocrystalline substance. The band gap, a substance‐specific quantity in macrocrystalline materials, increases by several electron volts in Q‐particles with decreasing particle size. In Q‐particles there are approximately as many molecules on the surface as in the interior of the particle. Therefore, the nature of the surface as well as the particle size is also largely responsible for the physico‐chemical properties of the particle. Q‐particles of many materials can be prepared in the form of colloidal solutions or embedded in porous matrices and are stable over a long period of time. In sandwich colloids, in which Q‐particles of different materials are coupled, as well as in porous semiconductor electrodes containing Q‐particles in the pores, very efficient primary charge separation is observed. As a result, sandwich colloids have greatly enhanced photocatalytic activity relative to the individual particles, while electrodes modified with Q‐particles show high photocurrents. This article deals with the size quantization effect, the synthesis and characterization of Q‐particles, as well as with the spectroscopic, electrochemical, and electron‐microscopic investigation of these particles.
New Generalized Transducing Bacteriophage in Echerichia coli (1970)

A new generalized transducing bacteriophage similar to P1 was isolated from Salmonella oranienburg.
Percutaneous coronary intervention in diabetic patients with non-ST-segment elevation acute coronary syndromes (2004)

Key pathophysiologic mechanisms of diabetes-related coronary disease include inflammation and a prothrombotic state. In the setting of non-ST-segment elevation acute coronary syndromes diabetic patients are at high risk for subsequent cardiovascular events. At the same time, they derive greater benefit than non-diabetic counterparts from aggressive antithrombotic therapy, early coronary angiography, and stent-based percutaneous coronary intervention. The mainstays of antithrombotic therapy for diabetic patients undergoing percutaneous revascularization include aspirin, clopidogrel, platelet glycoprotein IIb/IIIa receptor antagonists, and heparin or low-molecular-weight heparin. Despite dramatic reduction in restenosis conferred by drug-eluting stents, diabetic patients remain at increased risk for repeat revascularization. More efforts are needed both in terms of local drug elution as well as systemic pharmacologic therapies to further contain the excessive neointimal proliferation that characterizes the diabetic response to vascular injury.
Alignment methods for averaging of high-resolution cardiac signals: a comparative study of performance (1991)

Accurate signal estimation by means of coherent averaging techniques needs temporal alignment methods. A known low-pass filtering effect is yielded when alignment errors are present. This is very critical in the estimation of low-level high-frequency potentials in high-resolution ECG analysis. A comparative study of the performance of three alignment methods (the double-level method, a new time-delay estimation method based on normalized integrals, and matched filtering) is presented in this paper. A real signal and additive random noise for several signal-to-noise ratios (SNR's) are selected to make an ensemble of computer-simulated beats. The relation between the standard deviation of temporal misalignment versus SNR is discussed. A second study with real ECG signals is also presented. Several morphologies of QRS and P waves are tested. The results are in agreement with the computer simulation study. Nevertheless, the power spectrum of the noise process can affect the results. Matched filter estimation has been tested in the presence of power line interference (50 Hz), with poor results. An application of the three alignment methods as a function of the SNR is proposed. The new time-delay estimation method has been observed to be robust, even in the presence of nonwhite noise.
Identification of two determinants that attenuate vaccine-related type 2 poliovirus (1991)

The poliovirus P2/P712 strain is an attenuated virus that is closely related to the type 2 Sabin vaccine strain. By using a mouse model for poliomyelitis, sequences responsible for attenuation of the P2/P712 strain were previously mapped to the 5' noncoding region of the genome and a central region encoding VP1, 2Apro, 2B, and part of 2C. To identify specific determinants that attenuate the P2/P712 strain, recombinants between this virus and the mouse-adapted P2/Lansing were constructed and their neurovirulence in mice was determined. By using this approach, the attenuation determinant in the central region was mapped to capsid protein VP1. Candidate attenuating sequences in VP1 and the 5' noncoding region were identified by comparing the P2/P712 sequence with that of vaccine-associated isolate P2/P117, and the P2/117 sequences were introduced into the P2/Lansing-P2/P712 recombinants by site-directed mutagenesis. Results of neurovirulence assays in mice indicate that an A at nucleotide 481 in the 5' noncoding region and isoleucine (Ile) at position 143 of capsid protein VP1 are the major determinants of attenuation of P2/P712. These determinants also attenuated neurovirulence in transgenic mice expressing human poliovirus receptors, a new model for poliomyelitis in which virulent viruses are not host restricted. These results demonstrate that A-481 and Ile-143 are general determinants of attenuation.
Simian Virus 5 V Protein Acts as an Adaptor, Linking DDB1 to STAT2, To Facilitate the Ubiquitination of STAT1 (2005)

ABSTRACT The V protein of simian virus 5 (SV5) facilitates the ubiquitination and subsequent proteasome-mediated degradation of STAT1. Here we show, by visualizing direct protein-protein interactions and by using the yeast two-hybrid system, that while the SV5 V protein fails to bind to STAT1 directly, it binds directly and independently to both DDB1 and STAT2, two cellular proteins known to be essential for SV5-mediated degradation of STAT1. We also demonstrate that STAT1 and STAT2 interact independently of SV5 V and show that SV5 V protein acts as an adaptor molecule linking DDB1 to STAT2/STAT1 heterodimers, which in the presence of additional accessory cellular proteins, including Cullin 4a, can ubiquitinate STAT1. Additionally, we show that the avidity of STAT2 for V is relatively weak but is significantly enhanced by the presence of both STAT1 and DDB1, i.e., the complex of STAT1, STAT2, DDB1, and SV5 V is more stable than a complex of STAT2 and V. From these studies we propose a dynamic model in which SV5 V acts as a bridge, bringing together a DDB1/Cullin 4a-containing ubiquitin ligase complex and STAT1/STAT2 heterodimers, which leads to the degradation of STAT1. The loss of STAT1 results in a decrease in affinity of binding of STAT2 for V such that STAT2 either dissociates from V or is displaced from V by STAT1/STAT2 complexes, thereby ensuring the cycling of the DDB1 and SV5 V containing E3 complex for continued rounds of STAT1 ubiquitination and degradation.
Activation of CPP32-Like Caspases Contributes to Neuronal Apoptosis and Neurological Dysfunction after Traumatic Brain Injury (1997)

We examined the temporal profile of apoptosis after fluid percussion-induced traumatic brain injury (TBI) in rats and investigated the potential pathophysiological role of caspase-3-like proteases in this process. DNA fragmentation was observed in samples from injured cortex and hippocampus, but not from contralateral tissue, beginning 4 hr after TBI and continuing for at least 3 d. Double labeling of brain with terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) and an antibody directed to neuronal nuclear protein identified apoptotic neurons with high frequency in both traumatized rat cortex and hippocampus. Cytosolic extracts from injured cortex and hippocampus, but not from contralateral or control tissue, induced internucleosomal DNA fragmentation in isolated nuclei with temporal profiles consistent with those of DNA fragmentation observed in vivo. Caspase-3 mRNA levels, estimated by semiquantitative RT-PCR, were elevated fivefold in ipsilateral cortex and twofold in hippocampus by 24 hr after TBI. Caspase-1 mRNA content also was increased after trauma, but to a lesser extent in cortex. Increased caspase-3-like, but not caspase-1-like, enzymatic activity was found in cytosolic extracts from injured cortex. Intracerebroventricular administration of z-DEVD-fmk-a specific tetrapeptide inhibitor of caspase-3-before and after injury markedly reduced post-traumatic apoptosis, as demonstrated by DNA electrophoresis and TUNEL staining, and significantly improved neurological recovery. Together, these results implicate caspase-3-like proteases in neuronal apoptosis induced by TBI and suggest that the blockade of such caspases can reduce post-traumatic apoptosis and associated neurological dysfunction.
Creating time-optimal commands for systems with denominator dynamics (2002)

Many high-performance applications demand that machines execute rapid and precise point-to-point motions. In order to achieve these motions, time-optimal command profiles can typically be employed. This work presents a strategy for deriving time-optimal commands that takes into account all possible types of system denominator dynamics. Unlike other approaches, the method presented here can account for real modes as well as rigid-body and flexible modes. Since this is a more general strategy for deriving time-optimal commands, results illustrate that this technique always meets or exceeds the performance of existing methods.
Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization (2017)

Clinical tissues are prepared for histological analysis and long-term storage via formalin fixation and paraffin embedding (FFPE). The FFPE process results in fragmentation and chemical modification of RNA, rendering it less suitable for analysis by techniques that rely on reverse transcription (RT) such as RT-qPCR and RNA-Seq. Here we describe a broadly applicable technique called 'Ligation in situ Hybridization' ('LISH'), which is an alternative methodology for the analysis of FFPE RNA. LISH utilizes the T4 RNA Ligase 2 to efficiently join adjacent chimeric RNA-DNA probe pairs hybridized in situ on fixed RNA target sequences. Subsequent treatment with RNase H releases RNA-templated ligation products into solution for downstream analysis. We demonstrate several unique advantages of LISH-based assays using patient-derived FFPE tissue. These include >100-plex capability, compatibility with common histochemical stains and suitability for analysis of decade-old materials and exceedingly small microdissected tissue fragments. High-throughput DNA sequencing modalities, including single molecule sequencing, can be used to analyze ligation products from complex panels of LISH probes ('LISH-seq'), which can be amplified efficiently and with negligible bias. LISH analysis of FFPE RNA is a novel methodology with broad applications that range from multiplexed gene expression analysis to the sensitive detection of infectious organisms.
Clarifying the Catalytic Roles of Conserved Residues in the Amidase Signature Family (2000)

Fatty acid amide hydrolase (FAAH) is a mammalian integral membrane enzyme responsible for the hydrolysis of a number of neuromodulatory fatty acid amides, including the endogenous cannabinoid anandamide and the sleep-inducing lipid oleamide. FAAH belongs to a large class of hydrolytic enzymes termed the "amidase signature family," whose members are defined by a conserved stretch of approximately 130 amino acids termed the "amidase signature sequence." Recently, site-directed mutagenesis studies of FAAH have targeted a limited number of conserved residues in the amidase signature sequence of the enzyme, identifying Ser-241 as the catalytic nucleophile and Lys-142 as an acid/base catalyst. The roles of several other conserved residues with potentially important and/or overlapping catalytic functions have not yet been examined. In this study, we have mutated all potentially catalytic residues in FAAH that are conserved among members of the amidase signature family, and have assessed their individual roles in catalysis through chemical labeling and kinetic methods. Several of these residues appear to serve primarily structural roles, as their mutation produced FAAH variants with considerable catalytic activity but reduced expression in prokaryotic and/or eukaryotic systems. In contrast, five mutations, K142A, S217A, S218A, S241A, and R243A, decreased the amidase activity of FAAH greater than 100-fold without detectably impacting the structural integrity of the enzyme. The pH rate profiles, amide/ester selectivities, and fluorophosphonate reactivities of these mutants revealed distinct catalytic roles for each residue. Of particular interest, one mutant, R243A, displayed uncompromised esterase activity but severely reduced amidase activity, indicating that the amidase and esterase efficiencies of FAAH can be functionally uncoupled. Collectively, these studies provide evidence that amidase signature enzymes represent a large class of serine-lysine catalytic dyad hydrolases whose evolutionary distribution rivals that of the catalytic triad superfamily.
Non‐expression of HLA‐B*5111N is caused by an insertion into the cytosine island at exon 4 creating a frameshift stop codon (2001)

The identification of the "blank" allele HLA-B*5111N, which was detected in German and Czech individuals, is described. In the pedigree analysis this new allele segregates with the serological haplotype HLA-A2; B-; DR4 which is frequent in Czech population. The non-expression of B*5111N is caused by the insertion of an additional cytosine molecule at the cytosine island between the nucleotides 621-626 (codons 183-185, first three codons of exon 4) leading to a frame shift that creates a stop codon at codon 196. This insertion may be explained either by conversion with the pseudogene HLA-J or by slipped-strand mispairing. In order not to overlook the presence of alleles with altered expression in case of hematopoietic stem cell transplantation, both serological and DNA-based typing should be performed (Note).
Characterizing and Patterning of PDMS‐Based Conducting Composites (2007)

Conducting polydimethylsiloxane (PDMS) composites are synthesized by mixing conductive nano- or microparticles witha PDMS gel. Experiments show that such composites exhibit good electrical conductivity and mechanical reliability, as well as desirable thermal characteristics. 3D microstructures, such as for the use of bio-microchips, can be realized by a simple lithographic technique and a realistic 3D application is demonstrated (see figure).