gebhart/patrepeval huggingface dataset:
Discriminative Learning of Local Image Descriptors (2010)

In this paper, we explore methods for learning local image descriptors from training data. We describe a set of building blocks for constructing descriptors which can be combined together and jointly optimized so as to minimize the error of a nearest-neighbor classifier. We consider both linear and nonlinear transforms with dimensionality reduction, and make use of discriminant learning techniques such as Linear Discriminant Analysis (LDA) and Powell minimization to solve for the parameters. Using these techniques, we obtain descriptors that exceed state-of-the-art performance with low dimensionality. In addition to new experiments and recommendations for descriptor learning, we are also making available a new and realistic ground truth data set based on multiview stereo data.
Low-temperature silicon selective deposition and epitaxy on silicon using the thermal decomposition of silane under ultraclean environment (1989)

An ultraclean hot-wall low-pressure chemical vapor deposition (CVD) system was developed and Si films were deposited on single-crystal Si and SiO2 using ultraclean SiH4 and H2 gases in the temperature range 600–850 °C under an ultraclean environment. As a result of ultraclean processing, an incubation period of Si deposition only on SiO2 was found, and low-temperature Si selective deposition and epitaxy on Si were achieved without addition of HCl under deposition conditions where only nonselective polycrystalline Si growth could be obtained in conventional CVD systems.
The “Frankenplasmid” lab: An investigative exercise for teaching recombinant DNA methods (2011)

We describe an investigative laboratory module designed to give college undergraduates strong practical and theoretical experience with recombinant DNA methods within 3 weeks. After deducing restriction enzyme maps for two different plasmids, students ligate the plasmids together in the same reaction, transform E. coli with this mixture of ligated DNA, and plate the cells on media that specifically select for hybrid plasmids. The main goal of the assignment is for students to deduce the gene map of one hybrid "Frankenplasmid" using the LacZ phenotype of its transformants, PCR, and restriction mapping. Our protocol results in a number of possible outcomes, meaning that students are mapping truly unknown plasmids. The open-ended nature of this assignment results in an effective module that teaches recombinant DNA procedures while engaging students with its investigative approach, increasing complexity, and puzzle-like quality. Moreover, the modular design of the activity allows it to be adapted to a more limited schedule, introductory courses, or more advanced courses.
Vaccination with a Synthetic Zona Pellucida Peptide Produces Long-Term Contraception in Female Mice (1989)

The zona pellucida surrounding mouse oocytes is an extracellular matrix composed of three sulfated glycoproteins, ZP1, ZP2, and ZP3. It has been demonstrated that a monoclonal antibody to ZP3 injected into female mice inhibits fertilization by binding to the zona pellucida and blocking sperm penetration. A complementary DNA encoding ZP3 was randomly cleaved and 200- to 1000-base pair fragments were cloned into the expression vector lambda gt11. This epitope library was screened with the aforementioned contraceptive antibody, and the positive clones were used to map the seven-amino acid epitope recognized by the antibody. Female mice were immunized with a synthetic peptide containing this B cell epitope coupled to a carrier protein to provide helper T cell epitopes. The resultant circulating antibodies to ZP3 bound to the zona pellucida of immunized animals and produced long-lasting contraception. The lack of ovarian histopathology or cellular cytotoxicity among the immunized animals may be because of the absence of zona pellucida T cell epitopes in this vaccine.
Collaborative Spam Filtering Using E-Mail Networks (2006)

A distributed spam-filtering system that leverages e-mail networks' topological properties is more efficient and scalable than client-server-based solutions. Large-scale simulations of a prototype system reveal that this approach achieves a near-perfect spam detection rate while minimizing bandwidth cost.
Using Temporal Data for Making Recommendations (2013)

We treat collaborative filtering as a univariate time series estimation problem: given a user's previous votes, predict the next vote. We describe two families of methods for transforming data to encode time order in ways amenable to off-the-shelf classification and density estimation tools, and examine the results of using these approaches on several real-world data sets. The improvements in predictive accuracy we realize recommend the use of other predictive algorithms that exploit the temporal order of data.
Organization of projections from the ventromedial nucleus of the hypothalamus: A Phaseolus vulgaris‐Leucoagglutinin study in the rat (1994)

The organization of projections from the four parts of the ventromedial nucleus (VMH) and a ventrolaterally adjacent region tentatively identified as the tuberal nucleus (TU) have been analyzed with small injections of the anterograde axonal tracer Phaseolus vulgaris-leucoagglutinin (PHA-L). Extrinsic and intranuclear projections of each part of the VMH display clear quantitative differences, whereas the overall patterns of outputs are qualitatively similar. Overall, the VMH establishes massive intrahypothalamic terminal fields in other parts of the medial zone, tending to avoid the periventricular and lateral zones. The ventrolateral VMH is more closely related to other parts of the hypothalamus that also express gonadal steroid hormone receptors, including the medial preoptic, tuberal, and ventral premammillary nuclei, whereas other parts of the VMH are more closely related to the anterior hypothalamic and dorsal premammillary nuclei. All parts of the VMH project to the zona incerta (including the A13 region) and parts of the midline thalamus, including the paraventricular and parataenial nuclei and nucleus reuniens. The densest inputs to the septum are to the bed nuclei of the stria terminalis, where the ventrolateral and central VMH innervate the anteroventral and anterodorsal areas and transverse and interfascicular nuclei, whereas the anterior and dorsomedial VMH innervate the latter two. The central, lateral, and medial amygdalar nuclei receive substantial inputs from various parts of the VMH. Other regions of the telencephalon, including the nucleus accumbens and the piriform-amygdaloid, infralimbic, prelimbic, anterior cingulate, agranular insular, piriform, perirhinal, entorhinal, and postpiriform transition areas, also receive sparse inputs. All parts of the VMH send a massive, topographically organized projection to the periaqueductal gray. Other brainstem terminal fields include the superior colliculus, peripeduncular area, locus coeruleus, Barrington's nucleus, parabrachial nucleus, nucleus of the solitary tract, and the mesencephalic, pontine, gigantocellular, paragigantocellular, and parvicellular reticular nuclei. The projections of the TU are similar to, and a subset of, those from the VMH and are thus not nearly as widespread as those from adjacent parts of the lateral hypothalamic area. Because of these similarities, the TU may eventually come to be viewed most appropriately as the lateral component of the VMH itself. The functional implications of the present findings are discussed in view of evidence that the VMH plays a role in the expression of ingestive, affective, and copulatory behaviors.
Three-dimensional Type I Collagen Lattices Induce Coordinate Expression of Matrix Metalloproteinases MT1-MMP and MMP-2 in Microvascular Endothelial Cells (1998)

Matrix metalloproteinases (MMPs) are hypothesized to play a key role in the processes of endothelial cell migration and matrix remodeling during angiogenesis. We utilized an in vitro model of microvascular endothelial cell angiogenesis, cells cultured within a collagen matrix, to investigate the MMP profile of endothelial cells undergoing angiogenesis. We demonstrated by gelatin zymography that monolayer cultures (two-dimensional) of endothelial cells constitutively expressed low levels of latent MMP-2, but that culture in a three-dimensional collagen matrix increased the total amount of MMP-2 mRNA and protein. Furthermore, 51% of total MMP-2 protein was activated in the three-dimensional culture lysates, compared with 3.5% in two-dimensional culture. The mRNA and protein of MT1-MMP, the putative activator of MMP-2, were up-regulated in endothelial cells cultured in three-dimensional as compared with two-dimensional culture. Treatment of cultures with MMP inhibitors blocked activation of MMP-2 and inhibited formation of endothelial cell networks within the collagen gel. Induction of MT1-MMP and MMP-2 appeared to be specific to collagen, inasmuch as culture of the endothelial cells on top of, or within, a Matrigel(R) matrix neither increased total MMP-2 nor increased activation of MMP-2. These results suggest that MT1-MMP activation of MMP-2 occurs in endothelial cells undergoing angiogenesis, that this activation has a functional role in endothelial cell organization, and that specific matrix interactions may be critical for the increased expression of MT1-MMP and MMP-2.
Inducible Nitric-oxide Synthase Generates Superoxide from the Reductase Domain (1998)

In the absence of L-arginine, the heme center of the oxygenase domain of neuronal nitric-oxide synthase reduces molecular oxygen to superoxide (O-2). Our recent work has provided evidence that inducible NOS (iNOS) may also catalyze O-2 formation in macrophages. However, there has been a lack of direct evidence of superoxide generation from the purified iNOS, and it was previously hypothesized that significant O-2 production does not occur. Moreover, the mechanism and enzyme site responsible for O-2 generation is unknown. To determine whether iNOS produces O-2 and to identify the mechanism of this process, we performed electron paramagnetic resonance measurements on purified iNOS using the spin trap 5,5-dimethyl-1-pyrroline N-oxide. In the presence of NADPH, prominent O-2 adduct signals were detected from iNOS. These signals were totally abolished by superoxide dismutase but not affected by catalase. High concentrations of L-arginine decreased this O-2 formation, whereas its enantiomer D-arginine did not. Pre-incubation of iNOS with the flavoprotein inhibitor diphenyleneiodonium totally blocked these O-2 signals. Conversely, pretreatment of the enzyme with the heme blocker cyanide had no effect on O-2 generation. Furthermore, strong O-2 generation was directly detected from the isolated iNOS reductase domain. Together, these data demonstrate that iNOS does generate O-2, and this mainly occurs at the flavin-binding sites of the reductase domain.
Five Minds Our Children Deserve: Why The y're Needed, How To Nurture The m (2012)

We describe the five minds that should be nurtured in all children to prepare them to become both good workers and good citizens of a complex, every­changing society. In light of the central role that digital media technologies play in such a society, we explore the way in which digital media affect the development and expression of the five minds, as well as the distinct challenges of cultivating each mind in a digital era. We then delineate the types of schools we believe are best suited to meet these challenges. In conclusion, we consider the pedagogical practices required to develop the five minds and the policies and practices that powerfully affect what happens within the classroom walls.
Specificity of IS6110-based amplification assays for Mycobacterium tuberculosis complex (1996)

The specificity of IS6110 for the Mycobacterium tuberculosis complex has recently been questioned. We observed no cross-reaction with 27 nontuberculous mycobacteria using strand displacement- and PCR-based amplification of the nucleotide 970 to 1026 and 762 to 865 regions of IS6110. These data support use of selected regions of IS6110 as M. tuberculosis complex-specific targets.
Geometry of architectural freeform structures (2008)

Complex freeform structures are one of the most striking trends in contemporary architecture. This direction has been pioneered by architects such as F. Gehry, who exploit digital technology originally developed for the automotive and airplane industry for architectural design and construction. This is not a simple task at all, since the architectural application differs from the original target industries in many ways, including aesthetics, statics, scale and manufacturing technologies.
Potent induction of phase 2 enzymes in human prostate cells by sulforaphane. (2001)

Two population-based, case-control studies have documented reduced risk of prostate cancer in men who consume cruciferous vegetables. Cruciferae contain high levels of the isothiocyanate sulforaphane. Sulforaphane is known to bolster the defenses of cells against carcinogens through up-regulation of enzymes of carcinogen defense (phase 2 enzymes). Prostate cancer is characterized by an early and near universal loss of expression of the phase 2 enzyme glutathione S-transferase (GST)-pi. We tested whether sulforaphane may act in prostatic cells by increasing phase 2 enzyme expression. The human prostate cancer cell lines LNCaP, MDA PCa 2a, MDA PCa 2b, PC-3, and TSU-Pr1 were treated with 0.1-15 microM sulforaphane in vitro. LNCaP was also treated with an aqueous extract of broccoli sprouts. Quinone reductase enzymatic activity, a surrogate of global phase 2 enzyme activity, was assayed by the menadione-coupled reduction of tetrazolium dye. Expression of NQO-1, GST-alpha, gamma-glutamylcysteine synthetase-heavy and -light chains, and microsomal GST was assessed by Northern blot analysis. Sulforaphane and broccoli sprout extract potently induce quinone reductase activity in cultured prostate cells, and this induction appears to be mediated by increased transcription of the NQO-1 gene. Sulforaphane also induces expression of gamma-glutamylcysteine synthetase light subunit but not the heavy subunit, and this induction is associated with moderate increases in intracellular glutathione levels. Microsomal and alpha-class glutathione transferases were also induced transcriptionally. Sulforaphane induces phase 2 enzyme expression and activity significantly in human prostatic cells. This induction is accompanied by, but not because of, increased intracellular glutathione synthesis. Our findings may help explain the observed inverse correlation between consumption of cruciferae and prostate cancer risk.
Peptide and peptidomimetic libraries (1998)

Various techniques for generation of peptide and peptidomimetic libraries are summarized in this article. Multipin, tea bag, and split-couple-mix techniques represent the major methods used to make peptides and peptidomimetics libraries. The synthesis of these libraries were made in either discrete or mixture format. Peptides and peptidomimetics combinatorial libraries were screened to discover leads against a variety of targets. These targets, including bacteria, fungus, virus, receptors, and enzymes were used in the screening of the libraries. Discovered leads can be further optimized by combinatorial approaches.
Expression and activity of matrix metalloproteases in human malignant mesothelioma cell lines (2001)

The extracellular matrix metalloproteases (MMPs) secreted by various human tumor cells play a crucial role in tumor cell invasion and metastasis, but their expression in malignant mesothelioma (MM) cells has not been examined. In this study, we have investigated the spectrum of MMPs and tissue inhibitors of metalloproteases (TIMPs) produced by 8 MM cell lines. Using RT-PCR, we found that all investigated MM cell lines expressed genes encoding mRNA for MMP-1 (interstitial collagenase), MMP-2 (gelatinase A), MMP-3 (stromelysin-1), MMP-9 (gelatinase B) and TIMPs 1, 2 and 3. We also found that 6/8 MM cell lines expressed MMP-7 (matrilysin) and 3/8 MM cell lines expressed MMP-10 (stromelysin-2). MMP-11 (stromelysin-3) was not detected in any of the MM cell lines. Production of MMP-2 and MMP-9 was confirmed using gelatin zymography. In addition, all MM cell lines secreted a 66 kDa metalloprotease, while 3/8 MM cell lines secreted 46, 48, 51 and 63 kDa metalloproteases which specifically degraded the extracellular matrix components fibronectin, vitronectin and laminin. The 66 kDa protease was identified as MMP-3 by Western blot. Our results reveal a broad spectrum of MMPs and TIMPs produced by MM cells and indicate that different substrate specificities of MMPs may play a role in MM cell invasion.
Subthalamic Nucleus Deep Brain Stimulation: Accurate Axonal Threshold Prediction with Diffusion Tensor Based Electric Field Models (2006)

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) has become the therapy of choice for medically intractable Parkinson's Disease. However, the physiological mechanisms responsible for the therapeutic effects of DBS remain unknown, and quantitative understanding of the interaction between the electric field generated by DBS and the underlying neural tissue is lacking. Recently our group has developed various computational techniques to study the neural response to DBS. The goal of this study was to incrementally incorporate increasing levels of complexity into our computer models of STN DBS and address activation of the corticospinal tract (CST). Our model system was customized to an STN DBS patient and CST thresholds were calculated with electric field models that ranged from an electrostatic, homogeneous, isotropic model to one that explicitly incorporated the capacitance of the electrode-tissue interface, tissue encapsulation of the electrode, and diffusion-tensor based 3D tissue anisotropy and inhomogeneity. The model predictions were compared to clinical CST thresholds defined from electromyographic recordings from eight muscle groups in the arm and leg of the STN DBS patient. Coupled evaluation of the model and clinical data showed that accurate prediction of axonal thresholds required our most detailed model. In addition, the simplifications and assumptions typically utilized in neurostimulation models substantially overestimate neural activation
New Cyclooxygenase-2/5-Lipoxygenase Inhibitors. 3. 7-tert-Butyl-2,3-dihydro-3,3-dimethylbenzofuran Derivatives as Gastrointestinal Safe Antiinflammatory and Analgesic Agents:  Variations at the 5 Position (1998)

We report an expansion of the scope of our initial discovery that 5-keto-substituted 7-tert-butyl-2,3-dihydro-3,3-dimethylbenzofurans (DHDMBFs) are antiinflammatory and analgesic agents. Several other functional groups have been introduced at the 5 position: amides, amidines, ureas, guanidines, amines, heterocycles, heteroaromatics, and heteroaryl ethenyl substituents in the 5 position all provide active compounds. These compounds are dual cyclooxygenase (COX) and 5-lipoxygenase (5-LOX) inhibitors. They inhibit both COX-1 and COX-2 with up to 33-fold selectivity for COX-2.
Acoustic wavefield propagation using paraxial extrapolators (1988)

Modeling by paraxial extrapolators is applicable to wave propagation problems in which most of the energy is traveling within a restricted angular cone about a principle axis of the problem. Frequency domain finite-difference solutions are readily generated by using this technique. Input models can be described either by specifying velocities or appropriate media parameters on a two or three dimensional grid of points. For heterogeneous models, transmission and reflection coefficients are determined at structural boundaries within the media. The direct forward scattered waves are modeled with a single pass of the extrapolator operator in the paraxial direction for each frequency. The first-order back scattered energy can then be modeled by extrapolation (in the opposite direction) of the reflected field determined on the first pass. Higher order scattering can be included by sweeping through the model with more passes.
Altered Repair of Targeted Psoralen Photoadducts in the Context of an Oligonucleotide-mediated Triple Helix (1995)

Oligonucleotides can bind as third strands of DNA in a sequence-specific manner to form triple helices. Psoralen-conjugated, triplex-forming oligonucleotides (TFOs) have been used for the site-specific modification of DNA to inhibit transcription and to target mutations to selected genes. Such strategies, however, must take into account the ability of the cell to repair the triplex-directed lesion. We report experiments showing that the pattern of mutations produced by triplex-targeted psoralen adducts in an SV40 shuttle vector in monkey COS cells can be influenced by the associated third strand. Mutations induced by psoralen adducts in the context of a TFO of length 10 were the same as those generated by isolated adducts but were found to be different from those generated in the presence of a TFO of length 30 at the same target site. In complementary experiments, HeLa whole cell extracts were used to directly assess repair of the TFO-directed psoralen adducts in vitro. Excision of the damaged DNA was inhibited in the context of the 30-mer TFO, but not the 10-mer. These results suggest that an extended triple helix of length 30, which exceeds the typical size of the nucleotide excision repair patch in mammalian cells, can alter repair of an associated psoralen adduct. We present a model correlating these results and proposing that the incision steps in nucleotide excision repair in mammalian cells can be blocked by the presence of a third strand of sufficient length and binding affinity, thereby changing the pattern of mutations. These results may have implications for the use of triplex-forming oligonucleotides for genetic manipulation, and they may lead to the use of such oligonucleotides as tools to probe DNA repair pathways.
USING THE TRANSEPICONDYLAR AXIS TO DEFINE THE SAGITTAL MORPHOLOGY OF THE DISTAL PART OF THE FEMUR (2002)

Blaha, J. David MD; Mancinelli, Corrie A. PhD; Simons, William H. PhD Author Information
Metal Ion Leachates and the Physico-Chemical Stability of Biotherapeutic Drug Products (2014)

Metal ions that leach into biotherapeutic drug product solution during manufacturing and storage, result in contamination that can cause physico-chemical degradation of the active molecule. In this review, we describe various mechanisms by which metal ion leachates can interact with therapeutic proteins and antibodies. Site-specific modifications due to metal catalyzed oxidation (MCO) of the therapeutic proteins cause them to become destabilized and potentially increasingly aggregation prone. We have examined the molecular sequences and structures for three case studies, human relaxin (hRlx), human growth hormone (hGH) and an IgG2 mAb to rationalize the experimental findings related to their MCO. The analysis indicates that metal-binding sites lie in close spatial proximities to predicted aggregation prone regions in these molecules. From the perspective of pharmaceutical development of biotherapeutic drugs, this link between molecular origins of MCO and subsequent aggregation is undesirable. This article further suggests molecular design strategies involving disruption of APRs that may also help mitigate the impact of metal ion leachates on biotherapeutic drug products as well as improving their solubility.
Evidence of a Role of Tumor Necrosis Factor α in Refractory Asthma (2006)

Patients with refractory asthma have evidence of up-regulation of the TNF-alpha axis. (ClinicalTrials.gov number, NCT00276029.).