gebhart/patrepeval huggingface dataset:
Protocols for Nucleic Acid Analysis by Nonradioactive Probes (1993)

In assembling this book, Protocols for Nucleic Acid Analysis by Nonradioactive Probes, I have endeavored to select protocols that have wide applicability. My aim in doing so is to allow nucleic acid analysis to move from the confines of specialized research labora- ries and into general purpose and teaching laboratories. In particular, disciplines such as population biology and clinical diagnostics (where the application of the technology is important, not the technology itself) will find the newer techniques easier to perform with the qu- tity of samples that are normally required in these fields. Die-hard molecular biologists with hot fingers will find, by trying some of the protocols in this book, that nonradioactive protocols are normally faster than their radioactive brethren, and give more reliable results. An expanded description of the subject areas covered by this book is given in Chapter 1. The technology herein has very broad application; for instance, in conventional molecular biology research, population biology, plant and animal breeding, genetic mapping, paternity testing, forensics, prenatal diagnosis, and clinical and food microbiology. I have tried to include comprehensive protocols for both basic and more complex analyses. There are chapters dealing with the fundamentals of nucleic acid extraction from plants and a- mals, and with the procedures necessary to immobilize nucleic acids on solid supports. A range of labeling procedures is included, f- lowed by a selection of hybridization procedures
Structural Features of Prolactins and Growth Hormones That Can Be Related to Their Biological Properties* (1986)

IN THIS review we have compared the amino acid sequences of the GHs of eight mammalian species and the domestic chicken with the sequences of the PRLs of seven mammalian species. Individual amino acids, clusters of residues, and regions of the molecules were identified that were highly conserved among all of the hormones. Other individual amino acids, clusters of residues, and regions were identified that were specific to PRLs only or to GHs only. Attempts were made to associate these hormone-specific and commonly conserved features to the hormone-specific and shared biological properties of PRLs, GHs, and placental lactogens (PLs) by relating them to predicted secondary structure and hydropathy analysis. The latter involves predicting which regions of the molecules would be interior or exterior, based on the hydrophobicity or hydrophilicity of the regions. External clusters of conserved residues (consisting of both hormone-specific and commonly conserved) were identified that could be specifically associated with molecules that have GH activity or with those with lactogenic activity [including human (h) GH and PL]. Other external clusters were conserved in common among the PRLs and the GHs. The validity of our proposal that certain clusters of residues may be associated with GH and PRL binding determinants found support from the known structure and properties of two variant forms of hGH (i.e. 20 K and hGH-V). The residues that are likely to be responsible for hGH having PRL activity and for hPL not having GH activity were also identified.
Receptor complexes for each of the Class 3 Semaphorins (2012)

The Class 3 Semaphorins (Sema3s) are a sub-family of proteins whose known biological roles are varied and growing. The mechanism of action of the Sema3s requires binding to transmembrane receptors that comprise heteromeric complexes of Neuropilins, Plexins and cell adhesion molecules (CAMs). However, knowledge of the receptor components of the Sema3s remains incomplete, and there may be receptor components which are as yet undiscovered. The receptor complexes of the Sema3s share receptor components with each other, and it is the specific combination of these components within a heteromeric complex that is thought to give rise to selective binding and signalling for individual Sema3s. This crosstalk makes it experimentally difficult to define a single holoreceptor for each Sema3. Furthermore, the receptor composition for a given Sema3 may differ between cell types, and change as a function of developmental state or pathological situation. Nevertheless, there are at least some known differences in the constitutive structure of the receptors for the Sema3s. For example in neural cells, Sema3a and Sema3f signal through different Neuropilins (Nrp1 and Nrp2 respectively) and L1cam only appears important for Sema3a signaling, while Nrcam forms a complex with Nrp2. Further complexity arises from crosstalk of other families of ligands (e.g., VEGF) with Sema3 receptor components. Thus the Sema3s, which have been shown as antagonists for each other, can also act as antagonists for other families of molecules. This review compiles experimental evidence describing the receptor components for the Sema3s, detailing the current state of knowledge of which components are important for signaling of each Sema3 before going on to consider possible future directions for the field.
HMDB: the Human Metabolome Database (2007)

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca.
Cerebral Asymmetry of the “Top-Down” Allocation of Attention to Global and Local Features (2000)

Neuropsychological and neuroimaging studies have indicated that global and local features of a visual scene are processed differentially by the two hemispheres. Although visual selective attention is suggested to play a role in the hemispheric asymmetry, the precise mechanism of attentional control for the global-local processing is not fully understood. We investigated the neural correlates of cerebral asymmetry in directing attention to the global pattern and local components of a hierarchical stimulus. Event-related brain potentials (ERPs) were recorded while the subjects shifted their attention to the global or local level of a hierarchically structured letter. The shift direction was controlled by a preceding cue stimulus. The ERPs to the cue stimuli demonstrated that the right temporal-parietal and left posterior temporal regions were differentially activated during attentional allocation to the global and local levels, respectively. These effects started 240 msec after the cue stimulus. The late ERP components to the target stimuli also manifested the hemispheric global-local asymmetry as seen during the attentional shift. These electrophysiological results provided an asymmetrical neural basis for the "top-down" allocation of attention to global and local features and revealed the contribution of the temporal-parietal cortex to this attentional mechanism.
Discourse obligations in dialogue processing (1994)

We show that in modeling social interaction, particularly dialogue, the attitude of obligation can be a useful adjunct to the popularly considered attitudes of belief, goal, and intention and their mutual and shared counterparts. In particular, we show how discourse obligations can be used to account in a natural manner for the connection between a question and its answer in dialogue and how obligations can be used along with other parts of the discourse context to extend the coverage of a dialogue system.
Architectural analysis of multiple fiber ring networks employing optical paths (1997)

Analyzes the performance of various types of multiple fiber ring networks employing optical paths (OP's). The multiple fiber ring network architecture is suitable for achieving failure resilient networks that have extremely large bandwidth but are still upgradable against future increases in traffic. This architecture will overcome the limitation of conventional WDM rings in terms of network expansion capabilities, the number of nodes within the ring, and the number of OP's accommodated in the network. The generic node architecture suitable for multiple fiber ring networks is presented and functionality requirements are identified. The OP accommodation design algorithms that minimize the required node system scale are proposed. Based on the generic node architecture and proposed OP accommodation design algorithms, we evaluated the performance of several types of multiple fiber rings in terms of the required node system scale for rings under various conditions. The effect of the ring architecture (uni-/bidirectional rings), optical path schemes (wavelength path/virtual wavelength path), and different node connectivity patterns are demonstrated for the first time. The obtained results elucidate the criteria for selecting the most suitable multiple fiber ring architecture.
Association of p62, a Multifunctional SH2- and SH3-Domain-Binding Protein, with src Family Tyrosine Kinases, Grb2, and Phospholipase Cγ-1 (1995)

src family tyrosine kinases contain two noncatalytic domains termed src homology 3 (SH3) and SH2 domains. Although several other signal transduction molecules also contain tandemly occurring SH3 and SH2 domains, the function of these closely spaced domains is not well understood. To identify the role of the SH3 domains of src family tyrosine kinases, we sought to identify proteins that interacted with this domain. By using the yeast two-hybrid system, we identified p62, a tyrosine-phosphorylated protein that associates with p21ras GTPase-activating protein, as a src family kinase SH3-domain-binding protein. Reconstitution of complexes containing p62 and the src family kinase p59fyn in HeLa cells demonstrated that complex formation resulted in tyrosine phosphorylation of p62 and was mediated by both the SH3 and SH2 domains of p59fyn. The phosphorylation of p62 by p59fyn required an intact SH3 domain, demonstrating that one function of the src family kinase SH3 domains is to bind and present certain substrates to the kinase. As p62 contains at least five SH3-domain-binding motifs and multiple tyrosine phosphorylation sites, p62 may interact with other signalling molecules via SH3 and SH2 domain interactions. Here we show that the SH3 and/or SH2 domains of the signalling proteins Grb2 and phospholipase C gamma-1 can interact with p62 both in vitro and in vivo. Thus, we propose that one function of the tandemly occurring SH3 and SH2 domains of src family kinases is to bind p62, a multifunctional SH3 and SH2 domain adapter protein, linking src family kinases to downstream effector and regulatory molecules.
Essential and dispensable roles of ATR in cell cycle arrest and genome maintenance (2003)

A Cre/lox-conditional mouse line was generated to evaluate the role of ATR in checkpoint responses to ionizing radiation (IR) and stalled DNA replication. We demonstrate that after IR treatment, ATR and ATM each contribute to early delay in M-phase entry but that ATR regulates a majority of the late phase (2-9 h post-IR). Double deletion of ATR and ATM eliminates nearly all IR-induced delay, indicating that ATR and ATM cooperate in the IR-induced G2/M-phase checkpoint. In contrast to the IR-induced checkpoint, checkpoint delay in response to stalled DNA replication is intact in ATR knockout cells and ATR/ATM and ATR/p53 double-knockout cells. The DNA replication checkpoint remains intact in ATR knockout cells even though the checkpoint-stimulated inhibitory phosphorylation of Cdc2 on T14/Y15 and activating phosphorylation of the Chk1 kinase no longer occur. Thus, incomplete DNA replication in mammalian cells can prevent M-phase entry independently of ATR and inhibitory phosphorylation of Cdc2. When DNA replication inhibitors are removed, ATR knockout cells proceed to mitosis but do so with chromosome breaks, indicating that ATR provides a key genome maintenance function in S phase.
Interaction of Focal Adhesion Kinase with Cytoskeletal Protein Talin (1995)

The interaction of cells with extracellular matrix proteins plays a critical role in a variety of biological processes. Recent studies suggest that cell-matrix interactions mediated by integrins can transduce biochemical signals to the cell interior that regulate cell proliferation and differentiation. These studies have placed the focal adhesion kinase (FAK), an intracellular protein tyrosine kinase, in a central position in integrin-initiated signal transduction pathways (Zachary, I., and Rozengurt, E. (1992) Cell 71, 891-894; Schaller, M., and Parsons, J. T. (1993) Trends Cell Biol. 3, 258-262). Here, we report data suggesting a possible association of FAK with the cytoskeletal protein talin in NIH 3T3 cells. We have identified a 48-amino acid sequence in the carboxyl-terminal domain of FAK necessary for talin binding in vitro. Furthermore, we have correlated the ability of integrin to induce FAK phosphorylation with its ability to bind talin using a mutant integrin lacking the carboxyl-terminal 13 amino acids. These studies suggest talin may be a mediator for FAK activation in signaling initiated by integrins and may provide an explanation for the dependence on the integrity of actin-cytoskeleton of multiple intracellular signaling pathways converging to FAK activation and autophosphorylation.
Study of human precorneal tear film thickness and structure using laser interferometry. (1992)

The authors previously found that measurements of precorneal tear film thickness in animals, using laser interferometry and confocal microscopy, were larger than earlier estimates. They proposed that this occurred because optical methods did not disturb film structure and measured full thickness, including mucus. In the present study, tear film thickness was measured in humans. Coherent light was reflected from eyes and formed interference patterns. Thickness was determined from spacing of fringes. Mean thickness in six subjects was 34-45 microns, more than four times larger than earlier values. Validity and accuracy of measurements by interferometry were examined in our earlier study using confocal microscopy. Here it provided supportive evidence. Tear film thickness was estimated from optical sections through the corneas of three subjects to be 41-46 microns. Mucus content of the film also was examined. Interferometry was used to measure thinning after application of a mucolytic agent. There was no change in thickness after 5 min exposure to 0.1% (weight/volume) acetylcysteine. Solutions of 20% caused thinning to 11 microns, and thickness slowly increased to reach its original value over 40 min. Thus, the film seemed to be composed substantially of mucus, not aqueous fluid. The results also provided evidence that measurements by interferometry did not include underlying epithelium. Earlier nonoptical methods probably did not include the portion of the film that contained mucus. They seem to have greatly underestimated human tear film thickness.
Enhanced Diffusion in Boron Implanted Silicon (1985)

The cause of enhanced diffusion when boron is implanted into crystalline silicon is examined. A report is presented on an experimental non-local diffusion model. Samples are annealed with and without the heavily damaged surface region and profiled by SIMS. Preliminary results show similar diffusion in both sample lots in contradiction to the Fair proposal, implying that the enhanced tail diffusion is a local phenomenon.
Safety and efficacy of canakinumab in Japanese patients with phenotypes of cryopyrin-associated periodic syndrome as established in the first open-label, phase-3 pivotal study (24-week results). (2013)

Canakinumab 150 mg s.c. every 8 weeks was well-tolerated, highly efficacious and offered a convenient dosing regimen for treating Japanese patients with CAPS.
Human hemoglobin G-Makassar variant masquerading as sickle cell anemia (2018)

Human hemoglobin of G-Makassar variant has been reported very rarely with Beta Thalassemia. In year 1969 Hb GMakassar was first identified in Makassar, Sulawesi (Celebes), Republic of Indonesia. The disease was first published in 1969 and 33 years later it has been reported at a family of Thailand origin. We report a 45-yearold Malay man who was investigated for anemia and thrombocytopenia then diagnosed with Hb G-Makassar. This finding describes as a new Hemoglobin GMakassar discovered in Malaysia after 14 years diagnosed in Thailand.
The molecular structure of lubricating glycoprotein-I, the boundary lubricant for articular cartilage. (1981)

Lubricating glycoprotein-I (LGP-I) was prepared from bovine synovial fluid by density gradient sedimentation and gel-permeation chromatography. The LGP-I sample obtained was able to lubricate articular cartilage in a manner equivalent to that of whole synovial fluid. Chemical, physical, and electron microscope measurements were carried out to determine the structure of the LGP-I molecules. The molecular weight calculated from sedimentation equilibrium measurements was 2 X 10(5), and the solute distribution obtained indicated that LGP-I was relatively monodisperse. The s(0)20,w value was 4.84, and the intrinsic viscosity was 92 ml/g. The molecular weight and diffusion coefficient calculated from later light-scattering measurements was 2.06 x 10(5) and 1.10 x 10(-7) cm2/s, respectively. The electron microscope measurements showed that the LGP-I molecules had a number average length of 204 nm, a weight average length of 222 nm (with a standard deviation of 54 nm), and a width of 1-2 nm. These data and the kinked appearance of the molecules indicate that LGP-I is a partially extended flexible rod. The hydrodynamic measurements also indicate that LGP-I has the same structure in solution, although the apparently high s(0)20,w value, compared to other rod-like molecules, suggests that due to its flexibility LGP-I can occupy a more compact domain than would be expected based on its extended dimensions. The name of "lubricin" is suggested for this lubricating glycoprotein.
Antibody response to serotype-specific and cross-reactive neutralization epitopes on VP4 and VP7 after rotavirus infection or vaccination (1991)

By using a competitive solid-phase immunoassay with serotype-specific and cross-reactive neutralizing monoclonal antibodies directed at VP4 and VP7, we tested the antibody responses to some neutralization epitopes on VP4 and VP7 in individuals infected or vaccinated with rotavirus. Antibody responses to VP7 epitopes of the infecting serotype of virus were found at a high frequency in both infants and children. In contrast, antibody responses to VP4 and heterotypic VP7 were observed only when the individuals possessed antibodies to any serotype of rotavirus in their acute-phase or prevaccination sera.
224. The triterpene resinols and related acids. Part VI (1939)

C. W. Picard, K. S. Sharples and F. S. Spring, J. Chem. Soc., 1939, 1045 DOI: 10.1039/JR9390001045
Quantification of integrin subunits on human prostatic cell lines—Comparison of nontumorigenic and tumorigenic lines (1997)

Comparison of nontumorigenic and cancerous lines suggests that a loss of the alpha 4-subunit correlates with the acquisition of tumorigenicity and perhaps metastatic potential. The ability to quantify expression of integrin subunits on prostate cell lines allows the determination of regulation by factors responsible for growth, tumorigenicity, and/or metastasis.
Multiple DNA-Protein Complexes at a Circadian-Regulated Promoter Element. (1995)

Higher plant CAB genes encode chlorophyll a/b binding proteins that are part of light-harvesting complexes in chloroplasts. Transcription of the Arabidopsis CAB2 (lhcb1*1) gene is under the control of a circadian oscillator and exhibits high amplitude diurnal oscillations that persist within a period close to 24 hr in the absence of environmental time cues. Initial deletion studies in transgenic tobacco have demonstrated that the region between -111 and -38 of the CAB2 promoter sequence confers circadian regulation to a luciferase (luc) reporter gene. We dissected this element further and characterized five DNA binding complexes from Arabidopsis whole-cell extracts that bind within this region of the promoter and may be components of the signal transduction pathway for the control of transcription by the circadian clock. The in vivo analysis of cab2::luc fusion constructs in transgenic Arabidopsis demonstrated that a circadian-regulated element lies within a 36-bp sequence that overlaps a conserved CCAAT box and contains binding sites for three putative transcription factors.
Transferable erythromycin resistance in Listeria spp. isolated from food (1996)

An erythromycin-resistant (Emr) Listeria innocua and an Emr Listeria monocytogenes isolate both carried ermC genes, which code for rRNA methylases. The ermC genes were transferable by conjugation to recipient L. monocytogenes, Listeria ivanovii, and Enterococcus faecalis but did not appear to be associated with conjugative plasmids.
Multiparameter seismic inversion of noisy data (1984)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1984Multiparameter seismic inversion of noisy dataAuthors: Douglas W. HansonB. Bertram ChangRamarao InguvaDouglas W. HansonO'Connor Research, Inc;, B. Bertram ChangO'Connor Research, Inc;, and Ramarao InguvaUniv. of Wyominghttps://doi.org/10.1190/1.1894139 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1894139FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1984ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1984 Pages: 856 publication data© 1984 Copyright © 1984 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 24 Mar 2005 CITATION INFORMATION Douglas W. Hanson, B. Bertram Chang, and Ramarao Inguva, (1984), "Multiparameter seismic inversion of noisy data," SEG Technical Program Expanded Abstracts : 649-652. https://doi.org/10.1190/1.1894139 Plain-Language Summary PDF DownloadLoading ...
ATXN2 Is Regulated by a Promoter Associated Antisense Long Noncoding RNA (lncRNA) (P05.030) (2013)

OBJECTIVE: Our study objective is to characterize the role of a novel ATXN2 promoter associated antisense long non-coding RNA (ATXN2-lncRNA) in regulating the spinocerebellar ataxia type 2 gene ATXN2.
Rapid interpretation of EKG's : an interactive course (2000)

The reader's rapid assimilation of medical concepts is the key to the continuing success of this best-selling book. A caption explains the concept illustrated on each page, and a few simple sentences reinforce the concept with interactive (programmed) learning, which links to the following page. Dr. Dubin's light and entertaining style, known world-wide, makes learning enjoyable. Practice twelve-lead tracings at the end establish self-confidence, and summarised reference sheets with examples (designed to be copied) provide an excellent review. This work is most recently updated in February 2006.