gebhart/patrepeval huggingface dataset:
Novel Naphthalene Derivatives as Inhibitors of Human Immunoglobulin E Antibody Production (1997)

A series of naphthalene derivatives with a variety of substituents at the 2-position was prepared in order to evaluate their suppressive effect on immunoglobulin E (IgE) antibody production by human peripheral blood mononuclear cells provoked with anti-CD40 antibody (alpha-CD40), interleukin-4 (IL-4), and interleukin-10 (IL-10). Compounds having a 1,4-phenylene spacer moiety tethered between the 2-naphthyl nucleus and anthranilic acid suppressed IgE antibody production in vitro in preference to that of IgG antibody without affecting cell viability. Deletion of the anthranilic acid moiety diminished the inhibitory activities. Changing the 2-naphthyl to a 1-naphthyl or phenyl nucleus led to no change in the potency, indicating that the aromatic group at this position is indispensable for the inhibitory activities. On the other hand, changing the 1,4-phenylene spacer to a 1,3-phenylene one resulted in reduced potency. Similarly, inhibitory activities were lost when the CO2H moiety at the 2-position was moved to the 3- or 4-position on the terminal benzene. These observations suggest that the conformation around the anthranilic acid moiety affects the inhibitory activities toward IgE biosynthesis. 2-(4-(2-Naphthyloxy)benzamido)benzoic acid (29) seemed to be a more potent inhibitor of IgE production than of IgG production. Insertion of a methylene between the inter-phenylene and the amide moiety resulted in 2-((4-(2-naphthyloxy)phenyl)acetamido)benzoic acid (31), which provided a stronger inhibition of both IgE and IgG production, although the selectivity toward IgE was lower than that of 29. Introduction of a benzyl group at the 6-position on the naphthalene ring considerably increased the inhibitory activity toward IgE production with an IC50 of 8.3 nM (36). The potency of 31 and 36 was retained when hydrocortisone or lipopolysaccharide was used instead of alpha-CD40 and IL-10 as costimulatory factors with IL-4, implying that these compounds may interfere with signal transduction between IL-4/IL-4 receptor cognition and genetic transcription that induce class-switching of immunoglobulin in B cells. These novel naphthalene derivatives are thus excellent candidates for further investigation with a view toward a therapeutic remedy against IgE-mediated allergic diseases.
Reduced-Intensity Conditioning Regimens for Hematologic Malignancies: What Have We Learned over the Last 10 Years? (2005)

Reduced-intensity conditioning (RIC) regimens have been investigated for more than 10 years as an alternative to traditional myeloablative conditioning regimens. RIC regimens are being commonly used in older patients as well as in disorders in which traditional myeloablative conditioning regimens are associated with high rates of non-relapse mortality. Hodgkin disease, myeloma, and low-grade lymphoid malignancies have been the diseases most impacted by RIC regimens. RIC regimens have also been shown to be safe and effective in older patients as well as patients with co-morbidities, although patients with chemorefractory disease still have high relapse rates and poor outcomes. Patients with chemosensitive disease have outcomes similar to those obtained with conventional ablative therapies, and thus comparative trials are warranted. RIC regimens are associated with lower rates of severe toxicity and non-relapse mortality; however, infections, graft-versus-host disease, and relapse of primary disease remain the most common obstacles to a successful outcome. The impact on survival and the relative benefits of RIC allografting compared with traditional conditioning regimens or alternative therapy remain to be defined. Incorporating targeted therapies as part of the conditioning regimens or as maintenance therapies is currently being explored to reduce relapse rates without increasing toxicity.
Photonic crystal fiber tip sensor for precision temperature sensing (2009)

We demonstrate that monolithic 2-dimensional photonic crystals (PCs) confined to the facet, or tip, of single-mode optical fibers can be designed as highly sensitive temperature sensors. Monolithic 2-D photonic-crystals are fabricated on silicon wafers and subsequently released and micro-assembled onto the tip of optical fibers. The PC's reflection spectrum is modulated by the temperature of the sensor and its environment and shows sensitivity comparable to Fiber Bragg Gratings (FBGs). In contrast to FBGs, the compact sensing element is localized at the tip of the fiber and the active sensor element is a disk of 10 mum diameter and 480 nm thickness. The sensor system is made of robust, high-temperature dielectric materials and therefore has the potential to be used for many applications including measurements in harsh environments.
Augmentation of Postnatal Neovascularization With Autologous Bone Marrow Transplantation (2001)

Direct local transplantation of autologous BM-MNCs seems to be a useful strategy for therapeutic neovascularization in ischemic tissues in adults, consistent with "therapeutic vasculogenesis."
Defects in the opioid growth factor receptor in human squamous cell carcinoma of the head and neck (2003)

These data demonstrate that OGFr is defective in SCCHN and that translation/posttranslation of OGFr protein, but not transcriptional levels of the OGFr gene, is involved. In addition, the attenuated levels of OGFr binding capacity may serve as a marker for SCCHN. These subnormal levels of OGFr may be responsible in part for tumor progression, diminishing the interaction of OGF with OGFr that aids in stabilizing cell replication by an inhibitory mechanism. Gene therapy to reinstate OGFr and/or function could provide a useful treatment for inhibiting tumor progression.
Introduction to Orthonormal Wavelet Analysis with Shift Invariance: Application to Observed Atmospheric Blocking Spatial Structure (2000)

Orthonormal wavelet analysis (OWA) is a special form of wavelet analysis, especially suitable for analyzing spatial structures, such as atmospheric fields. For this purpose, OWA is much more efficient and accurate than the nonorthogonal wavelet transform (WT), which was introduced to the meteorological community recently and which is more suitable for time series analysis. Whereas the continuous WT is strictly correct only for infinite domains, OWA is derived from periodizing and discretizing the infinite-domain case and so is correct for periodic boundary conditions. Unlike Fourier spectra, OWA is not shift invariant. Nor is it equivariant like the WT; that is, the OWA output does not shift as its input shifts. Two remedies are to combine all possible shifts, known as the overcomplete, nonorthogonal shift equivariant WT, or else to use a “best shift,” known as best shift wavelet analysis. Although shift invariant and orthonormal w.r.t. arbitrary inputs, the latter’s optimization generally depends nonlinearly on a reference structure. OWA is a generalization of Fourier series, and the associated multiresolution analysis (MRA) generalizes Reynolds averaging. Like these, OWA/MRA on discrete and continuous domains satisfy analogous identities arithmetically exactly, unlike the WT. OWA/MRA is much more efficient than Fourier series for analyzing several examples, including nearly singular synthetic structures, and a 90-day Hovmöller diagram of observed geopotential height, containing five atmospheric blocking events. OWA’s variance compression is comparable to that of EOF analysis, but is much faster and less data-dependent. Implementing the basic OWA operations is documented with WaveLab, a freely available package requiring MATLAB.
A Double-Blind Trial of a 16-Hour Transdermal Nicotine Patch in Smoking Cessation (1991)

The nicotine skin patch proved to be safe and effective, as demonstrated by a higher rate of abstinence than with placebo. However, the absolute rate of abstinence after one year was only 17 percent, which is lower than the rate in studies that have combined the use of nicotine chewing gum with behavioral therapy.
The hinge as a spacer contributes to covalent assembly and is required for function of IgG (1997)

Chimeric IgG3 lacking a genetic hinge but with Cys residues in CH2 between position 231 and 232 (IgG3 deltaH+Cys) and position 279 (IgG3 deltaH+2Cys) produced by site-directed mutagenesis have been found to be deficient in their intermolecular assembly. Although some H2L2 molecules are formed, significant quantities of assembly intermediates, in particular HL, are found in the secretions. Both IgG3 deltaH+Cys and IgG3 deltaH+2Cys were greatly reduced in their ability to bind Fc gammaRI. They also failed to bind C1q and activate the complement cascade. Addition of the tailpiece from IgM (microtp) to IgG3 deltaH+Cys (yielding IgG3 deltaH+Cys microtp) failed to lead to efficient oligomerization. IgG3 deltaH+Cys microtp failed to bind Fc gammaRII. However, at high concentrations it was able to bind C1q and effect complement-dependent cytolysis. It consumed complement in the absence of added Ag, indicating that removing the flexible hinge was not sufficient to yield polymeric IgG that resembled IgM in its dependence on added Ag for complement activation.
Expression of Receptor-Type Tyrosine Kinase, Axl, and its Ligand, Gas6, in Pediatric Thyroid Carcinomas Around Chernobyl (2002)

Protein-tyrosine kinases (PTKs) play a crucial role in regulating thyroid cell growth and differentiation. It is known that PTKs are activated by ionizing radiation, but the critical pathways through ionizing radiation-induced malignant transformation are not well defined. The Axl protein is a member of a new family of receptor tyrosine kinases, which the ligand, Gas6, a protein S-related molecule, has recently been identified. We previously clarified the expression of Axl and mitogenic action of Gas6 in thyroid carcinoma cells. To investigate the involvement of Gas6-Axl signaling in pediatric thyroid carcinoma further, we examined tissues obtained from 17 patients with thyroid papillary carcinomas from Gomel, Belarus, by immunohistochemistry and in situ hybridization. Axl and Gas6 were overexpressed in 76.5% and 70.6 % of cases, respectively. Solid component and invasive front tended to overexppress Gas6 and Axl in papillary carcinomas. Eighty-five percent of Axl positive cases coexpressed Gas6. In situ hybridization also confirmed the presence of axl mRNA in thyroid carcinoma tissues. These findings suggest that Axl and Gas6 expression might be involved in childhood thyroid tumorigenesis around Chernobyl.
Biological responses to polyethylene oxide modified polyethylene terephthalate surfaces (1991)

Polyethylene oxide (PEO) of molecular weights 5,000, 10,000, 18,500, and 100,000 g/mol was covalently grafted to surfaces of otherwise cell adhesive polyethylene terephthalate (PET) films. Analysis of these surfaces by measurement of contact angles and ESCA verified the presence of the grafted PEO. Protein adsorption assays of radiolabeled albumin and fibrinogen showed a marked reduction in adsorbed protein for the 18,500 and 100,000 molecular weight PEO coupled surfaces. Cell growth assays using human foreskin fibroblasts in culture showed that the higher-molecular-weight PEO surfaces supported cell growth to a much lower extent than the two lower-molecular-weight PEOs. Flow of whole blood over these surfaces and visualization of platelet adherence using epifluorescence video-microscopy showed very low platelet adherence only on the two higher-molecular-weight PEO coupled surfaces. Scanning electron microscopy corroborated these results. It was concluded that PEO of molecular weights neighboring 18,500 and higher was effective in reducing protein adsorption and cellular interactions on these surfaces.
The role of growth factors in the activity of pharmacological differentiation agents. (2002)

Bryostatin-1 inhibits acute myeloid leukemia (AML) in vitroat doses that stimulate the growth of normal hematopoietic progenitors.Although bryostatin-1 has a number of distinct biological activities, those specifically responsible for its antileukemic activity are unclear. We found that bryostatin-1 (10(-8) M) inhibited cell cycling at G(1), induced phenotypic evidence of differentiation, and limited the clonogenic growth of both AML cell lines and patient specimens. This activity was markedly enhanced by granulocyte/macrophage-colony stimulating factor, whereas growth factor-neutralizing antibodies completely inhibited both the differentiating and antileukemic activities of bryostatin-1. Cell cycle inhibition and growth factors were also required for the differentiating activities of two unrelated agents, hydroxyurea and phenylbutyrate. These data suggest that many pharmacological differentiating agents require both cell cycle arrest and lineage-specific growth factors for full activity and may explain why these agents have demonstrated only limited clinical efficacy.
Using the Mutual k-Nearest Neighbor Graphs for Semi-supervised Classification on Natural Language Data (2011)

The first step in graph-based semi-supervised classification is to construct a graph from input data. While the k-nearest neighbor graphs have been the de facto standard method of graph construction, this paper advocates using the less well-known mutual k-nearest neighbor graphs for high-dimensional natural language data. To compare the performance of these two graph construction methods, we run semi-supervised classification methods on both graphs in word sense disambiguation and document classification tasks. The experimental results show that the mutual k-nearest neighbor graphs, if combined with maximum spanning trees, consistently outperform the k-nearest neighbor graphs. We attribute better performance of the mutual k-nearest neighbor graph to its being more resistive to making hub vertices. The mutual k-nearest neighbor graphs also perform equally well or even better in comparison to the state-of-the-art b-matching graph construction, despite their lower computational complexity. 1
Waveform recognition and classification using an unsupervised network (2005)

This article describes the modified version of a neural network which learns by experience. It is enhanced with the analog signal processing capability. Basically, it is a kind of unsupervised learning neural networks, with two operating parameters-learning rate and mean square error. By using different values of the parameter, mean square error, this network can provide either an one-to-one mapping (recognition) or a clustering function (classification). Also, it needs less memory storage and takes less steps to provide stable outputs as compared with other unsupervised neural networks. This network can also accept discrete data with continuous values, so now it can recognize patterns encoded with continuous values instead of binary values. Hence, it needs much less input neurons as compared to the binary ones when dealing with patterns of the same complexity.
Reducing Complexity of HEVC: A Deep Learning Approach (2018)

High Efficiency Video Coding (HEVC) significantly reduces bit-rates over the preceding H.264 standard but at the expense of extremely high encoding complexity. In HEVC, the quad-tree partition of coding unit (CU) consumes a large proportion of the HEVC encoding complexity, due to the brute-force search for rate-distortion optimization (RDO). Therefore, this paper proposes a deep learning approach to predict the CU partition for reducing the HEVC complexity at both intra-and inter-modes, which is based on convolutional neural network (CNN) and long-and short-term memory (LSTM) network. First, we establish a large-scale database including substantial CU partition data for HEVC intra-and inter-modes. This enables deep learning on the CU partition. Second, we represent the CU partition of an entire coding tree unit (CTU) in the form of a hierarchical CU partition map (HCPM). Then, we propose an early-terminated hierarchical CNN (ETH-CNN) for learning to predict the HCPM. Consequently, the encoding complexity of intra-mode HEVC can be drastically reduced by replacing the brute-force search with ETH-CNN to decide the CU partition. Third, an early-terminated hierarchical LSTM (ETH-LSTM) is proposed to learn the temporal correlation of the CU partition. Then, we combine ETH-LSTM and ETH-CNN to predict the CU partition for reducing the HEVC complexity at inter-mode. Finally, experimental results show that our approach outperforms other state-of-the-art approaches in reducing the HEVC complexity at both intra-and inter-modes.
Lock elision for read-only critical sections in Java (2010)

It is not uncommon in parallel workloads to encounter shared data structures with read-mostly access patterns, where operations that update data are infrequent and most operations are read-only. Typically, data consistency is guaranteed using mutual exclusion or read-write locks. The cost of atomic update of lock variables result in high overheads and high cache coherence traffic under active sharing, thus slowing down single thread performance and limiting scalability.
The Physiology of L-Methionine Catabolism to the Secondary Metabolite Ethylene by Escherichia coli (1989)

Catabolism of L-methionine by Escherichia coli strain B SPAO led to the formation of ethylene as a secondary metabolite (ethylenogenesis). Methionine was initially deaminated by a transamination reaction to the 2-oxo acid 2-oxo-4-methylthiobutyric acid (KMBA) which was then converted to ethylene. The utilization of L-methionine as an additional nitrogen source was investigated by examining ethylene synthesis under different nitrogen supply conditions. Ethylene formation in batch culture was unaffected by the concentration of the precursor L-methionine in the medium although increasing concentrations of NH4Cl resulted in progressively less ethylene formation. Cultures grown without L-methionine did not produce ethylene but were able to synthesize ethylene when L-methionine or KMBA was provided. Addition of L-tyrosine to batch cultures reduced the yield of ethylene after 42 h by 54%. Under these conditions the maximum transient level of KMBA was reduced by 32% and occurred later compared to when L-methionine was the only amino acid supplement. Continuous cultures grown under ammonia limitation produced both ethylene and KMBA. In contrast, when glucose was limiting, neither of these metabolites were produced. Cells harvested from continuous cultures grown under glucose or ammonia limitation were able to synthesize ethylene from either L-methionine or KMBA although their capacity for ethylene synthesis (ethylenogenic capacity) was optimal under ammonia limitation (C:N ratio = 20).
Estrogen receptor mutations and their role in breast cancer progression (2014)

Endocrine therapy is the mainstay of treatment in estrogen receptor-positive breast cancers and significantly reduces disease recurrence and breast cancer-related mortality. However, acquired resistance to therapy has been noted in nearly one-third of women treated with tamoxifen and other endocrine therapies. Mutations in the estrogen receptor have long been speculated to play a role in endocrine therapy resistance but have been rarely detected. However, recent studies utilizing next-generation sequencing on estrogen receptor-positive, metastatic clinical samples have revealed that recurrent ESR1 mutations are far more frequent than previously thought and may play an important role in acquired endocrine therapy resistance. Here we review recent advances in detection and characterization of ESR1 mutations in advanced, endocrine therapy-resistant breast cancers.
Application of antenna arrays to mobile communications. II. Beam-forming and direction-of-arrival considerations (1997)

Array processing involves manipulation of signals induced on various antenna elements. Its capabilities of steering nulls to reduce cochannel interferences and pointing independent beams toward various mobiles, as well as its ability to provide estimates of directions of radiating sources, make it attractive to a mobile communications system designer. Array processing is expected to play an important role in fulfilling the increased demands of various mobile communications services. Part I of this paper showed how an array could be utilized in different configurations to improve the performance of mobile communications systems, with references to various studies where feasibility of apt array system for mobile communications is considered. This paper provides a comprehensive and detailed treatment of different beam-forming schemes, adaptive algorithms to adjust the required weighting on antennas, direction-of-arrival estimation methods-including their performance comparison-and effects of errors on the performance of an array system, as well as schemes to alleviate them. This paper brings together almost all aspects of array signal processing.
Sphingolipid Activator Proteins Are Required for Epidermal Permeability Barrier Formation (1999)

The epidermal permeability barrier is maintained by extracellular lipid membranes within the interstices of the stratum corneum. Ceramides, the major components of these multilayered membranes, derive in large part from hydrolysis of glucosylceramides mediated by stratum corneum beta-glucocerebrosidase (beta-GlcCerase). Prosaposin (pSAP) is a large precursor protein that is proteolytically cleaved to form four distinct sphingolipid activator proteins, which stimulate enzymatic hydrolysis of sphingolipids, including glucosylceramide. Recently, pSAP has been eliminated in a mouse model using targeted deletion and homologous recombination. In addition to the extracutaneous findings noted previously, our present data indicate that pSAP deficiency in the epidermis has significant consequences including: 1) an accumulation of epidermal glucosylceramides together with below normal levels of ceramides; 2) alterations in lipids that are bound by ester linkages to proteins of the cornified cell envelope; 3) a thickened stratum lucidum with evidence of scaling; and 4) a striking abnormality in lamellar membrane maturation within the interstices of the stratum corneum. Together, these results demonstrate that the production of pSAP, and presumably mature sphingolipid activator protein generation, is required for normal epidermal barrier formation and function. Moreover, detection of significant amounts of covalently bound omega-OH-GlcCer in pSAP-deficient epidermis suggests that deglucosylation to omega-OH-Cer is not a requisite step prior to covalent attachment of lipid to cornified envelope proteins.
Prenatal fragile X detection using cytoplasmic and nuclear-specific monoclonal antibodies (1999)

We have been carrying out studies aimed at improving prenatal detection of the fragile X chromosome/mutation. Our current protocol requires a turnaround time (TAT) of several days. In an attempt to reduce the TAT, we have turned to the use of monoclonal antibodies (mAbs). Monoclonal antibody 1A1 (provided by Dr. Mandel of INSERM) immunostaining was performed according to a modified three-step immunocytochemical procedure. We found that cytoplasmic staining intensities, using mAb 1A1/avidin biotinylated complex/diaminobenzidine, varied from light to heavy within each sample, with controls exhibiting a majority of heavily stained cells in both chorionic villus (CV) sample and amniotic fluid cultured cells. Using mAb 1A1 and a new nuclear-specific antibody, mAb 3F11, we found that CV cultured cells harboring the FMR1 full mutation could be distinguished from controls as early as 10 weeks of gestation in both male and female specimens. Western blot analysis showed that the antibodies have similar staining patterns but that mAb 3F11 has fewer background/nonspecific bands. Our results demonstrate that it is feasible to detect fragile X full mutations within one day after obtaining cells from CV specimens taken as early as 10 weeks of gestation.