gebhart/patrepeval huggingface dataset:
Phospholipid binding properties of bovine prothrombin peptide residues 1-45. (1988)

The present study investigates the unique contribution of the NH2-terminal 33 residues of prothrombin, the gamma-carboxyglutamic acid (Gla) domain, to the Ca(II) and phospholipid-binding properties of prothrombin. Two Gla domain peptides, 1-42 and 1-45, produced by chymotryptic cleavage of prothrombin fragment 1 (residues 1-156 of the amino terminus of bovine prothrombin) and isolated by anion-exchange chromatography were utilized to characterize the Gla domain of prothrombin. This investigation utilized several experimental approaches to examine the properties of the Gla domain peptides. These studies were somewhat hampered by the metal ion-induced insolubility of the peptides. However, the 1-45 peptide was specifically radioiodinated, which facilitated the study of this peptide at low concentrations. In contrast to prothrombin fragment 1, the intrinsic fluorescence of both 1-42 and 1-45 was not quenched upon the addition of 1 mM Ca(II) or any concentration of Mg(II). Equilibrium dialysis studies revealed that the 1-42 peptide bound three Ca(II) ions noncooperatively, whereas fragment 1 binds seven Ca(II) ions in a positive cooperative manner. Ca(II)-promoted conformational changes are observed by comparison of electrophoretic mobility changes in the presence of increasing Ca(II) concentrations. Prothrombin, fragment 1, and the Gla domain peptides 1-42 and 1-45 exhibited similar electrophoretic mobility behavior in the presence of Ca(II) ions. The radiolabeled 1-45 peptide was found to comigrate with phospholipid vesicles on gel permeation chromatography in the presence of Ca(II). Fragment 1 was shown to inhibit this Ca(II)-dependent phospholipid binding of 1-45, demonstrating that the 1-45 peptide does possess the necessary phospholipid-binding structure. Furthermore, a metal ion-dependent conformational monoclonal antibody, F9.29, was inhibited from binding fragment 1 by the 1-42 peptide.
Fluoride Salts on Alumina as Reagents for Alkylation of Phenols and Alcohols (1982)

Abstract The effectiveness of alkali metal fluorides impregnated on alumina as a reagent for promoting alkylation was optimized with respect to the metal cation, the amount of impregnation, and the reaction solvent. Potassium or caesium fluoride on alumina in acetonitrile or 1,2-dimethoxyethane was concluded to be the best reaction system for general use. O-Alkylation of substituted phenols, primary and secondary alcohols, and a glycol was carried out mostly in good yields under mild conditions with simple experimental procedures.
Study of Immunization against Anthrax with the Purified Recombinant Protective Antigen of Bacillus anthracis (1998)

Protective antigen (PA) of anthrax toxin is the major component of human anthrax vaccine. Currently available human vaccines in the United States and Europe consist of alum-precipitated supernatant material from cultures of toxigenic, nonencapsulated strains of Bacillus anthracis. Immunization with these vaccines requires several boosters and occasionally causes local pain and edema. We previously described the biological activity of a nontoxic mutant of PA expressed in Bacillus subtilis. In the present study, we evaluated the efficacy of the purified mutant PA protein alone or in combination with the lethal factor and edema factor components of anthrax toxin to protect against anthrax. Both mutant and native PA preparations elicited high anti-PA titers in Hartley guinea pigs. Mutant PA alone and in combination with lethal factor and edema factor completely protected the guinea pigs from B. anthracis spore challenge. The results suggest that the mutant PA protein may be used to develop an effective recombinant vaccine against anthrax.
PD-L1 genetic overexpression or pharmacological restoration in hematopoietic stem and progenitor cells reverses autoimmune diabetes (2017)

Immunologically based clinical trials performed thus far have failed to cure type 1 diabetes (T1D), in part because these approaches were nonspecific. Because the disease is driven by autoreactive CD4 T cells, which destroy β cells, transplantation of hematopoietic stem and progenitor cells (HSPCs) has been recently offered as a therapy for T1D. Our transcriptomic profiling of HSPCs revealed that these cells are deficient in programmed death ligand 1 (PD-L1), an important immune checkpoint, in the T1D nonobese diabetic (NOD) mouse model. Notably, the immunoregulatory molecule PD-L1 plays a determinant role in controlling/inhibiting activated T cells and thus maintains immune tolerance. Furthermore, our genome-wide and bioinformatic analysis revealed the existence of a network of microRNAs (miRNAs) controlling PD-L1 expression, and silencing one of key altered miRNAs restored PD-L1 expression in HSPCs. We therefore sought to determine whether restoration of this defect would cure T1D as an alternative to immunosuppression. Genetically engineered or pharmacologically modulated HSPCs overexpressing PD-L1 inhibited the autoimmune response in vitro, reverted diabetes in newly hyperglycemic NOD mice in vivo, and homed to the pancreas of hyperglycemic NOD mice. The PD-L1 expression defect was confirmed in human HSPCs in T1D patients as well, and pharmacologically modulated human HSPCs also inhibited the autoimmune response in vitro. Targeting a specific immune checkpoint defect in HSPCs thus may contribute to establishing a cure for T1D.
Opsonophagocytosis of Chlamydia pneumoniae by Human Monocytes and Neutrophils (2020)

The human respiratory tract pathogen <i>Chlamydia pneumoniae</i>, which causes mild to severe infections, has been associated with the development of chronic inflammatory diseases. To understand the biology of <i>C. pneumoniae</i> infections, several studies have investigated the interaction between <i>C. pneumoniae</i> and professional phagocytes. However, these studies have been conducted under nonopsonizing conditions, making the role of opsonization in <i>C. pneumoniae</i> infections elusive. Thus, we analyzed complement and antibody opsonization of <i>C. pneumoniae</i> and evaluated how opsonization affects chlamydial infectivity and phagocytosis in human monocytes and neutrophils. We demonstrated that IgG antibodies and activation products of complement C3 and C4 are deposited on the surface of <i>C. pneumoniae</i> elementary bodies when incubated in human serum. Complement activation limits <i>C. pneumoniae</i> infectivity <i>in vitro</i> and has the potential to induce bacterial lysis by the formation of the membrane attack complex. Coculture of <i>C. pneumoniae</i> and freshly isolated human leukocytes showed that complement opsonization is superior to IgG opsonization for efficient opsonophagocytosis of <i>C. pneumoniae</i> in monocytes and neutrophils. Neutrophil-mediated phagocytosis of <i>C. pneumoniae</i> was crucially dependent on opsonization, while monocytes retained minor phagocytic potential under nonopsonizing conditions. Complement opsonization significantly enhanced the intracellular neutralization of <i>C. pneumoniae</i> in peripheral blood mononuclear cells and neutrophils and almost abrogated the infectious potential of <i>C. pneumoniae</i> In conclusion, we demonstrated that complements limit <i>C. pneumoniae</i> infection <i>in vitro</i> by interfering with <i>C. pneumoniae</i> entry into permissive cells by direct complement-induced lysis and by tagging bacteria for efficient phagocytosis in both monocytes and neutrophils.
Interactions between oestradiol and danazol on the growth of gastrointestinal tumour cells. (1993)

The gastrointestinal tumour cell lines, MKN45G and C146 possessed oestrogen receptors (ER) of affinities 1.8 x 10(-8) and 5.2 x 10(-9) M respectively. C146 and MKN45G had enhanced proliferation in the presence of oestradiol (10(-8) and 10(-10) M). Fifty-six percent (5/9) of primary gastric and colorectal tumours had their proliferation enhanced by oestradiol. The anti-steroidal drug, danazol, inhibited the basal growth of MKN45G (10 micrograms ml-1 45% of the untreated control), C146 (10 and 5 micrograms ml-1, 20 and 48% of control, respectively) and 3/9 GI primary tumours (10 micrograms ml-1). Danazol competed with 3 [H]-Oestradiol for binding to ER on MKN45G and C146, at concentrations from 10 to 1 micrograms ml-1.
A Japanese patient with frontotemporal dementia and parkinsonism by a tau P301S mutation (2000)

The authors report a patient carrying a missense mutation in exon 10 of tau that causes a substitution at codon 301 (P301S). Although the patient shares the rapidly progressive frontotemporal dementia of the other reported pedigrees with P301S, the clinical phenotype is unique in that parkinsonism was a major symptom in the early stage and because behavioral symptoms with dementia became prominent 2 years after the onset of the disease. This study substantiates the notion that tau mutations at codon 301 can show various phenotypes.
Development of a competitive lateral flow immunoassay for progesterone: influence of coating conjugates and buffer components (2008)

Several aspects of the development of competitive lateral flow immunoassays (LFIAs) are described. The quantitation of progesterone is taken as an example. The LFIA format consisted of a nitrocellulose membrane spotted with various progesterone conjugates as the test line. A mixture of primary antibody and secondary antibody adsorbed to colloidal carbon was used for signal generation. A digital scanner and dedicated software were used to quantitate the response. A reappraisal of the checkerboard titration, often used in the optimisation of immunoassays, is discussed. Surprisingly, the highest sensitivity of the LFIA format (IC(50) of 0.6 microg L(-1) progesterone in buffer) was achieved by using a high coating concentration of the analyte-protein conjugate and a high dilution of the antibody solution. Immediate addition of all reagents in LFIA was superior to premixing the components and allowing prereaction. Of several blocking agents tested bovine serum albumin was superior in performance, whereas the combination of ovalbumin and progesterone substantially influenced test results.
Domain Adaptation for MRI Organ Segmentation using Reverse Classification Accuracy (2018)

The variations in multi-center data in medical imaging studies have brought the necessity of domain adaptation. Despite the advancement of machine learning in automatic segmentation, performance often degrades when algorithms are applied on new data acquired from different scanners or sequences than the training data. Manual annotation is costly and time consuming if it has to be carried out for every new target domain. In this work, we investigate automatic selection of suitable subjects to be annotated for supervised domain adaptation using the concept of reverse classification accuracy (RCA). RCA predicts the performance of a trained model on data from the new domain and different strategies of selecting subjects to be included in the adaptation via transfer learning are evaluated. We perform experiments on a two-center MR database for the task of organ segmentation. We show that subject selection via RCA can reduce the burden of annotation of new data for the target domain.
Data science for business (2013)

Written by renowned data science experts Foster Provost and Tom Fawcett, Data Science for Business introduces the fundamental principles of data science, and walks you through the data-analytic thinking necessary for extracting useful knowledge and business value from the data you collect. This guide also helps you understand the many data-mining techniques in use today. Based on an MBA course Provost has taught at New York University over the past ten years, Data Science for Business provides examples of real-world business problems to illustrate these principles. You'll not only learn how to improve communication between business stakeholders and data scientists, but also how participate intelligently in your company's data science projects. You'll also discover how to think data-analytically, and fully appreciate how data science methods can support business decision-making. Understand how data science fits in your organization - and how you can use it for competitive advantage Treat data as a business asset that requires careful investment if you're to gain real value Approach business problems data-analytically, using the data-mining process to gather good data in the most appropriate way Learn general concepts for actually extracting knowledge from data Apply data science principles when interviewing data science job candidates
A data preparation framework based on a multidatabase language (2002)

Integration and analysis of data from different sources have to deal with several problems resulting from potential heterogeneities. The activities addressing these problems are called data preparation and are supported by various available tools. However, these tools process mostly in a batch-like manner, not supporting the iterative and explorative nature of the integration and analysis process. The authors present a framework for important data preparation tasks based on a multidatabase language. This language offers features for solving common integration and cleaning problems as part of query processing. Combining data preparation mechanisms and multidatabase query facilities permits applying and evaluating different integration and cleaning strategies without explicit loading and materialization of data. The paper introduces the language concepts and discusses their application for individual tasks of data preparation.
Camera-based estimation of needle pose for ultrasound percutaneous procedures (2008)

A pose estimation method is proposed for measuring the position and orientation of a biopsy needle. The technique is to be used as a touchless needle guide system for guidance of percutaneous procedures with 4D ultrasound. A pair of uncalibrated, light-weight USB cameras are used as inputs. A database is prepared offline, using both the needle line estimated from camera-captured images and the true needle line recorded from an independent tracking device. A nonparametric learning algorithm determines the best fit model from the database. This model can then be used in real-time to estimate the true position of the needle with inputs from only the camera images. Simulation results confirm the feasibility of the method and show how a small, accurately made database can provide satisfactory results. In a series of tests with cameras, we achieved an average error of 2.4mm in position and 2.61° in orientation. The system is also extended to real ultrasound imaging, as the two miniature cameras capture images of the needle in air and the ultrasound system captures a volume as the needle moves through the workspace. A new database is created with the estimated 3D position of the needle from the ultrasound volume and the 2D position and orientation of the needle calculated from the camera images. This study achieved an average error of 0.94 mm in position and 3.93° in orientation.
Sequence‐Unrestricted, Watson–Crick Recognition of Double Helical B‐DNA by (R)‐MiniPEG‐γPNAs (2011)

Invasion of the strand snatchers: We have synthesized chiral γ-peptide nucleic acids containing miniPEG side chains. Using gel shift assays we show that this particular type of nucleic acid mimic can invade any sequence of double helical B-form DNA (see figure), and this recognition occurs through direct Watson–Crick base pairing.
Transcript Analysis of The Equine Herpesvirus 1 Glycoprotein B Gene Homologue and Its Expression by a Recombinant Vaccinia Virus (1990)

Transcript mapping of the equine herpesvirus 1 (EHV-1) glycoprotein B (gB) gene homologue by Northern blot, S1 nuclease and primer extension analyses indicated that two overlapping transcripts of 3.4 and 4.6 kb originated from the same strand and were transcribed from left to right between coordinates 0.40 and 0.43 of the EHV-1 genome. The 3.4 kb transcript encoded EHV-1 gB and the 5' RNA terminus was located approximately 30 bases downstream from a probable TATA element. The coding region of the gB gene homologue was reconstructed from two subclones using oligonucleotide mutagenesis and inserted into vaccinia virus by homologous recombination. Cells infected with the recombinant virus synthesized EHV-1 gB antigen, which was detectable in the cytoplasm and on the cell surface by immunofluorescence using an EHV-1 neutralizing horse serum and EHV-1 monoclonal antibodies. On Western blots, bands of 138K to 143K, 80K to 90K and 55K to 57K were identified in recombinant virus-infected cells, by both EHV-1 monoclonal antibodies and the polyclonal horse serum. These were similar in Mr to bands identified by these sera in EHV-1-infected cells. Mice vaccinated with the recombinant virus produced antibodies which recognized proteins of the same Mr as EHV-1 gB, on Western blots, but did not have in vitro neutralizing activity.
New therapeutic strategies for type 2 diabetes : small molecule approaches (2012)

Preface, Type 2 Diabetes - Disease Overview Marketed Small Molecule Dipeptidyl Peptidase IV (DPP4) Inhibitors as a New Class of Oral Anti-diabetics SGLT2 Inhibitors in Development Glucokinase Activators in Development 11 -Hydroxysteroid dehydrogenase type 1 (11 -HSD1) inhibitors in development Recent Advances in PTP1B Inhibitor Development for the Treatment of Type-2 Diabetes and Obesity Recent advances in the discovery of GPR119 agonists Acyl-CoA:diacylglycerol acyltransferase-1 inhibition as an approach to the treatment of type 2 diabetes Stearoyl-CoA Desaturase 1 (SCD1) Inhibitors: Bench to Bedside Must Only Go through Liver TGR5 Agonists in Development The discovery and development of MB07803, a second generation fructose-1,6-bisphosphatase inhibitor with improved pharmacokinetic properties, as a potential treatment of type 2 diabetes Inhibition of Glycogen Phosphorylase as a Strategy for the Treatment of Type 2 Diabetes SIRT1 Activators in Development Long-Chain Free Fatty Acid Receptor Agonists Glucagon Receptor Antagonists in Development ACC Inhibitors in Development Index
Distribution of cholinergic neurons in rat brain: Demonstrated by the immunocytochemical localization of choline acetyltransferase (1983)

The neuroanatomical location and cytological features of cholinergic neurons in the rat brain were determined by the immunocytochemical localization of the biosynthetic enzyme, choline acetyltransferase (ChAT). Perikarya labeled with ChAT were detected in four major cell groups: (1) the striatum, (2) the magnocellular basal nucleus, (3) the pontine tegmentum, and (4) the cranial nerve motor nuclei. Labeled neurons in the striatum were observed scattered throughout the neostriatum (caudate, putamen) and associated areas (nucleus accumbens, olfactory tubercle). Larger ChAT-labeled neurons were seen in an extensive cell system which comprises the magnocellular basal nucleus. This more or less continuous set of neuronal clusters consists of labeled neurons in the nucleus of the diagonal band (horizontal and vertical limbs), the magnocellular preoptic nucleus, the substantia innominata, and the globus pallidus. Labeled neurons in the pontine tegmentum were seen as a group of large neurons in the caudal midbrain, dorsolateral to the most caudal part of the substantia nigra, and extended in a caudodorsal direction through the midbrain reticular formation into the area surrounding the superior cerebellar peduncle. The neurons in this latter group constitute the pedunculopontine tegmental nucleus (PPT). An additional cluster of cells was observed medially adjacent to the PPT, in the lateral part of the central gray matter at the rostral end of the fourth ventricle. This group corresponds to the laterodorsal tegmental nucleus. Large ChAT-labeled neurons were also observed in all somatic and visceral motor nerve nuclei. The correspondence of the distribution of ChAT-labeled neurons identified by our methods to earlier immunocytochemical and acetylcholinesterase histochemical studies and to connectional studies of these groups argues for the specificity of the ChAT antibody used.
Differences in the embryonic expression patterns of mouse Foxf1 and ‐2 match their distinct mutant phenotypes (2003)

Murine genes encoding the forkhead transcription factors Foxf1 and -2 are both expressed in derivatives of the splanchnic mesoderm, i.e., the mesenchyme of organs derived from the primitive gut. In addition, Foxf2 is also expressed in limbs and the central nervous system. Targeted mutagenesis of Foxf1 and -2 suggests that Foxf1 is the more important of the two mammalian FoxF genes with early embryonic lethality of null embryos and a haploinsufficiency phenotype affecting foregut-derived organs. In contrast, the only reported defect in Foxf2 null embryos is cleft palate. To investigate if the differences in mutant phenotype can be attributed to nonoverlapping expression patterns or if distinct functions of the encoded proteins have to be inferred, we analyzed the early embryonic expression of Foxf2 and compared it with that of the better investigated Foxf1. We find that in the early embryo, Foxf1 is completely dominating-in terms of expression-in extraembryonic and lateral plate mesoderm, consistent with the malformations and early lethality of Foxf1 null mutants. Along the developing gut, Foxf1 is highly expressed throughout, whereas Foxf2 expression is concentrated to the posterior part-fitting the foregut haploinsufficiency phenotypes of Foxf1 mutants. Foxf2, on the other hand, is more prominent than Foxf1 in mesenchyme around the oral cavity, as would be predicted from the cleft palate phenotype. The differences in expression pattern also highlight areas where defects should be sought for in the Foxf2 mutant, for example limbs, the posterior gut, genitalia, and derivatives of the neural crest mesenchyme.
Purification of the major mammalian heat shock proteins. (1982)

The major mammalian heat shock or "stress" proteins (molecular masses of 90,000, 72,000, and 73,000 daltons) have been purified from stressed HeLa cells. The 90,000-dalton protein co-purified with small amounts of a 100,000-dalton protein which was identified as one of the other stress proteins in these cells. The 72,000- and 73,000-dalton proteins co-purified throughout the fractionation scheme, apparently as a mixture of monomeric forms of the two proteins. From sedimentation velocity and gel filtration analysis, it was found that the 90,000/100,000-dalton protein mixture had a Stokes radius of 69A and a s20,w value of 5.8 while the 72,000/73,000-dalton protein mixture had a Stokes radius of 42.6A and a s20,w value of 4.3. The purified proteins migrated identically in two-dimensional gel electrophoretograms with their counterparts from total cell lysates of [35S]methionine-labeled stressed HeLa cells. Peptide mapping experiments indicated that the 72,000- and 73,000-dalton proteins contained common peptides while the 90,000- and 100,000-dalton proteins appeared to be distinct. Amino acid analysis of the 90,000- and a mixture of the 72,000/73,000-dalton proteins showed that both contained relatively high amounts of Asp/Asn and Glu/Gln.
The Structure of New Oligosaccharide Antibiotics, 13-384 Components 1 and 5 (1989)

b i o t i c s have been deduced based on chemical degradation aqd spectroscopic evidence.
Expression profile of Tripartite motif family (TRIM) in human fibroblasts (NHDF) infected with porcine endogenous retrovirus (PERV) (2020)

Porcine endogenous retrovirus infection of NHDF cells is accompanied by TRIM14 down regulation suggesting TRIM14 as a possible marker of retroviral infection. None of the selected miRNAs had statistically significant potential to regulate the expression of the selected TRIMs in any of the analyzed conditions.