gebhart/patrepeval huggingface dataset:
Effect of crosslinking on the elasticity of polyelectrolyte multilayer films measured by colloidal probe AFM (2006)

A homemade colloidal probe atomic force microscope was used to perform nanoindentation with a spherical probe of 5 microm in diameter, at different approach velocities in order to extract the Young's modulus, E0, of poly(L-lysine)/hyaluronan (PLL/HA) films. This parameter is of prime importance to control cellular adhesion. The films were either kept in their native form or cross-linked with a mixture of 1-ethyl-3-(3-dimethyl aminopropyl)carbodiimide (EDC) and N-hydrosulfosuccinimide (sulfo-NHS), where the EDC concentration was varied from 1 up to 100 mg mL(-1) (approximately from 5 to 500 mM). A model based on Hertz mechanics was used to account for the interactions between film and probe. It is shown that the Young's modulus varies with the approach velocity for the native (PLL/HA) films, whereas for cross-linked ones, E0 is independent from the velocity over the whole range investigated. It is found that for native films, E0 takes a value of 3 kPa at low approach velocities, a velocity domain that should be relevant in cellular adhesion processes. The Young's modulus increases with the EDC concentration used to cross-link the films and levels off at a value of about 400 kPa for EDC concentrations exceeding 40 mg mL(-1). Thus, it is possible by crosslinking PLL/HA films to control their elastic properties with the aim to alter their behavior as to the cellular adhesion.
THE ENTIRE COMPOUND AUTOSOMES OF DROSOPHILA MELANOGASTER (1981)

Three new unusual compound chromosomes have been synthesized in Drosophila melanogaster. They consist of two homologous autosomes joined together in the new order: right arm, left arm, centromere, left arm, right arm, for each of the two major autosomes, and one in which chromosomes 2 and 3 have been combined in the order: right arm of 2, left arm of 2, centromere, left arm of 3, right arm of 3. The attachments of the autosomal arms were accomplished by obtaining chromosome breaks at or very close to the ends of the left arms of the autosomes such that no essential chromosome material has been removed; the compounds derived from them are therefore referred to as entire compounds. These large chromosomes are recovered in progeny with frequencies lower than expectation partly because of zygote mortality associated with these chromosomes, and partly because of a failure of spermiogenesis.
Regulation of Transcription of the Human Presenilin-1 Gene by Ets Transcription Factors and the p53 Protooncogene (2000)

The expression of the human presenilin-1 cellular gene is suppressed by the p53 protooncogene. The rapid kinetic of the down-regulation has suggested that it may result from a primary mechanism. We show here that p53 also suppresses the transcription of a presenilin-1 promoter-chloramphenicol acetyltransferase reporter synthetic gene in transient infection assays in neuroblastoma (SK-N-SH) and hepatoma (HepG2) cell lines. Only a minimum promoter including sequences from -35 to + 6 from the transcription initiation is sufficient to confer down-regulation. We have previously defined a crucial DNA element controlling 90% of the expression of the gene within the same short area, and the identification of the transcription factors involved should also provide insights into the regulation of PS1 by p53. This region contains an Ets transcription factor binding motif, and a 2-base pair alteration within the core sequence (GGAA to TTAA) of the Ets consensus also reduced transcription by more than 90%. We now show that Ets1 and Ets2 indeed transactivate a PS1 promoter-chloramphenicol acetyltransferase reporter including the (-35 to +6) fragment. Furthermore, in vitro translated Ets2 binds specifically to the -10 Ets motif in electrophoretic mobility shift assays. Therefore, Ets1/2 factors bind specifically to the -10 Ets element and activate PS1 transcription. We also show that the coactivator p300 enhances the activation by Ets1 and Ets2 as well as the repression by p53. p300 is known to interact with p53 as well as with Ets1 and Ets2. We show that p53 does not bind directly to the PS1 promoter. Hence the repression of PS1 transcription by p53 is likely to be mediated through protein-protein interactions.
Measurement of Surgically Induced Corneal Deformations Using Three-Dimensional Confocal Microscopy (1996)

The goal of this study was to develop and apply a new set of experimental techniques for measuring the local deformations induced by partial-thickness corneal incisions in situ. Eight adult cat eyes were enucleated and cannulated, with corneal viability maintained as close to in vivo conditions as possible and intraocular pressure (IOP) carefully controlled. Experimental measurements were made pre/post radial keratotomy (RK) surgery in situ at IOPs of 15, 30, and 45 mm Hg. Incision depth and cross-sectional profiles were measured at the midpoint of selected incisions using three-dimensional (3-D) tandem scanning confocal microscopy (TSCM); central corneal curvature was estimated using a commercial corneal topographical analysis system, and corneal thickness was assessed by both 3-D TSCM and ultrasonic pachymetry. Corneas were then processed for light microscopy and incision depth was measured histologically. Finite element models were developed for comparison with the experimental measurements. There was no significant change in central corneal thickness (-5.3 +/- 3.9%, n = 8) over the course of the experiments, demonstrating that normal endothelial cell function and normal stromal hydration was maintained. The in situ TSCM incision depth measurements were significantly correlated with the histological measurements (slope = 0.95, R = 0.854, p < 0.01, n = 13 incisions). Measured incision gape at the top (anterior) of the stroma was 64.9 +/- 13.4, 87.3 +/- 12.6, and 108.7 +/- 14 microns at IOPs of 15, 30, and 45 mm Hg, respectively. The 3-D incision profiles were nonlinear in shape; comparison with the finite element models suggests that the shape of the wound profile may provide unique information regarding the shear stiffness of the cornea. Overall, the data suggest that TSCM measurements of the cross-sectional profile of the incisions immediately after RK under controlled in situ conditions provide important data regarding the mechanical behavior of the cornea after refractive surgery. These data should provide the foundation for future studies into the relationships between local tissue mechanics and corneal wound healing.
Recent Changes to Privacy Enhanced Electronic Mail (1993)

Privacy enhanced electronic mail is a set of protocols which provide confidentiality, authenticity, and integrity for electronic mail. A version of these protocols was released in August 1989, and revised two years later. Since then, several other changes were made to the protocols, many of them minor, but some major. This note describes these changes. 1. IntroductionPG A previous paper [1] described the privacy enhanced electronic mail protocols proposed in RFC 1113, RFC 1114, and RFC 1115 [2][3][4], along with changes made through June 1991. These protocols provide sender authenticity, message integrity and confidentiality, and under certain circumstances non-repudiation. A key tool for these protocols is cryptography; first, the message is encrypted using one cryptosystem and key (the session key), and then that key and algorithm identifier are themselves encrypted by a second cryptosystem and key (the interchange key). Support for both symmetric and asymmetric session and interch...
CD4 T Helper Type 1 and Regulatory T Cells Induced against the Same Epitopes on the Core Protein in Hepatitis C Virus–Infected Persons (2002)

The factors that determine persistence or clearance of hepatitis C virus (HCV) infection are poorly understood. The CD4 T cell responses to the HCV core protein were examined in a cohort of women infected with a single genotype of HCV. CD4 T cells from HCV-infected patients secreted interferon (IFN)-gamma in response to peptides from 4 immunodominant regions of the core protein, and these responses were stronger in persistently infected women. Interleukin (IL)-10 was also produced by CD4 T cells from HCV-infected subjects in response to the same core peptides. Furthermore, HCV core-specific CD4 T cell clones secreted either IFN-gamma or IL-10 but not IL-4. These findings demonstrate that T helper type 1 and regulatory T cells are induced against the same epitopes on the core protein during HCV infection.
Effect of culture medium and cryoprotectants on the growth and survival of probiotic lactobacilli during freeze drying (2009)

The survival of probiotic strains during freeze drying was shown to be dependent on the cryoprotectant used and the growth medium.
Matrix metalloproteinases and diabetic foot ulcers: the ratio of MMP‐1 to TIMP‐1 is a predictor of wound healing (2008)

A high level of MMP-1 seems essential to wound healing, while an excess of MMP-8 and -9 is deleterious, and could be a target for new topical treatments. The MMP-1/TIMP-1 ratio is a predictor of wound healing in diabetic foot ulcers.
A Matter of Opinion: Sentiment Analysis and Business Intelligence (position paper) (2005)

A general-audience introduction to the area of "sentiment analysis", the computational treatment of subjective, opinion-oriented language (an example application is determining whether a review is "thumbs up" or "thumbs down"). Some challenges, applications to business-intelligence tasks, and potential future directions are described.
CD146 expression is associated with a poor prognosis in human breast tumors and with enhanced motility in breast cancer cell lines (2009)

In addition to its expression in the vascular compartment, CD146 is expressed on a subset of epithelial cells in malignant breast. CD146 may directly or indirectly contribute to tumor aggressiveness by promoting malignant cell motility. Changes in molecular signatures following downmodulation of CD146 expression suggest that CD146 downmodulation is associated with the reversal of several biological characteristics associated with epithelial to mesenchymal transition, and the phenomenon associated with the metastatic process.
Overuse of proton pump inhibitors (2000)

Whereas the proton pump inhibitors are undoubtedly effective agents, studies of their prescribing in practice consistently suggest over-use prior to endoscopy, use in patients who do not fit the approved criteria, and prescribing for indications in which 'less powerful' agents should have been sufficiently effective for the patient's symptoms. This poses economic and safety concerns, particularly in light of the suggestion that these drugs could delay the diagnosis of gastric cancer.
Studies in Red Blood Cell Preservation (1993)

Studies were conducted to examine whether an experimental additive solution (EAS-2) containing, in mM: 20 NH4Cl, 30 Na2HPO4, 2 adenine, 110 dextrose, 55 mannitol, pH 7.15, would be useful to extend the storage shelf life of human RBCs. With 6 pairs of split units, ATP concentrations were better maintained for 12 weeks with EAS-2 than with Adsol (1.8 vs. 1.1 mumol/g Hb, respectively, p = 0.002). Autologous 24-hours 51Cr viability values for split units in the same donors were: on 6 paired units at 8 weeks, EAS-2 87.0 +/- 4.5%, Adsol 72.6 +/- 2.3%, p = 0.004; on 11 paired units at 9 weeks, EAS-2 79.5 +/- 7.1%, Adsol 68.2 +/- 10.1%, p = 0.0003. The data suggest that packed RBCs stored for 9 weeks with EAS-2 will be suitable for transfusion following the removal of supernatant with a single washing step.
Using an Ensemble of One-Class SVM Classifiers to Harden Payload-based Anomaly Detection Systems (2006)

Unsupervised or unlabeled learning approaches for network anomaly detection have been recently proposed. In particular, recent work on unlabeled anomaly detection focused on high speed classification based on simple payload statistics. For example, PAYL, an anomaly IDS, measures the occurrence frequency in the payload of n-grams. A simple model of normal traffic is then constructed according to this description of the packets' content. It has been demonstrated that anomaly detectors based on payload statistics can be "evaded" by mimicry attacks using byte substitution and padding techniques. In this paper we propose a new approach to construct high speed payload-based anomaly IDS intended to be accurate and hard to evade. We propose a new technique to extract the features from the payload. We use a feature clustering algorithm originally proposed for text classification problems to reduce the dimensionality of the feature space. Accuracy and hardness of evasion are obtained by constructing our anomaly-based IDS using an ensemble of one-class SVM classifiers that work on different feature spaces.
α11β1 Integrin Recognizes the GFOGER Sequence in Interstitial Collagens (2003)

The integrins alpha(1)beta(1), alpha(2)beta(1), alpha(10)beta(1), and alpha(11)beta(1) are referred to as a collagen receptor subgroup of the integrin family. Recently, both alpha(1)beta(1) and alpha(2)beta(1) integrins have been shown to recognize triple-helical GFOGER (where single letter amino acid nomenclature is used, O = hydroxyproline) or GFOGER-like motifs found in collagens, despite their distinct binding specificity for various collagen subtypes. In the present study we have investigated the mechanism whereby the latest member in the integrin family, alpha(11)beta(1), recognizes collagens using C2C12 cells transfected with alpha(11) cDNA and the bacterially expressed recombinant alpha(11) I domain. The ligand binding properties of alpha(11)beta(1) were compared with those of alpha(2)beta(1). Mg(2+)-dependent alpha(11)beta(1) binding to type I collagen required micromolar Ca(2+) but was inhibited by 1 mm Ca(2+), whereas alpha(2)beta(1)-mediated binding was refractory to millimolar concentrations of Ca(2+). The bacterially expressed recombinant alpha(11) I domain preference for fibrillar collagens over collagens IV and VI was the same as the alpha(2) I domain. Despite the difference in Ca(2+) sensitivity, alpha(11)beta(1)-expressing cells and the alpha(11) I domain bound to helical GFOGER sequences in a manner similar to alpha(2)beta(1)-expressing cells and the alpha(2) I domain. Modeling of the alpha I domain-collagen peptide complexes could partially explain the observed preference of different I domains for certain GFOGER sequence variations. In summary, our data indicate that the GFOGER sequence in fibrillar collagens is a common recognition motif used by alpha(1)beta(1), alpha(2)beta(1), and also alpha(11)beta(1) integrins. Although alpha(10) and alpha(11) chains show the highest sequence identity, alpha(2) and alpha(11) are more similar with regard to collagen specificity. Future studies will reveal whether alpha(2)beta(1) and alpha(11)beta(1) integrins also show overlapping biological functions.
Tumor blood flow modifying effects of electrochemotherapy: a potential vascular targeted mechanism (2003)

Background. The aim of this study was to determine the tumor blood flow modifying, and potential vascular targeted effect of electrochemotherapy with bleomycin or cisplatin. Materials and methods. Electrochemotherapy was performed by application of short intense electric pulses to the tumors after systemic administration of bleomycin or cisplatin. Evaluated were antitumor effectiveness of electrochemotherapy by tumor measurement, tumor blood flow modifying effect by Patent blue staining technique, and sensitivity of endothelial and tumor cells to the drugs and electrochemotherapy by clonogenicity assay. Results. Electrochemotherapy was effective in treatment of SA-1 tumors in A/J mice resulting in substantial tumor growth delay and also tumor cures. Tumor blood flow reduction following electrochemotherapy correlated well with its antitumor effectiveness. Virtually complete shut down of the tumor blood flow was observed already at 24 h after electrochemotherapy with bleomycin whereas only 50% reduction was observed after electrochemotherapy with cisplatin. Sensitivity of human endothelial HMEC-1 cells to electrochemotherapy suggests a vascular targeted effect for electrochemotherapy in vivo with bleomycin as well as with cisplatin. Conclusion. These results show that, in addition to direct electroporation of tumor cells, other vascular targeted mechanisms are involved in electrochemotherapy with bleomycin or cisplatin, potentially mediated by tumor blood flow reduction, and enhanced tumor cell death as a result of endothelial damage by electrochemotherapy.
Biomolecular Interaction Monitoring of Autoantibodies by Scanning Surface Plasmon Resonance Microarray Imaging (2007)

A new commercial surface plasmon resonance (SPR) imaging analysis system with a novel SPR dip angle scanning principle allows the measurement, without the need for labeling, of the exact SPR dip angle. With this system hundreds of biomolecular interactions can be monitored on microarrays simultaneously and with great precision. The potency of this system is demonstrated by automatically monitoring the interactions between citrullinated peptides and serum autoantibodies of 50 rheumatoid arthritis (RA) patients and 29 controls in a single step. The smallest antibody concentration that could be measured in this experimental setup was 0.5 pM.
A NEURAL NETWORK PRIMER (1994)

Neural networks are composed of basic units somewhat analogous to neurons. These units are linked to each other by connections whose strength is modifiable as a result of a learning process or algorithm. Each of these units integrates independently (in paral lel) the information provided by its synapses in order to evaluate its state of activation. The unit response is then a linear or nonlinear function of its activation. Linear algebra concepts are used, in general, to analyze linear units, with eigenvectors and eigenvalues being the core concepts involved. This analysis makes clear the strong similarity between linear neural networks and the general linear model developed by statisticians. The linear models presented here are the perceptron and the linear associator. The behavior of nonlinear networks can be described within the framework of optimization and approximation techniques with dynamical systems (e.g., like those used to model spin glasses). One of the main notions used with nonlinear unit networks is the notion of attractor. When the task of the network is to associate a response with some specific input patterns, the most popular nonlinear technique consists of using hidden layers of neurons trained with back-propagation of error. The nonlinear models presented are the Hopfield network, the Boltzmann machine, the back-propagation network and the radial basis function network.
Modification by Analgesics of Lesion Development in the Urinary Tract and Various Other Organs of Rats Pretreated with Dihydroxy‐di‐N‐propylnitrosamine and Uracil (1995)

Effects of the analgesics phenacetin, acetaminophen and antipyrine on lesion development in the urinary tract and other organs in male F344 rats were investigated. Animals were concurrently administered with 0.1% dihydroxy-di-N-propylnitrosamine (DHPN) in drinking water and 3.0% uracil in the diet for 4 weeks and then, starting 1 week after the cessation of this treatment, received basal diet or diet containing phenacetin, acetaminophen or antipyrine for 35 weeks. The occurrences of renal cell tumors were increased in the groups given phenacetin or antipyrine, as compared with the DHPN + uracil alone controls. Antipyrine, but not the two other compounds, also enhanced development of hyperplastic lesions in the renal pelvis and ureter. In the urinary bladder, phenacetin and antipyrine treatments were both associated with increased incidence of preneoplastic or neoplastic lesions. Furthermore, phenacetin alone, without the initiating agent pretreatments, induced simple hyperplasias of the urinary bladder at high incidence. Antipyrine enhanced induction of hyperplastic lesions in the ureter and was also found to increase the incidences of preneoplastic and neoplastic lesions in the liver. Although decreased incidences of tumor development of lung and thyroid were observed for the group given phenacetin, this might have been linked to the decreased weight gain. The results confirmed that combination treatment with DHPN + uracil is effective for wide-spectrum initiation of carcinogenesis in the urological tract and demonstrated significant modification potential for both phenacetin and antipyrine.
Aggregation Events Occur Prior to Stable Intermediate Formation during Refolding of Interleukin 1β (1999)

A point mutation, lysine 97 --> isoleucine (K97I), in a surface loop in the beta-sheet protein interleukin 1beta (IL-1beta), exhibits increased levels of inclusion body (IB) formation relative to the wild-type protein (WT) when expressed in Escherichia coli. Despite the common observation that less stable proteins are often found in IBs, K97I is more stable than WT. We examined the folding pathway of the mutant and wild-type proteins at pH 6.5 and 25 degrees C with manual-mixing and stopped-flow optical spectroscopy to determine whether changes in the properties of transiently populated species in vitro correlate with the observation of increased aggregation in vivo. The refolding reactions of the WT and K97I proteins are both described by three exponential processes. Two exponential processes characterize fast events (0.1-1.0 s) in folding while the third exponential process correlates with a slow (70 s) single pathway to and from the native state. The K97I replacement affects the earlier steps in the refolding pathway. Aggregation, absent in the WT refolding reaction, occurs in K97I above a critical protein concentration of 18 microM. This observation is consistent with an initial nucleation step mediating protein aggregation. Stopped-flow kinetic studies of the K97I aggregation process demonstrate that K97I aggregates most rapidly during the earliest refolding times, when unfolded protein conformers remain highly populated and the concentration of folding intermediates is low. Folding and aggregation studies together support a model in which the formation of stable folding intermediates afford protection against further K97I aggregation.
Quantitative Models in Supply Chain Management (2011)

Moreover, a wide review given by Terzi and Cavalieri (2004) on more than 80 papers about simulation in the supply chain context is used in this chapter. The main goal of this review is to determine which objectives simulation is used to solve the problems, which simulation models are more appropriate and useful for supporting the decision making in the supply chain.
Death caused by recreational cocaine use (1979)

Sixty-eight deaths associated with the recreational use of illicit cocaine were investigated by the Medical Examiner's Office of Dade County in Florida. Most fatalities occurred since 1975. Although 29 involved the use of other drugs (usually heroin), 24 persons died directly of the toxic effects of cocaine. Respiratory collapse and death occurred rapidly after the intravenous injection of cocaine. Oral or nasal ingestion resulted in a symptom-free interval lasting as long as an hour followed suddenly by generalized seizures and death. Toxicological analysis could not causally relate lidocaine hydrochloride or other adulterants to the untoward reactions. The data suggest that the rate of absorption, the peak blood concentration, and the prior use of cocaine all contribute to the possibility of a fatal reaction. Despite current belief, cocaine cannot be considered a safe recreational drug. (<i>JAMA</i>241:2519-2522, 1979)