gebhart/patrepeval huggingface dataset:
Scene Graph Generation With External Knowledge and Image Reconstruction (2019)

Scene graph generation has received growing attention with the advancements in image understanding tasks such as object detection, attributes and relationship prediction, etc. However, existing datasets are biased in terms of object and relationship labels, or often come with noisy and missing annotations, which makes the development of a reliable scene graph prediction model very challenging. In this paper, we propose a novel scene graph generation algorithm with external knowledge and image reconstruction loss to overcome these dataset issues. In particular, we extract commonsense knowledge from the external knowledge base to refine object and phrase features for improving generalizability in scene graph generation. To address the bias of noisy object annotations, we introduce an auxiliary image reconstruction path to regularize the scene graph generation network. Extensive experiments show that our framework can generate better scene graphs, achieving the state-of-the-art performance on two benchmark datasets: Visual Relationship Detection and Visual Genome datasets.
Screening method to identify inhibitors of siderophore biosynthesis in the opportunistic fungal pathogen,<i>Aspergillus fumigatus</i> (2009)

The increasing incidence of life-threatening fungal infections has produced an urgent need for novel antifungal agents. The method described in this report will facilitate the identification of novel antifungal compounds that inhibit a pathway critical for A. fumigatus virulence and have a reduced probability of affecting host metabolism.
Enhancing the light-extraction efficiency of AlGaN deep-ultraviolet light-emitting diodes using highly reflective Ni/Mg and Rh as p-type electrodes (2018)

Improving the light-extraction efficiency (LEE) is a major issue for the development of deep-ultraviolet (DUV) light-emitting diodes (LEDs). For this improvement, we introduced a transparent p-AlGaN contact layer and a reflective p-type electrode. In this work, we investigated the improvements obtained by replacing conventional Ni/Au p-type electrodes with highly reflective Ni/Mg and Rh electrodes. The external quantum efficiencies (EQEs) of 279 nm DUV LEDs were increased from 4.2 to 6.6% and from 3.4 to 4.5% by introducing Ni/Mg and Rh p-type electrodes, respectively. The LEE enhancement factors for the Ni/Mg and Rh electrodes were 1.6 and 1.4, respectively. These results are explained by the fact that the measured reflectances of the Ni/Mg and Rh electrodes were approximately 80 and 55%, respectively. Moreover, it was concluded that a passivation layer is required for Ni/Mg electrodes to prevent the degradation of the LED properties by the oxidation of Mg.
TOWARD A PLUG-AND-PLAY APPROACH FOR ACTIVE POWER FACTOR CORRECTION (2004)

The feasibility of producing a modular Active Power Factor Correction (APFC) system was studied analytically and experimentally. It is shown that the novel control scheme that does not need the sensing of the input voltage is highly compatible with the modular, plug-and-play concept. Modularity is achieved by aggregating practically all the electronics in an IC or hybrid unit that may also include the power switch. This unit plus a line rectifier, inductor and bus capacitor are all that it takes to form an APFC system. It is demonstrated that dynamic stability is assured by the proposed inherent robust control method. This plug-and-play solution will greatly simplify and reduce the cost of the design and manufacturing of APFC front ends.
Targeting membrane heat-shock protein 70 (Hsp70) on tumors by cmHsp70.1 antibody (2010)

Immunization of mice with a 14-mer peptide TKDNNLLGRFELSG, termed "TKD," comprising amino acids 450-461 (aa(450-461)) in the C terminus of inducible Hsp70, resulted in the generation of an IgG1 mouse mAb cmHsp70.1. The epitope recognized by cmHsp70.1 mAb, which has been confirmed to be located in the TKD sequence by SPOT analysis, is frequently detectable on the cell surface of human and mouse tumors, but not on isogenic cells and normal tissues, and membrane Hsp70 might thus serve as a tumor-specific target structure. As shown for human tumors, Hsp70 is associated with cholesterol-rich microdomains in the plasma membrane of mouse tumors. Herein, we show that the cmHsp70.1 mAb can selectively induce antibody-dependent cellular cytotoxicity (ADCC) of membrane Hsp70(+) mouse tumor cells by unstimulated mouse spleen cells. Tumor killing could be further enhanced by activating the effector cells with TKD and IL-2. Three consecutive injections of the cmHsp70.1 mAb into mice bearing CT26 tumors significantly inhibited tumor growth and enhanced the overall survival. These effects were associated with infiltrations of NK cells, macrophages, and granulocytes. The Hsp70 specificity of the ADCC response was confirmed by preventing the antitumor response in tumor-bearing mice by coinjecting the cognate TKD peptide with the cmHsp70.1 mAb, and by blocking the binding of cmHsp70.1 mAb to CT26 tumor cells using either TKD peptide or the C-terminal substrate-binding domain of Hsp70.
A Micro Device for Separation of Erythrocytes and Leukocytes in Human Blood (2005)

We report a MEMS device for continuous and binary separation of leukocytes (white blood cells, WBCs) and erythrocytes (red blood cells, RBCs) by their sizes. The system consists of PDMS cylindrical pillars inside fluidic chamber on glass slides. A 420 μm lateral separation was achieved for 5 μm and 10 μm beads. The critical particle size for separation was successful predicted by simulation and experimentally determined by calibration with polystyrene beads. The separation function (lateral displacement versus particle size) was also measured experimentally. Diluted whole blood and blood fraction of concentrated leukocytes were tested with the devices with erythrocyte to leukocyte ratio in agreement with blood count results. Experiments with fluorescent labeled leukocytes confirm the separation of leukocytes from erythrocytes and measured the separation efficiency.
Structure−Affinity Relationship Study on<i>N</i>-(1,2,3,4-Tetrahydronaphthalen-1-yl)-4-Aryl-1-Piperazinealkylamides, a New Class of 5-Hydroxytryptamine<sub>7</sub>Receptor Agents (2004)

A series of N-(1,2,3,4-tetrahydronaphthalen-1-yl)-4-aryl-1-piperazinealkylamides was prepared and their affinity for serotonin (5-hydroxytryptamine, 5-HT) 5-HT7, 5-HT(1A), and 5-HT(2A) receptors was measured by in vitro binding assays. In relation to 5-HT7 receptor affinity, receptor binding studies indicated that (i) the optimal alkyl chain length was five methylenes, (ii) an unsubstituted 1,2,3,4-tetrahydronaphthalenyl nucleus was preferred, and (iii) the substitution pattern of the aryl ring linked to the piperazine ring played a crucial role. Several compound with high affinity for 5-HT7 receptors were identified. Among them, 4-(2-methoxyphenyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-1-piperazinehexanamide (28), 4-(2-acetylphenyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-1-piperazinehexanamide (34), 4-(2-methylthiophenyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-1-piperazinehexanamide (44), 4-(2-hydroxyphenyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-1-piperazinehexanamide (46), and 4-(2-methylphenyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-1-piperazinehexanamide (49) were assayed for the 5-HT7 receptor-mediated relaxation of substance P-induced guinea pig ileum contraction. Compounds 28, 44, and 49 behaved as full agonists and compound 34 as a partial agonist, whereas derivative 46 acted as an antagonist. Among the compounds presented here, it emerged that 44 was identified as a potent 5-HT7 receptor agonist (Ki = 0.22 nM, EC50 = 2.56 microM), endowed with selectivity over 5-HT(1A) and 5-HT(2A) receptors (200-fold and >1000-fold, respectively).
Volumetric imaging of holographic optical traps (2006)

The holographic optical trapping technique creates arbitrary three-dimensional configurations of optical traps, each with individually specified characteristics. Holographic modification of the individual traps' wavefronts can transform conventional point-like optical tweezers into traps with different structures and properties, and can position them independently in three dimensions. Here, we describe a technique for rapidly characterizing holographic optical traps' three-dimensional intensity distributions. We create volumetric representations by by holographically translating the traps through the optical train's focal plane, acquiring a stack of two-dimensional images in the process. We apply this technique to holographic line traps, which are used to create tailored one-dimensional potential energy landscapes for mesoscopic objects. These measurements highlight problems that can arise when projecting extended traps with conventional optics and demonstrates the effectiveness of shape-phase holography for creating nearly ideal line traps.
CHAPTER 10. Antimicrobial Polymeric Dental Materials (2013)

Resin-based dental restorative materials (such as dental composites) have been widely used in dentistry to restore the function and esthetics of decayed teeth. However, dental composites usually have limited life (5–7 years). The leading cause for the failure and replacement of dental composite restoration is secondary (recurrent) caries. To reduce secondary caries, various materials and methods, such as fluoride-releasing materials, remineralization materials, and antimicrobial materials have been extensively studied. In this chapter, a systematic review is provided for the antimicrobial (antibacterial and antifungal) polymeric materials used in dentistry, including dental composites, bonding agents, sealants, and denture-base materials. The focus is on the development of antibacterial dental composites that release antibacterial agents, contain silver nanoparticles or quaternary ammonium monomers, and fluoride-releasing dental materials. The chemical structures, antimicrobial effects, and limitations of different types of antimicrobial polymeric dental materials are presented. The combination of different types of antimicrobial polymeric dental materials may reduce secondary caries and prolong the service life of the restorations.
Gene transfer to the tendon‐bone insertion site (2004)

This study investigated whether gene transfer to the tendon-bone insertion site is possible during early tendon-transplant healing using viral vectors. In addition, we evaluated the optimal gene delivery technique for an in vivo adenoviral gene transfer to a tendon-bone insertion site in a bone tunnel. Twenty-six rabbits underwent a bilateral transfer of the flexor digitorum longus tendon into a bone canal in the calcaneus. The animals were divided into two groups. The first group (n=18) received a direct injection of an adenoviral vector carrying the luciferase marker gene into the tendon on the left side, while on the right side the adenoviral vector was first injected into the bone trough and the tendon was later inserted into the trough. The analysis of this experiment showed that over a 4-week period a higher luciferase activity was achieved using the bone trough immersion technique. In the second group (n=8) we therefore used the qualitative marker virus (Ad/-LacZ) with the bone trough immersion technique in order to show the site of gene expression. The histological analysis of this experiment demonstrated the presence of beta-galactosidase positive cells within the tendon-bone interface over a 4-week period. Therefore we showed in the first part of this study that the bone canal provides a more efficient target for direct adenoviral gene delivery than the tendon. In the second part of the study we demonstrated the feasibility of the bone trough immersion technique since sustained gene expression within the tendon-bone interface was obtained for up to 4 weeks. This study has shown the feasibility of gene delivery to the tendon-bone interface and provides the basis for the application adenoviral delivery of growth factor genes to the tendon-bone insertion site.
Rate equation analysis of dynamic response in strongly injection-locked semiconductor microring lasers (2011)

A novel optical injection-locking scheme for modulation bandwidth enhancement is proposed, involving a distributed Bragg reflector master laser monolithically integrated with a strongly injection-locked unidirectional microring laser. Enhanced high-speed performance of the proposed scheme is confirmed in numerical modeling by comparing it with the scheme where weak optical injection is provided by a waveguide directional coupler adjacent to the ring laser.
Cloning and characterization of the gene that encodes acetyl-coenzyme A carboxylase in the alga Cyclotella cryptica. (1993)

The gene that encodes acetyl-coenzyme A carboxylase (ACCase; EC 6.4.1.2) in the eukaryotic alga Cyclotella cryptica has been isolated and cloned, representing the first time that a full-length gene for this enzyme has been isolated from a photosynthetic organism. The gene contains a 447-base pair intron that is located near the putative translation initiation codon and a 73-base pair intron that is located slightly upstream from the region that encodes the biotin binding site of the enzyme. The gene encodes a polypeptide that is predicted to be composed of 2089 amino acids and to have a molecular mass of 230 kDa. The deduced amino acid sequence exhibits strong similarity to the sequences of animal and yeast ACCases in the biotin carboxylase and carboxyltransferase domains. There is less sequence similarity in the biotin carboxyl carrier protein domain, although the highly conserved Met-Lys-Met of the biotin binding site is present. The amino terminus of the predicted ACCase sequence has characteristics of a signal sequence, suggesting that the enzyme is imported into chloroplasts via the endoplasmic reticulum, as has been shown to be the case for certain nuclear-encoded proteins that are transported into the chloroplasts of the diatom Phaeodactylum tricornutum. Southern blot analyses suggest that a single copy of this gene is present in C. cryptica.
Genetic Engineering of Streptavidin-Binding Peptide Tagged Single-Chain Variable Fragment Antibody to Venezuelan Equine Encephalitis Virus (2002)

A recombinant gene encoding a single-chain variable fragment (scFv) antibody against Venezuelan equine encephalitis virus (VEE) was cloned into a prokaryotic T7 RNA polymerase-regulated expression vector. A streptavidin-binding peptide gene fused to a 6His tag was attached downstream to the scFv gene. The recombinant fusion protein was expressed in bacteria as inclusion bodies that were subsequently solubilized with 8 M urea and renatured by an arginine system. Purification of the fusion protein was achieved by immobilized metal affinity chromatography. Enzyme-linked immunosorbent assay (ELISA) and Western blotting results revealed that the fusion protein not only retained VEE antigen binding and specificity properties similar to those of its parent native monoclonal antibody (MAb), but also possessed streptavidin-binding activity. This experimental approach can eliminate the need for chemical biotinylation of antibodies and the risk associated of antibody denaturation and can provide a stable and reproducible reagent for rapid and efficient immunoassay of VEE when detected by horseradish peroxidase (HRP)-conjugated streptavidin.
Automated and portable native code isolation (2005)

The coexistence of programs written in a safe language with user-supplied unsafe (native) code is convenient (e.g., it enables direct access to operating system resources), but at the same time it is problematic (e.g., it may decrease reliability and debuggability). This work aims at retaining most of the benefits of interfacing a safe language with native code while addressing its problems. It is carried out in the context of the Java/sup TM/ Native Interface (JNI). Our approach is to execute the native code in an operating system process different than that of the safe language application. A technique presented in this paper accomplishes this transparently, automatically,, and without sacrificing any of the JNI functionality. No changes to the Java virtual machine (JVM/sup TM/) or its runtime are necessary. The resulting prototype does not depend on a particular implementation of the JVM, and is highly portable across hardware architectures and operating systems. This approach can be used to improve reliability of applications consisting of a mix of safe and native code and to facilitate debugging them.
Distributed oblivious load balancing using prioritized job replication (2012)

Load balancing in large distributed server systems is a complex optimization problem of critical importance in cloud systems and data centers. However, any full (i.e., optimal) solution incurs significant, often prohibitive, overhead due to the need to collect state-dependent information.We propose a novel scheme that incurs no communication overhead between the users and the servers upon job arrivals, thus removing any scheduling overhead from the job execution's critical path. Furthermore, our scheme is oblivious, that is, it does not use any state information.Our approach is based on creating, in addition to the regular job requests that are assigned to randomly chosen servers, also replicas that are sent to different servers; these replicas are served in low priority, such that they do not add any real burden on the servers. Through analysis and simulations we show that the expected system performance improves up to a factor of 2 (even under high load conditions), if job lengths are exponentially distributed, and over a factor of 5, when job lengths adhere to heavy-tailed distributions. We implemented a load balancing system based on our approach and deployed it on the Amazon Elastic Compute Cloud (EC2). Realistic load tests on that system indicate that the actual performance is as predicted.
Accurate Query Optimization by Sub-plan Memoization (1999)

Query optimizers use approximate techniques such as histograms or sampling for result size and distinct value estimation, even though these techniques may incur high estimation errors, leading the optimizer to choose sub-optimal query execution plans. In this report, we propose a novel approach to query optimization that provides the query optimizer with exact values for the result size of operators and operator trees, which we call sub-plans, and for the number of distinct values in the output of these subplans. In our approach, the query optimizer optimizes the query and records all the sub-plans for which result size or distinct value estimates are required in a data structure that we call the sub-plan memo. After query optimization is completed, the sub-plans in the sub-plan memo are executed and their actual result sizes and the number of distinct values in their outputs are recorded in the memo. The optimizer then re-optimizes the query using the more accurate result size and distinct value information in the subplan memo, which results in potentially choosing a better query execution plan. The process is repeated if re-optimization encounters sub-plans that are not in the sub-plan memo. This technique can result in potentially increasing the optimization time sharply. However, it is very effective in choosing the optimal query execution plan. Therefore, this approach is primarily suitable for frequently executed queries embedded in application programs. We present an experimental evaluation of our proposed approach based on a prototype implementation in Microsoft SQL Server 2000.
Promoter Deletion and Comparative Expression Analysis of the Mirabilis mosaic caulimovirus (MMV) Sub-genomic Transcript (Sgt) Promoter in Transgenic Plants (2003)

35 A sub-genomic transcript (Sgt) promoter was isolated from a genomic clone of the Mirabilis mosaic virus (MMV), a double-stranded DNA plant pararetrovirus belonging to the Caulimoviridae family. The MMV Sgt promoter fragment (genomic co-ordinates 4830 to 5840) was mapped by 5′-3′-deletion analysis to define the boundaries required for maximal promoter expression. Expression patterns of promoter fragments coupled to GUS reporter gene were evaluated both in protoplast transient expression experiments and in transgenic Nicotiana tabacum cv. Samsun NN plants. A 333 bp MMV Sgt promoter fragment (sequence –306 to +27 from the transcription start site, TSS) was found sufficient for strong promoter activity in protoplast transient expression experiments. The transcription start site (TSS) of the MMV Sgt promoter was determined by primer extension analysis using total RNA isolated from transgenic plants containing a MMV Sgt promoter:uidA fusion gene. In seedlings, the level of GUS expression was in the order of leaf ≥ root >stem. Histochemical GUS-staining of seedlings showed highest GUS activity in root tips, leaf midribs, veins and vascular tissues. The MMV Sgt promoter fragment is a strong constitutive promoter, with strength comparable to that of the MMV full-length transcript (FLt) promoter. MMV Sgt promoter also demonstrated much greater activity, 8-fold more compared to the CaMV 19S promoter and 2-fold stronger than the CaMV 35S promoter.
Clinical usefulness of wave intensity analysis (2008)

Wave intensity (WI) is a hemodynamic index, which can evaluate the working condition of the heart interacting with the arterial system. It can be defined at any site in the circulatory system and provides a great deal of information. However, we need simultaneous measurements of blood pressure and velocity to obtain wave intensity, which has limited the clinical application of wave intensity, in spite of its potential. To expand the application of wave intensity in the clinical setting, we developed a real-time non-invasive measurement system for wave intensity based on a combined color Doppler and echo-tracking system. We measured carotid arterial WI in normal subjects and patients with various cardiovascular diseases. In the coronary artery disease group, the magnitude of the first peak of carotid arterial WI (W (1)) increased with LV max. dP/dt (r = 0.74, P < 0.001), and the amplitude of the second peak (W (2)) decreased with an increase in the time constant of LV pressure decay (r = -0.77, P < 0.001). In the dilated cardiomyopathy group, the values of W (1) were much lower than those in the normal group (P < 0.0001). In the hypertrophic cardiomyopathy group, the values of W (2) were much smaller than those in the normal group (P < 0.0001). In mitral regurgitation before surgery, W (2) decreased or disappeared, but after surgery W (2) appeared clearly. In the hypertension group, the magnitude of reflection from the head was considerably greater than that in the normal group (P < 0.0001). We also evaluated hemodynamic effects of sublingual nitroglycerin in normal subjects. Nitroglycerin increased W (1) significantly (P < 0.001). WI can be obtained non-invasively using an echo-Doppler system in the clinical setting. This method will increase the clinical usefulness of wave intensity.
Algorithms for Interactive Editing of Level Set Models (2005)

Abstract Level set models combine a low‐level volumetric representation, the mathematics of deformable implicit surfaces and powerful, robust numerical techniques to produce a novel approach to shape design. While these models offer many benefits, their large‐scale representation and numerical requirements create significant challenges when developing an interactive system. This paper describes the collection of techniques and algorithms (some new, some pre‐existing) needed to overcome these challenges and to create an interactive editing system for this new type of geometric model. We summarize the algorithms for producing level set input models and, more importantly, for localizing/minimizing computation during the editing process. These algorithms include distance calculations, scan conversion, closest point determination, fast marching methods, bounding box creation, fast and incremental mesh extraction, numerical integration and narrow band techniques. Together these algorithms provide the capabilities required for interactive editing of level set models.