gebhart/patrepeval huggingface dataset:
On the structure of polymeric IgM (1988)

The cysteine at position 575 of the immunoglobulin mu heavy chain is thought to provide the only disulfide bonds joining the monomer subunits of mouse polymeric IgM. The importance of this cysteine in the assembly of polymeric IgM was investigated by using site-directed mutagenesis to produce mu chains with serine at position 575. Thirty percent of the secreted mutant IgM was covalently assembled polymer implying that cysteines other than Cys575 can form inter-subunit disulfide bonds. The polymeric IgM lacked J chain, mediated complement-dependent cytolysis and appeared to have a higher molecular weight than conventional IgM pentamers, as judged by sucrose gradient sedimentation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis mobility. Electron microscopy revealed that the mutant IgM molecule contained six subunits. Wild-type IgM, while synthesized predominantly as a pentameric molecule, was assembled in at least two other forms, which were distinguished by their electrophoretic mobility. The apparently higher molecular weight forms of wild-type IgM include hexameric molecules which, like the hexameric mutant IgM, contained much less J chain that the pentameric form and were 20-fold more efficient at activating complement-dependent cytolysis.
Carbohydrate–Aromatic Interactions (2012)

The recognition of saccharides by proteins has far reaching implications in biology, technology, and drug design. Within the past two decades, researchers have directed considerable effort toward a detailed understanding of these processes. Early crystallographic studies revealed, not surprisingly, that hydrogen-bonding interactions are usually involved in carbohydrate recognition. But less expectedly, researchers observed that despite the highly hydrophilic character of most sugars, aromatic rings of the receptor often play an important role in carbohydrate recognition. With further research, scientists now accept that noncovalent interactions mediated by aromatic rings are pivotal to sugar binding. For example, aromatic residues often stack against the faces of sugar pyranose rings in complexes between proteins and carbohydrates. Such contacts typically involve two or three CH groups of the pyranoses and the π electron density of the aromatic ring (called CH/π bonds), and these interactions can exhibit a variety of geometries, with either parallel or nonparallel arrangements of the aromatic and sugar units. In this Account, we provide an overview of the structural and thermodynamic features of protein-carbohydrate interactions, theoretical and experimental efforts to understand stacking in these complexes, and the implications of this understanding for chemical biology. The interaction energy between different aromatic rings and simple monosaccharides based on quantum mechanical calculations in the gas phase ranges from 3 to 6 kcal/mol range. Experimental values measured in water are somewhat smaller, approximately 1.5 kcal/mol for each interaction between a monosaccharide and an aromatic ring. This difference illustrates the dependence of these intermolecular interactions on their context and shows that this stacking can be modulated by entropic and solvent effects. Despite their relatively modest influence on the stability of carbohydrate/protein complexes, the aromatic platforms play a major role in determining the specificity of the molecular recognition process. The recognition of carbohydrate/aromatic interactions has prompted further analysis of the properties that influence them. Using a variety of experimental and theoretical methods, researchers have worked to quantify carbohydrate/aromatic stacking and identify the features that stabilize these complexes. Researchers have used site-directed mutagenesis, organic synthesis, or both to incorporate modifications in the receptor or ligand and then quantitatively analyzed the structural and thermodynamic features of these interactions. Researchers have also synthesized and characterized artificial receptors and simple model systems, employing a reductionistic chemistry-based strategy. Finally, using quantum mechanics calculations, researchers have examined the magnitude of each property's contribution to the interaction energy.
Locomotion of a legged capsule in the gastrointestinal tract: theoretical study and preliminary technological results (2005)

This work illustrates the analysis of locomotion in the gastrointestinal tract obtainable by a legged capsule for diagnostic and therapeutic purposes. A preliminary simulation of the legged locomotion onto slippery and deformable substrates has been performed and -simultaneously- mechanisms for on board actuation of the legs have been developed and tested. Moreover, an engineering translation of medical needs in endoscopy is presented, with some ad hoc solutions for improving diagnostic capabilities.
RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1 (1995)

The selective encapsidation of retroviral RNA requires sequences in the Gag protein, as well as a cis-acting RNA packaging signal (psi site) near the 5' end of the genomic transcript. Gag protein of human immunodeficiency virus type 1 (HIV-1) has recently been found to bind specifically to the HIV-1 psi element in vitro. Here we report studies aimed at mapping features within the genetically defined psi locus that are required for binding of HIV-1 Gag or of its processed nucleocapsid derivative. The full-length HIV-1 Gag (p55) and nucleocapsid (p15) sequences were expressed as glutathione S-transferase (GST) fusion proteins in Escherichia coli. In a gel shift assay containing excess competitor tRNA, affinity-purified GST-p15 and GST-p55 proteins bound to a 206-nucleotide psi RNA element spanning the major splice donor and gag start codons but did not bind to antisense psi transcripts. Quantitative filter-binding assays revealed that both GST-p55 and GST-p15 bound to this RNA sequence with identical affinities (apparent Kd congruent to 5 x 10(-8) M), indicating that all major determinants of psi binding affinity reside within the nucleocapsid portion of Gag. Chemical and RNase accessibility mapping, coupled with computerized sequence analysis, suggested a model for psi RNA structure comprising four independent stem-loops. Filter-binding studies revealed that RNAs corresponding to three of these hypothetical stem-loops can each function as a independent Gag binding site and that each is bound with approximately fourfold-lower apparent affinity than the full-length psi locus. Interaction of Gag with these regions is likely to play a major role in directing HIV-1 RNA encapsidation in vivo.
Insulin-Like Growth Factor-I (IGF-I) and IGF Binding Protein-3 as Predictors of Advanced-Stage Prostate Cancer (2002)

Circulating levels of IGF-I and IGFBP-3 may predict the risk of developing advanced-stage prostate cancer, but their utility for screening patients with incident prostate cancer may be limited.
Peanut Allergy, Allergen Composition, and Methods of Reducing Allergenicity: A Review (2013)

Peanut allergy affects 1-2% of the world's population. It is dangerous, and usually lifelong, and it greatly decreases the life quality of peanut-allergic individuals and their families. In a word, peanut allergy has become a major health concern worldwide. Thirteen peanut allergens are identified, and they are briefly introduced in this paper. Although there is no feasible solution to peanut allergy at present, many methods have shown great promise. This paper reviews methods of reducing peanut allergenicity, including physical methods (heat and pressure, PUV), chemical methods (tannic acid and magnetic beads), and biological methods (conventional breeding, irradiation breeding, genetic engineering, enzymatic treatment, and fermentation).
Analysis of mode structure in hollow dielectric waveguide fibers (2003)

In this paper, we analyze the electromagnetic mode structure of an OmniGuide fiber-a hollow dielectric waveguide in which light is confined by a large index-contrast omnidirectional dielectric mirror. In particular, we find that the modes in an OmniGuide fiber are similar to those in a hollow metallic waveguide in their symmetries, cutoff frequencies, and dispersion relations. We show that the differences can be predicted by a model based on a single parameter-the phase shift upon reflection from the dielectric mirror. The analogy to the metal waveguide extends to the transmission properties, resulting in the identification of the TE01 mode as the lowest-loss mode of the OmniGuide fiber.
Apoptotic photoreceptor degeneration in experimental retinal detachment. (1995)

Results are consistent with the hypothesis that photoreceptor degeneration after retinal detachment occurs through apoptosis, usually associated with intrinsic, programmed cell death mechanisms. The detection of a rapid wave of photoreceptor degeneration seems to suggest that early therapeutic interventions might be recommended; agents capable of interfering with the apoptotic mechanism could have a role in the prevention of cell losses that represent a critical complication of retinal detachment.
Light-scattering models for spheres on a conducting plane: comparison with experiment (1987)

Three models have been developed to describe light scattering from a sphere in contact with a mirror. With two of the models the mirror was replaced with an image sphere. Light scattering from each sphere is assumed to follow the Mie theory: no further interaction between the sphere and mirror is assumed. The models differ in their consideration of the interaction of scattered fields from the spheres. The results of the models are compared to experimental values obtained for polystyrene spheres, 0.984 microm in diameter, with incident radiation lambda= 0.6328 and 0.4416 microm. The comparison indicates that a best fit can be obtained by assuming that the real sphere and its image sphere are coherent light sources with a phase difference of pi.
Heparin as an Inducer of Hepatocyte Growth Factor1 (1993)

Hepatocyte growth factor (HGF) has mitogenic and unique morphoregulatory functions, and is considered to act as a hepatotrophic and a renotrophic factor for regeneration of the liver and kidney subjected to various insults. We have now obtained evidence that heparin is a potent inducer of HGF production. The addition of heparin to a culture of MRC-5 human embryonic lung fibroblasts increased the HGF concentration in the conditioned medium, in a dose-dependent manner. The maximal stimulation was obtained at 1 microgram/ml heparin and stimulation was 4-fold compared to control cultures. The rate of HGF synthesis in MRC-5 cells, as measured by pulse-labeling with [35S]methionine, and subsequent immunoprecipitation of HGF from both conditioned medium and a cell lysate, was 3-4-fold stimulated by 1 microgram/ml heparin, whereas heparin apparently had no significant effect on the HGF mRNA level. The stimulatory effect of heparin on HGF production was evident in various types of cells, such as MRC-9, IMR-90, and WI-38 human embryonic lung fibroblasts, human skin fibroblasts, HL-60 human promyelocytic leukemic cells and human umbilical vein endothelial cells. In addition to heparin, heparan sulfate also stimulated HGF production, albeit to a lesser extent than heparin; 1.7-fold stimulation with 2 micrograms/ml heparan sulfate. However, other glycosaminoglycans, such as hyaluronic acid, chondroitin sulfate, dermatan sulfate, keratan sulfate, and keratan polysulfate, had no stimulatory effect on HGF production.(ABSTRACT TRUNCATED AT 250 WORDS)
The horse as a model of naturally occurring osteoarthritis (2012)

Osteoarthritis (OA) is an important cause of pain, disability and economic loss in humans, and is similarly important in the horse. Recent knowledge on post-traumatic OA has suggested opportunities for early intervention, but it is difficult to identify the appropriate time of these interventions. The horse provides two useful mechanisms to answer these questions: 1) extensive experience with clinical OA in horses; and 2) use of a consistently predictable model of OA that can help study early pathobiological events, define targets for therapeutic intervention and then test these putative therapies. This paper summarises the syndromes of clinical OA in horses including pathogenesis, diagnosis and treatment, and details controlled studies of various treatment options using an equine model of clinical OA.
Persistent Sodium Current in Mammalian Central Neurons (1996)

Neurons from the mammalian CNS have a noninactivating component of the tetrodotoxin-sensitive sodium current (INaP). Although its magnitude is < 1% of the transient sodium current, INaP has functional significance because it is activated about 10 mV negative to the transient sodium current, where few voltage-gated channels are activated and neuron input resistance is high. INaP adds to synaptic current, and evidence indicates that it is present in dendrites where relatively small depolarizations will activate INaP, thereby increasing effectiveness of distal depolarizing synaptic activity. The mechanism for INaP is not known. Research in striated muscle and neurons suggests a modal change in gating of conventional sodium channels, but it is also possible that INaP flows through a distinct subtype of noninactivating sodium channels. Modulation of INaP could have a significant effect on the transduction of synaptic currents by neurons.
Design of a flexible coprocessor unit (1999)

Todays FPGA technology allows reconfigurable hardware to be integrated into standard PC hardware. A hardware like this allows for on-the-fly reconfigurable hardware. It is possible to remove and insert complete subsystems just by reinitializing the configurable components. These systems make new demands on software that often can't be fulfilled by the classical device driver concept used in todays operating systems. This paper presents a flexible and on-the-fly reconfigurable hardware subsystem for interworking systems. Furthermore, a software integration for fast and efficient reconfiguration of the hardware is introduced. It provides a flexible integration into a Unix environment.
Contemporary Management of Overactive Bladder (2012)

Overactive bladder is a prevalent condition with bothersome symptoms that greatly impact health-related quality of life. Despite a multitude of treatment options, many patients go untreated or undertreated. This article addresses the contemporary management of overactive bladder, including behavioral and lifestyle modifications, pelvic floor muscle therapy, biofeedback, drug therapy, neuromodulation, and botulinum toxin. We highlight the new drugs and therapies that have been brought into clinical use over the past few years, and discuss important clinical implications of therapy as well as promising new agents that are currently in advanced stages of development.
Safety And Immunogenicity Of A Polyvalent Escherichia Coli Vaccine In Human Volunteers (1994)

Since a limited number of O serogroups account for nearly 70% of bacteremic and meningitic Escherichia coli isolates, a polyvalent vaccine was made by conjugating a Pseudomonas aeruginosa exotoxin A carrier protein to the O polysaccharide of 12 serogroups of E. coli (O1, O2, O4, O6-O8, O12, O15, O16, O18, O25, O75). No serious reactions occurred in 88 vaccinees. Four-fold or greater increases in ELISA antibody levels over baseline were greatest (> 60% of vaccinees) for O1, O2, O6-O8 and O15; intermediate (approximately 50%) for O18 and O75, and poorest (> or = 45%) for O4, O12, O16, and O25. Responses with functionally active opsonophagocytic antibody generally paralleled ELISA antibody responses. With the availability of a safe, immunogenic E. coli vaccine, active and passive immunization strategies merit further development as adjunctive treatment for E. coli bacteremia and neonatal meningitis.
Preservation of hypothalamic dopaminergic neurons in Parkinson's disease (1985)

The integrity of the hypothalamic neuroendocrine dopaminergic neurons in Parkinson's disease was assessed by comparing the numbers and distribution of melanin-pigmented neurons in the arcuate and periventricular nuclei in 7 parkinsonian and 5 normal brains. No significant differences were observed. In contrast to theories suggesting that Parkinson's disease involves a universal degeneration of central catecholaminergic neurons, the hypothalamic neuroendocrine dopaminergic neurons do not appear to be involved by the disease.
Response to B-cell–depleting therapy with rituximab reverts the abnormalities of T-cell subsets in patients with idiopathic thrombocytopenic purpura (2007)

Rituximab, an anti-CD20 monoclonal antibody, has been used to treat autoimmune disorders such as idiopathic thrombocytopenic purpura (ITP). However, its mechanisms of action as well as the effects on cellular immunity remain poorly defined. We investigated the changes of different peripheral blood T-cell subsets, the apoptosis profile, as well as the changes of T-cell receptor (TCR) beta-variable (VB) region gene usage of CD4+ and CD8+ T-cell subpopulations following rituximab therapy. The study involved 30 patients with chronic ITP who received rituximab, of whom 14 achieved a durable (> 6 months) response. Compared with the control group, pretreatment abnormalities of T cells in ITP patients included an increase of the Th1/Th2 ratio and of the Tc1/Tc2 ratios (P < .001), increased expression of Fas ligand on Th1 and Th2 cells (P < .001), increased expression of Bcl-2 mRNA (P = .003) and decreased expression of bax mRNA (P = .025) in Th cells, and expansion of oligoclonal T cells with no preferential use of any TCR VB subfamily. These abnormalities were reverted in responders at 3 and 6 months after treatment, whereas they remained unchanged in nonresponders. Our findings indicate that in patients with ITP, response to B-cell depletion induced by rituximab is associated with significant changes of the T-cell compartment.
Autoantibodies against Erythropoietin in a Patient with Pure Red-Cell Aplasia (1996)

Autoimmunity is often implicated in pure red-cell aplasia. Approximately 10 to 15 percent of patients with pure red-cell aplasia have thymomas,1 and remission of the anemia occurs in 25 to 30 percent of these patients after the thymoma is removed.2 In other patients there are immunologic abnormalities, such as hypogammaglobulinemia,3 monoclonal immunoglobulins,4 antithyroid antibodies,5 antinuclear antibodies,6,7 and autoimmune hemolytic anemia.3,8 Immunosuppressive therapy is successful in many patients,2,9–12 and a good response to plasmapheresis has been reported in two patients.13,14 In 1967 Krantz and Kao reported that plasma from a patient with pure red-cell aplasia inhibited . . .
Liver transplantation for familial amyloidotic polyneuropathy: Impact on Swedish patients' survival (2009)

Liver transplantation (LTx) for familial amyloidotic polyneuropathy (FAP) is an accepted treatment for this fatal disease. However, the long-term outcome with respect to that of nontransplanted patients has not been fully elucidated. The aim of this study was to compare the long-term survival of Swedish LTx FAP patients with that of historical controls, especially with respect to the age at onset of the disease and gender. In order to evaluate the outcome of LTx as a treatment for FAP, survival was calculated from the onset of disease. One hundred forty-one FAP patients, 108 transplanted and 33 not transplanted, were included in the study. Significantly increased survival was noted for LTx patients in comparison with controls. The outcome was especially favorable for those with an early onset of the disease (age at onset < 50 years) in comparison with early-onset controls (P < 0.001). In contrast, no significant difference for late-onset cases (> or = 50 years) was found. Transplanted late-onset females had significantly improved survival in comparison with transplanted late-onset males (P = 0.02). We were unable to find significant differences in survival between patients with long (> or = 7 years) or short (<7 years) disease duration at transplantation. The survival of male patients with late-onset disease appeared not to improve with LTx. LTx is an efficacious treatment for improving the survival of early-onset FAP patients. Further studies are needed to analyze the cause of the poorer outcome for late-onset male patients.
Findings on the suitability of 802.11 for highly mobile broadband networks (2009)

As the world becomes increasingly dependent on dynamic and up-to-the-moment information, we recognize that broadband networks must be able to convey this information timely and wirelessly, to and from users in motion. Varieties of 802.11 compliant equipment and other types of broadband wireless equipment have been proposed for, and in some areas, being used to meet this need. There have been questions about the suitability of 802.11-based equipment for broadband networks that have to operate at vehicular speeds. Prior literature in the field has illustrated some of the problems, but is generally short on specific results from testing. At our facility, we have a wireless networking testbed that includes 802.11-based equipment, as well as equipment supporting other protocols. We conducted mobile connectivity and throughput experiments at different rates of speed to examine how 802.11-based equipment performs in the mobile broadband wireless network role. We also conducted the same experiments using Motorola's Mesh-Enabled Architecture. This paper presents those results. After summarizing the previous work by others in this area, we describe the layout of the wireless testbed, the structure of the experiments and how the experiments were conducted. Next, we present and analyze the results of the experiments, and finally offer our conclusions.
Review and meta‐analysis of the epidemiology of congenital cytomegalovirus (CMV) infection (2007)

We reviewed studies that reported results of systematic cytomegalovirus (CMV) screening on fetuses and/or live-born infants. The overall birth prevalence of congenital CMV infection was 0.64%, but varied considerably among different study populations. About 11% of live-born infants with congenital CMV infection were symptomatic, but the inter-study differences in definitions of symptomatic cases limit the interpretation of these data. Non-white race, low socioeconomic status (SES), premature birth, and neonatal intensive care unit admittance were risk factors for congenital CMV infection. Birth prevalence increased with maternal CMV seroprevalence. Maternal seroprevalence accounted for 29% of the variance in birth prevalence between study populations. Maternal seroprevalence and birth prevalence were both higher in study populations that were ascertained at birth rather than in the prenatal period. Thus, timing of ascertainment should be considered when interpreting birth prevalence estimates. Birth prevalence was inversely correlated with mean maternal age, but this relationship was not significant when controlling for maternal seroprevalence. The rate of transmission to infants born to mothers who had a primary infection or a recurrent infection during pregnancy was 32% and 1.4%, respectively. Possible maternal primary infections (i.e. seropositive mother with CMV IgM) resulted in congenital infections about 20% of the time, but are likely to represent a mixture of primary and recurrent infections. In summary, CMV is a common congenital infection worldwide that can lead to permanent disabilities. There is an urgent need for interventions that can reduce the substantial burden of this often overlooked disease.