gebhart/patrepeval huggingface dataset:
Phenylketonuria: contemporary screening and diagnosis. (1991)

Screening newborns for phenylketonuria (PKU) is a mandatory practice based on measuring a raised blood phenylalanine level. Many factors influence the rate of blood phenylalanine rise so that there are many pitfalls in detecting the 1:10,000 affected infant. About one percent of all babies tested proves to be "false positives." Two-thirds of those with persistent hyperphenylalaninemia prove to have classic PKU. Non-classic PKU with less intense, persistent hyperphenylalaninemia is due to different alterations in the enzyme, phenylalanine hydroxylase. Additionally, about one percent of the confirmed positive patients is due to either a defect in the synthesis or regeneration of the cofactor, tetrahydrobiopterin; these latter forms are not amenable to treatment with the low phenylalanine diet. Screening programs have developed directives regarding the timing and conditions for obtaining the specimens for testing. Specific confirmatory tests of those with positive results must be performed. Even so, about one in 70 affected babies is "missed," resulting in mental retardation, seizures, and neurologic deficits.
Reduction of Anti-HIV-1 Gag Immune Responses During Co-Immunization: Immune Interference by the HIV-1 Envelope (2007)

Immunization with more than one immunogen (co-immunization) is an efficient regimen to induce immunity to multiple antigens. However, immune interference has been reported using multi-plasmid DNA immunizations. HIV-1 envelope (Env) and Gag gene products are the predominant immunogens used in current AIDS vaccines, although, few studies have evaluated possible immune interference when these two antigens are co-administered. Therefore, in this study, immune interference during co-inoculation was examined using DNA vaccines expressing lentiviral Envs and Gag from gene sequences optimized for efficient expression in mammalian cells (codon-optimized). BALB/c mice vaccinated in separate hind legs with each plasmid individually elicited high titer immune responses, however, when HIV-1 Env(gp120) and HIV-1 Gag(p55) DNA plasmids were co-inoculated, there was a reduction in the immune responses elicited to HIV-1 Gag(p55). To determine if the anti-HIV-1 Gag(p55) immune interference was specific to HIV-1 Env(gp120), mice were co-immunized with plasmids expressing the surface envelope protein from two additional lentiviruses, Env(gp130)-SIV or Env(gp90)-EIAV, or a soluble form of hemagglutinin (sHA) from influenza virus and HIV-1 Gag(p55)- or SIV Gag(p55)-DNA. Interestingly, there was no reduction in anti-HIV-1 Gag(p55) immune responses using other lentiviral envelopes or the influenza sHA. Also, none of the lentiviral envelopes reduced anti-SIV Gag(p55) immune responses during co-immunization. Therefore, anti-HIV-1 Gag immune interference appears specific to co-immunizations with HIV-1 Env(gp120) and may involve a yet undefined immunological mechanism(s).
Characterization of the ϒ-Glutamyl Carboxylase (1997)

Studies on the vitamin K-dependent carboxylase are still in their infancy, but the cloning and purification of the enzyme have permitted a number of advances in our understanding of both the molecular biology, and mechanism of the carboxylase. Advances in our knowledge of the molecular biology of the carboxylase include chromosomal location, characterization of messenger RNA transcript(s) and the study of patients with carboxylase mutations. Our understanding of the mechanism of the carboxylase has been enhanced by the expression of peptides in E. coli which contain multiple carboxylation sites and more closely resemble the native carboxylase substrates. These peptides have been utilized to identify elements within the substrates which are critical for carboxylation and to demonstrate that the vitamin K-dependent carboxylase is one of the first examples of a processive post-translational modification enzyme.
Marrow Cell Transplantation for Infantile Hypophosphatasia (2003)

An 8-month-old girl who seemed certain to die from the infantile form of hypophosphatasia, an inborn error of metabolism characterized by deficient activity of the tissue-nonspecific isoenzyme of alkaline phosphatase (TNSALP), underwent the first trial of bone marrow cell transplantation for this heritable type of rickets. After cytoreduction, she was given T-cell-depleted, haplo-identical marrow from her healthy sister. Chimerism in peripheral blood and bone marrow became 100% donor. Three months later, she was clinically improved, with considerable healing of rickets and generalized skeletal remineralization. However, 6 months post-transplantation, worsening skeletal disease recurred, with partial return of host hematopoiesis. At the age of 21 months, without additional chemotherapy or immunosuppressive treatment, she received a boost of donor marrow cells expanded ex vivo to enrich for stromal cells. Significant, prolonged clinical and radiographic improvement followed soon after. Nevertheless, biochemical features of hypophosphatasia have remained unchanged to date. Skeletal biopsy specimens were not performed. Now, at 6 years of age, she is intelligent and ambulatory but remains small. Among several hypotheses for our patient's survival and progress, the most plausible seems to be the transient and long-term engraftment of sufficient numbers of donor marrow mesenchymal cells, forming functional osteoblasts and perhaps chondrocytes, to ameliorate her skeletal disease.
Group B streptococcal conjugate vaccines (2003)

Linkage of bacterial capsular polysaccharides to proteins to create conjugate vaccines has had a dramatic impact on the health of children. Although unconjugated polysaccharides are poorly immunogenic in infants and some older children and adults, their covalent coupling with proteins stimulates T cell dependent antigenic recognition that profoundly enhances immunogenicity. In the decade since the introduction and widespread use of Haemophilus influenzae type b polysaccharide conjugate vaccines in the United States, invasive H influenzae infections have become a rarity in childhood. Similarly, the conjugation of polysaccharides of Streptococcus pneumoniae to a derivative of diphtheria toxoid and the addition of pneumococcal conjugate vaccine to infant immunisation schedules carries with it promise for a similar decline in the incidence of invasive pneumococcal disease in paediatric patients.
Identification of secreted proteins that reflect autophagy dynamics within tumor cells (2014)

Macroautophagy, a catabolic process of cellular self-digestion, is an important tumor cell survival mechanism and a potential target in antineoplastic therapies. Recent discoveries have implicated autophagy in the cellular secretory process, but potential roles of autophagy-mediated secretion in modifying the tumor microenvironment are poorly understood. Furthermore, efforts to inhibit autophagy in clinical trials have been hampered by suboptimal methods to quantitatively measure tumor autophagy levels. Here, we leveraged the autophagy-based involvement in cellular secretion to identify shed proteins associated with autophagy levels in melanoma. The secretome of low-autophagy WM793 melanoma cells was compared to its highly autophagic metastatic derivative, 1205Lu in physiological 3-dimensional cell culture using quantitative proteomics. These comparisons identified candidate autophagy biomarkers IL1B (interleukin 1, β), CXCL8 (chemokine (C-X-C motif) ligand 8), LIF (leukemia inhibitory factor), FAM3C (family with sequence similarity 3, member C), and DKK3 (dickkopf WNT signaling pathway inhibitor 3) with known roles in inflammation and tumorigenesis, and these proteins were subsequently shown to be elevated in supernatants of an independent panel of high-autophagy melanoma cell lines. Secretion levels of these proteins increased when low-autophagy melanoma cells were treated with the autophagy-inducing tat-BECN1 (Beclin 1) peptide and decreased when ATG7 (autophagy-related 7) was silenced in high-autophagy cells, thereby supporting a mechanistic link between these secreted proteins and autophagy. In addition, serum from metastatic melanoma patients with high tumor autophagy levels exhibited higher levels of these proteins than serum from patients with low-autophagy tumors. These results suggest that autophagy-related secretion affects the tumor microenvironment and measurement of autophagy-associated secreted proteins in plasma and possibly in tumors can serve as surrogates for intracellular autophagy dynamics in tumor cells.
Abnormal cancellous bone collagen metabolism in osteoarthritis. (1998)

Biochemical investigations into the pathogenesis of osteoarthritis have, for the last two decades, concentrated on the mechanisms involved in the destruction of the articular cartilage. Although bone changes are known to occur, the biochemistry of the collagenous matrix within osteoarthritic bone has received scant attention. We report that bone collagen metabolism is increased within osteoarthritic femoral heads, with the greatest changes occurring within the subchondral zone. Collagen synthesis and its potential to mineralize were determined by the carboxy-terminal propeptide content and alkaline phosphatase activity, respectively. These data supported elevated new matrix formation. Our finding of a three- to fourfold increase in TGF-beta in osteoarthritic bone indicates that this might represent a stimulus for the increased collagen synthesis observed. Of additional significance is the hypomineralization of deposited collagen in the subchondral zone of osteoarthritic femoral heads, supporting a greater proportion of osteoid in the diseased tissue. The cross-linking of collagen was similar to that observed for controls. In addition, the degradative potential of osteoarthritic bone was considerably higher as demonstrated by increased matrix metalloproteinase 2 activity, and again the greater activity was associated with the subchondral bone tissue. The polarization exhibited in the metabolism of bone collagen from osteoarthritic hips might exacerbate the processes involved in joint deterioration by altering joint morphology. This in turn may alter the distribution of mechanical forces to the various tissues, to which bone is a sensitive responder. Bone collagen metabolism is clearly an important factor in the pathogenesis of osteoarthritis and certainly warrants further biochemical study.
HER2 therapy. HER2 (ERBB2): functional diversity from structurally conserved building blocks (2007)

EGFR-type receptor tyrosine kinases achieve a broad spectrum of cellular responses by utilizing a set of structurally conserved building blocks. Based on available crystal structures and biochemical information, significant new insights have emerged into modes of receptor control, its deregulation in cancer, and the nuances that differentiate the four human receptors. This review gives an overview of current models of the control of receptor activity with a special emphasis on HER2 and HER3.
Architecture and art : the influence of art in the design process (2005)

Architecture and artDesign and the process of making works of art surround us in our everyday lives. Design has become more a part of the mainstream culture as quality design ideas reach the masses. From television shows about design to Target stores that utilize quality designers to design their products, people are realizing the benefits of good design in their everyday lives. As architects there is a responsibility to respond to this trend through future design decisions.Below are a list of questions raised by the idea of architecture and art. Not all were addressed in the thesis process but all are interwoven into any study of architecture and art. How does art influence the process of design in architecture? Architects are artists that communicate through space and form. Ideas are built in three dimensions that can be inhabited by others. Does the built work become a piece of art for future inspiration of architects and artists? How are architects inspired by art and how are artists inspired by architecture? What is the common element between architecture and art? Can architects and artists work together to develop ideas? How does art in the process of design inform the architectural project? Can art inform the design process and be an influence through out the architectural project? Architects use technology to create works of art; however, does art contribute to the making of technology?Objectives of this thesis include: creating and defining space through artistic endeavors that shape the architecture; make the impossibility within art possible through architectonical means; to reveal the opportunities and languages of art that have an influence on architectural design; creation unrestrained by the logical thought of the architect and at the same grounded by what sets it free; freedom from the functional and programmatic constraints that are placed on space and form.What is the common language between architecture and art that bind them in a close relationship? A reciprocal relationship between the architectural design and the artistic work is the basis of the thesis. The intention is to discover artistic moments that breathe life into the architectural design process and add to the design.
Metabotropic glutamate receptor agonists reduce epileptiform activity in the rat cortex (1992)

Slices of rat cingulate cortex, when incubated in magnesium-free medium, produce spontaneous epileptiform spikes. Here it is demonstrated that the metabotropic glutamate receptor (mGluR) agonists +/- trans-1-amino-cyclopentane-1,3-dicarboxylic acid (+/- Trans-ACPD), IS3R-ACPD and quisqualic acid (quis) can reduce the frequency of these bursts in a concentration-dependent manner. The IC50 values were 16, 12 and 26 microM, respectively. The low concentrations of +/- trans- and IS3R-ACPD used, plus the lack of NMDA antagonism shown by these compounds, suggest that the effect may be via a presynaptic reduction in glutamate release. The relative potency of the agonists IS3R-ACPD > Trans-ACPD > quis would seem to suggest that the mGluR1 receptor is not involved.
An Inorganic Hole Conductor for Organo-Lead Halide Perovskite Solar Cells. Improved Hole Conductivity with Copper Iodide (2013)

Organo-lead halide perovskite solar cells have emerged as one of the most promising candidates for the next generation of solar cells. To date, these perovskite thin film solar cells have exclusively employed organic hole conducting polymers which are often expensive and have low hole mobility. In a quest to explore new inorganic hole conducting materials for these perovskite-based thin film photovoltaics, we have identified copper iodide as a possible alternative. Using copper iodide, we have succeeded in achieving a promising power conversion efficiency of 6.0% with excellent photocurrent stability. The open-circuit voltage, compared to the best spiro-OMeTAD devices, remains low and is attributed to higher recombination in CuI devices as determined by impedance spectroscopy. However, impedance spectroscopy revealed that CuI exhibits 2 orders of magnitude higher electrical conductivity than spiro-OMeTAD which allows for significantly higher fill factors. Reducing the recombination in these devices could render CuI as a cost-effective competitor to spiro-OMeTAD in perovskite solar cells.
On-chip immuno-agglutination assay with analyte capture by dynamic manipulation of superparamagnetic beads (2009)

Magnetic bead-based lab-on-a-chip systems offer significant advantages compared to more conventional systems, mainly through the possibility of controlled manipulation of the magnetic carriers on-chip. In particular, microfluidic immunoassays using functionalized magnetic beads raise increasing interest. We present here a new approach for performing immuno-agglutination assays on-chip. Our system is based on a quadrupolar magnetic field set-up. Dynamic actuation of a confined plug of functionalized magnetic beads is used for analyte capture in a microchannel. A simple detection method based on the swelling of the released plug after agglutination is presented. We demonstrate the feasibility of on-chip agglutination tests by means of a streptavidin/biotinylated-bovine serum albumin (bBSA) model assay. A detection limit of about 200 pg/mL (approximately 3 pM) is achieved.
Danger Signaling in Atherosclerosis (2015)

All aspects of the pathogenesis of atherosclerosis are critically influenced by the inflammatory response in vascular plaques. Research in the field of innate immunity from the past 2 decades has uncovered many novel mechanisms elucidating how immune cells sense microbes, tissue damage, and metabolic derangements. Here, we summarize which triggers of innate immunity appear during atherogenesis and by which pathways they can contribute to inflammation in atherosclerotic plaques. The increased understanding gained from studies assessing how immune activation is associated with the pathogenesis of atherosclerosis has provided many novel targets for potential therapeutic intervention. Excitingly, the concept that inflammation may be the core of cardiovascular disease is currently being clinically evaluated and will probably encourage further studies in this area.
SNRPE is involved in cell proliferation and progression of high-grade prostate cancer through the regulation of androgen receptor expression (2011)

Clinically high-grade prostate cancers (PC) with high Gleason scores of 8-10 exhibit rapid growth and are more likely to spread beyond the prostate. These cancer types demonstrate a poor response to androgen deprivation therapy and eventually acquire a castration-resistant phenotype. To identify novel molecular cancer drug targets, we previously analyzed the gene expression profiles of high-grade PC using a cDNA microarray combined with laser microbeam microdissection and found a number of genes that are transactivated in high-grade PC. Among these genes, we report the identification of a novel molecular target, small nuclear ribonucleoprotein polypeptide E (SNRPE). Semi-quantitative RT-PCR confirmed that SNRPE is overexpressed in high-grade PC cells compared with normal prostatic epithelial cells. Knockdown of SNRPE expression by short interfering RNA (siRNA) resulted in the marked suppression of PC cell proliferation. By contrast, SNRPE overexpression promoted PC cell proliferation, indicating its oncogenic effects. Furthermore, we demonstrated that SNRPE regulates androgen receptor (AR) mRNA expression in PC cells. Knockdown of SNRPE expression by siRNA resulted in the marked suppression of AR and its downstream target genes at the mRNA level. We suggest that the regulation of AR expression by SNRPE is essential for cell proliferation and progression of high-grade PC and that it may be a novel molecular target for cancer drugs.
Synthesis of α- and γ-fluoroalkylphosphonates (1986)

α-Fluorobenzylphosphonate esters are conveniently made by treating α-hydroxybenzylphosphonate esters with diethylaminosulphur trifluoride. The reaction is not subject to steric impedance and is extended to the α-fluorination of an α-hydroxybenzylphosphine oxide. For α-hydroxyallyl and α-hydroxycinnamylphosphonates, the replacement of the hydroxy group by fluorine proceeds via an SN2′ rearrangement to give the γ-fluoroalk-1-enylphosphonates exclusively. Dehydration rather than substitution occurs in the case of alcohols of secondary alkylphosphonates.
Direct Observation of Spin-Trapped Carbon Dioxide Radicals in Hepatocytes Exposed to Carbon Tetrachloride (1990)

Carbon dioxide radical adducts of the spin trapping agent, alpha-phenyl N-t-butyl nitrone (PBN), have been observed to occur in the urine and bile of rats exposed to carbon tetrachloride as well as in perfusates of liver in which the perfusion medium contained carbon tetrachloride (Connor et al., J. Biol. Chem., 261, 4542, (1986]. The carbon dioxide adduct was proven to be derived from CCl4 by use of 13-C-labelled compound. These adducts were not observed in the liver itself suggesting that they might be rapidly secreted from the liver. However, using isolated hepatocytes, we have demonstrated that the carbon dioxide radical adduct can be observed directly in the liver cells as it is formed. Since this water-soluble adduct cannot be extracted by non-aqueous solvents such as chloroform or toluene, its formation in liver in vivo or in perfused livers was not detected. Lowering the oxygen tension in the system diminished the intensity of production of the carbon dioxide adduct, consistent with the adduct being produced as a result of .OOCCl3 generation. It is not clear the extent to which this adduct is formed as a result of the .CO2 radical or is produced by metabolic oxidation of the trichloromethyl radical adduct of PBN per se to the carbon dioxide radical adduct. The intensity of the signal of the carbon dioxide radical adduct suggests that adduct conversion may be the route of formation since it seems unlikely that a sufficient amount of the halocarbon could be metabolized to .COCl or .CO2 radicals to generate a signal of the magnitude involved.(ABSTRACT TRUNCATED AT 250 WORDS)
Design of Core−Shell-Type Nanoparticles Carrying Stable Radicals in the Core (2009)

Utilizing the self-assembled core-shell-type polymeric micelle technique, high-performance nanoparticles possessing stable radicals in the core and reactive groups on the periphery were prepared. The anionic ring-opening polymerization of ethylene oxide (EO) was carried out using potassium 3,3-diethoxypropanolate as an initiator, followed by mesylation with methanesulfonyl chloride to obtain acetal-poly(ethylene glycol)-methanesulfonate (acetal-PEG-Ms; 1). Compound 1 was reacted with potassium O-ethyldithiocarbonate, followed by treatment with n-propylamine to obtain heterobifunctional PEG derivatives containing both sulfanyl and acetal terminal groups (acetal-PEG-SH) (2) in a highly selective and quantitative manner. Poly(ethylene glycol)-block-poly(chloromethylstyrene) (acetal-PEG-b-PCMS) (3) was synthesized by the free-radical telomerization of chloromethylstyrene (CMS) using 2 as a telogen. The chloromethyl groups in the PCMS segment of the block copolymer (3) were quantitatively converted to 2,2,6,6-tetramethylpiperidinyloxys (TEMPOs) via the amination of 3 with 4-amino-TEMPO to obtain acetal-PEG-b-PCMS containing TEMPO moieties (4). The obtained 4 formed core-shell-type nanoparticles in aqueous media when subjected to the dialysis method: the cumulant average diameter of the nanoparticles was about 40 nm, and the nanoparticles emitted intense electron paramagnetic resonance (EPR) signals. The TEMPO radicals in the core of the nanoparticles showed reduction resistance even in the presence of 3.5 mM ascorbic acid. This means that these nanoparticles are anticipated as high-performance bionanoparticles that can be used in vivo.
Nucleotide sequence of 5' portion ofsrfAthat contains the region required for competence establishment inBacillus subtilus (1993)

The nucleotide sequence of the 20,535 base pairs of the 5' end of the srfA operon, containing the region required for competence development, was determined. This included the srfA promoter region, the first open reading frame, srfAA, encoding surfactin synthetase I and part of the second open reading frame, srfAB, encoding surfactin synthetase II. Three amino acid-activating domains characteristic of those found in peptide synthetases could be discerned in both srfAA (activating Glu, Leu and D-Leu) and srfAB (activating Val, Asp, and D-Leu). The presence of a conserved spacer motif in the amino-terminal end of srfAA suggests that the srfAA product may not initiate surfactin synthesis. The portion of srfA that contains the region required for competence is composed of srfAA and the first amino acid-activating domain of srfAB.