gebhart/patrepeval huggingface dataset:
Soluble E-selectin, ICAM-1 and VCAM-1 levels in systemic and coronary circulation in patients with variant angina (1997)

The purpose of this study was to assess whether the plasma levels of soluble adhesion molecules including E-selectin, . . intercellular adhesion molecule-1 ICAM-1 and vascular cell adhesion molecule-1 VCAM-1 are elevated in patients with variant angina and whether they are released in the coronary circulation. Methods: Antecubital venous plasma samples were collected from 33 patients . with variant angina, 22 patients with stable effort angina and 20 control subjects. Samples were also collected from the aortic root AO . and the coronary sinus CS in 18 patients with variant angina before and after left coronary spasm induced by intracoronary injection of acetylcholine. The soluble adhesion molecules were assayed by enzyme immunoassay. Results: Antecubital venous plasma soluble . .
Clinical flow cytometry : principles and application (1993)

Approach to the patient obstetrics - antepartum care intrapartum care postpartum care gynaecology - disorders of the breast chronic pelvic pain and dysmenorrhea sexuality vulvitis and vaginitis endometriosis reproductive endocrinology and infertility - neuro-ovarian cycle - normal menstrual cycle disorders of menstruation menopause gynaecologic oncology and neoplasia.
Approaches to carbocyclic analogues of the potent neuraminidase inhibitor 4-guanidino-Neu5Ac2en. X-Ray molecular structure of N-[(1S,2S,6R)-2-azido-6-benzyloxymethyl-4-formylcyclohex-3-enyl]acetamide (1995)

Various approaches using Diels–Alder chemistry have been established for the synthesis of truncated carbocyclic analogues 4 and 6 of 4-guanidino-Neu5Ac2en. In the case of compound 4, elaboration of an initial adduct from Danishefsky's diene and the dienophile 7 allowed access to the key enone 26. Methylenation of the carbonyl group and azide-induced opening of an intermediate oxazoline established the required framework regio- and stereo-specifically. Compounds 4 and 6 were found to retain interesting levels of antiviral activity comparable to those shown by their oxygen-containing counterparts.
Effects of pH Adjustment and Sodium Ions on Sour Taste Intensity of Organic Acids (2009)

Protonated organic acid species have been shown to be the primary stimuli responsible for sour taste of organic acids. However, we have observed that sour taste may be modulated when the pH of acid solutions is raised using sodium hydroxide. Objectives were to evaluate the effect of pH adjustment on sour taste of equimolar protonated organic acid solutions and to investigate the potential roles of organic anions and sodium ions on sour taste perception. Despite equal concentrations of protonated acid species, sour taste intensity decreased significantly with increased pH for acetic, lactic, malic, and citric acids (P < 0.05). Total organic anion concentration did not explain the suppression of sour taste in solutions containing a blend of 3 organic acids with constant concentration of protonated organic acid species and hydrogen ions and variable organic anion concentrations (R(2)= 0.480, P = 0.12). Sour taste suppression in these solutions seemed to be more closely related to sodium ions added in the form of NaOH (R(2)= 0.861, P = 0.007). Addition of 20 mM NaCl to acid solutions resulted in significant suppression of sour taste (P = 0.016). However, sour taste did not decrease with further addition of NaCl up to 80 mM. Presence of sodium ions was clearly shown to decrease sour taste of organic acid solutions. Nonetheless, suppression of sour taste in pH adjusted single acid solutions was greater than what would be expected based on the sodium ion concentration alone, indicating an additional suppression mechanism may be involved.
s-Block metal inverse crowns: synthetic and structural synergism in mixed alkali metal–magnesium (or zinc) amide chemistry (2001)

This article focuses on the special chemistry that can take place when certain lithium (or other heavier alkali metal) amides are combined with certain magnesium (or zinc) bisamides. Some of the reaction mixtures studied follow a straightforward path leading to simple heterobimetallic compositions with predictable structures, whereas others take an unexpected turn to behave as powerful oxygen scavengers or as regioselective bases to yield novel products with unpredictable host–guest macrocyclic structures. We refer to these new compounds as ‘inverse crown ethers’ or ‘inverse crowns’ because their arrangement of Lewis acidic and Lewis basic sites is opposite to that encountered in conventional crown ether complexes. This developing phenomenon appears to be a direct result of pairing together the two distinct metal types in the same complex, as the chemistry cannot be replicated by complexes containing one or the other metal type on its own.
EFFECT OF LIGHT ON CALCIUM UPTAKE BY MACROPHAGES (1990)

The effect of light on calcium uptake by U937 cells was studied using 45Ca radiotracer techniques. Cells were treated with light while suspended in phosphate buffered saline, and the effects of variation in energy density, pulse frequency and wavelength investigated. The results showed that calcium uptake by the cells was dependent upon the energy density of the light source. Calcium uptake increased from 0 to 4 J/cm2 but then declined steadily as the energy density was increased up to 16 J!cm2, remaining at this level which was not significantly different from the control level, as the energy density was increased up to 32 J/cm2, the maximum tested. Calcium uptake was also shown to be both frequency- and wavelength-dependent. The most effective of the frequencies tested were in the range 16-36.48 Hz, The most effective of the wavelengths tested were 660, 820 and 870 nm. The alteration in intracellular calcium levels in response to exposure to light therapy may have considerable biological and clinical significance, since calcium ions act as second messengers in many forms of cell activity, including synthesis, secretion and intracellular communication.
Common culture conditions for maintenance and cardiomyocyte differentiation of the human embryonic stem cell lines, BG01 and HUES-7 (2005)

Development of generic differentiation protocols that function in a range of independently-derived human embryonic stem cell (hESC) lines remains challenging due to considerable diversity in culture methods practiced between lines. Maintenance of BG01 and HUES-7 has routinely been on mouse embryonic fibroblast (MEF) feeder layers using manual- and trypsin-passaging, respectively. We adapted both lines to trypsin-passaging on feeders or on Matrigel in feeder-free conditions and assessed proliferation and cardiac differentiation. On feeders, undifferentiated proliferation of BG01 and HUES-7 was supported by all three media tested (BG-SK, HUES-C and HUES-nL), although incidence of karyotypic instability increased in both lines in BG-SK. On Matrigel, KSR-containing conditioned medium (CM) promoted undifferentiated cell proliferation, while differentiation occurred in CM containing Plasmanate or ES-screened Fetal Bovine Serum (FBS) and in unconditioned medium containing 100 ng/ml bFGF. Matrigel cultures were advantageous for transfection but detrimental to embryoid body (EB) formation. However, transfer of hESCs from Matrigel back to feeders and culturing to confluence was found to rescue EB formation. EBs formed efficiently when hESCs on feeders were treated with collagenase, harvested by scraping and then cultured in suspension in CM. Subsequent culture in FBS-containing medium produced spontaneously contracting EBs, for which the mean beat rate was 37.2 +/- 2.3 and 41.1 +/- 3.1 beats/min for BG01-EBs and HUES-7-EBs, respectively. Derived cardiomyocytes expressed cardiac genes and responded to pharmacological stimulation. Therefore the same culture and differentiation conditions functioned in two independently-derived hESC lines. Similar studies in other lines may facilitate development of universal protocols.
Integration of functional myotubes with a Bio-MEMS device for non-invasive interrogation (2007)

We have developed a biological micro-electromechanical system (Bio-MEMS) device consisting of surface-modified microfabricated silicon cantilevers and an AFM detection apparatus for the study of cultured myotubes. With this system we are able to selectively stimulate the myotubes as well as report on a variety of physiological properties of the myotubes in real time and in a high-throughput manner. This system will serve as the foundation for future work integrating multiple tissue types for the creation of Bio-MEMS analogues of complex tissues and biological circuits.
Tunnelling theories of non-volatile semiconductor memories (1976)

The discovery that charge storage in layered insulator field effect transistors enables them to function to advantage as non-volatile memory elements, has spurred widespread activity in the fabrication of many types of these devices. There is also much analytical work attempting to describe the device characteristics, particularly retention time, in terms of material and operational parameters. Here some of the different tunnelling theories that have been proposed are compared and discussed. Die Entdeckung, daß Ladungsspeicherung in geschichtenten Isolator-Feldeffekttransistoren deren Funktion als stabile Gedächtniselemente ermöglicht, hat eine breite Aktivität bei der Herstellung unterschiedlicher Arten dieser Bauelemente hervorgerufen. Es existieren analytische Arbeiten, die die Charakteristiken der Elemente, insbesondere die Speicherzeit mit Material- und Arbeitspunktparametern, zu beschreiben versuchen. Hier werden einige der vorgeschlagenen Tunneltheorien verglichen und diskutiert.
MRI visualisation of wood samples with ultra short TE sequences. (2005)

A. H. Herlihy, T. L. Eberhardt, C-L. So, H. G. Parkes, J. D. Bell, P-W. So Biological Imaging Centre, Imaging Sciences Department, MRC Clinical Sciences Centre, Hammersmith Hospital, Imperial College London, London, United Kingdom, Utilization of Southern Forest Resources, Southern Research Station, USDA Forest Service, Pineville, LA, United States, Wellcome Trust High Field Laboratory, Department of Medical Physics and Bioengineering, University College London, London, United Kingdom, Molecular Imaging Group, Imaging Sciences department, MRC Clinical Sciences Centre, Hammersmith Hospital, Imperial College London, London, United Kingdom
The CD39 lymphoid cell activation antigen. Molecular cloning and structural characterization. (1994)

CD39, a 70- to 100-kDa molecule expressed primarily on activated lymphoid cells, was previously shown to mediate B cell homotypic adhesion when ligated with a subset of anti-CD39 mAbs. In the present study, we describe the cloning and molecular characterization of human and murine CD39. The nucleotide sequence of human CD39 includes an open reading frame encoding a putative 510 amino acid protein with six potential N-linked glycosylation sites, 11 Cys residues, and two potential transmembrane regions. Murine CD39 shares 75% amino acid sequence identity with human CD39 but fails to cross-react with anti-human CD39 mAbs. Although there were no significant similarities with other mammalian genes, considerable homology was found between CD39 and a guanosine diphosphatase from yeast. A series of mouse-human hybrid molecules was constructed to determine the general topology of CD39 and the location of a biologically functional epitope. These findings and supporting evidence from an anti-CD39 mAb-selected phage peptide display library indicate a likely model wherein a short intracellular N-terminus is followed by a large extracellular loop containing the epitope recognized by stimulatory anti-CD39 mAbs, and a short intracellular C terminus. The results demonstrate that CD39 is a novel cell surface glycoprotein with unusual structural characteristics.
Evaluation of a Modified Sanitary Napkin as a Sample Self-Collection Device for the Detection of Genital Chlamydial Infection in Women (2001)

A modified sanitary napkin was compared with endocervical swab and urine specimens for the detection of urogenital Chlamydia trachomatis infection. Endocervical swabs and/or first-catch urine were collected from 510 women at medical or community settings in Quebec City. Participants were also asked to wear a modified sanitary napkin (Ezy-Detek) during 4 consecutive hours and to bring it back to the clinic or mail it to the laboratory. Endocervical and urine specimens were tested using the Cobas Amplicor CT/NG assay (Roche Diagnostic Systems) according to the manufacturer's instructions, as were specimens collected with the napkin after adequate preparation. If the PCR test result was positive on the endocervical sample or on any two samples, a woman was considered to be infected. PCR testing results on paired samples were identical for 493 (96.6%) of 510 women. According to the definition given above, 58 (11.3%; 95% confidence interval [CI], 8.7 to 14.5%) women were infected with C. trachomatis. The sensitivity and specificity of PCR testing on modified sanitary napkin specimens were, respectively, 93.1% (54 of 58; 95% CI, 83.3 to 98.1%) and 98.9% (447 of 452; 95% CI, 97.4 to 99.6%) compared to 81.0% (47 of 58; 95% CI, 68.6 to 90.1%) and 100% (451 of 451; 95% CI, 99.2 to 100%) for urine specimens. The positive and negative predictive values were, respectively, 91.5% (54 of 59) and 99.1% (447 of 451) for the sanitary napkin specimens compared to 100% (47 of 47) and 97.6% (451 of 462) for urine samples. These results suggest that a modified sanitary napkin represents an effective noninvasive device for self-collection of specimens to detect urogenital C. trachomatis infection.
MolProbity: all-atom structure validation for macromolecular crystallography (2009)

MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.
Process fluid mechanics (1979)

1. Introduction. 2. Dimensional Analysis and Experimentation. 3. Macroscopic Problems. 4. Detailed Flow Structure. 5. Approximate Methods. 6. Advanced Topics. Author Index. Subject Index.
Regulated Intramembrane Proteolysis of the Interleukin-1 Receptor II by α-, β-, and γ-Secretase (2007)

Ectodomain shedding and intramembrane proteolysis of the amyloid precursor protein (APP) by alpha-, beta- and gamma-secretase are involved in the pathogenesis of Alzheimer disease (AD). Increased proteolytic processing and secretion of another membrane protein, the interleukin-1 receptor II (IL-1R2), have also been linked to the pathogenesis of AD. IL-1R2 is a decoy receptor that may limit detrimental effects of IL-1 in the brain. At present, the proteolytic processing of IL-1R2 remains little understood. Here we show that IL-1R2 can be proteolytically processed in a manner similar to APP. IL-1R2 expressed in human embryonic kidney 293 cells first undergoes ectodomain shedding in an alpha-secretase-like manner, resulting in secretion of the IL-1R2 ectodomain and the generation of an IL-1R2 C-terminal fragment. This fragment undergoes further intramembrane proteolysis by gamma-secretase, leading to the generation of the soluble intracellular domain of IL-1R2. Intramembrane cleavage of IL-1R2 was abolished by a highly specific inhibitor of gamma-secretase and was absent in mouse embryonic fibroblasts deficient in gamma-secretase activity. Surprisingly, the beta-secretase BACE1 and its homolog BACE2 increased IL-1R2 secretion resulting in C-terminal fragments nearly identical to the ones generated by the alpha-secretase-like cleavage. This suggests that both proteases may act as alternative alpha-secretase-like proteases. Importantly, BACE1 and BACE2 did not cleave several other membrane proteins, demonstrating that both proteases do not contribute to general membrane protein turnover but only cleave specific proteins. This study reveals a similar proteolytic processing of IL-1R2 and APP and may provide an explanation for the increased IL-1R2 secretion observed in AD.
Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels (2015)

We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus <500 kPa including alginate, collagen, and fibrin. Computer-aided design models of 3D optical, computed tomography, and magnetic resonance imaging data were 3D printed at a resolution of ~200 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3D internal and external anatomical architectures.
Ecto‐enzyme and signaling functions of lymphocyte CD 7 3 (1998)

Summary: CD73 or ecto‐5′‐nucleotidase (S‐NT) is a widely expressed ecto‐enzyme which catalyzes the dephosphorylation of AMP and other nucleoside monophosphates. CD 73 participates in purine salvage through this enzymatic activity, supplying cells with precursors for energy metabolism and nucleic acid biosynthesis. As an enzyme that produces adenosine, CD 73 can also regulate adenosine receptor engagement in many tissues. However, CD73 also has functions independent of its enzyme activity like many glycosyl phosphatidylinositol (GPI)‐anchored molecules, it transmits potent activation signals in T cells when ligated by antibodies. Less compelling evidence suggests that CD 73 may function as a cell adhesion molecule. In the human immune system, CD73 is expressed on subsets of T and B cells, on germinal center follicular dendritic cells, and on thymic medullary reticular fibroblasts and epithelial cells. Many challenging areas remain to be explored before the role of CD73 in the immune system will be fully understood. These include an evaluation of the role of adenosine receptors in lymphoid development, the identification of physiological CD73 ligands, a functional assessment of the GPI anchor, and an analysis of the intricate cell‐type‐specific and developmental regulation of CD 73 expression.
Pharmacokinetics (2009)

Pharmacokinetics is the study of the movement of a drug through the compartments of the body and the transformations (activation and metabolism) that affect it. Pharmacokinetics is often referred to as ‘what the body does to the drug’. Figure PK1 shows an overview of these processes.
Vectors : cloning applications (1998)

General cloning vectors in vitro transcription/translation vectors bacteriophage lambda vectors cosmid vectors cloning of PCR products manipulation of cloned DNA preparation and sizes of molecular size markers.
Improved MtDNA Sequence Analysis of Forensic Remains Using a “Mini-Primer Set” Amplification Strategy (2001)

Mitochondrial DNA (mtDNA) analysis of highly degraded skeletal remains is often used for forensic identification due largely to the high genome copy number per cell. Literature from the "ancient DNA" field has shown that highly degraded samples contain populations of intact DNA molecules that are severely restricted in size (1-4). Hand et al. have demonstrated the targeting and preferential amplification of authentic human DNA sequences with small amplicon products of 150 bp or less (1,2). Given this understanding of ancient DNA preservation and amplification, we report an improved approach to forensic mtDNA analysis of hypervariable regions 1 and 2 (HV1/HV2) in highly degraded specimens. This "mini-primer set" (MPS) amplification strategy consists of four overlapping products that span each of the HV regions and range from 126 to 170 bp, with an average size of 141 bp. For this study, 11 extracts representing a range of sample quality were prepared from nonprobative forensic specimens. We demonstrate a significant increase in MPS amplification success when compared to testing methods using approximately 250 bp amplicons. Further, 16 of 17 independent amplifications previously "unreported" due to mixed sequences provided potentially reportable sequence data from a single, authentic template with MPS testing.
A novel gantry for proton therapy at the Paul Scherrer Institute (2001)

PSI has gained in the last few years the unique experience of using a proton therapy system based on a beam scanning delivery technique and on a compact gantry. This knowledge is now bringing forth new initiatives. We are continuously producing significant modifications and improvements to the present system, gantry 1. The major new step is however the decision of PSI to purchase a dedicated accelerator for the medical project. In the context of the expansion of the medical project of PSI (project PROSCAN) we have also started to plan the realisation of a second proton gantry, gantry 2. In this lecture we present the main ideas for the novel gantry, which will be based on one hand on the experience with the present technology, but on the other hand should be designed as a system more open to further developments and needs. The established and the future requirements for the beam delivery on the new gantry were routed into the specification list for the dedicated accelerator.
Safety and immunogenicity of an oral, replicating adenovirus serotype 4 vector vaccine for H5N1 influenza: a randomised, double-blind, placebo-controlled, phase 1 study (2013)

Wellcome Trust Foundation, PaxVax.