gebhart/patrepeval huggingface dataset:
Short tandem repeat profiling provides an international reference standard for human cell lines (2001)

Cross-contamination between cell lines is a longstanding and frequent cause of scientific misrepresentation. Estimates from national testing services indicate that up to 36% of cell lines are of a different origin or species to that claimed. To test a standard method of cell line authentication, 253 human cell lines from banks and research institutes worldwide were analyzed by short tandem repeat profiling. The short tandem repeat profile is a simple numerical code that is reproducible between laboratories, is inexpensive, and can provide an international reference standard for every cell line. If DNA profiling of cell lines is accepted and demanded internationally, scientific misrepresentation because of cross-contamination can be largely eliminated.
Direct isolation in cell culture of human rotaviruses and their characterization into four serotypes (1983)

Of 73 rotavirus-positive fecal specimens tested, 39 yielded a human rotavirus that could be cultivated serially in MA104 or primary African green monkey kidney cells or both; 18 were serotyped. Four distinct serotypes were identified by plaque reduction or tube neutralization assay or both, and three of these serotypes were the same as those established previously by plaque reduction, using human rotaviruses cultivated by genetic reassortment with a cultivable bovine rotavirus. Ten human rotavirus strains received from Japan were found to be similar, if not identical, to our candidate prototype strains representing these four human rotavirus serotypes.
Training non-parametric features for statistical machine translation (2007)

Modern statistical machine translation systems may be seen as using two components: feature extraction, that summarizes information about the translation, and a log-linear framework to combine features. In this paper, we propose to relax the linearity constraints on the combination, and hence relaxing constraints of monotonicity and independence of feature functions. We expand features into a non-parametric, non-linear, and high-dimensional space. We extend empirical Bayes reward training of model parameters to meta parameters of feature generation. In effect, this allows us to trade away some human expert feature design for data. Preliminary results on a standard task show an encouraging improvement.
Control of a Teleoperated Nanomanipulator with Time Delay under Direct Vision Feedback (2007)

Remote manipulation tasks in the small scale can often not be performed autonomously, due to the unstructured nature of the environments and the limited capabilities of sensor and localization technologies. For these tasks, teleoperated systems are used, in which the human operator is integral part of the control. In time-delayed teleoperation, the operator gradually adopts discrete control strategies, such as 'move-and-wait'. In this paper, we present and compare three different control strategies for driving a nanomanipulation system with direct vision feedback. Two strategies are based on a fixed step size to move the manipulator, while the third uses a variable step size. The strategies are compared on a 2D fine positioning task. Experimental results are in agreement with Fitts' law and show that the third strategy, besides allowing movements of size ranging across several orders of magnitude, also allows to complete the fine positioning task in less time. The control strategies can be used in general to control vision-guided teleoperation systems affected by time delay.
Platelet‐derived growth factor in human glioma (1995)

Platelet-derived growth factor (PDGF) is a 30 kDa protein consisting of disulfide-bonded dimers of A- and B-chains. PDGF receptors are of two types, alpha- and beta-receptors, which are members of the protein-tyrosine kinase family of receptors. The receptors are activated by ligand-induced dimerization, whereby the receptors become phosphorylated on tyrosine residues. These form attachment sites for signalling molecules, which inter alia activate the Ras.Raf pathway. PDGF has important functions in development and is required for a proper timing of oligodendrocyte differentiation. The v-sis oncogene of simian sarcoma virus (SSV) is a retroviral homolog of the B-chain gene, and induces transformation by an autocrine activation of PDGF receptors at the cell surface. SSV induces malignant glioma in experimental animals, suggesting a role for autocrine PDGF in glioma development. PDGF and PDGF receptors are frequently coexpressed in human glioma cell lines. Specific and nonspecific PDGF antagonists block the growth of some glioma cell lines in vitro and in vivo, suggesting that autocrine PDGF is involved in transformation and tumorigenesis. In situ studies of human gliomas show overexpression of alpha-receptors in glioma cells of high-grade tumors. In a few cases, overexpression is caused by receptor amplification. Since high-grade glioma cells also express the PDGF A-chain, an autocrine activation of the alpha-receptor may drive the proliferation of glioma cells in vivo.
Multiple myeloma cancer stem cells (2016)

Multiple myeloma (MM) remains incurable despite much progress that has been made in the treatment of the disease. MM cancer stem cell (MMSC), a rare subpopulation of MM cells with the capacity for self-renewal and drug resistance, is considered to lead to disease relapse. Several markers such as side population (SP) and ALDH1+ have been used to identify MMSCs. However, ideally and more precisely, the identification of the MMSCs should rely on MMSCs phenotype. Unfortunately the MMSC phenotype has not been properly defined yet. Drug resistance is the most important property of MMSCs and contributes to disease relapse, but the mechanisms of drug resistance have not been fully understood. The major signaling pathways involved in the regulation of self-renewal and differentiation of MMSCs include Hedgehog (Hh), Wingless (Wnt), Notch and PI3K/Akt/mTOR. However, the precise role of these signaling pathways needs to be clarified. It has been reported that the microRNA profile of MMSCs is remarkably different than that of non-MMSCs. Therefore, the search for targeting MMSCs has also been focused on microRNAs. Complex and mutual interactions between the MMSC and the surrounding bone marrow (BM) microenvironment sustain self-renewal and survival of MMSC. However, the required molecules for the interaction of the MMSC and the surrounding BM microenvironment need to be further identified. In this review, we summarize the current state of knowledge of MMSCs regarding their phenotype, mechanisms of drug resistance, signaling pathways that regulate MMSCs self-renewal and differentiation, abnormal microRNAs expression, and their interactions with the BM microenvironment.
Interaction of α-Synuclein and a Cell Penetrating Fusion Peptide with Higher Eukaryotic Cell Membranes Assessed by 19F NMR (2012)

We show that fluorine NMR can be used to monitor the insertion and change in conformation of a ¹⁹F-labeled cell-penetrating peptide upon interacting with the cellular plasma membrane. α-Synuclein and a construct comprising a cell-penetrating peptide covalently attached to its N-terminus were studied. Important information about the interaction of the proteins with CHO-K1 cells was obtained by monitoring the diminution of ¹⁹F resonances of 3-fluoro-l-tyrosine labeled proteins. For α-synuclein, a decrease in the resonance from position 39 was observed indicating that only the N-terminal third region of the protein interacts with plasma membrane. However, when the fusion construct was incubated with the cells, a decrease in the resonance from the fusion peptide region was noted with no change in the resonances from α-synuclein region. Longer incubation, studied by using confocal fluorescence microscopy, revealed that the fusion construct translocates into the cells, but α-synuclein alone did not cross the membrane in significant amounts.
Evaluation of species-specific recA-based PCR tests for genomovar level identification within the Burkholderia cepacia complex (2002)

The Burkholderia cepacia complex presently comprises nine genomovars: B. cepacia (genomovar I), B. multivorans (genomovar II), B. cepacia genomovar III, B. stabilis (genomovar IV), B. vietnamiensis (genomovar V), B. cepacia genomovar VI, B. ambifaria (genomovar VII), B. anthina (genomovar VIII) and B. pyrrocinia (genomovar IX). Strains of each genomovar can colonise the respiratory tract of cystic fibrosis (CF) patients. However, the majority of infections in CF patients are caused by B. multivorans and B. cepacia genomovar III isolates. Accurate genomovar-level identification is best achieved through a polyphasic approach combining phenotypic and genotypic analyses. In the present study, the sensitivity and specificity of recA-based genomovar specific primer pairs were evaluated with a collection of 508 B. cepacia complex isolates representing all nine genomovars. The assays for the identification of B. multivorans (sensitivity and specificity, 100%), B. cepacia genomovar III (sensitivity, 92%; specificity, 100%), and B. ambifaria (sensitivity and specificity, 100%) were the most efficient. However, the B. cepacia genomovar I assay lacked sensitivity (72%) and cross-reacted with all B. pyrrocinia isolates examined. Several new recA RFLP types were also revealed within the B. cepacia complex. One of these profiles was shared by a clinical and an environmental B. cepacia-like isolate and by the B. ubonensis type strain. The latter organism is a recently described soil bacterium. Its relationship to the various B. cepacia complex genomovars needs further study.
The Fractional Free Volume of the Sorbed Vapor in Modeling the Viscoelastic Contribution to Polymer-Coated Surface Acoustic Wave Vapor Sensor Responses (2000)

Surface acoustic wave (SAW) vapor sensors with polymeric sorbent layers can respond to vapors on the basis of mass loading and modulus decreases of the polymer film. The modulus changes are associated with volume changes that occur as vapor is sorbed by the film. A factor based on the fractional free volume of the vapor as a liquid has been incorporated into a model for the contribution of swelling-induced modulus changes to observed SAW vapor sensor responses. In this model, it is not the entire volume added to the film by the vapor that contributes to the modulus effect; it is the fractional free volume associated with the vapor molecules that causes the modulus to decrease in a manner that is equivalent to free volume changes from thermal expansion. The amplification of the SAW vapor sensor response due to modulus effects that are predicted by this model has been compared to amplification factors determined by comparing the responses of polymer-coated SAW vapor sensors with the responses of similarly coated thickness shear mode (TSM) vapor sensors, the latter being gravimetric. Results for six to eight vapors on each of two polymers, poly(isobutylene) and poly(epichlorohydrin), were examined. The model predicts amplification factors of the order of about 1.5-3, and vapor-dependent variations in the amplification factors are related to the specific volume of the vapor as a liquid. The fractional free volume factor provides a physically meaningful addition to the model and is consistent with conventional polymer physics treatments of the effects of temperature and plasticization on polymer modulus.
Neurotrophin‐3 Delivered Locally via Fibronectin Mats Enhances Peripheral Nerve Regeneration (1997)

A better understanding of the mechanisms of nerve regeneration could improve the outcome of surgical nerve repair. We have previously shown that axonal regeneration is increased by nerve growth factor. Neurotrophin-3 (NT-3) belongs to the same family as nerve growth factor but acts on a distinct neuron subpopulation. As little is known about its role following nerve injury, we have investigated the effect of NT-3 delivered via fibronectin mats, previously shown to support nerve regeneration comparable to nerve grafts. NT-3 stimulation (0.1-1000 ng/ml) of neurite extension from embryonic chick dorsal root ganglia in vitro has shown that fibronectin can bind and release bioactive NT-3. Fibronectin mats impregnated with NT-3 (500 ng/ml) were grafted into 1 cm sciatic nerve defects in adult Lewis rats. Plain mats were used as controls. Computerized quantification of penetration distance, volume of axonal regeneration and myelinated fibre counts was undertaken using immunostaining for axonal markers (growth-associated protein 43, calcitonin gene-related peptide, substance P, vasoactive intestinal peptide and neuropeptide tyrosine), or S100 or thionine blue staining up to 8 months postoperatively. The maximal effect of NT-3 occurred at day 15, when for GAP43-immunostained axons both penetration distance (NT-3, 6.10 +/- 0.42 mm; control, 4.11 +/- 0.41 mm; P < 0.01) and staining area (NT-3, 0.137 +/- 0.012 mm2; control, 0.077 +/- 0.018 mm2; P < 0.05) were significantly increased. Similar results were found for each neuronal subpopulation investigated. By 8 months after repair, the NT-3 group supported a significantly greater number of myelinated axons (NT-3, 7003 +/- 402; control, 4932 +/- 725; P < 0.05) of similar diameter and g-ratio to controls. These results demonstrate the contribution of NT-3 to the increase of nerve regeneration promoted by growth factors.
Machine learning-based automatic detection of pulmonary trunk (2011)

Pulmonary embolism is a common cardiovascular emergency with about 600,000 cases occurring annually and causing approximately 200,000 deaths in the US. CT pulmonary angiography (CTPA) has become the reference standard for PE diagnosis, but the interpretation of these large image datasets is made complex and time consuming by the intricate branching structure of the pulmonary vessels, a myriad of artifacts that may obscure or mimic PEs, and suboptimal bolus of contrast and inhomogeneities with the pulmonary arterial blood pool. To meet this challenge, several approaches for computer aided diagnosis of PE in CTPA have been proposed. However, none of these approaches is capable of detecting central PEs, distinguishing the pulmonary artery from the vein to effectively remove any false positives from the veins, and dynamically adapting to suboptimal contrast conditions associated the CTPA scans. To overcome these shortcomings, it requires highly efficient and accurate identification of the pulmonary trunk. For this very purpose, in this paper, we present a machine learning based approach for automatically detecting the pulmonary trunk. Our idea is to train a cascaded AdaBoost classifier with a large number of Haar features extracted from CTPA image samples, so that the pulmonary trunk can be automatically identified by sequentially scanning the CTPA images and classifying each encountered sub-image with the trained classifier. Our approach outperforms an existing anatomy-based approach, requiring no explicit representation of anatomical knowledge and achieving a nearly 100% accuracy tested on a large number of cases.
Factor VIII-bypassing activity of bovine tissue factor using the canine hemophilic model. (1988)

The bleeding disorder of hemophilia A currently treated by replacement therapy of the missing coagulation factor, factor VIII, is frequently complicated by the development of neutralizing antibodies. The therapeutic potential of attenuated forms of the lipid-associated glycoprotein tissue factor, a known initiator of coagulation, was investigated as a factor VIII-by-passing activity. The protein moiety of tissue factor (Apo-TF) was partially purified and exhibited minimal procoagulant activity before relipidation in vitro. In pilot studies, Apo-TF injection into rabbits previously anticoagulated with an antibody to factor VIII was found to have a procoagulant effect. The efficacy of the material was further demonstrated when injection of Apo-TF in hemophilic dogs resulted in a normalization of the cuticle bleeding time. Little or no change in the blood parameters associated with disseminated intravascular coagulation was observed at lower doses, although mild to moderate effects were seen at higher doses. These data suggest a novel role for Apo-TF preparations as a potential therapeutic agent for hemophiliacs with antibodies to factor VIII once the potential thrombogenicity of such materials is evaluated.
Expression of four CEA family antigens (CEA, NCA, BGP and CGM2) in normal and cancerous gastric epithelial cells: Up-regulation of BGP and CGM2 in carcinomas (1998)

Four human carcinoembryonic antigen (CEA) family members, CEA (CD66e), non-specific cross-reacting antigen (NCA, CD66c), biliary glycoprotein (BGP, CD66a) and CEA gene-family member 2 (CGM2), are expressed in normal mucosal epithelia of the colon. Expression of BGP and CGM2 has recently been demonstrated to be down-regulated in colorectal adenocarcinomas. We have now investigated the expression of the 4 CEA family antigens in gastric adenocarcinoma and carcinoma cell lines in comparison with adjacent normal gastric mucosa. The transcripts of the CEA, NCA and BGP genes evaluated by reverse transcription-polymerase chain reaction were detectable at various levels in all the gastric adenocarcinoma cell lines tested, while CGM2 mRNA was detectable in the cell lines of poorly differentiated but not of well-differentiated carcinomas. The levels of CEA mRNA in normal gastric mucosa were variable but mostly increased in adenocarcinomas. The sparse expression of NCA observed in the normal tissues was markedly up-regulated in the carcinomas. In contrast to previous findings on normal and cancerous colonic tissues, the transcripts of CGM2 were totally undetectable and those of BGP were recognized only marginally, if at all, in normal gastric mucosa, while both messages were detected at significant levels in most of the gastric adenocarcinomas. This was confirmed by in situ hybridization. Our findings indicate that expression of the CEA family antigens, particularly that of BGP and CGM2, is differently regulated in epithelial cells of the colon and the stomach.
Site‐specific N ‐glycosylation analysis: matrix‐assisted laser desorption/ionization quadrupole‐quadrupole time‐of‐flight tandem mass spectral signatures for recognition and identification of glycopeptides (2004)

Abstract The identification of glycosylation sites in proteins is often possible through a combination of proteolytic digestion, separation, mass spectrometry (MS) and tandem MS (MS/MS). Liquid chromatography (LC) in combination with MS/MS has been a reliable method for detecting glycopeptides in digestion mixtures, and for assigning glycosylation sites and glycopeptide sequences. Direct interfacing of LC with MS relies on electrospray ionization, which produces ions with two, three or four charges for most proteolytic peptides and glycopeptides. MS/MS spectra of such glycopeptide ions often lead to ambiguous interpretation if deconvolution to the singly charged level is not used. In contrast, the matrix‐assisted laser desorption/ionization (MALDI) technique usually produces singly charged peptide and glycopeptide ions. These ions require an extended m/z range, as provided by the quadrupole‐quadrupole time‐of‐flight (QqTOF) instrument used in these experiments, but the main advantages of studying singly charged ions are the simplicity and consistency of the MS/MS spectra. A first aim of the present study is to develop methods to recognize and use glycopeptide [M+H] + ions as precursors for MS/MS, and thus for glycopeptide/glycoprotein identification as part of wider proteomics studies. Secondly, this article aims at demonstrating the usefulness of MALDI‐MS/MS spectra of N ‐glycopeptides. Mixtures of diverse types of proteins, obtained commercially, were prepared and subjected to reduction, alkylation and tryptic digestion. Micro‐column reversed‐phase separation allowed deposition of several fractions on MALDI plates, followed by MS and MS/MS analysis of all peptides. Glycopeptide fractions were identified after MS by their specific m/z spacing patterns (162, 203, 291 u) between glycoforms, and then analyzed by MS/MS. In most cases, MS/MS spectra of [M+H] + ions of glycopeptides featured peaks useful for determining sugar composition, peptide sequence, and thus probable glycosylation site. Peptide‐related product ions could be used in database search procedures and allowed the identification of the glycoproteins. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Dynamic properties of micro-particles in ultrasonic transportation using phase-controllable standing waves (2014)

Ultrasonic manipulation has become an attractive method for surface-sensitive objects in micro-technology. Related phenomena, such as radiation force, multiple scattering, and acoustic streaming, have been widely studied. However, in current studies, the behavior of micro-particles in potential force fields is always analyzed in a quasi-static manner. We developed a dynamic model of a dilute micro-particle in the commonly used two-dimensional ultrasonic manipulation system to provide a systemic and quantitative analysis of the transient properties of particle movement. In this model, the acoustic streaming and hydrodynamic forces, omitted in previous work, were both considered. The trajectory of a spherical silica particle with different initial conditions was derived by numerically solving the established nonlinear differential integral equation system, which was then validated experimentally. The envelope of the experimental data on the x-axis showed good agreement with the theoretical calculation, and the greater influence on the y-axis of the deviation between the actual sound field and the ideal distribution employed in our dynamic model could account for the differences in displacement in that direction. Finally, the influence of particle size on its movement and the effect of acoustic streaming on calculating the hydrodynamic forces for an isolated particle with motion relative to the fluid were analyzed theoretically. It was found that the ultrasonic manipulation system will translate from an under-damped system to an over-damped system with a decrease in particle size and the micro-scale acoustic streaming velocity was negligible when calculating the hydrodynamic forces on the particle in the ultrasonic manipulation system.
Endotoxin/Lipopolysaccharide Activates NF-κB and Enhances Tumor Cell Adhesion and Invasion Through a β1 Integrin-Dependent Mechanism (2003)

Beta(1) integrins play a crucial role in supporting tumor cell attachment to and invasion into the extracellular matrix. Endotoxin/LPS introduced by surgery has been shown to enhance tumor metastasis in a murine model. Here we show the direct effect of LPS on tumor cell adhesion and invasion in extracellular matrix proteins through a beta(1) integrin-dependent pathway. The human colorectal tumor cell lines SW480 and SW620 constitutively expressed high levels of the beta(1) subunit, whereas various low levels of alpha(1), alpha(2), alpha(4), and alpha(6) expression were detected. SW480 and SW620 did not express membrane-bound CD14; however, LPS in the presence of soluble CD14 (sCD14) significantly up-regulated beta(1) integrin expression; enhanced tumor cell attachment to fibronectin, collagen I, and laminin; and strongly promoted tumor cell invasion through the Matrigel. Anti-beta(1) blocking mAbs (4B4 and 6S6) abrogated LPS- plus sCD14-induced tumor cell adhesion and invasion. Furthermore, LPS, when combined with sCD14, resulted in NF-kappaB activation in both SW480 and SW620 cells. Inhibition of the NF-kappaB pathway significantly attenuated LPS-induced up-regulation of beta(1) integrin expression and prevented tumor cell adhesion and invasion. These results provide direct evidence that although SW480 and SW620 cells do not express membrane-bound CD14, LPS in the presence of sCD14 can activate NF-kappaB, up-regulate beta(1) integrin expression, and subsequently promote tumor cell adhesion and invasion. Moreover, LPS-induced tumor cell attachment to and invasion through extracellular matrix proteins is beta(1) subunit-dependent.