gebhart/patrepeval huggingface dataset:
Smoothing-based Optimization (2008)

We propose an efficient method for complex optimization problems that often arise in computer vision. While our method is general and could be applied to various tasks, it was mainly inspired from problems in computer vision, and it borrows ideas from scale space theory. One of the main motivations for our approach is that searching for the global maximum through the scale space of a function is equivalent to looking for the maximum of the original function, with the advantage of having to handle fewer local optima. Our method works with any non-negative, possibly non-smooth function, and requires only the ability of evaluating the function at any specific point. The algorithm is based on a growth transformation, which is guaranteed to increase the value of the scale space function at every step, unlike gradient methods. To demonstrate its effectiveness we present its performance on a few computer vision applications, and show that in our experiments it is more effective than some well established methods such as MCMC, Simulated Annealing and the more local Nelder-Mead optimization method.
Investigation into the survival of epitaxial bipolar transistors in current mode second breakdown (1978)

Measurements have been obtained of the time for which epitaxial transistors are able to survive when pulsed into the current mode second breakdown condition. The results have been analysed to provide information on the nature of the constricted current distribution. The work indicates the effects that emitter geometry has on the extent of the current constriction.
The Mouse <i>Clock</i> Mutation Behaves as an Antimorph and Maps Within the <i>W19H</i> Deletion, Distal of <i>Kit</i> (1997)

Clock is a semidominant mutation identified from an N-ethyl-N-nitrosourea mutagenesis screen in mice. Mice carrying the Clock mutation exhibit abnormalities of circadian behavior, including lengthening of endogenous period and loss of rhythmicity. To identify the gene affected by this mutation, we have generated a high-resolution genetic map (> 1800 meioses) of the Clock locus. We report that Clock is 0.7 cM distal of Kit on mouse chromosome 5. Mapping shows that Clock lies within the W19H deletion. Complementation analysis of different Clock and W19H compound genotypes indicates that the Clock mutation behaves as an antimorph. This antimorphic behavior of Clock strongly argues that Clock defines a gene centrally involved in the mammalian circadian system.
Antigenic analysis of the repeat domain of the circumsporozoite protein of <i>Plasmodium vivax</i>. (1987)

In the present study we analyzed the fine specificity of mouse monoclonal and human polyclonal antibodies directed against the repeat domain of the circumsporozoite (CS) protein of the human malaria parasite, Plasmodium vivax. Five synthetic peptides, representing monomeric and dimeric repeats of this malarial antigen, were assayed for their capacity to inhibit the binding of these antibodies to a yeast-derived recombinant CS protein. The results revealed the existence of at least two distinct repeated overlapping epitopes in the CS protein of P. vivax. Furthermore, polyclonal sera contain antibodies which recognize additional determinants not represented by the synthetic repeat peptides. Some of these sera contain antibodies recognizing a region flanking the repeat domain (region I). The present findings are in contrast with the antibody response in rodents and humans to the Plasmodium falciparum CS protein, which is directed against a single repeated immunodominant epitope.
Candida Antigen Latex Test for Detection of Invasive Candidiasis in Immunocompromised Patients (1989)

Candida antigen latex agglutination testing was performed twice weekly during 217 admissions of 200 patients undergoing intensive chemotherapy alone or supported by autologous or allogeneic bone marrow transplantation. Eleven patients developed invasive candidiasis, three of whom survived; 6 (54.5%) of the 11 had positive Candida antigens. In 206 admissions, invasive candidiasis could not be documented. Of the 60 patients who died, 41 underwent autopsy examination, and 29 (71%) had positive Candida antigens. The latex test was also positive in 30 (20.5%) of the survivors and 10 (53%) of the unautopsied patients. Serum creatinine levels were greater than 2 mg/dL in 61% and 13% of patients with positive and negative Candida antigens, respectively (P less than .0001). For patients in whom the presence or absence of invasive candidiasis could be unequivocally demonstrated, the sensitivity, specificity, and positive and negative predictive values of the latex test at a titer of 1:4 were 54.5%, 29%, 17%, and 70.5%, respectively, suggesting that the latex test should not be used to diagnose invasive candidiasis in immunocompromised patients.
Isolation and characterization of an apoptosis-resistant variant of human leukemia HL-60 cells that has switched expression from Bcl-2 to Bcl-xL. (1996)

Human promyelocytic leukemia HL-60 cells treated with 8-chloroadenosine-3',5'-cyclic monophosphate (8-Cl-cAMP) undergo growth arrest and subsequently die by apoptosis. We describe here the isolation of a variant of HL-60 cells, HCW-2, which was resistant to the cytotoxic effects of 8-Cl-cAMP, but still underwent growth arrest. Thus, HCW-2 cells appeared to be altered in their ability to undergo apoptosis. HCW-2 cells were also completely refractory to the apoptotic action of cycloheximide and staurosporine, two compounds which were very potent inducers of apoptosis in the parental HL-60 cells, suggesting that the resistance to apoptosis was not unique to 8-Cl-cAMP. Western blot analysis demonstrated that the parental HL-60 cells expressed both Bcl-2 and Bax, two factors known to be intimately involved in the control of apoptosis. Surprisingly, HCW-2 cells no longer expressed Bcl-2 protein and paradoxically contained Bax protein at a level that was approximately 50-fold higher than in HL-60 cells. However, Northern and Western analyses indicated that the apoptotic suppressor gene, bcl-xL, which is not expressed in the parental HL-60 cells, was expressed in HCW-2 cells. Thus, the Bcl-2-independent resistance of HCW-2 cells to apoptotic induction is discussed in terms of the expression of bcl-xL.
Impaired CD28-mediated co-stimulation in anergic T cells (1995)

We have investigated a CD28 co-stimulation in anergic T cells in staphylococcal enterotoxin B-inoculated mice by stimulating the cells with a plate-coated anti-TCR antibody in the presence or absence of an anti-CD28 antibody. CD28 co-stimulation increased the levels of IL-2 and IL-4 mRNAs in naive CD4+V beta 8+ T cells. However, it did not increase the levels of IL-4 mRNA at all and only partially increased those of IL-2 mRNA in anergic T cells. It was demonstrated that CD28 co-stimulation was impaired so that it no longer stabilized cytokine mRNAs in anergic cells. The levels of IL-4 mRNA in response to TCR stimulation were higher in anergic T cells than those in naive T cells in spite of the defective CD28 co-stimulation in the former cells. Anergy induction and generation of a Th2-type immune response in vivo are discussed.
Identification and Characterization of a<i>Brucella abortus</i>ATP-Binding Cassette Transporter Homolog to<i>Rhizobium meliloti</i>ExsA and Its Role in Virulence and Protection in Mice (2002)

Brucella abortus is a facultative intracellular bacterial pathogen that causes abortion in domestic animals and undulant fever in humans. The mechanism of virulence of Brucella spp. is not fully understood yet. Furthermore, genes that allow Brucella to reach the intracellular niche and to interact with host cells need to be identified. Using the genomic survey sequence (GSS) approach, we identified the gene encoding an ATP-binding cassette (ABC) transporter of B. abortus strain S2308. The deduced amino acid sequence encoded by this gene exhibited 69 and 67% identity with the sequences of the ABC transporters encoded by the exsA genes of Rhizobium meliloti and Mesorhizobium loti, respectively. Additionally, B. abortus ExsA, like R. meliloti and M. loti ExsA, possesses ATP-binding motifs and the ABC signature domain features of a typical ABC transporter. Furthermore, ortholog group analysis placed B. abortus ExsA in ortholog group 6 of ABC transporters more likely to be involved in bacterial pathogenesis. In R. meliloti, ExsA is an exopolysaccharide transporter essential for alfalfa root nodule invasion and establishment of infection. To test the role of ExsA in Brucella pathogenesis, an exsA deletion mutant was constructed. Replacement of the wild-type exsA by recombination was demonstrated by Southern blot analysis of Brucella genomic DNA. Decreased survival in mice of the Brucella DeltaexsA mutant compared to the survival of parental strain S2308 demonstrated that ExsA is critical for full bacterial virulence. Additionally, the B. abortus exsA deletion mutant was used as a live vaccine. Challenge experiments revealed that the exsA mutant strain induced superior protective immunity in BALB/c mice compared to the protective immunity induced by strain S19 or RB51.
Predicting Individual Behavior with Social Networks (2013)

With the availability of social network data, it has become possible to relate the behavior of individuals to that of their acquaintances on a large scale. Although the similarity of connected individuals is well established, it is unclear whether behavioral predictions based on social data are more accurate than those arising from current marketing practices. We employ a communications network of over 100 million people to forecast highly diverse behaviors, from patronizing an off-line department store to responding to advertising to joining a recreational league. Across all domains, we find that social data are informative in identifying individuals who are most likely to undertake various actions, and moreover, such data improve on both demographic and behavioral models. There are, however, limits to the utility of social data.In particular, when rich transactional data were available, social data did little to improve prediction.
SAmBA: An interactive software for optimizing the design of biological macromolecules crystallization experiments (1997)

SAmBA is a new software for the design of minimal experimental protocols using the notion of orthogonal arrays of strength 2. The main application of SAmBA is the search of protein crystallization conditions. Given a user input defining the relevant effectors/variables (e.g., pH, temperature, salts) and states (e.g., pH: 5, 6, 7 and 8), this software proposes an optimal set of experiments in which all tested variables and the pairwise interactions between them are symmetrically sampled. No a priori restrictions on the number and range of experimental variables is imposed. SAmBA consists of two complementary programs, SAm and BA, using a simulated annealing approach and a backtracking algorithm, respectively. The software is freely available as C code or as an interactive JAVA applet at http:/(/)igs-server.cnrs-mrs.fr.
Ketoconazole in Cushing's Disease: Is It Worth a Try? (2014)

Ketoconazole is an effective drug with acceptable side effects. It should be used under close liver enzyme monitoring. Hepatotoxicity is usually mild and resolves after drug withdrawal.
Computationally efficient variational Bayesian method for <scp>PAPR</scp> reduction in multiuser <scp>MIMO</scp> ‐ <scp>OFDM</scp> systems (2019)

This paper investigates the use of the inverse-free sparse Bayesian learning (SBL) approach for peak-to-average power ratio (PAPR) reduction in orthogonal frequency-division multiplexing (OFDM)-based multiuser massive multiple-input multiple-output (MIMO) systems. The Bayesian inference method employs a truncated Gaussian mixture prior for the sought-after low-PAPR signal. To learn the prior signal, associated hyperparameters and underlying statistical parameters, we use the variational expectation-maximization (EM) iterative algorithm. The matrix inversion involved in the expectation step (E-step) is averted by invoking a relaxed evidence lower bound (relaxed-ELBO). The resulting inverse-free SBL algorithm has a much lower complexity than the standard SBL algorithm. Numerical experiments confirm the substantial improvement over existing methods in terms of PAPR reduction for different MIMO configurations.
The Effect of Ink Jet Paper Roughness on Print Gloss (2005)

Roughness of a variety of commercial Epson and Kodak ink jet papers was tested by Parker Print Surf (PPS), EMVECO stylus profilometer and Atomic Force Microscopy (AFM). The papers were printed on three Epson ink jet printers. Correlations between paper roughness and paper and print gloss were studied. From all three roughness testing methods used, the best correlation was found for AFM. Pigment based and dye based inks were found to have different effects on print gloss of Epson and Kodak papers. Topography of ink film was also studied by atomic force microscopy.
Cellular Permeability and Extracellular Formation of Glutamic Acid in Brevibacterium flavum (1963)

Journal Article Cellular Permeability and Extracellular Formation of Glutamic Acid in Brevibacterium flavum Get access ISAMU SHIIO, ISAMU SHIIO Central Research Laboratory of Ajinomoto Co., Inc.Kawasaki Search for other works by this author on: Oxford Academic PubMed Google Scholar SHIN-ICHIRO ÔTSUKA, SHIN-ICHIRO ÔTSUKA Central Research Laboratory of Ajinomoto Co., Inc.Kawasaki Search for other works by this author on: Oxford Academic PubMed Google Scholar NOBORU KATSUYA NOBORU KATSUYA Central Research Laboratory of Ajinomoto Co., Inc.Kawasaki Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Biochemistry, Volume 53, Issue 5, May 1963, Pages 333–340, https://doi.org/10.1093/oxfordjournals.jbchem.a127706 Published: 01 May 1963 Article history Received: 25 June 1962 Published: 01 May 1963
Regenerative Potential of Decellularized Porcine <i>Nucleus Pulposus</i> Hydrogel Scaffolds: Stem Cell Differentiation, Matrix Remodeling, and Biocompatibility Studies (2012)

Nucleus pulposus (NP) tissue regeneration has been proposed as an early stage interventional therapy to combat intervertebral disc degeneration. We have previously reported on the development and characterization of a novel biomimetic acellular porcine NP (APNP) hydrogel. Herein, we aimed to evaluate this material for use as a suitable scaffold for NP tissue regeneration. Human-adipose-derived stem cells (hADSCs) were cultured for 14 days on APNP hydrogels in chemically defined differentiation media and were analyzed for an NP-cell-like mRNA expression profile, evidence of hydrogel remodeling including hydrogel contraction measurements, extracellular matrix production, and compressive dynamic mechanical properties. The innate capacity of the hydrogel itself to induce stem cell differentiation was also examined via culture in media lacking soluble differentiation factors. Additionally, the in vivo biocompatibility of non-crosslinked and ethyldimethylaminopropyl carbodiimide/N-hydroxysuccinimide and pentagalloyl glucose crosslinked hydrogels was evaluated in a rat subdermal model. Results indicated that hADSCs expressed putative NP-cell-positive gene transcript markers when cultured on APNP hydrogels. Additionally, glycosaminoglycan and collagen content of hADSC-seeded hydrogels was significantly greater than nonseeded controls and cell-seeded hydrogels exhibited evidence of contraction and tissue inhibitors of metalloproteinase-1 production. The dynamic mechanical properties of the hADSC-seeded hydrogels increased with time in culture in comparison to noncell-seeded controls and approached values reported for native NP tissue. Immunohistochemical analysis of explants illustrated the presence of mononuclear cells, including macrophages and fibroblasts, as well as blood vessel infiltration and collagen deposition within the implant interstices after 4 weeks of implantation. Taken together, these results suggest that APNP hydrogels, in concert with autologous ADSCs, may serve as a suitable scaffold for NP tissue regeneration.
Assessment of human colorectal biopsies by <sup>1</sup>H MRS: Correlation with histopathology (1993)

Samples (3 mm3) of histopathologically normal (n = 15) and carcinomatous tissue (n = 15) were obtained from colectomy specimens and examined by 1H MRS. A combination of one- and two-dimensional spectra, obtained with appropriate acquisition and processing parameters, provide multiple diagnostic parameters allowing the distinction between normal and carcinomatous tissue. The diagnostic parameters include resonances from choline, choline-based, and other metabolites, cell surface fucosylation, and altered lipid profiles. Tissues histopathologically classified as normal, while remaining distinct from the malignant spectral profile, were found to fit into two categories, one of which had some of the spectral characteristics of malignancy. These results indicate that 1H MRS identifies abnormal colorectal mucosa, which is not morphologically manifest. Such abnormalities have been reported previously to exist in premalignant colorectal tissue by monoclonal antibody studies. Collectively, these results suggest that a clinical study of colorectal biopsies by 1H MRS could provide support for the use of MRS as an adjunct to current pathological procedures.
Novel therapy for therapy‐resistant mantle cell lymphoma: Multipronged approach with targeting of hedgehog signaling (2012)

Mantle cell lymphoma (MCL) is one of the most aggressive B-cell lymphomas with a median patient survival of only 5-7 years. The failure of existing therapies is mainly due to disease relapse when therapy-resistant tumor cells remain after chemotherapy. Therefore, development and testing of novel therapeutic strategies to target these therapy-resistant MCL are needed. Here, we developed an in vivo model of therapy-resistant MCL by transplanting a patient-derived MCL cell line (Granta 519) into NOD/SCID mice followed by treatment with combination chemotherapy. Cytomorphologic, immunophenotypic, in vitro and in vivo growth analyses of these therapy-resistant MCL cells confirm their MCL origin and resistance to chemotherapy. Moreover, quantitative real-time PCR revealed the upregulation of GLI transcription factors, which are mediators of the hedgehog signaling pathway, in these therapy-resistant MCL cells. Therefore, we developed an effective therapeutic strategy for resistant MCL by treating the NOD/SCID mice bearing Granta 519 MCL with CHOP chemotherapy to reduce tumor burden combined with GLI-antisense oligonucleotides or bortezomib, a proteosome inhibitor, to target therapy-resistant MCL cells that remained after chemotherapy. This regimen was followed by treatment with MCL-specific cytotoxic T lymphocytes to eliminate all detectable leftover minimal residual disease. Mice treated with this strategy showed a significantly increased survival and decreased tumor burden compared to the mice in all other groups. Such therapeutic strategies that combine chemotherapy with targeted therapy followed by tumor-specific immunotherapy are effective and have excellent potential for clinical application to provide long-term, disease-free survival in MCL patients.
Adaptive Slave Controller Assignment for Fault-Tolerant Control Plane in Software-Defined Networking (2018)

Multi-controller is a promising control plane solution for the large-scale Software-Defined Networks (SDN). Some existing works (e.g., OpenFlow 1.2) propose to use backup controllers named slave controllers to achieve fault- tolerance in the control plane. In this paper, we identify the unreasonable slave controller assignment could cause the controller chain failure and eventually crash the entire network. We consider some important factors for designing fault-tolerant control plane and formulating Slave Controller Assignment (SCA) problem. SCA is an NP-complete problem, and we solve it with Adaptive Slave Controller Assignment (ASCA) scheme, which adaptively assigns slave controller according to load variance difference. The numerical results validate the efficiency of ASCA.
PREDICTING KEY POLYMER PROPERTIES TO REDUCE EROSION IN IRRIGATED SOIL (1994)

The ability to understand and/or predict the physical properties of polymers is important in efforts to help reduce erosion in irrigated land by treating irrigation water with minute amounts of certain polymers. The key properties of polymers for this application (water solubility and water absorption capability, dilute solution properties, and stability) are discussed. Methods used to predict the properties of polymers include quantitative structure-property relationships, statistical mechanical theories, atomistic simulations, and quantum mechanical calculations. Each general method is best applied to different types of problems. For example, combination of quantum mechanical calculations and atomistic simulations may shed light on the solution conformation of a polymer and hence on its soil activity. On the other hand, a new method, based mainly on topological descriptors called connectivity indices, predicts key polymer physical properties very rapidly from the structures of polymeric repeat units via empirical and semi-empirical quantitative structure-property relationships. This new method can be used for the overall evaluation of the potential of candidate polymers for erosion reduction. Applications of this method to polyacrylamide and structural variants and copolymers are discussed. An outlook is provided for the future of applications of computational chemistry to water-soluble polymers. It is suggested that significant future advances can be expected from further developments of each of the different types of theoretical methods, as well as from their more synergistic and interdisciplinary utilization
Fetal and adult hemoglobin production during adult erythropoiesis: coordinate expression correlates with cell proliferation (2002)

The design and evaluation of therapies for the sickle cell and beta-thalassemia syndromes rely on our understanding of hemoglobin accumulation during human erythropoiesis. Here we report direct measurements of hemoglobin composition and messenger RNA (mRNA) levels in cultured CD34(+) cells and correlate those measurements with studies of freshly obtained bone marrow samples. Hemoglobin levels in differentiating cells were also compared with morphologic, immunophenotypic, and cell cycle assessments. A population of large preproerythroblasts was first identified within 24 hours and became the dominant population by day 5. The transition from proerythroblast to basophilic normoblast occurred later, from days 7 to 9, and correlated with a peak of 74.1% +/- 3.9% of the cells in the S phase of cell cycle. Orthochromatic normoblasts were the dominant and final cell type by day 13. High-performance liquid chromatography-based quantitation of fetal (HbF) and adult (HbA) hemoglobin and real-time polymerase chain reaction globin mRNA quantitation demonstrated a coordinate rise in the accumulation of both proteins and mRNA among these developmentally staged populations. Quantitative analyses on freshly sorted bone marrow populations demonstrated a similar rising pattern with beta-globin and HbA as the dominant species at both early and late stages of differentiation. We found no evidence for HbF dominant populations or switching during differentiation in adult cells. Instead, rapid increases in both HbF (heterocellular) and HbA (pancellular) content were observed, which coincided with the apex in cell cycling and the proerythroblast-basophilic normoblast transition. Based on these measurements, we conclude that HbF and HbA content are regulated with the rate of proliferation during adult erythropoiesis.