gebhart/patrepeval huggingface dataset:
Strategy for Signaling Molecule Detection by Using an Integrated Microfluidic Device Coupled with Mass Spectrometry to Study Cell-to-Cell Communication (2012)

Cell-to-cell communication is a very important physiological behavior in life entity, and most of human behaviors are related to it. Although cell-to-cell communications are attracting much attention and financial support, rare methods have been successfully developed for in vitro cell-to-cell communication study. In this work, we developed a novel method for cell-to-cell communication study on an integrated microdevice, and signaling molecule and metabolites were online-detected by an electrospray ionization-quadrupole-time-of-flight-mass spectrometer (ESI-Q-TOF-MS) after on-chip solid-phase extraction. Moreover, we presented a "Surface Tension Plug" on a microchip to control cell-to-cell communication. The microdevice consists of three functional sections: cell coculture channel, targets pretreatment, and targets detection sections. To verify the feasibility of cell-to-cell communications on the integrated microdevice, we studied the communication between the 293 and the L-02 cells. Epinephrine and glucose were successfully detected using an ESI-Q-TOF-MS with short analysis time (<10 min). The results demonstrated that the developed microfluidic device is a potentially useful tool for high throughput cell-to-cell communication study.
Memory-savvy distributed interactive ray tracing (2004)

Interactive ray tracing in a cluster environment requires paying close attention to the constraints of a loosely coupled distributed system. To render large scenes interactively, memory limits and network latency must be addressed efficiently. In this paper, we improve previous systems by moving to a page-based distributed shared memory layer, resulting in faster and easier access to a shared memory space. The technique is designed to take advantage of the large virtual memory space provided by 64-bit machines. We also examine task reuse through decentralized load balancing and primitive reorganization to complement the shared memory system. These techniques improve memory coherence and are valuable when physical memory is limited.
Pitfalls of vaccinations with WT1-, Proteinase3- and MUC1-derived peptides in combination with MontanideISA51 and CpG7909 (2010)

T cells with specificity for antigens derived from Wilms Tumor gene (WT1), Proteinase3 (Pr3), and mucin1 (MUC1) have been demonstrated to lyse acute myeloid leukemia (AML) blasts and multiple-myeloma (MM) cells, and strategies to enhance or induce such tumor-specific T cells by vaccination are currently being explored in multiple clinical trials. To test safety and immunogenicity of a vaccine composed of WT1-, Pr3-, and MUC1-derived Class I-restricted peptides and the pan HLA-DR T helper cell epitope (PADRE) or MUC1-helper epitopes in combination with CpG7909 and MontanideISA51, four patients with AML and five with MM were repetitively vaccinated. No clinical responses were observed. Neither pre-existing nor naive WT1-/Pr3-/MUC1-specific CD8+ T cells expanded in vivo by vaccination. In contrast, a significant decline in vaccine-specific CD8+ T cells was observed. An increase in PADRE-specific CD4+ T helper cells was observed after vaccination but these appeared unable to produce IL2, and CD4+ T cells with a regulatory phenotype increased. Taken into considerations that multiple clinical trials with identical antigens but different adjuvants induced vaccine-specific T cell responses, our data caution that a vaccination with leukemia-associated antigens can be detrimental when combined with MontanideISA51 and CpG7909. Reflecting the time-consuming efforts of clinical trials and the fact that 1/3 of ongoing peptide vaccination trails use CpG and/or Montanide, our data need to be taken into consideration.
Ezrin self-association involves binding of an N-terminal domain to a normally masked C-terminal domain that includes the F-actin binding site. (1995)

Ezrin is a membrane-cytoskeletal linking protein that is concentrated in actin-rich surface structures. It is closely related to the microvillar proteins radixin and moesin and to the tumor suppressor merlin/schwannomin. Cell extracts contain ezrin dimers and ezrin-moesin heterodimers in addition to monomers. Truncated ezrin fusion proteins were assayed by blot overlay to determine which regions mediate self-association. Here we report that ezrin self-association occurs by head-to-tail joining of distinct N-terminal and C-terminal domains. It is likely that these domains, termed N- and C-ERMADs (ezrin-radixin-moesin association domain), are responsible for homotypic and heterotypic associations among ERM family members. The N-ERMAD of ezrin resided within amino acids 1-296; deletion of 10 additional residues resulted in loss of activity. The C-ERMAD was mapped to the last 107 amino acids of ezrin, residues 479-585. The two residues at the C-terminus were required for activity, and the region from 530-585 was insufficient. The C-ERMAD was masked in the native monomer. Exposure of this domain required unfolding ezrin with sodium dodecyl sulfate or expressing the domain as part of a truncated protein. Intermolecular association could not occur unless the C-ERMAD had been made accessible to its N-terminal partner. It can be inferred that dimerization in vivo requires an activation step that exposes this masked domain. The conformationally inaccessible C-terminal region included the F-actin binding site, suggesting that this activity is likewise regulated by masking.
AFS-Assisted Trailer Reversing (2006)

Reversing with a trailer is very difficult and many drivers hesitate to even try it. This thesis examines if active steering, particularly AFS (Active Front Steering), can be used to provide assistance. For analysis and controller design a simple geometric model of car and trailer is used. The model seems to be accurate enough at the low speeds relevant for trailer reversing. It is shown that the only trailer dependent model parameter can be estimated while driving. This enables use with different trailers. Different schemes to control the system are tested. The main approach is to use the steering wheel as reference for some appropriate output signal, for example the angle between car and trailer. This makes reversing with a trailer more like reversing without a trailer. To turn left, the driver simply turns the steering wheel left and drives. Test driving, as well as theoretical analysis, shows that the resulting system is stable. Of the eight drivers that have tested this type of control, five found it to be a great advantage while two considered it more confusing than helpful. A major problem with this control approach has to do with the way AFS is constructed. With AFS, the torque required to turn the front wheels results in a reaction torque in the steering wheel. Together with the reference tracking controllers, this makes the steering wheel unstable. Theoretical analysis implies that this problem has to be solved mechanically. One solution would be to combine AFS with electric power steering. This thesis also presents a trajectory tracking scheme to autonomously reverse with a trailer. Starting from the current trailer position and the desired trajectory an appropriate turning radius for the trailer is decided. Within certain limits, this will stabilize the car as well. The desired trajectory can be programmed beforehand, but it can also be saved while driving forward. Both variants have been tested with good results.
Synthesis and Structure-Activity Studies of a Series of 1-Oxa-2,8-diazaspiro(4.5)decan-3-ones and Related Compounds as M1 Muscarinic Agonists. (1995)

A series of novel 2,8-dialkyl-1-oxa-2,8-diazaspiro[4.5]decan-3-ones and 2,8-dimethyl-1,2,8-triazaspiro[4.5]-decan-3-one (13), related to M1 muscarinic agonists YM796 and RS86, were synthesized by using Michael addition reaction of hydroxyurea or methylhydrazine to alpha, beta-unsaturated esters followed by cyclization reaction. These compounds were assessed for binding affinities for M1 and M2 receptors and in vivo muscarinic activity: namely, amelioration of scopolamine-induced impairment in rat passive avoidance tasks and induction of hypothermia, tremor, and salivation. 2,8-Dimethyl-1-oxa-2,8-diazaspiro[4.5]decan-3-one (6a) exhibited high affinities for both M1 and M2 receptors, showed antiamnesic activity (0.1 mg/kg, s.c.) and induced hypothermia (3 mg/kg, s.c.). In addition, 6a stimulated phosphoinositide hydrolysis in rat hippocampal slices, indicating partial agonistic activity for M1 muscarinic receptors. The alteration of the methyl group at N2 of 6a increased the selectivity in binding affinities for M1 over M2 receptors, but resulted in loss of M1 agonistic activity or antiamnesic activity. Compound 13 exhibited only low affinity for M1 receptors, suggesting that a basic nitrogen atom is not tolerated in M1 receptor binding as a substitute for an oxygen atom or a carbonyl group at the 1-position of 6a or RS86. None of these derivatives exhibited high selectivity for antiamnesic effect over induction of hypothermia compared to YM796.
PEX11 family members are membrane elongation factors that coordinate peroxisome proliferation and maintenance (2010)

Dynamic changes of membrane structure are intrinsic to organelle morphogenesis and homeostasis. Ectopic expression of proteins of the PEX11 family from yeast, plant or human lead to the formation of juxtaposed elongated peroxisomes (JEPs),which is evocative of an evolutionary conserved function of these proteins in membrane tubulation. Microscopic examinations reveal that JEPs are composed of independent elongated peroxisomes with heterogeneous distribution of matrix proteins. We established the homo- and heterodimerization properties of the human PEX11 proteins and their interaction with the fission factor hFis1, which is known to recruit the GTPase DRP1 to the peroxisomal membrane. We show that excess of hFis1 but not of DRP1 is sufficient to fragment JEPs into normal round-shaped organelles, and illustrate the requirement of microtubules for JEP formation. Our results demonstrate that PEX11-induced JEPs represent intermediates in the process of peroxisome membrane proliferation and that hFis1 is the limiting factor for progression. Hence, we propose a model for a conserved role of PEX11 proteins in peroxisome maintenance through peroxisome polarization, membrane elongation and segregation.
How the Egg Regulates Sperm Function during Gamete Interaction: Facts and Fantasies1 (1991)

Although details of the molecular mechanism are not yet clear, considerable evidence suggests that the egg-specific extracellular matrix component ZP3 regulates an essential event of sperm function, the acrosome reaction. Spatial control of this exocytotic event appears to be exerted by immobilization of the triggering ligand, ZP3, in the zona pellucida matrix surrounding the egg. Our data suggest that the signal transduction pathway in sperm activated by this ligand involves highly conserved components that are involved in many other eukaryotic signalling events. Recent experiments indicate that the murine zona pellucida glycoprotein ZP3 regulates acrosomal exocytosis by aggregating its corresponding receptors (ZP3-Rs) located in the mouse sperm plasma membrane. In other experiments, we have identified a putative ZP3-R of mouse sperm with Mr 95,000. Indirect immunofluorescence localizes this ZP3-R, termed p95, to the acrosomal region of the mouse sperm head, which is the anticipated location for ZP3-Rs. Membrane fractionation studies indicate that p95 cofractionates with a plasma membrane-enriched preparation from sperm that contains zona pellucida-receptor activity. In addition to its role as a ZP3-R, p95 also serves as a substrate for a tyrosine kinase in response to zona pellucida binding. On the basis of the data presented here, and borrowing heavily from findings for other signalling systems, we have formulated two testable hypotheses that are compatible with the available data: either p95 is itself a protein tyrosine kinase receptor, or p95 serves as a ZP3 receptor and is separate from a protein tyrosine kinase that is activated during gamete interaction.(ABSTRACT TRUNCATED AT 250 WORDS)
Synthesis of polyacrylamides N-substituted with PNA-like oligonucleotide mimics for molecular diagnostic applications (1999)

Two types of oligonucleotide mimics relative to peptide nucleic acids (PNAs) were tested as probes in nucleic acid hybridisation assays based on polyacrylamide technology. One type of mimic oligomers represented a chimera constructed of PNA and phosphono-PNA (pPNA) monomers, and the other one contained pPNA residues alternating with PNA-like monomers on the base of trans -4-hydroxy-L-proline (HypNA). A chemistry providing efficient and specific covalent attachment of these DNA mimics to acrylamide polymers using a convenient approach based on the co-polymerisation of acrylamide and some reactive acrylic acid derivatives with oligomers bearing 5'- or 3'-terminal acrylamide groups has been developed. A comparative study of polyacrylamide conjugates with oligonucleotides and mimic oligomers demonstrated the suitability and high potential of PNA-pPNA and HypNA-pPNA chimeras as sequence-specific probes in capture and detection of target nucleic acid fragments to serve current forms of DNA arrays.
Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon (1977)

Ten Bacteroides species found in the human colon were surveyed for their ability to ferment mucins and plant polysaccharides ("dietary fiber"). A number of strains fermented mucopolysaccharides (heparin, hyaluronate, and chondroitin sulfate) and ovomucoid. Only 3 of the 188 strains tested fermented beef submaxillary mucin, and none fermented porcine gastric mucin. Many of the Bacteroides strains tested were also able to ferment a variety of plant polysaccharides, including amylose, dextran, pectin, gum tragacanth, gum guar, larch arabinogalactan, alginate, and laminarin. Some plant polysaccharides such as gum arabic, gum karaya, gum ghatti and fucoidan, were not utilized by any of the strains tested. The ability to utilize mucins and plant polysaccharides varied considerably among the Bacteroides species tested.
Synthesis and evaluation of antiinflammatory activities of a series of corticosteroid 17.alpha.-esters containing a functional group (1991)

A series of 21-desoxy-21-chlorocorticosteroids that contain a functionalized ester group at 17 alpha has been prepared and examined to separate their systemic activity from topical antiinflammatory activity. Introduction of the functionalized ester group at 17 alpha was carried out by an acid-catalyzed formation of cyclic ortho esters with 17 alpha,21-hydroxyl groups of corticosteroids and subsequent acid-catalyzed hydrolysis. As for the functional group, chloro, methoxy, acetoxy, cyano, cyclopropyl, or alkoxycarbonyl group was introduced at the terminal carbon atom of the 17 alpha-alkanoate group. The topical antiinflammatory activity and systemic activity of these compounds were examined and found to be significantly dependent on the functionalities in the 17 alpha-esters. Among these derivatives, a series of 17 alpha-(alkoxycarbonyl)alkanoates (17 alpha-OCO(CH2)nCOOR) showed an excellent separation of the systemic activity from topical activity. The effects of the number of methylene groups (n) and of the alkyl groups of the ester (R) on either topical or systemic activity of the corticosteroid derivatives were also investigated.
Augmented reality system for surgical navigation using robust target vision (2002)

This paper presents a robust and accurate vision-based augmented reality system for surgical navigation. The key point of our system is a robust and real-time monocular vision algorithm to estimate the 3D pose of surgical tools, utilizing specially designed code markers and Kalman filter-based position updating. The vision system is not impaired by occlusion and rapid change of illumination. The augmented reality system superimposes the 3D object wireframe onto the live viewing image taken from the surgical microscope as well as displaying other useful navigation information, while allowing the surgeons to freely change its zoom and focus for viewing. The experimental results verified the robustness and usefulness of the system, and acquired the image registration error less than 2 mm.
Navigation in Endoscopic Soft Tissue Surgery: Perspectives and Limitations (2008)

Despite rapid developments in the research areas of medical imaging, medical image processing, and robotics, the use of computer assistance in surgical routine is still limited to diagnostics, surgical planning, and interventions on mostly rigid structures. In order to establish a computer-aided workflow from diagnosis to surgical treatment and follow-up, several proposals for computer-assisted soft tissue interventions have been made in recent years. By means of different pre- and intraoperative information sources, such as surgical planning, intraoperative imaging, and tracking devices, surgical navigation systems aim to support surgeons in localizing anatomical targets, observing critical structures, and sparing healthy tissue. Current research in particular addresses the problem of organ shift and tissue deformation, and obstacles in communication between navigation system and surgeon. In this paper, we review computer-assisted navigation systems for soft tissue surgery. We concentrate on approaches that can be applied in endoscopic thoracic and abdominal surgery, because endoscopic surgery has special needs for image guidance due to limitations in perception. Furthermore, this paper informs the reader about new trends and technologies in the area of computer-assisted surgery. Finally, a balancing of the key challenges and possible benefits of endoscopic navigation refines the perspectives of this increasingly important discipline of computer-aided medical procedures.
Effect of vaccination with live or killed Pasteurella haemolytica on resistance to experimental bovine pneumonic pasteurellosis (1985)

Using 6- to 8-month-old beef calves, 3 experiments were conducted to compare the effect of vaccination with live or killed Pasteurella haemolytica on resistance to a transthoracic challenge exposure with the organism and to correlate serum antibody response with resistance. In each experiment, calves were vaccinated twice at 1-week intervals and were challenge exposed 21 days after the first inoculation. Lung lesions were evaluated by a system, such that higher scores indicated the more severe lesions. In each experiment, calves immunized with live P haemolytica had lower lesion scores than calves vaccinated with saline solution or bacterin. In 2 of the experiments, the differences were significant (P less than 0.05). In all experiments, calves vaccinated parenterally with a commercial P haemolytica/P multocida bacterin or with a formalin-killed P haemolytica bacterin had lesion scores that were not significantly different (P greater than 0.05) than for control calves vaccinated with saline solution. Live and killed bacterial preparations induced a significant serum antibody response to P haemolytica as measured by a quantitative fluorometric immunoassay. The antibody response to vaccination was not affected by preexisting titers to P haemolytica. Serum antibody titers were not consistently as high for calves vaccinated with bacterins as for calves vaccinated with live organisms. Although high antibody titers correlated with low lesion scores when calves vaccinated with saline solution or live organisms were analyzed collectively, there was not a significant correlation between the 2 variables when calves, vaccinated with saline solution or with bacterin, were analyzed collectively. These data indicate that, although bacterins may induce a detectable serum antibody response, they do not induce protection against transthoracic challenge exposure to P haemolytica.
Masquerade detection using truncated command lines (2003)

A masquerade attack, in which one user impersonates another, can be the most serious form of computer abuse. Automatic discovery of masqueraders is sometimes undertaken by detecting significant departures from normal user behavior, as represented by a user profile formed from system audit data. While the success of this approach has been limited, the reasons for its unsatisfying performance are not obvious, possibly because most reports do not elucidate the origins of errors made by the detection mechanisms. This paper takes as its point of departure a recent series of experiments framed by Schonlau et al. (2001). In extending that work with a new classification algorithm, a 56% improvement in masquerade detection was achieved at a corresponding false-alarm rate of 1.3%. A detailed error analysis, based on an alternative data configuration, reveals why some users are good masqueraders and others are not.
Targeting Specific Regions of the Notch3 Ligand-Binding Domain Induces Apoptosis and Inhibits Tumor Growth in Lung Cancer (2010)

Like many signaling pathways in development, the Notch receptor pathway plays an important role in cancer pathobiology when it is dysregulated. Potential ligand-binding sites within the epidermal growth factor (EGF)-like repeats of Notch1 have been identified, but the ligand-binding domains in Notch3, which is implicated in lung cancer, are not known. In screening a library of 155 peptides representing all 34 EGF-like repeats in Notch3, we discovered two distinct ligand-binding regions involving the 7-10 and 21-22 repeats that are distinct from the putative ligand-binding domain of Notch1. In cell-based assays, peptides from these regions induced apoptosis and reduced expression of the Notch3-dependent gene Hey1. They also bound directly to the Notch ligand Jagged1, suggesting that their mechanism of action involves disrupting interactions between Notch3 and Jagged1. Recombinant Fc fusion peptides engineered for in vivo testing showed that the Notch3 peptides defined could trigger apoptosis and suppress tumor growth in tumor xenograft assays. These findings rationalize a mechanistic approach to lung cancer treatment based on Notch3 receptor-targeted therapeutic development.
[Blood microfiltration methods]. (1983)

Red cell deformability can be approached by filtration through narrow channels either at constant pressure or at constant flow. A very simplified constant pressure method is described, measuring relative flow of 8% hematocrit red cells resuspended in buffer. A constant flow method is also described, using again 8 to 10% hematocrit, which the authors consider as more physiological than the very low hematocrits used by others. Significant results are obtained after incubation with pentoxifylline.