gebhart/patrepeval huggingface dataset:
Control of Copper in Wilson’s Disease and Diseases of Neovascularization, such as Cancer (2002)

Over the last 20 yr our group has worked on the development of new anticopper drugs for the treatment of Wilson’s disease. This has led to the development of zinc and tetrathiomolybdate for specific indications in Wilson’s disease, which we will discuss in detail shortly.
Reactivity of catecholamines and related substances in the mouse lymphoma L5178Y cell assay for mutagens (1988)

Using the L5178Y mouse lymphoma cell thymidine kinase locus and the Salmonella his locus assays, the mutagenic potentials of several catecholamines and related compounds were examined. No supplementary metabolic activation systems were used. In the mouse lymphoma assay, the dihydroxybenzenes catechol and hydroquinone had similar and appreciable mutagenic potentials, whereas resorcinol was less active. Derivatives of catechol, such as dopamine and epinephrine, were mutagenic, whereas the related monohydroxylated compounds tyramine and synephrine were inactive. The primary amine, arterenol, and the corresponding secondary amine, epinephrine, induced similar mutagenic responses. Carboxylation of the side chain of dopamine, giving L-dopa, reduced the maximum mutagenic response. The introduction of charged groups directly on to the aromatic ring also reduced mutagenic activity, while an intervening methylene reversed this effect. Thus, 3,4-dihydroxyhydrocinnamic acid was more active than 3,4-dihydroxybenzoic acid. The compound active at the lowest doses was 4-tert-butyl catechol. The activities of these compounds are highly dependent upon substituent groups. Experiments with superoxide dismutase gave circumstantial evidence for some of the mutagenic activity being due to superoxide anion. Active oxygen species might be responsible for some of the observed effects, but this cannot be concluded from the superoxide dismutase experiments. Mutagenic responses in Salmonella were very low but were significant for L-dopa in three strains and for epinephrine and arterenol in one strain. Limited DNA association studies of 14C-dopamine suggest interactions in L5178Y and Salmonella cells and in mouse liver. The mutagenicity of dopamine in L5178Y is reduced by high serum concentrations during the exposure period, while the apparent association with DNA is unaffected.
Neutral sugar composition and gravimetric yield of plant and bacterial fractions of feces (1990)

Separating dietary fiber from other polysaccharides in digesta and feces is necessary to understand its mechanisms of action. A gravimetric method that separates fecal plant and bacterial matter based on size and density was evaluated and modified to determine the plant and bacterial mass of lyophilized whole and blended rat and human feces. Three screen mech combinations (150 and 75 microns, 150 and 35 microns, 35 microns) were used with rat feces. Filtration of a homogenized rat fecal slurry sequentially through 150- and 35-microns-mesh screens versus 150- and 75-microns-mesh screens decreased the gravimetric recovery of bacteria from congruent to 35 to congruent to 25% of fecal dry weight and increased the plant fraction weight. Neutral sugar composition, determined by gas chromatography of alditol acetates, and bacterial counts of the fractions suggested that the decreased yield of bacterial fraction represented removal of plant material and not a loss of bacteria. Rat excreta contained 29.5% (dry weight) total neutral sugar, 88% of which was recovered in the plant material. Human feces containing wheat bran, fractionated with the 150- and 35-microns-mesh screens, was 21% neutral sugar, congruent to 65% of which was in the plant fraction. The plant fractions had more xylose and arabinose and less glucose than the bacterial fractions. Processing samples in a Waring blender had no adverse effect on the rat or human fecal bacterial counts. The use of this gravimetric method in combination with the sugar analysis of the fractions provided a better measure of plant and bacteria than only gravimetric yield.
The Heterogeneity of Glucan Preparations from the Walls of Various Yeasts (1974)

Previous studies have shown that the insoluble glucan from the walls of baker’s yeast (Saccharomyces cerevisiae) is heterogeneous. It consists of about 85 % of an insoluble branched β-(1 → 3)-glucan and about 15 % of a soluble branched β-(1 → 6)-glucan. Glucan preparations from the walls of the yeasts Kloeckera apiculata, Schizosaccharomyces pombe, Saccharomyces fragilis and Saccharomyces fermentati have now been shown to be similarly heterogeneous. Quantitative periodate oxidation and enzymic degradation studies suggest that in these four yeasts, the amount of β-(1 → 6)-glucan is rather greater than in baker’s yeast.
Understanding the shape of the hazard rate: a process point of view (With comments and a rejoinder by the authors) (2001)

Survival analysis as used in the medical context is focused on the concepts of survival function and hazard rate, the latter of these being the basis both for the Cox regression model and of the counting process approach. In spite of apparent simplicity, hazard rate is really an elusive concept, especially when one tries to interpret its shape considered as a function of time. It is then helpful to consider the hazard rate from a different point of view than what is common, and we will here consider survival times modeled as first passage times in stochastic processes. The concept of quasistationary distribution,which is a well-defined entity for various Markov processes, will turn out to be useful. We study these matters for a number of Markov processes, including the following: finite Markov chains; birth-death processes; Wiener processes with and without randomization of parameters; and general diffusion processes. An example of regression of survival data with a mixed inverse Gaussian distribution is presented. The idea of viewing survival times as first passage times has been much studied by Whitmore and others in the context of Wiener processes and inverse Gaussian distributions. These ideas have been in the background compared to more popular appoaches to survival data, at least within the field of biostatistics,but deserve more attention.
Irritable Bowel Syndrome (2012)

Irritable bowel syndrome (IBS) is one of the commonest disorders seen by gastroenterologists. Patients complain of abdominal pain or discomfort associated with an erratic bowel habit. The peak age of onset is in the third and fourth decades when females outnumber males 3:1. This gender predominance is less evident in older patients. Precipitants include gastrointestinal infection, stress, or dietary factors. Irritable bowel syndrome is often associated with anxiety and multiple unexplained somatic complaints. Visceral hypersensitivity and disturbed transit are common. Treatments include anti-spasmodics, tricyclic antidepressants, loperamide, and 5-HT3 antagonists for diarrhoea-predominant IBS, and 5-HT4 agonists for constipation-predominant IBS.
Nanotoxicity assessment of quantum dots: from cellular to primate studies (2012)

Tremendous research efforts have been devoted to fabricating high quality quantum dots (QDs) for applications in biology and medicine. Much of this research was pursued with an ultimate goal of using QDs in clinical applications. However, a great deal of concern has been voiced about the potential hazards of QDs due to their heavy-metal content. Many studies have demonstrated toxicity of various QDs in cell culture studies. However, in a smaller number of studies using small animal models (mice and rats), no abnormal behaviour or tissue damage was noticed over periods of months after the systemic administration of QDs. Nevertheless, the correlation of these results with the potential for negative effects of QD on humans remains unclear. Many urgent questions must be answered before the QDs community moves into the clinical research phase. This review provides an overview of the toxicity assessment of QDs, ranging from cell culture studies to animal models and discusses their findings. Guidelines for using various nonhuman primate models for QD toxicity studies are highlighted. This review article is intended to promote the awareness of current developments of QD applications in biology, the potential toxicity of QDs, and approaches to minimizing toxicity.
Cataract blindness--challenges for the 21st century. (2001)

Cataract prevalence increases with age. As the world's population ages, cataract-induced visual dysfunction and blindness is on the increase. This is a significant global problem. The challenges are to prevent or delay cataract formation, and treat that which does occur. Genetic and environmental factors contribute to cataract formation. However, reducing ocular exposure to UV-B radiation and stopping smoking are the only interventions that can reduce factors that affect the risk of cataract. The cure for cataract is surgery, but this is not equally available to all, and the surgery which is available does not produce equal outcomes. Readily available surgical services capable of delivering good vision rehabilitation must be acceptable and accessible to all in need, no matter what their circumstances. To establish and sustain these services requires comprehensive strategies that go beyond a narrow focus on surgical technique. There must be changes in government priorities, population education, and an integrated approach to surgical and management training. This approach must include supply of start-up capital equipment, establishment of surgical audit, resupply of consumables, and cost-recovery mechanisms. Considerable innovation is required. Nowhere is this more evident than in the pursuit of secure funding for ongoing services.
Oral BCG vaccine in Crohn's disease. (1979)

In a randomised double-blind trial over one year oral BCG has been compared with a control preparation in the treatment of chronic Crohn's disease. Overall assessment scores deteriorated in nine of 22 patients taking BCG, and 11 of 26 in the control group (P = 0.25); this deterioration was great enough to be regarded as a clinical relapse in three patients taking BCG and in seven taking the control preparation (P greater than 0.1). No significant benefit from oral BCG treatment has been demonstrated.
Estimation of forest leaf area index from SPOT imagery using NDVI distribution over forest stands (2006)

Abstract Leaf area index (LAI) is a key parameter of atmosphere–vegetation exchanges, affecting the net ecosystem exchange and the productivity. At regional or continental scales, LAI can be estimated by remotely‐sensed spectral vegetation indices (SVI). Nevertheless, relationships between LAI and SVI show saturation for LAI values greater than 3–5. This is one of the principal limitations of remote sensing of LAI in forest canopies. In this article, a new approach is developed to determine LAI from the spatial variability of radiometric data. To test this method, in situ measurements for LAI of 40 stands, with three dominant species (European beech, oak and Scots pine) were available over 5 years in the Fontainebleau forest near Paris. If all years and all species are pooled, a good linear relationship without saturation is founded between average stand LAI measurements and a model combining the logarithm of the standard deviation and the skewness of the normalized difference vegetation index (NDVI) (R 2 = 0.73 rmse = 1.08). We demonstrate that this relation can be slightly improved by using different linear models for each year and each species (R 2 = 0.82 rmse = 0.86), but the standard deviation is less sensitive to the species and the year effects than the mean NDVI and is therefore a performing index. Acknowledgments We would like to thank the Office National des Forêts (ONF), Paris, France, for giving us facilities for in situ LAI measurements. This work was supported by the National Centre of Scientific Research (CNRS), Paris, France. We also thank all the people who helped us to collect the ground data. We acknowledge Guerric le Maire and Nick Barrett for their comments on an earlier version of the manuscript.
Mixed Color Sequential Technique for Reducing Color Breakup and Motion Blur Effects (2007)

This paper proposes a mixed color sequential (MCS) algorithm with high contrast enhancement technique in RGB light-emitting diode (LED) backlight display. Owing to synchronous control of liquid crystal display (LCD) and LED panels, high quality image with suppressed color breakup (CBU) and motion blur effects is achieved by our novel color sequential technique. Importantly, MCS algorithm is useful for color filter-less optical compensated bend (OCB) panel display for alleviating CBU and motion blur effects. Furthermore, high contrast image is also presented on LCD panel because of mixed red-green-blue (RGB) and cyan-magenta-yellow (CMY) backlights with optimum power consumption. In other words, MCS algorithm with high contrast enhancement technique can have the better performance compared with other field sequential color techniques. Experimental results demonstrate by an actual RGB backlight module for 32-in 1366*768 LCD panel the improvement of CBU and motion blur effects.
A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells (2015)

T cell immunity directed against tumor-encoded amino acid substitutions occurs in some melanoma patients. This implicates missense mutations as a source of patient-specific neoantigens. However, a systematic evaluation of these putative neoantigens as targets of antitumor immunity is lacking. Moreover, it remains unknown whether vaccination can augment such responses. We found that a dendritic cell vaccine led to an increase in naturally occurring neoantigen-specific immunity and revealed previously undetected human leukocyte antigen (HLA) class I-restricted neoantigens in patients with advanced melanoma. The presentation of neoantigens by HLA-A*02:01 in human melanoma was confirmed by mass spectrometry. Vaccination promoted a diverse neoantigen-specific T cell receptor (TCR) repertoire in terms of both TCR-β usage and clonal composition. Our results demonstrate that vaccination directed at tumor-encoded amino acid substitutions broadens the antigenic breadth and clonal diversity of antitumor immunity.
Prospects for urinary proteomics: Exosomes as a source of urinary biomarkers (Review Article) (2005)

Recent progress in biotechnology offers the promise of better medical care at lower costs. Among the techniques that show the greatest promise is mass spectrometry of proteins, which can identify proteins present in body fluids and tissue specimens at a large scale. Because urine can be collected in large amounts in a non-invasive fashion, the potential exists to use mass spectrometry to discover urinary biomarkers that are early predictors of renal disease, or useful in making therapeutic choices. Recently, the authors demonstrated that both membrane proteins and cytosolic proteins from renal epithelia are highly enriched in low-density urinary structures identified as exosomes. Exosomes were found to contain many disease-associated proteins including aquaporin-2, polycystin-1, podocin, non-muscle myosin II, angiotensin-converting enzyme, Na+ K+ 2Cl- cotransporter (NKCC2), thiazide-sensitive Na-Cl cotransporter (NCC), and epithelial sodium channel (ENaC). Potentially, other disease biomarkers could be discovered by mass spectrometry-based proteomic studies in well-defined patient populations. Herein is described the advantages of using urinary exosomes as a starting material for biomarker discovery. In addition, the purpose of this review is to present an overall strategy for biomarker discovery in urine using exosomes and for developing cost-effective clinical assays for these biomarkers, which can potentially be used for early detection of disease, as a means of differential diagnosis, or as a means of guiding therapy. Finally, potential barriers that need to be overcome before urinary proteomics can be applied clinically, are emphasized.
Application of genetically engineered finite-state-machine sequences to sequential circuit ATPG (1998)

New methods for fault-effect propagation and state justification that use finite-state-machine sequences are proposed for sequential circuit test generation. Distinguishing sequences are used to propagate the fault effects from the flip-flops to the primary outputs by distinguishing the faulty machine state from the fault-free machine state. Set, clear, and pseudoregister justification sequences are used for state justification via a combination of partial state justification solutions. Reengineering of existing finite-state machine sequences may be needed for specific target faults. Moreover, conflicts imposed by the use of multiple sequences may need to be resolved. Genetic-algorithm-based techniques are used to perform these tasks. Very high fault coverages have been obtained as a result of this technique.
The Aldehyde Trap NS2 Reduces Ocular Inflammation in an Endotoxin-Induced Model in Rats (2015)

Purpose: NS2 is an investigational drug in development for acute noninfectious anterior uveitis and other ocular indications. The mechanism of action of NS2 involves neutralizing toxic free-aldehydes, which are mediators of inflammatory disease, both in the eye and elsewhere. The purpose of this study was to evaluate efficacy of a topical NS2 eye drop formulation in a rat model of ocular inflammation.
Mitogenic leukoagglutinin from Phaseolus vulgaris binds to a pentasaccharide unit in N-acetyllactosamine-type glycoprotein glycans. (1982)

The carbohydrate binding specificity of leukoagglutinin (La; Phaseolus vulgaris isolectin L4) was studied by using quantitative precipitation and precipitation-inhibition. A series of purified glycopeptides and synthetic oligosaccharides were used as inhibitors. The minimal structural unit required for La binding was the disaccharide GlcNac(1 leads to beta 2)Man. Additions for this basic unit of different sugar residues gave a positive or negative contribution to binding. The most complementary structure was the pentasaccharide (formula: see text). This pentasaccharide units occurs in tetraantennary N-acetyllactosamine-type glycoprotein glycans. Glycoproteins containing such structures were accordingly precipitated by La. Selected glycopeptides and oligosaccharides were also tested as inhibitors of La-induced DNA synthesis in human lymphocytes. The pattern of inhibition was essentially the same as that obtained by precipitation-inhibition, indicating that binding to lymphocytes via the carbohydrate binding site of the lectin is an essential step in the activation process.
Vi antigen from Salmonella typhosa and immunity against typhoid fever. 11. Safety and antigenicity in humans (1975)

Safety and antigenicity of a purified preparation of Salmonella typhosa Vi antigen was evaluated in human volunteers. Dosages of Vi antigen at 25, 50, and 100 mug were less toxic than U.S. standard typhoid vaccine (lot 6A) containing 5 X 10(8) bacteria per dosage. Vi antigen in comparison with the standard typhoid vaccine induced higher hemagglutinating antibody but lower bactericidal antibody responses.
The implications of medical and psychiatric comorbidity with panic disorder. (2005)

The frequent presentation of patients with panic disorder in medical settings may, in part, be explained by the physical symptoms inherent in panic disorder. However, a number of medical disorders have symptoms that overlap with panic disorder symptoms, and elevated panic disorder prevalence is comorbid with a number of medical illnesses, including respiratory disorders, vestibular dysfunction, and hyperthyroidism and hypothyroidism. The presence of medical comorbidity complicates the identification, presentation, and treatment of panic disorder. In addition, comorbid mood disorders occur commonly and result in greater severity, poorer quality of life, and greater impairment. Recent work suggests that panic disorder occurs more commonly with bipolar disorder than major depressive disorder, resulting in substantial impairment, as well as poorer response to treatment. The implications of mood disorder and its medical comorbidity for the identification and treatment of panic disorder are discussed.
Density, porosity, and structure of dried cell walls isolated from Bacillus megaterium and Saccharomyces cerevisiae (1977)

Helium displacement and nitrogen adsorption techniques were used to determine the density and porosity, respectively, of freeze-dried cell walls isolated from Bacillus megaterium KM and Saccharomyces cerevisiae. The densities were 1.302 and 1.180 g/cm3, respectively, suggesting noncrystalline solids. The porosities were extremely small, indicating that the cell walls had collapsed and become essentially impervious upon lyophilization.
Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery (2015)

We show that assessment of ctDNA is a non-invasive, exquisitely specific and highly sensitive approach for monitoring disease load, which has the potential to provide clinically relevant lead times compared with conventional methods. Furthermore, we provide a low-coverage protocol optimised for identifying SSVs with excellent correlation between SSVs identified in tumours and matched metastases. Application of ctDNA analysis has the potential to change clinical practice in the management of CRC.
The Extent and Condition of US Coral Reefs (1998)

The United States has substantial coral reef holdings in the Atlantic and Pacific Oceans.In the Atlantic, off the coast of Florida, is the planet's third largest barrier reef system; other coral reef systems are found off Puerto Rico and the U.S. Virgin Islands.Many other notable systems are found throughout the Pacific, including significant coral reefs located off of Hawaii.Recent declines in coral reef health, and disturbances caused by hurricanes, diseases, and predator outbreaks, have captured the attention of governments and the public worldwide.Scientists have only recently begun the extensive studies necessary to determine whether and why coral reefs are in decline, and to understand the direct and indirect effects of human activities on reefs and reef resources.
A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP):  Theory and Application (2007)

A fast new algorithm (Fingerprints for Ligands And Proteins or FLAP) able to describe small molecules and protein structures using a common reference framework of four-point pharmacophore fingerprints and a molecular-cavity shape is described in detail. The procedure starts by using the GRID force field to calculate molecular interaction fields, which are then used to identify particular target locations where an energetic interaction with small molecular features would be very favorable. The target points thus calculated are then used by FLAP to build all possible four-point pharmacophores present in the given target site. A related approach can be applied to small molecules, using directly the GRID atom types to identify pharmacophoric features, and this complementary description of the target and ligand then leads to several novel applications. FLAP can be used for selectivity studies or similarity analyses in order to compare macromolecules without superposing them. Protein families can be compared and clustered into target classes, without bias from previous knowledge and without requiring protein superposition, alignment, or knowledge-based comparison. FLAP can be used effectively for ligand-based virtual screening and structure-based virtual screening, with the pharmacophore molecular recognition. Finally, the new method can calculate descriptors for chemometric analysis and can initiate a docking procedure. This paper presents the background to the new procedure and includes case studies illustrating several relevant applications of the new approach.