gebhart/patrepeval huggingface dataset:
A radiosity method for non-diffuse environments (1986)

A general radiosity method accounting for all interreflections of light between diffuse and nondiffuse surfaces in complex environments is introduced. As contrasted with previous radiosity methods, surfaces are no longer required to be perfectly diffuse reflectors and emitters. A complete, viewer independent description of the light leaving each surface in each direction is computed, allowing dynamic sequences of images to be rendered with little additional computation per image. Phenomena such as "reflection tracking", reflections following a moving observer across a specular surface are produced. Secondary light sources, such as the light from a spotlight reflecting off a mirror onto a wall are also accounted for.
ADDME – Avoiding Drug Development Mistakes Early: central nervous system drug discovery perspective (2009)

The advent of early absorption, distribution, metabolism, excretion, and toxicity (ADMET) screening has increased the attrition rate of weak drug candidates early in the drug-discovery process, and decreased the proportion of compounds failing in clinical trials for ADMET reasons. This paper reviews the history of ADMET screening and its place in pharmaceutical development, and central nervous system drug discovery in particular. Assays that have been developed in response to specific needs and improvements in technology that result in higher throughput and greater accuracy of prediction of human mechanisms of absorption and toxicity are discussed. The paper concludes with the authors' forecast of new models that will better predict human efficacy and toxicity.
Antigenic and genetic diversity among swine influenza A H1N1 and H1N2 viruses in Europe (2002)

Three subtypes of influenza A viruses, H1N1, H1N2 and H3N2, co-evolve in pigs in Europe. H1N2 viruses isolated from pigs in France and Italy since 1997 were closely related to the H1N2 viruses which emerged in the UK in 1994. In particular, the close relationship of the neuraminidases (NAs) of these viruses to the NA of a previous UK H3N2 swine virus indicated that they had not acquired the NA from H3N2 swine viruses circulating in continental Europe. Moreover, antigenic and genetic heterogeneity among the H1N2 viruses appeared to be due in part to multiple introductions of viruses from the UK. On the other hand, comparisons of internal gene sequences indicated genetic exchange between the H1N2 viruses and co-circulating H1N1 and/or H3N2 subtypes. Most genes of the earlier (1997-1998) H1N2 isolates were more closely related to those of a contemporary French H1N1 isolate, whereas the genes of later (1999-2000) isolates, including the HAs of some H1N2 viruses, were closely related to those of a distinct H1N1 antigenic variant which emerged in France in 1999. In contrast, an H3N2 virus isolated in France in 1999 was closely related antigenically and genetically to contemporary human A/Sydney/5/97-like viruses. These studies reveal interesting parallels between genetic and antigenic drift of H1N1 viruses in pig and human populations, and provide further examples of the contribution of genetic reassortment to the antigenic and genetic diversity of swine influenza viruses and the importance of the complement of internal genes in the evolution of epizootic strains.
Human 5-hydroxytryptamine(5A) receptors activate coexpressed G(i) and G(o) proteins in Spodoptera frugiperda 9 cells. (2000)

The ability of the human 5-hydroxytryptamine serotonin type 5A (h5-ht(5A)) receptor to couple to G proteins from distinct families was investigated through the simultaneous infection of Spodoptera frugiperda 9 insect cells with recombinant baculoviruses encoding the various proteins. Expression of G proteins was demonstrated in immunoblots. Receptor-G protein coupling was monitored by high-affinity agonist binding and agonist-induced stimulation of [(35)S]guanosine-5'-O-(3-thio) triphosphate binding to membranes. Receptors expressed alone displayed low-affinity agonist binding, and endogenous G proteins were only poorly stimulated on the addition of 5-hydroxytryptamine. When receptors were coexpressed with mammalian G(i)/G(o) proteins (Galpha(i) or Galpha(o) plus Gbeta(1)gamma(2)), the coupled phenotype was achieved: agonists bound with high affinity in a guanosine-5'-(beta, gamma-imido)triphosphate-sensitive manner and stimulated [(35)S]guanosine-5'-O-(3-thio)triphosphate binding to high levels. These effects were not observed on coexpression with G(z)/G(s)/G(q/11/16) or G(12/13). Various ligands were evaluated for their agonistic, antagonistic, or inverse agonistic behavior in both receptor binding and activation assays. Although G(o) displayed different receptor coupling characteristics than G(i) proteins, no clear coupling preference was evident. Coexpression of receptors and Galpha(i) subunits without Gbeta(1)gamma(2) produced increases in both agonist affinity and maximum G protein activation that were smaller than those in the presence of Gbeta(1)gamma(2), suggesting that Gbeta(1)gamma(2) coexpression improves receptor-G protein coupling. Similarly, coexpression of receptors with Gbeta(1)gamma(2) alone resulted in an improved interaction with endogenous G proteins. Our results demonstrate that h5-ht(5A) receptors expressed in Spodoptera frugiperda 9 cells selectively and functionally couple to coexpressed mammalian G(i) and G(o) proteins.
CRISPR‐Based Technologies and the Future of Food Science (2015)

The on-going CRISPR craze is focused on the use of Cas9-based technologies for genome editing applications in eukaryotes, with high potential for translational medicine and next-generation gene therapy. Nevertheless, CRISPR-Cas systems actually provide adaptive immunity in bacteria, and have much promise for various applications in food bacteria that include high-resolution typing of pathogens, vaccination of starter cultures against phages, and the genesis of programmable and specific antibiotics that can selectively modulate bacterial population composition. Indeed, the molecular machinery from these DNA-encoded, RNA-mediated, DNA-targeting systems can be harnessed in native hosts, or repurposed in engineered systems for a plethora of applications that can be implemented in all organisms relevant to the food chain, including agricultural crops trait-enhancement, livestock breeding, and fermentation-based manufacturing, and for the genesis of next-generation food products with enhanced quality and health-promoting functionalities. CRISPR-based applications are now poised to revolutionize many fields within food science, from farm to fork. In this review, we describe CRISPR-Cas systems and highlight their potential for the development of enhanced foods.
Co-Evolution of Bargaining Strategies in a Decentralized Multi-Agent System (2001)

Software agents will personalize smart devices to act autonomously on behalf of their human owner. In dynamical electronic commerce environments, these agents could buy and sell goods and services from each other, without using a central market maker. From a system perspective, this creates a decentralized and continuously changing multi-agent system with the need for coordination of supply and demand. In this article we show how such a multi-agent system may be decentrally coordinated while software agents bargain with each other under the constraints of incomplete information, non-equilibrium and time pressure. The agents adapt to a changing environment with an evolutionary learning mechanism. It can be shown that the multi-agent system as a whole shows emergent coordination in absence of a centralized coordination institution.
Tau Aggregation and Toxicity in Tauopathic Neurodegenerative Diseases (2008)

Since its discovery as a structural component of neurofibrillary lesions of Alzheimer's disease more than twenty years ago, tau protein has been implicated in the cascade of events associated with neurodegeneration. Specifically, the "tau hypothesis" posits that misfunction of tau, which occurs in response to unknown stimuli, results in its intracellular assembly into filaments that eventually prove toxic to the cells that produce them. The tau hypothesis is supported by numerous neuropathological and genetic observations of authentic human disease cases. However, experiments designed to study aggregate toxicity in biological models suggest that some aggregate species may be inert or could potentially serve a neuroprotective function. Distinguishing these possibilities experimentally has been complicated by currently available biological models, which do not fully recapitulate aggregation conditions seen in disease. Additional model systems which better approximate physiological conditions may help elucidate the molecular mechanisms involved in aggregation associated toxicity. Here we examine the accumulated evidence linking aggregation and neurodegeneration, and experimental approaches to the problem of tau aggregation-mediated toxicity.
Retinal vein occlusion and macular edema &ndash; critical evaluation of the clinical value of ranibizumab (2011)

Abstract: Retinal vein occlusions (RVOs) constitute the second most common cause of retinal vascular disease after diabetic retinopathy, with a prevalence of between 1% and 2% in persons older than 40 years of age. Despite the existence of numerous potential therapeutic options, none is entirely satisfactory, and many patients with RVO suffer irreversible visual loss. Fortunately however, the recent introduction of antivascular endothelial growth factor (VEGF) agents, such as ranibizumab (Lucentis ® , Genentech, South San Francisco, CA) and bevacizumab (Avastin ® , Genentech), offers a potentially new treatment approach for clinicians managing this disorder. The results of the BRAVO and CRUISE trials have provided the first definitive evidence for the efficacy and safety of ranibizumab in the treatment of RVO. As a result, ranibizumab has recently been approved by the US Food and Drug Administration for the treatment of RVO-associated macular edema. In this review, we provide a critical evaluation of clinical trial data for the safety and efficacy of ranibizumab, and address unresolved issues in the management of this disorder. Keywords: ranibizumab, retinal vein occlusion, vascular endothelial growth factor, macular edema
An NMR Comparison of the Whole Lignin from Milled Wood, MWL, and REL Dissolved by the DMSO/NMI Procedure (2007)

Abstract Lignins isolated from pine milled wood, milled wood lignin (MWL), and residual enzyme lignin (REL) were compared using modified thioacidolysis, modified DFRC, gel permeation chromatography (GPC), two‐dimensional Heteronuclear Multiple Quantum Coherence (HMQC) NMR, and quantitative 13C NMR. Dissolution of the lignin for solution‐state NMR was accomplished by utilizing the recently reported DMSO/N‐methylimidazole/acetic anhydride solvent system. Contrary to previous reports, comparison of the lignin preparations by thioacidolysis indicated that REL was more structurally similar to the lignin in the milled wood and Wiley wood meal than MWL. Total monomer yields indicated that the MWL was lower in β‐aryl ether content than the other preparations, and this was verified by quantitative 13C NMR. NMR analysis indicated that the inter‐unit linkages present in all the lignin preparations are consistent with the present knowledge about lignin biosynthesis. The contribution of minor end group structures in the MWL are further decreased in the milled wood, indicating that they are preferentially isolated as low molecular weight material, possibly generated during the milling process. All other structural moieties were similar in all preparations. GPC data indicated that the milled wood and REL both contain a portion of lignin with a molecular weight of 55,000 g/mol. Data indicate that the inefficiency of the DFRC method may be related to molecular mobility or accessibility in higher molecular weight portions of the lignin polymer.
Induction of hepatocyte growth factor in fibroblasts by tumor-derived factors affects invasive growth of tumor cells: in vitro analysis of tumor-stromal interactions. (1997)

Invasive and metastatic potentials of several types of carcinoma cells are regulated through interactions with host stromal cells, e.g., tumor-stromal interactions. Because hepatocyte growth factor (HGF), a ligand for the c-Met proto-oncogene product, is a mesenchymal- or stromal-derived factor that induces mitogenic, motogenic, and morphogenic responses, we examined the mechanisms involved in tumor-stromal interactions in vitro. The c-Met/HGF receptor was expressed in A431 human epidermoid carcinoma cells, A549 human non-small cell lung cancer cells, HuCC-T1 human cholangiocellular carcinoma cells, and SBC-3 human small cell lung carcinoma cells. HGF stimulated cell growth, scattering, and invasion of these cells. Although these cells did not produce biologically significant levels of HGF, these cells did secrete soluble factors that potently stimulated HGF production in human skin fibroblasts. These carcinoma cell-derived HGF inducers proved to be interleukin-1 (IL-1) in A431 cells, IL-1 plus basic fibroblast growth factor (bFGF) in A549 and HuCC-T1 cells, and bFGF plus platelet-derived growth factor in SBC-3 cells. When these carcinoma cells were cocultured with fibroblasts, HGF levels in the coculture system were much higher than the levels in fibroblasts alone, without cocultured carcinoma cells. Together with the increase in HGF levels, the number of invasive cells increased, but in vitro invasion of carcinoma cells in the coculture system was strongly inhibited by anti-HGF antibodies. Thus, there are mutual interactions between carcinoma cells and fibroblasts: IL-1, bFGF, and platelet-derived growth factor derived from tumor cells play a role in inducing HGF expression in stromal fibroblasts, whereas fibroblast-derived HGF, in turn, leads to invasive growth in carcinoma cells. The mutual interactions, as mediated by HGF and HGF inducers, may play a significant role in the occurrence of invasion and metastasis of carcinoma cells.
Screening for single nucleotide variants, small indels and exon deletions with a next‐generation sequencing based gene panel approach for U sher syndrome (2014)

Usher syndrome is an autosomal recessive disorder characterized both by deafness and blindness. For the three clinical subtypes of Usher syndrome causal mutations in altogether 12 genes and a modifier gene have been identified. Due to the genetic heterogeneity of Usher syndrome, the molecular analysis is predestined for a comprehensive and parallelized analysis of all known genes by next-generation sequencing (NGS) approaches. We describe here the targeted enrichment and deep sequencing for exons of Usher genes and compare the costs and workload of this approach compared to Sanger sequencing. We also present a bioinformatics analysis pipeline that allows us to detect single-nucleotide variants, short insertions and deletions, as well as copy number variations of one or more exons on the same sequence data. Additionally, we present a flexible in silico gene panel for the analysis of sequence variants, in which newly identified genes can easily be included. We applied this approach to a cohort of 44 Usher patients and detected biallelic pathogenic mutations in 35 individuals and monoallelic mutations in eight individuals of our cohort. Thirty-nine of the sequence variants, including two heterozygous deletions comprising several exons of USH2A, have not been reported so far. Our NGS-based approach allowed us to assess single-nucleotide variants, small indels, and whole exon deletions in a single test. The described diagnostic approach is fast and cost-effective with a high molecular diagnostic yield.
Vitamin B6 in Clinical Neurology (1990)

Many conditions in clinical neurology may be responsive to pyridoxine as a therapeutic agent. The current difficulty is in trying to isolate the conditions that are most likely to respond. Treating seizures is a major part of a neurologic practice. Our current therapeutic agents are only partially successful and limited by multiple side effects. One problem is that patients often have to take these agents for an entire lifetime, further raising the risk of toxicity. If pyridoxine supplementation can improve the efficacy of currently used medications, it will be gladly accepted into our therapeutic arsenal. Headache, chronic pain, and depression all appear to run together in many of our patients. The observations that serotonin deficiency is a common thread between them and that pyridoxine can raise serotonin levels open a wide range of therapeutic options. Small studies have been carried out with mixed success. Comparison with amitriptyline in the treatment of headache appears to show about equal efficacy, although side effects would be expected to be more of a problem with the amitriptyline. Behavioral disorders are relatively common and continue to be a major problem, disrupting the lives of the patients and their families. Current treatments are not acceptable to most people because of the risk of side effects with long-term usage. If, as Dr. Feingold suggests, many of these problems are caused by "toxic" exposures to chemicals that are pyridoxine antagonists, supplementation at early ages may reduce the incidence of hyperactivity and aggressive behavior. This raises the question of safety. Is pyridoxine safe for long-term use in large segments of the population, including children? The studies on children with Down's syndrome and autism, utilizing much higher doses than are used for other therapeutic purposes, seem to indicate relative safety if carefully monitored. Studies involving large population groups with carpal tunnel syndrome, all adults, using 100-150 mg/day have shown minimal or no toxicity in five- to 10-year studies. Women self-medicating for PMS taking 500 to 5000 mg/day have shown peripheral neuropathy within one to three years. It would appear from this retrospective analysis that pyridoxine is safe at doses of 100 mg/day or less in adults. In children there is not enough data to make any sort of suggestion. Because the major neurologic complication is a peripheral neuropathy and the causes of this condition are myriad, pyridoxine may cause neuropathy only in patients with a pre-existing susceptibility to this condition.
A Randomized Study of the Relative Pharmacokinetics, Pharmacodynamics, and Safety of Alirocumab, a Fully Human Monoclonal Antibody to PCSK9, After Single Subcutaneous Administration at Three Different Injection Sites in Healthy Subjects (2014)

These results suggest that alirocumab can be interchangeably injected in the abdomen, upper arm, or thigh.
Coagulin, a bacteriocin-like inhibitory substance produced by Bacillus coagulans I4 (1998)

A protease-sensitive antibacterial substance produced by Bacillus coagulans I4 strain, isolated from cattle faeces, was classified as a bacteriocin-like inhibitory substance and named coagulin. The inhibitory spectrum included B. coagulans and unrelated bacteria such as Enterococcus, Leuconostoc, Oenococcus, Listeria and Pediococcus. Coagulin was stable at 60 degrees C for 90 min, at a pH ranging from 4 to 8 and appeared to be unaffected by alpha-amylase, lipase or organic solvents (10% v/v). Coagulin exhibited a bactericidal and a bacteriolytic mode of action against indicator cells. The apparent molecular mass was estimated to be about 3-4 kDa by SDS-PAGE. The B. coagulans I4 strain harbours a plasmid, pI4, approximately 14 kb in size. Novobiocin curing experiments yielded two derivatives that no longer produced the bacteriocin-like inhibitory substance. Plasmid content of these two derivatives showed that one had lost pI4, whereas the second harboured a deleted form of this plasmid, thus suggesting a plasmid location for the genes for coagulin production.
CD134L Engagement Enhances Human B Cell Ig Production: CD154/CD40, CD70/CD27, and CD134/CD134L Interactions Coordinately Regulate T Cell-Dependent B Cell Responses (2000)

CD134 is a member of the TNFR family expressed on activated T cells, whose ligand, CD134L, is found preferentially on activated B cells. We have previously reported that the CD70/CD27 interaction may be more important in the induction of plasma cell differentiation after the expansion phase induced by the CD154/CD40 interaction has occurred. When CD134-transfected cells were added to PBMCs stimulated with pokeweed mitogen, IgG production was enhanced in a dose-dependent fashion. Addition of CD134-transfected cells to B cells stimulated with Staphylococcus aureus Cowan I strain/IL-2 resulted in little if any enhancement of B cell IgG production and proliferation. We found that while CD134-transfected cells induced no IgG production by themselves, it greatly enhanced IgG production in the presence of CD40 stimulation or T cell cytokines such as IL-4 and IL-10. The addition of CD134-transfected cells showed only a slight increase in the number of plasma cells compared with that in the culture without them, indicating that an increased Ig production rate per cell is responsible for the observed enhancing effect of CD134L engagement rather than increase in plasma cell generation. These results strongly suggest different and sequential roles of the TNF/TNFR family molecules in human T cell-dependent B cell responses through cell-cell contacts and the cytokine network.
Signalling constellations for power-efficient bit-interleaved coded modulation schemes (2003)

Bit-interleaved coded modulation (BICM) is a bandwidth-efficient coding technique consisting of serial concatenation of binary error-correcting coding, bit-by-bit interleaving, and high-order modulation. The author addresses the problem of finding the signal sets that are most suitable for designing power-efficient BICM schemes over an additive white Gaussian noise channel. To this end, the expression of the BICM capacity limit is exploited and evaluated for several 8- and 16-ary constellations. It is also shown that the bit error probability curves of the modulation schemes without coding can be used to determine the most attractive constellations. Finally, the bit error rate performance of some BICM schemes made up of turbo codes and various signal sets is investigated to illustrate the theoretical results.
Varicella Vaccine (VARIVAX) in Healthy Children and Adolescents: Results From Clinical Trials, 1987 to 1989 (1991)

A total of 3303 healthy children and adolescents, aged 12 months to 17 years, were vaccinated with one of five production lots of a live attenuated varicella vaccine (VARIVAX) containing 1000 to 1625 plaque-forming units per dose. The vaccine was generally well tolerated. Ninety-six percent (2381/2475) of vaccinees responded to vaccination by producing antibody as measured by a glycoprotein-based enzyme-linked immunosorbent assay; 99% (569/576) of those tested maintained antibody at 1 year following vaccination. The incidence of varicella following household exposure in vaccinees was approximately 12%; household contact historically results in 87% infection. Nearly all of the vaccinees who had varicella after vaccination had a clinically modified disease.