gebhart/patrepeval huggingface dataset:
<title>Ultimate Q of optical microsphere resonators</title> (1996)

We demonstrate the quality factor Q equals (0.8 plus or minus 0.1) multiplied by 10<SUP>10</SUP> of whispering-gallery modes in fused silica microspheres at 633 nm, close to the limit determined by fundamental material attenuation. The lifetime of ultimate Q is limited by adsorption of atmospheric water. Optical effects of adsorption are investigated and conditions for fabrication of long-lifetime microspheres are clarified.
Expression Cloning and Characterization of a Transporter for Large Neutral Amino Acids Activated by the Heavy Chain of 4F2 Antigen (CD98) (1998)

A cDNA was isolated from rat C6 glioma cells by expression cloning which encodes a novel Na+-independent neutral amino acid transporter designated LAT1. For functional expression in Xenopus oocytes, LAT1 required the heavy chain of 4F2 cell surface antigen (CD98), a type II membrane glycoprotein. When co-expressed with 4F2 heavy chain, LAT1 transported neutral amino acids with branched or aromatic side chains and did not accept basic amino acids or acidic amino acids. The transport via LAT1 was Na+-independent and sensitive to a system L-specific inhibitor 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid. These functional properties correspond to those of the classically characterized amino acid transport system L, a major nutrient transporter. In in vitro translation, LAT1 was shown to be a nonglycosylated membrane protein consistent with the property of 4F2 light chain, suggesting LAT1 is at least one of the proteins formerly referred to as 4F2 light chain. LAT1 exhibits relatively low but significant amino acid sequence similarity to mammalian cationic amino acid transporters and amino acid permeases of bacteria and yeasts, indicating LAT1 is a new member of the APC superfamily. Because of highly regulated nature and high level of expression in tumor cell lines, LAT1 is thought to be up-regulated to support the high protein synthesis for cell growth and cell activation. The cloning of LAT1 is expected to facilitate the research on the protein-protein interaction in the transporter field and to provide a clue to the search for still unidentified transporters.
Electron spin resonance of pulsed plasma-enhanced chemical vapor deposited fluorocarbon films (1997)

Pulsed-rf excitation of hexafluoropropylene oxide has been used to deposit poly(tetrafluoroethylene)-like thin films. Films were deposited at pulse rates of 10/20, 10/50, 10/200, and 10/400 ms on/ms off and analyzed using electron spin resonance spectroscopy (ESR). All four films produced similar broad ESR spectra, with an average width at maximum slope of ∼60 G and a g value of 2.0045. The number of free electrons in a sample decreased with increasing pulse off time. This behavior can be modeled by the reaction of a free radical with a gas species, assuming that free radicals are generated only during the pulse on time.
Human fetal hippocampal development: II. The neuronal cytoskeleton (1996)

In this study of the developing human hippocampus, we monitor the timing of onset and the sequential patterns of expression of 11 developmentally regulated proteins that are important components of the neuronal cytoskeleton. Immunohistochemistry using well-characterized antibodies was conducted with fixed paraffin-embedded sections from hippocampi at various stages of fetal and postnatal development. At 9 weeks gestational age, immunoreactivity was evident for the microtubule-associated proteins (MAPs), MAP2 and MAP5, low molecular weight (Mr) neurofilament (NF) protein (NF-L), poorly phosphorylated mid-Mr NF protein (NF-M/P-), vimentin, and alpha-and beta-tubulins within the somatodendritic domain of neurons of the hippocampal plate. Weak immunoreactivity for moderately phosphorylated, high Mr NF protein (NF-H/P + + +), tau, and nestin was observed. Highly phosphorylated mid-Mr NF protein (NF-M/P + + +) and alpha-internexin were first detected at 15 weeks and highly phosphorylated, high Mr NF protein (NF-H/P+3) at 20 weeks. At 15 weeks, MAP2, MAP5, and tubulins were expressed in an "inside-out" gradient and in a gradient between hippocampal subfields with subiculum > ammonic subfields > dentate gyrus. These gradients paralleled the maturational gradients seen in cytoarchitectural and neuronal morphologic studies. The adult pattern of neuronal cytoskeletal protein expression in the hippocampus was attained by the second postnatal year for all proteins. Our findings demonstrate an elaborate orchestration of cytoskeletal protein expression within the hippocampus that is qualitatively similar to what is seen in other brain regions and in nonhuman species but which also has some important differences in timing and pattern. The differences in the developmentally regulated expression of neuronal cytoskeletal proteins in separate regions of the central nervous system (CNS) suggest that there are region-specific differences in composition and function of the neuronal cytoskeleton. These observations have implications for understanding the role of the neuronal cytoskeleton in the developing, mature, and diseased CNS.
Controlled synthesis of dendritic Au@Pt core–shell nanomaterials for use as an effective fuel cell electrocatalyst (2008)

We report the controlled synthesis of dendritic Au@Pt core-shell nanomaterials. The size and morphology of the Au cores and the Pt shell thickness of the Au@Pt core-shell nanostructures could be easily tuned. It was found that the directing agent and the reducing agent play critical roles in the synthesis of dendritic Au@Pt core-shell nanomaterials. For comparison purposes, conventional Au@Pt core-shell nanoparticles and monometallic Pt nanoparticles were also synthesized by the successive reduction method. Transmission electron microscopy (TEM) observations demonstrated the dendritic surface of the products obtained. The UV-visible (UV-vis) spectroscopy results and a comparison of the average diameter between the dendritic Au@Pt and conventional Au@Pt confirmed the relatively loose Pt shells around Au cores for the dendritic Au@Pt. The as-prepared dendritic Au@Pt showed enhanced electrocatalytic activity for methanol oxidation in acid medium, compared to the conventional Au@Pt and monometallic Pt.
Chimeric Molecules between Keratinocyte Growth Factor and Basic Fibroblast Growth Factor Define Domains That Confer Receptor Binding Specificities (1995)

Basic fibroblast growth factor (FGF) and keratinocyte growth factor (KGF) are structurally related fibroblast growth factors, yet they exhibit distinct receptor binding specificity. Basic FGF binds with high affinity to FGFR1, FGFR2, and FGFR4, whereas KGF does not interact with these receptors and can only bind an isoform of FGFR2 known as the KGFR. Basic GFG binds KGFR but with lower affinity than KGF. In order to identify domains that confer this specificity, four reciprocal chimeras were generated between the two growth factors and were analyzed for receptor recognition and biological activity. The chimeras are designated BK1 (bFGF1-54:KGF91-194), BK2 (bFGF1-74:KGF111-194), KB1 (KGF31-90:bFGF55-155), and KB2 (KGF31-110:bFGF75-155). The two BK chimera similarly interacted with FGFR1 and FGFR4 but differed from each other with respect to KGFR recognition. BK1 displayed a slightly better affinity for KGFR than BK2 and induced a higher level of DNA synthesis in keratinocytes compared with bFGF and BK2. A neutralizing monoclonal antibody directed against bFGF specifically neutralized the biological activity of the BK chimeras. The reciprocal chimeras, KB1 and KB2, exhibited KGF-like receptor binding and activation properties. However, KB2 displayed higher affinity for KGFR and was significantly more potent mitogen that KB1. Altogether, our results suggest that the amino-terminal part of KGF and bFGF plays an important role in determining their receptor binding specificity. In addition, the results point to the contribution of a segment from the middle part of KGF (residues 91-110) for recognition and activation of the KGFR, as the two chimeras containing these residues (BK1 and KB2) displayed an enhanced interaction with the KGFR.
The chemical basis of morphogenesis (1952)

Abstract It is suggested that a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis. Such a system, although it may originally be quite homogeneous, may later develop a pattern or structure due to an instability of the homogeneous equilibrium, which is triggered off by random disturbances. Such reaction-diffusion systems are considered in some detail in the case of an isolated ring of cells, a mathematically convenient, though biologically unusual system. The investigation is chiefly concerned with the onset of instability. It is found that there are six essentially different forms which this may take. In the most interesting form stationary waves appear on the ring. It is suggested that this might account, for instance, for the tentacle patterns on Hydra and for whorled leaves. A system of reactions and diffusion on a sphere is also considered. Such a system appears to account for gastrulation. Another reaction system in two dimensions gives rise to patterns reminiscent of dappling. It is also suggested that stationary waves in two dimensions could account for the phenomena of phyllotaxis. The purpose of this paper is to discuss a possible mechanism by which the genes of a zygote may determine the anatomical structure of the resulting organism. The theory does not make any new hypotheses; it merely suggests that certain well-known physical laws are sufficient to account for many of the facts. The full understanding of the paper requires a good knowledge of mathematics, some biology, and some elementary chemistry. Since readers cannot be expected to be experts in all of these subjects, a number of elementary facts are explained, which can be found in text-books, but whose omission would make the paper difficult reading.
Deep Variational Information Bottleneck (2016)

We present a variational approximation to the information bottleneck of Tishby et al. (1999). This variational approach allows us to parameterize the information bottleneck model using a neural network and leverage the reparameterization trick for efficient training. We call this method "Deep Variational Information Bottleneck", or Deep VIB. We show that models trained with the VIB objective outperform those that are trained with other forms of regularization, in terms of generalization performance and robustness to adversarial attack.
Ammonium Acetate-Basic Alumina Catalyzed Knoevenagel Condensation Under Microwave Irradiation Under Solvent-Free Condition (2000)

Abstract Ammonium acetate and basic alumina catalyzed efficiently the Knoevenagel condensation of aldehydes and ketones with active methylene compounds under solvent-free condition where olefinic products were obtained in high yields.
Mucin production by colon cancer cells cultured in serum‐free medium (1991)

Although many colon cancer cell lines are available for study, few of them exhibit differentiated properties. When cultured in medium containing fetal bovine serum, WiDr cells (WiDr-FBS) show an undifferentiated phenotype: growth as a multilayer of cells adherent to plastic and lack of polarization, brush border, and mucin vacuoles. In contrast, WiDr cells cultured in a chemically-defined serum-free medium containing insulin, transferrin and selenium (WiDr-ITS) grow as clusters of nonadherent cells with abundant desmosomes and tight junctions, microvilli and electron-lucid vacuoles. As WiDr-FBS cells, WiDr-ITS are not polarized. WiDr-ITS cells show a marked enhancement in mucin synthesis as demonstrated by: periodic acid-Schiff and Alcian blue stains, electron microscopy, immunohistochemistry using monoclonal antibodies (MAbs) reactive with mucin-associated epitopes, immune electron microscopy and immunochemical analysis using Western blots. In comparison with WiDr-FBS cells, WiDr-ITS cells showed strong expression of Tn, sialyl-Tn, blood group A and CEA. When mouse MAbs were used, higher levels of the MUCI gene product were detected in WiDr-ITS than in WiDr-FBS cells. The full spectrum of phenotypic changes was observed after I month of culture in ITS medium, and transfer of WiDr-ITS cells to FBS medium was accompanied by a partial phenotypic reversal, suggesting that these phenotypic changes result from an adaptative--rather than selective--process.
Limitations of clonality analysis of B cell proliferations using CDR3 polymerase chain reaction (2000)

The minimum amount of template for CDR3 PCR is approximately 20 ng of high molecular weight DNA or 1 mm3 of B cell rich paraffin wax embedded normal tonsillar tissue, but care has to be taken to avoid pseudoclonality when low numbers of B cells are present. Duplicate or triplicate tests should be performed to avoid misinterpretation. The specificity of the PCR assay is almost 100%, whereas sensitivity depends on a combination of factors, such as lymphoma type and tissue fixation. Because frozen samples yield better results, obtaining fresh material for the PCR assay is recommended, especially when analysing FL and MALT lymphomas.
Dry Eye as a Major Complication Associated with Chronic Graft-Versus-Host Disease after Hematopoietic Stem Cell Transplantation (2003)

We report a significant role for stromal fibroblasts in the pathogenic processes of dry eye related to chronic GVHD. Although several supportive therapies can reduce the symptoms, specific therapies that suppress fibrotic and immune processes in the lacrimal glands are necessary to control dry eye associated with chronic GVHD.
Characterization of humoral immunity after DNA injection. (1994)

Antibodies to the influenza virus nucleoprotein are produced after injection of a plasmid DNA expression vector containing the nucleoprotein gene. A single injection of 10 to 100 micrograms of DNA produces IgG antibodies which first appear four to six weeks post injection. Antibody titres peak at six to eight weeks and then remain stable in most animals for many months. The antibody response at early times is dose-dependent, with higher amounts of DNA producing a faster immune response as well as higher antibody titres. Titres observed many months after injection are less dependent on DNA dose.
YY1 Facilitates the Association of Serum Response Factor with the c- fos Serum Response Element (1995)

YY1 is a multifunctional transcription factor that acts as an activator or repressor in different contexts. YY1 binds to multiple sites in the mouse c-fos promoter, inducing at each site a sharp DNA bend. Binding of YY1 to a site situated between the cyclic AMP response element (CRE) and the TATA box bends the DNA in a way that interferes with the interaction of proteins bound at the CRE and TATA elements, resulting in repression of transcription. Here, we show that binding of YY1 to a different site in the c-fos promoter has a different result. Binding of YY1 to the c-fos serum response element (SRE) enhances the binding of serum response factor (SRF). This enhancement requires the binding of YY1 to SRE DNA. YY1 and SRF can cooccupy the SRE at least transiently. In the region of overlapping contact, YY1 contacts DNA in the major groove, while SRF contacts DNA in the minor groove. YY1 also enhances the association of SRF with the SRE in transfected insect cells. Thus, although YY1 induces similar structural changes in DNA at different binding sites, it can have distinct local effects on protein-DNA and protein-protein interactions. These data support a general role for YY1 in the building of highly organized promoter complexes.
Nitric Oxide-Induced Decrease in Calcium Sensitivity of Resistance Arteries Is Attributable to Activation of the Myosin Light Chain Phosphatase and Antagonized by the RhoA/Rho Kinase Pathway (2003)

NO dilates RA by activating the MLCP in a cGMP-dependent manner, thereby reducing the apparent Ca2+ sensitivity of the contractile apparatus. MLCP inactivation via the RhoA/Rho kinase pathway antagonizes this Ca2+-desensitizing effect that, in turn, can be restored using RhoA/Rho kinase inhibitors.
Modified vaccinia virus Ankara for delivery of human tyrosinase as melanoma-associated antigen: induction of tyrosinase- and melanoma-specific human leukocyte antigen A*0201-restricted cytotoxic T cells in vitro and in vivo. (1999)

Vaccination with tumor-associated antigens is a promising approach for cancer immunotherapy. Because the majority of these antigens are normal self antigens, they may require suitable delivery systems to promote their immunogenicity. A recombinant vector based on the modified vaccinia virus Ankara (MVA) was used for expression of human tyrosinase, a melanoma-specific differentiation antigen, and evaluated for its efficacy as an antitumor vaccine. Stable recombinant viruses (MVA-hTyr) were constructed that have deleted the selection marker lacZ and efficiently expressed human tyrosinase in primary human cells and cell lines. Tyrosinase-specific human CTLs were activated in vitro by MVA-hTyr-infected, HLA-A*0201-positive human dendritic cells. Importantly, an efficient tyrosinase- and melanoma-specific CTL response was induced in vitro using MVA-hTyr-infected autologous dendritic cells as activators for peripheral blood mononuclear cells derived from HLA-A*0201-positive melanoma patients despite prior vaccination against smallpox. Immunization of HLA-A*0201/Kb transgenic mice with MVA-hTyr induced A*0201-restricted CTLs specific for the human tyrosinase-derived peptide epitope 369-377. These in vivo primed CTLs were of sufficiently high avidity to recognize and lyse human melanoma cells, which present the endogenously processed tyrosinase peptide in the context of A*0201. Tyrosinase-specific CTL responses were significantly augmented by repeated vaccination with MVA-hTyr. These findings demonstrate that HLA-restricted CTLs specific for human tumor-associated antigens can be efficiently generated by immunization with recombinant MVA vaccines. The results are an essential basis for MVA-based vaccination trials in cancer patients.
Multimodal affect recognition in learning environments (2005)

We propose a multi-sensor affect recognition system and evaluate it on the challenging task of classifying interest (or disinterest) in children trying to solve an educational puzzle on the computer. The multimodal sensory information from facial expressions and postural shifts of the learner is combined with information about the learner's activity on the computer. We propose a unified approach, based on a mixture of Gaussian Processes, for achieving sensor fusion under the problematic conditions of missing channels and noisy labels. This approach generates separate class labels corresponding to each individual modality. The final classification is based upon a hidden random variable, which probabilistically combines the sensors. The multimodal Gaussian Process approach achieves accuracy of over 86%, significantly outperforming classification using the individual modalities, and several other combination schemes.
Sequential synthesis of 5'-proximal vesicular stomatitis virus mRNA sequences (1982)

We examined the kinetics of synthesis in vitro of the 5' ends of the vesicular stomatitis virus mRNAs by analysis of specific RNase T1 oligonucleotides located near the 5' ends of the mRNAs. Our results indicate that, like synthesis of full-length mRNAs, the 5' ends of the mRNAs are synthesized sequentially, following the gene order N, NS, and M. Additional experiments with UV-irradiated virus demonstrated that synthesis of the mRNA regions containing these oligonucleotides is dependent on synthesis of the mRNA from the preceding gene. These results are inconsistent with a model of vesicular stomatitis virus transcription involving simultaneous initiation and presynthesis of leader RNAs 30 to 70 nucleotides long for each mRNA. We also characterized two small RNA species whose synthesis is highly resistant to UV irradiation. Partial sequence analysis indicates that these RNAs are a 5'-capped fragment of the N mRNA and a 5' fragment of the leader RNA.
Translation of Vascular Endothelial Growth Factor mRNA by Internal Ribosome Entry: Implications for Translation under Hypoxia (1998)

Vascular endothelial growth factor (VEGF) is a hypoxia-inducible angiogenic growth factor that promotes compensatory angiogenesis in circumstances of oxygen shortage. The requirement for translational regulation of VEGF is imposed by the cumbersome structure of the 5' untranslated region (5'UTR), which is incompatible with efficient translation by ribosomal scanning, and by the physiologic requirement for maximal VEGF production under conditions of hypoxia, where overall protein synthesis is compromised. Using bicistronic reporter gene constructs, we show that the 1,014-bp 5'UTR of VEGF contains a functional internal ribosome entry site (IRES). Efficient cap-independent translation is maintained under hypoxia, thereby securing efficient production of VEGF even under unfavorable stress conditions. To identify sequences within the 5'UTR required for maximal IRES activity, deletion mutants were analyzed. Elimination of the majority (851 nucleotides) of internal 5'UTR sequences not only maintained full IRES activity but also generated a significantly more potent IRES. Activity of the 163-bp long "improved" IRES element was abrogated, however, following substitution of a few bases near the 5' terminus as well as substitutions close to the translation start codon. Both the full-length 5'UTR and its truncated version function as translational enhancers in the context of a monocistronic mRNA.
Mitogenic Properties of Fab and F(ab′)2 Fragments of Rabbit Anti‐Human β2‐Microglobulin for Human Lymphocytes (1977)

Bivalent F(ab')2 fragments and monovalent Fab fragments of rabbit anti-human beta2-microglobulin (anti-beta2m) stimulated DNA synthesis in human lymphocytes. Mitogenicity of anti-beta2m antibodies can therefore be ascribed to the antigen-binding site and not to the Fc portion of the molecule. The mitogenic response to F(ab')2, and sometimes Fab, fragments of anti-beta2m IgG was comparable to that obtained with original IgG antibodies when tested at the same protein concentration. Since Fab monomers of anti-beta2m can cause lymphocyte activation, 'cross-linking' of hypothetical beta2-microblobulin-containing lymphocyte receptors does not seem necessary for activation. F(ab')2, as well as Fab, fragments of anti-beta2m blocked the cytotoxic effect of anti-beta2m IgG, showing that the fragments did indeed react with beta2-microblobulin on the cell surface. F(ab')2 dimers, but not Fab monomers, of anti-beta2m were capable of inhibiting the cytotoxic effect of an anti-HLA-A2 antiserum. The mitogenic activity of both anti-beta2m IgG and Fab monomers of such antibodies disappeared after absorption with highly purified beta2-microblobulin. The mitogenic effect of anti-beta2m IgG was inhibited to a minor extent by exposure of cells to high concentrations of pooled multispecific anti-HLA antibodies. This effect was probably nonspecific.
Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA. (1984)

Plasmids containing (C-G)n inserts have been used to study the inhibition of cleavage by restriction endonucleases due to Z-DNA formation in negatively supercoiled plasmids. The enzyme BssHII, which recognizes G-C-G-C-G-C, is strongly inhibited when the insert forms Z-DNA. The BamHI recognition sequence (G-G-A-T-C-C) was placed in four different positions near the B-Z junction and the inhibition of BamHI cleavage was determined as a function of negative superhelical density. Formation of Z-DNA in the (C-G)n insert inhibited cleavage by BamHI when its recognition sequence was located immediately adjacent to the insert or four base pairs away from it. However, no inhibition was found when the BamHI recognition site was eight base pairs away. These experiments help to define the limits of the structural perturbation associated with the B-Z junction.