gebhart/patrepeval huggingface dataset:
The Role of Sialic Acid in Determining the Survival of Glycoproteins in the Circulation (1971)

Evidence is presented to indicate a generalized role for the terminal sialic acid residues of circulating glycoproteins. Upon injection into rats, all of the desialylated plasma proteins tested, with the exception of transferrin, were promptly removed from the circulation and were recovered from the liver. The materials examined included orosomucoid, fetuin, ceruloplasmin, haptoglobin, α2-macroglobulin, thyroglobulin, lactoferrin, and the two gonadotropic hormones, human chorionic gonadotropin and follicle-stimulating hormone. Competitive inhibition of hepatic uptake was demonstrated by the injection of tracer amounts of 64Cu-ceruloplasmin together with substantive amounts of the above-mentioned desialylated proteins or the glycopeptides derived from them. Uptake was not inhibited by the fully sialylated protein or their glycopeptides.
Hydrogen Implantation into Silicon. Infra-Red Absorption Spectra and Electrical Properties (1985)

Hydrogen and deuterium implantations into crystalline silicon (c-Si) are carried out at room temperature. Infra-red spectra and electrical property studies are performed on these samples before and following annealing. Analysis of the vibrational spectra shows at least two types of bonding for hydrogen in c-Si, which are identified as SiH1, (SiH2)2 units. A strong evidence of SiH2 group formation is obtained for the relatively low hydrogen concentration in c-Si in comparison with a-Si:H. On the basis of the kinetics of formation and annealing of SiH vibrations and scanning micrograph data it is concluded that the microvoids with reconstructed inner surfaces, and hydrogen passivating dangling bonds, are effectively produced due to divacancy type defect agglomeration followed by hydrogen trapping. The electrical properties of c-Si:H are discussed also. [Russian Text Ignored].
PAK in Alzheimer disease, Huntington disease and X-linked mental retardation (2012)

Developmental cognitive deficits including X-linked mental retardation (XLMR) can be caused by mutations in P21-activated kinase 3 (PAK3) that disrupt actin dynamics in dendritic spines. Neurodegenerative diseases such as Alzheimer disease (AD), where both PAK1 and PAK3 are dysregulated, may share final common pathways with XLMR. Independent of familial mutation, cognitive deficits emerging with aging, notably AD, begin after decades of normal function. This prolonged prodromal period involves the buildup of amyloid-β (Aβ) extracellular plaques and intraneuronal neurofibrillary tangles (NFT). Subsequently region dependent deficits in synapses, dendritic spines and cognition coincide with dysregulation in PAK1 and PAK. Specifically proximal to decline, cytoplasmic levels of actin-regulating Rho GTPase and PAK1 kinase are decreased in moderate to severe AD, while aberrant activation and translocation of PAK1 appears around the onset of cognitive deficits. Downstream to PAK1, LIM kinase inactivates cofilin, contributing to cofilin pathology, while the activation of Rho-dependent kinase ROCK increases Aβ production. Aβ activation of fyn disrupts neuronal PAK1 and ROCK-mediated signaling, resulting in synaptic deficits. Reductions in PAK1 by the anti-amyloid compound curcumin suppress synaptotoxicity. Similarly other neurological disorders, including Huntington disease (HD) show dysregulation of PAKs. PAK1 modulates mutant huntingtin toxicity by enhancing huntingtin aggregation, and inhibition of PAK activity protects HD as well as fragile X syndrome (FXS) symptoms. Since PAK plays critical roles in learning and memory and is disrupted in many cognitive disorders, targeting PAK signaling in AD, HD and XLMR may be a novel common therapeutic target for AD, HD and XLMR.
The Neutralization Breadth of HIV-1 Develops Incrementally over Four Years and Is Associated with CD4 + T Cell Decline and High Viral Load during Acute Infection (2011)

An understanding of how broadly neutralizing activity develops in HIV-1-infected individuals is needed to guide vaccine design and immunization strategies. Here we used a large panel of 44 HIV-1 envelope variants (subtypes A, B, and C) to evaluate the presence of broadly neutralizing antibodies in serum samples obtained 3 years after seroconversion from 40 women enrolled in the CAPRISA 002 acute infection cohort. Seven of 40 participants had serum antibodies that neutralized more than 40% of viruses tested and were considered to have neutralization breadth. Among the samples with breadth, CAP257 serum neutralized 82% (36/44 variants) of the panel, while CAP256 serum neutralized 77% (33/43 variants) of the panel. Analysis of longitudinal samples showed that breadth developed gradually starting from year 2, with the number of viruses neutralized as well as the antibody titer increasing over time. Interestingly, neutralization breadth peaked at 4 years postinfection, with no increase thereafter. The extent of cross-neutralizing activity correlated with CD4(+) T cell decline, viral load, and CD4(+) T cell count at 6 months postinfection but not at later time points, suggesting that early events set the stage for the development of breadth. However, in a multivariate analysis, CD4 decline was the major driver of this association, as viral load was not an independent predictor of breadth. Mapping of the epitopes targeted by cross-neutralizing antibodies revealed that in one individual these antibodies recognized the membrane-proximal external region (MPER), while in two other individuals, cross-neutralizing activity was adsorbed by monomeric gp120 and targeted epitopes that involved the N-linked glycan at position 332 in the C3 region. Serum antibodies from the other four participants targeted quaternary epitopes, at least 2 of which were PG9/16-like and depended on the N160 and/or L165 residue in the V2 region. These data indicate that fewer than 20% of HIV-1 subtype C-infected individuals develop antibodies with cross-neutralizing activity after 3 years of infection and that these antibodies target different regions of the HIV-1 envelope, including as yet uncharacterized epitopes.
Combined Deficiency of Coagulation Factors Ii, Vii, IX, and X: A Case of Probable Congenital Origin (1986)

Combined deficiency of coagulant activity of the vitamin K-dependent factors was found in a 14-year-old boy suffering from severe hemorrhages. Immunoassays revealed the presence of acarboxyprothrombin. The bleedings could be controlled, but the coagulation defects persisted during more than 2 years' follow-up and could not be corrected by oral or parenteral vitamin K. No intoxication or underlying disease was found. The abnormality was considered a congenital disorder of the carboxylation of prothrombin.
Chronic Erosions of the Stomach - A Clinical, Endoscopic and Histological Evaluation - (1984)

A clinical, endoscopic and histological study was performed in 300 patients with chronic gastric erosions. The male-female ratio was 4:1. The antrum was the preferential site of erosions. Chronic erosions were classified into two categories: "active" (with a dark clot or whitish coat of fibrin) and "inactive" (covered by a normal pink mucosa). All the lesions showed foveolar hyperplasia, partial obliteration of the lamina propria by fibrous and smooth muscle bundles, a greatly thickened muscularis mucosae and an increased number of submucosal thick-walled vessels. In the "active" stage the central umbilicated area was covered by a collection of granulocytes, while in some of the "inactive" erosions the central depression showed the presence of a channel-like structure penetrating into the lamina propria. In two cases the lesion mimicked a gastric adenomyoma. Gastric acid secretion was significantly increased in the tested patients as compared with normal. The similarity of the histological findings with those in ischemic conditions of the gastro-intestinal tract suggests that both hypersecretion and localized ischemia may play a role in the pathogenesis of chronic erosions.
Mutational Analysis of Norrin-Frizzled4 Recognition (2006)

Norrin and Frizzled4 (Fz4) function as a ligand-receptor pair to control vascular development in the retina and inner ear. In mice and humans, mutations in either of the corresponding genes lead to defects in vascular development. The present work is aimed at defining the sequence determinants of binding specificity between Norrin and the Fz4 amino-terminal ligand-binding domain (the "cysteine-rich domain" (CRD)). The principal conclusions are as follows: 1) Norrin binds to the Fz4 CRD and does not detectably bind to the 14 other mammalian Frizzled and secreted Frizzled-related protein CRDs; 2) Norrin and Xenopus Wnt8 recognize largely overlapping regions of the Fz4 CRD; 3) surface determinants on the Fz4 and Fz8 CRDs that allow Norrin to distinguish between these two CRDs reside within several small regions on one face of the CRD; 4) Norrin function depends critically on three pairs of cysteines that form the highly conserved trio of disulfide bonds shared among all cystine knot proteins, but the remaining two putative disulfide bonds are less important; 5) Norrin-CRD binding depends on a largely contiguous group of amino acids in the extended beta-sheet domain of Norrin that are predicted to face away from the interface between the two monomers in the Norrin homodimer; 6) Norrin-CRD binding is strongly modulated by interactions involving charged amino acid side chains; and 7) Norrin-CRD binding is enhanced approximately 10-fold by the addition of heparin. These observations are discussed in the context of Frizzled signaling and the structure and function of other cystine knot proteins.
Identification of the Putative MAP Kinase Docking Site in the Thyroid Hormone Receptor-β1 DNA-Binding Domain:  Functional Consequences of Mutations at the Docking Site (2003)

In CV-1 cells transfected with wild-type (wt) nuclear thyroid hormone receptor TRbeta1 (TR), L-thyroxine (T(4)) causes activation and nuclear translocation of mitogen-activated protein kinase (MAPK, ERK1/2), co-immunoprecipitation of MAPK and TR, and MAPK-dependent serine phosphorylation of TR. In the present studies, we have identified (1) the likely site of TR serine phosphorylation in the TR DNA-binding domain (DBD) by T(4)-activated MAPK, (2) the site of MAPK docking on TR induced by T(4), and (3) functional consequences of TR docking site and serine phosphorylation site mutations on co-repressor and co-activator binding and on transcriptional activation by wt and mutant receptors in T(4)-treated cells. Plasmids containing TR(wt), serine 142-substituted TR (TR(S142A) or TR(S142E)), TR(K128A), TR(R132A), or TR(R133A) were transfected into CV-1 cells, and the cells were treated with 10(-7) M T(4) for 30 min. Activated MAPK was present in nuclear fractions of all T(4)-treated cells and co-immunoprecipitated prominently with TR(wt), TR(S142A), and TR(S142E). TR(K128A) complexing with activated MAPK was minimally detectable, but no association of MAPK with TR(R132A) or TR(R133A) was seen in cells treated with T(4). Serine phosphorylation of TR(wt), but not of any mutants, occurred with T(4). In in vitro phosphorylation studies, constitutively activated MAPK phosphorylated only TR(wt). We concluded that serine 142 of the TR DBD is the likely site of phosphorylation by T(4)-activated MAPK and that the docking site on TR for activated MAPK includes residues 128-133 (KGFFRR), a basic amino acid-enriched motif novel for MAPK substrates. TR mutations in the proposed MAPK docking domain and at residue 142 modulated T(4)-conditioned shedding of co-repressor and recruitment of co-activator proteins by the receptor, and they altered transcriptional activity of TR in a thyroid hormone response element-luciferase reporter assay.
Transmission Electron Microscopy (2024)

Abstract Presentation slides for the ISTFA 2024 Tutorial session “Transmission Electron Microscopy.”
Prediction of molecular subtypes in acute myeloid leukemia based on gene expression profiling (2008)

We examined the gene expression profiles of two independent cohorts of patients with acute myeloid leukemia [n=247 and n=214 (younger than or equal to 60 years)] to study the applicability of gene expression profiling as a single assay in prediction of acute myeloid leukemia-specific molecular subtypes. The favorable cytogenetic acute myeloid leukemia subtypes, i.e., acute myeloid leukemia with t(8;21), t(15;17) or inv(16), were predicted with maximum accuracy (positive and negative predictive value: 100%). Mutations in NPM1 and CEBPA were predicted less accurately (positive predictive value: 66% and 100%, and negative predictive value: 99% and 97% respectively). Various other characteristic molecular acute myeloid leukemia subtypes, i.e., mutant FLT3 and RAS, abnormalities involving 11q23, -5/5q-, -7/7q-, abnormalities involving 3q (abn3q) and t(9;22), could not be correctly predicted using gene expression profiling. In conclusion, gene expression profiling allows accurate prediction of certain acute myeloid leukemia subtypes, e.g. those characterized by expression of chimeric transcription factors. However, detection of mutations affecting signaling molecules and numerical abnormalities still requires alternative molecular methods.
Chemical structure and biological activity relationship of bacterial cell walls and muramyl peptides. (1986)

The biological activities of the cell walls of bacteria having different types of peptidoglycans, and those of stereoisomers and analogs of muramyl dipeptide (MDP), of N-acetylglucosaminyl-beta(1-4)-N-acetylmuramyl tetrapeptides having different L- and D-amino acids at the COOH-terminus, and of 6-O-acyl-MDPs were examined to elucidate the relationship between structure and activity. Replacement of the L-alanine residue of MDP with glycine and replacement of the D-isoglutamine residue with L-isoglutamine, L-glutamic acid, and D-isoasparagine, but not with D-glutamic acid, caused a marked decrease in the biological activities of the MDP molecule. Test disaccharide tetrapeptides, irrespective of the configuration of COOH-terminal amino acid, showed strong immunoadjuvant activity and stimulation of macrophages, whereas those having COOH-terminal L-amino acids exhibited greater pyrogenicity, induction of acute joint inflammation, and hemorrhagic necrosis at a primed site than those having COOH-terminal D-amino acids. Introduction of an alpha-branched higher fatty acid to the muramic acid residue resulted in the disappearance of pyrogenicity after i.v. injection, an increase of adjuvanticity, and a loss of dependence on administration vehicles. The lack of the immunopotentiating activity (adjuvanticity) in cell walls from group B-type bacterial species was explained by the combined inhibitory effects of the replacement of the L-alanine residue by glycine and involvement of the alpha-carboxyl group of the D-glutamic acid residue in linking with neighboring peptide subunits.
Subacute Thrombosis and Vascular Injury Resulting From Slotted-Tube Nitinol and Stainless Steel Stents in a Rabbit Carotid Artery Model (1996)

Slotted-tube stainless steel stents were more thrombogenic and created more extensive vascular injury than nitinol stents in a rabbit carotid artery model. The mechanisms underlying these differences probably are related to metallurgic and design geometry properties of the two stent types.
SLO-driven right-sizing and resource provisioning of MapReduce jobs (2011)

There is an increasing number of MapReduce applications, e.g., personalized advertising, spam detection, real-time event log analysis, that require completion time guarantees or need to be completed within a given time window. Currently, there is a lack of performance models and workload analy-sis tools available to system administrators for automated performance management of such MapReduce jobs. In this work, we outline a novel framework for SLO-driven resource provisioning and sizing of MapReduce jobs. First, we pro-pose an automated profiling tool that extracts a compact job profile from the past application run(s) or by executing it on a smaller data set. Then, by applying a linear regression technique, we derive scaling factors to accurately project the application performance when processing a larger data-set. The job profile (with scaling factors) forms the basis of a MapReduce performance model that computes the lower and upper bounds on the job completion time. Finally, we provide a fast and efficient capacity planning model that for a MapReduce job with timing requirements generates a set of resource provisioning options. We validate the accuracy of our models by executing a set of realistic applications with different timing requirements on the 66-node Hadoop cluster. 1.
Electrosurgery (1996)

In this paper the author reviews the development of electrosurgery in neurosurgical procedures. Particular stress is placed on bipolar coagulation and the more recent addition of bipolar cutting. Basic electric principles are discussed as well as the electrophysiological basis of coagulating and cutting currents. Neurosurgical techniques and instrumentation criteria are presented. The material is planned to provide the neurosurgeon with greater understanding of the function of the equipment and, perhaps, to improve usage.
Increased Collagen IV Excretion in Diabetes (2001)

Because not all patients with microalbuminuria progress to declining renal function and some patients who develop nephropathy do not manifest albuminuria, the findings in this cross-sectional analysis suggest that measurement of urine collagen IV may be a useful noninvasive indicator to detect diabetic renal disease entering a phase of compromised renal function.
INFLUENCE OF AN ANTI-OXIDANT ON THE FORMATION OF ALLERGENIC COMPOUNDS DURING AUTO-OXIDATION OF <italic>d</italic>-LIMONENE (1994)

Butylated hydroxytoluene (BHT), a common anti-oxidant, was added to different samples of d-limonene. The decrease in concentration of d-limonene and the formation of oxidation products were compared between the samples and with samples without anti-oxidant using gas chromatography. The aim of the study was to investigate how long d-limonene to which BHT was added could be handled when air-exposed at room temperature, without formation of oxidation products which according to previous studies increase the risk of skin sensitization. In experiments trying to mimic the handling of limonene products at workplaces the addition of BHT prevented auto-oxidation for periods depending on the purity of the products and on the room temperature. Cold and dark storage of d-limonene in closed vessels prevented auto-oxidation for 1 year without addition of anti-oxidant.
An Implantable Seal‐less Centrifugal Pump with Integrated Double‐Disk Motor (1995)

Thrombus formation and sealing problems at the shaft as well as the compact and efficient design of the driving unit have been major difficulties in the construction of a long-term implantable centrifugal pump. To eliminate the problems of the seal, motor size, and efficiency, two major steps were taken by modifying the Vienna implantable centrifugal pump. First, a special driving unit was developed, in which the permanent magnets of the motor themselves are used for coupling the force into the rotor. Second, the rotor shaft in the pumping chamber was eliminated by adopting a concept recently presented by Ohara. The rotor is supported by 3 pins, which run on a carbon disk, whose concave shape leads to stabilization. The device has the following specifications: size: 65 mm (diameter) by 35 mm (height), 101 cm3; priming volume 30 cm3, 240 g; and a 6-pole brushless double disk DC motor. The required input power of the described prototype is 15 W at 150 mm Hg, 5 L/min (overall eta = 11%), and has an in vitro index of hemolysis (IH) of 0.0046 g/100 L. The test for in vitro thrombus growth exhibited far less thrombus formation in the new design than in designs with axles. In conclusion, the design of a special driving unit and the elimination of the axle led to the construction of a small pump with very low blood traumatization.
Toll-like receptors in innate immunity (2004)

Functional characterization of Toll-like receptors (TLRs) has established that innate immunity is a skillful system that detects invasion of microbial pathogens. Recognition of microbial components by TLRs initiates signal transduction pathways, which triggers expression of genes. These gene products control innate immune responses and further instruct development of antigen-specific acquired immunity. TLR signaling pathways are finely regulated by TIR domain-containing adaptors, such as MyD88, TIRAP/Mal, TRIF and TRAM. Differential utilization of these TIR domain-containing adaptors provides specificity of individual TLR-mediated signaling pathways. Several mechanisms have been elucidated that negatively control TLR signaling pathways, and thereby prevent overactivation of innate immunity leading to fatal immune disorders. The involvement of TLR-mediated pathways in autoimmune and inflammatory diseases has been proposed. Thus, TLR-mediated activation of innate immunity controls not only host defense against pathogens but also immune disorders.
Consumption of polyphenolic-rich beverages (mostly pomegranate and black currant juices) by healthy subjects for a short term increased serum antioxidant status, and the serum’s ability to attenuate macrophage cholesterol accumulation (2010)

The present study analyzed the antioxidative effects of various beverages, in vitro, and also the effect of short term consumption of beverages richest in polyphenols by healthy subjects on serum anti-atherogenic properties. Healthy subjects consumed 250 mL of the selected beverages for 2 h, or daily, for up to 1 week.We hypothesized that differences in the anti-atherogenic properties of the studied beverages could be related, not only to the quantity of polyphenols, but also to their quality. Furthermore, we hypothesized that consumption of these juices by healthy subjects for just a short-term, will increase their serum anti-atherogenic properties, as was demonstrated previously in long-term consumption studies.Of 35 beverages studied, both 100% Wonderful-variety pomegranate and 100% black currant juices were the most potent antioxidants in vitro, as they inhibited copper ion-induced LDL oxidation by up to 94% and AAPH-induced serum lipid peroxidation by up to 38%. Furthermore, they increased in vitro serum paraoxonase 1 (PON1) lactonase activity by up to 51%. Consumption of five selected polyphenol rich beverages by healthy subjects increased serum sulfhydryl group (SH) levels and serum PON1 activities after 2 h, and more so after 1 week of drinking these beverages. These effects were most pronounced after the consumption of 100% Wonderful-variety pomegranate and 100% black currant juices. In conclusion, polyphenolic-rich juices with impressive in vitro antioxidant properties, also demonstrate antioxidant effects in vivo when analyzed for short term consumption. In this respect, 100% Wonderful-variety pomegranate and 100% black currant juices were most the potent.
The elasticity and strength of paper and other fibrous materials (1952)

An analysis is made of the effect of orientation of the fibres on the stiffness and strength of paper and other fibrous materials. It is shown that these effects may be represented completely by the first few coefficients of the distribution function for the fibres in respect of orientation, the first three Fourier coefficients for a planar matrix and the first fifteen spherical harmonics for a solid medium. For the planar case it is shown that all possible types of elastic behaviour may be represented by composition of four sets of parallel fibres in appropriate ratios. The means of transfer of load from fibre to fibre are considered and it is concluded that the effect of short fibres may be represented merely by use of a reduced value for their modulus of elasticity. The results of the analysis are applied to certain samples of resin bonded fibrous filled materials and moderately good agreement with experimental results is found.