gebhart/patrepeval huggingface dataset:
Worm-like locomotion as a problem of nonlinear dynamics (2007)

Non-pedal forms of locomotion show their advantages in inspection tech-niques or applications to the medical technology for diagnostic systems and minimally invasive surgery. Observing the locomotion of worms, one recognizes conversion of (mostly periodic) internal and internally dri-ven motions into a change in the external position (undulatory locomo-tion). This paper presents some theoretical and practical investigations of worm-like motion systems that have the earthworm as a live pro-totype. The locomotion of worms can be described by introduction of nonlinear non-symmetric frictional forces. In the first part of the paper these systems are modelled in form of straight chains of interconnected mass points. The ground contact can be described by non-symmetric dry friction. The investigations are concentrated on motion in a tube or channel, and on motion on a horizontal plane as well. In both cases, the body is modeled as a viscous Newtonian fluid. The effect of the mass flow through a cross section on the disturbance and material parameters (viscosity, dimensions) is discussed. The paper presents first prototypes of technically implemented artificial worms.
Cell therapy of a highly invasive human breast carcinoma implanted in immunodeficient (SCID) mice. (1997)

Although enormous progress has been made in the detection and treatment of localized (nonmetastatic) breast cancer, there has been relatively moderate progress toward the effective treatment of advanced disease. This study investigates the antitumor efficacy of a potent MHC nonrestricted cytotoxic human T cell line (TALL-104) upon transfer into a clinically relevant mouse model of metastatic breast cancer. Fragments from a surgical specimen of a patient with infiltrating ductal carcinoma were implanted s.c. in the flank region of severe combined immunodeficient (SCID) mice. One hundred % of the animals developed a local tumor mass that metastasized to subaxillary and inguinal lymph nodes, bones, lungs, liver, kidneys, ovaries, and brain, very closely mimicking the human disease. Multiple i.p. transfers of gamma-irradiated (nonproliferating) TALL-104 cells into mice bearing low tumor burden (the primary tumor mass weighed only 150 mg) completely arrested local tumor growth and prevented systemic spread into local lymph nodes and distant organs. Remarkably, cell therapy administered in an advanced disease stage (when the tumor weighed 2 g) induced a significant or total regression of established metastasis with no obvious effects on the primary tumor mass. Profound antitumor effects against both local and systemic disease were instead seen in mice that received cell therapy after surgical excision of the primary tumor. The implications of these data in adjuvant breast cancer therapy are discussed.
Synthesis and antimicrobial activity of some novel heterocycles. Azolo-as-triazines (1976)

A general method for the preparation of substituted azolo-as-triazines is reported. The various alpha-aminoazoles (3-aminopyrazole, 3-amino-s-triazole, 5-amino-v-triazole, 2-aminoimidazole, 4(5)-aminoimidazole, and their substituted derivatives) were diazotized and coupled with active methylene reagents (beta-diketones, beta-keto esters, beta-keto acids, ethyl cyanoacetate and malononitrile) to afford intermediates which were then cyclized in methanol, acetic acid, or benzene. The cyclized products were the corresponding pyrazolo[2,3-c]- (2), s-triazolo[2,3-c]- (3), imidazo[3,4-c]- (4), v-triazolo[1,2-c]- (5), and imidazo[3,4-c]-as-triazines (6) with substituents such as amino, alkyl (or hydrogen), ester, ketone, or nitrile, depending on the methylene reagent used. Of the 28 compounds synthesized (representative of the five heterocycles) six, with various substituents, exhibited specific in vitro antimicrobial activity. Compounds 2b and 2d inhibited the gram-negative bacterium Pseudomonas, 3a, and 5a inhibited the gram-positive Staphylococcus, 2h inhibited the dermatophyte Trichophyton, and 2c inhibited the yeast Candida in the MIC (minimum inhibitory concentration) range of 0.40-0.16 mumol/ml.
Characterization of a plasmid from Helicobacter pylori encoding a replication protein common to plasmids in Gram‐positive bacteria (1991)

A 1.5 kb cryptic plasmid was isolated from Helicobacter pylori. Low-stringency hybridization analysis using this plasmid as a DNA probe revealed base sequence homology with other plasmids in this species. Nucleotide sequence analysis identified an open reading frame encoding a putative polypeptide of 25 kDa. This protein showed marked amino acid sequence similarity to replication-initiation proteins commonly found in small plasmids endogenous to Gram-positive bacteria which replicate by the 'rolling-circle' mechanism. Sequence motifs corresponding to the origins-of-replication consensus sequences were found on this cryptic plasmid. DNA and oligonucleotide probes to these plasmid replication sequences were used in hybridization analysis to identify similar sequences in other H. pylori plasmids. We believe this is the first plasmid isolated from a Gram-negative bacterium to show replication determinants characteristic of the 'rolling-circle' group of plasmids from Gram-positive bacteria. The cloned plasmid will be used to develop a shuttle-vector for H. pylori.
Up-regulation of human secreted frizzled homolog in apoptosis and its down-regulation in breast tumors (1998)

In the screening of apoptosis-related genes, an elevated 4.5-kb transcript representing the full-length cDNA of human secreted frizzled-related protein (hsFRP) was cloned. To investigate its possible role in the regulation of cell proliferation, gene expression of hsFRP was examined in human immortalized breast epithelial cell line HBL-100 during growth arrest and apoptosis. Serum deprivation caused G arrest and induction of hsFRP. When serum was re-introduced into the cell culture, the expression of hsFRP declined. Adriamycin treatment induced accumulation of hsFRP mRNA and decrease of beta-catenin. This indicates that the regulation of hsFRP may be involved in the cell-cycle/apoptosis mechanism and possibly in the wnt signaling pathway. hsFRP transcripts were undetectable in cells derived from malignant breast carcinomas, but detectable in 3 immortalized non-malignant breast epithelial cell lines, indicating the involvement of hsFRP in the breast malignant transformation. When tumor and adjacent normal tissues from the same patients were examined, lower expression was found in 5/5 of breast tumors, 2/4 of ovary tumors and 3/5 of kidney tumors. These data suggest the possible involvement of hsFRP in regulation of cell proliferation and breast tumorigenesis.
Exploiting the power of relational databases for efficient stream processing (2009)

Stream applications gained significant popularity over the last years that lead to the development of specialized stream engines. These systems are designed from scratch with a different philosophy than nowadays database engines in order to cope with the stream applications requirements. However, this means that they lack the power and sophisticated techniques of a full fledged database system that exploits techniques and algorithms accumulated over many years of database research.
Taxol and Taxane Production by Taxomyces andreanae , an Endophytic Fungus of Pacific Yew (1993)

Taxomyces andreanae, a fungal endophyte, was isolated from the phloem (inner bark) of the Pacific yew, Taxus brevifolia. The fungus is hyphomyceteous and, when grown in a semi-synthetic liquid medium, produced taxol and related compounds. Taxol was identified by mass spectrometry, chromatography, and reactivity with monoclonal antibodies specific for taxol. Both [1-14C]acetic acid and L-[U-14C]phenylalanine served as precursors of [14C]taxol in fungal cultures. No taxol was detected in zero-time cultures or in the small agar plugs used to inoculate the culture flasks.
European/Canadian multicenter, double-blind, randomized, placebo-controlled study of the effects of glatiramer acetate on magnetic resonance imaging--measured disease activity and burden in patients with relapsing multiple sclerosis. European/Canadian Glatiramer Acetate Study Group. (2001)

Two prior double-blind, placebo-controlled, randomized trials demonstrated that glatiramer acetate (GA) reduces relapse rates in patients with relapsing remitting multiple sclerosis (RRMS). This study was designed to determine the effect, onset, and durability of any effect of GA on disease activity monitored with magnetic resonance imaging (MRI) in patients with RRMS. Two hundred thirty-nine eligible patients were randomized to receive either 20 mg GA (n = 119) or placebo (n = 120) by daily subcutaneous injection. Eligibility required one or more relapses in the 2 years before entry and at least one enhancing lesion on a screening MRI. The study was a randomized, double-blind, placebo-controlled phase during which all patients studied underwent monthly MRI scans and clinical assessments over 9 months. The primary outcome measure was the total number of enhancing lesions on T1-weighted images. Secondary outcome measures included the proportion of patients with enhancing lesions, the number of new enhancing lesions and change in their volume; the number of new lesions detected on T2-weighted images and change in their volume, and the change in volume of hypointense lesions seen on unenhanced T1-weighted images. Clinical measures of disease activity were also evaluated. The active treatment and placebo groups were comparable at entry for all demographic, clinical, and MRI variables. Treatment with GA showed a significant reduction in the total number of enhancing lesions compared with placebo (-10.8, 95% confidence interval -18.0 to -3.7; p = 0.003). Consistent differences favoring treatment with GA were seen for almost all secondary end points examined: number of new enhancing lesions (p < 0.003), monthly change in the volume of enhancing lesions (p = 0.01), and change in volume (p = 0.006) and number of new lesions seen on T2-weighted images (p < 0.003). The relapse rate was also significantly reduced by 33% for GA-treated patients (p = 0.012). All effects increased over time. Glatiramer acetate significantly reduced MRI-measured disease activity and burden.
Expression of the T-cell surface molecule CD2 and an epitope-loss CD2 mutant to define the role of lymphocyte function-associated antigen 3 (LFA-3) in T-cell activation. (1988)

To define the role of the CD2-lymphocyte function-associated antigen 3 (LFA-3) interaction in T-cell activation, we have expressed a cDNA encoding the human CD2 molecule in a murine antigen-specific T-cell hybridoma. Expression of the CD2 molecule greatly enhances T-cell responsiveness to antigen; this enhancement is inhibited by anti-CD2 and anti-LFA-3 monoclonal antibodies (mAbs). CD2+ hybridomas produce interleukin 2 in response to combinations of anti-CD2 mAbs 9.6 and 9-1 and, in the presence of mAb 9-1, to sheep erythrocytes or to the LFA-3 antigen. Furthermore, hybridomas expressing a mutant CD2 molecule that has lost mAb 9.6 binding do not exhibit the enhanced response to antigen or the ability to respond to LFA-3 plus mAb 9-1, but these hybridomas retain the ability to respond to combinations of anti-CD2 mAbs. The role of the CD2-LFA-3 interaction in T-cell activation and the potential for other physiologic ligands for CD2 are discussed.
Long term file migration: development and evaluation of algorithms (1981)

The steady increase in the power and complexity of modern computer systems has encouraged the implementation of automatic file migration systems which move files dynamically between mass storage devices and disk in response to user reference patterns. Using information describing 13 months of user disk data set file references, we develop and evaluate (replacement) algorithms for the selection of files to be moved from disk to mass storage. Our approach is general and demonstrates a general methodology for this type of problem. We find that algorithms based on both the file size and the time since the file was last used work well. The best realizable algorithms tested condition on the empirical distribution of the times between file references. Acceptable results are also obtained by selecting for replacement that file whose size times time to most recent reference is maximal. Comparisons are made with a number of standard algorithms developed for paging, such as Working Set, VMIN, and GOPT. Sufficient information (parameter values, fitted equations) is provided so that our algorithms may be easily implemented on other systems.
Adaptation of Robot Locomotion Patterns with Dynamic Movement Primitives (2015)

Functional locomotion requires continuous modulation of coordination within and between legs to flexibly accommodate demands of real-word environments. In this context, dynamic movement primitives (DMP) is a powerful tool for motion planning based on demonstrations, being used as a compact policy representation well-suited for robot learning. In this work, we study on-line adaptation of robot biped locomotion patterns when employing DMP as trajectory representations. Here, the adaptation of learned walking movements is obtained from a single demonstration. The goal is to demonstrate and evaluate how new movements can be generated by simply modifying the parameters of rhythmic DMP learned in task space. The formulation in task space allows recreating new movements such that the DMP's parameters directly relate to task variables, such as step length, hip height, foot clearance and forward velocity. Several experiments are conducted using the V-REP robotics simulator, including the adaptation of the robot's gait pattern to irregularities on the ground surface and stepping over obstacles.
Multi‐way principal components‐and PLS‐analysis (1987)

Abstract The Lohmöller–Wold decomposition of multi‐way (three‐way, four‐way, etc.) data arrays is combined with the non‐linear partial least squares (NIPALS) algorithms to provide multi‐way solutions of principal components analysis (PCA) and partial least squares modelling in latent variables (PLS). The decomposition of a multi‐way array is developed as the product of a score vector and a loading array, where the score vectors have the same properties as those of ordinary two‐way PCA and PLS. In image analysis, the array would instead be decomposed as the product of a loading vector and an image score matrix. The resulting methods are equivalent to the method of unfolding a multi‐way array to a two‐way matrix followed by ordinary PCA or PLS analysis. This automatically proves the eigenvector and least squares properties of the multi‐way PCA and PLS methods. The methodology is presented; the algorithms are outlined and illustrated with a small chemical example.
Photonucleolysis of intervertebral disc and its herniation. Preparation to percutaneous laser discectomy. (1990)

Making use of a whole-body stereotactic device under model conditions a human intervertebral disc and its herniations could be targeted and removed with a laser by photocoagulation. The applicable cannulae are 3 mm in diameter and of a 6 to 12 W output power. The required effect is reached within one minute. The situation is now prepared for the clinical introduction of the new technique of discectomy, which is still performed with chemicals or mechanically section and suction.
Induction of Apoptosis by a Secreted Lipocalin That is Transcriptionally Regulated by IL-3 Deprivation (2001)

Many hematopoietic cells undergo apoptosis when deprived of specific cytokines, and this process requires de novo RNA/protein synthesis. Using DNA microarrays to analyze interleukin-3 (IL-3)-dependent murine FL5.12 pro-B cells, we found that the gene undergoing maximal transcriptional induction after cytokine withdrawal is 24p3, which encodes a secreted lipocalin. Conditioned medium from IL-3-deprived FL5.12 cells contained 24p3 and induced apoptosis in naive FL5.12 cells even when IL-3 was present. 24p3 also induced apoptosis in a wide variety of leukocytes but not other cell types. Apoptotic sensitivity correlated with the presence of a putative 24p3 cell surface receptor. We conclude that IL-3 deprivation activates 24p3 transcription, leading to synthesis and secretion of 24p3, which induces apoptosis through an autocrine pathway.
A Comparison of Two Noninvasive Techniques to Measure Total Body Lipid in Live Birds (1991)

Total body electrical conductivity (TOBEC) and near infrared interactance (IRI) are noninvasive techniques with potential utility for monitoring body composition of free-ranging birds or captive experimental subjects. I used live Northern Bobwhites (Colinus virginianus) to validate these methods for estimation of total body lipid. Total body electrical conductivity and IRI measurements were compared with body composition as determined by solvent extraction of carcasses. I measured IRI at three body sites (subscapular, pectoralis, and subfemoral) on 42 bobwhites. Only the subscapular and pectoralis sites yielded IRI measurements that were significantly correlated with percent body lipid, but IRI from these sites explained only 17.5% and 10.0% of the variation in percent body lipid, respectively. The cause of the low correlations is unknown, but it was not a function of differences in subject posture or light-wand position between replicate measures on the same subject. Total body electrical conductivity measurements explained 92% of the variation in lean body mass in a sample of 62 bobwhites. Measurements were affected by small differences in subject movement and position in the measurement chamber. There was no significant difference in TOBEC of subjects with or without aluminum leg bands. Measurements obtained from the same subjects with two different SA-1 TOBEC analyzers were not significantly different. The residuals about the regression of TOBEC against lean body mass were not correlated significantly with body temperature, but were significantly correlated with hydration. Total body electrical conductivity explained 99.1% of the variation in lean body mass when only those data from normally hydrated and properly restrained subjects were included (n = 38). Estimated body lipid from TOBEC measurements was highly correlated with total body lipid (R = 0.96) as determined by solvent extraction. The 95% confidence limits from the inverse regression procedure for the estimate of total body lipid from TOBEC measurements were Â±4.75 g at 25 g lipid, Â±4.85 g at 10 g lipid, and Â±5.62 g at 50 g lipid. Estimated total body lipid from TOBEC measurements was on average within 10% of total body lipid from solvent extraction. Although IRI analysis failed to yield a suitable index to body composition, TOBEC analysis provided an accurate estimate of total body lipid in live bobwhites.
Synthesis of Novel Tyrosinyl FRET Cassettes, Terminators, and Their Potential Use in DNA Sequencing (2003)

Fluorescence resonance energy transfer (FRET) dye labeled cassettes and terminators with one or more donor dyes (fluorescein) and acceptor dye (rhodamine dyes) with benzofuran or tyrosine linker moieties were synthesized. These terminators were evaluated for their energy transfer and DNA sequencing potential using thermostable DNA polymerase.
TFEB Links Autophagy to Lysosomal Biogenesis (2011)

Autophagy is a cellular catabolic process that relies on the cooperation of autophagosomes and lysosomes. During starvation, the cell expands both compartments to enhance degradation processes. We found that starvation activates a transcriptional program that controls major steps of the autophagic pathway, including autophagosome formation, autophagosome-lysosome fusion, and substrate degradation. The transcription factor EB (TFEB), a master gene for lysosomal biogenesis, coordinated this program by driving expression of autophagy and lysosomal genes. Nuclear localization and activity of TFEB were regulated by serine phosphorylation mediated by the extracellular signal-regulated kinase 2, whose activity was tuned by the levels of extracellular nutrients. Thus, a mitogen-activated protein kinase-dependent mechanism regulates autophagy by controlling the biogenesis and partnership of two distinct cellular organelles.
Prodrugs in Cardiovascular Therapy (2008)

Prodrugs are biologically inactive derivatives of an active drug intended to solve certain problems of the parent drug such as toxicity, instability, minimal solubility and non-targeting capabilities. The majority of drugs for cardiovascular diseases undergo first-pass metabolism, resulting in drug inactivation and generation of toxic metabolites, which makes them appealing targets for prodrug design. Since prodrugs undergo a chemical reaction to form the parent drug once inside the body, this makes them very effective in controlling the release of a variety of compounds to the targeted site. This review will provide the reader with an insight on the latest developments of prodrugs that are available for treating a variety of cardiovascular diseases. In addition, we will focus on several drug delivery methodologies that have merged with the prodrug approach to provide enhanced target specificity and controlled drug release with minimal side effects.
Feasibility of adenovirus-mediated gene transfer in vivo. (1992)

We have evaluated the use of Adenovirus as a new vector for gene transfer in vivo. The capacity of this virus to express a foreign gene even in the absence of viral and cellular replication makes it attractive to deliver a gene to quiescent cells. We show here that organs like lung, liver and muscles are relevant to this strategy.
Implications of Genetic and Epigenetic Alterations of CDKN2A (p16 INK4a ) in Cancer (2016)

Aberrant gene silencing is highly associated with altered cell cycle regulation during carcinogenesis. In particular, silencing of the CDKN2A tumor suppressor gene, which encodes the p16(INK4a) protein, has a causal link with several different types of cancers. The p16(INK4a) protein plays an executional role in cell cycle and senescence through the regulation of the cyclin-dependent kinase (CDK) 4/6 and cyclin D complexes. Several genetic and epigenetic aberrations of CDKN2A lead to enhanced tumorigenesis and metastasis with recurrence of cancer and poor prognosis. In these cases, the restoration of genetic and epigenetic reactivation of CDKN2A is a practical approach for the prevention and therapy of cancer. This review highlights the genetic status of CDKN2A as a prognostic and predictive biomarker in various cancers.