gebhart/patrepeval huggingface dataset:
Distribution and subcellular localization of surfactant-associated glycoproteins in human lung. (1985)

Human surfactant contains lung-specific, high molecular weight glycoproteins which are composed of disulfide-linked 34-kilodalton peptide subunits. We prepared antibodies to both isolated HMW glycoproteins and 34-kilodalton peptides and tested the antisera for specificity with immunochemical procedures. In the present study we have investigated the cellular distribution and subcellular localization of these glycoproteins in surgically excised human lung tissue with or without type II cell hyperplasia. An immunoperoxidase technique was used, and cytoplasmic staining reflecting labeling with antibodies to either high molecular weight glycoproteins or the 34-kilodalton peptide subunits was consistently observed in normal type II cells, Clara cells, and some alveolar macrophages and was more intense and diffuse in hyperplastic type II cells. The ultrastructural localization of surfactant-associated glycoproteins was investigated using the periodate-lysine-paraformaldehyde fixative and a peroxidase-labeled antibody technique. In both normal and proliferating type II cells the staining was localized in the rough endoplasmic reticulum, perinuclear cisternas, vesicles of the Golgi complex, vesicles and lamellar membranes of the multivesicular bodies, and some multivesicular body-lamellar body forms. In addition, staining was frequently found in peripheral portions of partially preserved lamellar bodies including those at the stage of secretion, as well as in association with of alveolar tubular myelin. Labeling was also observed in the rough endoplasmic reticulum of Clara cells. We conclude that antibodies against human surfactant-associated glycoproteins are markers for normal and regenerating type II cells, as well as for Clara cells which apparently retain limited ability to produce surfactant-associated glycoproteins independently of surfactant phospholipids. The results indicate that, in type II cells, synthesis and secretion of these glycoproteins involve the same cytoplasmic organelles that are responsible for synthesis, packaging, storage, and exocytosis of surfactant phospholipids. However, maturation of the lamellar bodies, known to be characterized by progressive accumulation of phospholipids, may not require parallel storage of surfactant-associated glycoproteins within the entire lamellar body compartment.
Isolation of Oct4-Expressing Extraembryonic Endoderm Precursor Cell Lines (2009)

Our findings (i) suggest strongly that the ExEn precursor is a self-renewable entity, (ii) indicate that active Oct4 gene expression (transcription plus translation) is part of its molecular identity, and (iii) provide an in vitro model of early ExEn differentiation.
Risk Factors for Pediatric Human Immunodeficiency Virus–Related Malignancy (2003)

Route of infection, demographic characteristics, and zidovudine use were not associated with the development of malignancy in HIV-infected children. High viral burden with EBV was associated with the development of malignancy in HIV-infected children although the effect was modified by CD4 cell count. The pathogenesis of HIV-related pediatric malignancies remains unclear and other contributing risk factors can be elucidated only through further study.
Phosphorylation Controls Timing of Cdc6p Destruction: A Biochemical Analysis (1999)

The replication initiation protein Cdc6p forms a tight complex with Cdc28p, specifically with forms of the kinase that are competent to promote replication initiation. We now show that potential sites of Cdc28 phosphorylation in Cdc6p are required for the regulated destruction of Cdc6p that has been shown to occur during the Saccharomyces cerevisiae cell cycle. Analysis of Cdc6p phosphorylation site mutants and of the requirement for Cdc28p in an in vitro ubiquitination system suggests that targeting of Cdc6p for degradation is more complex than previously proposed. First, phosphorylation of N-terminal sites targets Cdc6p for polyubiquitination probably, as expected, through promoting interaction with Cdc4p, an F box protein involved in substrate recognition by the Skp1-Cdc53-F-box protein (SCF) ubiquitin ligase. However, in addition, mutation of a single, C-terminal site stabilizes Cdc6p in G2 phase cells without affecting substrate recognition by SCF in vitro, demonstrating a second and novel requirement for specific phosphorylation in degradation of Cdc6p. SCF-Cdc4p- and N-terminal phosphorylation site-dependent ubiquitination appears to be mediated preferentially by Clbp/Cdc28p complexes rather than by Clnp/Cdc28ps, suggesting a way in which phosphorylation of Cdc6p might control the timing of its degradation at then end of G1 phase of the cell cycle. The stable cdc6 mutants show no apparent replication defects in wild-type strains. However, stabilization through mutation of three N-terminal phosphorylation sites or of the single C-terminal phosphorylation site leads to dominant lethality when combined with certain mutations in the anaphase-promoting complex.
Induction of revertant fibres in the mdx mouse using antisense oligonucleotides (2006)

This work demonstrates the feasibility of AO cocktails to by-pass dystrophin mutation hotspots through multi-exon skipping. Multi-exon skipping could be important in expediting an exon skipping therapy to treat DMD, so that the same AO formulations may be applied to several different mutations within particular domains of the dystrophin gene.
Seizures in low- and high-grade gliomas: current management and future outlook (2010)

Major difficulties in patients with epilepsy and brain tumors include refractory seizures, potential interactions between anticonvulsants and chemotherapeutic agents and enhanced risks of toxicity, including cognitive deterioration. For seizure control, levetiracetam, valproic acid, topiramate and lamotrigine can each be considered as agents of first choice. We advocate starting with levetiracetam monotherapy, based on efficacy, good tolerability and the absence of interactions. If levetiracetam alone is not sufficiently effective, we propose adding a second antiepileptic drug, rather than switching to monotherapy with another anticonvulsant. Under these circumstances we advise the use of valproic acid as an add-on over topiramate or lamotrigine, based on its reported clinical activity in brain tumor patients. The combination of levetiracetam and valproic acid seems synergistic, and produces few or no cognitive side effects. Antitumor therapy by neurosurgery, cranial radiation or chemotherapy contribute substantially to reducing seizure activity. Future research on seizure management in brain tumor patients should focus on better insight into the influence of multidrug resistance proteins on anticonvulsant drug transport over the blood-brain barrier, efficacy of new anticonvulsants with no or few interactions with other drugs, synergistic combinations of anticonvulsants in order to limit toxicity and therapeutic drug monitoring of anticonvulsants in current clinical practice and in new drug studies, including the effects of concomitant administration of chemotherapeutic agents.
A leucine zipper structure present in the measles virus fusion protein is not required for its tetramerization but is essential for fusion (1992)

The biological role of a leucine zipper motif present in the measles virus fusion (F) protein has been investigated. This motif is present in all paramyxovirus F proteins, all coronavirus spike proteins and many if not all retrovirus envelope proteins. By analogy to its role in certain transcription factors, it has been suggested that the motif may be responsible for the oligomerization of these viral membrane proteins. In this study, one, two or four heptadic leucines in the motif were substituted using site-directed mutagenesis. We found that fusion is prevented when all four heptadic leucines present in the motif are mutated whereas cellular transport and the oligomeric state of the F protein are unaffected.
Analysis and optimization of elliptic-curve single-scalar multiplication (2008)

Let P be a point on an elliptic curve over a finite field of large characteristic.Exactly how many points 2P, 3P, 5P, 7P, 9P, . . ., mP should be precomputed in a sliding-window computation of nP ?Should some or all of the points be converted to affine form, and at which moments during the precomputation should these conversions take place?Exactly how many field multiplications are required for the resulting computation of nP ?The answers depend on the size of n, the I/M ratio, the choice of curve shape, the choice of coordinate system, and the choice of addition formulas.This paper presents answers that, compared to previous analyses, are more carefully optimized and cover a much wider range of situations.
Serological divergence of Dobrava and Saaremaa hantaviruses: evidence for two distinct serotypes (2002)

In order to investigate the serological relationship of Dobrava hantavirus (DOBV, originating from Slovenia) and the Dobrava-like Saaremaa virus (SAAV, recently discovered in Estonia) we analysed 37 human serum samples, 24 from Estonia and 13 from the Balkans, by focus reduction neutralization test (FRNT). Most of the Estonian sera (19), including all sera from Saaremaa island (12), reacted with higher FRNT end-point titres to the local SAAV; the majority of them (15 and 11, respectively), with at least fourfold or higher titres to SAAV than to DOBV. In contrast, out of the 13 sera collected in Slovenia, Bosnia-Herzegovina and Greece, only one reacted more strongly with SAAV (with a twofold higher titre), while 10 of these sera reacted more strongly with the local DOBV (9/10 with fourfold or higher titres). These results indicate that DOBV and SAAV define unique hantavirus serotypes.
Cutaneous manifestations of intravenous vasopressin therapy. (1985)

A 79-year-old woman with primary biliary cirrhosis was admitted with esophageal variceal hemorrhage. She was initially managed with sclerosing of esophageal varices with no relief from the bleeding. Intravenous Vasopressin was started, but had to be discontinued because of cutaneous changes. A portocaval shunt was performed to control the variceal bleeding. Postoperatively she did poorly from sepsis and hepatic encephalopathy and died 46 days after admission to the hospital.
PROCHECK: a program to check the stereochemical quality of protein structures (1993)

The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing. These give an assessment of the overall quality of the structure as compared with well refined structures of the same resolution and also highlight regions that may need further investigation. The PROCHECK programs are useful for assessing the quality not only of protein structures in the process of being solved but also of existing structures and of those being modelled on known structures.
Experimental Pulmonary Aspergillosis Due toAspergillus terreus:Pathogenesis and Treatment of an Emerging Fungal Pathogen Resistant to Amphotericin B (2003)

Aspergillus terreus is an uncommon but emerging fungal pathogen, which causes lethal infections that are often refractory to amphotericin B (AmB). In comparison to Aspergillus fumigatus, A. terreus was resistant to the in vitro fungicidal effects of safely achievable concentrations of AmB. These in vitro findings correlated directly with resistance of A. terreus to AmB in experimental invasive pulmonary aspergillosis. Residual fungal pulmonary burden and galactomannan antigenemia demonstrated persistent infection, despite therapy with deoxycholate AmB or liposomal AmB. By comparison, posaconazole and itraconazole resolved GM antigenemia, reduced residual fungal burden, and improved survival. There were no differences in phagocytic host response to A. terreus versus A. fumigatus; however, the rate of conidial germination of A. terreus was slower. The strain of A. terreus with the highest minimum inhibitory and minimum lethal concentration of AmB also had the lowest membrane ergosterol content. The hyphae of A. terreus in vivo displayed distinctive aleurioconidia, which may be a practical microscopic feature for rapid preliminary diagnosis.
On the speed requirement for optimal deadline scheduling in overloaded systems (2005)

We consider the problem of scheduling jobs with deadlines in an on-line single-processor system. It is known for long that unless the system is underloaded, any on-line algorithm is not optimal in the sense that it may fail to match the optimal offline algorithm on the total work of jobs meeting their deadlines. In this paper, we extend this fact with two new lower bound results. First, we show that even if the on-line scheduler can use a processor times faster than the offline scheduler, where is any real number less than the golden ratio (i.e. ), no online algorithm can be optimal. Furthermore, if we restrict our attention to on-line algorithms that decide at the release time of a job whether the job will be processed to meet its deadline, then the speed requirement for optimal on-line algorithms is at least . These lower bound results should be contrasted with the recent upper bound result [11] that with a two times faster processor, a simple extension of the earliest deadline first strategy (EDF) is optimal.
Defining the kinetochore’s rules of engagement (2014)

Quantitative analyses and computer modeling reveal how a “molecular lawn” fine-tunes the interactions between kinetochores and microtubules.
Dengue-Virus Recovery by Direct and Delayed Plaques in LLC-MK2 Cells (1968)

SummaryA method for detecting and propagating dengue viruses in LLC-MK2 cells has been developed by direct plaquing and by fluid maintenance of inoculated cultures 7 to 14 days before plaquing (delayed plaquing). This procedure was used in support of studies of hemorrhagic fever and has resulted in the recovery of 69 dengue viruses, including all four serotypes. About half of these were detected by delayed plaques when direct plaques were not seen. Most of these dengue strains were inoculated simultaneously into mice and cell cultures. The direct and delayed plaque method was more sensitive and efficient than the use of suckling mice. Comparisons of the direct and delayed plaque method with other methods of recovery of dengue virus are discussed.Early in the study, occasional difficulty in preparing low-passage cell-culture seed virus of adequate titer was encountered. Consequently, the growth of dengue virus in LLC-MK2 cells was studied. Virus growth was synchronous and cyclic. In order to avoid inadvertent harvesting of virus during eclipse, live cells, rather than cell lysates, were passaged. This has resulted in consistent production of low-passage seed-virus suspensions.
Brain mechanical property measurement using MRE with intrinsic activation (2012)

Many pathologies alter the mechanical properties of tissue. Magnetic resonance elastography (MRE) has been developed to noninvasively characterize these quantities in vivo. Typically, small vibrations are induced in the tissue of interest with an external mechanical actuator. The resulting displacements are measured with phase contrast sequences and are then used to estimate the underlying mechanical property distribution. Several MRE studies have quantified brain tissue properties. However, the cranium and meninges, especially the dura, are very effective at damping externally applied vibrations from penetrating deeply into the brain. Here, we report a method, termed 'intrinsic activation', that eliminates the requirement for external vibrations by measuring the motion generated by natural blood vessel pulsation. A retrospectively gated phase contrast MR angiography sequence was used to record the tissue velocity at eight phases of the cardiac cycle. The velocities were numerically integrated via the Fourier transform to produce the harmonic displacements at each position within the brain. The displacements were then reconstructed into images of the shear modulus based on both linear elastic and poroelastic models. The mechanical properties produced fall within the range of brain tissue estimates reported in the literature and, equally important, the technique yielded highly reproducible results. The mean shear modulus was 8.1 kPa for linear elastic reconstructions and 2.4 kPa for poroelastic reconstructions where fluid pressure carries a portion of the stress. Gross structures of the brain were visualized, particularly in the poroelastic reconstructions. Intra-subject variability was significantly less than the inter-subject variability in a study of six asymptomatic individuals. Further, larger changes in mechanical properties were observed in individuals when examined over time than when the MRE procedures were repeated on the same day. Cardiac pulsation, termed intrinsic activation, produces sufficient motion to allow mechanical properties to be recovered. The poroelastic model is more consistent with the measured data from brain at low frequencies than the linear elastic model. Intrinsic activation allows MRE to be performed without a device shaking the head so the patient notices no differences between it and the other sequences in an MR examination.
Computational Methods for Integral Equations (1985)

Integral equations form an important class of problems, arising frequently in engineering, and in mathematical and scientific analysis. This textbook provides a readable account of techniques for their numerical solution. The authors devote their attention primarily to efficient techniques using high order approximations, taking particular account of situations where singularities are present. The classes of problems which arise frequently in practice, Fredholm of the first and second kind and eigenvalue problems, are dealt with in depth. Volterra equations, although attractive to treat theoretically, arise less often in practical problems and so have been given less emphasis. Some knowledge of numerical methods and linear algebra is assumed, but the book includes introductory sections on numerical quadrature and function space concepts. This book should serve as a valuable text for final year undergraduate or postgraduate courses, and as an introduction or reference work for practising computational mathematicians, scientists and engineers.
Application of Denaturing Gradient Gel Electrophoresis (DGGE) To Study the Diversity of Marine Picoeukaryotic Assemblages and Comparison of DGGE with Other Molecular Techniques (2001)

ABSTRACT We used denaturing gradient gel electrophoresis (DGGE) to study the diversity of picoeukaryotes in natural marine assemblages. Two eukaryote-specific primer sets targeting different regions of the 18S rRNA gene were tested. Both primer sets gave a single band when used with algal cultures and complex fingerprints when used with natural assemblages. The reproducibility of the fingerprints was estimated by quantifying the intensities of the same bands obtained in independent PCR and DGGE analyses, and the standard error of these estimates was less than 2% on average. DGGE fingerprints were then used to compare the picoeukaryotic diversity in samples obtained at different depths and on different dates from a station in the southwest Mediterranean Sea. Both primer sets revealed significant differences along the vertical profile, whereas temporal differences at the same depths were less marked. The phylogenetic composition of picoeukaryotes from one surface sample was investigated by excising and sequencing DGGE bands. The results were compared with an analysis of a clone library and a terminal restriction fragment length polymorphism fingerprint obtained from the same sample. The three PCR-based methods, performed with three different primer sets, revealed very similar assemblage compositions; the same main phylogenetic groups were present at similar relative levels. Thus, the prasinophyte group appeared to be the most abundant group in the surface Mediterranean samples as determined by our molecular analyses. DGGE bands corresponding to prasinophytes were always found in surface samples but were not present in deep samples. Other groups detected were prymnesiophytes, novel stramenopiles (distantly related to hyphochytrids or labyrinthulids), cryptophytes, dinophytes, and pelagophytes. In conclusion, the DGGE method described here provided a reasonably detailed view of marine picoeukaryotic assemblages and allowed tentative phylogenetic identification of the dominant members.
Construction, binding properties, metabolism, and tumor targeting of a single-chain Fv derived from the pancarcinoma monoclonal antibody CC49. (1991)

CC49 is a "second generation" monoclonal antibody to B72.3, which reacts with the pancarcinoma antigen TAG-72. CC49 has been shown to efficiently target human colon carcinoma xenografts and is currently being evaluated in both diagnostic and therapeutic clinical trials. We describe here the construction and characterization of a recombinant single-chain Fv (sFv) of CC49. The sFv was shown to be a Mr 27,000 homogeneous entity which could be efficiently radiolabeled with 125I or 131I. Comparative direct binding studies and competition radioimmunoassays using CC49 intact IgG, F(ab')2, Fab', and sFv revealed that the monomeric CC49 Fab' and sFv had relative binding affinities 8-fold lower than the dimeric F(ab')2 and intact IgG. Nonetheless, the 131I-labeled sFv was shown to bind biopsies of TAG-72-expressing tumors. Metabolism studies in mice, using radiolabeled CC49 IgG, F(ab')2, Fab', and sFv, demonstrated an extremely rapid plasma and whole body clearance for the sFv. CC49 sFv plasma pharmacokinetic studies in rhesus monkeys also showed a very rapid plasma clearance (T1/2 alpha of 3.9 min and T1/2 beta of 4.2 h). Tumor targeting studies with all four radiolabeled Ig CC49 forms, using the LS-174T human colon carcinoma xenograft model, revealed a much lower percentage injected dose/g tumor binding for the CC49 monomeric sFv and Fab' as compared to the dimeric F(ab')2 and intact IgG. However, tumor:normal tissue ratios (radiolocalization indices) for the sFv were comparable to or greater than those of the other Ig forms. High kidney uptake with 125I-labeled Fab' and F(ab')2 was not seen with 125I-sFv. Gamma scanning studies also showed that 131I-CC49 sFv could efficiently localize tumors. The CC49 sFv may thus have utility in diagnostic and perhaps therapeutic applications for a range of human carcinomas.
A Labeling-Free Approach to Supervising Deep Neural Networks for Retinal Blood Vessel Segmentation (2017)

Segmenting blood vessels in fundus imaging plays an important role in medical diagnosis. Many algorithms have been proposed. While deep Neural Networks have been attracting enormous attention from computer vision community recent years and several novel works have been done in terms of its application in retinal blood vessel segmentation, most of them are based on supervised learning which requires amount of labeled data, which is both scarce and expensive to obtain. We leverage the power of Deep Convolutional Neural Networks (DCNN) in feature learning, in this work, to achieve this ultimate goal. The highly efficient feature learning of DCNN inspires our novel approach that trains the networks with automatically-generated samples to achieve desirable performance on real-world fundus images. For this, we design a set of rules abstracted from the domain-specific prior knowledge to generate these samples. We argue that, with the high efficiency of DCNN in feature learning, one can achieve this goal by constructing the training dataset with prior knowledge, no manual labeling is needed. This approach allows us to take advantages of supervised learning without labeling. We also build a naive DCNN model to test it. The results on standard benchmarks of fundus imaging show it is competitive to the state-of-the-art methods which implies a potential way to leverage the power of DCNN in feature learning.