gebhart/patrepeval huggingface dataset:
Underway physical oceanography and carbon dioxide measurements during Roger A. Revelle cruise 33RR20160321 (2017)

Wanninkhof, Rik; Pierrot, Denis (2017): Underway physical oceanography and carbon dioxide measurements during Roger A. Revelle cruise 33RR20160321 [dataset]. NOAA-Atlantic Oceanographic and Meteorological Laboratory, Miami, PANGAEA, https://doi.org/10.1594/PANGAEA.878375, In supplement to: Bakker, Dorothee C E; O'Brien, Kevin M; Pfeil, Benjamin; Currie, Kim I; Kozyr, Alexander; Landa, Camilla S; Lauvset, Siv K; Metzl, Nicolas; Nakaoka, Shin-Ichiro; Nojiri, Yukihiro; Nonaka, Isao; Olsen, Are; Omar, Abdirahman M; Pierrot, Denis; Saito, Shu; Smith, Karl; Sutton, Adrienne; Sullivan, Kevin; Tilbrook, Bronte; Wanninkhof, Rik; Akl, John; Alin, Simone R; Barbero, Leticia; Barrera, Kira E; Beaumont, Laurence; Becker, Meike; Bernard, Christophe; Bott, Randy; Byrne, Robert; Cai, Wei-Jun; Cosca, Catherine E; Cross, Jessica; Daly, Kendra L; Danguy, Théo; De Carlo, Eric Heinen; Dietrich, Colin; Feely, Richard A; Fiedler, Björn; Glockzin, Michael; Gove, Matthew D; Goyet, Catherine; Guillot, Antoine; Hales, Burke; Hartman, Sue E; Herndon, Julian; Hoppema, Mario; Humphreys, Matthew P; Hunt, Christopher W; Huss, Betty; Hydes, David; Ibánhez, J Severino P; Ishii, Masao; Johannessen, Truls; Jones, Steve D; Kitidis, Vassilis; Knorr, Paul O; Körtzinger, Arne; Kosugi, Naohiro; Lee, Charity M; Lefèvre, Nathalie; Lo Monaco, Claire; Liu, Xuewu; Maenner, Stacy M; Manke, Ansley; Manzello, Derek P; Mathis, Jeremy T; Mickett, John; Millero, Frank J; Monacci, Natalie; Monteiro, Pedro; Morell, Julio; Munro, David R; Musielewicz, Sylvia; Neill, Craig; Newberger, Timothy; Newton, Jan; Noakes, Scott; Noh, Jae Hoon; Ohman, Mark; Ólafsdóttir, Sólveig Rósa; Ólafsson, Jón; Osborne, John; Padín, Xose Antonio; Rehder, Gregor; Reimer, Janet J; Robbins, Lisa L; Rutgersson, Anna; Sabine, Christopher L; Salisbury, Joe; Sasano, Daisuke; Schlitzer, Reiner; Schuster, Ute; Send, Uwe; Sieger, Rainer; Skjelvan, Ingunn; Steinhoff, Tobias; Sutherland, Stewart C; Sweeney, Colm; Takahashi, Taro; Telszewski, Maciej; Vandemark, Douglas C; van Heuven, Steven; Wallace, Douglas WR; Woosley, Ryan J; Wynn, Jonathan G; Yates, Kimberly Kaye (in prep.): Version 5 of the Surface Ocean CO2 Atlas (SOCAT).
Use of a cellular ELISA for the detection of cell surface antigens. (1992)

A sensitive, convenient and inexpensive enzyme-linked immunosorbent assay (ELISA) is described for the detection and relative quantitation of cell surface antigens. The cells to be tested are rapidly glutaraldehyde-fixed to the wells of microtiter plates, which can be stored for later assay, if desired. Alternatively, adherent cells may be left unfixed. Following incubation with antibodies specific for the antigens of interest, an enzyme-linked second antibody conjugate is added, followed by the substrate for the enzyme, as in a conventional ELISA for soluble proteins. The method is a sensitive and accurate alternative to immunofluorescence flow cytometry for rapid and inexpensive screening of large numbers of cell samples.
The Development of an Acne Quality of Life Scale: Reliability, Validity, and Relation to Subjective Acne Severity in Mild to Moderate Acne Vulgaris (1998)

We developed a disease-specific 9-item Acne Quality of Life scale that is sensitive to changes in patient-rated indices of acne severity and the psychological morbidity that is associated with acne. Seventy patients with mild to moderate acne vulgaris completed a 12-item scale that was developed to assess both the social and vocational impacts of acne. Factor analysis revealed the presence of two dimensions underlying the quality of life construct. The first dimension consisted of 9 items and addressed the social impact of acne, while the second dimension consisted of 3 items and addressed the vocational impact of acne. Only the first dimension correlated with indices of acne severity, such as pustules and scarring, and all 3 scales correlated with a wide range of psychopathologic measures. The 9-item scale had a very high degree of internal consistency and test-retest reliability. This 9-item scale may be used to evaluate the relation between acne severity and quality of life, especially among mildly to moderately affected patients for whom quality of life issues are often a major consideration in deciding whether or not to institute therapies for the acne.
SdrG, a Fibrinogen-binding Bacterial Adhesin of the Microbial Surface Components Recognizing Adhesive Matrix Molecules Subfamily from Staphylococcus epidermidis, Targets the Thrombin Cleavage Site in the Bβ Chain (2001)

Staphylococcus epidermidis is an important opportunistic pathogen and is a major cause of foreign body infections. We have characterized the ligand binding activity of SdrG, a fibrinogen-binding microbial surface component recognizing adhesive matrix molecules from S. epidermidis. Western ligand blot analysis showed that a recombinant form of the N-terminal A region of SdrG bound to the native Bbeta chain of fibrinogen (Fg) and to a recombinant form of the Bbeta chain expressed in Escherichia coli. By analyzing recombinant truncates and synthetic peptide mimetics of the Fg Bbeta chain, the binding site for SdrG was localized to residues 6-20 of this polypeptide. Recombinant SdrG bound to a synthetic 25-amino acid peptide (beta1-25) representing the N terminus of the Fg Bbeta chain with a KD of 1.4 x 10(-7) m as determined by fluorescence polarization experiments. This was similar to the apparent K(D) (0.9 x 10(-7) m) calculated from an enzyme-linked immunosorbent assay where SdrG bound immobilized Fg in a concentration-dependent manner. SdrG could recognize fibrinopeptide B (residues 1-14), but with a substantially lower affinity than that observed for SdrG binding to synthetic peptides beta1-25 and beta6-20. However, SdrG does not bind to thrombin-digested Fg. Thus, SdrG appears to target the thrombin cleavage site in the Fg Bbeta chain. In fact, SdrG was found to inhibit thrombin-induced fibrinogen clotting by interfering with fibrinopeptide B release.
Reflection and transmission coefficients for seismic waves in ellipsoidally anistropic media (1979)

Abstract The deficiency of an isotropic model of the earth in the explanation of observed traveltime phenomena has led to the mathematical investigation of elastic wave propagation in anisotropic media. A type of anisotropy dealt with in the literature (Potsma, 1955; Cerveny and Psencik, 1972; and Vlaar, 1968) is uniaxial anisotropy or transverse isotropy. A special case of transverse isotropy which assumes the wavefronts to be ellipsoids of revolution has been used by Cholet and Richard (1954) and Richards (1960) in accounting for the observed traveltimes at Berraine in the Sahara and in the foothills of Western Canada.The kinematics of this problem have been treated in a number of papers, the most notable being Gassmann (1964). However, to appreciate fully the effect of anisotropy, the dynamics of the problem must be explored.Assuming a model of the earth consisting of plane transversely isotropic layers with the axes of anisotropy perpendicular to the interfaces, a prime requisite for obtaining amplitude distance curves or synthetic seismograms is the calculation of reflection and transmission coefficients at the interfaces.In this paper the special case of ellipsoidal anisotropy will be considered. That the quasi-shear SV wavefront is forced to be spherical by this assumption is unfortunate, but it is instructive to investigate this simple anisotropic model as it incorporates many features inherent to wave propagation in a more general anisotropic medium.A brief outline of the theory for wave propagation in an ellipsoidally anisotropic medium is given and the analytic expressions for the reflection and transmission coefficients are listed. A complete derivation of reflection and transmission coefficients in transversely isotropic media can be found in Daley and Hron (1977). Finally, all 24 possible reflection and transmission coefficients and surface conversion coefficients are displayed for varying degrees of anisotropy.
Ring Closing Metathesis in the Synthesis of Sultones and Sultams (2004)

Unsaturated sultones with normal, medium and large ring sizes were efficiently synthesized by ring closing metathesis (RCM) of sulfonates. The resulting α,β-unsaturated sultones act as dienophiles in intermolecular Diels-Alder reactions. A first cyclic sulfate formation through RCM has been discovered, and a rapid access to β-lactams fused to a sultam moiety of variable ring size was developed from inexpensive, commercially available starting materials using RCM as the key operation. An efficient RCM of 4-vinyl-azetidin-2-ones to give 1-aza-bicyclo[4.2.0]oct-4-en-8-ones is also described.
Isolation of the Novel Human Guanine Nucleotide Exchange Factor Src Homology 3 Domain-Containing Guanine Nucleotide Exchange Factor (SGEF) and of C-Terminal SGEF, an N-Terminally Truncated Form of SGEF, the Expression of Which Is Regulated by Androgen in Prostate Cancer Cells (2003)

In searching for androgen-responsive genes in human prostate cancer cells, we have isolated two cDNAs that encode alternate forms of a novel Src homology 3 domain-containing guanine nucleotide exchange factor (SGEF). The SGEF mRNA is widely expressed in human tissues, and the predicted 871-amino acid SGEF protein contains Dbl homology and pleckstrin homology domains as well as an N-terminal proline-rich domain, a C-terminal Src homology 3 domain, and two nuclear localization signals. The second cDNA encodes a 139-amino acid N-terminally truncated form of SGEF designated C-terminal SGEF (CSGEF). In contrast to SGEF, CSGEF mRNA expression is restricted to prostate and liver. Moreover, CSGEF expression is up-regulated by androgens in LNCaP cells, whereas that of SGEF is not. Up-regulation of CSGEF was sensitive to actinomycin D but did not require new protein synthesis. The SGEF gene is located on chromosome 3q25.2 and consists of at least 15 exons. Based on the structure of the SGEF and CSGEF cDNAs, we deduced that CSGEF expression is controlled by an alternate androgen-responsive promoter of the SGEF gene. We hypothesize that SGEF is a ubiquitous regulator of Rho guanosine triphosphatases, whereas CSGEF may function as an androgen-induced regulator of Rho guanosine triphosphatase activity in epithelial cells of the human prostate.
Label-free imaging of blood vessel morphology with capillary resolution using optical microangiography. (2012)

Several tissue pathologies are correlated with changes in the blood vessel morphology and microcirculation that supplies the tissue. Optical coherence tomography (OCT) is an imaging technique that enables acquiring non-invasive three-dimensional images of biological structures with micrometer resolution. Optical microangiography (OMAG) is a method of processing OCT data which enables visualizing the three-dimensional blood vessel morphology within biological tissues. OMAG has high spatial resolution which allows visualizing single capillary vessels, and does not require the use of contrast agents. The intrinsic optical signals backscattered by the moving blood cells inside blood vessels are used as the contrast for which OMAG images are based on. In this paper, we discuss a brief review of the OMAG theory, and present some examples of applications for this technique.
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants (2015)

Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands and tandem repeats) in a promoter or a set of plant promoters. Additionally, TFBSs, CpG islands, and tandem repeats in the conserve regions between similar gene promoters are also identified. The current PlantPAN release (version 2.0) contains 16 960 TFs and 1143 TF binding site matrices among 76 plant species. In addition to updating of the annotation information, adding experimentally verified TF matrices, and making improvements in the visualization of transcriptional regulatory networks, several new features and functions are incorporated. These features include: (i) comprehensive curation of TF information (response conditions, target genes, and sequence logos of binding motifs, etc.), (ii) co-expression profiles of TFs and their target genes under various conditions, (iii) protein-protein interactions among TFs and their co-factors, (iv) TF-target networks, and (v) downstream promoter elements. Furthermore, a dynamic transcriptional regulatory network under various conditions is provided in PlantPAN 2.0. The PlantPAN 2.0 is a systematic platform for plant promoter analysis and reconstructing transcriptional regulatory networks.
Biological responses to electromagnetic fields <sup>1</sup> (1998)

Electrification in developed countries has progressively increased the mean level of extremely low-frequency electromagnetic fields (ELF-EMFs) to which populations are exposed; these humanmade fields are substantially above the naturally occurring ambient electric and magnetic fields of approximately 10(-4) Vm(-1) and approximately 10(-13) T, respectively. Several epidemiological studies have concluded that ELF-EMFs may be linked to an increased risk of cancer, particularly childhood leukemia. These observations have been reinforced by cellular studies reporting EMF-induced effects on biological systems, most notably on the activity of components of the pathways that regulate cell proliferation. However, the limited number of attempts to directly replicate these experimental findings have been almost uniformly unsuccessful, and no EMF-induced biological response has yet been replicated in independent laboratories. Many of the most well-defined effects have come from gene expression studies; several attempts have been made recently to repeat these key findings. This review analyses these studies and summarizes other reports of major cellular responses to EMFs and the published attempts at replication. The opening sections discuss quantitative aspects of exposure to EMFs and the incidence of cancers that have been correlated with such fields. The concluding section considers the problems that confront research in this area and suggests feasible strategies.
Setting Service Standards for Local Government Reception Services (1994)

Analyses the number, distribution and nature of enquiries made at Stirling District Council’s central reception and the times taken by staff to deal with them satisfactorily in order to measure meaningful service standards. A survey of customers was conducted to try to establish a profile of the users of the reception service. With the aid of queuing theory, tries to obtain a better understanding of the way in which reception service quality target levels can be defined, measured, monitored and improved.
Cluster analysis of molecular conformations (1994)

Abstract We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single‐link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.
Automated sample preparation of protein solid dosage forms: Novel application for the tablet processing workstation (2023)

Biological macromolecule solid dosage forms represent the frontier of orally administered pharmaceuticals. Analysis of these drug products poses new challenges compared to traditional small molecule tablets. In this study we demonstrate the first, to our knowledge, automated Tablet Processing Workstation (TPW) sample preparation of large molecule tablets. Tablets containing a modified version of human insulin were tested for content uniformity and the automated method was successfully validated for recovery, carryover and displayed manual method equivalency in repeatability and in-process stability. Per TPW's ability to process one sample sequentially, the total analysis cycle time is, in fact, increased. In lieu, a net gain in scientist productivity is realized by enabling continuous operation reducing analytical scientist labor time by 71% compared to manually conducted sample preparation.
Enzyme Immobilization on magnetic nanoparticles for enhancing biocatalysis (2018)

Magnetic nanoparticles have a wide range of applications in catalysis, separation, magnetic resonance imaging and drug delivery. This talk focuses on the synthesis, functionalization and application of magnetic nanoparticles for improving biocatalysis. Great progress in synthesizing uniform superaramagnetic nanoparticles with high saturation magnetization has been achieved, and various functional magnetic nanoparticles with specific components have been fabricated for enzyme immobilization in enhancing biocatalysis. Achievements in our research group together with recent progress in the world will be critically reviewed in this talk, and future trends and perspectives in the biocatalysis areas with robust magnetic nanoparticles will be outlined.
Interferon-gamma induces dipeptidylpeptidase IV expression in human glomerular epithelial cells. (1993)

Because dipeptidylpeptidase IV (DPP IV) is present in vivo on glomerular visceral epithelial cells and possesses immunogenic properties, as shown by the capability of anti-DPP IV antibody to induce the Heymann model of glomerulonephritis, we studied the expression and regulation of DPP IV in cultured human glomerular visceral epithelial cells. DPP IV is an ectoenzyme, as indicated by the rapid detection of the product of the reaction in the incubation medium of intact cells and the staining of paraformaldehyde-fixed cells in the presence of a specific anti-DPP IV antibody. DPP IV activity was inhibited by diisopropylfluorophosphate and phenylmethyl sulphonylfluoride. Its optimum pH was alkaline (7.7-8) and it exhibited a Km value of 0.94 mM. DPP IV expression was induced in cells treated by interferon-gamma (IFN-gamma). The effect was significant after a 3-day treatment with 100 U/ml. It increased with time, reaching a plateau after 11 days, and was dose-dependent with a maximum at a concentration of 1000 U/ml. Staining of the cells with anti-DPP IV antibody was also increased after a 6-day treatment with 100 U/ml IFN-gamma. It was shown by Northern analysis that, after 24 hr of exposure to 500 U/ml of IFN-gamma, DPP IV mRNA transcript was stimulated. Transcriptional activation by IFN-gamma did not require new protein synthesis. Interleukin-1 (IL-1) and cyclic AMP had a small stimulatory effect, whereas dexamethasone and phorbol esters were inefficient. These results suggest that DPP IV of glomerular epithelial cells may be up-regulated by IFN-gamma from activated T lymphocytes in glomerular diseases and during lymphocyte-mediated graft rejection.
Loop‐mediated isothermal amplification (LAMP): An effective molecular point‐of‐care technique for the rapid diagnosis of coronavirus SARS‐CoV‐2 (2021)

The novel coronavirus disease-2019 (Covid-19) public health emergency has caused enormous loss around the world. This pandemic is a concrete example of the existing gap between availability of advanced diagnostics and current need for cost-effective methodology. The advent of the loop-mediated isothermal amplification (LAMP) assay provided an innovative tool for establishing a rapid diagnostic technique based on the molecular amplification of pathogen RNA or DNA. In this review, we explore the applications, diagnostic effectiveness of LAMP test for molecular diagnosis and surveillance of severe acute respiratory syndrome coronavirus 2. Our results show that LAMP can be considered as an effective point-of-care test for the diagnosis of Covid-19 in endemic areas, especially for low- and middle-income countries.
Towards semantic visual SLAM (2014)

Summary form only given. Visual Simultaneous Localisation and Mapping is the process whereby a camera builds a map of a previously unseen environment, and localises itself with respect to that environment, often in real-time. Although there has been remarkable progress, and it is now possible, for example, to build dense maps in real-time using high-end commodity hardware, most SLAM research has remained rooted in geometry. Geometric representations are limited though, in that they rarely encode higher-level information to describe the scene, are wasteful of storage, and brittle to changes. I am therefore interested extending SLAM beyond geometry to more semantically meaningful representations in which a scene can be segmented into components, and compactly described and represented. In work towards that end, in this talk I will describe work i my group from the last few years that progresses to this end:. First, I will describe a system that combines detection, segmentation and tracking of instances of a known 3D object class with a system for real-time dense visual mapping. We learn a low dimensional space of shapes to encode prior shape knowledge, and then perform simultaneous segmentation and tracking of an instance of a 3D shape class by optimising for shape and pose. This tracking methodology is then incorporated into a system for real-time dense visual mapping of a scene demonstrating that prior knowledge of objects can be incorporated into a SLAM map to improve map fidelity. Second I will present work that shows how structured learning methods can be used within SLAM scene understanding methods. I will discuss a method for reconstructing building interiors using a combination of point-based parallel tracking and mapping, with single-view reconstruction techniques. Here, by leveraging prior knowledge of shape (namely that the building interior conforms to a "Manhattan" model), we develop an efficient global optimisation method for inferring key semantic properties of the scene, namely its boundaries: the floor, ceiling and walls. This method makes use of single-view pixel-level texture cues, as well as opportunistic use of 3D information such as photo-consistency, and sparse 3d map data. Finally I will discuss progress in using structured learning methods for interpreting RGB-D data using Decision Tree Fields.
Infrared rotating-analyzer ellipsometry: calibration and data processing (1993)

The necessary relationships and a calibration procedure are presented for a rotating-analyzer IR ellipsometer that uses wire grid polarizing optics. The wire grid polarizers contribute significant ellipticity because of relatively low extinction ratios. Jones matrices are used for a configuration consisting of a quarter-wave plate, a polarizer, a sample, and a rotating-analyzer ellipsometer. Results from a calibrated IR- and visible-light ellipsometer for silicon dioxide films on silicon are compared.