gebhart/patrepeval huggingface dataset:
Preservation of Cone Photoreceptors after a Rapid yet Transient Degeneration and Remodeling in Cone-OnlyNrl−/−Mouse Retina (2012)

Cone photoreceptors are the primary initiator of visual transduction in the human retina. Dysfunction or death of rod photoreceptors precedes cone loss in many retinal and macular degenerative diseases, suggesting a rod-dependent trophic support for cone survival. Rod differentiation and homeostasis are dependent on the basic motif leucine zipper transcription factor neural retina leucine zipper (NRL). The loss of Nrl (Nrl(-/-)) in mice results in a retina with predominantly S-opsin-containing cones that exhibit molecular and functional characteristics of wild-type cones. Here, we report that Nrl(-/-) retina undergoes a rapid but transient period of degeneration in early adulthood, with cone apoptosis, retinal detachment, alterations in retinal vessel structure, and activation and translocation of retinal microglia. However, cone degeneration stabilizes by 4 months of age, resulting in a thinner but intact outer nuclear layer with residual cones expressing S- and M-opsins and a preserved photopic electroretinogram. At this stage, microglia translocate back to the inner retina and reacquire a quiescent morphology. Gene profiling analysis during the period of transient degeneration reveals misregulation of genes related to stress response and inflammation, implying their involvement in cone death. The Nrl(-/-) mouse illustrates the long-term viability of cones in the absence of rods and retinal pigment epithelium defects in a rodless retina. We propose that Nrl(-/-) retina may serve as a model for elucidating mechanisms of cone homeostasis and degeneration that would be relevant to understanding diseases of the cone-dominant human macula.
Argumentation-enabled interest-based personalised recommender system (2014)

Recommender systems (RSs) use information filtering to recommend information of interest (to a user). Similarly, personalisation can be adopted for recommendations in e-market. We propose a new and innovative system called as interest-based recommender system (IBRS) for personalisation of recommendations. The IBRS is an agent-based RS that takes into account user's preferences. It can transform a standard product (or service) into a dedicated solution for an individual. The system discovers interesting product alternatives based on user's underlying mental attitudes (likes and dislikes) during the repair process using argumentation. The proposed method combines a hybrid RS approach with automated argumentation-based reasoning between agents. The system improves results by improving the recommendation repair activity. We consider a book recommendation application, for experiment to carry out the system's (objective and subjective) evaluation using standard metrics. The experiments confirm that the proposed IBRS improves user's acceptance of the product as compared with a traditional hybrid method and an argumentation-enabled state-of-the-art recommendation method. The system has been found to be more effective than its traditional counterpart when dealing with the new user problems.
Effect of Proton Pump Inhibitors and Antacid Therapy on 13C Urea Breath Tests and Stool Test for Helicobacter Pylori Infection (2004)

False negative breath and stool tests are equally common in patients taking proton pump inhibitors. Antacids do not impair the sensitivity of the breath tests or the stool test.
An Expedient Route to the Tetrazole Analogues of α-Amino Acids (2002)

[reaction: see text] Convenient conditions are described for the transformation of alpha-aminonitriles to the tetrazole analogues of alpha-amino acids. Refluxing the starting material in water/2-propanol at 80 degrees C with sodium azide and catalytic zinc bromide affords the tetrazole product in yields generally exceeding 90%.
Phenolic sulfates as new and highly abundant metabolites in human plasma after ingestion of a mixed berry fruit purée (2015)

Bioavailability studies are vital to assess the potential impact of bioactive compounds on human health. Although conjugated phenolic metabolites derived from colonic metabolism have been identified in the urine, the quantification and appearance of these compounds in plasma is less well studied. In this regard, it is important to further assess their potential biological activity in vivo. To address this gap, a cross-over intervention study with a mixed fruit purée (blueberry, blackberry, raspberry, strawberry tree fruit and Portuguese crowberry) and a standard polyphenol-free meal was conducted in thirteen volunteers (ten females and three males), who received each test meal once, and plasma metabolites were identified by HPLC-MS/MS. Sulfated compounds were chemically synthesised and used as standards to facilitate quantification. Gallic and caffeic acid conjugates were absorbed rapidly, reaching a maximum concentration between 1 and 2 h. The concentrations of sulfated metabolites resulting from the colonic degradation of more complex polyphenols increased in plasma from 4 h, and pyrogallol sulfate and catechol sulfate reached concentrations ranging from 5 to 20 μm at 6 h. In conclusion, phenolic sulfates reached high concentrations in plasma, as opposed to their undetected parent compounds. These compounds have potential use as biomarkers of polyphenol intake, and their biological activities need to be considered.
Light-Inducible Spatiotemporal Control of Gene Activation by Customizable Zinc Finger Transcription Factors (2012)

Advanced gene regulatory systems are necessary for scientific research, synthetic biology, and gene-based medicine. An ideal system would allow facile spatiotemporal manipulation of gene expression within a cell population that is tunable, reversible, repeatable, and can be targeted to diverse DNA sequences. To meet these criteria, a gene regulation system was engineered that combines light-sensitive proteins and programmable zinc finger transcription factors. This system, light-inducible transcription using engineered zinc finger proteins (LITEZ), uses two light-inducible dimerizing proteins from Arabidopsis thaliana, GIGANTEA and the LOV domain of FKF1, to control synthetic zinc finger transcription factor activity in human cells. Activation of gene expression in human cells engineered with LITEZ was reversible and repeatable by modulating the duration of illumination. The level of gene expression could also be controlled by modulating light intensity. Finally, gene expression could be activated in a spatially defined pattern by illuminating the human cell culture through a photomask of arbitrary geometry. LITEZ enables new approaches for precisely regulating gene expression in biotechnology and medicine, as well as studying gene function, cell-cell interactions, and tissue morphogenesis.
Oxidation of glycated proteins: age-dependent accumulation of N.epsilon.-(carboxymethyl)lysine in lens proteins (1989)

N epsilon-(Carboxymethyl)lysine (CML) has been identified as a product of oxidation of fructoselysine (FL) in glycated (nonenzymatically glycosylated) proteins in vitro and has also been detected in human tissues and urine [Ahmed et al. (1986) J. Biol. Chem. 261, 4889-4894]. In this study, we compare the amounts of CML and FL in normal human lens proteins, aged 0-79 years, using specific and sensitive assays based on selected ion monitoring gas chromatography-mass spectrometry. Our results indicate that the lens content of FL increases significantly between infancy and about age 5 but that there is only a slight, statistically insignificant increase in FL between age 5 and 80 (mean +/- SD = 1.4 +/- 0.4 mmol of FL/mol of Lys). In contrast, the lens content of the oxidation product, CML, increased linearly with age, ranging from trace levels at infancy up to 8 mmol of CML/mol of lysine at age 79. The ratio of CML to FL also increased linearly from 0.5 to 5 mol of CML/mol of FL between age 1 and 79, respectively. These results indicate that CML, rather than FL, is the major product of glycation detectable in adult human lens protein. The age-dependent accumulation of CML in lens protein indicates that products of both glycation and oxidation accumulate in the lens with age, while the constant rate of accumulation of CML in lens with age argues against an age-dependent decline in free radical defense mechanisms in this tissue.
An incremental data-stream sketch using sparse random projections (2007)

We propose the use of random projections with a sparse matrix to maintain a sketch of a collection of high-dimensional data-streams that are updated asynchronously. This sketch allows us to estimate L2 (Euclidean) distances and dot-products with high accuracy. We verify the validity of this sketch by applying it to an online clustering problem, where we compare our results to the offline algorithm and an existing L2 sketch, and observe comparable results in terms of accuracy, and a reduced runtime cost.
A Formal Foundation for the Security Features of Physical Functions (2011)

Physical attacks against cryptographic devices typically take advantage of information leakage (e.g., side-channels attacks) or erroneous computations (e.g., fault injection attacks). Preventing or detecting these attacks has become a challenging task in modern cryptographic research. In this context intrinsic physical properties of integrated circuits, such as Physical(ly) Unclonable Functions (PUFs), can be used to complement classical cryptographic constructions, and to enhance the security of cryptographic devices. PUFs have recently been proposed for various applications, including anti-counterfeiting schemes, key generation algorithms, and in the design of block ciphers. However, currently only rudimentary security models for PUFs exist, limiting the confidence in the security claims of PUF-based security primitives. A useful model should at the same time (i) define the security properties of PUFs abstractly and naturally, allowing to design and formally analyze P UF-based security solutions, and (ii) provide practical quantification tools allowing engineers to evaluate PUF instantiations. In this paper, we present a formal foundation for security primitives based on PUFs. Our approach requires as little as possible from the physics and focuses more on the main properties at the heart of most published works on PUFs: robustness (generation of stable answers), unclonability (not provided by algorithmic solutions), and unpredictability. We first formally define these properties and then show that they can be achieved by previously introduced PUF instantiations. We stress that such a consolidating work allows for a meaningful security analysis of security primitives taking advantage of physical properties, becoming increasingly important in the development of the next generation secure information systems.
Joint prosody prediction and unit selection for concatenative speech synthesis (2002)

We describe how prosody prediction can be efficiently integrated with the unit selection process in a concatenative speech synthesizer under a weighted finite-state transducer (WFST) architecture. WFSTs representing prosody prediction and unit selection can be composed during synthesis, thus effectively expanding the space of possible prosodic targets. We implemented a symbolic prosody prediction module and a unit selection database as the synthesis components of a travel planning system. Results of perceptual experiments show that by combining the steps of prosody prediction and unit selection we are able to achieve improved naturalness of synthetic speech compared to the sequential implementation.
A second neutralizing epitope of B19 parvovirus implicates the spike region in the immune response (1991)

We used 18 monoclonal antibodies against B19 parvovirus to identify neutralizing epitopes on the viral capsid. Of the 18 antibodies, 9 had in vitro neutralizing activity in a bone marrow colony culture assay. The overlapping polypeptide fragments spanning the B19 structural proteins were produced in a pMAL-c Escherichia coli expression system and used to investigate the binding sites of the neutralizing antibodies. One of the nine neutralizing antibodies reacted with both VP1 and VP2 capsid proteins and a single polypeptide fragment on an immunoblot, identifying a linear neutralizing epitope between amino acids 57 and 77 of the VP2 capsid protein. Eight of nine neutralizing antibodies failed to react with either of the capsid proteins or any polypeptide fragments, despite reactivities with intact virions in a radioimmunoassay, suggesting that additional conformationally dependent neutralizing epitopes exist.
Transcriptional and Translational Regulation of β-Cell Differentiation Factor Nkx6.1 (2000)

In the mature pancreas, the homeodomain transcription factor Nkx6.1 is uniquely restricted to beta-cells. Nkx6.1 also is expressed in developing beta-cells and plays an essential role in their differentiation. Among cell lines, both beta- and alpha-cell lines express nkx6.1 mRNA; but no protein can be detected in the alpha-cell lines, suggesting that post-transcriptional regulation contributes to the restriction of Nkx6.1 to beta-cells. To investigate the regulator of Nkx6.1 expression, we outlined the structure of the mouse nkx6.1 gene, and we identified regions that direct cell type-specific expression. The nkx6.1 gene has a long 5'-untranslated region (5'-UTR) downstream of a cluster of transcription start sites. nkx6.1 gene sequences from -5.6 to +1.0 kilobase pairs have specific promoter activity in beta-cell lines but not in NIH3T3 cells. This activity is dependent on sequences located at about -800 base pairs and on the 5'-UTR. Electrophoretic mobility shift assays demonstrate that homeodomain transcription factors PDX1 and Nkx2.2 can bind to the sequence element located at -800 base pairs. In addition, dicistronic assays establish that the 5'-UTR region functions as a potent internal ribosomal entry site, providing cell type-specific regulation of translation. These data demonstrate that complex regulation of both Nkx6.1 transcription and translation provides the specificity of expression required during pancreas development.
Sequence and overexpression of the menD gene from Escherichia coli (1989)

The menD gene of Escherichia coli codes for the first enzyme of menaquinone biosynthesis, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) synthase. DNA sequence analysis of menD shows an open reading frame encoding a 52-kilodalton protein. Possible promoter and ribosome binding sites are present. Insertion of the menD gene into a tac promoter expression vector leads to nearly a 100-fold increase in the level of SHCHC synthase activity upon induction with isopropyl-beta-D-thiogalactoside (IPTG). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of [35S]methionine-labeled proteins shows a 61-kilodalton protein produced upon induction of the menD-containing expression vector. This is the first reported sequence analysis of a men gene and the first significant amplification of any of the menaquinone biosynthetic enzymes.
Evidence that tyrosine phosphorylation may increase tight junction permeability (1995)

Tight junction permeability control is important in a variety of physiological and pathological processes. We have investigated the role of tyrosine phosphorylation in the regulation of tight junction permeability. MDCK epithelial cells and brain endothelial cells were grown on filters and tight junction permeability was determined by transcellular electrical resistance (TER). The tyrosine phosphatase inhibitor pervanadate caused a concentration- and time-dependent decrease in TER in both MDCK and brain endothelial cells. However, as expected, pervanadate resulted in the tyrosine phosphorylation of many proteins; hence interpretation of its effects are extremely difficult. Phenylarsine oxide, a more selective tyrosine phosphatase inhibitor, caused the tyrosine phosphorylation of relatively few proteins as analyzed by immunoblotting of whole cell lysates. This inhibitor, like pervanadate, also elicited a decrease in TER in the two cell types. In the MDCK cells, the action of phenylarsine oxide could be reversed by the subsequent addition of the reducing agent 2,3-dimercaptopropanol. Immunocytochemistry revealed that phenylarsine oxide rapidly stimulated the tyrosine phosphorylation of proteins associated with intercellular junctions. Because of the known influence of the adherens junction on tight junctions, we analyzed immunoprecipitates of the E-cadherin/catenin complex from MDCK cells treated with phenylarsine oxide. This revealed an increase in the tyrosine phosphorylation of beta-catenin, but not of alpha-catenin. However, the tight junction associated protein ZO-1 was also tyrosine phosphorylated after PAO treatment. These data indicate that tight junction permeability may be regulated via mechanisms involving tyrosine phosphorylation of adherens junction and tight junction proteins.
‘SITUATIONAL HYPERACTIVITY’ IN A U.S. CLINICAL SETTING (1986)

Eight of 69 males referred to a Hyperactivity Clinic for participation in psychopharmacological trials were not rated hyperactive by their primary caretaker on a parent symptom questionnaire. In comparison to eight boys for whom both parent and teacher ratings of hyperactivity were high, the group differed only in caretaker status. 'Situational' children were less likely to be living with both biological parents (P less than 0.05). In contrast, direct observation and actometer measurement of activity did not differ significantly between the groups. The findings suggest that at least in clinical settings, a distinction between 'situational' and 'pervasive' hyperactivity reflects caretaker status or attitude and not characteristics of the child.
Etudes microlithographiques de résines négatives renfermant des unités tétrathiafulvalènes sensibles aux électrons (1993)

Abstract Pour résoudre le phénomène de gonflement qui limite la résolution des résines micro lithographiques classiques, nous nous sommes intéressés à de nouvelles résines avec lesquelles ce phénomène n'apparaǐt pas. Nous avons retenu pour notre étude les résines R qui renferment en mélange un polymère porteur de radicaux tétrathiafulvalénylcarbonyloxyméthyles et le dibromotétrachloroéthane. Afin de voir l'influence de la nature du radical porteur de l'unité tetrathiafulvalène dans le polymère sur les propriétés microlithographiques des résines R, nous nous sommes également intéressés aux polymères renfermant des radicaux tétrathiafulvalénoxyméthyles. Les résines R ont été testées sous irradiation électronique. Leurs sensibilités dépendent en outre de la valeur de la masse molaire du polymère. Des résolutions comprises entre 0,1 et 0,4 μm ont été obtenues. Ce type de résines possèdent un certain nomber de propriétés intéressantes telles que des sensibilités élevées et de bonnes résolutions.
Water‐Balance Calculations for Solid‐Polymer‐Electrolyte Fuel Cells (1990)

The proper balance between water production and removal is particularly important for successfully operating solid‐polymer‐electrolyte fuel cells. Imbalance between production and evaporation rates can result in either flooding of the electrodes or membrane dehydration, both of which severely limit performance. We present a mathematical model of the solid‐polymer‐electrolyte fuel cell that identifies operating conditions that result in a water balance. The model is one‐dimensional and is derived from basic principles of gas‐phase transport. The mechanisms of membrane water transport are not included explicitly in the model, and the membrane is taken as uniformly wetted, which renders the model most applicable to thin membranes. We suggest how humidification of reactant gases can be adjusted as current density is varied during an experiment (at constant temperature, pressure, and reactant feed rates) in order to accommodate the fuel cell's changing demands for water. Humidification requirements of inlet reactant gases for a wide range of practical operating temperatures, pressures, and gas feed rates have been identified. The analysis also identifies conditions in which reactant transport limitations govern the behavior of the fuel cell.
ApoE Polymorphism and Fish Oil Supplementation in Subjects With an Atherogenic Lipoprotein Phenotype (2000)

The study assessed the efficacy of fish oil supplementation in counteracting the classic dyslipidemia of the atherogenic lipoprotein phenotype (ALP). In addition, the impact of the common apolipoprotein E (apoE) polymorphism on the fasting and postprandial lipid profile and on responsiveness to the dietary intervention was established. Fifty-five ALP males (aged 34 to 69 years, body mass index 22 to 35 kg/m(2), triglyceride [TG] levels 1.5 to 4.0 mmol/L, high density lipoprotein cholesterol [HDL-C] <1.1 mmol/l, and percent low density lipoprotein [LDL]-3 >40% total LDL) completed a randomized placebo-controlled crossover trial of fish oil (3.0 g eicosapentaenoic acid/docosahexaenoic acid per day) and placebo (olive oil) capsules with the 6-week treatment arms separated by a 12-week washout period. In addition to fasting blood samples, at the end of each intervention arm, a postprandial assessment of lipid metabolism was carried out. Fish oil supplementation resulted in a reduction in fasting TG level of 35% (P<0.001), in postprandial TG response of 26% (TG area under the curve, P<0.001), and in percent LDL-3 of 26% (P<0.05). However, no change in HDL-C levels was evident (P=0.752). ANCOVA showed that baseline HDL-C levels were significantly lower in apoE4 carriers (P=0.035). The apoE genotype also had a striking impact on lipid responses to fish oil intervention. Individuals with an apoE2 allele displayed a marked reduction in postprandial incremental TG response (TG incremental area under the curve, P=0.023) and a trend toward an increase in lipoprotein lipase activity relative to non-E2 carriers. In apoE4 individuals, a significant increase in total cholesterol and a trend toward a reduction in HDL-C relative to the common homozygous E3/E3 profile was evident. Our data demonstrate the efficacy of fish oil fatty acids in counteracting the proatherogenic lipid profile of the ALP but also that the apoE genotype influences responsiveness to this dietary treatment.
Detection and Quantification of Neurotensin in Human Brain Tissue by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (2000)

A method was developed for mass spectrometric detection of neurotensin (NT)-like immunoreactivity and quantification of NT in human brain tissue. The method is based on immunoprecipitation followed by analysis using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The identity of the major component of the immunoprecipitates as neurotensin was confirmed by fragment ion analysis on an electrospray ionization quadrupole time-of-flight instrument. MALDI-TOF-MS quantification of NT was achieved using stable-isotope-labeled NT as the internal standard, yielding an error of less than 5%. The method allowed detection of low-femtomole amounts of NT, staring from low-milligram amounts of lyophilized brain tissue. In addition to NT, several other peptides were detected in the purified samples, most of which, according to their molecular masses, corresponded to fragments of NT. The method is demonstrated with quantification of NT from human hypothalamus tissue, and a comparison is made with results obtained from competitive radioimmunoassay.