gebhart/patrepeval huggingface dataset:
Progression elevated gene‐3, PEG‐3, induces genomic instability in rodent and human tumor cells (2002)

Genomic instability is a fundamental component of cancer progression. Subtraction hybridization identified a novel rodent gene, progression elevated gene-3 (PEG-3) whose expression directly correlates with cancer aggressiveness and progression. Moreover, ectopic expression of PEG-3 in rodent or human tumor cells produces an aggressive transformed phenotype. We demonstrate that PEG-3 expression in rodent tumor cells correlates directly with genomic instability as characterized by alterations in chromosome composition and structure. Additionally, elevated endogenous or ectopic expression of PEG-3 in rodent and human tumor cells, respectively, enhances gene amplification, as monitored by resistance to methothrexate (MTX) and amplification of the dihydrofolate reductase (dhfr) gene. Stable expression of PEG-3 in normal cloned rat embryo fibroblast (CREF) cells marginally elevates MTX resistance, but morphology remains unaltered and anchorage independence is not induced, suggesting that these phenotypes are separable in immortal cells and gene amplification may precede the acquisition of morphological and oncogenic transformation. The present studies document that stable, inducible, and transient expression of PEG-3 in cancer cells augments genomic instability. In these contexts, one mechanism by which PEG-3 influences cancer progression may be by preferentially facilitating the development of genomic changes in evolving cancer cells.
Function of Trehalose and Glycogen in Cell Cycle Progression and Cell Viability in Saccharomyces cerevisiae (1999)

Trehalose and glycogen accumulate in Saccharomyces cerevisiae when growth conditions deteriorate. It has been suggested that aside from functioning as storage factors and stress protectants, these carbohydrates may be required for cell cycle progression at low growth rates under carbon limitation. By using a mutant unable to synthesize trehalose and glycogen, we have investigated this requirement of trehalose and glycogen under carbon-limited conditions in continuous cultures. Trehalose and glycogen levels increased with decreasing growth rates in the wild-type strain, whereas no trehalose or glycogen was detected in the mutant. However, the mutant was still able to grow and divide at low growth rates with doubling times similar to those for the wild-type strain, indicating that trehalose and glycogen are not essential for cell cycle progression. Nevertheless, upon a slight increase of extracellular carbohydrates, the wild-type strain degraded its reserve carbohydrates and was able to enter a cell division cycle faster than the mutant. In addition, wild-type cells survived much longer than the mutant cells when extracellular carbon was exhausted. Thus, trehalose and glycogen have a dual role under these conditions, serving as storage factors during carbon starvation and providing quickly a higher carbon and ATP flux when conditions improve. Interestingly, the CO2 production rate and hence the ATP flux were higher in the mutant than in the wild-type strain at low growth rates. The possibility that the mutant strain requires this steady higher glycolytic flux at low growth rates for passage through Start is discussed.
Receptor-mediated endocytosis in Xenopus oocytes. I. Characterization of the vitellogenin receptor system. (1987)

We have investigated the vitellogenin (VTG) receptor system in Xenopus oocytes since these cells are specialized for endocytosis. Oocytes have between 0.2 and 3 X 10(11) receptors per 1-mm cell. There is only a single class of receptors of low affinity (1.3 X 10(-6) M at 22 degrees C and 2-4 X 10(-6) M at 0 degree C), but high specificity (less than 5% nonspecific binding at 2 X 10(-6) M). The specific internalization rate of the VTG receptor (around 2 X 10(-3) s-1) is first order, highly variable, and at the upper end of the range of values reported for mammalian cells. The receptor association rate constant (9.6 X 10(2) M-1 s-1) is extremely low although the dissociation rate constant was immeasurable. Calcium is required for VTG binding, and low pH does not dissociate the VTG-receptor complex. Monensin treatment at 100 microM caused the loss of surface receptors with a t1/2 of 3 h and the accumulation of internalized ligand in a "pre-lysosomal" endocytic compartment. Conversely, the recovery of surface VTG receptors that were removed with trypsin occurred with a t1/2 of about 2 h. These observations indicate that oocytes have very large intracellular pools of receptors and that although surface receptors are internalized on the time scale of minutes, the intracellular pool is recycled on the time scale of hours.
Presentation of endogenous viral proteins in association with major histocompatibility complex class II: On the role of intracellular compartmentalization, invariant chain and the TAP transporter system (1995)

Major histocompatibility complex (MHC) class II-associated antigen presentation is mainly linked to processing of exogenous antigens upon cellular uptake by endocytosis, but has also been observed for endogenously synthesized antigens. We have studied the MHC class II-associated presentation of the endogenously synthesized membrane associated glycoprotein (GP) and the cytosolic nucleoprotein (NP) of lymphocytic choriomeningitis virus (LCMV) in professional antigen presenting cells (APC) of mice. Since LCMV is a noncytopathic virus and minimally affects cellular protein synthesis, it is a convenient virus for the study of antigen presentation. In contrast, most other studies assessing class II-associated presentation of endogeneously synthesized viral antigens used cytolytic viruses such as vaccinia, measles and influenza virus, which drastically interfere with host cell functions. In addition, most studies were performed using non-professional APC. We found that class II-associated presentation of endogenously synthesized membrane associated LCMV-GP was efficient and could not be inhibited by chloroquine or leupeptin. Neither the transporter associated with processing (TAP) system nor the invariant chain (Ii) were significantly involved in this process. In contrast, MHC class II-associated presentation of endogenously synthesized cytosolic LCMV-NP was not observed even in Ii-deficient APC. Thus, MHC class II loading of endogenously synthesized LCMV-GP apparently does not require processing in acidic endosomal compartments as defined by chloroquine and leupeptin insensitivity. Furthermore, although the TAP molecules transport peptides of up to 15 amino acids in length, which potentially could bind to MHC class II molecules in the endoplasmic reticulum, such a process apparently does not occur for either the glycoprotein or the nucleoprotein. Therefore, the subcellular localization of an endogenously synthesized protein influences crucially whether or not MHC class II loading can occur independently of the acidic compartments usually involved in MHC class II loading.
THE STRUCTURE AND FUNCTION OF THE PROXIMAL END OF THE FEMUR (1961)

Many analyses of the geometric arrangement of trabeculae in the proximal end of the femur have accepted and perpetuated the theories of Ward (1838), Culmann (1866) and Meyer (1867), and have contributed to the belief that the structure of the femoral neck embodies mechanical principles which are foreign to bony formations elsewhere. This isolated departure from the normal pattern of skeletal behaviour is considered to be most unlikely, and an attempt has been made to show that the structure of the femoral head and neck departs but little from the normal anatomy of the long bone. From a developmental point of view, the proximal end of the human femur is believed, in its simplest interpretation, to represent an upward continuation of the original shaft which has undergone rotation and expansion. The cancellous arrangements of the internal weight-bearing system are likewise believed to represent the expanded and rotated lamellae of the neck as they are presented radiologically or on coronal section. The forces acting upon the proximal end of the femur are considered to be mainly compressive in nature, and both crane and street-lamp bracket theories have therefore been rejected. The spiral conformity of the proximal end of the femur has been related to the spiral disposition of the soft-tissue structures that surround the hip, and in the interpretation of hip joint mechanics the principle of the screw has been preferred to the principle ofthe lever.
[Magnetic resonance imaging in the exploration of hepatic masses]. (1984)

Exploration was conducted by magnetic resonance imaging (MRI) at 0.15 T in 33 patients with hepatic masses, including 18 with malignant tumors, 11 with benign tumors and 4 with non-tumoral masses. All tumors appeared hyperintensive in relation to liver on images acquired by long TR spin echos (SE) and all, except for one fatty tumor, appeared hypointense in relation to liver on images acquired in inversion-recuperation (IR). The study seemed to provide data demonstrating that MRI at 0.15 T enables visualization of hepatic masses with a degree of precision that approaches that of other imaging methods. Tumors of the small size of the order of a centimetre can be detected. Tumor outlines and vascular relations are clearly demonstrated without use of contrast. Characterization of masses is still insufficient since the simple play of contrasts between tumor, parenchyma and vessels does not allow differentiation of malignant from benign tumors, nor the identification of a given histologic type.
Apoptosis in human fibrosarcoma cells is induced by a multimeric synthetic Tyr-Ile-Gly-Ser-Arg (YIGSR)-containing polypeptide from laminin. (1994)

The YIGSR (Tyr-Ile-Gly-Ser-Arg) peptide, derived from the laminin beta 1 chain, decreases tumor metastasis and growth in experimental animals. The mechanism responsible for this inhibition is not known. We now report that a 16-mer branched form of YIGSR, synthesized by the multimeric antigen peptide system, induced the apoptosis of HT-1080 cells in vitro at 30 micrograms/ml (approximately 3 microM). Tumor cells treated with this peptide showed the expected morphological changes associated with apoptosis, acridine orange staining of nuclei, increased numbers of 3'-OH ends of DNA in nuclei, a DNA ladder pattern on agarose gels, and increased transforming growth factor beta 1 mRNA by Northern blot. The specificity of this peptide was confirmed by inhibition of apoptosis with a neutralizing antibody to the peptide. In addition, the branched 16-mer peptides of scrambled sequence did not induce apoptosis. Our in vitro results suggest that apoptosis may play a role in the antimetastatic and antitumor effects associated with the YIGSR peptide.
Perfect quantum-error-correction coding in 24 laser pulses (1997)

An efficient coding circuit is given for the perfect quantum-error correction of a single quantum bit (qubit) against arbitrary one-qubit errors within a five-qubit code. The circuit presented employs a double ``classical'' code, i.e., one for bit flips and one for phase shifts. An implementation of this coding circuit on an ion-trap quantum computer is described that requires 26 laser pulses. Another circuit is presented requiring only 24 laser pulses, making it an efficient protection scheme against arbitrary one-qubit errors. In addition, the performances of two error-correction schemes, one based on the quantum Zeno effect and the other using standard methods, are compared. The quantum Zeno error correction scheme is found to fail completely for a model of noise based on phase diffusion.
What Ails Education Research (1988)

My purpose is to reflect on the state of education research and on what ails it. Part of what ails it, of course, is that the public regards much of our work with more than a trace of skepticism. Education research rarely gets credit for such headway as is being made in American education. Rather, it tends to be associated with educational faddism on the one hand and pointy-headed intellectualism on the other.
Binding of factors IX and IXa to cultured vascular endothelial cells. (1983)

Factor IX and its activated form IXa have been found to bind to confluent cultured bovine aortic and human umbilical vein endothelial cells. Binding of bovine factors IX and IXa to the bovine endothelial cells was saturable and specific and reached a plateau in 75 min at 4 degrees C and 30 min at 37 degrees C. Binding was half-maximal at a total factor IX or IXa concentration of 2.3 +/- 0.2 nM. At 4 degrees C, a maximum of 42 fmol of tritiated factor IX or IXa bound to 10(6) cells (an average of 20,000 molecules per cell). The binding of tritiated factor IX or IXa was inhibited by excess unlabeled factor IX or IXa but not by factor X, prothrombin, or thrombin. Competition studies indicated that factors IX and IXa interacted with the same site. Binding was reversible, with 50% of the specifically bound factor IX or IXa eluted in 40 min by a 400-fold excess of unlabeled protein. Specific binding required Ca2+ with half-maximal binding at 1.2 mM CaCl2. Factor IXa bound to the cells was tested for procoagulant activity in a clotting assay with factor IX-deficient plasma, cephalin, and CaCl2. Cell-bound factor IXa was at least 3-fold more active than was factor IXa in solution. The retention of procoagulant activity by cell surface-bound factor IXa provides a mechanism for the localization of clot-promoting activity.
Cytokine Signals in T-Cell Homeostasis (2005)

Thymic production of T cells declines rapidly with age, and therefore homeostatic cycling (HC) of mature lymphocytes plays an important role in maintaining stable numbers of mature T lymphocytes bearing sufficient repertoire diversity. Following lymphocyte depletion, HC changes in quality and magnitude, resulting in homeostatic peripheral expansion (HPE), a state of widespread T-cell cycling that serves to increase T-cell number and to maintain T-cell repertoire diversity to the greatest extent possible. Recent studies delineating the requirements for HC and HPE have shown that naive CD4+ cells and naive CD8+ cells require both IL7 and TCR engagement for survival, cycling, and homeostatic expansion, whereas CD8+ memory cells are maintained and expanded by cytokine signals alone, independent of TCR engagement. While basal levels of IL15 are sufficient for HC and HPE of CD8+ memory cells, supranormal levels of IL7 will also suffice. The requirements for memory CD4+ cells remain unclear, but current models hypothesize that either IL7 or TCR triggering may be sufficient. Thus, the changes in immune physiology that are present in lymphopenic hosts can be largely accounted for by cytokine-driven signals, especially those rendered by IL7 or IL15. As the alterations in immune physiology present in lymphopenic hosts may be conducive to stronger antitumor immune responsiveness, careful delineation of the factors responsible may be expected to give rise to approaches to augment the effectiveness of current antitumor immunotherapies.
Influence of Source and Receiver Geometry on the Testing of Pavements by the Surface Waves Method (1989)

The spectral analysis of surface waves (SASW) method is a nondestructive testing procedure under development for determining the elastic modulus profile of pavement systems in situ. The ultimate goal in the development of the SASW method is a totally automated, moveable test rig for conducting the investigation. An important step toward this objective is the development of a multiple transducer testing procedure. A significant variable with respect to a multiple transducer testing procedure is the choice of source and receiver geometry. A series of tests were conducted on an asphaltic concrete pavement to study the influence of source and receiver geometry. It was found that the results obtained from two different geometries, the common receivers midpoint (CRMP) geometry and the common source (CS) geometry, were nearly identical. The common source (CS) geometry was concluded to be preferable because of its practical advantage of a fixed source location.
Second messenger systems as targets for new therapeutic agents: focus on selective phosphodiesterase inhibitors. (1995)

Second messengers are intracellular substances whose concentration is regulated by the action on their specific receptors of extracellular regulatory molecules globally known as first messengers. In particular, the cyclic nucleotides cAMP and cGMP help in the coordination of cellular functions, mainly through their stimulatory effect on multisubstrate protein kinases. The pharmacological modulation of cyclic nucleotide levels has been classically attained by acting on the first messenger receptors. However, the possibility exists that an intervention on the enzymes responsible for the synthesis or degradation of such second messengers could yield similar effects. The enzymes involved in the degradation of cAMP and cGMP, the so-called cyclic nucleotide phosphodiesterases (PDEs), are a group of at least 7 enzyme families that share the property of hydrolysing the cyclic nucleotides to their corresponding 5-monophosphate counterparts. At the present time, most of the interest on the potential utility of selective PDE inhibitors is focused on drugs capable of inhibiting PDE IV, one of the cAMP specific phosphodiesterases, because the tissue distribution of PDE IV strongly suggests that pathologies related to the central nervous and immune systems, could be treated in this way. PDE IV inhibitors can be divided into three structural classes: 1) structural analogues of rolipram, 2) structural analogues of nitraquazone and 3) structures related to the xanthine nucleus, such as denbufylline. An overview of the structure-activity relationships for these classes of compounds and a summary of their possible therapeutic potential will be given.
Experimental results on fast 2D-encoded magnetic particle imaging (2008)

This paper presents the first experimental results on magnetic particle imaging with full 2D encoding. The encoding speed achieved was 3.88 ms for a field of view of 1x1 cm2. Small phantoms composed of several dots each filled with 200 nl undiluted Resovist (500 mmol(Fe) l(-1)) were scanned. A resolution of better than 1 mm was achieved for a frame rate of 25 frames s(-1).
Treatment of Post–Electroconvulsive Therapy Agitation With Dexmedetomidine (2013)

Post-electroconvulsive therapy (ECT) delirium is commonly encountered in practice, occurring in up to 12% of treatments. Although often easily managed nonpharmacologically, more severe or persistent cases are generally treated with benzodiazepines or propofol. We describe a patient who failed to respond adequately to these medications but responded quite favorably to dexmedetomidine, a centrally acting α2 agonist. There is evidence that dexmedetomidine may have unique, "delirium-sparing" properties; this makes it an attractive option for this indication.
Model Checking Hierarchical Communicating Real-Time State Machines (2006)

Hierarchical communicating real-time state machines (H-CRSM) is a formal modelling language for the modular development of distributed real-time systems. The formalism is characterized by the use of state transitions with guarded commands and timing constraints, the adoption of a few distilled statecharts constructs, and the modular specification of timing constraints along a state hierarchy. This paper proposes a translation of H-CRSM into UPPAAL which enables model checking. Translation rests on unfolding a hierarchical model on a flat representation
Structural diversity of heparan sulfate binding domains in chemokines (2002)

Heparan sulfate (HS) molecules are ubiquitous in animal tissues where they function as ligands that are dramatically involved in the regulation of the proteins they bind. Of these, chemokines are a family of small proteins with many biological functions. Their well-conserved monomeric structure can associate in various oligomeric forms especially in the presence of HS. Application of protein surface analysis and energy calculations to all known chemokine structures leads to the proposal that four different binding modes are created by the folding and oligomerization of these proteins. So, based on the present state of our knowledge, four different clusters of amino acids should be involved in the recognition process. Our results help to rationalize how unique sequences of HS specifically bind any given chemokine. The conclusions open the route for a rational design of compounds of therapeutical interest that could influence chemokine activity.
Zinc Binding in HDAC Inhibitors:  A DFT Study (2007)

Histone deacetylases (HDACs) are attractive targets for the treatment of cancers and a variety of other diseases. Most currently studied HDAC inhibitors contain hydroxamic acids, which are potentially problematic in the development of practical drugs. DFT calculations of the binding modes and free energies of binding for a variety of other functionalities in a model active site of HDAC are described. The protonation state of hydroxamic acids in the active site and the origin of the high affinity are discussed. These results emphasize the importance of a carefully chosen pKa for zinc binding and provide guidance for the design of novel, non-hydroxamic acid HDAC inhibitors.
Dissociation between vasospasm and functional improvement in a murine model of subarachnoid hemorrhage (2006)

These results demonstrate a dissociation between vasospasm and neurological outcomes that is consistent with findings of previous clinical trials.
Superantigen properties of a human sialoprotein involved in gut-associated immunity. (1995)

Protein Fv (pFv) is a recently described 175-kD gut-associated sialoprotein with a potent capacity for augmentation of antibody-dependent immune functions. To investigate the molecular basis for Fab-mediated binding of pFv, we evaluated a panel of 52 monoclonal IgM and found that approximately 40% bound pFv. Whereas the majority (> or = 75%) of V H3 and V H6 IgM strongly bound pFv, only a small minority (< 20%) of IgM from other V H families bound pFv, and these antibodies had weaker binding interactions. Inhibition studies suggested that all binding occurred at the same (or overlapping) site(s) on pFv. Surface plasmon resonance studies demonstrated binding affinity constants up to 6.7 x 10(8) M-1 for pFv. Biopanning of IgM and IgG Fab phage-display libraries with pFv preferentially selected for V H3 and V H6 antibodies, but also obtained certain V H4 IgM. V H sequence analyses of 36 pFv-binding antibodies revealed that binding did not correlate with CDR sequence, JH, or L chain usage. However, there was preferential selection of pFv binders with V H CDR3 of small size. These studies demonstrate that a protein which enhances immune defense in the gut has structural and functional properties similar to known superantigens.
Spatial Programming for Industrial Robots through Task Demonstration (2013)

Abstract We present an intuitive system for the programming of industrial robots using markerless gesture recognition and mobile augmented reality in terms of programming by demonstration. The approach covers gesture-based task definition and adaption by human demonstration, as well as task evaluation through augmented reality. A 3D motion tracking system and a handheld device establish the basis for the presented spatial programming system. In this publication, we present a prototype toward the programming of an assembly sequence consisting of several pick-and-place tasks. A scene reconstruction provides pose estimation of known objects with the help of the 2D camera of the handheld. Therefore, the programmer is able to define the program through natural bare-hand manipulation of these objects with the help of direct visual feedback in the augmented reality application. The program can be adapted by gestures and transmitted subsequently to an arbitrary industrial robot controller using a unified interface. Finally, we discuss an application of the presented spatial programming approach toward robot-based welding tasks.