gebhart/patrepeval huggingface dataset:
Development and Characterization of a Human In Vitro Resorption Assay: Demonstration of Utility Using Novel Antiresorptive Agents (1999)

A human in vitro resorption assay has been developed using osteoclastoma-derived osteoclasts and used to evaluate novel antiresorptive agents including antagonists of the alphavbeta3 integrin, and inhibitors of cathepsin K and the osteoclast ATPase. The potency of novel compounds in the in vitro resorption assay correlates with functional assays for each class of inhibitor: the human alphavbeta3-mediated cell adhesion assay for the vitronectin receptor antagonists (r2 = 0.82), the chick osteoclast vacuolar ATPase enzyme assay for the H+-ATPase inhibitors (r2 = 0.77) and the recombinant human cathepsin K enzyme assay for the cathepsin K inhibitors (r2 = 0.80). Cell suspensions, rich in osteoclasts, are prepared by collagenase digestion of the tumor tissue. These cells can be stored long-term in liquid nitrogen and upon thawing maintain their bone-resorbing phenotype. The cryopreserved cells can be cultured on bovine cortical bone for 24-48 h and resorption can be measured by either confocal microscopy or biochemical assays. The resorptive activity of osteoclasts derived from a number of tumors can be inhibited reproducibly using a number of mechanistically unique antiresorptive compounds. In addition, the measurement of resorption pits by laser confocal microscopy correlates with the release of type I collagen C-telopeptides or N-telopeptides, as measured by enzyme-linked immunosorbent assay. Resorption can be measured reproducibly using a 48-h incubation of osteoclasts on bone slices, or a 24-h incubation with bone particles. This in vitro human osteoclast resorption assay provides a robust system for the evaluation of inhibitors of osteoclastic function that may be developed for the treatment of metabolic bone diseases such as osteoporosis.
Blood Genomics in Human Stroke (2007)

Advances in microarray technology and the sequencing of the human genome are opening up new possibilities for applying genomic information in clinical medicine, using information about structural polymorphisms in DNA and changes in gene expression as measured by mRNA. Gene expression profiling studies in cancer samples have led to the identification of clinical signatures that are already being applied in some centers. In stroke, it may be possible to use peripheral blood as a source of mRNA to study gene expression. After stroke, there is a selective recruitment and migration of white blood cells to the ischemic focus in the brain. This appears to involve all white cell types and is believed to impact significantly on tissue and clinical outcome through the exacerbation of ischemic injury, particularly after reperfusion, on the one hand, and conversely contributing to tissue remodeling and repair days to weeks after stroke. The first results from clinical studies in ischemic stroke suggest that a gene expression signature can be demonstrated from peripheral white blood cells and that this represents at least a partial adaptation to the altered cerebral microenvironment. Further studies are indicated to see whether these methods may lead to new management approaches for stroke.
In situclick chemistry: from small molecule discovery to synthetic antibodies (2012)

Advances in the fields of proteomics, molecular imaging, and therapeutics are closely linked to the availability of affinity reagents that selectively recognize their biological targets. Here we present a review of Iterative Peptide In Situ Click Chemistry (IPISC), a novel screening technology for designing peptide multiligands with high affinity and specificity. This technology builds upon in situ click chemistry, a kinetic target-guided synthesis approach where the protein target catalyzes the conjugation of two small molecules, typically through the azide-alkyne Huisgen cycloaddition. Integrating this methodology with solid phase peptide libraries enables the assembly of linear and branched peptide multiligands we refer to as Protein Catalyzed Capture Agents (PCC Agents). The resulting structures can be thought of as analogous to the antigen recognition site of antibodies and serve as antibody replacements in biochemical and cell-based applications. In this review, we discuss the recent progress in ligand design through IPISC and related approaches, focusing on the improvements in affinity and specificity as multiligands are assembled by target-catalyzed peptide conjugation. We compare the IPISC process to small molecule in situ click chemistry with particular emphasis on the advantages and technical challenges of constructing antibody-like PCC Agents.
Indoor seismology by probing the Earth's interior by using sound velocity measurements at high pressures and temperatures (2007)

The adiabatic bulk (K(S)) and shear (G) moduli of mantle materials at high pressure and temperature can be obtained directly by measuring compressional and shear wave velocities in the laboratory with experimental techniques based on physical acoustics. We present the application of the current state-of-the-art experimental techniques by using ultrasonic interferometry in conjunction with synchrotron x radiation to study the elasticity of olivine and pyroxenes and their high-pressure phases. By using these updated thermoelasticity data for these phases, velocity and density profiles for a pyrolite model are constructed and compared with radial seismic models. We conclude that pyrolite provides an adequate explanation of the major seismic discontinuities at 410- and 660-km depths, the gradient in the transition zone, as well as the velocities in the lower mantle, if the uncertainties in the modeling and the variations in different seismic models are considered. The characteristics of the seismic scaling factors in response to thermal anomalies suggest that anticorrelations between bulk sound and shear wave velocities, as well as the large positive density anomalies observed in the lower mantle, cannot be explained fully without invoking chemical variations.
Optical coherence tomography: high-resolution imaging in nontransparent tissue (1999)

Optical coherence tomography (OCT) is a method of high-resolution imaging originally developed for the transparent tissue of the eye. Recently, the technology has been advanced toward the difficult challenge of imaging in nontransparent tissue. In the paper, three topics are addressed. First, the principles behind OCT imaging are discussed. Second, the difficulties associated with OCT imaging in nontransparent tissue are outlined. Finally, the feasibility of OCT for medical imaging is discussed. Specifically, OCT demonstrates its greatest potential in situations where conventional biopsy is either dangerous or ineffective.
Enzyme Assembly after de Novo Synthesis in Rabbit Reticulocyte Lysate Involves Molecular Chaperones and Immunophilins (1995)

The folding kinetics of two luciferases were studied after synthesis in reticulocyte lysates to investigate whether molecular chaperones and/or folding catalysts are involved in the folding reactions. Two bacterial luciferases were used as model proteins: heterodimeric Vibrio harveyi luciferase (LuxAB), and a monomeric luciferase fusion protein (Fab2). Data indicate that folding of these enzymes to the native state occurs in the translation system, and that the extent of folding can be quantified. It was found that (i) folding of LuxAB and Fab2 can clearly be separated in time from synthesis, (ii) folding of Fab2 and LuxAB is slow because it involves either transient (Fab2) or permanent (LuxAB) interaction of polypeptides, (iii) preservation of the assembly competent state of LuxA and/or LuxB and folding of Fab2 depend on ATP-hydrolysis, (iv) folding of Fab2 and LuxAB is partially sensitive to cyclosporin A (CsA) and FK506, i.e. inhibitors of two distinct peptidylprolyl cis/trans-isomerases. Thus, bacterial luciferases provide a unique system for direct measurement of the effects of ATP-dependent molecular chaperones on protein folding and enzyme assembly in reticulocyte lysates. Furthermore, these two luciferases provide the first direct evidence documenting the involvement of peptidylprolyl cis/trans-isomerases in protein biogenesis in a eukaryotic cytosol.
Alpha1-Antichymotrypsin Level in Cerebrospinal Fluid Is Closely Associated with Late Onset Alzheimer's Disease. (1995)

The levels of alpha 1-antichymotrypsin (ACT) in cerebrospinal fluid (CSF) from 66 sporadic Alzheimer's disease (AD) patients and 54 normal controls were measured by enzyme immunoassay and compared. There was no correlation (r = 0.259, n = 54) between the ACT level and normal aging. The levels of ACT were significantly higher in the total AD group (p < 0.01) than in the normal control group. Dividing AD patients into early onset AD (n = 27) and late onset AD groups (n = 39), the mean level of CSF ACT in the late onset AD group was significantly higher than that in the normal control group (p < 0.001) and that in the early onset AD group (p < 0.01). Thus, the level of ACT in CSF is closely associated with late onset AD.
Activation of human dendritic cells through CD40 cross-linking. (1994)

Dendritic cells, the professional antigen-presenting cells (APC) involved in T cell priming, express CD40, a molecule which triggering plays a key role in B cell growth and differentiation as well as monocyte activation. Herein we demonstrate that dendritic Langerhans cells (D-Lc) generated by culturing cord blood CD34+ progenitor cells with granulocyte/macrophage colony-stimulating and tumor necrosis factor alpha (TNF-alpha) express functional CD40 at a density higher than that found on B cells. Culturing D-Lc on CD40-ligand (CD40L) transfected L cells allowed D-Lc survival as 50 +/- 15% of seeded cells were recovered after 4 d while only 5% survived over control L cells. CD40 activation induced important morphological changes with a reduction of cytoplasmic content and a remarkable increase of dendrite development as well as an altered phenotype. In particular, CD40 triggering induced maintenance of high levels of major histocompatibility complex class II antigens and upregulation of accessory molecules such as CD58, CD80 (B7-1) and CD86 (B7-2). CD40 engagement also seems to turn on D-Lc maturation as illustrated by upregulation of CD25, a molecule usually expressed on interdigitating dendritic cells of secondary lymphoid organs. Finally, CD40 activated D-Lc secreted a limited set of cytokines (TNF-alpha, IL-8, and macrophage inflammatory protein 1 alpha [MIP-1 alpha]) whereas a similar activation induced elutriated monocytes to secrete IL-1 alpha, IL-1 beta, IL-6, IL-8, IL-10, TNF-alpha, and MIP-1 alpha. As D-Lc activated T cells upregulated CD40L, it is likely that CD40 activation of D-Lc observed herein with a fibroblast cell line stably expressing CD40L, mimics physiological interactions between dendritic cells and T cells.
The effect of artificial antigen-presenting cells with preclustered anti-CD28/-CD3/-LFA-1 monoclonal antibodies on the induction of ex vivo expansion of functional human antitumor T cells (2008)

Our artificial antigen-presenting cells might represent an efficient tool to rapidly obtain a sufficient number of functional T cells for adoptive immunotherapy in patients with cancer.
Traumeel vs. diclofenac for reducing pain and improving ankle mobility after acute ankle sprain: A multicentre, randomised, blinded, controlled and non‐inferiority trial (2013)

T-O and T-G decreased pain and improved joint function to the same extent as D-G in acute ankle sprain, and were well tolerated.
Diversity Before Life (2006)

ASTROBIOLOGY SCIENCE CONFERENCE 2006WASHINGTON, D.C.-- According to a researcher at the Astrobiology Science Conference 2006, held here from 26 to 30 March, the final assembly of molecules leading to life must have happened somewhere between deep-sea vents, warm little ponds, and any number of other chemical stew pots rather than in any one type of environment. ([Read more][1].)

 [1]: http://www.sciencemag.org/cgi/content/full/312/5771/179b
Bovine Collagen Implant: Histologic Chronology in Pig Dermis (1983)

The histologic fate of an injectable form of type I bovine dermal collagen (Zyderm Collagen Implant, ZCI) in the pig dermis and subcutaneous tissue has been studied. Biopsies were taken sequentially and analyzed by hematoxylin and eosin (H&E) and Weigert's stain, by birefringence, by direct immunofluorescence (using a highly specific rabbit anti-Zyderm antibody), and by electron microscopy. The implant material was found to stimulate a host response resulting in implant degradation and replacement by newly generated host collagen.
A New Functional Suppressor tRNA/Aminoacyl−tRNA Synthetase Pair for the in Vivo Incorporation of Unnatural Amino Acids into Proteins (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA New Functional Suppressor tRNA/Aminoacyl−tRNA Synthetase Pair for the in Vivo Incorporation of Unnatural Amino Acids into ProteinsLei Wang, Thomas J. Magliery, David R. Liu, and Peter G. SchultzView Author Information Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037 Cite this: J. Am. Chem. Soc. 2000, 122, 20, 5010–5011Publication Date (Web):May 4, 2000Publication History Received18 February 2000Published online4 May 2000Published inissue 1 May 2000https://pubs.acs.org/doi/10.1021/ja000595yhttps://doi.org/10.1021/ja000595yrapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views3547Altmetric-Citations106LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Assays,Elements,Genetics,Monomers,Peptides and proteins Get e-Alerts
The Kinetics of Ammonia Exchange between Nickel Ammine Complexes and Ammonia in Aqueous and Anhydrous Ammonia Solutions Measured by Nuclear Magnetic Resonance of Nitrogen-14. II (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Kinetics of Ammonia Exchange between Nickel Ammine Complexes and Ammonia in Aqueous and Anhydrous Ammonia Solutions Measured by Nuclear Magnetic Resonance of Nitrogen-14. IIHans H. Glaeser, George A. Lo, Harold W. Dodgen, and John P. HuntCite this: Inorg. Chem. 1965, 4, 2, 206–208Publication Date (Print):February 1, 1965Publication History Published online1 May 2002Published inissue 1 February 1965https://pubs.acs.org/doi/10.1021/ic50024a017https://doi.org/10.1021/ic50024a017research-articleACS PublicationsRequest reuse permissionsArticle Views67Altmetric-Citations17LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Sprinklers, Crop Water Use, and Irrigation Time: Box Elder County (2001)

Sprinkler irrigation has been an important part of Utah's agricultural production since the early 1950s.About 40% of Utah's 1.3 million irrigated acres are watered with sprinklers, including hand move, wheel move, center pivot and other types.Sprinklers can be a good investment when properly designed, installed, maintained and managed.For every acre-foot of water supplied to an efficient sprinkler system a farmer can expect to harvest about 1 3/4 tons of alfalfa and 46 bushels of wheat.In contrast, the expected harvest with a typical surface irrigation system (flood or furrow) is less than 1 1/4 tons of alfalfa or about 30 bushels of wheat for each acre-foot of water applied.Sprinklers apply water more efficiently and uniformly than typical surface irrigation systems, thus they produce more yield for each acre-foot of water.Not all water applied by an irrigation system is used by the crop.Some water is lost to deep percolation, evaporation, or runoff.Application efficiency (Ea) is a term that tells how much of the water applied by the system is actually stored in the root zone for crop use.In Utah a typical sprinkler system has an Ea of 70% which means that 70% of the water applied by the sprinkler heads is actually stored in the soil for crop use.The actual Ea depends upon how evenly the sprinklers distribute water as well as other factors such as operating pressure, nozzle size and spacing, sprinkler maintenance condition, wind, air temperature and humidity (day versus night), and irrigation scheduling.In Utah, the average efficiency of surface irrigation in Utah is less than 50% as compared to the higher sprinkler efficiency values of more than 65% for well managed systems.
Metabolism-Based Identification of a Potent Thrombin Receptor Antagonist (2006)

The metabolism of our prototypical thrombin receptor antagonist 1, Ki = 2.7 nM, was studied and three major metabolites (2, 4, and 5) were found. The structures of the metabolites were verified independently by synthesis. Compound 4 was shown to be a potent antagonist of the thrombin receptor with a Ki = 11 nM. Additionally, compound 4 showed a 3-fold improvement in potency with respect to 1 in an agonist-induced ex-vivo platelet aggregation assay in cynomolgus monkeys after oral administration; this activity was sustained with 60% inhibition observed at 24 h post-dose. Compound 4 was highly active in functional assays and showed excellent oral bioavailability in rats and monkeys. Compound 4 showed a superior rat enzyme induction profile relative to compound 1, allowing it to replace compound 1 as a development candidate.
Differential location of nucleic acids within interchromatin granule clusters. (1993)

We have examined in great detail the distribution of nucleic acids within interchromatin granule clusters in different cell types by means of various immunocytochemical approaches. Using the in situ polyadenylate nucleotidyl transferase-immunogold technique for RNA detection or anti-RNA antibodies, we decisively demonstrate the presence of appreciable amount of RNA in clusters of interchromatin granules of untreated cells. Neither the in situ terminal deoxynucleotidyl transferase-immunogold technique nor anti-DNA antibodies, nor the in situ nick-translation technique for DNA detection have revealed any DNA in the interchromatin granule clusters. However, dispersed chromatin sensitive to DNase I are found at the borders and in the close vicinity of interchromatin granule clusters. The results indicate that interchromatin granule clusters should not be nuclear structures directly involved in RNA transcription but rather in some other steps of RNA metabolism.
Differences in the infrared bright pupil response of human eyes (2002)

In this paper, we describe experiments conducted to explain observed differences in the bright pupil response of human eyes. Many people observe the bright pupil response as the red-eye effect when taking flash photography. However, there is significant variation in the magnitude of the bright pupil response across the population. Since many commercial gaze-tracking systems use the infrared bright pupil response for eye detection, a clear understanding of the magnitude and cause of the bright pupil variation gives critical insight into the robustness of gaze tracking systems. This paper documents studies we have conducted to measure the bright pupil differences using infrared light and hypothesis factors that lead to these differences.
Method for identifying microbial antigens that stimulate specific lymphocyte responses: application to Salmonella. (1990)

Vaccine development and understanding of cellular immune stimulatory mechanisms have been impeded by the paucity of data on microbial antigens that stimulate protective immunity. We describe here a general method for identifying and isolating peptide antigens that specifically stimulate sensitized lymphocytes. First, Salmonella typhimurium C5 genomic DNA fragments were subcloned into Escherichia coli by use of the lambda gt11 expression vector. Next, antigens expressed by recombinant phage from this genomic library were tested for their capacity to stimulate proliferative responses in pooled lymphocytes obtained from BALB/c mice infected 14 days earlier with S. typhimurium. Of 2000 recombinant phages tested, 5 stimulated a polypeptide-antigen-specific proliferative response. Physical analyses of these 5 recombinant phages revealed cloned inserts of 0.5-2.4 kilobase pairs representing nonoverlapping regions of the C5 chromosome. Four of the five insert DNAs hybridized at high stringency to both S. typhimurium and Salmonella typhi total chromosomal DNA, suggesting that these pathogens of different host specificity share several antigenic determinants. Use of sensitized primary polyclonal lymphocytes provides a rapid and simple method for screening recombinant DNA libraries for clones that stimulate specific immune responses and avoids the use of cloned lymphocyte cell lines. This approach should be generally applicable to similar studies in different hosts of many other microbial pathogens.
The α-helical neck region of human lung surfactant protein D is essential for the binding of the carbohydrate recognition domains to lipopolysaccharides and phospholipids (1996)

We have expressed the carbohydrate recognition domains (CRDs) of human lung surfactant protein D (SP-D) in Escherichia coli as a trimeric structure held together by the alpha-helical neck region of the molecule. The DNA sequence coding for the neck-region peptide and the CRD of SP-D was subcloned and expressed as a fusion protein containing the E. coli maltose binding protein (MBP). After removal of the MBP, the recombinant structure, containing three CRDs of SP-D, was found to be comparable to native SP-D in terms of carbohydrate binding specificity, the binding to lipopolysaccharides (LPSs) of Gram-negative bacteria, and interaction with phospholipids. The CRD of SP-D, without the neck region peptide, was also expressed and shown to behave as a monomer that showed a very weak affinity for maltose-agarose, LPSs and phospholipids. The alpha-helical neck region on its own showed affinity for phospholipids and thus might contribute to the binding of SP-D to these structures. However, the possibility that hydrophobic patches, which are exposed only in the isolated neck region and not in the intact SP-D, plays a role in neck region-phospholipid interaction, cannot be excluded. The results confirm the importance of the neck region as a trimerizing agent in bringing together three CRDs and suggest that multivalency is important in the strong binding of SP-D to carbohydrate targets.