gebhart/patrepeval huggingface dataset:
Fcγ Receptor-like Activity of Hepatitis C Virus Core Protein (2004)

We have previously demonstrated that viral particles with the properties of nonenveloped hepatitis C virus (HCV) nucleocapsids occur in the serum of HCV-infected individuals (1). We show here that nucleocapsids purified directly from serum or isolated from HCV virions have FcgammaR-like activity and bind "nonimmune" IgG via its Fcgamma domain. HCV core proteins produced in Escherichia coli and in the baculovirus expression system also bound "nonimmune" IgG and their Fcgamma fragments. Folded conformation was required for IgG binding because the FcgammaR-like site of the core protein was inactive in denaturing conditions. Studies with synthetic core peptides showed that the region spanning amino acids 3-75 was essential for formation of the IgG-binding site. The interaction between the HCV core and human IgG is more efficient in acidic (pH 6.0) than in neutral conditions. The core protein-binding site on the IgG molecule differs from those for C1q, FcgammaRII (CD32), and FcgammaRIII (CD16) but overlaps with that for soluble protein A from Staphylococcus aureus (SpA), which is located in the CH2-CH3 interface of IgG. These characteristics of the core-IgG interaction are very similar to those of the neonatal FcRn. Surface plasmon resonance studies suggested that the binding of an anti-core antibody to HCV core protein might be "bipolar" through its paratope to the corresponding epitope and by its Fcgamma region to the FcgammaR-like motif on this protein. These features of HCV nucleocapsids and HCV core protein may confer an advantage for HCV in terms of survival by interfering with host defense mechanisms mediated by the Fcgamma part of IgG.
Energy-efficient resource allocation in SDMA systems with large numbers of base station antennas (2012)

In this paper, resource allocation for energy efficient communication in space division multiple access (SDMA) downlink networks with large numbers of transmit antennas is studied. The considered problem is modeled as a non-convex optimization problem which takes into account the circuit power consumption and a minimum required data rate. By exploiting the properties of fractional programming, the considered non-convex optimization problem in fractional form is transformed into an equivalent optimization problem in subtractive form, which enables the derivation of an efficient iterative resource allocation algorithm. The optimal power allocation solution for each iteration is derived based on a low complexity user selection policy for maximization of the energy efficiency of data transmission (bit/Joule delivered to the users). Simulation results illustrate that the proposed iterative resource allocation algorithm converges in a small number of iterations and unveil the trade-off between energy efficiency and the number of antennas.
BAG-1: A Novel Biomarker Predicting Long-Term Survival in Early-Stage Breast Cancer (2001)

These findings provide preliminary evidence that BAG-1 represents a potential marker of improved survival in early-stage breast cancer patients, independent of the status of axillary lymph nodes.
Rab7 and the CMT2B disease (2009)

The CMT2B (Charcot-Marie-Tooth type 2B) disease is an autosomal dominant axonal neuropathy. Sensory loss, distal muscle weakness and wasting, frequent foot ulcers and amputations of the toes due to frequent infections characterize this neuropathy. Four missense mutations in the rab7 gene have been identified as causative of the disease. Rab7 is a small G-protein of the Rab family that controls vesicular transport to late endosomes and lysosomes in the endocytic pathway. The CMT2B-associated mutant Rab7 proteins show altered nucleotide dissociation rates and impaired GTPase activity. In addition, these mutant proteins are predominantly in the GTP-bound form when expressed in human cells and they are able to rescue Rab7 function in Rab7-depleted cells. Thus these mutations generate activated forms of Rab7 that are responsible for the development of the disease. In spite of these results, there are still important gaps in our understanding of the mechanism underlying CMT2B. Indeed, how these mutations in the rab7 gene affect specifically peripheral neurons leading to an axonal pathology in CMT2B is not clear, and it is a particularly puzzling and challenging issue in view of the fact that Rab7 is a ubiquitous protein. The present review discusses possible molecular mechanisms underlying CMT2B.
Peripheral Blood Fibrocytes: Differentiation Pathway and Migration to Wound Sites (2001)

Fibrocytes are a distinct population of blood-borne cells that display a unique cell surface phenotype (collagen I+/CD11b+/CD13+/CD34+/CD45RO+/MHC class II+/CD86+) and exhibit potent immunostimulatory activities. Circulating fibrocytes rapidly enter sites of tissue injury, suggesting an important role for these cells in wound repair. However, the regulatory processes that govern the differentiation of blood-borne fibrocytes and the mechanisms that underlie the migration of these cells to wound sites are currently not known. We report herein that ex vivo cultured fibrocytes can differentiate from a CD14+-enriched mononuclear cell population and that this process requires contact with T cells. Furthermore, we demonstrate that TGF-beta1 (1-10 ng/ml), an important fibrogenic and growth-regulating cytokine involved in wound healing, increases the differentiation and functional activity of cultured fibrocytes. Because fibrocytes home to sites of tissue injury, we examined the role of chemokine/chemokine receptor interactions in fibrocyte trafficking. We show that secondary lymphoid chemokine, a ligand of the CCR7 chemokine receptor, acts as a potent stimulus for fibrocyte chemotaxis in vitro and for the homing of injected fibrocytes to sites of cutaneous tissue injury in vivo. Finally, we demonstrate that differentiated, cultured fibrocytes express alpha smooth muscle actin and contract collagen gels in vitro, two characteristic features of wound-healing myofibroblasts. These data provide important insight into the control of fibrocyte differentiation and trafficking during tissue repair and significantly expand their potential role during wound healing.
Design of the linkers which effectively separate domains of a bifunctional fusion protein (2001)

With the aim of separating the domains of a bifunctional fusion protein, the ability of several lengths of helix-forming peptides to separate two weakly interacting beta-can domains was compared with that of flexible linkers or of a three alpha-helices bundle domain. We introduced helix-forming peptide linkers A(EAAAK)nA (n = 2-5) between two green fluorescent protein variants, EBFP and EGFP, and investigated their spectral properties. The fluorescence resonance energy transfer from EBFP to EGFP decreased as the length of the linkers increased. The circular dichroism spectra analysis suggested that the linkers form an alpha-helix and the alpha-helical contents increased as the length of the linkers increased. The results clearly suggested the ability of the helical linkers to control the distance and reduce the interference between the domains. This 'linker engineering' may open a way to the rational design of linkers which maximize the multiple functions of fusion proteins or de novo multi-domain proteins.
Collecting back-reflected photons in photoacoustic microscopy (2010)

Since the photoacoustic effect relies only on the absorbed optical energy, the back-reflected photons from samples in optical-resolution photoacoustic microscopy are usually discarded. By employing a 2 x 2 single-mode fiber optical coupler in a laser-scanning optical-resolution photoacoustic microscope for delivering the illuminating laser light and collecting the back reflected photons, a fiber-optic confocal microscope is integrated with the photoacoustic microscope. Thus, simultaneous multimodal imaging can be achieved with a single light source and images from the two modalities are intrinsically registered. Such capabilities are demonstrated in imaging both phantoms and small animals in vivo.
Diced cartilage grafts to correct enophthalmos. (1980)

A technique is described using diced cartilage grafts to correct the volume deficit which is responsible for many of the unsatisfactory cosmetic features following enucleation.
Reflectance spectroscopy of pancreatic microcirculation (1996)

A technique employing diffuse reflectance spectroscopy (DRS) is described to assess and mirror dynamic changes of pancreatic tissue perfusion. An especially designed reflectance spectrophotometer was initially used to derive the quantitative relation between hemoglobin concentration ([Hb]) and reflectance measurements in vitro. Over a wide range of scattering related to the medium in which the measurements were made (scattering coefficient: 6.5-13 cm-1), a close, direct correlation existed with a slope of 0.376 +/- 0.012. In Sprague-Dawley rats under general anesthesia, the pancreas was isolated in situ and perfused with graded infusions of hemoglobin solutions. A correlation, comparable to the in vitro setting, was found between a [Hb] of 0 and 14 g/dl in the perfusate with slopes of 0.0037 and 0.0035. Changes in perfusion induced by adrenergic drugs produced changes in hemoglobin oxygen saturation and [Hb] that correspond with measured alterations of systemic arterial pressure and aortic blood flow. We conclude that diffuse reflectance spectroscopy reliably provides data on intrapancreatic hemoglobin oxygen saturation and [Hb] that can be a valuable tool for minimally invasive on-line evaluation of these aspects of pancreatic perfusion in the rat. This newly designed device is superior to previously used ones in that it analyzes the entire spectrum and therefore can account for changes in scattering that are very likely to occur with pathophysiological alterations such as edema formation.
Design of a Web-based distributed location-aware infrastructure for mobile devices (2010)

Since GPS receivers have become a commodity anyone could access and use location information simply and freely. Such an easy access to ones' location is instrumental to development of location-aware applications. However, existing applications are static in that they do not model relations between places and mobile things. Moreover, these applications do not allow to easily map the physical location of mobile devices to virtual resources on the Internet. We attempt to bridge this gap by extending the base concepts that make up the Internet with the physical location of devices, in order to facilitate the development of Web-based location-aware applications for embedded mobile devices. In this paper, we describe and evaluate a simple infrastructure for the ¿Web of Things¿ that extends the existing Web to enable location-aware applications. By introducing the concept ¿here/*¿, we enable a naturally hierarchic way to search for location-aware devices and the services they provide.
Interactions with Sinefungin. (2016)

&lt;p&gt;The SAM analog Sinefungin is tightly bound within the MTase domain via extensive hydrogen bonding (dashed lines) and hydrophobic contacts.&lt;/p&gt;
Bacterial morphine dehydrogenase further defines a distinct superfamily of oxidoreductases with diverse functional activities. (1994)

Pseudomonas putida morphine dehydrogenase is shown to be closely homologous to 18 proteins, defining a superfamily within which morphine dehydrogenase particularly resembles two bacterial, 2,5-dioxo-D-gluconic acid reductases, and two eukaryotic proteins of unknown functions. Relationships within the superfamily are extensive and complex. Residue identities between protein pairs range from 29-90%. Three subgroups are proposed. Nevertheless, on the basis of residue conservations/exchanges it is suggested that the nicotinamide coenzyme binding and substrate reduction occur in all the enzymes by broadly analogous mechanisms, among which some probable differences are identified.
Synthesis and immunological activity of 5,6,6a,8,9,11a-hexahydronaphth[1',2':4,5]imidazo[2,1-b]thiazoles and 5,6,6a,9,10,11a-hexahydronaphth[2',1':4,5]imidazo[2,1-b]thiazoles (1980)

A series of 5,6,6a,8,9,11a-hexahydroanaphth[1',2':4,5]imidazo[2,q-b]thiazoles (17 and 20) and 5,6,6a,9,10,11a-hexahydronaphth[2',1':4,5]imidazo[2,1-b]thiazoles has been synthesized with cis- and/or trans-1,2-diamino-1,2,3,4-tetrahydronaphthalenes as the key intermediates and subsequently evaluated for immunological activity (effects on antibody formation and delayed-type hypersensitivity reaction). Among the compounds tested trans-5,6,6a,8,9,11a-hexahydronaphth[1',2':4,5]imidazo[2,1-b]thiazole (trans-17a) and (+/-)-5,6,6a beta,8,9,11a alpha-hexahydro-8 beta-hydroxy-9 beta-methyl-8 alpha-phenylnaphth[1',2':4,5]imidazo[2,1-b]thiazole (20a) showed the largest immunological activity in mice with a magnitude comparable to that of levamisole and were found to be considerably less toxic than levamisole in acute toxicological study. The structures of 18a and 20a were determined by X-ray crystallography.
Mucosal immunogenicity of a recombinant Salmonella typhimurium-cloned heterologous antigen in the absence or presence of coexpressed cholera toxin A2 and B subunits (1997)

An avirulent Salmonella typhimurium vaccine strain expressing a streptococcal protein adhesin and a similar clone which produces the same streptococcal antigen linked to the cholera toxin (CT) A2 and B subunits (CTA2/B) were compared for the ability to induce antibody responses to the expressed heterologous antigen after oral or intranasal immunization of mice. Expression of cloned immunogens in these systems is temperature regulated, being optimal at 37 degrees C, and the two clones under comparison were shown to produce similar levels of the streptococcal antigen. Both clones were found to stimulate high levels of serum immunoglobulin G (IgG) and mucosal IgA antibodies to the cloned immunogen. A consistent trend was observed toward higher mucosal IgA but lower serum IgG responses in the case of the S. typhimurium vector that coexpressed CTA2/B, a potential mucosal adjuvant, regardless of the route of administration. Also noteworthy was the capacity of these antigen delivery systems to induce anamnestic systemic and secretory responses to the cloned immunogen 15 weeks after the primary immunization, despite preexisting immunity to the Salmonella vectors. These antibody responses were sustained for at least 7 months following the booster immunization, at which time the secretory IgA antibody levels were significantly higher in mice given the Salmonella clone that coexpressed CTA2/B. Although the serum IgG response against the Salmonella vector was characterized by a high IgG2a/IgG1 ratio (indicative of the T helper type 1 [Th1]/Th2 profile), a mixed IgG1 and IgG2a pattern was observed for the carried heterologous antigen, which displayed a dominant IgG1 response when administered as a purified immunogen. Our findings indicate that the recombinant streptococcal antigen and CTA2/B are strong immunogens when expressed by the antigen delivery system used in this study and suggest that CTA2/B may have an additional immunoenhancing activity in the mucosal compartment besides its ability to target antigen uptake into the mucosal inductive sites. CTA2/B may thus be useful as an S. typhimurium-cloned adjuvant for coexpressed protein antigens.
Identification of a human cDNA encoding a protein that is structurally and functionally related to the yeast adenylyl cyclase-associated CAP proteins. (1992)

The adenylyl cyclases of both Saccharomyces cerevisiae and Schizosaccharomyces pombe are associated with related proteins named CAP. In S. cerevisiae, CAP is required for cellular responses mediated by the RAS/cyclic AMP pathway. Both yeast CAPs appear to be bifunctional proteins: the N-terminal domains are required for the proper function of adenylyl cyclase, while loss of the C-terminal domains results in morphological and nutritional defects that appear to be unrelated to the cAMP pathways. Expression of either yeast CAP in the heterologous yeast suppresses phenotypes associated with loss of the C-terminal domain of the endogenous CAP but does not suppress loss of the N-terminal domain. On the basis of the homology between the two yeast CAP proteins, we have designed degenerate oligonucleotides that we used to detect, by the polymerase chain reaction method, a human cDNA fragment encoding a CAP-related peptide. Using the polymerase chain reaction fragment as a probe, we isolated a human cDNA clone encoding a 475-amino-acid protein that is homologous to the yeast CAP proteins. Expression of the human CAP protein in S. cerevisiae suppresses the phenotypes associated with loss of the C-terminal domain of CAP but does not suppress phenotypes associated with loss of the N-terminal domain. Thus, CAP proteins have been structurally and, to some extent, functionally conserved in evolution between yeasts and mammals.
Efficient transformation of human fibroblasts by adenovirus-simian virus 40 recombinants. (1984)

The origin-defective simian virus 40 (SV40) mutant 6-1 has been useful in transforming human cells (Small et al., Nature [London] 296:671-672, 1982; Nagata et al., Nature [London] 306:597-599, 1983). However, the low efficiency of transformation achieved by DNA transfection is a major drawback of the system. To increase the efficiency of SV40-induced transformation of human fibroblasts, we used recombinant adenovirus-SV40 virions which contain a complete SV40 early region including either a wild-type or defective (6-1) origin of replication. The SV40 DNA was cloned into the adenovirus vector in place of early region 1. Cell lines transformed by viruses containing a functional origin of replication produced free SV40 DNA. These cell lines were subcloned, and some of the subclones lost the ability to produce free viral DNA. Subclones that failed to produce free viral DNA were found to possess a mutated T antigen. Cell lines transformed by viruses containing origin-defective SV40 mutants did not produce any free DNA. Because of the high efficiency of transformation, we suggest that the origin-defective chimeric virus is a convenient system for establishing SV40-transformed cell lines from any human cell type that is susceptible to infection by adenovirus type 5.
Global rover localization by matching lidar and orbital 3D maps (2010)

Current rover localization techniques such as visual odometry have proven to be very effective on short to medium-length traverses (e.g., up to a few kilometres). This paper deals with the problem of long-range rover localization (e.g., 10km and up). An autonomous method to globally localize a rover is proposed by matching features detected from a 3D orbital elevation map and rover-based 3D lidar scans. The accuracy and efficiency of the algorithm is enhanced with visual odometry, and inclinometer/sun-sensor orientation measurements. The methodology was tested with real data, including 37 lidar scans of terrain from a Mars-Moon analogue site on Devon Island, Nunavut. When a scan contained a sufficient number of good topographic features, localization produced position errors of no more than 100m, and as low as a few metres in many cases. On a 10km traverse, the developed algorithm's localization estimates were shown to significantly outperform visual odometry estimates. It is believed that this architecture could be used to accurately and autonomously localize a rover on long-range traverses.
Lexical cohesion computed by thesaural relations as an indicator of the structure of text (1991)

In text, lexical cohesion is the result of chains of related words that contribute to the continuity of lexical meaning. These lexical chains are a direct result of units of text being the same thing, and finding text structure involves finding units of text that are about the same thing. Hence, computing the chains is useful, since they will have a correspondence to the structure of the text. Determining the structure of text is an essential step in determining the deep meaning of the text. In this paper, a thesaurus is used as the major knowledge base for computing lexical chains. Correspondences between lexical chains and structural elements are shown to exist. Since the lexical chains are computable, and exist in non-domain-specific text, they provide a valuable indicator of text structure. The lexical chains also provide a semantic context for interpreting words, concepts, and sentences.
Type II collagen defects in the chondrodysplasias. I. Spondyloepiphyseal dysplasias. (1989)

The spondyloepiphyseal dysplasias (SEDs) and spondyloepimetaphyseal dysplasias (SEMDs) are a heterogeneous group of skeletal dysplasias (dwarfing disorders) characterized by abnormal epiphyses, with and without varying degrees of metaphyseal irregularities, flattened vertebral bodies, and myopia. To better define the underlying cause of these disorders, we have analyzed the collagens from costal cartilage from several of these patients, using SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and high-performance liquid chromatography (HPLC) of intact chains and cyanogen bromide (CNBr) peptides and amino acid analysis. In almost all of the patients in this study group, the type II collagen exhibited a slower electrophoretic mobility when compared with that in normal controls. The mobility of many, but not all, of the CNBr peptides was also retarded. Peptides near the amino terminus were almost always altered, while the mobility of peptides close to the carboxyl terminus were normal in all but the severely affected cases. Analysis of the CNBr peptides on an HPLC sieving column confirmed that the electrophoretically abnormal peptides were of a higher molecular weight than were control peptides. Amino acid analysis indicated that the abnormal collagens have a higher ratio of hydroxylysine to lysine than does control collagen, suggesting that overmodification may be involved in the altered mobility. Our results are consistent with a defect in the collagen helix that results in overmodification of the molecule from that point toward the amino terminus. We propose that some forms of SED and SEMD are associated with abnormalities in type II collagen that results in delayed helix formation and consequent overmodification of the collagen. Cases of SED fit onto a continuous spectrum of clinical severity that correlates positively with both the extent of alteration and the proximity of the defect to the carboxyl terminus.
Problem Statement for SIP-signalled Peer-to-Peer Communication across Middleboxes (2006)

Middleboxes, particularly firewalls and network address translators,
are essential components of today's Internet infrastructure. They
are designed to support client-server applications well, but very
often they are obstacles for peer-to-peer communication. This memo
discusses middlebox traversal issues of SIP-based peer-to-peer
communication. Required communication steps are analyzed concerning
their potential constraints caused by middleboxes. The requirements
derived from this analysis are compared with the capabilites of
currently available middlebox traversal methods and SIP signaling
standards. The comparison identifies open issues that need to be
considered when designing standards for a SIP-based peer-to-peer
communication infrastructure.