gebhart/patrepeval huggingface dataset:
3-D Technology Assessment: Path-Finding the Technology/Design Sweet-Spot (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> It is widely acknowledged that three-dimensional (3-D) technologies offer numerous opportunities for system design. In recent years, significant progress has been made on these 3-D technologies, and they have become probably the best hope for carrying the semiconductor industry beyond the path of Moore's law. However, a clear roadmap is missing to successfully introduce this 3-D technology onto the market. Today, a plurality of 3-D technology options exists, which requires different design and test strategies. To crystallize the many technology options in a few mainstream technologies, it is mandatory to coexplore both technology and design options. The contribution of this paper is to introduce a novel path finding methodology to untangle the many intertwined design/technology options. This holistic approach will be applied on a representative 3-D case study. Initial results demonstrate the benefits of the proposed path-finding methodology to steer the technology development and fine-tune design strategies. </para>
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction (2013)

Tumor heterogeneity is a limiting factor in cancer treatment and in the discovery of biomarkers to personalize it. We describe a computational purification tool, ISOpure, to directly address the effects of variable normal tissue contamination in clinical tumor specimens. ISOpure uses a set of tumor expression profiles and a panel of healthy tissue expression profiles to generate a purified cancer profile for each tumor sample and an estimate of the proportion of RNA originating from cancerous cells. Applying ISOpure before identifying gene signatures leads to significant improvements in the prediction of prognosis and other clinical variables in lung and prostate cancer.
Pitch perception by cochlear implant subjects (1987)

Direct electrical stimulation of the auditory nerve can be used to restore some degree of hearing to the profoundly deaf. Percepts due to electrical stimulation have characteristics corresponding approximately to the acoustic percepts of loudness, pitch, and timbre. To encode speech as a pattern of electrical stimulation, it is necessary to determine the effects of the stimulus parameters on these percepts. The effects of the three basic stimulus parameters of level, repetition rate, and stimulation location on subjects' percepts were examined. Pitch difference limens arising from changes in rate of stimulation increase as the stimulating rate increases, up to a saturation point of between 200 and 1000 pulses per second. Changes in pitch due to electrode selection depend upon the subject, but generally agree with a tonotopic organization of the human cochlea. Further, the discriminability of such place-pitch percepts seems to be dependent on the degree of current spread in the cochlea. The effect of stimulus level on perceived pitch is significant but is highly dependent on the individual tested. The results of these experiments are discussed in terms of their impact on speech-processing strategies and their relevance to acoustic pitch perception.
Application of lentivirus‐mediated RNAi in studying gene function in mammalian tooth development (2006)

RNA interference (RNAi) has recently become a powerful tool to silence gene expression in mammalian cells, but its application in assessing gene function in mammalian developing organs remains highly limited. Here we describe several unique developmental properties of the mouse molar germ. Embryonic molar mesenchyme, but not the incisor mesenchyme, once dissociated into single cell suspension and re-aggregated, retains its odontogenic potential, the capability of a tissue to instruct an adjacent tissue to initiate tooth formation. Dissociated molar mesenchymal cells, even after being plated in cell culture, retain odontogenic competence, the capability of a tissue to respond to odontogenic signals and to support tooth formation. Most interestingly, while dissociated epithelial and mesenchymal cells of molar tooth germ are mixed and re-aggregated, the epithelial cells are able to sort out from the mesenchymal cells and organize into a well-defined dental epithelial structure, leading to the formation of a well-differentiated tooth organ after sub-renal culture. These unique molar developmental properties allow us to develop a strategy using a lentivirus-mediated RNAi approach to silence gene expression in dental mesenchymal cells and assess gene function in tooth development. We show that knockdown of Msx1 or Dlx2 expression in the dental mesenchyme faithfully recapitulates the tooth phenotype of their targeted mutant mice. Silencing of Barx1 expression in the dental mesenchyme causes an arrest of tooth development at the bud stage, demonstrating a crucial role for Barx1 in tooth formation. Our studies have established a reliable and rapid assay that would permit large-scale analysis of gene function in mammalian tooth development.
An overview of dexterous manipulation (2002)

Presents an overview of research in dexterous manipulation. We first define robotic dexterous manipulation in comparison to traditional robotics and human manipulation. Next, kinematics, contact types and forces are used to formulate the dexterous manipulation problem. Dexterous motion planning is described, which includes grasp planning and quality measures. We look at mid- and low-level control frameworks, and then compare manipulation versus exploration. Finally, we list accomplishments in the different areas of dexterous manipulation research, and highlight important areas for future work.
Pharmaceutical applications of cyclodextrins: effects on drug permeation through biological membranes (2011)

A mechanism-based understanding of cyclodextrin complexation is essential for the appropriate formulation of contemporary drug candidates.
Rigiflex Lithography for Nanostructure Transfer (2005)

Rigiflex lithography combines the mold rigidity of imprint lithography, which permits fine patterning, with the mold flexibility of soft lithography, allowing intimate contact of the mold with the surface substrate over a large area. A UV-curable mold based on poly(urethane acrylate) is prepared as a film on a flexible poly(ethylene terephthalate) support, allowing nanopatterns to be prepared by a bilayer-transfer technique (see Figure).
Automatic prefetching in a WAN (2002)

File systems have become slow relative to processor, memory and network speeds. The high latencies of distributed file systems (particularly wide area file systems) have only exacerbated the problem. The authors believe that file system prefetching provides an effective method for alleviating the latency bottleneck. File system prefetching requires knowledge of future file accesses. The authors are currently investigating efficient methods for accurately predicting future file activity automatically without application intervention. They have designed and implemented a system which uses past file activity to predict future file system needs. The initial results indicate that reasonable accuracy can be obtained even when relatively simple algorithms are employed.
A Human Immunoglobulin λ Locus Is Similarly Well Expressed in Mice and Humans (1999)

Transgenic mice carrying a 380-kb region of the human immunoglobulin (Ig) lambda light (L) chain locus in germline configuration were created. The introduced translocus on a yeast artificial chromosome (YAC) accommodates the most proximal Iglambda variable region (V) gene cluster, including 15 Vlambda genes that contribute to >60% of lambda L chains in humans, all Jlambda-Clambda segments, and the 3' enhancer. HuIglambdaYAC mice were bred with animals in which mouse Igkappa production was silenced by gene targeting. In the kappa-/- background, human Iglambda was expressed by approximately 84% of splenic B cells. A striking result was that human Iglambda was also produced at high levels in mice with normal kappa locus. Analysis of bone marrow cells showed that human Iglambda and mouse Igkappa were expressed at similar levels throughout B cell development, suggesting that the Iglambda translocus and the endogenous kappa locus rearrange independently and with equal efficiency at the same developmental stage. This is further supported by the finding that in hybridomas expressing human Iglambda the endogenous L chain loci were in germline configuration. The presence of somatic hypermutation in the human Vlambda genes indicated that the Iglambda-expressing cells function normally. The finding that human lambda genes can be utilized with similar efficiency in mice and humans implies that L chain expression is critically dependent on the configuration of the locus.
Energy dissipation during nanoscale indentation of polymers with an atomic force microscope (1994)

Nanometer size indentations on polypropylene and polymethylmethacrylate were made with the atomic force microscope and were 200-nm wide and 20-nm deep for a tip penetration depth of 75 nm. To image the indentations with the same tip used for writing, the tip was retracted at high speed, thus detaching any polymer sticking on it. Nanomechanical properties of polymer are studied in the limit of shallow indentations and slow penetration speed. From the hysteresis of the force versus tip motion curve, the dissipated energy during the indentation and the inelastic deformation of the polymer surface can be measured. We find that the measured dissipated energy is proportional to the volume of the indentation times the activation energy needed to excite chain segments motion during the deformation.
4-(Fluoromethyl)phenyl Phosphate Acts as a Mechanism-based Inhibitor of Calcineurin (1995)

The compound 4-(fluoromethyl)phenyl phosphate (FMPP), recently shown to be a mechanism-based inhibitor of prostatic acid phosphatase (Myers, J.K., and Widlanski, T.S. (1993) Science 262, 1451-1453), was examined for its effect on calcineurin. This compound inhibits calcineurin in a time-dependent, first order manner. Inactivation with [3H]FMPP led to a specific labeling of the catalytic subunit with a stoichiometry of 0.75 mol of label/mol of protein. A related substrate, 4-methylphenyl phosphate, is able to protect calcineurin from FMPP-mediated inhibition. Scavenging nucleophiles, such as cysteine, do not affect the rate of inhibition when included in the reaction. In addition, extensive dialysis indicates that inhibition is essentially irreversible. These results demonstrate that FMPP inactivates calcineurin in a mechanism-based fashion by forming a covalent adduct with calcineurin A, the catalytic subunit.
Long-term culture of chronic myelogenous leukemia marrow cells on stem cell factor-deficient stroma favors benign progenitors (1995)

Long-term culture of marrow from patients with chronic myelogenous leukemia (CML) has been reported to favor the outgrowth of bcr/abl- progenitor cells in some patients. We examined the effect of the presence of soluble or transmembrane forms of stem cell factor (SCF) in long-term cultures of CML marrow. CD34-enriched cells from CML patients in advanced chronic phase or accelerated phase were plated on immortalized fetal liver stromal cells from homozygous SCF-deficient SI/SI mice (SI/SI4) with or without the addition of soluble human SCF, SI/SI4 cells expressing high levels of the transmembrane form of human SCF (SI/SIh220), or primary human allogeneic stroma. Cells were removed from cultures and plated weekly in colony assays. The clonagenic cell output from cultures completely lacking SCF was lower over the first 2 to 3 weeks, but by 5 weeks was similar to the clonagenic cell output from the other culture conditions. Analysis of bcr/abl transcripts from individual colonies showed a lower percentage of malignant progenitors present in long-term cultures completely deficient in SCF than under the other culture conditions, particularly compared with primary human stroma-containing long-term cultures. SCF may specifically favor malignant versus benign progenitor cells present in the marrow of CML patients, and an abnormal proliferative response to SCF in very primitive cells may be an underlying defect in the pathophysiology of this disease.
Isolation ofMycobacterium paratuberculosisfrom Milk by Immunomagnetic Separation (1998)

An immunomagnetic separation (IMS) technique was developed to facilitate selective isolation of Mycobacterium paratuberculosis cells from milk. Rabbit polyclonal antibodies against radiation-killed intact M. paratuberculosis cells were produced and used to coat sheep anti-rabbit immunoglobulin G (IgG) type M-280 Dynabeads. The rabbit anti-M. paratuberculosis IgG-coated beads (IMB) reacted strongly with laboratory strains of M. paratuberculosis as determined by slide agglutination, and microscopic examination confirmed that M. paratuberculosis cells attached to the IMB. The IMB were found to have a maximum binding capacity of 10(4) to 10(5) CFU of M. paratuberculosis. Studies showed that IMS selectively recovered M. paratuberculosis from inoculated milk containing as few as 10 CFU of M. paratuberculosis per ml when 10 microliter IMB (ca. 10(6) beads) was added to 1 ml of milk and the preparation was incubated for 30 min at room temperature with gentle agitation. Larger volumes of milk (10 and 50 ml) were centrifuged and resuspended in 1 ml of phosphate-buffered saline-0.05% Tween 20 prior to IMS in order to increase the sensitivity of the method. Currently, primary isolation of M. paratuberculosis from a milk sample relies on chemical decontamination, followed by culturing on Herrold's egg yolk medium, which must be incubated at 37 degreesC for up to 18 weeks. The potential value of our IMS method is as an aid for rapid detection of M. paratuberculosis in milk when it is used in conjunction with end point detection methods, such as IS900 PCR or an enzyme-linked immunosorbent assay.
Tissue Engineered Artificial Skin Composed of Dermis and Epidermis (2000)

We made an artificial skin comprised of a stratified layer of keratinocytes and a dermal matrix with a type I collagen containing fibroblasts. In this work, we showed keratinocyte behavior under primary culture, gel contractions varying with concentration of collagen solution, and cell growth plots in the collagen gel. The optimum behavior of dermal equivalent could be obtained using 3.0 mg/ml collagen solution and attached gel culture. The attached gel culture had a jumping effect of growth factor on cell growth at the lag phase. To develop the artificial skin, 1x10(5) cells/cm2 of keratinocytes were cultured on the dermal equivalent at air-liquid interface. Finally, to overcome the problem that artificial skin of collagen gel was torn easily during suturing of grafting, we prepared histocompatible collagen mesh and attached the mesh to the bottom of the gel. Cultured artificial skins were successfully grafted onto rats.
Flip-Flop Jet Nozzle (1975)

A nozzle development program was undertaken to produce a time-dependent flow at the nozzle exit. The oscillatory character of the flow was achieved without the use of moving parts by incorporating a fluidic feedback loop into the nozzle design. The nozzle thrust efficiencies approached 90% and the half-width spreading rates attained exceeded that of the slot nozzle by a factor of more than three.
Growth stimulation of A431 cells by epidermal growth factor: identification of high-affinity receptors for epidermal growth factor by an anti-receptor monoclonal antibody. (1983)

Epidermal growth factor (EGF) at 3 nM maximally inhibits the proliferation of A431 epidermoid carcinoma cells. We show that at lower concentrations, in the range of 3-100 pM, EGF has a mitogenic effect on A431 cells. In the presence of 100 nM anti-EGF-receptor monoclonal IgG (designated 528), which inhibits A431 cell proliferation and blocks greater than 95% of EGF binding, EGF becomes mitogenic for A431 cells at concentrations up to 3 nM. These results suggest that a minor population of high-affinity EGF receptors may be involved in stimulation of A431 cell proliferation. Saturation binding assays with 125I-labeled EGF indicate that approximately equal to 0.1-0.2% of receptors for EGF are high-affinity receptors that bind EGF with an estimated Kd of 7 X 10(-11) M. This affinity is nearly 2 orders of magnitude higher than that of the remaining EGF receptors. Although A431 cell proliferation is maximally inhibited by nonsaturating amounts of EGF (3 nM), maximal inhibition by 528 IgG (approximately equal to 70% of maximal inhibition by EGF) requires saturating concentrations of antibody (approximately equal to 15 nM). Unlike EGF, rapid down-regulation is not observed with 528 IgG. These results indicate different mechanisms of growth inhibition of A431 cells by EGF and 528 IgG.
MafA Is a Glucose-regulated and Pancreatic β-Cell-specific Transcriptional Activator for the Insulin Gene (2002)

The insulin gene is specifically expressed in beta-cells of the Langerhans islets of the pancreas, and its transcription is regulated by the circulating glucose level. Previous reports have shown that an unidentified beta-cell-specific nuclear factor binds to a conserved cis-regulatory element called RIPE3b and is critical for its glucose-regulated expression. Based on the sequence similarity of the RIPE3b element and the consensus binding sequence of the Maf family of basic leucine zipper transcription factors, we here identified mammalian homologue of avian MafA/L-Maf, an eye-specific member of the Maf family, as the RIPE3b-binding transcriptional activator. Reverse transcription-PCR analysis showed that mafA mRNA is detected only in the eyes and in pancreatic beta-cells and not in alpha-cells. MafA protein as well as its mRNA is up-regulated by glucose, consistent with the glucose-regulated binding of MafA to the RIPE3b element in beta-cell nuclear extracts. In transient luciferase assays, we also showed that expression of MafA greatly enhanced insulin promoter activity and that a dominant-negative form of MafA inhibited it. Therefore, MafA is a beta-cell-specific and glucose-regulated transcriptional activator for insulin gene expression and thus may be involved in the function and development of beta-cells as well as in the pathogenesis of diabetes.
Multi-sensor 3D image fusion and interactive search (2000)

Describes a system under development for the 3D fusion of multi-sensor surface surveillance imagery, including electro-optical (EO), IR, SAR, multispectral and hyperspectral sources. Our approach is founded on biologically-inspired image processing algorithms. We have developed an image processing architecture enabling the unified interactive visualization of fused multi-sensor site data which utilizes a color image fusion algorithm based on retinal and cortical processing of color. We have also developed interactive Web-based tools for training neural network search agents that are capable of automatically scanning site data for the fused multi-sensor signatures of targets and/or surface features of interest. Each search agent is an interactively trained instance of a neural network model of cortical pattern recognition called a fuzzy ARTMAP. The utilization of 3D site models is central to our approach because it enables the accurate multi-platform image registration that is necessary for color image fusion and the designation, learning and searching for multi-sensor fused pixel signatures. Interactive stereo 3D viewing and fly-through tools enable efficient and intuitive site exploration and analysis. Web-based remote visualization and search agent training and utilization tools facilitate rapid, distributed and collaborative site exploitation and dissemination of results.
Microchip Emitter for Solid-Phase Extraction–Gradient Elution–Mass Spectrometry (2013)

A microchip electrospray emitter with a magnetic bead trap has been designed for solid-phase extraction-gradient elution-mass spectrometry (SPE-GEMS). The goal of this method is the detection of analytes at low concentrations and it is here demonstrated using reverse phase coated magnetic beads (Mbs) for the preconcentration and detection of the peptides. The sample is passed through the chip, and the peptides are retained and enriched in the trap. After washing, the peptides are released sequentially by stepwise gradient elution and electrosprayed for mass spectrometry analysis. This approach allows effective sample desalting, enrichment, sequential elution, and MS detection without the introduction of an additional separation step after SPE. Efficient preconcentration of model peptides by SPE and sequential release and analysis of peptides by GEMS were demonstrated for diluted sample solutions within the range of 1 μM to 10 nM. Fortified human blood serum, protein digest and fractions collected after protein digest OFFGEL separation were analyzed by SPE-GEMS allowing the detection of low abundance peptides usually not observed by direct mass spectrometry analysis. A mathematical model for gradient elution is proposed.
Remarkable Expression in the Colon Adenocarcinoma ofHmat-Xa, a Human Mannosyltransferase-Like Gene, That Is Homologous to Drosophila Gene GC15914 (2011)

We cloned a novel human mannosyltransferase-like gene, designated Hmat-Xa, as a gene homologous to the Drosophila GC15914 gene encoding the 9QVXN0 protein: see "Project Report for FY2002 on the 'Construction of Libraries of Human Genes Participating in Glycosylation' project" 43-45 (2003), New Energy and Industrial Technology Development Organization (NEDO), NEDO and Research Association for Biotechnology, Tokyo, Japan (in Japanese). After that, the GTDC1 gene, as reported by Zhao et al., DNA Cell Biol., 23, 183-187 (2004), was found to be the same as the Hmat-Xa gene. Domain EXFGI/L/VX(2)L/VE in the Hmat-Xa protein, also present in both human mannosyltransferase II/III and mannosyltransferase IV/V, which are involved in the synthesis of lipid-linked oligosaccharides, and some bacterial mannosyltransferases. A real-time PCR study of Hmat-Xa mRNA expression in human normal and tumor multiple tissue cDNA identified its tissue-specific expression and its remarkable expression in colon adenocarcinoma as compared to the normal counterpart. Thus the elevated expression of Hmat-Xa might serve as a candidate marker for colon adenocarcinoma.
Altered molecular pathways in melanocytic lesions (2009)

To identify gene expression changes in melanocytic lesions, biopsies from 18 common nevi (CMN), 11 dysplastic nevi (DN), 8 radial and 15 vertical growth phase melanomas (RGPM, VGPM), and 5 melanoma metastases (MTS) were analyzed using whole genome microarrays. The comparison between CMN and RGPM showed an enrichment of Gene Ontology terms related to inter and intracellular junctions, whereas the transition from RGPM to VGPM underlined the alteration of apoptosis. Upregulation of genes involved in dsDNA break repair and downregulation of cellular adhesion genes were observed in MTS with respect to VGPM. DN exhibited rather heterogeneous molecular profiles, with some proliferation genes expressed at higher levels than in CMN, altered regulation of transcription compared to RGPM and a subset of processes, such as mismatch repair, equally expressed as in VGPM. Furthermore, the expression profile of genes involved into cellular detoxification and antigen presentation split them into two classes, with different proliferation potential. Finally, molecular profiling of individual lesions identified altered biological processes, such as regulation of apoptosis, regulation of transcription and T-cell activation, not associated with specific histological classes but rather with subgroups of samples without apparent relationship. This holds true for dysplastic nevi in particular. Our data indicate that generally the intersection between stage specific and sample specific molecular alterations may lead to a more precise determination of the individual progression risk of melanocytic lesions.