gebhart/patrepeval huggingface dataset:
A Unified Framework for Metric Transfer Learning (2017)

Transfer learning has been proven to be effective for the problems where training data from a source domain and test data from a target domain are drawn from different distributions. To reduce the distribution divergence between the source domain and the target domain, many previous studies have been focused on designing and optimizing objective functions with the Euclidean distance to measure dissimilarity between instances. However, in some real-world applications, the Euclidean distance may be inappropriate to capture the intrinsic similarity or dissimilarity between instances. To deal with this issue, in this paper, we propose a metric transfer learning framework (MTLF) to encode metric learning in transfer learning. In MTLF, instance weights are learned and exploited to bridge the distributions of different domains, while Mahalanobis distance is learned simultaneously to maximize the intra-class distances and minimize the inter-class distances for the target domain. Unlike previous work where instance weights and Mahalanobis distance are trained in a pipelined framework that potentially leads to error propagation across different components, MTLF attempts to learn instance weights and a Mahalanobis distance in a parallel framework to make knowledge transfer across domains more effective. Furthermore, we develop general solutions to both classification and regression problems on top of MTLF, respectively. We conduct extensive experiments on several real-world datasets on object recognition, handwriting recognition, and WiFi location to verify the effectiveness of MTLF compared with a number of state-of-the-art methods.
A dynamic instruction set computer (2002)

A dynamic instruction set computer (DISC) has been developed that supports demand-driven modification of its instruction set. Implemented with partially reconfigurable FPGAs, DISC treats instructions as removable modules paged in and out through partial reconfiguration as demanded by the executing program. Instructions occupy FPGA resources only when needed and FPGA resources can be reused to implement an arbitrary number of performance-enhancing application-specific instructions. DISC further enhances the functional density of FPGAs by physically relocating instruction modules to available FPGA space.
Learning to predict indoor illumination from a single image (2017)

We propose an automatic method to infer high dynamic range illumination from a single, limited field-of-view, low dynamic range photograph of an indoor scene. In contrast to previous work that relies on specialized image capture, user input, and/or simple scene models, we train an end-to-end deep neural network that directly regresses a limited field-of-view photo to HDR illumination, without strong assumptions on scene geometry, material properties, or lighting. We show that this can be accomplished in a three step process: 1) we train a robust lighting classifier to automatically annotate the location of light sources in a large dataset of LDR environment maps, 2) we use these annotations to train a deep neural network that predicts the location of lights in a scene from a single limited field-of-view photo, and 3) we fine-tune this network using a small dataset of HDR environment maps to predict light intensities. This allows us to automatically recover high-quality HDR illumination estimates that significantly outperform previous state-of-the-art methods. Consequently, using our illumination estimates for applications like 3D object insertion, produces photo-realistic results that we validate via a perceptual user study.
Disintegration of chromosomes in dead sperm cells as revealed by injection into mouse oocytes (1997)

Intracytoplasmic sperm injection of immotile (dead) ejaculated human spermatozoa has been carried out by several centres for the treatment of infertility caused by severe asthenozoospermia (necrozoospermia). No healthy pregnancies have been reported as yet, suggesting irreversible damage to sperm DNA, centrioles and/or other important structures. We investigated this hypothesis by injection of immotile human spermatozoa obtained from several male infertility patients into mouse oocytes and analysis of the oocyte activation rate and sperm chromosome integrity. Motile spermatozoa of the same sample were used as a control. The proportion of living spermatozoa among the immotile was also assessed in each sample and was related to the results of the mouse oocyte injection test. The oocyte activation rate after injection of immotile human spermatozoa into mouse oocytes was the same or only slightly lower than after injection with initially motile spermatozoa (87-100% versus 100% respectively). The rate of normal sperm chromosome spreads correlated significantly (r = 0.90, P < 0.05) with the proportion of living immotile spermatozoa in a given sample. It varied from 4 to 48% for samples containing respectively 8 and 40% of living spermatozoa. Most of the mouse oocytes injected and activated with immotile human spermatozoa were arrested during a prolonged period of time at the interphase of the first cell cycle (from 22 to 60%). Others underwent a delayed nuclear envelope breakdown but showed signs of abnormal structure of both male and female or only the male pronuclear chromosomes. Our data demonstrate an irreversible damage of chromosomes in dead ejaculated human spermatozoa and provide an experimental basis for recommending the use of testicular or epididymal spermatozoa for treatment of male infertility due to necrozoospermia.
Order in Microcontact Printed Self-Assembled Monolayers (1997)

Self-assembled monolayers (SAMs) on Au(111) formed by microcontact printing of dodecanethiol and investigated by scanning tunneling microscopy and wettability measurements have, under certain conditions, characteristics indistinguishable from SAMs formed from solutions of dodecanethiol in ethanol. The monolayer product of microcontact printing demonstrates a sensitivity to the concentration of thiol used to ink a poly(dimethylsiloxane) (PDMS) stamp needed to make the print and an insensitivity to its duration of contact, for times >0.3 s, with the gold substrate. The wettability of the SAM, the distribution of domains within the monolayer, their size and organizational state, and the pattern of depressions on the surface each are reproducibly controlled by simply changing the concentration of dodecanethiol applied to the stamp. The inferred mode of growth of printed SAMs shares many features of monolayer formation through the gas phase of a thiol and corresponds to a highly controlled and self-limiting delivery of thiol from the interior parts of the PDMS. Our study shows that printed SAMs provide a wonderful opportunity to change controllably the order in monolayers at the nanometer scale and to examine its effects on microscopic and macroscopic properties of these films.
Kernel Based Discourse Relation Recognition with Temporal Ordering Information (2010)

Syntactic knowledge is important for discourse relation recognition. Yet only heuristically selected flat paths and 2-level production rules have been used to incorporate such information so far. In this paper we propose using tree kernel based approach to automatically mine the syntactic information from the parse trees for discourse analysis, applying kernel function to the tree structures directly. These structural syntactic features, together with other normal flat features are incorporated into our composite kernel to capture diverse knowledge for simultaneous discourse identification and classification for both explicit and implicit relations. The experiment shows tree kernel approach is able to give statistical significant improvements over flat syntactic path feature. We also illustrate that tree kernel approach covers more structure information than the production rules, which allows tree kernel to further incorporate information from a higher dimension space for possible better discrimination. Besides, we further propose to leverage on temporal ordering information to constrain the interpretation of discourse relation, which also demonstrate statistical significant improvements for discourse relation recognition on PDTB 2.0 for both explicit and implicit as well. 1
Iron Deficiency Generates Secondary Thrombocytosis and Platelet Activation in IBD (2013)

FCM lowers platelet counts and platelet activation in patients with IBD-associated secondary thrombocytosis.
Self-assembly and adsorption of diblock copolymers from selective solvents. 1. Self-assembly (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelf-assembly and adsorption of diblock copolymers from selective solvents. 1. Self-assemblyYongjian Zhan and Wayne L. MatticeCite this: Macromolecules 1994, 27, 3, 677–682Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://doi.org/10.1021/ma00081a009RIGHTS & PERMISSIONSArticle Views137Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (752 KB) Get e-Alerts Get e-Alerts
Is plant endophyte‐mediated defensive mutualism the result of oxidative stress protection? (2009)

In this review, we discuss the biology and beneficial effects of plant endophytes on host plants. The current explanation of endophyte protection (defensive mutualism) of host plants is based on the secondary metabolites (alkaloids) with antiherbivore properties produced by the symbiotic association between host plant and endophytes. We propose an alternative explanation of the mechanism of host protection through enhanced stress tolerance to oxidative stress. Several studies have demonstrated the production of different compounds (phenolics) with antioxidant capacity in endophyte-infected plants. Endophytes may also produce mannitol, other carbohydrates and small molecules (proline) with antioxidant capacity. We suggest that enhanced antioxidant production by symbiotic plants may be the result of the production of reactive oxygen species (ROS) by endophytes. In turn, symbiotic plants are protected from oxidative stress produced by plant diseases, droughts, heavy metals and other oxidative stressors by the production of antioxidants. We also discuss the lichen symbiosis and evaluate whether management of ROS also plays a role in this defensive mutualism. Future experiments are needed to evaluate the hypothesis that antioxidants are responsible for enhanced stress tolerance in endophyte-infected plants.
Functional chimeras of the Rous sarcoma virus and human immunodeficiency virus gag proteins (1993)

The Gag protein encoded by Rous sarcoma virus (RSV) is the only viral product required for the process of budding whereby virus particles are formed at the plasma membrane. Deletion analysis of this Gag molecule has revealed several regions (assembly domains) that are important for budding. One of these domains is located at the amino terminus and is needed for membrane binding. Another is located within the carboxy-terminal third of the protein. Though there is little sequence homology among the Gag proteins of unrelated retroviruses, it seemed possible that their assembly domains might be functionally conserved, and to explore this idea, numerous Gag chimeras were made. The results indicate that the first 10 amino acids of the human immunodeficiency virus (HIV) Gag protein can suppress the block to budding caused by deletions in the RSV MA sequence, much as described previously for the first 10 residues from the Src oncoprotein (J.W. Wills, R.C. Craven, R. A. Weldon, Jr., T. D. Nelle, and C.R. Erdie, J. Virol. 65:3804-3812, 1991). In addition, the carboxy-terminal half of the HIV Gag protein was fused to a truncated RSV Gag molecule, mutant Bg-Bs, which is unable to direct core assembly. This chimera was able to produce particles at a rate identical to that of RSV and of a density similar to that of authentic virions. Deletion analysis of the carboxy-terminal chimera revealed two small regions within the HIV NC protein that were sufficient for endowing mutant Bg-Bs with these properties. Chimeras lacking both regions produced particles of a low density, suggesting that these sequences may be involved in the tight packing of Gag molecules during assembly. In a related set of experiments, replacement of the RSV protease with that of HIV resulted in premature processing within the RSV sequence and a block to budding. Particle assembly was restored when the HIV PR activity was inactivated by mutagenesis. Collectively, the data presented here illustrate the functional similarities of Gag proteins from unrelated retroviruses.
Computation of external aerodynamics for a canard rotor/wing aircraft (2001)

The aerodynamic loads on a Canard Rotor/Wing vehicle are investigated using inviscid numerical simulations in order to understand the flight characteristics of the vehicle during conversion from rotor craft to fixed-wing flight. A series of numerical simulations at seven azimuthal rotor indices are presented covering a quarter turn of the rotor With symmetry arguments, these simulations produce 25 data points for a complete rotation. A Cartesian mesh approach is used to compute the flow field about a configuration with faired-over engine inlet and exhaust that matches the wind tunnel geometry. These simulations were performed using meshes with approximately nine Million Cartesian cells. To better understand the aerodynamic effects of the rotor hub on the configuration, the same set of simulations were repeated for a hub-less geometry. Overall loads for both configurations are similar but are due to somewhat different aerodynamic mechanisms.
Caspase-mediated cleavage of the stacking protein GRASP65 is required for Golgi fragmentation during apoptosis (2002)

The mammalian Golgi complex is comprised of a ribbon of stacked cisternal membranes often located in the pericentriolar region of the cell. Here, we report that during apoptosis the Golgi ribbon is fragmented into dispersed clusters of tubulo-vesicular membranes. We have found that fragmentation is caspase dependent and identified GRASP65 (Golgi reassembly and stacking protein of 65 kD) as a novel caspase substrate. GRASP65 is cleaved specifically by caspase-3 at conserved sites in its membrane distal COOH terminus at an early stage of the execution phase. Expression of a caspase-resistant form of GRASP65 partially preserved cisternal stacking and inhibited breakdown of the Golgi ribbon in apoptotic cells. Our results suggest that GRASP65 is an important structural component required for maintenance of Golgi apparatus integrity.
Hardware-software codesign with GRAPE (2002)

GRAPE-II (Graphical Rapid Prototyping Environment-II) is a hardware-software codesign environment for the real-time functional emulation of synchronous DSP systems. It allows one to specify the application's data dependency graph in a target-machine-independent way. After specifying the heterogeneous target machine's architecture, it estimates the resources needed by each application subtask. Based on these requirements, it assigns the subtasks to specific target devices at compile-time, be they processors or FPGAs, establishes routing paths and determines a static schedule. It generates a main shell for each target device and generates intra-device and inter-device communication code. After downloading the executable images on to the target machine, it allows the designer to modify end-user controls and application settings at run-time. This paper situates the tool in the application design cycle, explains GRAPE-II's design flow and shows the advantages of hardware-software codesign by evaluating the achievable sampling frequency for a small example application.
Cloning, Expression, Characterization, and Nucleophile Identification of Family 3, Aspergillus nigerβ-Glucosidase (2000)

The beta-glucosidase from Aspergillus niger (CMI CC 324262) was purified, and an N-terminal sequence and two internal sequences were determined. BglI genomic gene and the cDNA were cloned from a genomic library and by reverse transcriptase-polymerase chain reaction, respectively. The cDNA was successfully expressed in Saccharomyces cerevisiae and Pichia pastoris. Sequence analysis revealed that the gene encodes a 92-kDa enzyme that is a member of glycosidase family 3. (1)H-NMR analysis of the reaction catalyzed by this enzyme confirmed that, in common with other family 3 glycosidases, this enzyme hydrolyzes with net retention of anomeric configuration. Accordingly, the enzyme was inactivated by 2-deoxy-2-fluoro beta-glucosyl fluoride, with kinetic parameters of k(i) = 4.5 min(-1), K(I) = 35.4 mM, through the trapping of a covalent glycosyl enzyme intermediate. The catalytic competence of this intermediate was demonstrated by the fact that incubation with linamarin resulted in reactivation, presumably via a transglycosylation mechanism. Peptic digestion of the 2-deoxy-2-fluoroglucosyl enzyme and subsequent analysis of high pressure liquid chromatography eluates by electrospray ionization triple quadrupole mass spectrometry in the neutral loss mode allowed the localization of a 2-deoxy-2-fluoroglucosyl-peptide. Sequence determination of this labeled peptide by tandem mass spectrometry in the daughter ion scan mode permitted the identification of Asp-261 as the catalytic nucleophile within the sequence VMSDW. Asp-261 is fully conserved within this family, consistent with its key role, and aligns with the aspartic acid residue previously identified in the Aspergillus wentii enzyme by labeling with conduritol B epoxide (Bause, E., and Legler, G. (1974) Hoppe-Seyler's Z. Physiol. Chem. 355, 438-442).
Epitopes Recognized by a Nonautoreactive Murine Anti-N-Propionyl Meningococcal Group B Polysaccharide Monoclonal Antibody (2005)

The capsular polysaccharide of Neisseria meningitidis group B (MBPS) is a polymer of alpha (2-->8) N-acetyl neuraminic acid. The polysaccharide is chemically identical to an autoantigen, polysialic acid (PSA), and is a poor immunogen, even when conjugated to protein carriers. Immunization of mice with MBPS-protein conjugate vaccines, in which N-acetyl groups have been replaced by propionyl groups (N-Pr MBPS), elicits serum bactericidal antibodies. A subpopulation of these antibodies do not cross-react with human PSA. The reasons for the increased immunogenicity of N-Pr MBPS and the antigenic targets of the bactericidal nonautoreactive antibodies are unknown. In this study, we investigated the antigenic targets of a protective murine monoclonal antibody (MAb) prepared against a N-Pr MBPS-tetanus toxoid conjugate vaccine. Binding of the MAb to N-Pr MBPS (as demonstrated by an enzyme-linked immunosorbent assay) and bactericidal activity were inhibited by de-N-acetylated MBPS and re-N-acetylated MBPS, which indicate that N-propionyl groups are not obligatory determinants for binding. The results of affinity selection from a preparation of N-Pr MBPS and matrix-assisted laser desorption ionization-time of flight mass spectroscopic analysis indicated that the minimal epitope recognized by the MAb is a MBPS disaccharide containing one de-N-acetylated residue. Thus, the bacterial capsular epitope recognized by this bactericidal, nonautoreactive, anti-group-B MAb likely contains de-N-acetyl residues.
Detection of Aspergillus fumigatus by polymerase chain reaction (1993)

Aspergillus fumigatus is an opportunistic nosocomial pathogen causing an often fatal pneumonia, invasive aspergillosis (IA), in immunosuppressed patients. Oligonucleotide primers were used to amplify a 401-bp fragment spanning the 26S/intergenic spacer region of the rDNA complex of A. fumigatus by the polymerase chain reaction (PCR). The primers were highly sensitive and specific: as little as 1 pg of A. fumigatus genomic DNA could be detected, and the primers only amplified DNA from A. fumigatus and not any other fungal, bacterial, viral, or human DNA tested. Using the PCR, we were able to detect A. fumigatus DNA in lung homogenates from immunosuppressed mice experimentally infected with A. fumigatus but not from immunosuppressed uninfected controls. There was 93% correlation between the culture results and the PCR results. In a retrospective clinical study, the sensitivity of the PCR for the detection of A. fumigatus in clinical samples was confirmed by positive amplification in three of three culture-positive respiratory samples from confirmed cases of IA. Because isolation of Aspergillus spp. may reflect contamination and colonization without infection, the feasibility of using the PCR was evaluated by analyzing culture-negative samples from both immunosuppressed patients at high risk for IA and immunocompetent patients with other lung infections. Only 2 of 10 patients were culture negative and PCR positive in the high-risk group, and 2 of 7 patients were culture negative and PCR positive in the immunocompetent group. The results indicate that PCR detection might be a valuable adjunct to current laboratory methods to diagnose IA.
Structural elements regulating zein gene expression (1989)

Zeins are a group of alcohol-soluble proteins that are synthesized in the endosperm of developing maize seeds. These proteins are encoded by a large number of genes located on several chromosomes; based upon the number of mutants that have been isolated, zein gene regulation is complex. Comparisons of gene flanking regions reveal conserved sequences that may be important for their regulation. Studies of transformed plant tissues support the assertion that cis-acting elements with the 5' flanking regions of zein genes are required for accurate transcription. Although the genes are transcribed in transgenic tobacco and petunia plants, they are not properly regulated. This appears to be due to transcriptional effects rather than protein or mRNA instability.