gebhart/patrepeval huggingface dataset:
Non-radioactive localization of substance P binding sites in rat brain and spinal cord using peptides labeled with 1.4-nm gold particles. (1995)

We present here a new method for non-radioactive labeling of substance P (SP) to demonstrate the distribution of its binding sites in histological sections. The peptide was labeled at the primary amino group with a 1.4-nm gold particle. In Western blots of membrane fractions of rat spinal cord, specific binding occurred at 38 and 58 KD. This binding was competitively suppressed by adding the native peptide. In addition, the SP-gold conjugate was able to displace the corresponding 125I-labeled peptide from binding proteins. In histological sections, binding sites could be shown in various parts of rat brain and spinal cord. The distribution patterns were comparable to those found in studies using autoradiographic methods. Adding the native peptide or a neurokinin 1 receptor agonist markedly reduced labeling of the tissue, whereas only a slight reduction was obtained after adding neurokinin A. Therefore, SP could be specifically labeled with a 1.4-nm gold particle to demonstrate its binding sites. This new method combines the advantages of receptor-ligand affinity binding with a non-radioactive detection system. It can be used for labeling peptides in general and therefore offers an alternative or addition to other methods used in study of the distribution of membrane receptors.
A brief history of the object-oriented approach (2003)

Unlike other fads, the object-oriented paradigm is here to stay. The road towards an object-oriented approach is described and several object-oriented programming languages are reviewed. Since the object-oriented paradigm promised to revolutionize software development, in the 1990s, demand for object-oriented software systems increased dramatically; consequently, several methodologies have been proposed to support software development based on that paradigm. Also presented are a survey and a classification scheme for object oriented methodologies.
Relighting objects from image collections (2009)

We present an approach for recovering the reflectance of a static scene with known geometry from a collection of images taken under distant, unknown illumination. In contrast to previous work, we allow the illumination to vary between the images, which greatly increases the applicability of the approach. Using an all-frequency relighting framework based on wavelets, we are able to simultaneously estimate the per-image incident illumination and the persurface point reflectance. The wavelet framework allows for incorporating various reflection models. We demonstrate the quality of our results for synthetic test cases as well as for several datasets captured under laboratory conditions. Combined with multi-view stereo reconstruction, we are even able to recover the geometry and reflectance of a scene solely using images collected from the Internet.
An Interval Tightly Linked to but Distinct From the H2 Complex Controls Both Overt Diabetes (Idd16) and Chronic Experimental Autoimmune Thyroiditis (Ceat1) in Nonobese Diabetic Mice (2002)

The major histocompatibility complex (MHC) has long been associated with predisposition to several autoimmune diseases, including type 1 diabetes and autoimmune thyroiditis. In type 1 diabetes, a primary role has been assigned to class II genes, both in humans and in the nonobese diabetic (NOD) mouse model. However, an involvement of other tightly linked genes is strongly suspected. Here, through two independent sets of experiments, we provide solid evidence for the existence of at least one such gene. First, using a new recombinant congenic NOD strain, R114, we definitively individualized the Idd16 locus from the MHC in a 6-cM interval proximal to H2-K. It affords almost complete protection against diabetes and is associated with delayed insulitis. Second, by genome scan, we mapped non-H2 genes associated with the highly penetrant form of chronic experimental autoimmune thyroiditis (EAT) that is elicited in NOD and NOD.H2(k) mice by immunization with thyroglobulin. We identified one major dominant locus, Ceat1, on chromosome 17, overlapping with Idd16. Most importantly, R114 recombinant congenic mice challenged with thyroglobulin did not develop chronic EAT. This new major region defined by both Idd16 and Ceat1 might thus concur to the unique strength of the MHC in autoimmune susceptibility of NOD mice.
Noise effects on centroid tracker aim point estimation (1988)

An investigation of errors due to noise in centroid tracker aim-point estimation is presented. The centroid tracker discussed is similar to the tracker described by A.L. Gilbert et al. (1980). Simplifications to this algorithm were made so that the derived models would be consistent with the actual tracker algorithm. Two statistical models are derived which relate image noise effects to computation of the target centroid. The first model, the simplified aim-point error model, is derived by assuming that the probabilities of incorrectly classifying target and background pixels are equal. The second model, the extended aim-point error model, is derived by assuming that the probability of incorrectly classifying a target pixel can differ from the probability of incorrectly classifying a background pixel. These models are described and their mathematical implication is discussed. Simulation results which verify the models are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Approximate caches for packet classification (2005)

Many network devices such as routers and firewalls employ caches to take advantage of temporal locality of packet headers in order to speed up packet processing decisions. Traditionally, cache designs trade off time and space with the goal of balancing the overall cost and performance of the device. We examine another axis of the design space that has not been previously considered: accuracy. In particular, we quantify the benefits of relaxing the accuracy of the cache on the cost and performance of packet classification caches. Our cache design is based on the popular Bloom filter data structure. This paper provides a model for optimizing Bloom filters for this purpose, as well as extensions to the data structure to support graceful aging, bounded misclassification rates, and multiple binary predicates. Given this, we show that such caches can provide nearly an order of magnitude cost savings at the expense of misclassifying one billionth of packets for IPv6-based caches.
Association between IgM response to IgG damaged by glyoxidation and disease activity in rheumatoid arthritis. (2000)

IgM anti-IgG-AGE appears to be associated with clinical measurements of RA activity and represents a new marker of more active disease in RA.
Self-calibration of a light striping system by matching multiple 3-D profile maps (2003)

A novel method is proposed for refining the calibration of a light striping system including a projective transformation between the image plane of the camera and the plane of the laser sheet, and also the direction of the scanning with respect to the plane of the laser sheet. The refinement is obtained through weighted least squares matching of multiple profile maps acquired from different viewpoints and registered previously using an approximate calibration. Testing with synthetically generated profile maps shows that if the geometry of the object is appropriate and the registration parameters and the intrinsic parameters of the system are known exactly, then a calibration accuracy of 0.003...0.00003% relative to the scene dimensions can be achieved as the average noise level in the maps used for the calibration decreases from 0.3 down to zero pixels. It is also possible to adjust several calibrations at the same time. The registration and calibration parameters can be refined simultaneously, but a close initial estimate and rather complex object geometry are needed for an accuracy of 0.03% when the average noise level is 0.03 pixels. Determining the corresponding points by interpolation on the parametric domains of the maps yields higher accuracy than perpendicular projection to the tangent planes at the closest points in 3D in both registration and calibration tasks. The highest accuracy is achieved when the interpolation errors are as equal as possible within the overlapping areas.
A multi-scale, multi-layer, translucent virtual space (2002)

The dynamic nature of virtual display spaces can provide powerful tools for helping people comprehend phenomena that occur over widely disparate spatial scales. This paper presents the macroscope, an interactive technique for browsing very large spaces of displayed information at different scales. The macroscope takes as a point of departure the traditional 2D zoom and pan operations, but introduces multiple translucent layers to avoid the problem of losing visual context. The third dimension is used to visually separate the layers and provide an external point of view for controlling the presentation. The user can manipulate viewfinders in the virtual space, which control the relative scale and position of the layers.
Extended-Cavity Semiconductor Wavelength-Swept Laser for Biomedical Imaging (2004)

We demonstrate a compact high-power rapidly swept wavelength tunable laser source based on a semiconductor optical amplifier and an extended-cavity grating filter. The laser produces excellent output characteristics for biomedical imaging, exhibiting >4-mW average output power, <0.06-nm instantaneous linewidth, and >80-dB noise extinction with its center wavelength swept over 100 nm at 1310 nm at variable repetition rates up to 500 Hz.
Physical and functional domains of the herpes simplex virus transcriptional regulatory protein ICP4 (1988)

A characteristic common to DNA animal viruses is the expression early in infection of viral proteins that act in trans to regulate subsequent RNA polymerase II-dependent transcription of the remainder of the viral genome. The predominant transcriptional regulatory protein specified by herpes simplex virus type 1 is the immediate-early protein ICP4. ICP4 is a complex multifunctional protein required for the activation of many herpes simplex virus type 1 transcriptional units and for repression of its own transcription. In the present study we have introduced nonsense and deletion mutations into both genome copies of the ICP4 gene such that the resulting mutants express only defined subsets of the primary ICP4 amino acid sequence. The partial peptides retain activities and physical properties of the intact ICP4 molecule, permitting one to attribute individual activities and properties to defined amino acid sequences.
Risk-averse control of a three-dimensional wear process (2000)

The problem of maximizing the profit obtained by using a machine until it is worn out is solved explicitly in one special instance. The performance criterion takes into account the risk sensitivity of the optimizer, who is assumed to be risk-averse. The method of similarity solutions is used.
Complex DNA repair pathways as possible therapeutic targets to overcome temozolomide resistance in glioblastoma (2012)

Many conventional chemotherapeutic drugs exert their cytotoxic function by inducing DNA damage in the tumor cell. Therefore, a cell-inherent DNA repair pathway, which reverses the DNA-damaging effect of the cytotoxic drugs, can mediate therapeutic resistance to chemotherapy. The monofunctional DNA-alkylating agent temozolomide (TMZ) is a commonly used chemotherapeutic drug and the gold standard treatment for glioblastoma (GBM). Although the activity of DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) has been described as the main modulator to determine the sensitivity of GBM to TMZ, a subset of GBM does not respond despite MGMT inactivation, suggesting that another DNA repair mechanism may also modulate the tolerance to TMZ. Considerable interest has focused on MGMT, mismatch repair (MMR), and the base excision repair (BER) pathway in the mechanism of mediating TMZ resistance, but emerging roles for the DNA strand-break repair pathway have been demonstrated. In the first part of this review article, we briefly review the significant role of MGMT, MMR, and the BER pathway in the tolerance to TMZ; in the last part, we review the recent publications that demonstrate possible roles of DNA strand-break repair pathways, such as single-strand break repair and double-strand break repair, as well as the Fanconi anemia pathway in the repair process after alkylating agent-based therapy. It is possible that all of these repair pathways have a potential to modulate the sensitivity to TMZ and aid in overcoming the therapeutic resistance in the clinic.
Wound infection after metronidazole infiltration (2006)

In state-run hospitals in India, pre-existing malnutrition and anaemia with late presentation, septicaemia and gross peritoneal contamination lead to a very high wound infection rate despite the use of systemic antibiotics. We studied the wound infection rate of subcutaneous infiltration of metronidazole (group B) versus irrigation with saline (group A) in patients undergoing exploratory laprotomy for perforation peritonitis with pyoperitoneum. The study included 30 patients in group A and 30 in group B. In group A 66.6% of the patients developed wound infection, whereas in group B 26.6% only developed wound infection. This difference is found to be statistically significant at a level of P < 0.01. There was no local complication attributable to infiltration of metronidazole in group B. Thus, we concluded that local infiltration of metronidazole at the incision is a safe and effective measure to control wound infection in cases of perforation peritonitis with pyoperitoneum.
Overexpressed Ly-6A.2 mediates cell-cell adhesion by binding a ligand expressed on lymphoid cells. (1995)

The Ly-6 locus encodes several cell surface proteins whose functions are unknown. Although it is hypothesized that these proteins may be receptors, there is no direct evidence that they bind a ligand. Herein we present evidence that Ly-6A.2, a Ly-6 protein expressed on T lymphocytes, binds a ligand expressed on normal thymocytes and splenic B and T cells. We find that transgenic thymocytes that overexpress Ly-6A.2 spontaneously aggregate in culture. This homotypic adhesion requires the overexpression of Ly-6A.2 because it is not observed in cultures of nontransgenic thymocytes. The aggregation of Ly-6A.2 transgenic thymocytes is inhibited by phosphatidylinositol-specific phospholipase C (which removes Ly-6A.2 and other glycosylphosphatidylinositol-anchored proteins from the membrane). Some anti-Ly-6A.2 monoclonal antibodies, including nonactivating ones and Fab' fragments, inhibit this aggregation. In contrast, other anti-Ly-6A.2 monoclonal antibodies increase the aggregation of transgenic but not nontransgenic thymocytes. To further examine whether Ly-6A.2 mediates adhesion (versus inducing another adhesion pathway) reaggregation assays were performed with paraformaldehyde-fixed Tg+ thymocytes. Paraformaldehyde-fixed Tg+ thymocytes reaggregate in culture and this aggregation is also blocked by phosphatidyl-inositol-specific phospholipase C and anti-Ly-6A.2 monoclonal antibodies. These results indicate that the homotypic adhesion of cultured Ly-6A.2 transgenic thymocytes is directly mediated by Ly-6A.2 and, more importantly, strongly suggests that Ly-6A.2 binds a ligand that is expressed on thymocytes. Tg+ thymocytes also bind to nontransgenic thymocytes, B cells, and T cells, indicating that normal cells naturally express the Ly-6A.2 ligand.
Coexisting conformations of fibronectin in cell culture imaged using fluorescence resonance energy transfer (2001)

Fluorescence resonance energy transfer (FRET) between fluorophores attached to single proteins provides a tool to study the conformation of proteins in solution and in cell culture. As a protein unfolds, nanometer-scale increases in distance between donor and acceptor fluorophores cause decreases in FRET. Here we demonstrate the application of FRET to imaging coexisting conformations of fibronectin (Fn) in cell culture. Fn is a flexible 440-kDa extracellular matrix protein, with functional sites that are regulated by unfolding events. Fn was labeled with multiple donor and acceptor fluorophores such that intramolecular FRET could be used to distinguish a range of Fn conformations. The sensitivity of FRET to unfolding was tested by progressively denaturing labeled Fn using guanidium chloride. To investigate Fn conformation changes during cell binding and matrix assembly, we added labeled Fn to the culture medium of NIH 3T3 fibroblasts. Coexisting conformations of Fn were visualized using fluorescence microscopy, and spectra from specific features were measured with an attached spectrometer. Using FRET as an indicator of Fn conformation, Fn diffusely bound to cells was in a compact state, whereas Fn in matrix fibrils was highly extended. Matrix fibrils exhibited a range of FRET that suggested some degree of unfolding of Fn's globular modules. Fn in cell-associated clusters that preceded fibril formation appeared more extended than diffuse cell-bound Fn but less extended than fibrillar Fn, suggesting that Fn undergoes extension after cell binding and before polymerization. FRET thus provides an approach to gain insight into the integrin-mediated pathway of Fn fibrillogenesis.
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors (2003)

AGRIS provides the necessary software tools on Arabidopsis transcription factors and their putative binding sites on all genes to initiate the identification of transcriptional regulatory networks in the model dicotyledoneous plant Arabidopsis thaliana. AGRIS can be accessed from http://arabidopsis.med.ohio-state.edu.
Epstein-Barr virus latent membrane protein 1 is essential for B-lymphocyte growth transformation. (1993)

The gene encoding latent-infection membrane protein 1 (LMP1) was specifically mutated in Epstein-Barr virus (EBV) recombinants by inserting a nonsense linker after codon 9 or codon 84 or into an intron 186 bp 3' to the latter insertion site. EBV recombinants with the LMP1 intron mutation were wild type for LMP1 expression and for growth transformation of primary B lymphocytes. In contrast, EBV recombinants with the mutations in the LMP1 open reading frame expressed N-terminally truncated crossreactive proteins and could initiate or maintain primary B-lymphocyte transformation only when wild-type LMP1 was provided in trans by a coinfecting, transformation-defective EBV, P3HR-1. These data indicate that LMP1 is essential for EBV-mediated transformation of primary B lymphocytes, that the first 43 amino acids are critical for LMP1's function, and that codon 44-initiated LMP1 does not have a dominant negative effect on transformation.
Testicular Leukemia Inhibitory Factor (LIF) and LIF Receptor Mediate Phosphorylation of Signal Transducers and Activators of Transcription (STAT)-3 and STAT-1 and Induce c-fos Transcription and Activator Protein-1 Activation in Rat Sertoli But Not Germ Cells (1998)

Increasing amounts of evidence suggest noninflammatory roles for growth factor and cytokines in development and differentiation. Leukemia inhibitory factor (LIF) belongs to a gp130 pleiotropic family of growth factors that has recently been shown to enhance the survival of rat testicular gonocytes and Sertoli cells. In this study, we show the expression of gp130 and LIF messenger RNAs (mRNAs) in the somatic (the Sertoli and Leydig cells) and specific germ cells (spermatogonia, pachytene, round, and elongated spermatids) of rodent testis, suggestive of cell-specific LIF-mediated functions. LIF receptor mRNA was demonstrated in rat somatic cells, rat elongating spermatids, and all of the mouse germ cells. In addition, we characterized the effects of LIF on the signal transducers and activators of transcription (STAT)-3 and STAT-1, c-fos gene expression, and activator protein-1 regulation in primary rat Sertoli cells. Electrophoretic mobility shift assay and Western blot analysis demonstrated that LIF translocates STAT-3 (and to a lesser extent STAT-1) transcription
Differential size variations between transcriptionally active and inactive telomeres ofTrypanosoma brucei (1983)

We have studied the genes coding for the variant-specific surface antigen (VSA) in a series of seven trypanosome clones derived from AnTat 1.1: 1.1 leads to 1.3 leads to 1.6 leads to 1.16 leads to 1.1C leads to 1.3B leads to 1.18 These genes are all telomeric (1-5), and their surrounding, although sometimes similar, differs in each case. The length between these antigen genes and the corresponding DNA end appears to increase at each antigenic switch, with however occasional sharp size reductions, often linked to the involvement of the telomere in gene expression. This increase is due to a constant "growth" of the telomeres, at a rate of about 28 bp per day in at least four cases and probably linked to chromosome duplication. The telomere harbouring the transcribed VSA gene is growing slightly faster (about 36 bp per day), and it is the only one whose size reduction is progressive, leading to a terminal length heterogeneity within a clone. As a result, the active VSA gene is found in a population of telomeres which, as the trypanosomes divide, becomes increasingly heterogeneous, with however a preferred discrete size class about 1.4 kb smaller. The fact that the "active" telomere is the only one in a chromatin conformation highly sensitive to DNAaseI (1-4, 6), suggests that chromatin structure influences the rate and extent of both size increase and shortening of telomeres.
Glutamate Receptors of the Non-N-Methyl-D-Aspartic Acid Type Mediate the Increase in Luteinizing Hormone-Releasing Hormone Release by Excitatory Amino Acidsin Vitro (1990)

The present study was designed to analyze in detail the effects of L-glutamate (L-Glu) and its agonists on the release of LHRH from arcuate nucleus-median eminence (AN-ME) fragments in vitro. Fragments from adult male rats were incubated in Krebs-Ringer bicarbonate buffer in the presence of different concentrations of L-Glu, kainate (KA), N-methyl-D-aspartic acid (NMDA), and quisqualate (QA). L-Glu at 10-20 mM evoked a significant increase in basal LHRH release, while D-glutamate at similar concentrations was ineffective. Partial depolarization with 14 mM K+ significantly augmented the release of LHRH induced by L-Glu. L-Glu-induced LHRH release was blunted in a dose-related manner by the specific KA/QA receptor antagonist 6,7-dinitroquinoxaline-2,3-dione. Exposure to KA or QA significantly increased LHRH release at concentrations (1 mM) much lower than those required for L-Glu. In the presence of 14 mM K+ the potencies of KA and QA (0.075 and 0.1 mM, respectively) were significantly enhanced. 6,7-Dinitroquinoxaline-2,3-dione blocked KA-induced LHRH release, while AP-7, a competitive NMDA receptor antagonist, was inactive in preventing L-Glu- and KA-induced LHRH release. LHRH secretion from AN-ME fragments was unaffected by NMDA at concentrations up to 10 mM in the different media tested. A significant stimulatory effect of NMDA at 20 mM was observed when fragments were incubated in Mg2+-free medium. These results show the stereoselectivity of L-Glu to enhance LHRH release from AN-ME fragments in vitro. Moreover, in view of the respective potencies of excitatory amino acid agonists (KA = QA greater than L-Glu greater than NMDA) and the selective antagonism of excitatory amino acid effects, they provide evidence that non-NMDA receptors primarily mediate the excitatory actions of L-Glu on LHRH release from nerve terminals in the AN-ME.