gebhart/patrepeval huggingface dataset:
Normal and inhibited cholesterol synthesis in the cultured rat embryo. (1997)

The Smith-Lemli-Opitz syndrome-affected fetus presents a deficiency in delta7-dehydrocholesterol reductase, the last enzymatic step in the cholesterol biosynthesis pathway. Development of the abnormal human fetus takes place in a normal environment as the heterozygous mother's cholesterolemia remains normal. An animal model for this disease has been obtained from the offspring of pregnant rats treated with "distal" inhibitors of delta7-dehydrocholesterol reductase, AY-9944 or BM15766. In the animal model, embryonic development occurs in a disturbed environment characterized by hypocholesterolemia and accumulation of delta7-dehydrocholesterol and delta8-dehydrocholesterol in the maternal serum. The purpose of the present study was to assess, in cultured rat embryos at early developmental stages, the relative contributions of exogenous and de novo synthesized cholesterol in the total embryonic cholesterol, according to the conditions of normal and altered de novo biosynthesis. Cultured rat embryos are able to synthesize cholesterol as shown by 13C-incorporation into cholesterol from 13C-labeled precursors added to the culture medium. De novo cholesterol biosynthesis is altered by addition to the culture medium of AY-9944 which inhibits the delta7-dehydrocholesterol reductase and the delta8-delta7-sterol isomerase as suggested by the emergence of characteristic aberrant sterols in the embryonic tissues. Cholesterol-rich serum used for embryo culture alters the pattern in a way that confirms that the rat embryos are able to import exogenous cholesterol which down-regulates de novo cholesterol biosynthesis. Exogenous cholesterol substitutes for the deficit in a manner efficient enough to prevent the embryonic abnormalities induced by AY-9944.
The centromeric K-type repeat and the central core are together sufficient to establish a functional Schizosaccharomyces pombe centromere. (1994)

The DNA requirements for centromere function in fission yeast have been investigated using a minichromosome assay system. Critical elements of Schizosaccharomyces pombe centromeric DNA are portions of the centromeric central core and sequences within a 2.1-kilobase segment found on all three chromosomes as part of the K-type (K/K"/dg) centromeric repeat. The S. pombe centromeric central core contains DNA sequences that appear functionally redundant, and the inverted repeat motif that flanks the central core in all native fission yeast centromeres is not essential for centromere function in circular minichromosomes. Tandem copies of centromeric repeat K", in conjunction with the central core, exert an additive effect on centromere function, increasing minichromosome mitotic stability with each additional copy. Centromeric repeats B and L, however, and parts of the central core and its core-associated repeat are dispensable and cannot substitute for K-type sequences. Several specific protein binding sites have been identified within the centromeric K-type repeat, consistent with a recently proposed model for centromere/kinetochore function in S. pombe.
Extraction of the corner of checkerboard image (2008)

The extraction of the internal corners of planar checkerboard pattern image is of vital importance to camera calibration, for the accuracy of camera calibration depends on the accuracy of it. An effective approach is proposed to automatically extract the internal corners of the planar checkerboard calibration pattern image based on the characteristics of local intensity and the grid line architecture of the planar checkerboard pattern image. The proposed procedure consists of the detection of image corners, the recognition of the corners at the intersections of black and white squares and the recognition of the corners at the intersections of two groups of grid lines. The proposed approach obviously reduces the time cost for camera calibration, speeds up calibration process and is especially adapted for automatic calibration based on multiple images.
The unique cytoarchitecture of human pancreatic islets has implications for islet cell function (2006)

The cytoarchitecture of human islets has been examined, focusing on cellular associations that provide the anatomical framework for paracrine interactions. By using confocal microscopy and multiple immunofluorescence, we found that, contrary to descriptions of prototypical islets in textbooks and in the literature, human islets did not show anatomical subdivisions. Insulin-immunoreactive beta cells, glucagon-immunoreactive alpha cells, and somatostatin-containing delta cells were found scattered throughout the human islet. Human beta cells were not clustered, and most (71%) showed associations with other endocrine cells, suggesting unique paracrine interactions in human islets. Human islets contained proportionally fewer beta cells and more alpha cells than did mouse islets. In human islets, most beta, alpha, and delta cells were aligned along blood vessels with no particular order or arrangement, indicating that islet microcirculation likely does not determine the order of paracrine interactions. We further investigated whether the unique human islet cytoarchitecture had functional implications. Applying imaging of cytoplasmic free Ca2+ concentration, [Ca2+]i, we found that beta cell oscillatory activity was not coordinated throughout the human islet as it was in mouse islets. Furthermore, human islets responded with an increase in [Ca2+]i when lowering the glucose concentration to 1 mM, which can be attributed to the large contribution of alpha cells to the islet composition. We conclude that the unique cellular arrangement of human islets has functional implications for islet cell function.
Establishment of Agrobacterium tumefaciens -Mediated Transformation of an Oleaginous Fungus, Mortierella alpina 1S-4, and Its Application for Eicosapentaenoic Acid Producer Breeding (2009)

Gene manipulation tools for an arachidonic-producing filamentous fungus, Mortierella alpina 1S-4, have not been sufficiently developed. In this study, Agrobacterium tumefaciens-mediated transformation (ATMT) was investigated for M. alpina 1S-4 transformation, using the uracil-auxotrophic mutant (ura5(-) strain) of M. alpina 1S-4 as a host strain and the homologous ura5 gene as a selectable marker gene. Furthermore, the gene for omega3-desaturase, catalyzing the conversion of n-6 fatty acid to n-3 fatty acid, was overexpressed in M. alpina 1S-4 by employing the ATMT system. As a result, we revealed that the frequency of transformation surpassed 400 transformants/10(8) spores, most of the integrated T-DNA appeared as a single copy at a random position in chromosomal DNA, and most of the transformants (60 to 80%) showed mitotic stability. Moreover, the accumulation of n-3 fatty acid in transformants was observed under the conditions of optimal omega3-desaturase gene expression. In particular, eicosapentaenoic acid (20:5n-3), an end product of n-3 fatty acids synthesized in M. alpina 1S-4, reached a maximum of 40% of total fatty acids. In conclusion, the ATMT system was found to be effective and suitable for the industrial strain Mortierella alpina 1S-4 and will be a useful tool for basic mutagenesis research and for industrial breeding of this strain.
p53-Binding Protein 1 Is Fused to the Platelet-Derived Growth Factor Receptor β in a Patient with a t(5;15)(q33;q22) and an Imatinib-Responsive Eosinophilic Myeloproliferative Disorder (2004)

We describe the fusion of TP53BP1 to PDGFRB in a patient with a chronic myeloid leukemia-like disorder associated with eosinophilia and a t(5;15)(q33;q22). TP53BP1 encodes 53BP1, a p53-binding protein that plays a role in cellular responses to DNA damage. The 53BP1-PDGFRbeta fusion protein is predicted to retain the kinetochore-binding domain of 53BP1 fused to the transmembrane and intracellular tyrosine kinase domain of PDGFRbeta. The presence of the fusion was confirmed by two-color fluorescence in situ hybridization, reverse transcription-PCR, and by characterizing the genomic breakpoints. The reciprocal fusion, which would contain the p53-binding 53BP1 BRCA1 COOH-terminal domains, was not detectable by fluorescence in situ hybridization or nested PCR. Imatinib, a known inhibitor of PDGFRbeta, blocked the growth of patient colony-forming unit, granulocyte-macrophage in vitro and produced a clinically significant response before relapse and subsequent death with imatinib-resistant disease. We conclude that TP53BP1-PDGFRB is a novel imatinib target in atypical chronic myeloid leukemia.
Alterations in Receptor Activation and Divalent Cation Activation of Agonist Binding by Deletion of Intracellular Domains of the Glucagon Receptor (1997)

Deletion of residues 252-259 within the putative second intracellular loop of the human glucagon receptor results in a protein with high affinity for glucagon but with attenuated agonist activation of adenylyl cyclase. The Delta252-259 mutant has 4-fold higher affinity for glucagon than does the wild type receptor. The nonhydrolyzable GTP analog, guanosine 5'-(beta, gamma-imido)triphosphate (Gpp(NH)p), inhibits binding of 125I-glucagon to the wild type receptor but not to the Delta252-259 mutant. Divalent cations such as MgCl2 and CaCl2 stimulate the binding of 125I-glucagon to the wild type receptor by increasing glucagon affinity. The rate of dissociation of 125I-glucagon is decreased 4-fold by MgCl2 and increased 6-fold by Gpp(NH)p. However, divalent cations do not affect the binding of 125I-glucagon to the Delta252-259 mutant. The rate of dissociation of 125I-glucagon from the Delta252-259 mutant protein is equivalent to the rate of dissociation from the wild type receptor in the presence of MgCl2. These data suggest that at least three conformations of the glucagon receptor can exist in the membrane based on their differing affinities for 125I-glucagon. Deletion of residues 252-259 appears to lock the protein in the conformation promoted by divalent cations and prevents the protein from normal coupling to Gs.
Theoretical investigation of water formation on Rh and Pt Surfaces (2000)

Catalytic water formation from adsorbed H and O adatoms is a fundamental reaction step in a variety of technologically important reactions involving organic molecules. In particular, the water-formation rate determines the selectivity of the catalytic partial oxidation of methane to syngas. In this report we present a theoretical investigation of the potential-energy diagram for water formation from adsorbed O and H species on Rh(111) and Pt(111) surfaces. The study is based on accurate first-principles calculations applying density-functional theory. Our results are compared to the potential-energy diagram for this reaction inferred from experimental data by Hickman and Schmidt [AIChE. J. 39, 1164 (1993)]. The calculations essentially reproduce the scheme of Hickman and Schmidt for water formation on Rh(111) with the important difference that the OH molecule is significantly more stable than assumed by Hickman and Schmidt. On Pt(111) surfaces, however, the calculations predict a barrier to OH formation very similar to that found on Rh(111). In particular, the calculated barrier to OH formation of about 20 kcal/mol seems to contradict the small 2.5 kcal/mol barrier assumed in the Hickman–Schmidt scheme and the observed large rate of water formation on Pt. A possible explanation for the apparent discrepancy between the large calculated barrier for OH formation on Pt and the experimentally observed rapid formation of water even at low temperatures is that the active sites for water formation on Pt are at “defect” sites and not on the ideally flat terraces. A similar conclusion has been reached by Verheij and co-workers [Surf. Sci. 371, 100 (1997); Chem. Phys. Lett. 174, 449 (1990); Surf. Sci. 272, 276 (1991)], who did detailed experimental work on water formation on Pt surfaces. Analyzing our results, we develop an explicit picture of the interaction processes governing the formation of OH groups. This picture rationalizes the calculated weak dependence of OH formation on substrate material. An important conclusion from this work is that “good” catalysts for the partial oxidation of hydrocarbons should resist defect formation at their surfaces.
Combining Sequence-Specific Probes and DNA Binding Dyes in Real-Time PCR for Specific Nucleic Acid Quantification and Melting Curve Analysis (2006)

Currently, in real-time PCR, one often has to choose between using a sequence-specific probe and a nonspecific double-stranded DNA (dsDNA) binding dye for the detection of amplified DNA products. The sequence-specific probe has the advantage that it only detects the targeted product, while the nonspecific dye has the advantage that melting curve analysis can be performed after completed amplification, which reveals what kind of products have been formed. Here we present a new strategy based on combining a sequence-specific probe and a nonspecific dye, BOXTO, in the same reaction, to take the advantage of both chemistries. We show that BOXTO can be used together with both TaqMan probes and locked nucleic acid (LNA) probes without interfering with the PCR. The probe signal reflect formation of target product, while melting curve analysis of the BOXTO signal reveals primer-dimer formation and the presence of any other anomalous products.
Thin Film Rechargeable Lithium Batteries for Implantable Devices (1997)

Thin films of LiCoO2 have been synthesized in which the strongest x-ray reflection is either weak or missing, indicating a high degree of preferred orientation. Thin film solid state batteries with these textured cathode films can deliver practical capacities at high current densities. For example, for one of the cells, 70% of the maximum capacity between 4.2 and 3 V (∼0.2 mAh/cm2) was delivered at a current of 2 mA/cm2. When cycled at rates of 0.1 mA/cm2, the capacity loss was 0.001%/cycle. The reliability and performance of LiLiCoO2 thin film batteries make them attractive for application in implantable devices such as neural stimulators, pacemakers, and defibrillators.
High Level Expression of Active Human Prothrombin in a Vaccina Virus Expression System (1992)

We have worked out an efficient and time saving procedure for the expression of recombinant human prothrombin. The glycoprotein was expressed in the vaccinia virus expression system in several mammalian cell lines. The kidney cell lines Vero and BHK and the human cell line Hela were found to efficiently secrete prothrombin. Expression level of 3-4 micrograms of factor II per 10(6) cells per day corresponding to 18-23 mU per 10(6) cells per day were achieved. Since the expression levels obtained with the vaccinia virus/Vero cell system were comparable to those obtained in amplified transformed CHO cells it provides an alternative system for the efficient expression of human prothrombin and may allow to further elucidate structure-function relationships of (pro)thrombin and its various effectors.
Ketone Isosteres of 2-N-Acetamidosugars as Substrates for Metabolic Cell Surface Engineering (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTKetone Isosteres of 2-N-Acetamidosugars as Substrates for Metabolic Cell Surface EngineeringHoward C. Hang and Carolyn R. BertozziView Author Information Departments of Chemistry and Molecular and Cell Biology, University of California Center for Advanced Materials, Materials Sciences Division Lawrence Berkeley National Laboratory Howard Hughes Medical Institute, Berkeley, California 94720 Cite this: J. Am. Chem. Soc. 2001, 123, 6, 1242–1243Publication Date (Web):January 20, 2001Publication History Received9 August 2000Published online20 January 2001Published inissue 1 February 2001https://doi.org/10.1021/ja002962bCopyright © 2001 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1899Altmetric-Citations99LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (38 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Carbohydrates,Cells,Ketones,Metabolic engineering,Peptides and proteins Get e-Alerts
Optical coherence domain reflectometry by synthesis of coherence function (1993)

Reflectometry by synthesis of optical coherence function using a laser diode as a light source for high resolution measurements of optical systems and waveguide devices is proposed. This method has no mechanical moving parts. The oscillation frequency of the laser diode is controlled by the injection current with an appropriate waveform and the coherence function, which corresponds to the time-averaged spectrum shape, is synthesized. The principle that includes three types of synthesized coherence function is presented. The basic experiments of the three methods have been successfully carried out and the resolution about 10 mm in air is demonstrated using an ordinary Fabry-Perot-type single-mode laser diode. The performance deterioration factors of the most promising method are also discussed, in which a coherence function with a delta-function-like shape along the optical path is synthesized to obtain the reflectivity distribution directly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Obesity and Metabolic Syndrome in Circadian Clock Mutant Mice (2005)

The CLOCK transcription factor is a key component of the molecular circadian clock within pacemaker neurons of the hypothalamic suprachiasmatic nucleus. We found that homozygous Clock mutant mice have a greatly attenuated diurnal feeding rhythm, are hyperphagic and obese, and develop a metabolic syndrome of hyperleptinemia, hyperlipidemia, hepatic steatosis, hyperglycemia, and hypoinsulinemia. Expression of transcripts encoding selected hypothalamic peptides associated with energy balance was attenuated in the Clock mutant mice. These results suggest that the circadian clock gene network plays an important role in mammalian energy balance.
Overexpression of Nell-1, a Craniosynostosis-Associated Gene, Induces Apoptosis in Osteoblasts During Craniofacial Development (2003)

We show that Nell-1 expression modulates calvarial osteoblast differentiation and apoptosis pathways. Nell-1 overexpression disrupts these pathways resulting in craniofacial anomalies such as premature suture closure.
The precursor form of the human kallikrein 2, a kallikrein homologous to prostate-specific antigen, is present in human sera and is increased in prostate cancer and benign prostatic hyperplasia (1998)

Prostate-specific antigen (PSA, hK3) is a diagnostic marker for prostatic cancer but lacks the specificity to sufficiently distinguish between prostatic cancer and benign prostatic hyperplasia (BPH). Human glandular kallikrein 2 (hK2) has been proposed as a potential diagnostic marker for prostate cancer that could complement the current PSA test. Recently we demonstrated that proPSA is present in prostate cancer sera. This study examines the expression of prohK2 in prostate cells and its presence in human sera. Western blot analysis was used to assess prohK2 expression in the human carcinoma cell line, LNCaP. A highly specific and sensitive dual monoclonal immunoassay for prohK2 was developed and used to assess the presence of prohK2 in human sera. prohK2 was detected in the spent media of LNCaP cells. Furthermore, prohK2 was present at immunodetectable concentrations in human sera, and its concentration was increased in prostatic cancer and BPH. These results indicate for the first time that prohK2 is secreted by human prostate cells and is a major component of uncomplexed (free) hK2 in human sera. In addition, prohK2 in human sera is associated with prostate disease and thus may be a useful marker for prostatic cancer and BPH.
Respiration and Cardiac Activity Sensing Using 3-D Cameras (2020)

Remote vital sign monitoring at home with commercially viable hardware extends care from hospital wards to personal settings without overwhelming health care providers and resources. In this paper, we explore usage of Azure Kinect (Microsoft) to monitor respiration and cardiac activity of a subject. We propose a fusion sensing technique that ensures immunity to ambient lighting conditions and movements of the subject, two key limitations while employing cameras or radars respectively. The functionality of this process is enabled by the phenomenon of Photoplethysmography (PPG) and availability of commercial sensors that can leverage it. We investigate robustness of the proposed technique by conducting experiments in variable lighting conditions while the subject is in motion. A comparison is drawn to an RGB camera and the results are validated using a pulse oximeter, a contact PPG sensor.
Studies on the metal binding sites in the catalytic domain of 1,4-galactosyltransferase (2002)

The catalytic domain of bovine beta1,4-galactosyltransferase (beta4Gal-T1) has been shown to have two metal binding sites, each with a distinct binding affinity. Site I binds Mn(2+) with high affinity and does not bind Ca(2+), whereas site II binds a variety of metal ions, including Ca(2+). The catalytic region of beta4Gal-T1 has DXD motifs, associated with metal binding in glycosyltransferases, in two separate sequences: D(242)YDYNCFVFSDVD(254) (region I) and W(312)GWGGEDDD(320) (region II). Recently, the crystal structure of beta4Gal-T1 bound with UDP, Mn(2+), and alpha-lactalbumin was determined in our laboratory. It shows that in the primary metal binding site of beta4Gal-T1, the Mn(2+) ion, is coordinated to five ligands, two supplied by the phosphates of the sugar nucleotide and the other three by Asp254, His347, and Met344. The residue Asp254 in the D(252)VD(254) sequence in region I is the only residue that is coordinated to the Mn(2+) ion. Region II forms a loop structure and contains the E(317)DDD(320) sequence in which residues Asp318 and Asp319 are directly involved in GlcNAc binding. This study, using site-directed mutagenesis, kinetic, and binding affinity analysis, shows that Asp254 and His347 are strong metal ligands, whereas Met344, which coordinates less strongly, can be substituted by alanine or glutamine. Specifically, substitution of Met344 to Gln has a less severe effect on the catalysis driven by Co(2+). Glu317 and Asp320 mutants, when partially activated by Mn(2+) binding to the primary site, can be further activated by Co(2+) or inhibited by Ca(2+), an effect that is the opposite of what is observed with the wild-type enzyme.
Cutting Edge: Cationic Antimicrobial Peptides Block the Binding of Lipopolysaccharide (LPS) to LPS Binding Protein (2000)

We investigated the mechanism by which cationic antimicrobial peptides block the activation of macrophages by LPS. The initial step in LPS signaling is the transfer of LPS to CD14 by LPS binding protein (LBP). Because many cationic antimicrobial peptides bind LPS, we asked whether these peptides block the binding of LPS to LBP. Using an assay that measures the binding of LPS to immobilized LBP, we show for the first time that a variety of structurally diverse cationic antimicrobial peptides block the interaction of LPS with LBP. The relative ability of different cationic peptides to block the binding of LPS to LBP correlated with their ability to block LPS-induced TNF-alpha production by the RAW 264.7 macrophage cell line.