gebhart/patrepeval huggingface dataset:
PEG-Supported Synthesis of Cyclic Oligodeoxyribonucleotides (1993)

Abstract Cyclic oligodeoxyribonucleotides have been synthesized in satisfactory yields by an easy procedure using polyethylene glycol (PEG) as soluble supporting polymer. The present method is particularly suitable for a medium to large scale synthesis. Early studies involving biological properties of synthetic1 and natural2 cyclic oligonucleotides stimulated a great deal of interest in such kind of molecules. The recent findings3 that circular single-stranded oligodeoxyribonucleotides having two runs of pyrimidines can bind tightly and sequence selectively to single-stranded polypurine DNA and RNA by forming triple helical complexes open up new perspectives to the design of more efficient DNA-and RNA-binding molecules. Our attention is being focused on the synthesis of medium-sized rings, since none of the synthetic procedures described so far proved to be really suitable for the preparation of such molecules on a relatively large scale. Following „classical“ solution methods, which in principle should easily allow syntheses
Fast and flexible X-ray tomography using the ASTRA toolbox (2016)

Object reconstruction from a series of projection images, such as in computed tomography (CT), is a popular tool in many different application fields. Existing commercial software typically provides sufficiently accurate and convenient-to-use reconstruction tools to the end-user. However, in applications where a non-standard acquisition protocol is used, or where advanced reconstruction methods are required, the standard software tools often are incapable of computing accurate reconstruction images. This article introduces the ASTRA Toolbox. Aimed at researchers across multiple tomographic application fields, the ASTRA Toolbox provides a highly efficient and highly flexible open source set of tools for tomographic projection and reconstruction. The main features of the ASTRA Toolbox are discussed and several use cases are presented.
Limited Immunological Recognition of Critical Malaria Vaccine Candidate Antigens (1988)

Current vaccine development strategies for malaria depend on widespread immunological responsiveness to candidate antigens such as the zygote surface antigens and the sporozoite coat protein, the circumsporozoite (CS) protein. Since immunological responsiveness is controlled mainly by genes mapping within the major histocompatibility complex (MHC), the humoral immune response to the zygote surface antigens and the cytotoxic T lymphocyte (CTL) response to the CS protein were examined in MHC-disparate congenic mouse strains. Only two of six strains responded to the 230-kilodalton zygote surface antigen and another two strains responded to the 48/45-kilodalton surface antigen. From two mouse strains, expressing between them five different class I MHC molecules, there was recognition of only a single CTL epitope from the CS protein, which was from a polymorphic segment of the molecule. The restricted CTL response to this protein parallels the restricted antibody response to this protein observed in humans and mice. These findings suggest that subunit malaria vaccines now being developed may be ineffective.
Chemically Reactive Derivatives of Gramicidin A for Developing Ion Channel-Based Nanoprobes (2008)

Ion channel-forming peptides and proteins offer tremendous opportunities for fundamental and applied studies of function on individual molecules. An ongoing challenge in ion channel research is the lack of simple and accessible synthetic methods to engineer pores with tailored chemical and physical properties. This paper describes a practical synthetic route to rapidly generate C-terminally modified derivatives of gramicidin A (gA), an ion channel-forming peptide, through the use of two chemically reactive gA-based building blocks. These amine- and azide-containing building blocks can react readily with typical substrates for amidation and 1,3-dipolar cycloaddition ("click") reactions to present molecules with desired structure and functionality near the opening of a gA pore. These derivatives of gA are stable under typical aqueous conditions for ion channel recordings and retain characteristic single ion channel conductance properties in planar lipid bilayers. Additionally, the synthetic methods described here afford useful quantities of these gA derivatives in good purity and yield with minimal purification. We demonstrate that derivatives of gA can be used for studying, in situ, a change in conductance through a channel upon performing a "click" reaction on an azide moiety attached to the gA pore. We also demonstrate that these gA-based building blocks can be used to construct sensors for the recognition of specific protein-ligand binding interactions in solution. This widely accessible, enabling synthetic methodology represents a powerful new tool to study relationships between chemical structure and function on the single molecule level.
Organ Trafficking: Legislative Proposals to Protect Minors (1995)

This documented trade in adult organs and the paucity of organs for medical transplants have fueled fears of a thriving criminal market in children's organs. 5Beginning in 1987,6 rumors of such a trade to North America, 7 Europe, 8 and Israel, 9 have raged throughout Latin America.' 0 These rumors remain unsubstantiated."Nonetheless, the that shortage has led to the rise of commercial traffic [k] in human organs, particularly from living donors who are unrelated to recipients").See generally, Maud Beelman,
Porphyrin and Phthalocyanine Antiscrapie Compounds (2000)

The transmissible spongiform encephalopathies (TSEs) are fatal, neurodegenerative diseases for which no effective treatments are available. The likelihood that a bovine form of TSE has crossed species barriers and infected humans underscores the urgent need to identify anti-TSE drugs. Certain cyclic tetrapyrroles (porphyrins and phthalocyanines) have recently been shown to inhibit the in vitro formation of PrP-res, a protease-resistant protein critical for TSE pathogenesis. We now report that treatment of TSE-infected animals with three such compounds increased survival time from 50 to 300%. The significant inhibition of TSE disease by structurally dissimilar tetrapyrroles identifies these compounds as anti-TSE drugs.
Photoacoustic ultrasound: Pulse production and detection in 0.5% Liposyn (1994)

Theoretical predictions and experimental measurements of photoacoustic pulse production within a 0.5% solution of Liposyn, a highly scattering, optical propagation medium, are reported. A simple model for photoacoustic energetics is developed that predicts photoacoustic signal pressure as a function of depth within a turbid medium following surface irradiation from an infrared source. The model is valid for very short irradiation duration. The model predicts that the acoustic pressure produced at a distance r from the center of a small, highly absorbing sphere of radius R consists of two, opposite polarity pulses, one originating from the near and one from the far side of the sphere. The magnitude of these biphasic pulses is expected to be proportional to the energy fluence (E) incident on the surface of the sphere and to the ratio, R/r. Furthermore, the energy fluence (E) that reaches the sphere is roughly proportional to e-mu effZ, where mu eff is the effective attenuation coefficient of the turbid medium and Z is the depth of the embedded sphere below the irradiated surface. The variation of E with depth within the absorber and biphasic acoustic pulse production have been verified experimentally. Further experiments demonstrate that a small (3-mm diameter), highly absorbing sphere can be detected and localized at a depth of 37.5 mm within a 0.5% solution of Liposyn with a spatial resolution of 1 x 6 mm2, using a biologically safe level of infrared irradiation (lambda = 1064 nm) and a conventional ultrasound transducer (frequency = 2.25 MHz). These results suggest that photoacoustic ultrasound imaging may have application to biologic systems such as the human breast.
Surgical Site Infection in Elective Operations for Colorectal Cancer After the Application of Preventive Measures (2011)

The prevalence of SSI in elective colon and rectal operations remains high despite the application of evidence-based preventive measures.
Increased levels of NGF in sera of systemic lupus erythematosus patients (1993)

Using a specific enzyme-linked immunosorbent assay (ELISA) for human nerve growth factor (NGF), serum levels in patients with systemic lupus erythematosus (SLE) were measured. We found a consistent increase in NGF levels in SLE patients compared with controls. A good correlation exists between serum NGF level and severity of clinical manifestation. We hypothesize that NGF might play a role in the pathogenesis of autoimmune disorders such as SLE.
Radiation hybrid mapping of the zebrafish genome (1999)

The zebrafish is an excellent genetic system for the study of vertebrate development and disease. In an effort to provide a rapid and robust tool for zebrafish gene mapping, a panel of radiation hybrids (RH) was produced by fusion of irradiated zebrafish AB9 cells with mouse B78 cells. The overall retention of zebrafish sequences in the 93 RH cell lines that constitute the LN54 panel is 22%. Characterization of the LN54 panel with 849 simple sequence length polymorphism markers, 84 cloned genes and 122 expressed sequence tags allowed the production of an RH map whose total size was 11,501 centiRays. From this value, we estimated the average breakpoint frequency of the LN54 RH panel to correspond to 1 centiRay = 148 kilobase. Placement of a group of 235 unbiased markers on the RH map suggests that the map generated for the LN54 panel, at present, covers 88% of the zebrafish genome. Comparison of marker positions in RH and meiotic maps indicated a 96% concordance. Mapping expressed sequence tags and cloned genes by using the LN54 panel should prove to be a valuable method for the identification of candidate genes for specific mutations in zebrafish.
Robotic versus manual control in magnetic steering of an endoscopic capsule (2009)

Robotic control for magnetic steering of a capsular endoscope was demonstrated to be more precise and reliable than manual operation. Validation of the proposed robotic system paves the way for automation of capsular endoscopy and advanced endoscopic techniques.
Synthesis of α,ω‐isocyanate telechelic polymethacrylate soft segments with activated ester side functionalities and their use for polyurethane synthesis (2013)

The synthetic route for the preparation of α,ω‐isocyanate‐telechelic poly(methyl methacrylate‐ co ‐acryloxysuccinimide) and α,ω‐ isocyanate‐telechelic poly(methyl methacrylate‐ co ‐acrylamidohexanoic succinimide) soft segments is presented. The strategy includes reversible addition fragmentation chain transfer ( RAFT ) copolymerization and two post polymerization modification steps. The RAFT polymerizations result in copolymers with an activated ester proportion within the polymer chains of 8% N ‐acryloxysuccinimide and 5% 6‐acrylamidohexanoic succinimide. The reactivity ratios of the monomer pairs were determined. In a first post polymerization reaction carboxylic acid homo telechelic polymers were prepared by reacting the ω‐dithiobenzoate end‐group with an excess of azobis(cyanovaleric acid). In a second modification step the α‐ and ω‐carboxylic acid end‐groups were reacted with hexamethylene diisocyanate and 100% isocyanate telechelic copolymers were obtained. Finally segmented polyurethanes were prepared by coupling hexamethylene diisocyanate ( HDI ) end capped soft segments with hard segments composed of 1,4‐butanediol and HDI . © 2013 Society of Chemical Industry
Challenges to Diagnosis of HIV-Associated Wasting (2004)

There is a wide variability in the clinical presentation of the protein energy malnutrition often characterized as wasting in patients infected with HIV. Moreover, the clinical presentation has evolved over time. Initially, protein energy malnutrition was characterized by profound weight loss and depletion of body cell mass (BCM). Recently, unrelated concurrent metabolic abnormalities, such as lipodystrophy, may complicate the diagnosis of HIV wasting. Although measures of BCM are relatively accurate for the diagnosis of HIV wasting, the optimal tools for assessing BCM are not necessarily available to the clinician. From the practical standpoint, HIV wasting may be a self-evident diagnosis in advanced stages, but effective interpretation of the early signs of HIV wasting requires familiarity with other complications included in the differential diagnosis.
Glycosylphosphatidylinositol-anchored Fungal Polysaccharide in Aspergillus fumigatus (2005)

Galactomannan is a characteristic polysaccharide of the human filamentous fungal pathogen Aspergillus fumigatus that can be used to diagnose invasive aspergillosis. In this study, we report the isolation of a galactomannan fraction associated to membrane preparations from A. fumigatus mycelium by a lipid anchor. Specific chemical and enzymatic degradations and mass spectrometry analysis showed that the lipid anchor is a glycosylphosphatidylinositol (GPI). The lipid part is an inositol phosphoceramide containing mainly C18-phytosphingosine and monohydroxylated lignoceric acid (2OH-C(24:0) fatty acid). GPI glycan is a tetramannose structure linked to a glucosamine residue: Manalpha1-2Manalpha1-2Manalpha1-6Manalpha1-4GlcN. The galactomannan polymer is linked to the GPI structure through the mannan chain. The GPI structure is a type 1, closely related to the one previously described for the GPI-anchored proteins of A. fumigatus. This is the first time that a fungal polysaccharide is shown to be GPI-anchored.
Retinoid X receptors are essential for early mouse development and placentogenesis (1999)

Embryos carrying null mutations of both retinoid X receptors alpha and beta (RXRalpha-/-/RXRbeta-/- mutants) were generated. These mutant embryos die between 9.5 and 10.5 days of gestation and display a wide range of abnormalities. The cause of the lethality appears to be the lack of formation of the labyrinthine zone of the chorioallantoic placenta. In a thorough analysis of mutant conceptuses, we establish that RXRs, through heterodimerization with retinoic acid receptors, are essential for postimplantation embryonic development before placentogenesis. RXRs are also essential for the formation of the chorioallantoic placenta, most probably through RXR/peroxisomal proliferator-activated receptor-gamma heterodimers. Interestingly, as a RXR ligand appears dispensable, placentogenesis must be controlled by a yet unknown hormonal ligand(s) activating the heterodimerization partner(s) of RXRs.
Thrombopoietic potential and serial repopulating ability of murine hematopoietic stem cells constitutively expressing interleukin 11. (1996)

Based on transplantation studies with bone marrow cultured under various conditions, a role of interleukin 11 (IL-11) in the self-renewal and/or the differentiation commitment of hematopoietic stem cells has been indicated. To better evaluate the in vivo effects of IL-11 on stem/progenitor cell biology, lethally irradiated mice were serially transplanted with bone marrow cells transduced with a defective retrovirus, termed MSCV-mIL-11, carrying the murine IL-11 (mIL-11) cDNA and the bacterial neomycin phosphotransferase (neo) gene. High serum levels (i.e., > 1 ng/ml) of mIL-11 in all (20/20) primary and 86% (12/14) of secondary long-term reconstituted mice, as well as 86% (12/14) of tertiary recipients examined at 6 weeks posttransplant, demonstrated persistence of vector expression subsequent to transduction of bone marrow precursors functionally definable as totipotent hematopoietic stem cells. In agreement with results obtained with human IL-11 in other myeloablation models, ectopic mIL-11 expression accelerated recovery of platelets, neutrophils, and, to some extent, total leukocytes while preferentially increasing peripheral platelet counts in fully reconstituted mice. When analyzed 5 months posttransplant, tertiary MSCV-mIL-11 recipients had a significantly greater percentage of G418-resistant colony-forming cells in their bone marrow compared with control MSCV animals. Collectively, these data show that persistent stimulation of platelet production by IL-11 is not detrimental to stem cell repopulating ability; rather, they suggest that IL-11 expression in vivo may have resulted in enhanced maintenance of the most primitive hematopoietic stem cell compartment. The prolonged expression achieved by the MSCV retroviral vector, despite the presence of a selectable marker, contrasts with the frequent transcriptional extinction observed with other retroviral vectors carrying two genes. These findings have potentially important implications for clinical bone marrow transplantation and gene therapy of the hematopoietic system.
PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease (2003)

Peptidylarginine deiminase (PAD, EC 3.5.3.15) enzymes catalyze the conversion of protein-bound arginine to citrulline. This post-translational modification may have a big impact on the structure and function of the target protein. In this review, we will discuss the effects of citrullination and its involvement in several human diseases, including rheumatoid arthritis and multiple sclerosis. So far, four isotypes of PAD have been described in mammals. We describe the existence of PAD in non-mammalian vertebrates and the existence of a fifth mammalian PAD. In addition, tissue-specific expression, genomic organization and evolutionary conservation of the different PAD isotypes will be discussed in detail. This article contains supplementary material which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/2003/25/v25.1106.html.
Rapid synthesis of oligodeoxyribonucleotides VI. Effident, mechanised synthesis of heptadecadeoxyribonucleotides by an improved solid phase phosphotriester route (1981)

Efficient mechanised synthesis of heptadecadeoxyribonucleotides has been achieved on an economically small scale by an improved solid phase phosphotriester method on a polydimethylacrylamide resin. Improvements were made in the preparation of dinucleotide building blocks, reaction conditions for oligonucleotide assembly and in purification of deprotected oligonucleotides by h.p.l.c. Several milligrams of pure heptadecamers were obtained. Two of the heptadecamers were designed for sequencing in opposite directions of DNA cloned in phage M13mp2.
Identification of Scavenger Receptor SR-BI as a High Density Lipoprotein Receptor (1996)

High density lipoprotein (HDL) and low density lipoprotein (LDL) are cholesterol transport particles whose plasma concentrations are directly (LDL) and inversely (HDL) correlated with risk for atherosclerosis. LDL catabolism involves cellular uptake and degradation of the entire particle by a well-characterized receptor. HDL, in contrast, selectively delivers its cholesterol, but not protein, to cells by unknown receptors. Here it is shown that the class B scavenger receptor SR-BI is an HDL receptor. SR-BI binds HDL with high affinity, is expressed primarily in liver and nonplacental steroidogenic tissues, and mediates selective cholesterol uptake by a mechanism distinct from the classic LDL receptor pathway.
Inhibitors of the renin-angiotensin system ameliorates clinical and pathological aspects of experimentally induced nephrotoxic serum nephritis (2018)

This is the first study showing a comprehensive pathological description of the chronic features of the murine NTN model and that inhibiting the RAS pathway show a significant effect on functional and morphological parameters.
Immunochemical detection of oxidized proteins (1993)

An immunochemical assay was developed to detect carbonyl moieties that result from oxidative damage to proteins. Bovine serum albumin was reacted with hydroxyl radicals generated via a Fenton-like mechanism or by a radiolysis mechanism. The resulting albumin-derived carbonyls were reacted with 2,4-dinitrophenylhydrazine, giving the corresponding hydrazones, which were detected by Western blot using anti-dinitrophenyl antisera. The immunoblot demonstrated a concentration-dependent increase in carbonyl formation, as well as fragmentation of the albumin into two distinct bands with molecular masses of 51 and 45 kDa when oxidized with the Fenton-like mechanism, and 62 and 46 kDa when oxidized by radiolysis. Analysis of the immunoblot using laser densitometry indicated a linear relationship between carbonyl groups and increasing treatment from radiolysis. This immunochemical assay was approximately 3 orders of magnitude more sensitive than the spectrophotometric method and was able to determine the molecular mass of carbonyl-modified polypeptides in the detection of oxidative damage.
Locomotor Skills and Balance Strategies in Adolescents Idiopathic Scoliosis (2007)

Patients with AIS show substantial similarities with control subjects in adaptive strategies relative to locomotor velocity as well as balance control based on segmental stabilization. In contrast, the loss of the yaw head stabilization strategies, mainly based on the use of vestibular information, probably reflects the presence of vestibular deficits in the patients with AIS.
Chemicals from Biomass (2007)

Many chemicals used by the chemical industry can be derived from biomass, potentially reducing the industry's reliance on petroleum.
Mechanisms of immunity to malaria and the possibilities of a blood-stage vaccine: a critical appraisal (1989)

Resistance developed by the immune system in response to blood-stage malaria is complex in nature, involving humoral and non-antibody effector mechanisms. Different species of malarial parasites may vary in their ability to elicit, or their susceptibility to, those immune effectors. This complexity is enhanced by the different results obtained in vaccinated as opposed to drug-controlled infections. It is therefore important that some attempt be made to unravel these interactions. This is particularly so when we have to decide on methods for assessing the potentiality of antigens to induce protective immunity. In this review the limitations of some in vitro assays of immunity, as well as those of various host-parasite models, are discussed. The relative importance of cell-mediated and humoral immunity in laboratory models and natural infections is also considered in the context of vaccine development.