gebhart/patrepeval huggingface dataset:
A comparison of computational color constancy Algorithms. II. Experiments with image data (2002)

We test a number of the leading computational color constancy algorithms using a comprehensive set of images. These were of 33 different scenes under 11 different sources representative of common illumination conditions. The algorithms studied include two gray world methods, a version of the Retinex method, several variants of Forsyth's gamut-mapping method, Cardei et al.'s neural net method, and Finlayson et al.'s Color by Correlation method. We discuss a number of issues in applying color constancy ideas to image data, and study in depth the effect of different preprocessing strategies. We compare the performance of the algorithms on image data with their performance on synthesized data. All data used for this study are available online at http://www.cs.sfu.ca/(tilde)color/data, and implementations for most of the algorithms are also available (http://www.cs.sfu.ca/(tilde)color/code). Experiments with synthesized data (part one of this paper) suggested that the methods which emphasize the use of the input data statistics, specifically color by correlation and the neural net algorithm, are potentially the most effective at estimating the chromaticity of the scene illuminant. Unfortunately, we were unable to realize comparable performance on real images. Here exploiting pixel intensity proved to be more beneficial than exploiting the details of image chromaticity statistics, and the three-dimensional (3-D) gamut-mapping algorithms gave the best performance.
EVOLUTION OF ANTIGEN BINDING RECEPTORS (1999)

This review addresses issues related to the evolution of the complex multigene families of antigen binding receptors that function in adaptive immunity. Advances in molecular genetic technology now permit the study of immunoglobulin (Ig) and T cell receptor (TCR) genes in many species that are not commonly studied yet represent critical branch points in vertebrate phylogeny. Both Ig and TCR genes have been defined in most of the major lineages of jawed vertebrates, including the cartilaginous fishes, which represent the most phylogenetically divergent jawed vertebrate group relative to the mammals. Ig genes in cartilaginous fish are encoded by multiple individual loci that each contain rearranging segmental elements and constant regions. In some loci, segmental elements are joined in the germline, i.e. they do not undergo genetic rearrangement. Other major differences in Ig gene organization and the mechanisms of somatic diversification have occurred throughout vertebrate evolution. However, relating these changes to adaptive immune function in lower vertebrates is challenging. TCR genes exhibit greater sequence diversity in individual segmental elements than is found in Ig genes but have undergone fewer changes in gene organization, isotype diversity, and mechanisms of diversification. As of yet, homologous forms of antigen binding receptors have not been identified in jawless vertebrates; however, acquisition of large amounts of structural data for the antigen binding receptors that are found in a variety of jawed vertebrates has defined shared characteristics that provide unique insight into the distant origins of the rearranging gene systems and their relationships to both adaptive and innate recognition processes.
Parameter study and design of W-band micromachined tapered slot antenna (2013)

A parameter study of a W-band micromachined tapered slot antenna shows how key structural features affect the VSWR and gain of these antennas. By properly choosing the type of taper, exponential growth rate and corrugation length, a VSWR <; 1.75 and gain > 8 dBi over W-band can be achieved.
Sacral Neuromodulation for Lower Urinary Tract Dysfunction and Impact on Erectile Function (2008)

Our study showed a clinically important benefit of sexual function mainly for neurogenic retentionists. Future research should test SNM in a larger sample of subjects, exclusively with sexual dysfunctions, in order to better understand the mechanism of action of SNM on erectile function.
Facilitation of sodium currents in frog neuroglia by nerve impulses: dependence on external calcium (1993)

Facilitation of voltage-gated sodium currents in glial membranes by nerve impulses has been studied by using both the whole cell and loose-patch clamp techniques in the isolated intact optic nerve of the frog. During facilitation there is a shift in the voltage dependence of glial Na+ channels such that a given depolarization produces a larger inward Na+ current. Decreasing external calcium from 4 times normal to 0.2 times normal produced a similar shift in the current-voltage relation. Increasing the external calcium concentration to 4-5 times normal blocks facilitation. In reduced calcium, 0.1-0.2 times normal, the peak of facilitation was unaffected, but its decay was slowed. The addition of 1 mM nickel and 2 mM cobalt or 2 mM cadmium, to prevent depletion of extracellular calcium that might result from voltage-dependent entry of calcium into the axons, did not block the facilitation. The results suggest that, even though facilitation is blocked by high extracellular calcium, a decrease in extracellular calcium produced by axon impulses is not the cause of the facilitation.
Crystal Structure of P22 Tailspike Protein: Interdigitated Subunits in a Thermostable Trimer (1994)

The tailspike protein (TSP) of Salmonella typhimurium phage P22 is a part of the apparatus by which the phage attaches to the bacterial host and hydrolyzes the O antigen. It has served as a model system for genetic and biochemical analysis of protein folding. The x-ray structure of a shortened TSP (residues 109 to 666) was determined to a 2.0 angstrom resolution. Each subunit of the homotrimer contains a large parallel beta helix. The interdigitation of the polypeptide chains at the carboxyl termini is important to protrimer formation in the folding pathway and to thermostability of the mature protein.
A Sensitive Probe for the Detection of Zn(II) by Time-Resolved Fluorescence (2006)

A new, highly sensitive fluorescent sensor for Zn(II) ion (a tris(2-pyridylmethyl)amine derivative) shows very strong binding and Zn(II) concentration-dependent biexponential time-resolved fluorescence (TRF) decay profiles that can be used for ratiometric estimates of Zn(II) concentrations. The ligand-metal complexes were characterized in solution by spectroscopic techniques and in the solid state by X-ray crystallography. The TRF studies revealed that the sensor aggregates in the absence of Zn(II) in a ligand concentration-dependent manner, a complication that is discerned by TRF but not by steady-state fluorescence ratiometric sensing techniques. It is shown that the same TRF methods are highly useful for monitoring Zn(II) concentrations in A549 epithelial lung cells in vitro and that the results were consistent with those in solution.
Temporal Role of Chemokines in a Murine Model of Cockroach Allergen-Induced Airway Hyperreactivity and Eosinophilia (1998)

The increase in inner-city asthma among children appears to be due to allergic responses to several allergens. Recent studies have demonstrated that Ags derived from cockroaches are especially prominent in these settings and a significant health concern for the induction of asthma in children. In the present study, we have outlined the development of a murine model of cockroach allergen-induced airway disease and assessed specific mechanisms of the response, which resembles atopic human asthma. The allergic responses in this model include allergen-specific airway eosinophilia and significantly altered airway physiology, which directly correlates with inflammation. We have further utilized this allergen to establish primary and secondary rechallenge stages of late phase hyperreactivity exacerbation. This latter stage is characterized by greater changes in airway physiology than the primary stage, and it is likely due to the preexisting peribronchial inflammation present at the time of the second allergen rechallenge. We have identified specific roles for CC chemokines during these stages, with MIP-1alpha being an important eosinophil attractant during the primary stage and eotaxin during the secondary rechallenge stage. The development of these models allows the evaluation of mediators involved in both stages of cockroach allergen challenge, as well as the testing of specific therapeutic modalities.
Use of the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) and related protecting groups in oligoribonucleotide synthesis: stability of internucleotide linkages to aqueous acid (1994)

The internucleotide linkage of uridylyl-(3'-->5')-uridine (r[UpU]) does not undergo detectable hydrolytic cleavage or migration in ca. 24 hr in 0.01 mol dm-3 hydrochloric acid (pH 2.0) at 25 degrees C. However, unlike r[UpU] and previously examined relatively high molecular weight oligoribonucleotides, oligouridylic acids are very sensitive to aqueous acid under the latter conditions (pH 2.0, 25 degrees C). Thus when the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp) group is used to protect the 2'-hydroxy functions in the synthesis of r[(Up)9U] and r[(Up)19U], the final unblocking process must be carried out above pH 3 if hydrolytic cleavage and migration are to be avoided. It is demonstrated that the rate of acid-catalyzed hydrolysis of the internucleotide linkages of oligoribonucleotides is sequence dependent. As Fpmp groups may be virtually completely removed from average partially-protected oligoribonucleotides within ca. 24 hr at pH 3 and 25 degrees C, it is concluded that Fpmp is a suitable 2'-protecting group even in the synthesis of particularly acid-sensitive sequences.
Cryopreservation of Human Semen: Comparison of Cryopreservatives, Sources of Variability, and Prediction of Post‐thaw Survival (1992)

Human semen was cryopreserved using Human Sperm Preservation Medium, TEST-Yolk buffer, or glycerol alone. Sperm characteristics for each specimen were measured before and after freezing to determine which cryopreservative resulted in better cryosurvival and recovery of motile sperm. Sperm frozen in Human Sperm Preservation Medium had a significantly better recovery of all semen parameters (motility, velocity, and recovery) than either TEST-Yolk or glycerol alone. Statistical analyses also were done to examine the variability between and within donor semen specimens. Differences between donors, between specimens, and measurements within donors all contributed to variability of sperm characteristics. Specimen-to-specimen variability for a given donor represented 12% to 47% of the total variability, whereas processing and measurement variability represented 12% to 41%. Donors also varied in the ability of their sperm to tolerate freezing. There was a relationship between motile count after dilution with cryopreservative and post-thaw motile count. This relationship allows the prediction of poor-thaw survival before freezing a specimen.
An efficient location cache scheme for three‐level database architecture in PCS networks (2001)

Abstract Recently, hierarchical architecture for location databases has been proposed in order to accommodate the growing number of personal communication systems users. With the three‐level hierarchical database architecture, which is compatible with the current cellular mobile systems, newly developed additional databases, including the regional location database (RLR), are positioned between the HLR and the VLRs. We propose an efficient cache scheme, the double T‐thresholds location cache scheme , which could reduce the network and database costs to lookup a portable using the three‐level architecture. This scheme extends the existing T‐threshold location cache scheme, which is effective only under the two‐level architecture of location databases currently adopted by IS‐41 and GSM. The idea behind our proposed scheme is to use two pieces of cache information, VLR and RLR, which serve the called portables. These two pieces are required in order to exploit not only the locality of a registration area (RA), but also the locality of a regional registration area (RRA), a wide area covered by the RLR. We also use two threshold values in order to determine whether the two pieces are obsolete. In order to model the RRA residence time, the branching Erlang‐∞ distribution is introduced. The cost analysis presented in this paper shows that the double T ‐thresholds location cache scheme significantly reduces the network and database costs for most patterns of portables. Copyright © 2001 John Wiley &amp; Sons, Ltd.
The Genetics of Alzheimer's Disease (1977)

Relatives of probands with histologically confirmed Alzheimer's disease had excessive morbidity from Alzheimer's disease, Down's syndrome, and hematologic malignancies. These associations coupled with two previously reported ones, the indistinguishable histopathological changes in brain in Alzheimer's disease and Down's syndrome, and the 20-fold increased incidence of leukemia among persons with Down's syndrome, are evidence that some instances of those disorders are associated with a unitary genetic etiology. The genetic defect may be expressed through disorganization of microtubules. Other evidence suggests that the same process may be involved in aging and in other chromosomal aberrations.
Further evidence localising the gene for Hunter's syndrome to the distal region of the X chromosome long arm. (1989)

Cytogenetic re-evaluation of a fibroblast cell line from a female Hunter's syndrome case with a balanced X;autosome translocation, which had previously been reported to have a breakpoint in Xq26 to Xq27, showed the breakpoint to be either between Xq27 and Xq28 or within Xq28. The normal X chromosome was preferentially inactivated, supporting the view that the translocation had disrupted the Hunter gene. The new localisation is now in full agreement with our previous linkage work and other published data. Results of further linkage studies using probes defining the loci DXS86, DXS144, DXS100, DXS102, DXS105, F8C, and DXS134 are also consistent with our original conclusion that the Hunter locus lies within the distal region of the X chromosome long arm.
Redirecting anti-viral CTL against cancer cells by surface targeting of monomeric MHC class I-viral peptide conjugated to antibody fragments. (2001)

To combine the advantage of both the tumor targeting capacity of high affinity monoclonal antibodies (mAbs) and the potent killing properties of cytotoxic T lymphocytes (CTL), we investigated the activity of conjugates made by coupling single Fab' fragments, from mAbs specific for tumor cell surface antigens, to monomeric HLA-A2 complexes containing the immunodominant influenza-matrix peptide 58-66. In solution, the monovalent 95 kDa Fab-HLA-A2/Flu conjugates did not activate influenza-specific CTL. However, when targeted to tumor cells expressing the relevant tumor-associated antigen, the conjugates induced CTL activation and efficient tumor cell lysis, as a result of MHC/peptide surface oligomerization. The highly specific and sensitive in vitro cytotoxicity results presented suggest that injection of Fab-MHC/peptide conjugates could represent a new form of immunotherapy, bridging antibody and T lymphocyte attack on cancer cells.
Gate oxide integrity (GOI) of MOS transistors with W/TiN stacked gate (2002)

With W/TiN stack gate deposited at high temperature, excellent time-dependent dielectric breakdown (TDDB) characteristics of the gate oxide were obtained in MOS capacitors. In the case of negative gate bias where thin oxide reliability becomes critical, the TiN gate provides a much longer time to breakdown than that of n/sup +/-poly gate due to a larger barrier height and less F-N tunneling current. In spite of skipping the conventional reoxidation process, a breakdown field larger than 10 MV/cm could be obtained in MOS transistors by undercutting TiN with boiling H/sub 2/SO/sub 4/. With a double spacer and undercutting scheme, the short channel effect of NMOS and PMOS transistors could be suppressed up to L/sub gate//spl sim/0.3 /spl mu/m.
Macrocyclization of Organo‐Peptide Hybrids through a Dual Bio‐orthogonal Ligation: Insights from Structure–Reactivity Studies (2012)

Macrocycles constitute an attractive structural class of molecules for targeting biomolecular interfaces with high affinity and specificity. Here, we report systematic studies aimed at exploring the scope and mechanism of a novel chemo-biosynthetic strategy for generating macrocyclic organo-peptide hybrids (MOrPHs) through a dual oxime-/intein-mediated ligation reaction between a recombinant precursor protein and bifunctional, oxyamino/1,3-amino-thiol compounds. An efficient synthetic route was developed to access structurally different synthetic precursors incorporating a 2-amino- mercaptomethyl-aryl (AMA) moiety previously found to be important for macrocyclization. With these compounds, the impact of the synthetic precursor scaffold and of designed mutations within the genetically encoded precursor peptide sequence on macrocyclization efficiency was investigated. Importantly, the desired MOrPHs were obtained as the only product from all the different synthetic precursors probed in this study and across peptide sequences comprising four to 15 amino acids. Systematic mutagenesis of the "i-1" site at the junction between the target peptide sequence and the intein moiety revealed that the majority of the 20 amino acids are compatible with MOrPH formation; this enables the identification of the most and the least favorable residues for this critical position. Furthermore, interesting trends with respect to the positional effect of conformationally constrained (Pro) and flexible (Gly) residues on the reactivity of randomized hexamer peptide sequences were observed. Finally, mechanistic investigations enabled the relative contributions of the two distinct pathways (side-chain→C-end ligation versus C-end→side-chain ligation) to the macrocyclization process to be dissected. Altogether, these studies demonstrate the versatility and robustness of the methodology to enable the synthesis and diversification of a new class of organo-peptide macrocycles and provide valuable structure-reactivity insights to inform the construction of macrocycle libraries through this chemo-biosynthetic strategy.
Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing (2012)

Nuclear RNA decay factors are involved in many different pathways including rRNA processing, snRNA and snoRNA biogenesis, pre-mRNA processing, and the rapid decay of cryptic intergenic transcripts. In contrast to its yeast counterpart, the mammalian nuclear decay machinery is largely uncharacterized. Here we report interactions of several putative components of the human nuclear RNA decay machinery, including the TRAMP complex protein Mtr4 and the nuclear exosome constituents PM/Scl-100 and PM/Scl-75, with components of the U4/U6.U5 tri-snRNP complex required for pre-mRNA splicing. The tri-snRNP component Prp31 interacts indirectly with Mtr4 and PM/Scl-100 in a manner that is dependent on the phosphorylation sites in the middle of the protein, while Prp3 and Prp4 interact with the nuclear decay complex independent of Prp31. Together our results suggest recruitment of the nuclear decay machinery to the spliceosome to ensure production of properly spliced mRNA.
Selective up-regulation of PDE1B2 upon monocyte-to-macrophage differentiation (2004)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a major regulator of monocyte to macrophage differentiation. In both humans and mice, the main phenotype of decreased GM-CSF function is pulmonary proteinosis due to aberrant function of alveolar macrophages. Recently, this cytokine has been shown to up-regulate a cyclic nucleotide phosphodiesterase, PDE1B. Two PDE1B variants with unique N-terminal sequences, PDE1B1 and PDE1B2, have been identified. Here, we report that the previously uncharacterized PDE1B2 is selectively increased by GM-CSF by stimulation of transcription at a previously unknown transcriptional start site. Analysis of the exon and intron organization of the PDE1B gene reveals that PDE1B2 has a different N-terminal sequence because of a separate first exon that is located 11.5 kb downstream from the PDE1B1 first exon. By using 5'-RACE, alignment of EST sequences, and a luciferase-reporter system, we provide evidence that PDE1B2 has a separate transcriptional start site from PDE1B1 that can be activated by monocyte differentiation. Furthermore, IL-4 treatment in the presence of GM-CSF, which shifts the differentiation from a macrophage to a dendritic cell phenotype, suppresses the up-regulation of PDE1B2. Induction of PDE1B2 is also found in T cells upon activation by PHA. Therefore, PDE1B2 may have a regulatory role in multiple immune cell types. Last, characterization of the catalytic properties of recombinant PDE1B2 shows that it prefers cGMP over cAMP as a substrate and, thus, is likely to regulate cGMP in macrophages. Also, PDE1B2 has a nearly 3-fold lower EC(50) for activation by calmodulin than PDE1B1.
Phase modulation nanoscopy: a simple approach to enhanced optical resolution (2015)

A new modular super-resolution technique called Phase Modulation Nanoscopy (PhMoNa) has been developed in order to break the optical diffraction barrier in Confocal Laser Scanning Microscopy (LSCM). This technique is based on using spatially modulated illumination intensity, whilst harnessing the fluorophore's non-linear emission response. It allows experimental resolution in both lateral and axial domains to be improved by at least a factor of 2. The work is in its initial phase, but by using a custom built Electro Optical Modulator (EOM) in conjunction with functionalised Ln(III) complexes as probes, a sub-diffraction resolution of ∼60 nm was achieved of selected cellular organelles in long term live cell imaging experiments.
Trans fatty acids (TFA): analysis, occurrence, intake and clinical relevance. (2003)

More than one quarter of total daily calories are normally provided by fatty acids which contain at least one double bond. The usual configuration of these double bonds is the cis configuration. Trans fatty acids (TFA) are formed in technological and microbiological processes by isomerization of cis double bonds to trans double bonds. In the 1990s, there was public health concern about epidemiological studies suggesting that TFA increase the risk of coronary heart disease. High intakes of TFA may have an influence on total cholesterol and other blood parameters; but on the other hand there have been a lot of studies which have not been able to confirm these results. TFA are formed in varying amounts during the industrial hydrogenation of vegetable oils and in the first stomach of ruminants. Regular margarines contain varying contents of partially hydrogenated vegetable oils, and therefore of TFA. The main dietary TFA are the trans octadecenoic acids, which contribute to approximately 80-90 % of total TFA content in foods. The predominant isomer of milk fat is trans vaccenic acid, which is directly influenced by ruminant feeding conditions. For a reliable identification and quantification of TFA in foods and other biological matrices it is necessary to use a combination of chromatographic methods (GC-FID, GC-MS, GC-FTIR, Ag superset +-HPLC).
One‐step osteochondral repair with cartilage fragments in a composite scaffold (2012)

Autologous cartilage fragments loaded onto an HA felt/FG/PRP-scaffold provided an efficient cell source, and allowed for an improvement of the repair process of ostechondral defects in a rabbit model. Human FG, however, hampered the rabbit healing process. These results may have clinical relevance as they show the potential of a novel one-stage repair technique for osteochondral defects.