gebhart/patrepeval huggingface dataset:
Medicinal Mushroom Substances as Cancer Molecular Therapy (2005)

Medicinal mushrooms possess a variety of health promoting qualities as well as being a potential source of a variety of pharmaceuticals for some diseases, including cancer. Although most of the attention for their anticancer activity revolved around the activity of high-molecular-weight polysaccharides with no clear mechanism of action, our focus is on low-molecular-weight mushroom substances with a well-defined mechanism of action.A neoplasm is an abnormal mass or colony of cells produced by a relatively autonomous new growth of tissue arising from the clonal expansion of a single cell that has undergone neoplastic transformation, which is usually accompanied by the loss of some specialized functions and the acquisition of new biological properties mediated by alteration in the expression or function of specific molecular targets. Our research interest on mushroom substances that specifically modulate molecular targets implicated in carcinogenesis, especially in chronic myelogenous leukemia (CML) and prostate cancer (PCa).CML is a malignancy of pluripotent hematopoietic cells characterized by distinctive cytogenetic abnormality resulting in the creation of a p210 Bcr-Abl fusion protein with increased tyrosine kinase activity.Imatinib is a potent inhibitor of Bcr-Abl and is used as standard therapy for CML. Unfortunately, clinical efficacy continuously decreases with the advancement of the disease. Secondary resistance is mostly due to the acquisition of point mutations in Bcr-Abl, which argues for the need of developing alternative inhibitors of Bcr-Abl.Medicinal mushrooms exhibiting selective anti-CML activity were selected. Active mushroom substances induced apoptosis and erythroid differentiation in CML cells and caused a reduction in Bcr-Abl levels. Focusing on mushroom #540 and #514, we show that medicinal mushroom substances were effective in inhibiting auto-phosphorylation from wild types as well as from imatinib-resistance mutants of Bcr-Abl.PCa is the second leading cause of death in Western men. Primary PCa is hormone dependent and is manageable by hormonal therapy. However, it rapidly develops into hormone-refractory tumors due to the accumulation of mutations in the androgen receptor (AR) or to the acquisition of alternative cellular pathways that support proliferation and inhibit apoptosis of PCa in androgen-independent mechanisms.Whereas PCa is very common in Western countries, its levels are very low in several countries in Asia. Several reports linked Eastern diets and cancer occurrence, especially for PCa. Of special interest is the implication of several mushrooms in the prevention of PCa in Asia.We evaluate the ability of mushroom substances extracted from our collection ot mushroom strains to interfere selectively with the activity of AR, the leading molecular target implicated in the development and maintenance of hormone-refractory PCa. Data showing anti-prostate cancer activity and the ability to modulate AR and other molecular targets will be presented.
Novel Guided Head Expander Design Uses Close Coupled Inertial Masses and Hydrostatic Bearings to Minimize Cross-Axis Motion This paper is a peer-reviewed, technically edited, and updated revision of a paper originally published in the 2006 Space Simulation Conference Proceedings. (2010)

When vertical vibration testing of large test articles is required, it is common to install a head expander on the armature of a shaker. Larger test articles often have a center of gravity relatively far above the mounting surface. When combined with the armature and head expander, these test articles may exhibit multiple structural resonances within the desired test band that do not exist in the intended application. These test configuration-driven characteristics are likely to create unwanted cross-axis excitation during a vibration test. The difficulty in controlling unwanted cross-axis motion usually increases when testing large items. Excessive cross-axis motion can “over-test” the test item, creating the risk of damaging the test item, or can limit the input in the test axis, thus jeopardizing a successful test. Orbital Sciences commissioned the design of a guided head expander system that greatly reduces the cross-axis motion at the test article mounting surface of the head expander. The design submitted by Team Corporation couples large inertial masses to the head expander through high-stiffness, hydrostatic, self-aligning bearings. Together, the guided head expander and inertial mass structures have a first resonance higher than the test band of interest and provide high dynamic stiffness. The head expander and inertial masses are supported by a suspension system with a low first resonance, below the test band of interest. It is noteworthy that this design approach exhibits high “dynamic” stiffness and low static stiffness. Conventional designs for this type of equipment may have relatively high cross-axis load ratings, which might suggest that such designs would provide good cross-axis motion control, but these designs often suffer from structural resonances within the test band of interest that produce unwanted cross-axis motion.
A hybrid video codec based on extended block sizes, recursive integer transforms, improved interpolation, and flexible motion representation (2010)

This paper describes video coding technology proposal submitted by Qualcomm Inc. in response to a joint call for proposal (CfP) issued by ITU-T SG16 Q.6 (VCEG) and ISO/IEC JTC1/SC29/WG11 (MPEG) in January 2010. Proposed video codec follows a hybrid coding approach based on temporal prediction, followed by transform, quantization, and entropy coding of the residual. Some of its key features are extended block sizes (up to 64x64), recursive integer transforms, single pass switched interpolation filters with offsets (single pass SIFO), mode dependent directional transform (MDDT) for intra-coding, luma and chroma high precision filtering, geometry motion partitioning, adaptive motion vector resolution. It also incorporates internal bit-depth increase (IBDI), and modified quadtree based adaptive loop filtering (QALF). Simulation results are presented for a variety of bit rates, resolutions and coding configurations to demonstrate the high compression efficiency achieved by the proposed video codec at moderate level of encoding and decoding complexity. For random access hierarchical B configuration (HierB), the proposed video codec achieves an average BD-rate reduction of 30.88c/o compared to the H.264/AVC alpha anchor. For low delay hierarchical P (HierP) configuration, the proposed video codec achieves an average BD-rate reduction of 32.96c/o and 48.57c/o, compared to the H.264/AVC beta and gamma anchors, respectively.
Surface-enhanced Raman nanodomes (2010)

We demonstrate a surface-enhanced Raman scattering (SERS) substrate consisting of a closely spaced metal nanodome array fabricated on flexible plastic film. We used a low-cost, large-area replica molding process to produce a two-dimensional periodic array of cylinders that is subsequently overcoated with SiO(2) and silver thin films to form dome-shaped structures. Finite element modeling was used to investigate the electromagnetic field distribution of the nanodome array structure and the effect of the nanodome separation distance on the electromagnetic field enhancement. The SERS enhancement from the nanodome array substrates was experimentally verified using rhodamine 6G as the analyte. With a separation distance of 17 nm achieved between adjacent domes using a process that is precisely controlled during thin film deposition, a reproducible SERS enhancement factor of 1.37 × 10(8) was demonstrated. The nanoreplica molding process presented in this work allows for simple, low-cost, high-throughput fabrication of uniform nanoscale SERS substrates over large surface areas without the requirement for high resolution lithography or defect-free deposition of spherical microparticle monolayer templates.
Performance of an MLSE-based early stopping technique for turbo codes (2005)

A crucial issue in the practical application of turbo codes is decoding complexity. A common approach to reducing decoding complexity is to stop the iterative decoding process early. It is demonstrated that an early stopping technique based on maximum-likelihood sequence estimation (MLSE) can significantly reduce average decoder processing. Specifically, it is shown that an 8-state turbo code with 512 data bits and a nominal code rate of 1/3 can be decoded in less than 2 iterations on average when E/sub b//N/sub 0/ /spl ges/ 2 dB (packet error rate /spl ap/ 10/sup -7/). This reduction is achieved with virtually no loss in error rate performance relative to performing a large fixed number of iterations.
A class of reversible variable length codes for robust image and video coding (2002)

We describe a class of parameterized reversible variable length codes that have length distributions identical to Golomb-Rice codes and exp-Golomb codes. The pdfs to which these codes correspond are well matched to statistics of image and video data, thus enabling an increase in robustness to channel errors with no penalty in coding efficiency. These codes are applicable to MPEG-4 and other algorithms that aim to use variable length codes in error-prone environments.
SOMA-ME: A platform for the model-driven design of SOA solutions (2008)

The service-oriented modeling and architecture modeling environment (SOMA-ME) is first a framework for the model-driven design of service-oriented architecture (SOA) solutions using the service-oriented modeling and architecture (SOMA) method. In SOMA-ME, Unified Modeling Language (UML™) profiles extend the UML 2.0 metamodel to domain-specific concepts. SOMA-ME is also a tool that extends the IBM Rational® Software Architect product to provide a development environment and automation features for designing SOA solutions in a systematic and model-driven fashion. Extensibility, traceability, variation-oriented design, and automatic generation of technical documentation and code artifacts are shown to be some of the properties of the SOMA-ME tool.
Practical Realization of a Passive Coherent Population Trapping Frequency Standard (2005)

The paper outlines the practical realization and characteristics of a small, totally autonomous passive frequency standard based on the coherent population trapping (CPT) phenomenon. The frequency standard, including physical characteristics, block diagrams of the optical control CPT resonance system and of the digital control electronics, is described. The characteristics of the frequency standard relative to general functionality and frequency stability are given, as measured on several units.
New Before Closure Analysis Model for Unconventional Reservoirs (2014)

Abstract Minifrac/diagnostic fracture injection tests (DFITs) are an important and integral part of hydraulic fracture design and reservoir evaluation. Models for analysis of the before and after closure data have been developed. While several models exist and are being used to analyze the after closure data, before closure analysis (BCA) is not widely used, and only a handful of models have been developed. Additionally, the models are based on similar approaches and assumptions. This paper introduces a new BCA model based on rigorous treatment of the fluid flow equations in the fracture and the formation. In this new model, the assumptions of linear leakoff and short injection time for a minifrac test are made. In general, these assumptions are valid. In unconventional reservoirs, where permeability is expected to be very low, the assumption of linear leakoff is particularly valid and would last most of the duration of the before closure period. In most minifrac tests, the injection time is relatively small with respect to after shut-in time, which validates this new model assumption of short injection time. Fracture stiffness is a critical parameter when using this model, which can be easily calculated or measured from logging or experimental data. By using the before closure model presented here, formation permeability could be estimated by interpretation of the slope of straight line in the specialized Cartesian plot using before closure data. This paper details the development of the new model and compares it to existing models. In addition, several field examples from unconventional formations are presented and analyzed using various techniques, demonstrating the applicability of this new model. The results are also compared to the after closure analysis (ACA).
Intra Picture Prediction for Video Coding with Neural Networks (2019)

We train a neural network to perform intra picture prediction for block based video coding. Our network has multiple prediction modes which co-adapt during training to minimize a loss function. By applying the l1-norm and a sigmoid-function to the prediction residual in the DCT domain, our loss function reflects properties of the residual quantization and coding stages present in the typical hybrid video coding architecture. We simplify the resulting predictors by pruning them in the frequency domain, thus greatly reducing the number of multiplications otherwise needed for the dense matrix-vector multiplications. Also, by quantizing the network weights and using fixed point arithmetic, we allow for a hardware friendly implementation. We demonstrate significant coding gains over state of the art intra prediction.
Performance of Dengue Diagnostic Tests in a Single-Specimen Diagnostic Algorithm (2016)

The use of molecular or NS1 antigen tests to detect DENV and one to detect anti-DENV IgM in a single serum specimen collected during the first 10 days of illness accurately identified ≥90% of dengue primary and secondary cases.
Spectrum-based color reproduction system for motion picture (2003)

The architecture of color reproduction system based on spectral information is addressed. This system aims to realize the accurate color reproduction under arbitrary illuminants and color matching functions and anticipates the ultimate reproduction of spectral reflectance and spectrum of objects. This system is like an expanded version of that proposed by the International Color Consortium (ICC). One of the features of this system is the usage of the spectral space for the profile connection space alternative to the colorimetric space. It retains compatibility with the indigenous color management functions of the current system. The proposed system is further expanded to construct the spectrum-based color reproduction system for motion picture. Six-band HDTV camera and six-primary projection display system, which is realized in our laboratory as experimental spectrum-based color reproduction system for motion picture, is briefly introduced.
New Insights Into the Transmissibility of<i>Leishmania infantum</i>From Dogs to Sand Flies: Experimental Vector-Transmission Reveals Persistent Parasite Depots at Bite Sites (2016)

Canine leishmaniasis (CanL) is a chronic fatal disease of dogs and a major source of human infection through propagation of parasites in vectors. Here, we infected 8 beagles through multiple experimental vector transmissions with Leishmania infantum-infected Lutzomyia longipalpis. CanL clinical signs varied, although live parasites were recovered from all dog spleens. Splenic parasite burdens correlated positively with Leishmania-specific interleukin 10 levels, negatively with Leishmania-specific interferon γ and interleukin 2 levels, and negatively with Leishmania skin test reactivity. A key finding was parasite persistence for 6 months in lesions observed at the bite sites in all dogs. These recrudesced following a second transmission performed at a distal site. Notably, sand flies efficiently acquired parasites after feeding on lesions at the primary bite site. In this study, controlled vector transmissions identify a potentially unappreciated role for skin at infectious bite sites in dogs with CanL, providing a new perspective regarding the mechanism of Leishmania transmissibility to vector sand flies.
Defining host-symbiont collaboration in termite lignocellulose digestion: “The view from the tip of the iceberg” (2011)

Termites have the unique ability to exploit lignocellulose as a primary nutrition source. Traditionally, termite lignocellulose digestion has been considered as a gut-symbiont-mediated process; however, in recent years the importance of host digestive capabilities have become apparent. Despite this growing understanding, how digestive enzymes from different origins specifically collaborate (i.e., additively or synergistically) has remained largely unknown. In a recent study, we undertook translational-genomic studies to address these questions in the lower termite Reticulitermes flavipes (Isoptera: Rhinotermitidae) and its symbiotic gut fauna. We used a combination of native gut tissue preparations and recombinant enzymes derived from the host gut transcriptome to identify synergistic collaborations between host and symbiont, and also among enzymes produced exclusively by the host termite. These findings provided important new evidence of synergistic collaboration among enzymes in the release of fermentable monosaccharides from wood lignocellulose, and laid a foundation for future integrative studies into termite digestion, symbiosis and eusociality.
Evaluation of a Commercial Competitive ELISA Test Kit for the Detection of Group-Specific Antibodies to Bluetongue Virus (1993)

The performance of a competitive (c) enzyme-linked immunosorbent assay (ELISA) test kit, Blueplate Special (BPS), commercially produced by DiagXotics (Wilton, CT) for detection of group-specific antibodies to bluetongue virus (BTV) was compared with that of an internationally endorsed cELISA-I. A total of 1,026 serum samples were tested in this study: 133 samples from 23 calves and 3 sheep experimentally infected with South African isolates of 19 BTV serotypes and US isolates of 5 BTV serotypes and 7 calves infected with US isolates of 2 epizootic haemorrhagic disease of deer virus (EHDV); 102 paired sera from cattle, sheep, and goats experimentally infected with the Australian isolates of BTV, EHDV, and Palyam virus; 229 bovine and ovine samples of Canadian origin (BTV free); and 562 bovine and ovine field samples from the USA and Barbados (BTV endemic). Seroconversion was demonstrable by the BPS cELISA 10 days postinfection in all experimental animals inoculated with BTV, with the exception of 4 calves in which there was a delay of 10-20 days. Similar to the cELISA-I, none of the sera from calves inoculated with US and Australian isolates of EHDV and Palyam viruses cross-reacted with the BTV antigen in the BPS cELISA. The total agreement between the two assays for all the total bovine and ovine field sera was 98.1%. The overall results substantiate the usefulness of the BPS cELISA test kit for monitoring animal sera for group-specific antibodies to BTV.(ABSTRACT TRUNCATED AT 250 WORDS)
Maternal aryl hydrocarbon receptor activation protects newborns against necrotizing enterocolitis (2021)

Necrotizing enterocolitis (NEC) is a disease of premature infants characterized by acute intestinal necrosis. Current dogma suggests that NEC develops in response to post-natal dietary and bacterial factors, and so a potential role for in utero factors in NEC remains unexplored. We now show that during pregnancy, administration of a diet rich in the aryl hydrocarbon receptor (AHR) ligand indole-3-carbinole (I3C), or of breast milk, activates AHR and prevents NEC in newborn mice by reducing Toll-like receptor 4 (TLR4) signaling in the newborn gut. Protection from NEC requires activation of AHR in the intestinal epithelium which is reduced in mouse and human NEC, and is independent of leukocyte activation. Finally, we identify an AHR ligand ("A18") that limits TLR4 signaling in mouse and human intestine, and prevents NEC in mice when administered during pregnancy. In summary, AHR signaling is critical in NEC development, and maternally-delivered, AHR-based therapies may alleviate NEC.
An Efficient Chemoenzymatic Approach to (<i>S</i>)-γ-Fluoroleucine Ethyl Ester (2005)

[reaction: see text] An asymmetric synthesis of (S)-gamma-fluoroleucine ethyl ester 1 is described. The key transformation involves a lipase-catalyzed dynamic ring-opening of 2-(3-butenyl)azlactone 7b with EtOH to give amide ester (S)-6b in 84% enantiomeric excess. Removal of the N-pentenoyl group with N,N'-dibromodimethylhydantoin in the presence of trifluoroacetic acid afforded the titled compound, which was isolated as its hydrogen sulfate salt in 75% yield and >97% ee.
Transform method for laser speckle strain-rate measurements in biological tissues and biomaterials (1999)

Laser speckle strain measurements in biological tissues and some synthetic biomaterials, such as translucent dental composites and ceramics, are often complicated by the physical properties of the materials. For example, speckles generated by illuminating soft biological tissue with laser light are subject to rapid decorrelation due to the Brownian movement of water and scattering particles in the tissues and to cellular motions. In addition, the penetration of the laser beam into the tissue or translucent biomaterial results in multiple scattering and a complete depolarization of the speckle field. This may complicate the evaluation of the strain field when a force is applied to the material because the speckle pattern shift is providing information from the surface of the material as well as from the bulk sample, where the strains may or may not be the same as on the surface. This paper presents a variation of a speckle processing scheme originally called the `Transform Method' for evaluating both surface and bulk strain rates and total strains in biological tissues and translucent biomaterials. The method is not a correlation-based technique, but instead relies upon 2D frequency transforms of time series of 1D speckle pattern records stacked into 2D arrays. The method is insensitive to speckle field depolarization and, compared to correlation-based techniques, is relatively insensitive to speckle decorrelation. Strain rates and total in-plane strains were measured in both hard (cortical bone) and soft (artery segments) biological tissues and in translucent biomaterials (dental ceramics). Potential applications to medical diagnostics and biomaterials science are also discussed.
Evidence for Editing of Human Papillomavirus DNA by APOBEC3 in Benign and Precancerous Lesions (2008)

Cytidine deaminases of the APOBEC3 family all have specificity for single-stranded DNA, which may become exposed during replication or transcription of double-stranded DNA. Three human APOBEC3A (hA3A), hA3B, and hA3H genes are expressed in keratinocytes and skin, leading us to determine whether genetic editing of human papillomavirus (HPV) DNA occurred. In a study of HPV1a plantar warts and HPV16 precancerous cervical biopsies, hyperedited HPV1a and HPV16 genomes were found. Strictly analogous results were obtained from transfection experiments with HPV plasmid DNA and the three nuclear localized enzymes: hA3A, hA3C, and hA3H. Thus, stochastic or transient overexpression of APOBEC3 genes may expose the genome to a broad spectrum of mutations that could influence the development of tumors.