gebhart/patrepeval huggingface dataset:
Alkoxyamines: a new family of pro-drugs against cancer. Concept for theranostics (2013)

Development of anti-cancerous theranostic agents is a vivid field. This article describes a theranostic approach that relies on the triggering of cancer cell death by generation of alkyl radicals at the right place and at the right time using the presence of active proteases in the tumour environment. Alkoxyamines (R(1)R(2)NOR(3)) are labile molecules that homolyze into nitroxides (R(1)R(2)NO˙) and reactive alkyl radicals (R(3)˙). They are used as a source of active alkyl radicals for curing and nitroxides for monitoring by Overhauser-enhanced magnetic resonance imaging (OMRI). Herein, the requirements needed for applying alkoxyamines are described: (i) highly selective activation of the alkoxyamine by specific proteases; (ii) fast homolysis of the alkoxyamine C-ON bond at physiological temperature; (iii) activation of cell death processes through an increase of the local oxidative stress or potential re-activation of the immune system due to short-lived alkyl radicals; and (iv) imaging of the tumor and the drug release by sensing the nitroxide by OMRI.
Imaging using lateral bending modes of atomic force microscope cantilevers (2004)

Using scanning probe techniques, surface properties such as shear stiffness and friction can be measured with a resolution in the nanometer range. The torsional deflection or buckling of atomic force microscope cantilevers has previously been used in order to measure the lateral forces acting on the tip. This letter shows that the flexural vibration modes of cantilevers oscillating in their width direction parallel to the sample surface can also be used for imaging. These lateral cantilever modes exhibit vertical deflection amplitudes if the cantilever is asymmetric in thickness direction, e.g., by a trapezoidal cross section.
Gastric cancer progression may involve a shift in HLA‐E profile from an intact heterodimer to β2‐microglobulin‐free monomer (2013)

Phenotypic expression of human leukocyte antigen (HLA)-E on the surface of tumor lesions includes intact heterodimer [HLA-E heavy chain and β2-microglobulin (β2m)] and β2m-free monomer. Anti-HLA-E monoclonal antibodies (mAbs), MEM-E/02 or 3D12 bind to the peptide sequences in β2m-free HLA-E, which is common and shared with HLA-Ia monomers. A newly developed monospecific anti-HLA-E mAb (TFL-033) recognizes HLA-E-restricted peptide sequences on α1 and α2 helices away from β2-m-site. Tumor progression may involve shedding of β2-m from HLA-E or overexpression of β2m-free monomers. There is a need to identify and distinguish the different phenotypic expression of HLA-E, particularly the intact heterodimer from the β2m-free monomer on the surface of tumor lesions. Because of the unique peptide-binding affinities of the mAbs, it is hypothesized that TFL-033 and MEM-E/02 may distinguish the phenotypic expressions of cell surface HLA-E during stages of tumor progression. Only TFL-033 stained diffusely the cytoplasm of normal mucosa. The incidence and intensity of TFL-033 staining of the cell surface in early stages, poorly or undifferentiated and non-nodal lesions and in diffuse carcinoma is greater than that of MEM-E/02. Whereas MEM-E/02 stained terminal stages, adenocarcinoma and lymph node metastatic lesions intensely, either owing to increased expression of β2m-free HLA-E with tumor progression or owing to expression of HLA-Ia molecules. Our study evaluates the relative diagnostic potential of HLA-E-monospecific TFL-033 and the HLA-Ia-reactive MEM-E/02 for determining the specific distribution and immunodiagnosis of different phenotypic expression HLA-E in tumor lesions, and the structural and functional alterations undergone by HLA-E during tumor progression.
A photonic system for broadband microwave measurement (2018)

Aiming at fast detection speed and significant cost reduction, a photonic system exploring both wavelength- and time-division multiplexing is presented in this paper. The system is primarily consisted of a coherent dual electro-optical frequency comb which slices the broadband microwave spectrally in the optical domain, and an optical storage which snap-shots the input for later read-out. The proof-of-concept experimental setup measures a microwave burst of ~ 1 μs with up to 8 GHz bandwidth within 20 μs at ~ 1 MHz resolution, making the system especially attractive for a wide range of applications for microwave spectral analysis.
Surveillance of Cancer Stem Cell Plasticity Using an Isoform-Selective Fluorescent Probe for Aldehyde Dehydrogenase 1A1 (2018)

Cancer stem cells (CSCs) are progenitor cells that contribute to treatment-resistant phenotypes during relapse. CSCs exist in specific tissue microenvironments that cell cultures and more complex models cannot mimic. Therefore, the development of new approaches that can detect CSCs and report on specific properties (e.g., stem cell plasticity) in their native environment have profound implications for studying CSC biology. Herein, we present AlDeSense, a turn-on fluorescent probe for aldehyde dehydrogenase 1A1 (ALDH1A1) and Ctrl-AlDeSense, a matching nonresponsive reagent. Although ALDH1A1 contributes to the detoxification of reactive aldehydes, it is also associated with stemness and is highly elevated in CSCs. AlDeSense exhibits a 20-fold fluorescent enhancement when treated with ALDH1A1. Moreover, we established that AlDeSense is selective against a panel of common ALDH isoforms and exhibits exquisite chemostability against a collection of biologically relevant species. Through the application of surface marker antibody staining, tumorsphere assays, and assessment of tumorigenicity, we demonstrate that cells exhibiting high AlDeSense signal intensity have properties of CSCs. Using these probes in tandem, we have identified CSCs at the cellular level via flow cytometry and confocal imaging, as well as monitored their states in animal models.
When Not to Classify: Detection of Reverse Engineering Attacks on DNN Image Classifiers (2019)

This paper addresses detection of a reverse engineering (RE) attack targeting a deep neural network (DNN) image classifier; by querying, RE's aim is to discover the classifier's decision rule. RE can enable test-time evasion attacks, which require knowledge of the classifier. Recently, we proposed a quite effective approach (ADA) to detect test-time evasion attacks. In this paper, we extend ADA to detect RE attacks (ADA-RE). We demonstrate our method is successful in detecting "stealthy" RE attacks before they learn enough to launch effective test-time evasion attacks.
Characterization of a new human papillomavirus (HPV 41) from disseminated warts and detection of its DNA in some skin carcinomas (1988)

A new human papillomavirus type (HPV 41), distantly related to known HPV prototypes, was isolated from a patient with disseminated facial, peri-anal and foot warts (epidermodysplasia verruciformis was not diagnosed). The viral DNA was molecularly cloned in 2 BamH1 restriction fragments with sizes of 6.5 kb and 0.98 kb, respectively. The classification of this cloned DNA as a new type is based on the degree of cross-hybridization with 40 HPV types under conditions of varying stringency. A total of 106 benign and malignant skin lesions, as well as 71 malignant tumours of different origins, were screened for the presence of HPV-related sequences. In 2 out of 10 squamous-cell carcinomas and in 1 of 3 arsenic keratoses HPV 41 DNA sequences could be detected.
A Greedy Part Assignment Algorithm for Real-Time Multi-person 2D Pose Estimation (2018)

Human pose-estimation in a multi-person image involves detection of various body parts and grouping them into individual person clusters. While the former task is challenging due to mutual occlusions, the combinatorial complexity of the latter task is very high. We propose a greedy part assignment algorithm that exploits the inherent structure of the human body to lower the complexity of the graphical model, compared to any of the prior published works. This is accomplished by (i) reducing the number of part-candidates using the estimated number of people in the image, (ii) doing a greedy sequential assignment of partclasses, following the kinematic chain from head to ankle (iii) doing a greedy assignment of parts in each part-class set, to person-clusters (iv) limiting the candidate person clusters to the most proximal clusters using human anthropometric data and (v) using only a specific subset of pre-assigned parts for establishing pairwise structural constraints. We show that, these steps sparsify the bodyparts relationship graph and reduces the algorithm's complexity to be linear in the number of candidates of any single part-class. We also propose a method for spawning person-clusters from any unassigned significant body part to make the algorithm robust to occlusions. We show that, our proposed part-assignment algorithm, despite using a sub-optimal pre-trained DNN model, achieves state of the art results on both MPII and WAF pose datasets, demonstrating the robustness of our approach.
Discovering linkage points over web data (2013)

A basic step in integration is the identification of linkage points, i.e., finding attributes that are shared (or related) between data sources, and that can be used to match records or entities across sources. This is usually performed using a match operator, that associates attributes of one database to another. However, the massive growth in the amount and variety of unstructured and semi-structured data on the Web has created new challenges for this task. Such data sources often do not have a fixed pre-defined schema and contain large numbers of diverse attributes. Furthermore, the end goal is not schema alignment as these schemas may be too heterogeneous (and dynamic) to meaningfully align. Rather, the goal is to align any overlapping data shared by these sources. We will show that even attributes with different meanings (that would not qualify as schema matches) can sometimes be useful in aligning data. The solution we propose in this paper replaces the basic schema-matching step with a more complex instance-based schema analysis and linkage discovery. We present a framework consisting of a library of efficient lexical analyzers and similarity functions, and a set of search algorithms for effective and efficient identification of linkage points over Web data. We experimentally evaluate the effectiveness of our proposed algorithms in real-world integration scenarios in several domains.
Development of a New Qualitative Test for Fit Testing Respirators (1995)

A new qualitative fit test was developed using Bitrex (Macfarland Smith Limited) as the test agent. It was validated by running a series of paired qualitative and quantitative fit tests. Quantitative tests were conducted with a small corn oil aerosol, using a condensation nucleus counter as a detector. Qualitative fit tests were run with Bitrex and saccharin, following the established protocol for the saccharin fit test. Four models of National Institute for Occupational Safety and Health--approved replaceable filter respirators were used in the study. All were half mask models equipped with high efficiency filters. In some cases, respirators expected to be the correct size for test subjects were tested. In other cases, respirators expected to be too small or too large for the subjects were tested. Test results were analyzed using fit test method validation criteria recommended in the American National Standards Institute draft standard on fit testing (ANSIZ88.10). The Bitrex and saccharin tests were found to have virtually identical performance. Both met proposed American National Standards Institute requirements for a valid qualitative fit test.
Low-dose performance of a whole-body research photon-counting CT scanner (2016)

Photon-counting CT (PCCT) is an emerging technique that may bring new possibilities to clinical practice. Compared to conventional CT, PCCT is able to exclude electronic noise that may severely impair image quality at low photon counts. This work focused on assessing the low-dose performance of a whole-body research PCCT scanner consisting of two subsystems, one equipped with an energy-integrating detector, and the other with a photon-counting detector. Evaluation of the low-dose performance of the research PCCT scanner was achieved by comparing the noise performance of the two subsystems, with an emphasis on examining the impact of electronic noise on image quality in low-dose situations.
On variable clock methods for path delay testing of sequential circuits (1997)

We propose a delay test methodology for general sequential circuits. To test a combinational path between two flip-flops, the source flip-flop is initialized to the appropriate value, followed by creation of a transition, which is propagated through the path. An incorrect logic value is captured in the destination flip-flop if the path delay exceeds the clock period. The state of the destination flip-flop is observed at a primary output through path sensitization. Only one vector that propagates the transition through the path is applied with the rated clock period. All other vectors use a slow speed clock to ensure fault-free initialization and fault effect observation. The test generation method uses a 13-value algebra that represents the relevant transition and hazard states of signals. Since several path delay faults can be activated by the vector applied at the rated clock, only the flip-flops with hazard-free steady values are assumed to have deterministic states. This allows us to generate sequentially robust tests. We present the results of the test generation method on ISCAS benchmark circuits.
Program Boosting or Crowd-Sourcing for Correctness (2013)

A great deal of effort has been spent on both trying to specify software requirements and on ensuring that software actually matches these requirements. A wide range of techniques that includes theorem proving, model checking, type-based analysis, static analysis, runtime monitoring, and the like have been proposed. However, in many areas adoption of these techniques remains spotty. In fact, obtaining a specification or a precise notion of correctness is in many cases quite elusive. In this paper we investigate an approach we call program boosting, which involves crowd-sourcing imperfect solutions to a difficult programming problem from developers and then blending these programs together in a way that improves their correctness. We show how interesting and highly non-trivial tasks such as writing regular exepressions for URLs or email addresses can be effectively crowd-sourced. We demonstrate that carefully blending the crowd-sourced results together consistently produces a boost, yielding results that are better than any of the starting programs. Our experiments on 465 programs show consistent boosts in accuracy and demonstrate that program boosting can be performed at a relatively modest monetary cost. 1.
An embedded 90 nm SONOS nonvolatile memory utilizing hot electron programming and uniform tunnel erase (2003)

In this work, a new compact SONOS Flash EEPROM device with fast programming, high reliability, and uniform erase is demonstrated. This device has been embedded into a 90 nm high performance CMOS logic process with an advanced copper backend. This device utilizes hot electron injection for programming and uniform channel tunneling for erase. Uniform tunnel erase prevents residual electron build up over the channel and avoids the reliability concerns of hot hole erase. A single bit is stored in each nonvolatile memory transistor.
Performance of a traveling wave thermoacoustic-piezoelectric energy harvester: An electrical circuit analogy approach (2013)

The performance of a traveling wave thermoacoustic-piezoelectric energy harvester is developed using an electrical circuit analogy approach. The harvester converts thermal energy, such as solar or waste heat energy, directly into electrical energy without the need for any moving components. The input thermal energy generates a steep temperature gradient along a porous regenerator. At a critical threshold of the temperature gradient, self-sustained acoustic waves are developed inside an acoustic resonator. The associated pressure fluctuations impinge on a piezoelectric diaphragm, placed at the end of the resonator. The resulting interaction is accompanied by a direct conversion of the acoustic energy into electrical energy. The acoustic pressure oscillations are amplified by a specially designed acoustic feedback loop that introduces appropriate phasing to make the pulsations take the form of traveling waves. Such traveling waves render the harvester to be inherently reversible and thus highly efficient. The behavior of this class of harvesters is modeled using an electrical circuit analogy approach. The developed model is a multifield model that combines the descriptions of the acoustic resonator, feedback loop, and the regenerator with the characteristics of the piezoelectric diaphragm. The onset of self-sustained oscillations of the harvester is predicted using the root locus method. The predictions are validated against published results. The developed electrical analog and the associated analysis approach present invaluable tools for the design of efficient thermoacoustic-piezoelectric energy harvesters.
Real-time estimation of UPC parameters for arbitrary traffic sources in ATM networks (2002)

In networks based on the asynchronous transfer mode (ATM), traffic sources are subjected to a usage parameter control (UPC) function which controls the emitted cell stream by either discarding or delaying cells according to the parameters of a deterministic algorithm (e.g. the dual leaky bucket). The UPC parameters constitute a traffic descriptor which are used to allocate network resources to the traffic source. This paper presents a scheme for determining dual leaky bucket UPC parameter values for an arbitrary traffic source from observations of its emitted cell stream. The selection of UPC parameters is based on a novel statistical characterization of the observed cell stream, the user's tolerance for traffic shaping and a cost function based on the network resource allocation policy. Our scheme makes weak modeling assumptions and is robust for a wide class of traffic streams.
Modulation of aspect ratio for complete separation in an inertial microfluidic channel (2013)

Inertial microfluidics has been attracting considerable interest in recent years due to immensely promising applications in cell separations and sorting. Despite the intense attention, the moderate efficiencies and low purity of the reported devices have hindered their widespread acceptance. In this work, we report on a simple inertial microfluidic system with high efficiency (>99%) and purity (>90%). Our system builds on the concept of two-stage inertial migration which permits precise prediction of particle or cell position within the microchannel. Our design manipulates the inertial equilibrium positions by modulating channel aspect ratio to achieve a complete separation. Here, we successfully demonstrate a complete separation of particles and isolation of rare cells in blood spiked with human prostate epithelial tumor (HPET) cells. Based on the planar structure, large separation spacing and predictable focusing, we envision promising applications and easy integration of our system with existing lab-on-a-chip systems for cell separations.
Determinants of High Titer in Recombinant Porcine Endogenous Retroviruses (2004)

Porcine endogenous retroviruses (PERVs) pose a potential stumbling block for therapeutic xenotransplantation, with the greatest threat coming from viruses generated by recombination between members of the PERV subgroup A (PERV-A) and PERV-C families (PERV-A/C recombinants). PERV-A and PERV-B have been shown to infect human cells in culture, albeit with low titers. PERV-C has a more restricted host range and cannot infect human cells. A recombinant PERV-A/C virus (PERV-A14/220) contains the PERV-A sequence between the end of pol and the middle of the SU region in env. The remaining sequence is derived from PERV-C. PERV-A14/220 is approximately 500-fold more infectious than PERV-A. To determine the molecular basis for the increased infectivity of PERV-A14/220, we have made a series of vector constructs. The primary determinant for the enhanced replicative potential of the recombinant virus appeared to be the env gene. Using a series of chimeric env genes, we could identify two determinants of high infectivity; one was an isoleucine to valine substitution at position 140 between variable regions A and B, and the other lies within the proline rich region. Taken together, these results show that the novel juxtaposition of env gene sequences enhanced the infectivity of PERV-A14/220 for human cells, perhaps by stabilization of the envelope glycoprotein or increased receptor binding.
Microwave monitoring of silver nanoparticle sintering for surface‐enhanced Raman scattering substrates (2011)

One of the most widely used methods for surface‐enhanced Raman scattering (SERS) employs silver or gold nanoparticles either in colloidal suspension or in the dry‐drop form. In such substrates the SERS amplification factors depend critically on the interparticle distances. Here, we report that microwave absorption as a function of temperature in dry‐drop substrates can be used as a probe to demarcate temperature regions for thermal annealing to produce SERS substrates with very high amplification factors. Copyright © 2011 John Wiley & Sons, Ltd.
A Specific Method for Measurement of Equine Active Myeloperoxidase in Biological Samples and in in Vitro Tests (2006)

An original method called SIEFED (specific immunological extraction followed by enzymatic detection) was developed for the specific detection of the activity of equine myeloperoxidase (MPO). The method consists of the extraction of MPO from aqueous solutions by immobilized anti-MPO antibodies followed by washing (to eliminate proteins and interfering molecules) and measurement of MPO activity using a detection system containing a fluorogenic substrate, hydrogen peroxide, and nitrite as reaction enhancer. The SIEFED technique was applied to study active MPO in horse biological fluids and the effects of 2 polyphenolic molecules, curcumin and resveratrol, on MPO activity. The detection limit of the SIEFED was 0.23 mU/ml. The SIEFED exhibited good precision with intra-assay and interassay coefficients of variation below 10% and 20%, respectively, for MPO activities ranging from 0.25 to 6.4 mU/ml. The activity of MPO was generally higher than 1 mU/ml in the fluids collected from horses with inflammatory diseases. Curcumin and resveratrol exerted a dose-dependent inhibition on MPO activity and, as they were removed before the enzymatic detection of MPO, the results suggest a direct drug-nzyme interaction or an enzyme structure modification by the drug. The SIEFED is a new tool that would be useful for specific detection of active MPO in complex media and for selection of MPO activity modulators.