gebhart/patrepeval huggingface dataset:
A caveat for T cell transfer studies: generation of cytotoxic anti-Thy1.2 antibodies in Thy1.1 congenic mice given Thy1.2+ tumors or T cells (2010)

Thy1.1 congenic B6.PL mice were used to simultaneously monitor Thy1.2+ E.G7-OVA tumors transplanted in the a.c. of the eye and i.v.-transferred tumor-specific Thy1.2+ CTLs to determine mechanisms that inhibit the tumoricidal activity of CTL responses in mice with established ocular tumors. Transferred CTLs were systemically deleted in mice with established ocular tumors. However, this deletion was not a unique mechanism of immune evasion by ocular tumors. Rather, development of Thy1.2+ tumors in the eye or skin of B6.PL mice generated cytotoxic anti-Thy1.2 antibodies that eliminated a subsequent Thy1.2+ T cell transfer. Anti-Thy1.2 immune responses in B6.PL mice were influenced by the route of antigen administration, as the serum concentration of cytotoxic anti-Thy1.2 antibodies was 92-fold greater in mice with eye tumors in comparison with mice with skin tumors. In addition, anti-Thy1.2 immune responses were detected in B6.PL mice given naïve Thy1.2+ T cells i.p. but not i.v. Anti-Thy1.2 responses were augmented in B6.PL mice with ocular Thy1.2+ EL-4 tumors that did not express OVA, suggesting immunodominance of OVA antigen over Thy1.2. Thy1.1+ T cells given i.p. was not immunogenic in Thy1.2 congenic mice. These data reaffirm that the introduction of antigens in the a.c. induces robust antibody responses. Experimentation using allotypic differences in Thy1 between donor cells and recipient mice must consider cytotoxic anti-Thy1 antibody generation in the interpretation of results.
Contextual behavior and neural circuits (2013)

Animals including humans engage in goal-directed behavior flexibly in response to items and their background, which is called contextual behavior in this review. Although the concept of context has long been studied, there are differences among researchers in defining and experimenting with the concept. The current review aims to provide a categorical framework within which not only the neural mechanisms of contextual information processing but also the contextual behavior can be studied in more concrete ways. For this purpose, we categorize contextual behavior into three subcategories as follows by considering the types of interactions among context, item, and response: contextual response selection, contextual item selection, and contextual item-response selection. Contextual response selection refers to the animal emitting different types of responses to the same item depending on the context in the background. Contextual item selection occurs when there are multiple items that need to be chosen in a contextual manner. Finally, when multiple items and multiple contexts are involved, contextual item-response selection takes place whereby the animal either chooses an item or inhibits such a response depending on item-context paired association. The literature suggests that the rhinal cortical regions and the hippocampal formation play key roles in mnemonically categorizing and recognizing contextual representations and the associated items. In addition, it appears that the fronto-striatal cortical loops in connection with the contextual information-processing areas critically control the flexible deployment of adaptive action sets and motor responses for maximizing goals. We suggest that contextual information processing should be investigated in experimental settings where contextual stimuli and resulting behaviors are clearly defined and measurable, considering the dynamic top-down and bottom-up interactions among the neural systems for contextual behavior.
The structural impact of DNA mismatches (2015)

The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produced significant local structural alterations, especially in the case of purine transversions. Mismatched pairs often show promiscuous hydrogen bonding patterns, which interchange among each other in the nanosecond time scale. This therefore defines flexible base pairs, where breathing is frequent, and where distortions in helical parameters are strong, resulting in significant alterations in groove dimension. Even if the DNA structure is plastic enough to absorb the structural impact of the mismatch, local structural changes can be propagated far from the mismatch site, following the expected through-backbone and a previously unknown through-space mechanism. The structural changes related to the presence of mismatches help to understand the different susceptibility of mismatches to the action of repairing proteins.
The history of energetic efficiency research: Where have we been and where are we going? (2003)

The development of energetic efficiency concepts followed a recognized pattern of knowledge evolution that began with novel insights leading to cre- ative new concepts. The second phase integrated con- cepts from other fields to create new applicable princi- ples. The third phase was the adoptive or dissemination phase, yielding solutions to industry or societal prob- lems. It is our contention that animal energetics has been in the adoptive phase for approximately 100 yr. Concepts developed during the early phase of nutri- tional energetics included the concept that life is a com- bustion process, the laws of thermodynamics, and the Law of Hess. Subsequent efforts established relation- ships between gas exchange and heat production and established the concept that food not only functions as fuel, but also as a body-building material. Much of the research effort for the last 100 yr has been to 1) devise bases for evaluation of foods that could be related to energy requirements and energy expenditures and 2) establish causes of energy expenditures. Much of the effort has focused on general and broadly applicable
Identification of the ral and rac1 Gene Products, Low Molecular Mass GTP-binding Proteins from Human Platelets (1989)

Identification of the GTP-binding proteins from human platelet particulate fractions was attained by their purification via successive column chromatography steps followed by amino acid sequencing. To enhance the likelihood of identifying the GTP-binding proteins, two assays were employed to monitor GTP-binding activities: (i) guanosine 5'-(3-O-[35S]thio)triphosphate (GTP gamma S)-binding followed by rapid filtration and ii) [alpha-32P]GTP-binding following sodium dodecyl sulfate-polyacrylamide gel electrophoresis and electroblotting onto nitrocellulose membranes. The latter assay permitted the isolation of a 28-kDa GTP-binding protein that bound [alpha-32P]GTP prominently but was only poorly detected with the GTP gamma S-binding assay. The amino acid sequences of three peptide fragments derived from the 28-kDa protein were identical to regions of the amino acid sequence deduced from a simian ral cDNA with the exception of one conservative substitution (Asp147----Glu). A full length human ral cDNA was isolated from a placental cDNA library, and its deduced amino acid sequence, compared with simian ral, also contained the Asp----Glu substitution along with two other substitutions and an additional three NH2-terminal amino acids. In addition to the 28-kDa protein, two distinct 25-kDa GTP-binding proteins were purified from platelets. One of these proteins has been previously characterized as G25K, an abundant low molecular mass GTP-binding protein. Partial amino acid sequence obtained from the second unidentified 25-kDa protein indicates that it is the product of the rac1 gene; a member of a newly identified gene family which encode for low molecular mass GTP-binding proteins (Didsbury, J., Weber, R.F., Bokoch, G. M., Evans, T., and Snyderman, R. (1989) J. Biol. Chem. 264, 16378-16382). These results identify two new GTP-binding proteins in human platelets, ral, the major protein that binds [alpha-32P]GTP on nitrocellulose transfers, and rac1, a substrate for botulinum C3 ADP-ribosyltransferase.
Combining biocatalyzed electrolysis with anaerobic digestion (2008)

Biocatalyzed electrolysis is a microbial fuel cell based technology for the generation of hydrogen gas and other reduced products out of electron donors. Examples of electron donors are acetate and wastewater. An external power supply can support the process and therefore circumvent thermodynamical constraints that normally render the generation of compounds such as hydrogen unlikely. We have investigated the possibility of biocatalyzed electrolysis for the generation of methane. The cathodically produced hydrogen could be converted into methane at a ratio of 0.41 mole methane mole(-1) acetate, at temperatures of 22+/-2 degrees C. The anodic oxidation of acetate was not hampered by ammonium concentrations up to 5 g N L(-1). An overview is given of potential applications for biocatalyzed electrolysis.
Arabinogalactan−Folic Acid−Drug Conjugate for Targeted Delivery and Target-Activated Release of Anticancer Drugs to Folate Receptor-Overexpressing Cells (2009)

Folic acid (FA) is a high affinity ligand (K(d) = 0.1-1 nM) of folate receptors (FRs) responsible for cellular uptake of folates via receptor-mediated endocytosis. FRs are frequently overexpressed in malignant epithelial cells including ovary, brain, kidney, breast, colon, and lung. FR has emerged as a target for the differential-delivery of anticancer chemotherapeutics with several FA-linked therapeutic agents currently undergoing clinical trials. Here we show that by tethering both FA and the anticancer drug methotrexate (MTX) to arabinogalactan (AG), a highly branched natural polysaccharide with unusual water solubility, a targeted biomacromolecular nanovehicle is formed, which can differentially deliver a cytotoxic cargo into FR-overexpressing cells. Moreover, by linking MTX via an endosomally cleavable peptide (GFLG), we demonstrate a target-activated release mechanism. This FA-AG-GFLG-MTX drug conjugate displayed 6.3-fold increased cytotoxic activity to FR-overexpressing cells compared to their FR-lacking counterparts. These findings establish a novel FA-tethered polymeric nanoconjugate for the targeted delivery of antitumor agents into cancer cells overexpressing FR.
Bacterial Mutants Defective in Plasmid Formation: Requirement for the <i>lon</i> <sup>+</sup> Allele (1971)

Bacterial mutants defective in plasmid formation were selected for their inability to be transduced to chloramphenicol resistance by bacteriophage PlCM. The mutants isolated are indistinguishable from a lon mutant strain. Both the lon strain and the mutants isolated here show very poor lysogenization by P1 and very low transduction to Gal(+) by the plasmid formation of the lambdagal(8)-Nam7am53cI(857). The lon(+) gene function of the host bacteria is indispensable for plasmid formation, even though P1 and lambda(+) can grow normally on the lon strains and lambda(+) can be integrated normally in lon as well as in the lon(+) bacteria. Phage mutants that can persist as plasmids in lon strains were isolated from P1CM. The function of the lon(+) gene is discussed with regard to plasmid formation.
A fail-safe, three way, variable flow control valve for a commercially available, implantable insulin infusion pump (1985)

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1985.
Gadolinium-Enhanced Magnetic Resonance Imaging, Renal Failure and Nephrogenic Systemic Fibrosis /Nephrogenic Fibrosing Dermopathy (2008)

First described in 2000, nephrogenic systemic fibrosis (NSF)/nephrogenic fibrosing dermopathy (NFD) is a recently defined and sometimes fatal condition that, so far, has occurred only in people with some degree of renal failure, either during the conservative phase of chronic renal disease, the dialysis phase, or the kidney transplantation phase. The association between NSF/NFD and gadolinium-based magnetic resonance (MR) examination is so strong that public health agencies have sent out warnings concerning the use of gadolinium-enhanced MR in patients with renal failure. The prolonged residence of some gadolinium-chelates in the uremic milieu may allow free toxic gadolinium released from its chelate to extravasate into the extravascular space where it may accelerate fibrillogenesis. The medical community must be apprised of the concern surrounding the use of gadolinium contrast agent in patients with even moderate renal failure, considering that the number of at risk persons is 20 times greater than that of patients needing dialysis/transplantation, remember that the risk is particularly high in patients with liver transplantation in the presence of functional renal impairment, and not to forget that MR examination remains one of the three pillars of molecular medicine.
Species barrier in prion diseases: a kinetic interpretation based on the conformational adaptation of the prion protein (1998)

Prion diseases are thought to result from the conformational change of the normal cellular prion protein to a pathogenic protease-resistant isoform. However, brain extracts not containing the protease-resistant isoform of the prion protein can be infectious following interspecies transmission. The 'protein-only' hypothesis of pathogenesis is extended to provide possible explanations which could be interpreted in terms of a different infectious agent. It is proposed that normal cellular protein (PrPC) may be transformed into a form (PrP*) that is conformationally distinct from the host-specific abnormal isoform (PrPSc). In infection from a heterologous donor, the dimeric forms of heterologous PrPSc, which may catalyse the formation of host PrP* from PrPC, host PrP* and host PrPSc are all considered to be capable of catalysing, to some extent, the conversion of PrPC into PrPSc. However, depending on the species involved, PrP* may, or may not, be pathogenic, and may, or may not, be sensitive to proteolysis. It is shown, by numerical integration of the differential rate equations derived from this model, that a strain may be stabilized after two or three passages through a different species and that transmission might occur in the absence of detectable protease-resistant prion protein. The natural transmission of scrapie to cattle is discussed in relation to the model.
The first example of the generation and trapping of diazospiropentane by unsaturated compounds (1997)

Alkaline hydrolysis of N-spiropentyl-N-nitrosourea at –50 °C generates unknown diazospiropentane in situ, which is trapped with methyl methacrylate or 3,3-dimethylcyclopropene yielding the corresponding 1-pyrazolines with a spiropentane fragment in the molecule. Some chemical transformations of the products obtained are performed.
Comment on “First-Principles Calculation of Transport Properties of a Molecular Device” (2001)

A Comment on the Letter by M. Di Ventra, S. T. Pantelides, and N. D. Lang, Phys. Rev. Lett. 84, 979 (2000).Received 14 May 2001DOI:https://doi.org/10.1103/PhysRevLett.87.269701©2001 American Physical Society
Schedule and Cost Buffer Sizing: How to Account for the Bias between Project Performance and Your Model (2003)

Bias in project performance causes schedule and cost to overrun baseline estimates (your model). Bias is the onesided tendency of actual schedule or cost to overrun the model. A Guide to the Project Management Body of Knowledge (PMBOK® Guide) and supporting literature recommend estimating the variability for all project time and cost estimates, and sizing appropriate schedule or cost buffers (also known as contingency or management reserve) using Monte-Carlo analysis or PERT. This paper describes a number of sources of bias in performance of projects to schedule and cost estimates, and provides recommendations to size buffers that ensure your projects come in under your baseline schedule and budget.
The Effects of Panel Convexity on Visual Performance and Fatigue in Using Cathode-Ray Tube (CRT) Displays (2003)

An experiment was carried out to compare the suitability in visual tasks between flat and conventional (convex) cathode-ray tube (CRT) displays. The subjects performed visual search tasks during 2-h for detecting target words among distracters presented on the screen. The subjects' visual performance was evaluated with average time and number of errors made to complete the tasks. Visual fatigue after the search tasks was also evaluated in terms of degradations in accommodative power and subjective ratings. Difference was not found in task time between the two displays, but flat CRT showed a lower number of errors than conventional CRT. The difference in number of errors was statistically significant at 0=0.05. Although there was no difference between the displays in degradations of accommodative power, results from the subjective ratings showed that flat CRT yields less fatigue than conventional CRT. The results partially support the hypothesis that panel convexity of CRT displays has a significant effect on the performance and fatigue during visual tasks and thus flat CRT is the better display than conventional one.
Carbon Nanotubes (2011)

This chapter contains sections titled: Introduction Arming of CNTs Toxicity of CNTs Conclusions References
Effective Ionic Conductivity of a Novel Intermediate-Temperature Mixed Oxide-Ion and Carbonate-Ion Conductor (2010)

A systematic investigation on the effective ionic conductivity of a novel intermediate-temperature mixed oxide-ion and carbonate-ion conductor (MOCC) consisting of a ceria phase and a carbonate phase is reported. The study explicitly shows that the observed remarkable temperature-dependent is primarily the result of softening/melting of the carbonate phase as the physical state of the carbonate phase transforms from solid, softened to molten. Differential scanning calorimetry analysis complements the understanding of the observed electrical behavior by revealing temperatures of melting and solidification in agreement with the onset temperatures of . In addition, the measured agrees reasonably well with that simulated by the effective medium percolation theory. Furthermore, of the MOCC is independent of atmosphere at , exhibiting the characteristics of a good electrolyte. The MOCC– and MOCC–Ni composites are better cathode and anode materials than noble metals for MOCC-based fuel cells, respectively. Finally, no sign of degradation measured at in air is found over a period.
A Physician by Any Other Name (2001)

What's in a name? In Act II, scene ii of Romeo and Juliet, William Shakespeare's young hero says: "That which we call a rose/ By any other name would smell as sweet." It didn't matter to Romeo that Juliet bore the surname "Capulet," a name despised by his own Montague family. He loved her for who she was. In affairs of the heart, lovers may be both blind and "illiterate" to the connotations of names and titles, but as Shakespeare's most famous tale demonstrates, the consequences of their "illiteracy" can be fatal.
Functional rescue of a constitutively desensitized β2AR through receptor dimerization (1998)

We have recently demonstrated that wild-type beta2-adrenergic receptors (beta2AR) form homodimers and that disruption of receptor dimerization inhibits signalling via Gs [Hebert, Moffett, Morello, Loisel, Bichet, Barret and Bouvier (1996) J. Biol. Chem. 271, 16384-16392]. Here taking advantage of the altered functional properties of a non-palmitoylated, constitutively desensitized mutant beta2AR (C341Gbeta2AR), we sought to study whether physical interactions between mutant and wild-type beta2AR expressed in Sf9 cells could occur and have functional consequences. Using metabolic labelling with [3H]palmitate and co-immunoprecipitation we demonstrated the existence of heterodimerization between wild-type and C341Gbeta2AR. Furthermore, we show that, in co-expression experiments, wild-type receptors have a dominant positive effect resulting in the functional complementation of C341Gbeta2AR. Indeed, when expressed alone, the mutant C341G receptor displays altered functional characteristics in that (1) the response of the receptor to agonist is reduced as compared to the wild-type receptor and (2) the desensitization of the receptor in response to prolonged exposure to agonist is minimal. In contrast, when C341G and the wild-type beta2AR were expressed together, both the response to agonist and subsequent desensitization (at a constant level of total receptor) were equivalent to the wild-type beta2AR expressed alone. This dominant positive effect was also seen when C341G was co-expressed with a second receptor mutant in which the two protein kinase A phosphorylation sites (S261, 262, 345, 346A beta2AR) were mutated. Taken together these data suggest that intermolecular interactions between receptors may have both functional and structural implications for G-protein-mediated signalling.
Affine invariant features from the trace transform (2004)

The trace transform is a generalization of the Radon transform that allows one to construct image features that are invariant to a chosen group of image transformations. In this paper, we propose a methodology and appropriate functionals that can be computed from the image function and which can be used to calculate features invariant to the group of affine transforms. We demonstrate the usefulness of the constructed image descriptors in retrieving images from an image database and compare it with relevant state-of-the-art object retrieval methods.
Optimizing Restaurant Reservation Scheduling (2010)

available for noncommercial, educational purposes, provided that this copyright statement appears on the reproduced materials and notice is given that the copy-ing is by permission of the author. To disseminate otherwise or to republish re-quires written permission from the author. We consider a yield-management approach to determine whether a restau-rant should accept or reject a pending reservation request. This approach was examined by Bossert (2009), where the decision for each request is eval-uated by an approximate dynamic program (ADP) that bases its decision on a realization of future demand. This model only considers assigning requests to their desired time slot. We expand Bossert’s ADP model to in-corporate an element of flexibility that allows requests to be assigned to a time slot that differs from the customer’s initially requested time. To esti-mate the future seat utilization given a particular decision, a new heuristic is presented which evaluates time-slot/table assignments based on the ex-pected number of unused seats likely to result from a given assignment. When compared against naive seating models, the proposed model pro-duced average gains in seat utilization of 25%.