gebhart/patrepeval huggingface dataset:
A Prototype for Unsupervised Analysis of Tissue Microarrays for Cancer Research and Diagnostics (2004)

The tissue microarray (TMA) technique enables researchers to extract small cylinders of tissue from histological sections and arrange them in a matrix configuration on a recipient paraffin block such that hundreds can be analyzed simultaneously. TMA offers several advantages over traditional specimen preparation by maximizing limited tissue resources and providing a highly efficient means for visualizing molecular targets. By enabling researchers to reliably determine the protein expression profile for specific types of cancer, it may be possible to elucidate the mechanism by which healthy tissues are transformed into malignancies. Currently, the primary methods used to evaluate arrays involve the interactive review of TMA samples while they are viewed under a microscope, subjectively evaluated, and scored by a technician. This process is extremely slow, tedious, and prone to error. In order to facilitate large-scale, multi-institutional studies, a more automated and reliable means for analyzing TMAs is needed. We report here a web-based prototype which features automated imaging, registration, and distributed archiving of TMAs in multiuser network environments. The system utilizes a principal color decomposition approach to identify and characterize the predominant staining signatures of specimens in color space. This strategy was shown to be reliable for detecting and quantifying the immunohistochemical expression levels for TMAs.
Localized Dictionaries Based Orientation Field Estimation for Latent Fingerprints (2014)

Dictionary based orientation field estimation approach has shown promising performance for latent fingerprints. In this paper, we seek to exploit stronger prior knowledge of fingerprints in order to further improve the performance. Realizing that ridge orientations at different locations of fingerprints have different characteristics, we propose a localized dictionaries-based orientation field estimation algorithm, in which noisy orientation patch at a location output by a local estimation approach is replaced by real orientation patch in the local dictionary at the same location. The precondition of applying localized dictionaries is that the pose of the latent fingerprint needs to be estimated. We propose a Hough transform-based fingerprint pose estimation algorithm, in which the predictions about fingerprint pose made by all orientation patches in the latent fingerprint are accumulated. Experimental results on challenging latent fingerprint datasets show the proposed method outperforms previous ones markedly.
KNET (2015)

Neural network techniques are widely applied to obtain high-quality distributed representations of words (i.e., word embeddings) to address text mining, information retrieval, and natural language processing tasks. Most recent efforts have proposed several efficient methods to learn word embeddings from context such that they can encode both semantic and syntactic relationships between words. However, it is quite challenging to handle unseen or rare words with insufficient context. Inspired by the study on the word recognition process in cognitive psychology, in this article, we propose to take advantage of seemingly less obvious but essentially important morphological knowledge to address these challenges. In particular, we introduce a novel neural network architecture called KNET that leverages both words’ contextual information and morphological knowledge to learn word embeddings. Meanwhile, this new learning architecture is also able to benefit from noisy knowledge and balance between contextual information and morphological knowledge. Experiments on an analogical reasoning task and a word similarity task both demonstrate that the proposed KNET framework can greatly enhance the effectiveness of word embeddings.
A 158-mW 360-MHz BW 68-dB DR Continuous-Time 1-1-1 Filtering MASH ADC in 40-nm CMOS (2022)

This article presents a 5-GS/s continuous-time (CT) multi-stage noise-shaping (MASH) analog-to-digital converter (ADC). The ADC consists of three first-order modulators with a 3-bit quantizer/digital-to-analog converter (DAC) per stage. An RC-hybrid stabilization DAC is used to compensate for the excess loop delay and excess phase shift. A delay matching all-pass input filter with a low-pass feedforward filter is employed to suppress input signal leakage. As a result, inter-stage DACs are waived in residue generation, and low-power, area-saving Gm-C integrators are enabled in the back-end stages. The MASH ADC was implemented in 40-nm CMOS and occupies 0.21 mm2. The ADC achieves 68-dB dynamic range (DR) and 65-dB signal-to-noise and distortion ratio (SNDR) over a 360-MHz bandwidth (BW). The ADC consumes 158 mW from 1/1.1/1.8 V supplies, yielding 159-dB Schreier figure-of-merit (FOM) and 151-fJ/Conv. Walden FOM.
Wireless Test Structure for Integrated Systems (2008)

Contact-based wafer testing of complex integrated systems presents several drawbacks: inherent limitations in terms of pad pitch reduction and number of devices tested in parallel, eventual "touchdown" damage to the chip when recursive test is required. This paper presents a solution based on a wireless communication between the test equipment and the device under test.
Photo-active collagen systems with controlled triple helix architecture (2013)

The design of photo-active collagen systems is presented as a basis for establishing biomimetic materials with varied network architecture and programmable macroscopic properties. Following in-house isolation of type I collagen, reaction with vinyl-bearing compounds of varied backbone rigidity, i.e. 4-vinylbenzyl chloride (4VBC) and glycidyl methacrylate (GMA), was carried out. TNBS colorimetric assay, <sup>1</sup>H-NMR and ATR-FTIR confirmed covalent and tunable functionalization of collagen lysines. Depending on the type and extent of functionalization, controlled stability and thermal denaturation of triple helices were observed via circular dichroism (CD), whereby the hydrogen-bonding capability of introduced moieties was shown to play a major role. Full gel formation was observed following photo-activation of functionalized collagen solutions. The presence of a covalent network only slightly affected collagen triple helix conformation (as observed by WAXS and ATR-FTIR), confirming the structural organization of functionalized collagen precursors. Photo-activated hydrogels demonstrated an increased denaturation temperature (DSC) with respect to native collagen, suggesting that the formation of the covalent network successfully stabilized collagen triple helices. Moreover, biocompatibility and mechanical competence of obtained hydrogels were successfully demonstrated under physiologically-relevant conditions. These results demonstrate that this novel synthetic approach enabled the formation of biocompatible collagen systems with defined network architecture and programmable macroscopic properties, which can only partially be obtained with current synthetic methods.
Convenient and versatile subcellular extraction procedure, that facilitates classical protein expression profiling and functional protein analysis (2004)

Standardized sample preparation to reduce proteome complexity facilitates subsequent proteome analysis. Here we describe a robust sequential extraction method that enables simple fractionation of proteins in their native state according to their subcellular localization, yielding four subproteomes enriched in (a) cytosolic; (b) membrane and membrane organelle-localized; (c) soluble and DNA-associated nuclear and (d) cytoskeletal proteins. Efficiency and selectivity is demonstrated by morphological-, two-dimensional electrophoresis image-, immunological- as well as enzymatic-analysis. In pilot studies, subcellular redistribution of regulatory proteins was successfully measured.
Scatter Diagram Analysis: A New Technique for Discriminating Ventricular Tachyarrhythmias (1994)

With the increasing flexibility allowed by implantable cardioverter defibrillators that use tiered therapy, it is important to match the therapy with the arrhythmia. In this article we present scatter diagram analysis, a new computationally efficient two-channel algorithm for distinguishing monomorphic ventricular tachycardia (VT) from polymorphic ventricular tachycardia and ventricular fibrillation (VF). Scatter diagram analysis plots the amplitude from one channel versus the amplitude from another channel on a graph with a 15 x 15 grid. The fraction (percentage) of the 225 grid blocks occupied by at least one sample point is then determined. We found that monomorphic VT traces nearly the same path in space and occupies a smaller percentage of the graph than a nonregular rhythm such as polymorphic VT or VF. Scatter diagram analysis was tested on 27 patients undergoing intraoperative implantable cardioverter defibrillator testing. Passages of 4.096 seconds were obtained from rate (bipolar epicardial) and morphology (patch) leads, and digitized at 125 Hz. Scatter diagram analysis distinguished 13 episodes of monomorphic VT (28.6% +/- 4.0%) from 27 episodes of polymorphic VT or VF (48.0% +/- 8.2%) with P < 0.0005. There was overlap in only one monomorphic VT episode and one polymorphic VT or VF episode.
Detecting clandestine material with nuclear resonance fluorescence (2006)

We study the performance of a class of interrogation systems that exploit nuclear resonance fluorescence (NRF) to detect specific isotopes. In these systems the presence of a particular nuclide is inferred by observing the preferential attenuation of photons that strongly excite an electromagnetic transition in that nuclide. Estimates for the false positive/negative error rates, radiological dose, and detection sensitivity associated with discovering clandestine material embedded in cargo are presented. The relation between performance of the detection system and properties of the beam of interrogating photons is also considered. Bright gamma-ray sources with fine energy and angular resolution, such as those based on Thomson upscattering of laser light, are found to be associated with uniquely low radiological dose, scan times, and error rates. For this reason a consideration of NRF-based interrogation systems may provide impetus for efforts in light source development for applications related to national security and industry.
Transmission of 32-WDM 10-Gb/s channels over 640 km using broad-band, gain-flattened erbium-doped silica fiber amplifiers (1997)

We report 640-km transmission of 32 wavelength-division-multiplexed (WDM) 10-Gb/s channels with 100-GHz spacing (covering 25-nm bandwidth) using wide dynamic range, gain-flattened erbium-doped silica fiber amplifiers (EDSFAs) with an optical bandwidth of 35 nm. The EDSFA separation is 80 km, the system gain is 140 dB and the total end of system gain nonuniformity among the 32 channels is 4.9 dB.
Parasitic calibration by two-step ratio approaching technique for split capacitor array SAR ADCs (2009)

A calibration technique is proposed to apply for split capacitor array of successive approximation register (SAR) ADC. This technique calibrates the parasitic effects of the split capacitor array by two-step ratio approaching technique, and achieves medium-to-high resolution. The calibration technique is designed and simulated under a 10-bit 100 MS/s SAR ADC structure, with 15% to 25% of top plate parasitic capacitance. The simulation results show that the proposed technique can improve the THD from -41 dB to -59 dB at Nyquist input frequency for the worst case. The DNL/INL is improved from 5.02/5.6 LSB to 0.25/0.38 LSB, respectively.
Supramolecular Organic Nanowires as Plasmonic Interconnects (2016)

Metallic nanostructures are able to interact with an incident electromagnetic field at subwavelength scales by plasmon resonance which involves the collective oscillation of conduction electrons localized at their surfaces. Among several possible applications of this phenomenon, the theoretical prediction is that optical circuits connecting multiple plasmonic elements will surpass classical electronic circuits at nanoscale because of their much faster light-based information processing. However, the placement and coupling of metallic elements smaller than optical wavelengths currently remain a formidable challenge by top-down manipulations. Here, we show that organic supramolecular triarylamine nanowires of ≈1 nm in diameter are able to act as plasmonic waveguides. Their self-assembly into plasmonic interconnects between arrays of gold nanoparticles leads to the bottom-up construction of basic optical nanocircuits. When the resonance modes of these metallic nanoparticles are coupled through the organic nanowires, the optical conductivity of the plasmonic layer dramatically increases from 259 to 4271 Ω(-1)·cm(-1). We explain this effect by the coupling of a hot electron/hole pair in the nanoparticle antenna with the half-filled polaronic band of the organic nanowire. We also demonstrate that the whole hybrid system can be described by using the abstraction of the lumped circuit theory, with a far field optical response which depends on the number of interconnects. Overall, our supramolecular bottom-up approach opens the possibility to implement processable, soft, and low cost organic plasmonic interconnects into a large number of applications going from sensing to metamaterials and information technologies.
Novel mRNA-based VP8* vaccines against rotavirus are highly immunogenic in rodents (2023)

ABSTRACT Despite the availability of live-attenuated oral vaccines, rotavirus remains a major cause of severe childhood diarrhea worldwide. Due to the growing demand for parenteral rotavirus vaccines, we developed novel mRNA-based vaccine candidates targeting the viral spike protein VP8*. Our monomeric P2 (universal T cell epitope)-VP8* mRNA design is equivalent to a protein vaccine currently in clinical development, while LS (lumazine synthase)-P2-VP8* was designed to form nanoparticles. Cyro-electron microscopy and western blotting-based data presented here suggest that proteins derived from LS-P2-VP8* mRNA are secreted in vitro and self-assemble into 60-mer nanoparticles displaying VP8*. mRNA encoded VP8* was immunogenic in rodents and introduced both humoral and cellular responses. LS-P2-VP8* induced superior humoral responses to P2-VP8* in guinea pigs, both as monovalent and trivalent vaccines, with encouraging responses detected against the most prevalent P genotypes. Overall, our data provide evidence that trivalent LS-P2-VP8* represents a promising mRNA-based next-generation rotavirus vaccine candidate.
Filovirus-like particles as vaccines and discovery tools (2005)

Ebola and Marburg viruses are members of the family Filoviridae, which cause severe hemorrhagic fevers in humans. Filovirus outbreaks have been sporadic, with mortality rates currently ranging from 30 to 90%. Unfortunately, there is no efficacious human therapy or vaccine available to treat disease caused by either Ebola or Marburg virus infection. Expression of the filovirus matrix protein, VP40, is sufficient to drive spontaneous production and release of virus-like particles (VLPs) that resemble the distinctively filamentous infectious virions. The addition of other filovirus proteins, including virion proteins (VP)24, 30 and 35 and glycoprotein, increases the efficiency of VLP production and results in particles containing multiple filovirus antigens. Vaccination with Ebola or Marburg VLPs containing glycoprotein and VP40 completely protects rodents from lethal challenge with the homologous virus. These candidate vaccines are currently being tested for immunogenicity and efficacy in nonhuman primates. Furthermore, the Ebola and Marburg VLPs are being used as a surrogate model to further understand the filovirus life cycle, with the goal of developing rationally designed vaccines and therapeutics. Thus, in addition to their use as a vaccine, VLPs are currently being used as tools to learn lessons about filovirus pathogenesis, immunology, replication and assembly requirements.
HIV-1-Specific IgA Monoclonal Antibodies from an HIV-1 Vaccinee Mediate Galactosylceramide Blocking and Phagocytosis (2018)

Vaccine-elicited humoral immune responses comprise an array of antibody forms and specificities, with only a fraction contributing to protective host immunity. Elucidation of antibody effector functions responsible for protective immunity against human immunodeficiency virus type 1 (HIV-1) acquisition is a major goal for the HIV-1 vaccine field. Immunoglobulin A (IgA) is an important part of the host defense against pathogens; however, little is known about the role of vaccine-elicited IgA and its capacity to mediate antiviral functions. To identify the antiviral functions of HIV-1-specific IgA elicited by vaccination, we cloned HIV-1 envelope-specific IgA monoclonal antibodies (MAbs) by memory B cell cultures from peripheral blood mononuclear cells from an RV144 vaccinee and produced two IgA clonal cell lines (HG129 and HG130) producing native, nonrecombinant IgA MAbs. The HG129 and HG130 MAbs mediated phagocytosis by monocytes, and HG129 blocked HIV-1 Env glycoprotein binding to galactosylceramide, an alternative HIV-1 receptor. These findings elucidate potential antiviral functions of vaccine-elicited HIV-1 envelope-specific IgA that may act to block HIV-1 acquisition at the portal of entry by preventing HIV-1 binding to galactosylceramide and mediating antibody Fc receptor-mediated virion phagocytosis. Furthermore, these findings highlight the complex and diverse interactions of vaccine-elicited IgA with pathogens that depend on IgA fine specificity and form (e.g., multimeric or monomeric) in the systemic circulation and mucosal compartments.<b>IMPORTANCE</b> Host-pathogen interactions <i>in vivo</i> involve numerous immune mechanisms that can lead to pathogen clearance. Understanding the nature of antiviral immune mechanisms can inform the design of efficacious HIV-1 vaccine strategies. Evidence suggests that both neutralizing and nonneutralizing antibodies can mediate some protection against HIV in animal models. Although numerous studies have characterized the functional properties of HIV-1-specific IgG, more studies are needed on the functional attributes of HIV-1-specific IgA, specifically for vaccine-elicited IgA. Characterization of the functional properties of HIV-1 Env-specific IgA monoclonal antibodies from human vaccine clinical trials are critical toward understanding the capacity of the host immune response to block HIV-1 acquisition.
A minimal descriptor of an ancestral recombinations graph (2011)

Ancestral Recombinations Graph (ARG) is a phylogenetic structure that encodes both duplication events, such as mutations, as well as genetic exchange events, such as recombinations: this captures the (genetic) dynamics of a population evolving over generations. In this paper, we identify structure-preserving and samples-preserving core of an ARG G and call it the minimal descriptor ARG of G. Its structure-preserving characteristic ensures that all the branch lengths of the marginal trees of the minimal descriptor ARG are identical to that of G and the samples-preserving property asserts that the patterns of genetic variation in the samples of the minimal descriptor ARG are exactly the same as that of G. We also prove that even an unbounded G has a finite minimal descriptor, that continues to preserve certain (graph-theoretic) properties of G and for an appropriate class of ARGs, our estimate (Eqn 8) as well as empirical observation is that the expected reduction in the number of vertices is exponential. Based on the definition of this lossless and bounded structure, we derive local properties of the vertices of a minimal descriptor ARG, which lend itself very naturally to the design of efficient sampling algorithms. We further show that a class of minimal descriptors, that of binary ARGs, models the standard coalescent exactly (Thm 6).
Discovery of a Novel Class of Potent and Orally Bioavailable Sphingosine 1-Phosphate Receptor 1 Antagonists (2012)

A series of subtype selective sphingosine 1-phosphate receptor 1 (S1P(1)) antagonists are disclosed. Our high-throughput screening campaign revealed hit 1 for which an increase in potency and mouse oral exposure was achieved with minor modifications to the chemical scaffold. In vivo efficacy revealed that at high doses compounds 12 and 15 inhibited tumor growth. Further optimization of our lead series led to the discovery of proline derivatives 37 (XL541) and 38 which had similar efficacy as our first generation analogues at significantly lower doses. Analogue 37 displayed excellent pharmacokinetics and oral exposure in multiple species.
A Common Functional Polymorphism in the Promoter Region of the Microsomal Triglyceride Transfer Protein Gene Influences Plasma LDL Levels (1998)

Microsomal triglyceride transfer protein (MTP) is required for the assembly and cellular secretion of apolipoprotein B (apoB) -containing lipoproteins from the liver and intestine. The secretion pattern of apoB-containing lipoproteins is likely to influence the VLDL and LDL levels in plasma. By initial opportunistic screening for polymorphic sites in the regulatory region of the MTP gene by gene sequencing in 20 healthy male subjects, a common functional G/T polymorphism was detected 493 bp upstream from the transcriptional start point. There was differential binding of unique nuclear proteins at this site, as shown by electrophoretic mobility shift assay. The G variant seemed to bind two or three nuclear proteins that do not bind to the T variant. Expression studies with minimal promoter constructs linked to the chloramphenicol acetyltransferase reporter and transfected into HepG2 cells revealed marked enhancement of transcriptional activity with the T variant. The prevalence of the MTP promoter genotypes was investigated in a group of 184 healthy, middle-aged white men; the frequency of homozygosity for the MTP -493 T variant was .06 and the allele frequency of MTP -493T was .25 in the population. These homozygous subjects had a 22% lower LDL cholesterol concentration than did heterozygotes or subjects homozygous for the MTP -493 G variant (2.9+/-0.6 versus 3.7+/-0.8 mmol/L, P<.05). Analysis of apoB and triglyceride contents in VLDL subfractions revealed a markedly changed balance within the VLDL population. Subjects homozygous for the MTP -493 T variant had fewer but more lipid-rich VLDL particles, thereby arguing for an effect of MTP expression on the hepatic secretion of triglyceride-rich, apoB-containing lipoproteins. This common genetic variation of the MTP promoter is likely to have important implications for cardiovascular disease.
High-Speed Growth of 4H-SiC Single Crystal Using Si-Cr Based Melt (2013)

In this study, we have investigated the rate-limiting process of 4H-SiC solution growth using Si-Cr based melt, and have tried high-speed growth. It is revealed that the rate-limiting process of SiC growth under our experimental condition is interface kinetics, which can be controlled by such factors as temperature and supersaturation of carbon. By enhancing the interface kinetics, SiC crystal has been grown at a high rate of 2 mm/h. The FWHM values of X-ray rocking curves and threading dislocation density of the grown crystals are almost the same as those of seed crystal. Possibility of high-speed and high-quality growth of 4H-SiC has been indicated.