gebhart/patrepeval huggingface dataset:
Trellis-based scalar vector quantization of sources with memory (2000)

The trellis-based scalar-vector quantizer (TB-SVQ) can achieve the rate-distortion performance bound for memoryless sources. This paper extends the scope of this quantizer to coding of sources with memory. First considered is a simple extension, called the predictive TB-SVQ, which applies a closed-loop predictive coding operation in each survivor path of the Viterbi codebook search algorithm. Although the predictive TB-SVQ outperforms all other known structured fixed-rate vector quantizers, due to practical reasons, it may not approach the rate-distortion limit. A new quantization scheme motivated by the precoding idea of Laroia et al. (1993), called the precoded TB-SVQ, is also considered; the granular gain is realized by the underlying trellis code while the combination of the precoder and the SVQ structure provides the boundary gain. This new quantization scheme is asymptotically optimal and can, in principle, approach the rate-distortion bound for Markov sources.
Aberrant epigenetic silencing of neuronatin is a frequent event in human osteosarcoma (2020)

The paternally imprinted neuronatin (<i>NNAT</i>) gene has been identified as a target of aberrant epigenetic silencing in diverse cancers, but no association with pediatric bone cancers has been reported to date. In screening childhood cancers, we identified aberrant CpG island hypermethylation in a majority of osteosarcoma (OS) samples and in 5 of 6 human OS cell lines studied but not in normal bone-derived tissue samples. CpG island hypermethylation was associated with transcriptional silencing in human OS cells, and silencing was reversible upon treatment with 5-aza-2'-deoxycytidine. Expression of NNAT was detectable in osteoblasts and chondrocytes of human bone, supporting a potential role in bone homeostasis. Enforced expression of NNAT in human OS cells lacking endogenous expression resulted in significant reduction in colony formation and <i>in vitro</i> migration compared to nonexpressor control cells. We next analyzed the effect of NNAT expression on intracellular calcium homeostasis and found that was associated with an attenuated decay of calcium levels to baseline following ATP-induced release of calcium from endoplasmic reticulum (ER) stores. Furthermore, NNAT expression was associated with increased cytotoxicity in OS cells from thapsigargin, an inhibitor of calcium reuptake into ER and an inducer of the ER stress response. These results suggest a possible tumor suppressor role for NNAT in human osteosarcoma. Additional study is needed ascertain sensitization to ER stress-associated apoptosis as a mechanism of NNAT-dependent cytotoxicity. In that case, epigenetic modification therapy to effect <i>NNAT</i> transcriptional derepression may represent a therapeutic strategy potentially of benefit to a majority of osteosarcoma patients.
Large area sensing arrays for detection of thermal neutrons (2012)

Developments of flexible detection arrays suggest that portable robust detectors are indeed possible. A large area flexible array promises a large capture cross section in a light weight rugged format suitable for deployment at ports of entry. The approach for this detector uses a high neutron-capture cross-section layer, such as <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> B, which captures incident thermal neutrons, and emits energetic ionizing charged particles. These ionizing particles are sensed using an integrated diode. The resulting charge is then amplified via a low-noise thin film transistor amplifier. We present a low-noise optimized active pixel sensor (APS) design which can be implemented in either a low temperature InGaZnO or an a-Si:H thin film transistor (TFT) process compatible with plastic substrates. Here, we also present a detectable alpha particle response with our dual stage APS design in combination with an externally connected commercial PIN diode. Furthermore, we discuss detector and array modeling which will further aid in future designs.
The investigation of an equilibrium dependent reaction for the formation of enamines in a microchemical system (2001)

The paper describes the equilibrium dependant reaction for the formation of enamines in a microchemical system utilising electroosmotic flow (EOF) for fluid mobilisation. The authors have shown that the reaction can be carried out without the presence of a Lewis acid catalyst, in addition the enamine intermediate was synthesised at room temperature using mild solvent conditions. A 42% conversion of cyclohexanone into the enamine has been achieved to date.
Autoignition in a premixing-prevaporizing fuel duct using 3 different fuel injection systems at inlet air temperatures to 1250 K (1983)

Conditions were determined in a continuous-flow, premixing-prevaporizing duct at which autoignition occurred. Test conditions were representative of an advanced, regenerative-cycle, automotive gas turbine. The test conditions inlet air temperatures from 600 to 1250 K (a vitiated preheater was used), pressures from 170 to 600 kPa, air velocities of 10 to 30 m/sec, equivalence ratios from 0.3 to 1.0, mixing lengths from 10 to 60 cm, and residence times of 2 to 100 ms. The fuel was diesel number 2. The duct was insulated and had an inside diameter of 12 cm. Three different fuel injection systems were used: One was a single simplex pressure atomizer, and the other two were multiple-source injectors. The data obtained with the simplex and one of the multiple-source injectors agreed satisfactorily with the references and correlated with an Arrenhius expression. The data obtained with the other multiple source injector, which used multiple cones to improve the fuel-air distribution, did not correlate well with residence time.
The Neuroendocrine Protein 7B2 Is Intrinsically Disordered (2012)

The small neuroendocrine protein 7B2 has been shown to be required for the productive maturation of proprotein convertase 2 (proPC2) to an active enzyme form; this action is accomplished via its ability to block aggregation of proPC2 into nonactivatable forms. Recent data show that 7B2 can also act as a postfolding chaperone to block the aggregation of a number of other proteins, for example, α-synuclein. To gain insight into the mechanism of action of 7B2 in blocking protein aggregation, we performed structural studies of this protein using gel filtration chromatography, intrinsic tryptophan fluorescence, 1-anilino-8-naphthalenesulfonate (ANS) binding, circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopy. Gel filtration studies indicated that 7B2 exists as an extended monomer, eluting at a molecular mass higher than that expected for a globular protein of similar size. However, chemical cross-linking showed that 7B2 exhibits concentration-dependent oligomerization. CD experiments showed that both full-length 27 kDa 7B2 and the C-terminally truncated 21 kDa form lack appreciable secondary structure, although the longer protein exhibited more structural content than the latter, as demonstrated by intrinsic and ANS fluorescence studies. NMR spectra confirmed the lack of structure in native 7B2, but a disorder-to-order transition was observed upon incubation with one of its client proteins, α-synuclein. We conclude that 7B2 is a natively disordered protein whose function as an antiaggregant chaperone is likely facilitated by its lack of appreciable secondary structure and tendency to form oligomers.
Secure Image Inference Using Pairwise Activation Functions (2021)

Amongst most artificial neural networks, there is considerable reliance on (raw) data in their use, thus raising data privacy and security issues. A homomorphic encryption scheme affords the performing of computations on encrypted data though it has some challenges, including the lack of support for performing computations using transcendental functions such as logarithm and exponentiation, which exists in some of the typical activation functions in neural networks. Polynomial approximation, though can be used to derive polynomials as an approximation to these activation functions as homomorphic encryption scheme favours mostly addition and multiplication operations. While the literature has considered forming new activation functions as pairwise multiplication of well-known activation functions, the design space is mostly unexplored. Therefore this paper explores the design space of such pairwise, multiplied activation functions and their application in homomorphic image inferencing or prediction using the widely popular MNIST and CIFAR-10 benchmark datasets. Moreover, it analyses corresponding curve fitting parameters (range and degree), homomorphic-friendly pooling methods, and optimization methods in the ciphertext domain to avoid incurring huge computation costs via bootstrapping but not compromising accuracy. Results show new activation function combinations yielding similar or better results in ciphertext as compared to the ones in plaintext.
A de novo DNA Sequencing and Variant Calling Algorithm for Nanopores (2015)

The single-molecule accuracy of nanopore sequencing has been an area of rapid academic and commercial advancement, but remains insufficient for the de novo analysis of genomes. We introduce here a novel algorithm for the error correction of nanopore data, utilizing statistical models of the physical system in order to obtain high accuracy de novo sequences at a range of coverage depths. We demonstrate the technique by sequencing M13 bacteriophage DNA to 99% accuracy at moderate coverage as well as its use in an assembly pipeline by sequencing λ DNA at a range of coverages. We also show the algorithm’s ability to accurately classify sequence variants at far lower coverage than existing methods.
Toward the Comprehensive Systematic Enumeration and Synthesis of Novel Kinase Inhibitors Based on a 4-Anilinoquinazoline Binding Mode (2010)

There are currently eight small-molecule kinase inhibitors approved as cancer treatments, and a significantly larger number of compounds are in the earlier stages of clinical development. Although kinase inhibitors are most commonly developed in a cancer setting, other disease areas have been targeted. The vast majority of reported kinase small-molecule inhibitors contain functionalities that interact with the adenosine triphosphate (ATP) binding site of the kinase. The 4-anilinoquinazolines have previously been reported as potent epidermal growth factor receptor (EGFR) inhibitors, binding at the 'hinge' region of the ATP site. Subsequently, this chemical series has been optimized against a number of different kinases including Src and Aurora B. Here, we detail the computational enumeration of ring systems that have the ability to make comparable interactions to the 4-anilinoquinazoline core. These were prioritized by computational, medicinal, and synthetic chemistry input, and a number of libraries were subsequently synthesized.
Human Endogenous Retrovirus K Homologous Sequences and Their Coding Capacity in Old World Primates (1998)

The coding capacity for retroviral Gag and Env proteins has been maintained in human endogenous retroviruses of the HERV-K family. HERV-K homologous sequences have been found in all Old World primates. Here, we examined Old World primate species for the presence of full-length HERV-K gag and env genes and the presence of gag and env open reading frames as determined by the protein truncation test. Full-length HERV-K env genes were found in DNAs of all Old World primate species, whereas open reading frames for Env protein were found solely in human, chimpanzee, and gorilla DNAs. The mutational event leading to two HERV-K types was found to have occurred after the separation of hominids from lower Old World primates and before the expansion of hominids. Full-length HERV-K gag genes in hominids displayed a 96-bp deletion compared to those in lower Old World primates. The ancient gag variant has not been maintained during hominid evolution. Open reading frames for HERV-K Gag have been found in all Old World primates except chimpanzees. Our study of the HERV-K family during Old World primate evolution contributes to the understanding of their possible biological functions in the host genomes.
COMPARISON OF TWO METHODS OF PREPARATION OF THE STATIONARY PHASE FOR HPLC CHIRAL COLUMNS BASED ONtris(3,5-DIMETHYLPHENYLCARBAMOYL) CELLULOSE (1999)

Stationary phase based on tris(3,5-dimethylphenylcarbamoyl) cellulose is prepared under various conditions (precipitation, evaporation, sieving), and examined in HPLC columns for enantioseparation of racemic mixtures 1–10. Number of theoretical plates (N) and separation parameters (α and RS) are compared with those obtained with commercially available column based on the same polymeric material (Chiralcel OD, from Daicel Co.). Higher efficiency of the columns prepared by precipitation under specific conditions and followed by sieving of stationary phase, over those prepared by evaporation and (or without) sieving, is demonstrated.
Dielectric and Insulating Properties of Embedded Capacitor for Flexible Electronics Prepared by Aerosol-Type Nanoparticle Deposition (2013)

The rapid evolution in electronic equipment has created a demand for advanced devices that are flexible, thin, and light in weight. This demand is driving the development of a core technology for flexible and stretchable electronic devices. To produce wearable computers, we need to fabricate functional membranes that contain passive devices, such as capacitors and resistors, on resin sheets at low temperatures. These sheets can then serve as mounting boards for various electronic devices. By improving the technique for room-temperature aerosol-type nanoparticle deposition of a ceramic material, we have established a technology for forming a dielectric inorganic BaTiO 3 film with an excellent degree of crystallinity and favorable electric properties for use in the production of flexible and stretchable electronic devices on a polyimide sheet. By this method of forming a homogeneous nanoparticle structure inside a film, we produced a capacitor film with a dielectric constant of 200 on a polyimide sheet at room temperature.
Continuous radiant decomposition studies (1983)

To support ongoing research activities of the Renewable Resources Research Laboratory (R/sup 3/L), a double paraboloid downward facing beam arc image furnace was designed and fabricated in Princeton. The solar simulator was currently modified and upgraded to incorporate a 30 KW water-cooled, xenon compact arc lamp with all the associated electrical, optical and cooling systems. The solar furnace provides an intense light beam with a peak flux density as high as 1000 W/cm/sup 2/ (or 10,000 suns) at the focus of the concentrator. The parameters governing the design and operation of this solar furnace are described in detail. Considerable progress was made in the development of novel spouted/fluidized bed flash pyrolysis reactors which function as solar receivers. The reactors were employed at the focus of the arc image furnace under conditions of severe radiant energy transfer (with peak flux of about 1 KW/cm/sup 2/). The pyrolysis reactors employed under continuous radiant decomposition conditions performed well and provided sirup yields as high as 55% (by weight) using crushed corn cob particles (1000 > dp > 850 ..mu..m). Finally, an extensive literature search was carried out to compile the currently available data regarding decomposition of zinc sulfate. Several experiments using a Setaram Differential Scanning Calorimeter were preformed in order to investigate the mechanisms of ZnSO/sub 4/ decomposition under conditions of low heating rates.
Role of polymer ligands in the oxygenation of metal chlorophyllins (1976)

Abstract In order to obtain information about the characteristics of polymer‐(metal chlorophyllins), their redox and oxygenation reactions were studied. Complexes composed of metal chlorophyllins (MChn) and partially quaternized poly(4‐vinylpyridine) (QPVP) exhibited an increased stability due to electrostatic interaction between polymer cation and carboxylate anions of side groups in the MChn. The reduction of these polymer complexes by S 2 O 4 2‐ occurred easily with an decrease in their apparent reduction potentials. The resulting low‐valence complexes had an ability to absorb molecular oxygen. The oxygenation of these polymer complexes was not completely reversible; however the rate of the irreversible reoxidation was less by a factor of 10 10 for the polymeric complex than that for the monomeric MChn‐pyridine complex. The stability of these oxygen complexes is discussed in relation to the hydrophobicity of QPVPs.
Epitaxial Si, SiGe and Ge on binary and ternary rare earth oxide buffers (2012)

Abstract Lattice engineering by combining multilayer binary (Gd 2 O 3 and La 2 O 3 ) and ternary (Er x Nd 1‐x ) 2 O 3 rare earth oxide layers makes possible the accommodation of lattice mismatch between the silicon substrate and the grown semiconductor layer for semiconductor on insulator structures leading to a reduction of defect density. It also opens up the opportunity for stress engineering and the avoidance of the formation of structural defects and mechanical damages caused by different thermal‐mechanical properties of the substrate and the layers. In this work, some results of the development of epitaxial heterostructures with group IV semiconductors (Si, SiGe and Ge) on rare earth oxide buffer layers grown on Si(111) are desribed. Distributed Bragg reflectors designed with only three pairs exhibits 80% reflectivity for blue light. On ternary erbium neodymium oxide, SiGe layer grows with a 5x5 reconstructed surface and a roughness of 1.7 nm. We demonstrate a crack free 1 µm thick epitaxial single crystal Ge layer grown on a pseudomorphic cubic La 2 O 3 layer. (© 2012 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Photochemistry of Mycolactone A/B, the Causative Toxin of Buruli Ulcer (2012)

Photochemistry of mycolactone A/B and related unsaturated fatty acid esters is reported. On exposure to visible light, mycolactone A/B gave a mixture of four photomycolactones. Pentaenoates and tetraenoates, representing the unsaturated fatty acid portion of mycolactone A/B, were found to show the reactivity profile parallel with that of mycolactone A/B. The structure of the four photomycolactones was elucidated via (1) structure determination of the four photoproducts in the tetraenoate series; (2) their transformation to the photoproducts in the pentaenoate and then mycolactone series. Triplet quenchers did not affect the photochemical transformation, thereby indicating an event at the singlet state. A concerted, photochemically allowed [4πs + 2πa] cycloaddition was suggested to account for the observed result. This study provided the structurally defined and homogeneous material, which allowed demonstration that photomycolactones exhibit significantly reduced cytotoxicity, compared with mycolactone A/B.
Mitotic CDK1 and 4E-BP1 II: A single phosphomimetic mutation in 4E-BP1 induces glucose intolerance in mice (2023)

Objective Cyclin-dependent kinase 1 (CDK1)/cyclin B1 phosphorylates many of the same substrates as mTORC1 (a key regulator of glucose metabolism), including the eukaryotic initiation factor 4E-binding protein 1 (4E-BP1). Only mitotic CDK1 phosphorylates 4E-BP1 at residue S82 in mice (S83 in humans), in addition to the common 4E-BP1 phospho-acceptor sites phosphorylated by both CDK1 and mTORC1. We examined glucose metabolism in mice having a single aspartate phosphomimetic amino acid knock in substitution at the 4E-BP1 serine 82 (4E-BP1 S82D ) mimicking constitutive CDK1 phosphorylation. Methods Knock-in homozygous 4E-BP1 S82D and 4E-BP1 S82A C57Bl/6N mice were assessed for glucose tolerance testing (GTT) and metabolic cage analysis on regular and on high-fat chow diets. Gastrocnemius tissues from 4E-BP1 S82D and WT mice were subject to Reverse Phase Protein Array analysis. Since the bone marrow is one of the few tissues typically having cycling cells that transit mitosis, reciprocal bone-marrow transplants were performed between male 4E-BP1 S82D and WT mice, followed by metabolic assessment, to determine the role of actively cycling cells on glucose homeostasis. Results Homozygous knock-in 4E-BP1 S82D mice showed glucose intolerance that was markedly accentuated with a diabetogenic high-fat diet (p = 0.004). In contrast, homozygous mice with the unphosphorylatable alanine substitution (4E-BP1 S82A ) had normal glucose tolerance. Protein profiling of lean muscle tissues, largely arrested in G 0 , did not show protein expression or signaling changes that could account for these results. Reciprocal bone-marrow transplantation between 4E-BP1 S82D and wild-type littermates revealed a trend for wild-type mice with 4E-BP1 S82D marrow engraftment on high-fat diets to become hyperglycemic after glucose challenge. Conclusions 4E-BP1 S82D is a single amino acid substitution that induces glucose intolerance in mice. These findings indicate that glucose metabolism may be regulated by CDK1 4E-BP1 phosphorylation independent from mTOR and point towards an unexpected role for cycling cells that transit mitosis in diabetic glucose control.
Regulation of Neuropeptides in Adult Rat Forebrain by the Neurotrophins BDNF and NGF (1994)

The expression of neuropeptides and neurotrophic factors is altered in the hippocampus after seizure induction in rats. Because the increase in brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF) mRNAs precede changes in neuropeptide expression after seizure, it is possible that BDNF and NGF mediate subsequent alterations in peptide expression. To test this hypothesis directly, BDNF or NGF was infused into the hippocampus and cortex of adult rats. To ascertain the regional specificity of any observed effects of neurotrophin administration on neuropeptide expression, infusions into the striatum were also studied. To control for specificity, vehicle was also infused into the same sites. Peptide and mRNA alterations were assessed by Northern analysis, immunohistochemistry and radioimmunoassay. BDNF produced elevations of peptide and mRNA for neuropeptide Y and cholecystokinin in hippocampus and cortex, and somatostatin in cortex. BDNF increased mRNAs for neuropeptide Y, cholecystokinin, substance P and dynorphin in striatum. In contrast, BDNF decreased dynorphin peptide and mRNA in hippocampus. NGF's effects were limited to small mRNA increases, without corresponding changes in peptide levels, for neuropeptide Y in hippocampus and striatum, substance P in cortex and cholecystokinin in striatum. The distinct and limited effects of NGF infusion on neuropeptide expression demonstrate that BDNF's effects are not non-specific results of protein infusion into the brain. These findings indicate that BDNF may play a regionally specific role in modulating neuropeptide expression in the normal brain as well as in various pathophysiological states.