gebhart/patrepeval huggingface dataset:
Detection of Disseminated Medullary Thyroid Carcinoma Cells inCervical Lymph Nodes by Cytokeratin 20 Reverse Transcription‐PolymeraseChain Reaction (2002)

Local recurrence in differentiated and medullary thyroid carcinoma develops frequently from metastatic infiltration of cervical lymph nodes. Despite an aggressive surgical approach, postoperative calcitonin levels as biochemical evidence for residual cancer cells remain often elevated in patients with medullary thyroid carcinoma. In the present study, we compared the detection rates of disseminated medullary thyroid carcinoma cells in cervical lymph nodes by histopathology with reverse transcription-polymerase chain reaction (RT-PCR) amplification of cytokeratin 20 (CK20) transcripts as a more sensitive but still specific molecular parameter for residual thyroid cancer cells. Forty-two cervical lymph nodes obtained from 7 patients with CK20positive medullary thyroid carcinomas were cut into two halves, one used for conventional histology, the other subjected to RNA extraction and subsequent amplification of cytokeratin 20 transcripts. Matching results for CK20 RT-PCR and histopathology were found in 74% (31/42)of the examined lymph nodes (52% positive results, 48% negative results). Positive CK20 RT-PCR pointed to residual thyroid carcinoma cells in another 19% (8/42), in which no thyroid carcinoma cells were identified by histopathology. Histology and immunohistochemistry,however, identified tumor cells in 7% (3/42) of the analyzed lymph nodes, from which no CK20 transcript could be amplified (false-negative results). These data suggest that CK20 RT-PCR might be more sensitive to detect nodal involvement of CK20 positive medullary thyroid carcinomas than conventional histopathology. In combination with histology, it might help to identify patients with residual disease after surgery.
High-performance liquid chromatography of amino acids, peptides, and proteins. 123. Dynamics of peptides in reversed-phase high-performance liquid chromatography (1993)

The dynamics of several peptides in reversed-phase high-performance liquid chromatography (RP-HPLC) have been investigated on both n-octadecyl (C18) silica and n-butyl (C4) silica sorbents. In particular, the conformational interconversions and the relative rates of chromatographic relaxation of bombesin, glucagon, and beta-endorphin on both C18 and C4 n-alkylsilicas were monitored by examining changes in the experimental bandwidths of these peptides as a function of temperature and column residence time under linear gradient elution RP-HPLC conditions. The observed band-broadening trends were correlated with previously derived retention parameters and thermodynamic descriptors of the association process determined for bombesin, beta-endorphin, glucagon, and a control peptide, penta-L-phenylalanine. This study confirms that bandwidth measurements can be used as an integral experimental component to study the effect of the secondary structure of peptidic solutes on their RP-HPLC retention behavior. Further, the data demonstrate the utility of RP-HPLC as a tool to examine peptide conformational dynamics at hydrophobic surfaces. The relevance of these results to the general phenomenon of peptide-lipid interactions is discussed in terms of the associated evidence for lipid-induced changes in the conformation of these three bioactive peptides.
The diverse roles of RNA helicases in RNAi (2009)

RNA interference (RNAi) is a regulatory gene silencing system found in nearly all eukaryotic organisms that employs small RNAs, typically 20-25 nucleotides long, to target complementary sequences found in mRNAs. RNA helicases use ATP to unwind double-stranded RNA (dsRNA), and are known to participate at nearly every level of RNA metabolism. A multitude of RNA helicases have been isolated from screens for essential RNAi factors, and even the earliest models of the RNAi pathway have presumed an RNA helicase to function at the level of small RNA duplex unwinding. However, while many components that function in RNAi have been uncovered and characterized, the exact placement in the pathway and ascription of a specific biochemical function of an RNA helicase in RNAi remains elusive. Recent studies have delved deeper into the precise role of some RNA helicases. Surprisingly, these studies have revealed nontraditional roles, which may not even require the helicase activity. Such findings suggest that RNA helicases regulate gene silencing at nearly every level of the RNAi pathways.
Indium-111 T101 monoclonal antibody is superior to iodine-131 T101 in imaging of cutaneous T-cell lymphoma. (1987)

We have reported that [111In]T101 is highly effective in the detection of cutaneous T-cell lymphoma (CTCL) in nodal and cutaneous (erythroderma and tumor) sites. This study compares the biodistribution of [131I]T101 (1 to 7.1 mg, 2 mCi) in four patients with CTCL; two of these patients also received [111In]T101 (1 mg, 5 mCi). There was rapid clearance of [131I]T101 from whole-body, spleen, liver, and bone marrow, with evidence of loss of 131I tracer from the T101. Lymph node uptake was minimal in three of four patients, and there was no localization in skin lesions. This contrasted with [111In]T101 where there was prolonged retention of activity in these organs and excellent uptake in skin tumors, erythroderma, and lymph nodes. The study showed that [131I]T101 was suboptimal for imaging CTCL patients and demonstrates that the isotope or labeling method can dramatically alter the apparent biodistribution and tumor targeting of a given monoclonal antibody.
Sacral Neuromodulation in Children With Urinary and Fecal Incontinence: A Multicenter, Open Label, Randomized, Crossover Study (2010)

In a pediatric population sacral neuromodulation is effective for bladder and bowel dysfunction and should be considered before irreversible surgery.
Initial experiments with a flexible robot (2002)

A flexible three-degree-of-freedom robot is described, and its behavior is compared with a simple model of a vibrating system. The robot has three rotary joints and two flexible steel links, causing it to exhibit many complicated modes of vibration. A nondimensional analysis of the model showing how it responds to ramp commands and acceleration commands is presented, and the results are compared with those for the actual robot. Using the model, one can select input commands that minimize the vibration of the robot.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The vacuolar sorting domain of sporamin transports GUS, but not levansucrase, to the plant vacuole (1997)

SUMMARY Fructans (polyfructosylsucrose) are synthesized by a number of plants and micro‐organisms. Plant fructans are localized in the vacuole and have a low degree of polymerization (DP), whereas the fructans synthesized by microorganisms are usually much bigger. There is an increasing interest in fructans for both food and non‐food applications. In order to accumulate fructans of high DP in the plant vacuole, the levansucrase protein of Bacillus subtilis was fused to the vacuolar targeting sequence of sporamin and expressed in plants. Transgenic tobacco plants in which this fusion gene is expressed accumulate fructans to levels up to 21% of the d. wt. They showed a reduced translocation of carbohydrates, bleaching of the leaves, stunted growth and increased levels of hexoses and starch. The levansucrase protein was not translocated to the plant vacuole, but retained in the endomembrane system, even though the same targeting signal was able to translocate the E. coli GUS protein to the plant vacuole.
[Advance in study of induced pluripotent stem cells (iPS cells)]. (2008)

By retroviral transduction of four or three transcription factors, mouse and human somatic cells have been reprogrammed to an undifferentiated state similar to embryonic stem (ES) cells, and these cells have been termed induced pluripotent stem (iPS) cells. This technology has opened the avenue to generate patient- and disease-specific pluripotent stem cells, which are useful for not only customized cell transplantation therapy without rejection but also for understanding disease mechanisms, drug screening and toxicology. In this review, we discuss the overview of the advance of iPS cells.
Delivery of Non-Native Cargo into Mammalian Cells Using Anthrax Lethal Toxin (2016)

The intracellular delivery of peptide and protein therapeutics is a major challenge due to the plasma membrane, which acts as a barrier between the extracellular environment and the intracellular milieu. Over the past two decades, a nontoxic PA/LFN delivery platform derived from anthrax lethal toxin has been developed for the transport of non-native cargo into the cytosol of cells in order to understand the translocation process through a protective antigen (PA) pore and to probe intracellular biological functions. Enzyme-mediated ligation using sortase A and native chemical ligation are two facile methods used to synthesize these non-native conjugates, inaccessible by recombinant technology. Cargo molecules that translocate efficiently include enzymes from protein toxins, antibody mimic proteins, and peptides of varying lengths and non-natural amino acid compositions. The PA pore has been found to effectively convey over 30 known cargos other than native lethal factor (LF; i.e., non-native) with diverse sequences and functionalities on the LFN transporter protein. All together these studies demonstrated that non-native cargos must adopt an unfolded or extended conformation and contain a suitable charge composition in order to efficiently pass through the PA pore. This review provides insight into design parameters for the efficient delivery of new cargos using PA and LFN.
Amide proton transfer (APT) contrast for imaging of brain tumors (2003)

In this work we demonstrate that specific MR image contrast can be produced in the water signal that reflects endogenous cellular protein and peptide content in intracranial rat 9L gliosarcomas. Although the concentration of these mobile proteins and peptides is only in the millimolar range, a detection sensitivity of several percent on the water signal (molar concentration) was achieved. This was accomplished with detection sensitivity enhancement by selective radiofrequency (RF) labeling of the amide protons, and by utilizing the effective transfer of this label to water via hydrogen exchange. Brain tumors were also assessed by conventional T(1)-weighted, T(2)-weighted, and diffusion-weighted imaging. Whereas these commonly-used approaches yielded heterogeneous images, the new amide proton transfer (APT) technique showed a single well-defined region of hyperintensity that was assigned to brain tumor tissue.
Monoethanol Amine Modified Zeolite 13X for CO2Adsorption at Different Temperatures (2007)

Zeolite 13X has been modified with monoethanol amine (MEA). MEA loadings of 0.5–25 wt % have been achieved using the impregnation method in different solvents. The mode of incorporation based on methanol with stirring at room temperature appears to be the most feasible. The adsorbent has been characterized for crystallinity, surface area, pore volume, and pore size. The thermal stability of the adsorbent is studied using a thermal analyzer. The CO2 adsorption capacity of adsorbents is evaluated using the breakthrough adsorption method with a packed column on a 10 g scale. The adsorption capacities of adsorbents are estimated in the temperature range 30–120 °C. The adsorbents show improvement in CO2 adsorption capacity over the unmodified zeolite by a factor of ca. 1.6 at 30 °C, whereas at 120 °C the efficiency improved by a factor of 3.5. For adsorption at these temperatures, different MEA loading levels were found to be suitable as per the governing adsorption phenomena, that is, physical or chemical. The adsorbent is also studied for CO2 selectivity over N2 at 75 °C. The MEA-modified adsorbent shows better CO2 selectivity, which was improved further in the presence of moisture.
Mammalian sialidases: Physiological and pathological roles in cellular functions (2012)

Sialic acids are terminal acidic monosaccharides, which influence the chemical and biological features of glycoconjugates. Their removal catalyzed by a sialidase modulates various biological processes through change in conformation and creation or loss of binding sites of functional molecules. Sialidases exist widely in vertebrates and also in a variety of microorganisms. Recent research on mammalian sialidases has provided evidence for great importance of these enzymes in various cellular functions, including lysosomal catabolism, whereas microbial sialidases appear to play roles limited to nutrition and pathogenesis. Four types of mammalian sialidases have been identified and characterized to date, designated as NEU1, NEU2, NEU3 and NEU4. They are encoded by different genes and differ in major subcellular localization and enzymatic properties including substrate specificity, and each has been found to play a unique role depending on its particular properties. This review is an attempt to concisely summarize current knowledge concerning mammalian sialidases, with a special focus on their properties and physiological and pathological roles in cellular functions.
Brain transplantation of genetically engineered human neural stem cells globally corrects brain lesions in the mucopolysaccharidosis type VII mouse (2003)

In the present study, we investigated the feasibility of using human neural stem cells (NSCs) in the treatment of diffuse central nervous system (CNS) alterations in a murine model of mucopolysaccharidosis VII (MPS VII), a lysosomal storage disease caused by a genetic defect in the beta-glucuronidase gene. An immortalized NSC line derived from human fetal telencephalon was genetically engineered to overexpress beta-glucuronidase and transplanted into the cerebral ventricles of neonatal MPS VII mouse. Transplanted human NSCs were found to integrate and migrate in the host brain and to produce large amount of beta-glucuronidase. Brain contents of the substrates of beta-glucuronidase were reduced to nearly normal levels, and widespread clearing of lysosomal storage was observed in the MPS VII mouse brain at 25 days posttransplantation. The number of engrafted cells decreased markedly after the transplantation, and it appears that the major cause of the cell death was not the immune response of the host but apoptotic cell death of grafted human NSCs. Results showed that human NSCs would serve as a useful gene transfer vehicle for the treatment of diffuse CNS lesions in human lysosomal storage diseases and are potentially applicable in the treatment of patients suffering from neurological disorders.
Metallo‐β‐Lactamases: A Class Apart (1998)

Metallo-beta-lactamases have recently become more prominent among the beta-lactam-hydrolyzing enzymes. Two major functional groups of enzymes have been identified, with little structural similarity among the groups. One group is a set of enzymes with broad substrate specificities capable of hydrolyzing most beta-lactams except monobactams. A second group is composed of the "true" carbapenemases, enzymes that exhibit poor hydrolysis of penicillins and cephalosporins. This latter group has been found primarily in Aeromonas species. To date, only a small number of carbapenem-resistant isolates have been reported to produce metallo-beta-lactamases, in part because of the ease with which this resistance can be acquired by other means: permeability changes and an increase in chromosomal cephalosporinase production. However, the appearance of these enzymes on plasmids in Japan poses a worrisome problem. It is anticipated that plasmid-mediated resistance to carbapenems will continue to increase, perhaps compromising the use of these agents.
Proposed Cardiovascular Risk Assessment Algorithm Using High-Sensitivity C-Reactive Protein and Lipid Screening (2001)

Several prospective epidemiologic studies from the United States and Europe have demonstrated that high-sensitivity C-reactive protein (hs-CRP) is a predictor of future coronary events among apparently healthy men and women. For example, findings from the Multiple Risk Factors Intervention Trial demonstrated a correlation between hs-CRP and coronary heart disease mortality among male smokers followed over a 17-year period \[relative risk (RR) = 2.8; 95% confidence interval (CI), 1.4–5.4\] (1). A similar positive association between hs-CRP and future coronary events was noted in the Cardiovascular Health Study and Rural Health Promotion Project, which included elderly men and women with subclinical cardiovascular disease (2). A direct positive association between hs-CRP and future coronary events was also reported in apparently healthy men from the Physician’s Health Study (PHS); those in the highest quartile of hs-CRP had twice the risk of future stroke (RR = 1.9; 95% CI, 1.1–3.3), three times the risk of future myocardial infarction (RR = 2.9; 95% CI, 1.8–4.6), and four times the risk of future peripheral vascular disease (RR = 4.1; 95% CI, 1.2–6.0) (3)(4). Furthermore, both the MONICA-Augsburg cohort (5) and the Helsinki Heart Study (6) showed that compared with those with low hs-CRP, individuals with the highest hs-CRP concentrations were at approximately three times the risk of developing future coronary events. Finally, two reports from the Women’s Health Study (WHS) showed that hs-CRP is also a strong predictor of future cardiovascular events in women (RR = 4.4; 95% CI, 2.2–8.9) (7)(8). In fact, in that study, which directly compared several novel risk factors to standard lipid screening, hs-CRP was the single strongest predictor of future vascular risk …
Asthma: epidemiology, etiology and risk factors (2009)

Asthma is one of the most common chronic conditions affecting both children and adults, yet much remains to be learned of its etiology. This paper evolved from the extensive literature review undertaken as part of a proposal for a longitudinal birth cohort study to examine risk factors for the
Enhanced fold recognition using efficient short fragment clustering. (2012)

The main structure aligner in the CCP4 Software Suite, SSM (Secondary Structure Matching) has a limited applicability on the intermediate stages of the structure solution process, when the secondary structure cannot be reliably computed due to structural incompleteness or a fragmented mainchain. In this study, we describe a new algorithm for the alignment and comparison of protein structures in CCP4, which was designed to overcome SSM's limitations but retain its quality and speed. The new algorithm, named GESAMT (General Efficient Structural Alignment of Macromolecular Targets), employs the old idea of deriving the global structure similarity from a promising set of locally similar short fragments, but uses a few technical solutions that make it considerably faster. A comparative sensitivity and selectivity analysis revealed an unexpected significant improvement in the fold recognition properties of the new algorithm, which also makes it useful for applications in the structural bioinformatics domain. The new tool is included in the CCP4 Software Suite starting from version 6.3.
The Proprotein Convertase PCSK9 Induces the Degradation of Low Density Lipoprotein Receptor (LDLR) and Its Closest Family Members VLDLR and ApoER2 (2007)

The proprotein convertase PCSK9 gene is the third locus implicated in familial hypercholesterolemia, emphasizing its role in cardiovascular diseases. Loss of function mutations and gene disruption of PCSK9 resulted in a higher clearance of plasma low density lipoprotein cholesterol, likely due to a reduced degradation of the liver low density lipoprotein receptor (LDLR). In this study, we show that two of the closest family members to LDLR are also PCSK9 targets. These include the very low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) implicated in neuronal development and lipid metabolism. Our results show that wild type PCSK9 and more so its natural gain of function mutant D374Y can efficiently degrade the LDLR, VLDLR, and ApoER2 either following cellular co-expression or re-internalization of secreted human PCSK9. Such PCSK9-induced degradation does not require its catalytic activity. Membrane-bound PCSK9 chimeras enhanced the intracellular targeting of PCSK9 to late endosomes/lysosomes and resulted in a much more efficient degradation of the three receptors. We also demonstrate that the activity of PCSK9 and its binding affinity on VLDLR and ApoER2 does not depend on the presence of LDLR. Finally, in situ hybridization show close localization of PCSK9 mRNA expression to that of VLDLR in mouse postnatal day 1 cerebellum. Thus, this study demonstrates a more general effect of PCSK9 on the degradation of the LDLR family that emphasizes its major role in cholesterol and lipid homeostasis as well as brain development.
Wavelet estimation by prestack multiple elimination (1989)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1989Wavelet estimation by prestack multiple eliminationAuthors: D. J. VerschuurA. J. BerkhoutC. P. A. WapenaarD. J. VerschuurDelft University of Technology, Netherlands, A. J. BerkhoutDelft University of Technology, Netherlands, and C. P. A. WapenaarDelft University of Technology, Netherlandshttps://doi.org/10.1190/1.1889855 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1889855FiguresReferencesRelatedDetailsCited byResearch note: Inverse propagation in 1.5‐dimensional amplitude‐versus‐offset joint migration inversion29 September 2021 | Geophysical Prospecting, Vol. 70, No. 13D surface-related multiples elimination based on improved apex-shifted Radon transform3 August 2021 | Acta Geophysica, Vol. 69, No. 5References14 March 2018Wavelet estimation and multiple modeling in full wavefield inversionKe Wang, Spyros Lazaratos, and Ivan Chikichev25 May 2012References21 March 2012Kirchhoff scattering series: Insight into the multiple attenuation methodLuc T. Ikelle, Lasse Amundsen, Anthony Gangi, and Steven B. Wyatt27 February 2003 | GEOPHYSICS, Vol. 68, No. 1An optimization of the inverse scattering multiple attenuation method for OBS and VC dataLuc T. Ikelle, Lasse Amundsen, and Seung Yoo24 July 2002 | GEOPHYSICS, Vol. 67, No. 4Elimination of free‐surface related multiples without need of the source waveletLasse Amundsen7 February 2012 | GEOPHYSICS, Vol. 66, No. 1SLOPE DATA WATER-BOTTOM MULTIPLE ATTENUATION1Geophysical Prospecting, Vol. 40, No. 4 SEG Technical Program Expanded Abstracts 1989ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1989 Pages: 1375 publication data© 1989 Copyright © 1989 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 10 Feb 2005 CITATION INFORMATION D. J. Verschuur, A. J. Berkhout, and C. P. A. Wapenaar, (1989), "Wavelet estimation by prestack multiple elimination," SEG Technical Program Expanded Abstracts : 1129-1132. https://doi.org/10.1190/1.1889855 Plain-Language Summary PDF DownloadLoading ...