gebhart/patrepeval huggingface dataset:
PRELP Protein Inhibits the Formation of the Complement Membrane Attack Complex (2012)

PRELP is a 58-kDa proteoglycan found in a variety of extracellular matrices, including cartilage and at several basement membranes. In rheumatoid arthritis (RA), the cartilage tissue is destroyed and fragmented molecules, including PRELP, are released into the synovial fluid where they may interact with components of the complement system. In a previous study, PRELP was found to interact with the complement inhibitor C4b-binding protein, which was suggested to locally down-regulate complement activation in joints during RA. Here we show that PRELP directly inhibits all pathways of complement by binding C9 and thereby prevents the formation of the membrane attack complex (MAC). PRELP does not interfere with the interaction between C9 and already formed C5b-8, but inhibits C9 polymerization thereby preventing formation of the lytic pore. The alternative pathway is moreover inhibited already at the level of C3-convertase formation due to an interaction between PRELP and C3. This suggests that PRELP may down-regulate complement attack at basement membranes and on damaged cartilage and therefore limit pathological complement activation in inflammatory disease such as RA. The net outcome of PRELP-mediated complement inhibition will highly depend on the local concentration of other complement modulating molecules as well as on the local concentration of available complement proteins.
Truncated tau from sporadic Alzheimer's disease suffices to drive neurofibrillary degeneration in vivo (2006)

Truncated tau protein is the characteristic feature of human sporadic Alzheimer's disease. We have identified truncated tau proteins conformationally different from normal healthy tau. Subpopulations of these structurally different tau species promoted abnormal microtubule assembly in vitro suggesting toxic gain of function. To validate pathological activity in vivo we expressed active form of human truncated tau protein as transgene, in the rat brain. Its neuronal expression led to the development of the neurofibrillary degeneration of Alzheimer's type. Furthermore, biochemical analysis of neurofibrillary changes revealed that massive sarcosyl insoluble tau complexes consisted of human Alzheimer's tau and endogenous rat tau in ratio 1:1 including characteristic Alzheimer's disease (AD)-specific proteins (A68). This work represents first insight into the possible causative role of truncated tau in AD neurofibrillary degeneration in vivo.
2′-Deoxyadenosine Bearing Hydrophobic Carborane Pharmacophore (2007)

Modification of 2'-deoxyadenosine at position 8 with para-carborane boron cluster is described. Incorporation of boron cluster into nucleic base has been accomplished using Sonogashira palladium-catalyzed cross-coupling reaction or, alternatively, Huisgen "click" type reaction. These are the first examples of adenosine derivatives with hydrophobic carborane pharmacophore attached to purine base.
Cloning and expression of intercellular adhesion molecule 3 reveals strong homology to other immunoglobulin family counter-receptors for lymphocyte function-associated antigen 1. (1993)

Based on protein sequence, we have isolated a cDNA for intercellular adhesion molecule 3 (ICAM-3), the most recently defined counter-receptor for lymphocyte function-associated antigen 1 (LFA-1). Expression of the cDNA yields a product that reacts with monoclonal antibody to ICAM-3 and functions as a ligand for LFA-1. The deduced 518-amino acid sequence of the predicted mature protein defines a highly glycosylated type I integral membrane protein with five immunoglobulin (Ig)-like domains. The five Ig-like domains of ICAM-3 are highly homologous with those of human ICAM-1 (52% identity) and human ICAM-2 (37% identity).
A Machine Learning Framework for Programming by Example (2013)

Learning programs is a timely and interesting challenge. In Programming by Example (PBE), a system attempts to infer a program from input and output examples alone, by searching for a composition of some set of base functions. We show how machine learning can be used to speed up this seemingly hopeless search problem, by learning weights that relate textual features describing the provided input-output examples to plausible sub-components of a program. This generic learning framework lets us address problems beyond the scope of earlier PBE systems. Experiments on a prototype implementation show that learning improves search and ranking on a variety of text processing tasks found on help forums. 1.
Regularized Discriminant Analysis (1989)

Abstract Linear and quadratic discriminant analysis are considered in the small-sample, high-dimensional setting. Alternatives to the usual maximum likelihood (plug-in) estimates for the covariance matrices are proposed. These alternatives are characterized by two parameters, the values of which are customized to individual situations by jointly minimizing a sample-based estimate of future misclassification risk. Computationally fast implementations are presented, and the efficacy of the approach is examined through simulation studies and application to data. These studies indicate that in many circumstances dramatic gains in classification accuracy can be achieved.
Reassessment of the Diagnostic Value of Histology in Patients with GERD, Using Multiple Biopsy Sites and an Appropriate Control Group (2005)

In contrast with previous reports on the marginal role of histology in patients with GERD, our study shows that this technique can be a useful diagnostic tool, particularly in patients with NERD, when biopsies are taken at two sites including Z-line and 2 cm above it.
Activation of a local renin angiotensin system in podocytes by glucose (2008)

ANG II is a critical mediator of diabetic nephropathy. Pharmacologic inhibition of ANG II slows disease progression beyond what could be predicted by the blood pressure lowering effects alone, suggesting the importance of nonhemodynamic pathways of ANG II in mediating disease. Podocyte injury and loss are cardinal features of diabetic nephropathy. Mounting evidence suggests that the podocyte is a direct target of ANG II-mediated signaling in diabetic renal disease. We have tested the hypothesis that high glucose leads to the activation of a local angiotensin system in podocytes and delineated the underlying pathways involved. Cultured podocytes were exposed to standard glucose (5 mM), high glucose (40 mM), or mannitol as an osmotic control. ANG II levels in cell lysates were measured in the presence or absence of inhibitors of angiotensin-converting enzyme (captopril), chymase (chymostatin), and renin (aliskiren) activity. The effects of glucose on renin and angiotensin subtype 1 receptor expression and protein levels were determined. Exposure to high glucose resulted in a 2.1-fold increase ANG II levels mediated through increased renin activity, as exposure to high glucose increased renin levels and preincubation with Aliskiren abrogated glucose-induced ANG II production. Relevance to the in vivo setting was demonstrated by showing glomerular upregulation of the prorenin receptor in a podocyte distribution early in the course of experimental diabetic nephropathy. Furthermore, high glucose increased angiotensin subtype 1 receptor levels by immunofluorescence and Western blot. Taken together, the resultant activation of a local renin angiotensin system by high glucose may promote progressive podocyte injury and loss in diabetic nephropathy.
Large-Scale Mammalian Cell Culture: A Perspective (2018)

In many countries there are regulations governing pharmaceutical manufacture from suspension cell cultures and a number of products made in this way have been licensed for use. Indeed, mammalian cell cultures are now the preferred source of a number of important proteins for use in human and animal medicine, especially those which are relatively large, complex, or glycosylated. While the large-scale culture of mammalian cells may seem a comparatively recent development, both human and hamster cells had already been grown in 1000-liter culture tanks some 20 years ago. Work on such a scale was at first carried out in only a very few institutions whose special needs made it worthwhile to tackle the initially formidable technological and other problems. One such need was to produce foot-and-mouth disease (FMD) virus vaccines on a commercial scale for veterinary use; another was to make large amounts of human interferon (IFN) for clinical evaluation.
Phase noise in self-injection-locked oscillators - Theory and experiment (2003)

Phase-noise analysis of the self-injection-locked oscillator is presented in this paper. The analysis is developed for different oscillator models and arbitrary self-injection feedback loops. The results are illustrated with specific cases of simple time-delay cable and a high-Q factor resonator. It is shown that the behavior of the phase noise is similar to an oscillator locked to an external low phase-noise source. The output phase noise can be reduced at the noise offset frequency near the carrier frequency, and returning to the free-running oscillator noise far from the carrier frequency for certain stable feedback delay ranges. The phase-noise reduction is affected by the self-injection signal strength and feedback transfer function for different oscillator equivalent-circuit models. The theory is verified by using a self-injection-locked GaAs MESFET oscillator operating at the X-band with delay cable loops. The self-injection-locked technique may be used to improve the phase noise of the existing oscillators.
The Use of Grouping in Visual Object Recognition (1988)

The report describes a recognition system called GROPER, which performs grouping by using distance and relative orientation constraints that estimate the likelihood of different edges in an image coming from the same object. The thesis presents both a theoretical analysis of the grouping problem and a practical implementation of a grouping system. GROPER also uses an indexing module to allow it to make use of knowledge of different objects, any of which might appear in an image. We test GROPER by comparing it to a similar recognition system that does not use grouping.
Effect of glucocorticoids on oncogene transformed NIH3T3 cells. (1990)

We studied the differential response of oncogene transformed NIH3T3 cells to glucocorticoids. As demonstrated for transformed human fibroblasts, the morphology of neu-, ras-, src- and sis-transformed mouse fibroblasts became more normal after glucocorticoid treatment. This change was not due to inhibition of the expression of oncogene mRNA or protein. However, the abl-transformed NIH3T3 cells were resistant to glucocorticoid-induced morphology change. These results indicate that the glucocorticoid-induced morphology change is specific to certain oncogene-transformed NIH3T3 cells. Transformed human fibroblasts generally have reduced amounts of cell surface fibronectin. When treated with glucocorticoids, they incorporate higher levels of fibronectin in their extracellular matrix, which correlates with their change in morphology. However, we found that, except for abl-transformed cells, the fibronectin level of the other oncogene transformed mouse cells was similar to non-transformed cells. Moreover, treatment of the neu-, ras-, src- and sis-transformed cells with glucocorticoids resulted in a change in morphology but no increase in cell surface fibronectin. These studies demonstrate that the glucocorticoid-induced morphological change of oncogene-transformed NIH3T3 cells is not due to enhanced expression of fibronectin. Therefore, other mechanisms are responsible for this glucocorticoid-induced phenotypic change of oncogene-transformed cells.
Quantitative phase-contrast microscopy by a lateral shear approach to digital holographic image reconstruction (2006)

Combining the concept of lateral shear interferometry (LSI) within a digital holography microscope, we demonstrate that it is possible to obtain quantitative optical phase measurement in microscopy by a new single-image-processing procedure. Numerical lateral shear of the reconstructed wavefront in the image plane makes it possible to retrieve the derivative of the wavefront and remove the defocus aberration term introduced by the microscope objective. The method is tested to investigate a silicon structure and a mouse cell line.
Cloning, nucleotide sequence, and mutagenesis of the Bacillus subtilis ponA operon, which codes for penicillin-binding protein (PBP) 1 and a PBP-related factor (1995)

An oligonucleotide probe designed to hybridize to genes encoding class A high-molecular-weight penicillin-binding proteins (PBPs) was used to identify the ponA gene encoding PBP1a and -1b (PBP1) of Bacillus subtilis. The identity of the ponA product was established by (i) the presence of a sequence coding for a peptide generated from PBP1 and (ii) the disappearance of PBP1 in a ponA mutant. DNA sequence analysis revealed that the amino acid sequence of PBP1 was similar to those of other class A high-molecular-weight PBPs and that ponA appeared to be cotranscribed with an upstream gene (termed prfA) of unknown function. Null mutations in ponA resulted in a slight decrease in growth rate and a change in colony morphology but had no significant effect on cell morphology, cell division, sporulation, spore heat resistance, or spore germination. Mutations in prfA which did not effect ponA expression produced a more significant decrease in growth rate but had no other significant phenotypic effects. Deletion of both prfA and ponA resulted in extremely slow growth and a reduction in sporulation efficiency. Studies of expression of transcriptional fusions of ponA and prfA to lacZ demonstrated that these two genes constitute an operon. Expression of these genes was relatively constant during growth, decreased during sporulation, and was induced approximately 15 min into spore germination. The ponA locus was mapped to the 200 degrees region of the chromosomal physical map.
Gene profiling in murine corneas challenged with Aspergillus fumigatus. (2007)

MBL-A is among the primary responding genes during the onset of fungal keratitis. Also it was found that the microarray is a useful tool in elucidating the pathogenesis of FK.
Limited Trafficking of a Neurotropic Virus Through Inefficient Retrograde Axonal Transport and the Type I Interferon Response (2010)

Poliovirus is an enteric virus that rarely invades the human central nervous system (CNS). To identify barriers limiting poliovirus spread from the periphery to CNS, we monitored trafficking of 10 marked viruses. After oral inoculation of susceptible mice, poliovirus was present in peripheral neurons, including vagus and sciatic nerves. To model viral trafficking in peripheral neurons, we intramuscularly injected mice with poliovirus, which follows a muscle-sciatic nerve-spinal cord-brain route. Only 20% of the poliovirus population successfully moved from muscle to brain, and three barriers limiting viral trafficking were identified. First, using light-sensitive viruses, we found limited viral replication in peripheral neurons. Second, retrograde axonal transport of poliovirus in peripheral neurons was inefficient; however, the efficiency was increased upon muscle damage, which also increased the transport efficiency of a non-viral neural tracer, wheat germ agglutinin. Third, using susceptible interferon (IFN) alpha/beta receptor knockout mice, we demonstrated that the IFN response limited viral movement from the periphery to the brain. Surprisingly, the retrograde axonal transport barrier was equivalent in strength to the IFN barrier. Illustrating the importance of barriers created by the IFN response and inefficient axonal transport, IFN alpha/beta receptor knockout mice with muscle damage permitted 80% of the viral population to access the brain, and succumbed to disease three times faster than mice with intact barriers. These results suggest that multiple separate barriers limit poliovirus trafficking from peripheral neurons to the CNS, possibly explaining the rare incidence of paralytic poliomyelitis. This study identifies inefficient axonal transport as a substantial barrier to poliovirus trafficking in peripheral neurons, which may limit CNS access for other viruses.
Cellular Mechanisms Underlying Activity Patterns in the Monkey Thalamus During Visual Behavior (2000)

We show for the first time with in vitro recording that burst firing in thalamic relay cells of the monkey is evoked by activation of voltage-dependent, low threshold Ca(2+) spikes (LTSs), as has been described in other mammals. Due to variations in LTS amplitude, the number of action potentials evoked by an LTS could vary between 1 and 8. These data confirm the presence of two modes of firing in the monkey for thalamic relay cells, tonic and burst, the latter related to the activation of LTSs. With these details of the cellular processes underlying burst firing, we could account for many of the firing patterns we recorded from the lateral geniculate nucleus of the thalamus in behaving monkeys. In particular, we found clear evidence of burst firing during alert wakefulness, which had been thought to occur only during sleep or certain pathological states. This makes it likely that the burst firing seen in awake humans has the same cellular basis of LTSs, and this supports previous suggestions that burst firing represents an important relay mode for visual processing.
Multidrug-resistant human immunodeficiency virus type 1 strains resulting from combination antiretroviral therapy (1996)

Multidrug-resistant human immunodeficiency virus type 1 (HIV-1) strains with reverse transcriptase (RT) mutations at codons A62-->V, V75-->I, F77-->L, F116-->Y, and Q151-->M have been reported in patients receiving combination therapy with zidovudine (AZT) and didanosine (ddI). Infectious clones with each mutation alone, all five mutations together, and various combinations of mutations were created by site-directed mutagenesis. Mutation Q151-->M conferred partial resistance to AZT, ddI, zalcitibine, and stavudine, whereas a combination of four mutations conferred increased resistance to AZT, ddI, zalcitibine, and stavudine. The positions of residues 75, 77, and 151 in the three-dimensional crystal structure of HIV-1 RT suggest that these residues may affect the ability of the enzyme to discriminate between deoxynucleoside triphosphates and nucleoside analog RT inhibitors. Replication experiments showed that clones with mutation F77-->L but without V75-->I (HIV-1(77), HIV-1(77,151), and HIV-1(77,116,151) had attenuated growth compared with that of the original HIV-1NL4-3 strain and strains containing mutations at both positions 75 and 77 (HIV-1(75,77,151) and HIV-1(75,77,116,15)). Sequence analysis of viral RNA and proviral DNA from several patients indicated that RT mutations developed in a sequential and cumulative pattern over the course of a 2- to 4-year observation period. The present results suggest that drug resistance and viral replicative capacity both may play a role in selection of HIV-1 RT mutations.
A 1020-Node Modular Microphone Array and Beamformer for Intelligent Computing Spaces (2004)

Ubiquitous computing environments are characterized by an unboundedamount of noise and crosstalk. In these environments, traditionalmethods of sound capture are insufficient, and array microphones areneeded in order to obtain a clean recording of desired speech. In thiswork, we have designed, implemented, and tested LOUD, a novel 1020-nodemicrophone array utilizing the Raw tile parallel processorarchitecture for computation. To the best of our knowledge,this is currently the largest microphone array in the world. We haveexplored the uses of the array within ubiquitous computing scenarios byimplementing an acoustic beamforming algorithm for sound sourceamplification in a noisy environment, and have obtained preliminaryresults demonstrating the efficacy of the array. From one to 1020microphones, we have shown a 13.7dB increase in peak SNR on arepresentative utterance, an 87.2% drop in word error rate withinterferer present, and an 89.6% drop in WER without an interferer.
CXCL12 and Vascular Endothelial Growth Factor Synergistically Induce Neoangiogenesis in Human Ovarian Cancers (2005)

Ovarian carcinomas have a poor prognosis, often associated with multifocal i.p. dissemination accompanied by intense neovascularization. To examine tumor angiogenesis in the tumor microenvironment, we studied malignant ascites and tumors of patients with untreated ovarian carcinoma. We observed that malignant ascites fluid induced potent in vivo neovascularization in Matrigel assay. We detected a sizable amount of vascular endothelial cell growth factor (VEGF) in malignant ascites. However, pathologic concentration of VEGF is insufficient to induce in vivo angiogenesis. We show that ovarian tumors strongly express CXC chemokine stromal-derived factor (SDF-1/CXCL12). High concentration of CXCL12, but not the pathologic concentration of CXCL12 induces in vivo angiogenesis. Strikingly, pathologic concentrations of VEGF and CXCL12 efficiently and synergistically induce in vivo angiogenesis. Migration, expansion, and survival of vascular endothelial cells (VEC) form the essential functional network of angiogenesis. We further provide a mechanistic basis for explaining the interaction between CXCL12 and VEGF. We show that VEGF up-regulates the receptor for CXCL12, CXCR4 expression on VECs, and synergizes CXCL12-mediated VEC migration. CXCL12 synergizes VEGF-mediated VEC expansion and synergistically protects VECs from sera starvation-induced apoptosis with VEGF. Finally, we show that hypoxia synchronously induces tumor CXCL12 and VEGF production. Therefore, hypoxia triggered tumor CXCL12 and VEGF form a synergistic angiogenic axis in vivo. Hypoxia-induced signals would be the important factor for initiating and maintaining an active synergistic angiogeneic pathway mediated by CXCL12 and VEGF. Thus, interrupting this synergistic axis, rather than VEGF alone, will be a novel efficient antiangiogenesis strategy to treat cancer.
Material fundamentals and clinical performance of plasma‐sprayed hydroxyapatite coatings: A review (2001)

The clinical use of plasma-sprayed hydroxyapatite (HA) coatings on metal implants has aroused as many controversies as interests over the last decade. Although faster and stronger fixation and more bone growth have been revealed, the performance of HA-coated implants has been doubted. This article will initially address the fundamentals of the material selection, design, and processing of the HA coating and show how the coating microstructure and properties can be a good predictor of the expected behavior in the body. Further discussion will clarify the major concerns with the clinical use of HA coatings and introduce a comprehensive review concerning the outcomes experienced with respect to clinical practice over the past 5 years. A reflection on the results indicates that HA coatings can promote earlier and stronger fixation but exhibit a durability that can be related to the coating quality. Specific relationships between coating quality and clinical performance are being established as characterization methods disclose more information about the coating.