gebhart/patrepeval huggingface dataset:
A reduced QWERTY keyboard for mobile text entry (2004)

In this paper we describe a specialized keyboard for text entry that maps four rows of a standard keyboard onto the home row, with different characters encoded via modifier keys and multi-tap input. Use of the keyboard also relies on lexicon-based disambiguation. This design has two motivations: limiting physical space requirements and capitalizing on user knowledge of the standard QWERTY keyboard layout. The resulting stick keyboard is between 15% and 25% of the size of a standard keyboard. In a preliminary empirical study, users reached half of their normal typing speed using lexicon-based disambiguation (22.5 wpm) and a reasonable but lower speed with multi-tap input (10.4 wpm) with only a few minutes of practice.
Plastic Encapsulation of Stabilized Escherichia coli and Pseudomonas putida (2004)

Escherichia coli and Pseudomonas putida dried in hydroxyectoine or trehalose are shown to be highly resistant to the organic solvents chloroform and acetone, and consequently, they can be encapsulated in a viable form in solid plastic materials. Bacteria are recovered by rehydration after physical disruption of the plastic. P. putida incorporated into a plastic coating of maize seeds was shown to colonize roots efficiently after germination.
Purification of a Protein Palmitoyltransferase that Acts on H-Ras Protein and on a C-terminal N-Ras Peptide (1996)

Mammalian H-Ras and N-Ras are GTP-binding proteins that must be post-translationally lipidated to function as molecular switches in signal transduction cascades controlling cell growth and differentiation. These proteins contain a C-terminal farnesyl-cysteine alpha-methyl ester and palmitoyl groups attached to nearby cysteines. Data is presented showing that rat liver microsomes contain an enzyme that transfers the palmitoyl group from palmitoyl-coenzyme A to cysteine residues of H-Ras protein and of a synthetic peptide having the structure of the C terminus of N-Ras. This protein palmitoyltransferase (PPT) was solubilized from membranes and purified 10,500-fold to apparent homogeneity with an overall yield of 10%. On an SDS gel, PPT appears as two proteins of molecular masses of approximately 30 and approximately 33 kDa. If the palmitoylation sites of the N-Ras peptide (the non-farnesylated cysteine) or H-Ras protein (cysteines 181 and 184) are changed to serine, palmitoylation by PPT does not occur. Non-farnesylated H-Ras produced in bacteria as well as in vitro farnesylated bacterial H-Ras are not substrates for PPT nor is the non-farnesylated, methylated N-Ras peptide. These results suggest, but do not prove, that farnesylation and possibly C-terminal methylation are prerequisites for Ras palmitoylation. PPT shows a large preference for palmitoyl-coenzyme A over myristoyl-coenzyme as the acyl donor. Values of Km for palmitoyl-CoA and H-Ras are 4.3 +/- 1.2 and 0.8 +/- 0.3 microM, respectively. PPT is the first protein palmitoyltransferase to be purified, and the availability of pure enzyme should contribute to our understanding of the function and regulation of Ras palmitoylation in cells.
Distortion-invariant object recognition using adaptive resonance theory (2002)

Classification and recognition of multiple objects under changes in position, orientation and scale are needed in practical applications such as automation of assembly lines. One of the main drawbacks in the conventional pattern recognition technique is the enormous time and computational overhead required for classification. However, the conventional techniques are well-suited for extracting the features of objects. Recently, the advantages of artificial neural networks (ANNs) of having a high degree of fault-tolerance have been used in the field of pattern classification problems. The authors have combined the advantages of both the traditional pattern recognition methodology and the neural network paradigm for the distortion-invariant object recognition. The first part of this work deals with the traditional pattern recognition techniques for the extraction of the features of objects. To extract the invariant features of objects, geometrical moment-invariant techniques are used. In the case of multiple objects, the authors do segmentation of each object before extracting the features. A neural network paradigm called the ART2-analog version of adaptive resonance theory is employed to classify objects from the extracted features.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
3D deep shape descriptor (2015)

Shape descriptor is a concise yet informative representation that provides a 3D object with an identification as a member of some category. We have developed a concise deep shape descriptor to address challenging issues from ever-growing 3D datasets in areas as diverse as engineering, medicine, and biology. Specifically, in this paper, we developed novel techniques to extract concise but geometrically informative shape descriptor and new methods of defining Eigen-shape descriptor and Fisher-shape descriptor to guide the training of a deep neural network. Our deep shape descriptor tends to maximize the inter-class margin while minimize the intra-class variance. Our new shape descriptor addresses the challenges posed by the high complexity of 3D model and data representation, and the structural variations and noise present in 3D models. Experimental results on 3D shape retrieval demonstrate the superior performance of deep shape descriptor over other state-of-the-art techniques in handling noise, incompleteness and structural variations.
Graphitic carbon nanofiber (GCNF)/polymer materials. II. GCNF/epoxy monoliths using reactive oxydianiline linker molecules and the effect of nanofiber reinforcement on curing conditions (2005)

Abstract Reactive (r‐) graphitic carbon nanofibers (GCNFs) with 3,4'‐oxydianiline (ODA), r‐GCNF‐ODA, capable of covalent binding to an epoxy resin during thermal curing, are prepared by reaction of GCNFs surface‐derivatized with ODA linker molecules (GCNF‐ODA) with butyl glycidyl ether. The thermal curing characteristics of r‐GCNF‐ODA/epoxy resin mixtures having nanofiber loadings of 0.3 wt% and 1.3 wt% are analyzed by differential scanning calorimetry (DSC). The quality of the cured GCNF/epoxy nanocomposites is assessed through bending tests and scanning electron microscopy (SEM). These results indicate that the presence of r‐GCNF‐ODA nanofibers affects the thermal curing process, and that additional heating is required to achieve cured nanocomposites at higher nanofiber loadings. Reaction of GCNF‐ODA nanofibers with butyl glycidyl ether prior to mixing with an epoxy resin gives more well‐dispersed r‐GCNF‐ODA/epoxy resin mixtures and r‐GCNF‐ODA/epoxy nanocomposites having better flexural strength than the corresponding GCNF‐ODA/epoxy materials. POLYM. COMPOS., 26:128–135, 2005. © 2005 Society of Plastics Engineers
Identification of human genomic clones coding the major histocompatibility antigens HLA-a2 and HLA-B7 by DNA-mediated gene transfer. (1982)

We have screened a large number of isolated human genomic clones that hybridize to a cloned HLA cDNA probe for their ability to direct the synthesis of HLA-A, -B, and -C surface antigens on mouse L cells following DNA-mediated gene transfer. The surface expression of human histocompatibility antigens, monitored by indirect immunofluorescence and the fluorescence-activated cell sorter, was examined at 60 hr after transfection and on hypoxanthine/aminopterin/thymidine-resistant (HATR) populations derived from cotransfer with the herpes simplex virus thymidine kinase gene. Two unique genomic clones designated JY B3.2 and JY 158, isolated from the human lymphoblastoid cell line JY (homozygous HLA-A2, -B7), were shown to contain gene sequences capable of directing expression of an HLA-A, -B, -C determinant. By using allo-specific antibodies, the gene products of these clones were identified as HLA-A2 and HLA-B7, respectively. HATR clonal populations isolated from cotransfections with these genomic clones displayed varying levels of surface HLA expression that correlated with the number of intact donor HLA sequences present in the cells. In general, these levels of expression were stable during 3 months in culture. This system provides a powerful tool for the study of human surface antigen gene structure, expression, and function on a mouse cell background.
Plain Silver Surface Plasmon Resonance for Microarray Application (2015)

The application scope of surface plasmon resonance (SPR) and SPR imaging (SPRi) is rapidly growing, and tools such as high-performance and low-cost slides could enable more rapid growth of the field. We describe herein a novel silver slide, addressing the inherent instability of plain silver structure by improving adhesion between the glass substrate and the silver layer with a thin buffer layer of gold. Covered by a self-assembled monolayer (SAM) only, SPR characteristics of the slide remain steady for more than 3 months under regular storage. In a bioassay, the slide substantiates the predicted nearly 100% sensitivity improvement over gold slides and exhibits exceptional performance stability as determined by sensitivity and resolution measurements during the extended 40,000 s multicycle experiment. We demonstrate the suitability of this new slide for large-area SPRi, describing analysis results from a 1 296-ligand protein microarray. We predict this slide structure will provide a stable, high-sensitivity solution for high-throughput SPRi applications and other surface analysis platforms.
WIPI1 Coordinates Melanogenic Gene Transcription and Melanosome Formation via TORC1 Inhibition (2011)

Recent studies implicate a role for WD repeat domain, phosphoinositide-interacting 1 (WIPI1) in the biogenesis of melanosomes, cell type-specific lysosome-related organelles. In this study, we determined that WIPI1, an ATG18 homologue that is shown to localize to both autophagosomes and early endosomes, inhibited mammalian target of rapamycin (MTOR) signaling, leading to increased transcription of melanogenic enzymes and the formation of mature melanosomes. WIPI1 suppressed the target of rapamycin complex 1 (TORC1) activity, resulting in glycogen synthase kinase 3β inhibition, β-Catenin stabilization, and increased transcription of microphthalmia transcription factor and its target genes. WIPI1-depleted cells accumulated stage I melanosomes but lacked stage III-IV melanosomes. Inhibition of TORC1 by rapamycin treatment resulted in the accumulation of stage IV melanosomes but not autophagosomes, whereas starvation resulted in the formation of autophagosomes but not melanin accumulation. Taken together, our studies define a distinct role for WIPI1 and TORC1 signaling in controlling the transcription of melanogenic enzymes and melanosome maturation, a process that is distinct from starvation-induced autophagy.
Impaired Glial Glutamate Uptake Induces Extrasynaptic Glutamate Spillover in the Spinal Sensory Synapses of Neuropathic Rats (2010)

Glial cell dysfunction and excessive glutamate receptor activation in spinal dorsal horn neurons are hallmark mechanisms of pathological pain. The way in which glial cell dysfunction leads to excessive glutamate receptor activation in the spinal sensory synapses remains unknown. We and others recently reported the downregulation of glial glutamate transporter (GT) protein expression in the spinal dorsal horn of neuropathic rats. In this study, we showed that excitatory postsynaptic currents originating from N-methyl-d-aspartate receptor activation (NMDA EPSCs) elicited by peripheral synaptic input in the spinal sensory synapses were enhanced in neuropathic rats with mechanical allodynia induced by partial sciatic nerve ligation. The enhanced NMDA EPSCs were accompanied by an increased proportion of NR2B receptor activation. Physically blocking the extrasynaptic glutamate with dextran or chemically scavenging the glutamate with glutamic-pyruvic transaminase ameliorated the abnormal NMDA EPSCs in neuropathic rats. Pharmacological blockade of glial GTs with dihydrokainic acid enhanced NMDA receptor activation elicited by synaptic input or puffed glutamate in normal control rats, but this effect was precluded in neuropathic rats. Thus extrasynaptic glutamate spillover and extrasynaptic NMDA receptor activation induced by deficient glial glutamate uptake in the synapses resulted in the excessive activation of NMDA receptors in neuropathic rats. It is suggested that extrasynaptic glutamate spillover may be a key synaptic mechanism related to phenotypic alterations induced by nerve injury in the spinal dorsal horn and that glial GTs are potential new targets in the development of analgesics.
Therapeutic effect of tocilizumab on two patients with polymyositis (2011)

cells, or her B-cell subset. Like autoinflammatory diseases, our case strongly suggests that neutrophils and monocytes play important roles in the development of BD. Our case may help to explain the pathogenesis of BD.
Hindering auxiliary anchors are potent modulators of peptide binding and selection by I-Akclass II molecules (2000)

Selection of particular antigen-derived peptides by class II MHC molecules determines the population of complexes represented on the antigen-presenting cell surface and available for T cell receptor engagement. This discriminating selection process results from unique interactions between the spectrum of peptides generated during antigen processing and the MHC molecules. Here, we examined the selection of peptides by the class II MHC, I-A(k). Our results indicate that although peptide primary anchors are key in MHC binding, auxiliary anchors are a powerful regulatory component in the selection of peptides by I-A(k). Study of the segments surrounding the dominant hen egg white lysozome(48-61) epitope demonstrates that auxiliary anchors also are involved in determining the binding register of I-A(k) along an extended peptide. In addition, we found that unique combinations of auxiliary anchors can act in concert to modulate the binding of peptides to I-A(k).
Thermal Behavior and Kinetic Analysis of the Chain Unfolding and Refolding and of the Concomitant Nonpolar Solvation and Desolvation of Two Elastin-like Polymers (2003)

Water-induced chain dynamics alterations are of paramount importance in many protein-based polymers because they determine and affect to a great extent the temperature dependence of the end properties. In this study, the thermal behavior of the reversible unfolding and refolding of poly(Val-Pro-Gly-Val-Gly) and poly(Val-Pro-Ala-Val-Gly) and of their concurrent dehydration and hydration processes has been studied by differential scanning calorimetry (DSC) and turbidimetry. Contrary to the good reversibility shown by poly(Val-Pro-Gly-Val-Gly), the substitution of glycine by alanine in poly(Val-Pro-Ala-Val-Gly) perturbed to a large extent the process of chain unfolding. For the latter polymer, it was found that both chain unfolding and rehydration processes take place at large undercoolings, suggesting that both events occur far from equilibrium conditions and, therefore, are strongly dominated by kinetics. In this context, the existence of an hydration excess with a kinetic rather than a thermodynamic nature is a remarkable observation. The kinetics of folding and unfolding were also studied by using an isoconversional method of kinetic analysis, i.e., the model-free Friedmand's isoconversional method. As expected, the kinetics of the solvation of nonpolar moieties for both polymers indicated a complex and multistep process. Again, poly(Val-Pro-Ala-Val-Gly) showed a quite different pattern characterized by an acute hysteresis behavior which seems to govern the hydration process for this polymer. The differences observed between both polymers have been interpreted in terms of the hindrance provided by the methyl group in alanine during temperature-induced chain dynamics.
The 24 kDa N‐terminal sub‐domain of the DNA gyrase B protein binds coumarin drugs (1994)

A number of lines of evidence suggest that the N-terminal sub-domain of the DNA gyrase B protein contains the binding site for the coumarin antibiotics. We have engineered a clone which encodes a 24 kDa protein which represents this domain. Bacteria which overproduce this protein show an elevated level of resistance to coumarins, suggestive of binding of the 24 kDa protein to the drugs in vivo. In vitro we find that the 24 kDa protein does not interact with the gyrase A or B proteins or with DNA, and fails to hydrolyse ATP or show significant binding to ATP, ADP or ADPNP. However, we show that the 24 kDa protein binds coumarin drugs as tightly as the intact B protein. A number of experiments suggest that the interaction of the coumarins with the protein is predominantly hydrophobic in nature.
Author index (2006)

The non-Hodgkin's lymphomas (NHLs) comprise a heterogeneous collection of lymphoproliferative malignancies, which are most common in people aged over 55 years. Diffuse large B-cell lymphoma (DLBCL) is the most common type of NHL, accounting for approximately 30% of all new patients. Follicular lymphoma (FL) is the second most common NHL sub-type, and accounts for a further 22% of cases. While the incidence of most other cancers is decreasing, that of NHL is increasing steadily. During the 1970's and 1980's, worldwide NHL incidence rose by 3-4% per year. This rise has slowed in the 1990's, but an annual increase of 1-2% is still being recorded. Over the last five years, the introduction of monoclonal antibodies, and specifically the anti-CD20 monoclonal antibody, rituximab, has radically changed treatment of B-cell NHL. Rituximab is a genetically engineered chimeric mouse/human monoclonal antibody which binds to the transmembrane antigen, CD20, a non-glycosylated phosphoprotein, located on pre-B and mature B lymphocytes. This antigen is expressed on over 95% of all B cell NHLs, and on normal B cells, but not on haematopoietic stem cells, normal or malignant plasma cells. The Fc domain of rituximab recruits immune effector functions to mediate B cell lysis. Possible mechanisms of cytotoxicity include complement-dependent cytotoxicity (CDC) resulting from C1q binding, and antibody-dependent cellular cytotoxicity (ADCC) mediated by one or more of the Fcgamma receptors on the surface of granulocytes, macrophages and NK cells. It is also possible that the binding of rituximab to the CD20 antigen on the cell surface may directly induce apoptosis. For patients with both follicular and diffuse large B-cell NHL, several large scale prospective randomised trials have demonstrated prolongation of remission when rituximab is incorporated into first line treatment, and, in follicular lymphoma, as a component of salvage therapy. As a result of these studies, current European indications for rituximab include: the treatment of previously untreated patients with stage III-IV follicular lymphoma in combination with cyclophosphamide, vincristine and prednisone (CVP) chemotherapy; as maintenance therapy in patients with relapsed follicular lymphoma responding to induction therapy with chemotherapy or immuno-chemotherapy; the treatment of patients with diffuse large B cell NHL in combination with cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) chemotherapy. This paper examines the evidence supporting the use of rituximab in these settings, and places its use into the context of standard clinical practice.
A 4-MHz CMOS continuous-time filter with on-chip automatic tuning (1988)

A third-order elliptic low-pass continuous-time filter with a 4-MHz cutoff frequency, integrated in a 3- mu m p-well CMOS process, is presented. The design procedure is based on the direct simulation of a doubly terminated LC ladder filter by capacitors and fully balanced, current-controlled transconductance amplifiers with extended linear range. The on-chip automatic tuning circuit uses a phase-locked loop implemented with an 8.5-MHz controlled oscillator that matches a specific two-integrator loop of the filter. The complete circuit features 70-dB dynamic range (THD<-50 dB) and consumes only 16 mW from +or-2.5-V supplies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
SRT1720, SRT2183, SRT1460, and Resveratrol Are Not Direct Activators of SIRT1 (2010)

Sirtuins catalyze NAD(+)-dependent protein deacetylation and are critical regulators of transcription, apoptosis, metabolism, and aging. There are seven human sirtuins (SIRT1-7), and SIRT1 has been implicated as a key mediator of the pathways downstream of calorie restriction that have been shown to delay the onset and reduce the incidence of age-related diseases such as type 2 diabetes. Increasing SIRT1 activity, either by transgenic overexpression of the Sirt1 gene in mice or by pharmacological activation by small molecule activators resveratrol and SRT1720, has shown beneficial effects in rodent models of type 2 diabetes, indicating that SIRT1 may represent an attractive therapeutic target. Herein, we have assessed purported SIRT1 activators by employing biochemical assays utilizing native substrates, including a p53-derived peptide substrate lacking a fluorophore as well as the purified native full-length protein substrates p53 and acetyl-CoA synthetase1. SRT1720, its structurally related compounds SRT2183 and SRT1460, and resveratrol do not lead to apparent activation of SIRT1 with native peptide or full-length protein substrates, whereas they do activate SIRT1 with peptide substrate containing a covalently attached fluorophore. Employing NMR, surface plasmon resonance, and isothermal calorimetry techniques, we provide evidence that these compounds directly interact with fluorophore-containing peptide substrates. Furthermore, we demonstrate that SRT1720 neither lowers plasma glucose nor improves mitochondrial capacity in mice fed a high fat diet. SRT1720, SRT2183, SRT1460, and resveratrol exhibit multiple off-target activities against receptors, enzymes, transporters, and ion channels. Taken together, we conclude that SRT1720, SRT2183, SRT1460, and resveratrol are not direct activators of SIRT1.
Cell-to-Cell Trafficking of Macromolecules through Plasmodesmata Potentiated by the Red Clover Necrotic Mosaic Virus Movement Protein. (1993)

Direct evidence is presented for cell-to-cell trafficking of macromolecules via plasmodesmata in higher plants. The fluorescently labeled 35-kD movement protein of red clover necrotic mosaic virus (RCNMV) trafficked rapidly from cell to cell when microinjected into cowpea leaf mesophyll cells. Furthermore, this protein potentiated rapid cell-to-cell trafficking of RCNMV RNA, but not DNA. Electron microscopic studies demonstrated that the 35-kD movement protein does not unfold the RCNMV RNA molecules. Thus, if unfolding of RNA is necessary for cell-to-cell trafficking, it may well involve participation of endogenous cellular factors. These findings support the hypothesis that trafficking of macromolecules is a normal plasmodesmal function, which has been usurped by plant viruses for their cell-to-cell spread.
Wireless Neural Recording With Single Low-Power Integrated Circuit (2009)

We present benchtop and in vivo experimental results from an integrated circuit designed for wireless implantable neural recording applications. The chip, which was fabricated in a commercially available 0.6- mum 2P3M BiCMOS process, contains 100 amplifiers, a 10-bit analog-to-digital converter (ADC), 100 threshold-based spike detectors, and a 902-928 MHz frequency-shift-keying (FSK) transmitter. Neural signals from a selected amplifier are sampled by the ADC at 15.7 kSps and telemetered over the FSK wireless data link. Power, clock, and command signals are sent to the chip wirelessly over a 2.765-MHz inductive (coil-to-coil) link. The chip is capable of operating with only two off-chip components: a power/command receiving coil and a 100-nF capacitor.