gebhart/patrepeval huggingface dataset:
Deficiency of p53 accelerates mammary tumorigenesis in Wnt-1 transgenic mice and promotes chromosomal instability. (1995)

By crossing mice that carry a null allele of p53 with transgenic mice that develop mammary adenocarcinomas under the influence of a Wnt-1 transgene, we have studied the consequences of p53 deficiency in mammary gland neoplasia. In Wnt-1 transgenic mice homozygous for the p53 null allele, tumors appear at an earlier age than in animals heterozygous or wild-type at the p53 locus. About half of the tumors arising in p53 heterozygotes exhibit loss of the normal p53 allele, implying selection for p53-deficient cells. Mammary tumors lacking p53 display less fibrotic histopathology and increased genomic instability with aneuploidy, amplifications, and deletions, as detected by karyotype analysis and comparative genomic hybridization. In one tumor, the amplified region of chromosome 7 had an ectopically expressed int-2/FGF3 proto-oncogene, a gene known to cooperate with Wnt-1 in the production of mammary tumors. These findings favor a model in which p53 deficiency relaxes normal restraints on chromosomal number and organization during tumorigenesis.
The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents That Inhibit Uncoating (1986)

WIN 51711 and WIN 52084 are structurally related, antiviral compounds that inhibit the replication of rhino (common cold) viruses and related picornaviruses. They prevent the p H-mediated uncoating of the viral RNA. The compounds consist of a 3-methylisoxazole group that inserts itself into the hydrophobic interior of the VP1 β-barrel, a connecting seven-membered aliphatic chain, and a 4-oxazolinylphenoxy group (OP) that covers the entrance to an ion channel in the floor of the "canyon." Viral disassembly may be inhibited by preventing the collapse of the VP1 hydrophobic pocket or by blocking the flow of ions into the virus interior.
Molecular cloning, epigenetic regulation, and functional characterization of Prkd1 gene promoter in dopaminergic cell culture models of Parkinson's disease (2015)

We recently identified a compensatory survival role for protein kinase D1 (PKD1) in protecting dopaminergic neurons from oxidative insult. To investigate the molecular mechanism of Prkd1 gene expression, we cloned the 5'-flanking region (1620-bp) of the mouse Prkd1 gene. Deletion analyses revealed that the -250/+113 promoter region contains full promoter activity in MN9D dopaminergic neuronal cells. In silico analysis of the Prkd1 promoter uncovered binding sites for key redox transcription factors including Sp1 and NF-κB. Over-expression of Sp1, Sp3, and NF-κB-p65 proteins stimulated Prkd1 promoter activity. Binding of Sp3 and NF-κB-p65 to the Prkd1 promoter was confirmed using chromatin immunoprecipitation. Treatment with the Sp inhibitor mithramycin A significantly attenuated Prkd1 promoter activity and PKD1 mRNA and protein expression. Further mechanistic studies revealed that inhibition of histone deacetylation and DNA methylation up-regulated PKD1 mRNA expression. Importantly, negative modulation of PKD1 signaling by pharmacological inhibition or shRNA knockdown increased dopaminergic neuronal sensitivity to oxidative damage in a human mesencephalic neuronal cell model. Collectively, our findings demonstrate that Sp1, Sp3, and NF-κB-p65 can transactivate the mouse Prkd1 promoter and that epigenetic mechanisms, such as DNA methylation and histone modification, are key regulatory events controlling the expression of pro-survival kinase PKD1 in dopaminergic neuronal cells. Previously, we demonstrated that protein kinase D1 (PKD1) plays a survival role during the early stage of oxidative stress in dopaminergic neuronal cells.
Human brain fibroblast growth factor (1985)

Fibroblast growth factor (FGF) has been purified to homogeneity from human brain by a procedure involving salt precipitation, cation-exchange chromatography, Heparin-Sepharose affinity chromatography and reverse-phase HPLC. Isolation was monitored by radioimmunoassay and/or by testing column fractions for their capacity to stimulate the proliferation of vascular endothelial cells in vitro. The amino-terminal sequence of human brain FGF was determined as Pro-Ala-Leu-Pro-Glu-Asp-Gly-Gly-Ser-Gly-Ala-Phe-Pro-. This sequence is identical to that of the amino-terminal region of bovine FGF. Additional evidence, including amino acid composition, chromatographic retention behavior, and immunoreactivity suggest that the human and bovine mitogens are very similar in structure.
Dynamics based 3D skeletal hand tracking (2013)

Natural human computer interaction motivates hand tracking research, preferably without requiring the user to wear special hardware or markers. Ideally, a hand tracking solution would provide not only points of interest, but the full state of an entire hand. [Oikonomidis et al. 2011] demonstrated a particle swarm optimization that tracked a 3D skeletal hand model from a single depth camera, albeit using significant computing resources. In contrast, we track the hand from a single depth camera using an efficient physical simulation, which incrementally updates a model's fit and explores alternative candidate poses based on a variety of heuristics. Our approach enables real-time, robust 3D skeletal tracking of a user's hand, while utilizing a single x86 CPU core for processing.
Addition to Carbon–Hetero Multiple Bonds (2006)

This chapter contains sections titled: Mechanism and Reactivity Reactions Reactions in Which Hydrogen or a Metallic Ion Adds to the Heteroatom Acyl Substitution Reactions Reactions in Which Carbon Adds to the Heteroatom Addition to Isocyanides2124 Nucleophilic Substitution at a Sulfonyl Sulfur Atom2138
Design, Synthesis, and Biological Activity of Novel Polycyclic Aza-Amide FKBP12 Ligands (2006)

Since the discovery that FK-506 promotes neurite outgrowth, considerable attention has been focused on the development of potent nonimmunosuppressive ligands for FK-506 binding proteins (FKBPs). Such neuroimmunophilin agents have been reported to show neuroregenerative activity in a variety of cell and animal models including neurite outgrowth, age-related cognitive decline, Parkinson's disease, peripheral nerve injury, optic nerve degeneration, and diabetic neuropathy. We have designed and synthesized a unique series of tetracyclic aza-amides that have been shown to be potent FKBP12 rotamase inhibitors. The structure-activity relationships established in this study have demonstrated diverse structural modifications that result in potent rotamase inhibitory activity.
Functional and Structural Role of the Cytochrome b Subunit of the Membrane‐Bound Hydrogenase Complex of Alcaligenes Eutrophus H16 (1997)

This study shows that the product of the hoxZ gene of Alcaligenes eutrophus H16 is a b-type cytochrome (cytochrome b(z)), which is essential for anchoring the membrane-bound hydrogenase (MBH) complex to the periplasmic side of the membrane and for H2-coupled respiration. The hoxZ product is not required for MBH translocation and H2-dependent reduction of the redox dye, 2,3,5-triphenyl-2-tetrazolium chloride. The lack of cytochrome b(z) does not affect the electron-transport activities linked to oxidation of succinate and NADH, although it enhances the electron-flow rate through the cytochrome-c oxidase pathway in hoxZdelta membranes. We show that the hoxZ product is a dihaem cytochrome b (haems with E(m7.0) of +10 mV and +166 mV) involved in H2-dependent electron transfer. We conclude that cytochrome b(z) of the A. eutrophus MBH complex is the link necessary for transfer of electrons from H2 to the ubiquinone pool and that it is required for attachment of MBH to the membrane.
Requirement of CD4 cells for induction and maintenance of unresponsiveness in islet xenografted mice (1998)

Long-term survival of islet xenografts in the hamster to mouse model can be induced by a short-course treatment with a nondepleting anti-CD4 mAb but not with a depleting anti-CD4 mAb [Lu et al. Xenotransplantation 1998; 5:154-163]. Although CD4 cells are known to play a key role in the rejection of islet xenografts, it remains unclear whether CD4 cells are also required for the induction and/or maintenance of specific unresponsiveness to xenografts. To investigate this problem, islets were isolated from golden hamsters and transplanted into streptozotocin-induced diabetic CBA/J mice. Nondepleting mAb YTS 177.9 was used to block CD4 cells for the induction of islet xenograft unresponsiveness and subsequently depleting mAb GK1.5 to deplete CD4 cells in the unresponsive recipients. First, we now confirm that second donor-strain xenografts were permanently accepted in recipients that had been unresponsive to the first grafts, whereas Lewis rat islet xenografts, used as third-party grafts, were rejected like a primary graft within 7-8 days. Second, we depleted CD4 cells in recipient mice, which had been treated perioperatively with the nondepleting mAb YTS 177.9 and became unresponsive to their primary hamster islet graft, by using a depleting anti-CD4 mAb at different time points post-transplant. Depletion of CD4 cells in the unresponsive recipients by the depleting anti-CD4 mAb GK1.5 did abrogate this unresponsive state, since the grafts were always rejected within an average of 25.5 days after the mAb GK1.5 injections. Therefore, our results strongly suggest that CD4 positive cells play an active suppressive role and that their presence in the recipients appears essential for both induction and maintenance of long-term islet xenograft survival or specific unresponsiveness.
Auditory Scene Analysis (1990)

Auditory Scene Analysis addresses the problem of hearing complex auditory environments, using a series of creative analogies to describe the process required of the human auditory system as it analyzes mixtures of sounds to recover descriptions of individual sounds. In a unified and comprehensive way, Bregman establishes a theoretical framework that integrates his findings with an unusually wide range of previous research in psychoacoustics, speech perception, music theory and composition, and computer modeling. Bradford Books imprint
Thermal Inactivation Kinetics and Application of Phospho- and Galactolipid-Degrading Enzymes for Evaluation of Quality Changes in Frozen Vegetables (2001)

Lipid-acyl hydrolases (LAHases) play significant roles in lipid degradation during the storage of vegetables. In particular, spinach contains a large portion of galactolipids (59.5%) and phospholipids (22.4%) among its fat-soluble components, which are used as substrates for LAHases. Thermal inactivation of various LAHases, including phospholipases A, C, and D, phosphatase, and galactolipase, from spinach and carrot was investigated to optimize the blanching process prior to the frozen storage of vegetables. Thermostability of phospholipase C or galactolipase was greatest among the LAHases from both spinach and carrot. Galactolipase from spinach exhibited a D value of 3.39 x 10(2) s at 80 degrees C and a z value of 8.21 degrees C, whereas phospholipase C from spinach showed D(80) of 1.72 x 10(2) s with a z value of 9.26 degrees C. In the case of LAHases from carrot, the D(65) and z values of galactolipase were 6.66 x 10(2) s and 8.69 degrees C, respectively, whereas phospholipase C displayed D(85) of 3.12 x 10(2) s and a z value of 15.8 degrees C. Highly active and thermostable galactolipase and phospholipase C in spinach and carrot made it possible for them to be used as indicator enzymes for the determination of quality deterioration of the stored vegetables.
Artificial opal photonic crystals and inverse opal structures – fundamentals and applications from optics to energy storage (2015)

This review outlines the fundamentals and applications of artificial opal photonic crystals, their fabrication, development and adaption from optics to energy storage research.
PHOTOPROTECTION REVISITED:Genetic and Molecular Approaches (1999)

The involvement of excited and highly reactive intermediates in oxygenic photosynthesis poses unique problems for algae and plants in terms of potential oxidative damage to the photosynthetic apparatus. Photoprotective processes prevent or minimize generation of oxidizing molecules, scavenge reactive oxygen species efficiently, and repair damage that inevitably occurs. This review summarizes several photoprotective mechanisms operating within chloroplasts of plants and green algae. The recent use of genetic and molecular biological approaches is providing new insights into photoprotection, especially with respect to thermal dissipation of excess absorbed light energy, alternative electron transport pathways, chloroplast antioxidant systems, and repair of photosystem II.
A simultaneous single breath measurement of pulmonary diffusing capacity with nitric oxide and carbon monoxide (1989)

Pulmonary diffusing capacity (DL) for carbon monoxide (CO) and nitric oxide (NO) were simultaneously measured in man using the single breath method, by adding 4O ppm of NO to the inspired gas and analysing the expirate for NO by a chemiluminescent method. The mean ratio of DLNO to DLCO in thirteen subjects was 4.3 (SD 0.3), mean DLNO = 49 mmol.min-1.kPa-1 (SD 10) and mean DLCO = 11 mmol.min-1.kPa-1 (SD 2). An increase in alveolar oxygen concentration from a mean of 18 to 68% in five subjects was associated with a 54% fall in DLCO but no change in DLNO. A reduction of lung volume from total lung capacity (TLC) (mean of 7 l) to a mean volume of 3.9 l in five subjects caused a fall in both DLNO (by 34%) and DLCO (by 8%). With 175 watts cycle exercise in three subjects the DLCO rose by 45% and DLNO by 25%. Since NO reacts much faster with haemoglobin than CO, DLNO should be influenced much less by reaction with haemoglobin, and perhaps represents a better index for the diffusing capacity of the alveolar-capillary membrane (Dm) than DLCO.
Selective modulation of human natural killer cells in vivo after prolonged infusion of low dose recombinant interleukin 2. (1993)

The immunologic consequences of prolonged infusions of rIL-2 in doses that produce physiologic serum concentrations of this cytokine were investigated. rIL-2 in doses of 0.5-6.0 x 10(6) U/m2 per d (3.3-40 micrograms/m2 per d) was administered by continuous intravenous infusion for 90 consecutive days to patients with advanced cancer. IL-2 concentrations (25 +/- 25 and 77 +/- 64 pM, respectively) that selectively saturate high-affinity IL-2 receptors (IL-2R) were achieved in the serum of patients receiving rIL-2 infusions of 10 micrograms/m2 per d and 30 micrograms/m2 per d. A gradual, progressive expansion of natural killer (NK) cells was seen in the peripheral blood of these patients with no evidence of a plateau effect during the 3 mo of therapy. A preferential expansion of CD56bright NK cells was consistently evident. NK cytotoxicity against tumor targets was only slightly enhanced at these dose levels. However, brief incubation of these expanded NK cells with IL-2 in vitro induced potent lysis of NK-sensitive, NK-resistant, and antibody-coated targets. Infusions of rIL-2 at 40 micrograms/m2 per d produced serum IL-2 levels (345 +/- 381 pM) sufficient to engage intermediate affinity IL-2R p75, which is constitutively expressed by human NK cells. This did not result in greater NK cell expansion compared to the lower dose levels, but did produce in vivo activation of NK cytotoxicity, as evidenced by lysis of NK-resistant targets. There was no consistent change in the numbers of CD56- CD3+ T cells, CD56+ CD3+ MHC-unrestricted T cells, or B cells during infusions of rIL-2 at any of the dosages used. This study demonstrates that prolonged infusions of rIL-2 in doses that saturate only high affinity IL-2R can selectively expand human NK cells for an extended period of time with only minimal toxicity. Further activation of NK cytolytic activity can also be achieved in vivo, but it requires concentrations of IL-2 that bind intermediate affinity IL-2R p75. Clinical trials are underway attempting to exploit the differing effects of various concentrations of IL-2 on human NK cells in vivo.
Site-Specific Growth of Au–Pd Alloy Horns on Au Nanorods: A Platform for Highly Sensitive Monitoring of Catalytic Reactions by Surface Enhancement Raman Spectroscopy (2013)

Surface-enhanced Raman scattering (SERS) is a highly sensitive probe for molecular detection. The aim of this study was to develop an efficient platform for investigating the kinetics of catalytic reactions with SERS. To achieve this, we synthesized a novel Au-Pd bimetallic nanostructure (HIF-AuNR@AuPd) through site-specific epitaxial growth of Au-Pd alloy horns as catalytic sites at the ends of Au nanorods. Using high-resolution electron microscopy and tomography, we successfully reconstructed the complex three-dimensional morphology of HIF-AuNR@AuPd and identified that the horns are bound with high-index {11l} (0.25 < l < 0.43) facets. With an electron beam probe, we visualized the distribution of surface plasmon over the HIF-AuNR@AuPd nanorods, finding that strong longitudinal surface plasmon resonance concentrated at the rod ends. This unique crystal morphology led to the coupling of high catalytic activity with a strong SERS effect at the rod ends, making HIF-AuNR@AuPd an excellent bifunctional platform for in situ monitoring of surface catalytic reactions. Using the hydrogenation of 4-nitrothiophenol as a model reaction, we demonstrated that its first-order reaction kinetics could be accurately determined from this platform. Moreover, we clearly identified the superior catalytic activity of the rod ends relative to that of the rod bodies, owing to the different SERS activities at the two positions. In comparison with other reported Au-Pd bimetallic nanostructures, HIF-AuNR@AuPd offered both higher catalytic activity and greater detection sensitivity.
Protein-targeted corona phase molecular recognition (2016)

Corona phase molecular recognition (CoPhMoRe) uses a heteropolymer adsorbed onto and templated by a nanoparticle surface to recognize a specific target analyte. This method has not yet been extended to macromolecular analytes, including proteins. Herein we develop a variant of a CoPhMoRe screening procedure of single-walled carbon nanotubes (SWCNT) and use it against a panel of human blood proteins, revealing a specific corona phase that recognizes fibrinogen with high selectivity. In response to fibrinogen binding, SWCNT fluorescence decreases by >80% at saturation. Sequential binding of the three fibrinogen nodules is suggested by selective fluorescence quenching by isolated sub-domains and validated by the quenching kinetics. The fibrinogen recognition also occurs in serum environment, at the clinically relevant fibrinogen concentrations in the human blood. These results open new avenues for synthetic, non-biological antibody analogues that recognize biological macromolecules, and hold great promise for medical and clinical applications.
Target Detection With Impulse Radiating Antenna (2011)

A prolate spheroidal reflector antenna focuses subnanosecond pulsed radiation in the near field with a small beamwidth, allowing for applications such as target detection. Confocal imaging in free space has been demonstrated with such an antenna for both transmitting and receiving. A polarized beam allows for the detection of linear target orientation. We show that decreasing the focal spot size by adding a dielectric lens enables us to resolve a target with a typical dimension of 4 cm. The spatial resolution can be further enhanced by increasing the dielectric constant of the lens' innermost layer.
Enzymatic Cyclization of a Potent Bowman-Birk Protease Inhibitor, Sunflower Trypsin Inhibitor-1, and Solution Structure of an Acyclic Precursor Peptide (2003)

The most potent known naturally occurring Bowman-Birk inhibitor, sunflower trypsin inhibitor-1 (SFTI-1), is a bicyclic 14-amino acid peptide from sunflower seeds comprising one disulfide bond and a cyclic backbone. At present, little is known about the cyclization mechanism of SFTI-1. We show here that an acyclic permutant of SFTI-1 open at its scissile bond, SFTI-1[6,5], also functions as an inhibitor of trypsin and that it can be enzymatically backbone-cyclized by incubation with bovine beta-trypsin. The resulting ratio of cyclic SFTI-1 to SFTI-1[6,5] is approximately 9:1 regardless of whether trypsin is incubated with SFTI-1[6,5] or SFTI-1. Enzymatic resynthesis of the scissile bond to form cyclic SFTI-1 is a novel mechanism of cyclization of SFTI-1[6,5]. Such a reaction could potentially occur on a trypsin affinity column as used in the original isolation procedure of SFTI-1. We therefore extracted SFTI-1 from sunflower seeds without a trypsin purification step and confirmed that the backbone of SFTI-1 is indeed naturally cyclic. Structural studies on SFTI-1[6,5] revealed high heterogeneity, and multiple species of SFTI-1[6,5] were identified. The main species closely resembles the structure of cyclic SFTI-1 with the broken binding loop able to rotate between a cis/trans geometry of the I7-P8 bond with the cis conformer being similar to the canonical binding loop conformation. The non-reactive loop adopts a beta-hairpin structure as in cyclic wild-type SFTI-1. Another species exhibits an iso-aspartate residue at position 14 and provides implications for possible in vivo cyclization mechanisms.
Immunoscintigraphy of inflammatory processes with a technetium-99m-labeled monoclonal antigranulocyte antibody (MAb BW 250/183). (1990)

Antigranulocyte immunoscintigraphy with a technetium-99m- (99mTc) labeled monoclonal antigranulocyte antibody (MAb BW 250/183) was performed in 34 in-patients of the departments of accident surgery and internal medicine in order to prove or exclude inflammatory processes. After labeling with 99mTc, 555 MBq, 99mTc-MAb (0.5 mg antibody) were slowly injected intravenously over a period of 5 min. A whole-body scan was done 4-6 hr postinjection, and planar or SPECT images were performed 6, 18, and 24 hr postinjection. Leukocyte immunoscintigraphy proved inflammatory suppurating processes in 20 cases (true-positive) and excluded them in 11 cases (true-negative). The findings were false-positive in two patients (hematoma without signs of infection, pseudoarthrosis) and false-negative in one patient (encapsulated lung abscess with pleural fibrosis). Anti-idiotypic human anti-mouse antibodies (HAMA) were found only in one out of 20 patients. According to our experiences, immunoscintigraphy with 99mTc-MAb BW 250/183 has a sensitivity of 95%, and is, therefore, well suited for the identification of leukocytic inflammations.
Targeted disruption of the TGA3 locus in Arabidopsis thaliana (1995)

A major drawback to study gene functions in plant systems is the lack of an effective gene knockout strategy. With a large number of plant genes isolated and the accelerating pace by which this collection is growing, the need for their functional analyses at the whole plant level has become increasingly urgent. Here evidence is reported for the first successful disruption of a non-selectable gene in Arabidopsis thaliana by creating a mutant of the TGA3 locus via targeted insertion of the bacterial neo gene conferring kanamycin (Km) resistance. A beta-glucuronidase (GUS) expression unit outside the region of homology was used as a screenable marker to distinguish homologous recombination events from those of ectopic insertions. PCR amplification coupled with Southern blot screening identified two putative homologous recombination events among 2580 Kmr calli. One callus line was subsequently isolated and the structure of the targeted TGA3 allele confirmed by Southern blot analyses. This study demonstrates the feasibility of targeting a non-selectable locus in Arabidopsis. Combined with future improvements in negative selection strategies and efficient transformation methodologies, gene replacement studies in plants could become a routine technique.