gebhart/patrepeval huggingface dataset:
Cell cluster graph for prediction of biochemical recurrence in prostate cancer patients from tissue microarrays (2013)

Prostate cancer (CaP) is evidenced by profound changes in the spatial distribution of cells. Spatial arrangement and architectural organization of nuclei, especially clustering of the cells, within CaP histopathology is known to be predictive of disease aggressiveness and potentially patient outcome. Quantitative histomorphometry is a relatively new field which attempt to develop and apply novel advanced computerized image analysis and feature extraction methods for the quantitative characterization of tumor morphology on digitized pathology slides. Recently, graph theory has been used to characterize the spatial arrangement of these cells by constructing a graph with cell/nuclei as the node. One disadvantage of several extant graph based algorithms (Voronoi, Delaunay, Minimum Spanning Tree) is that they do not allow for extraction of local spatial attributes from complex networks such as those that emerges from large histopathology images with potentially thousands of nuclei. In this paper, we define a cluster of cells as a node and construct a novel graph called Cell Cluster Graph (CCG) to characterize local spatial architecture. CCG is constructed by first identifying the cell clusters to use as nodes for the construction of the graph. Pairwise spatial relationship between nodes is translated into edges of the CCG, each of which are assigned certain probability, i.e. each edge between any pair of a nodes has a certain probability to exist. Spatial constraints are employed to deconstruct the entire graph into subgraphs and we then extract global and local graph based features from the CCG. We evaluated the ability of the CCG to predict 5 year biochemical failures in men with CaP and who had previously undergone radical prostatectomy. Extracted features from CCG constructed using nuclei as nodal centers on tissue microarray (TMA) images obtained from the surgical specimens of 80 patients allowed us to train a support vector machine classifier via a 3 fold randomized cross validation procedure which yielded a classification accuracy of 83:1±1:2%. By contrast the Voronoi, Delaunay, and Minimum spanning tree based graph classifiers yielded corresponding classification accuracies of 67:1±1:8% and 60:7±0:9% respectively.
In vivo metabolic intermediates of phospholipid biosynthesis in Rhodopseudomonas sphaeroides (1983)

The in vivo metabolic pathways of phospholipid biosynthesis in Rhodopseudomonas sphaeroides have been investigated. Rapid pulse-chase-labeling studies indicated that phosphatidylethanolamine and phosphatidylglycerol were synthesized as in other eubacteria. The labeling pattern observed for N-acylphosphatidylserine (NAPS) was inconsistent with the synthesis of this phospholipid occurring by direct acylation of phosphatidylserine (PS). Rather, NAPS appeared to be kinetically derived from an earlier intermediate such as phosphatidic acid or more likely CDP-diglyceride. Tris-induced NAPS accumulation specifically reduced the synthesis of PS. Treatment of cells with a bacteriostatic concentration of hydroxylamine (10 mM) greatly reduced total cellular phospholipid synthesis, resulted in accumulation of PS, and stimulated the phosphatidylglycerol branch of phospholipid metabolism relative to the PS branch of the pathway. When the cells were treated with a lower hydroxylamine dosage (50 microM), total phospholipid synthesis lagged as PS accumulated, however, phospholipid synthesis resumed coincident with a reversal of PS accumulation. Hydroxylamine alone was not sufficient to promote NAPS accumulation but this compound allowed continued NAPS accumulation when cells were grown in medium containing Tris. The significance of these observations is discussed in terms of NAPS biosynthesis being representative of a previously undescribed branch of the phospholipid biosynthetic sequence.
An Ultra Low Noise Telecom Wavelength Free Running Single Photon Detector Using Negative Feedback Avalanche Diode (2016)

It is challenging to implement genuine free running single photon detectors for the 1550 nm wavelength range with simultaneously high detection efficiency (DE), low dark noise, and good time resolution. We report a novel read out system for the signals from a negative feedback avalanche diode (NFAD)1–3 which allows useful op-eration of these devices at a temperature of 193 K and results in very low dark counts ( ∼ 100 CPS), good time jitter ( ∼ 30 ps), and good DE (∼10 %). We char-acterized two NFADs with a time correlation method using photons generated from weak coherent pulses (WCP) and photon pairs produced by spontaneous parametric down conversion (SPDC). The inferred detector efficiencies for both types of pho-ton sources agree with each other. The best noise equivalent power of the device is estimated to be 8.1 × 10−18 W · Hz−1/2, more than 10 times better than typical InP/InGaAs SPADs show in free running mode. The afterpulsing probability was found to be less than 0.1 % per ns at the optimized operating point. In addition, we studied the performance of an entanglement-based quantum key distribution (QKD) using these detectors and develop a model for the quantum bit error rate (QBER) that incorporates the afterpulsing coefficients. We verified experimentally that using these NFADs it is feasible to implement QKD over 400 km of telecom fibre. Our NFAD photon detector system is very simple, and is well suited for single-photon applications where ultra-low noise and free-running operation is required, and some afterpulsing can be tolerated.
Synthesis of perylene-porphyrin dyads for light-harvesting studies (2002)

The spectral coverage of porphyrin-based light-harvesting arrays can be enhanced through the use of suitable accessory pigments. Perylene-monoimide dyes can serve as valuable accessory pigments with porphyrins. To investigate the choice of perylene-monoimide and the effects of molecular architecture on light-harvesting efficacy, five perylene-porphyrin dyads were prepared. Each dyad employs a diphenylethyne linker that bridges the perylene N-imide site and the porphyrin meso-position. Three dyads incorporate a mono-phenoxy perylene at the o-, m-, or p-position of the meso-aryl group on the porphyrin. The two remaining dyads incorporate a perylene-monoimide (bearing zero or three phenoxy substituents) at the p-position of the meso-aryl group on the porphyrin. The introduction of phenoxy groups on the perylenes increases the solubility, a key requirement for use in light-harvesting arrays. The long-wavelength absorption band of the perylene shifts from 506 nm to 532 or 533 nm upon substitution with one or three phenoxy groups, respectively. The synthesis of the dyads entails Pd -mediated coupling of a bromo-perylene and an ethynyl porphyrin, or the mixed-aldehyde condensation with a perylene-aldehyde, mesitaldehyde, and pyrrole. Five perylene-monoimide dyes bearing an ethyne or bromo substituent at the p-position of the N-aryl unit were developed for this modular chemistry. Each perylene-porphyrin dyad exhibits efficient energy transfer from the excited perylene to the ground-state porphyrin.
<i>In vivo</i>blockade of CTLA-4 enhances the priming of responsive T cells but fails to prevent the induction of tumor antigen-specific tolerance (1999)

The efficacy of therapeutic vaccination for the treatment of cancer is limited by peripheral tolerance to tumor antigens. In vivo blockade of CTLA-4, a negative regulator of T cell function, can induce the regression of established tumors and can augment the tumor rejection achieved through therapeutic vaccination. These outcomes may reflect enhanced tumor-specific T cell priming and/or interference with the development of tolerance to tumor antigens. We examined the effect of CTLA-4 blockade on the fate and function of T cells specific for a model tumor antigen in the tumor-bearing host. We found that while CTLA-4 blockade enhanced the priming of responsive T cells, it did not prevent the induction of tolerance to tumor antigens. These results demonstrate that there is a critical window in which the combination of CTLA-4 blockade and vaccination achieves an optimal response, and they point to mechanisms other than CTLA-4 engagement in mediating peripheral T cell tolerance to tumor antigens.
<title>New approach to diagnosis of pulmonary embolism using multislice CT</title> (2001)

Suspected pulmonary embolism (PE) is a common indication for CT scanning of the thorax. Usually, intravenous contrast agent is administered utilizing a power-injector and the vascular structures are examined for the presence of pulmonary emboli. Current Multi-Slice CT-technology allows extending this morphological analysis by adding a more functional visualization of the actual parenchymal perfusion disturbance. We have developed a new image processing technique which allows selective color encoded display of parenchymal enhancement of the lung, which will be reduced in the presence of PE. Based on thin slice reconstructions an automatic 3D segmentation of the lung is performed followed by threshold based extraction of the major airways and vascular structures. This allows applying an adaptive 3D low-pass filter to the parenchymal volume only. The filtered volume data are then color encoded and overlaid onto the original CT-images. This combination of low-resolution perfusion-weighted color maps and high-resolution gray scale structural data from the same data set greatly enhances visualization of spatial relationships. The resulting images can be displayed in axial, sagittal and coronal orientation. Initial experience indicates that this new technique provides relevant additional information for the clinical management of patients with proven PE. A larger controlled patient study is under way.
1091: Recombinant Anti-PSCA Antibodies Inhibit Prostate and Bladder Cancer Growthin Xenograft Models and are Superior to Parental Murine Antibody (2004)

You have accessJournal of UrologyDiscussed Poster, Monday, May 10, 2004, 1:00 - 5:00 pm1 Apr 20041091: Recombinant Anti-PSCA Antibodies Inhibit Prostate and Bladder Cancer Growthin Xenograft Models and are Superior to Parental Murine Antibody Robert E. Reiter, Anna Wu, Mark Sherman, and Zhennan Gu Robert E. ReiterRobert E. Reiter More articles by this author , Anna WuAnna Wu More articles by this author , Mark ShermanMark Sherman More articles by this author , and Zhennan GuZhennan Gu More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38328-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1091: Recombinant Anti-PSCA Antibodies Inhibit Prostate and Bladder Cancer Growthin Xenograft Models and are Superior to Parental Murine Antibody." The Journal of Urology, 171(4S), pp. 287–288 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 287-288 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Robert E. Reiter More articles by this author Anna Wu More articles by this author Mark Sherman More articles by this author Zhennan Gu More articles by this author Expand All Advertisement PDF downloadLoading ...
Priority-based Routing Framework for Image Transmission in Visual Sensor Networks: Experimental Analysis (2020)

A Visual Sensor Network (VSN) is a specialized Wireless Sensor Network (WSN) equipped with cameras. Its primary function is to capture images, videos and send them to power rich sink nodes for processing. As image data is much larger than scalar data sensed by a typical WSN, applications of VSN require much bigger amount of data to be transferred to the sink. Due to constraints of WSN such as low energy, limited CPU power and scarce memory, transmission of large amount of data becomes challenging. On the other hand, some VSN applications require critical image features sooner than the entire image to take action. In this paper, we provide the details of experiments done using our proposed Priority-based Routing Framework for Image Transmission (PRoFIT). PRoFIT is designed to deliver critical image features at high priority to the sink node for early processing. Peak signal-to-noise ratio (PSNR) analyses show that PRoFIT improves VSN application response time as compared to priority-less routing. This paper also contains the design of our VSN testbed. Multiple indoor and outdoor experiments were performed to validate the framework. This framework also improves the energy efficiency of the network. The results show that the PRoFIT is 40% efficient in terms of energy consumption.
White Electrophosphorescence from Semiconducting Polymer Blends (2004)

White emission from polymer light‐emitting diodes (PLEDs) is demonstrated using semiconducting polymers blended with organometallic emitters and spin‐cast from solution. Because a single semiconducting polymer was used as the common host for red, green, and blue emission, the color coordinates, color temperatures, and color rendering indices of the white emission are insensitive to the brightness, applied voltage, and applied current density. The PLEDs have luminous efficiency of 4.3 cd A –1 and luminance of 223 cd m –2 at current density of 5.2 mA cm –2 ( V = 14 V); at 17 V, L = 1.2 × 10 4 cd m –2 .
A figure of merit for assertions in verification (2019)

Assertion quality is critical to the confidence and claims in a design's verification. In current practice, there is no metric to evaluate assertions. We introduce a methodology to rank register transfer level (RTL) assertions. We define assertion importance and assertion complexity and present efficient algorithms to compute them. Our method ranks each assertion according to its importance and complexity. We demonstrate the effectiveness of our ranking for pre-silicon verification on a detailed case study. For completeness, we study the relevance of our highly ranked assertions in a post-silicon validation context, using traced and restored signal values from the design's netlist.
Comparative Study of Colorimetric DNA Hybridization Method and Conventional Culture Procedure for Detection of Salmonella in Foods (1990)

A second generation nucleic acid hybridization assay has been developed and evaluated against the conventional culture method for detection of salmonellae in foods. The assay involves a liquid hybridization with Salmonella-specific oligonucleotide probes, capture of probe:target hybrids onto a solid support (plastic dipstick), and a colorimetric end point detection. The assay can be completed in 2.5 h, following approximately 44 h of culture enrichment. One thousand samples representing 20 food types were analyzed in parallel by both methods. Samples included uninoculated test product, and product inoculated with Salmonella at 2 levels. Eighteen Salmonella serotypes were used as inocula. The data demonstrate that the colorimetric hybridization method and the conventional culture method are equivalent in their ability to detect Salmonella contamination of foods.
From Videos to Places: Geolocating the World's Videos (2011)

This paper explores the problem of large-scale automatic video geolocation. A methodology is developed to infer the location at which videos from Anonymized.com were recorded using video content and various additional signals. Specifically, multiple binary Adaboost classifiers are trained to identify particular places based on learning decision stumps on sets of hundreds of thousands of sparse features. A one-vs-all classification strategy is then used to classify the location at which videos were recorded. Empirical validation is performed on an immense data set of 20 million labeled videos. Results demonstrate that high accuracy video geolocation is indeed possible for many videos and locations and interesting relationships exist between between videos and the places where they are recorded.
Multidimensional benzobisoxazole rigid-rod polymers. I. Preparation and characterization (1997)

Two- and three-dimensional rigid-rod polymers containing benzobisoxazole structures were prepared through the polycondensation in polyphosphoric acid of 4-[5-amino-6-hydroxybenzoxazol-2-yl]benzoic acid (ABA) with trimesic acid and 1,3,5,7-tetrakis(4-carboxylatophenyl)adamantane, respectively. Thermal properties of the polymers were determined by differential scanning calorimetry, thermogravimetric/mass spectral analysis, and isothermal aging studies. The multidimensional polymers exhibited lower solution viscosities and lower thermooxidative stabilities than the one-dimensional polymer generated by the homopolymerization of ABA under identical reaction conditions. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 3451–3456, 1997
Supercurrent parity meter in a nanowire Cooper pair transistor (2022)

We study a Cooper pair transistor realized by two Josephson weak links that enclose a superconducting island in an InSb-Al hybrid nanowire. When the nanowire is subject to a magnetic field, isolated subgap levels arise in the superconducting island and, because of the Coulomb blockade, mediate a supercurrent by coherent cotunneling of Cooper pairs. We show that the supercurrent resulting from such cotunneling events exhibits, for low to moderate magnetic fields, a phase offset that discriminates even and odd charge ground states on the superconducting island. Notably, this phase offset persists when a subgap state approaches zero energy and, based on theoretical considerations, permits parity measurements of subgap states by supercurrent interferometry. Such supercurrent parity measurements could, in a series of experiments, provide an alternative approach for manipulating and protecting quantum information stored in the isolated subgap levels of superconducting islands.
High Internal Phase Polymeric Emulsions by Self-Assembly of Colloidal Systems (2003)

We propose a new procedure to synthesize high internal phase polymeric emulsions (polyHIPE) that is based on the self-assembly of colloidal systems. Colloidal suspensions were used as precursors of the final polyHIPE. These were obtained by dispersing 500 nm diameter, lightly cross-linked polystyrene (PS) emulsion particles in ethanol at room temperature under continuous sonification. A polystyrene-poly(2-vinylpyridine) (PS−PVP) block copolymer with a short PS block and a long PVP block was synthesized and dissolved in the ethanol-colloidal dispersion. After solvent removal, owing to the asymmetric composition of the block copolymer and the high volume fraction of the colloid, a closely packed colloidal system was obtained, where voids were partially filled by the block copolymer discrete phase. However, under appropriate annealing, the colloidal system was shown to undergo a rearrangement in which the particles deform to polyhedrons and closely pack within a percolating phase formed by the poly(2-vinylpyridine) block of the copolymer. The volume fraction threshold for percolation of this PVP domain structure was shown to be as low as 0.10 by doping the PVP and performing conductivity measurements. We argue that the physical driving force leading to this rearrangement is the reduction of the interfacial tension of the colloidal system.
Aligned Schwann cells derived from human dental pulp stem cells direct neurite growth in a tissue engineered collagen construct (2013)

A variety of traumas and diseases can cause peripheral nerve injury (PNI). In the process of spontaneous healing, Schwann cells (SC) are very important players. They not only reconstitute myelin, essential for proper nerve function, but also organize themselves into columns that lie within the endoneurial tubes to guide and support axonal regeneration from the proximal to the distal end of the injury. By contrast, large gap PNI requires artificial bridging strategies such as highly aligned scaffolds to promote directed neurite outgrowth. In the field of neural tissue engineering, hydrogels are very attractive biomaterials to encapsulate cells. Their high water content facilitates transport of oxygen, nutrients and waste and their viscoelastic properties can be relatively easy modulated. Recently, a new technique has been developed to efficiently and reproducibly align cells in a collagen type I hydrogel, thereby mimicking the environment required for nerve regeneration. This Engineered Neural Tissue (ENT) has given promising preliminary results with immortalized and primary rat SC both in vitro and in vivo. However, the use of human cells would be a significant advance in bringing this ENT from bench to bedside. Since autologous SC must be harvested from another peripheral nerve and are slowly growing in vitro, there is a high need for alternative cell types such as human dental pulp stem cells (hDPSC). hDPSC can be easily isolated from discarded teeth with very little ethical issues and their neural crest origin suggests a predisposition to differentiate into neural or glial cells. Preliminary experiments in our laboratory indicate the two-dimensional (2D) in vitro transdifferentiation capacity of human DPSC (hPDSC) into Schwann-like cells (SC-hDPSC). Here, we evaluate the potential of SC-hDPSC to align within a collagen type I hydrogel and determine the effects of this ENT on dorsal root ganglion neuron neurite outgrowth in vitro.
Orthogonal frequency coding for SAW device applications (2005)

This paper presents the concept of orthogonal frequency coding (OFC) for applications to SAW device technology. OFC is the use of orthogonal frequencies to encode a signal. which spreads the signal bandwidth in a manner similar to a fixed M-ary frequency shift signal. Also, a pseudo noise (PN) sequence can be added for additional coding. The OFC technique provides a wide bandwidth spread spectrum signal with all the inherent advantages obtained from the time-bandwidth product increase over the data bandwidth. The theory of OFC is presented and discussed, defining the fundamental equations and showing the time and frequency domain relationships. The application of OFC to SAW devices for tagging is introduced.
UV-Curable Resins Appropriate for UV Nanoimprint (2008)

Three types of UV-curable resins; radical curing type, cationic curing type, and hybrid curing type, a combination of radical and cationic curing type, have been developed for UV nanoimprint. Nanoimprint has a variety range of ways and finds extensive range of applications. For UV nanoimprint UV-curable resins play an important roll for the progress of the nanoimprint technology, but the material used for the study of UV nanoimprint has been so far limited to the radical curing type like acrylic resins. The cationic curing type consisting of epoxides, oxetanes, and vinyl ethers has been studied along with the radical curing type and the hybrid curing type, and has shown usefulness for UV-nanoimprint in reactivity of sub micron thin films. Also the condition for successful pattern transfer has been studied and it turned out that for thin films below 300nm no lower than 5MPas of imprint pressure is necessary. The demolding and the contact to substrate, another important concern for nanoimprint was studied from the view point of additives and some additives having potential for improving the contact to substrate and the demolding have been found.
Optoelectronic transmitters for medical ultrasound transducers (1994)

Optoelectronics and fiber optics can be used to miniaturize and improve the flexibility of the transducer cable and handle of medical diagnostic ultrasound scanners. The reduction in size gains importance as 2-D array transducers with up to 1000 independent channels are incorporated in diagnostic ultrasound systems. The design, fabrication, and analysis of a photoconductive semiconductor switch (PCSS) is described. The monolithic silicon PCSS was used in combination with a pulsed infrared semiconductor diode laser with a fiber optic `pigtail' to shock excite and burst excite a 2-D array transducer element resonant at 3.5 MHz. Optically controlled transducer voltage and ultrasound pulses are displayed for single shock excitation and burst excitation