gebhart/patrepeval huggingface dataset:
Potential trade-offs between biomineralization and immunity revealed by shell properties and gene expression profiles of two closely related Crassostrea species (2018)

Species of the Ostreidae family are key ecosystem engineers and many of them - including <i>Crassostrea gigas</i> and <i>Crassostrea</i><i>virginica</i> - are commercially important aquaculture species. Despite similarities in their morphology and ecology, these two species differ in their ability to defend against pathogens, potentially reflecting species-specific differential specialization of hemocytes on immune defense versus biomineralization. To test this hypothesis, we investigated the expression levels of immune- and biomineralization-related genes as well as mineralogical and mechanical properties of the shells and the calcium sequestration ability of the hemocytes of <i>C. gigas</i> and <i>C. virginica</i> The expression of biomineralization-related genes was higher in <i>C. virginica</i> than in <i>C. gigas</i> in multiple tissues including the mantle edge and hemocytes, while the expression of immune genes was higher in the hemocytes of <i>C. gigas</i> Hemocytes of <i>C. virginica</i> contained more calcium (stored intracellularly as calcium carbonate mineral) compared with those of <i>C. gigas</i> Analysis of the adult shells showed that the crystallinity of calcite was higher and the laths of the foliated layer of the shell were thicker in <i>C. virginica</i> than in <i>C. gigas</i> Mechanically, the shells of <i>C. virginica</i> were stiffer, harder and stronger than those of <i>C. gigas</i> Taken together, our results show that the species-specific differences in physiology (such as disease resistance and exoskeleton properties) are reflected at the cellular and molecular levels in the differential specialization of hemocytes on potentially competing functions (immunity and biomineralization) as well as different expression profiles of other tissues involved in biomineralization (such as the mantle edge).
Numerical Modeling of Fused Deposition Processing (1995)

Abstract A recently proposed ceramics production technique, Fused Deposition of Ceramics (FDC), utilizes the Fused Deposition Modeling™ method; with the introduction of ceramic particle filled thermoplastic filaments. This novel method will enable the manufacturers to produce net-shape structural ceramics parts, with little or no post-processing. Numerical simulation of FDC poses numerous provocative challenges. Three models have been developed to investigate the cooling process of deposited filaments and the quantification of vector-length bonding errors between deposited filaments. Finite difference and finite volume techniques are utilized in numerical models to address heat transfer issues regarding the melting and solidification of the thermoplastic binder. MDSC data of RU160 binder-particle system has been incorporated into the numerical models. Rectangular geometry has been used to demonstrate the capabilities of the two dimensional model.
Iron assisted formation of CO2 over condensed CO and its relevance to interstellar chemistry (2020)

Catalytic conversion of CO to CO<sub>2</sub> has been investigated in ultrahigh vacuum (UHV) under cryogenic conditions (10 K). This cryogenic oxidation is assisted by iron upon its co-deposition with CO, on a substrate. The study shows that the interaction of Fe and CO results in a Fe-CO complex that reacts in the presence of excess CO at cryogenic conditions leading to CO<sub>2</sub>. Here, the presence of CO on the surface is a prerequisite for the reaction to occur. Different control experiments confirm that the reaction takes place in the condensed phase and not in the gas phase. Surface sensitive reflection absorption infrared spectroscopy (RAIRS), temperature programmed desorption (TPD), and Cs<sup>+</sup> based low energy ion scattering are utilized for this study. The iron assisted formation of CO<sub>2</sub> may be proposed as another pathway relevant in interstellar ices, containing CO. This direct oxidation process, which occurs at extremely low temperatures and pressures, in the presence of a reactive metal species like iron (the most abundant metal in the interstellar medium) may have astrochemical importance. It does not require any external energy in the form of photo-irradiation or thermal processing. Such reactions are highly relevant in cold dense molecular clouds where interactions between neutral species are more favoured.
Towards a learning-algorithm agnostic generative policy model for coalitions (2019)

Autonomous systems are expected to have a major impact in future coalition operations. These systems are enabled by a variety of Artificial Intelligence (AI) learning algorithms that contextualize and adapt in varying, possibly unforeseen situations to assist humans in achieving complex tasks. Moreover, these systems will be required to operate in dynamic and challenging environments that impose certain constraints such as task formation and collaboration, ad-hoc resource availability, rapidly changing environmental conditions and the requirement to abide by mission objectives. Therefore, such systems require the capability to adapt and evolve so that they can behave autonomously at the edge of the network in new situations. Crucially, autonomous systems have to understand the bounds in which they can operate based on their own capability and the constraints of the environment. Policies are typically used by systems to define their behavior and constraints and often these policies are manually configured and managed by humans. AI-enabled systems will require novel approaches to rapidly learn, create, augment, and model emerging policies to support real-time decision making. Recent work has shown that such policy model generations are possible through symbolic learning to shallow and deep learning approaches for different classes of problems. Motivated by this observation, in this paper, we propose to apply recent advances in explainable-AI to develop an approach which is agnostic to the learning algorithm, thus enabling seamless policy generation in the coalition environment.
Abstract 4522: Akt2 and acid ceramidase cooperate to induce malignant transformation (2014)

Abstract The ability of Akt 2 and acid ceramidase (ASAH1) to cooperate and induce malignant transformation is not known. Here we show that in immortalized, non-transformed cells, ectopic co-expression of Akt2 and ASAH1 is significantly more effective than expression of each gene alone at inducing cell invasion and at conferring resistance to apoptosis. Consistent with these observations, siRNA-mediated depletion of both Akt2 and ASAH1 is much more potent than depleting each alone at inhibiting cell viability/proliferation and cell invasion. Furthermore, pharmacological inhibitors of Akt (TCN or MK-2206) and ASAH1 (B13) synergize to inhibit cell viability/proliferation, and combinations of these drugs are more effective than single agent treatments at inhibiting cell invasion. Taken together, the results suggest that these two enzymes cooperate to induce malignant transformation and warrant further preclinical studies to evaluate the potential of combining inhibitors of Akt and ASAH1 to treat cancer. Citation Format: Said M. Sebti, Norbert Berndt, Ronil Patel, Hua Yang, Maria Balasis. Akt2 and acid ceramidase cooperate to induce malignant transformation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4522. doi:10.1158/1538-7445.AM2014-4522
The Intentional Spring: A Strategy for Modeling Systems That Learn to Perform Intentional Acts (1992)

In motor task learning by instruction, the instructor's skill and intention, which, initially, are extrinsic constraints on the learner's perceiving and acting, eventually become internalized as intrinsic constraints by the learner. How is this process to be described formally? This process takes place via a forcing function that acts both as an anticipatory (informing) influence and a hereditary (controlling) influence. A mathematical strategy is suggested by which such intentions and skills might be dynamically learned. A hypothetical task is discussed in which a blindfolded learner is motorically instructed to pull a spring to a specific target in a specific manner. The modeling strategy involves generalizing Hooke's law to the coupled instructor-spring-Learner system. Specifically, dual Volterra functions express the anticipatory and hereditary influences passed via an instructor-controlled forcing function on the shared spring. Boundary conditions (task goals) on the instructor-spring system, construed as a mathematical (self-adjoint) operator, are passed to the learner-spring system. Psychological interpretation is given to the involved mathematical operations that are passed, and mathematical (Hilbert-Schmidt's and Green's function) techniques are used to account for the release of the boundary conditions by the instructor and their absorption by the learner, and an appropriate change of their power spectra.
Bequinostatins A and B, new inhibitors of glutathione S-transferase, produced by Streptomyces sp. MI384-DF12. Production, isolation, structure determination and biological activities. (1993)

New benzo[a]naphthacenequinone metabolites, designated bequinostatins A and B, have been isolated from the culture broth of the benastatin-producing strain Streptomyces sp. MI384-DF12. The structures of bequinostatins A and B were determined by spectral analyses to be 5,6,8,13-tetrahydro-1,6,7,9,11-pentahydroxy-8,13-dioxo-3- pentylbenzo[a]naphthacene-2-carboxylic acid and 2-decarboxybequinostatin A, respectively. Bequinostatin A showed considerable inhibitory activity against human pi class glutathione S-transferase (GST pi).
Recreational music-making modulates the human stress response: a preliminary individualized gene expression strategy. (2005)

The resultant amelioration of stress-induced genomic expression supports the underlying premise that RMM warrants additional consideration as a rational choice within our armamentarium of stress reduction strategies. Modulation of individualized genomic stress induction signatures in peripheral blood presents a new opportunity for elucidating the dynamics of the human stress response.
ChemInform Abstract: Tubelactomicin A, a Novel 16‐Membered Lactone Antibiotic, from Nocardia sp. Part 2. Structure Elucidation. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Robust MRF-based object tracking and graph-cut-based contour refinement for high quality 2D to 3D video conversion (2011)

Generation of object-boundary-matched accurate depth map is important to semi-automatic 2D to 3D conversion for high quality perception of converted 3D video. In this paper, we propose an accurate depth map generation scheme using an MRF-based initial contour tracking followed by a robust graph-cut-based contour refinement. To limit the propagation of potential tracking errors, key-frames as well as current and previous video frames are considered together in composing the graph cut seeds of the proposed contour refinement. In addition, the proposed scheme checks the ambiguity of seeds in foreground and background to eliminate the seeds, which may cause confusion in graph-cut segmentation, and thereby further improves the accuracy of contour tracking. Experiment results demonstrate the proposed scheme is especially useful when there is complex background or deformation of object, indicating the power of the proposed scheme in object-boundary-matched accurate depth map generation.
Guidelines for DC preparation and flow cytometry analysis of mouse nonlymphoid tissues (2022)

This article is part of the Dendritic Cell Guidelines article series, which provides a collection of state-of-the-art protocols for the preparation, phenotype analysis by flow cytometry, generation, fluorescence microscopy and functional characterization of mouse and human dendritic cells (DC) from lymphoid organs and various nonlymphoid tissues. DC are sentinels of the immune system present in almost every mammalian organ. Since they represent a rare cell population, DC need to be extracted from organs with protocols that are specifically developed for each tissue. This article provides detailed protocols for the preparation of single-cell suspensions from various mouse nonlymphoid tissues, including skin, intestine, lung, kidney, mammary glands, oral mucosa and transplantable tumors. Furthermore, our guidelines include comprehensive protocols for multiplex flow cytometry analysis of DC subsets and feature top tricks for their proper discrimination from other myeloid cells. With this collection, we provide guidelines for in-depth analysis of DC subsets that will advance our understanding of their respective roles in healthy and diseased tissues. While all protocols were written by experienced scientists who routinely use them in their work, this article was also peer-reviewed by leading experts and approved by all coauthors, making it an essential resource for basic and clinical DC immunologists.
One-pot chemoselective functionalization of arylsilanes via cascade metal–metal exchange reactions (2002)

A cascade-transmetallation sequence allows a one-pot conversion of arylsilanes into functionalized arylcoppers; they react with various types of electrophiles (allylic halides, acid chlorides, bromoalkynes); bimetallic zinc–copper-reagents can be prepared by this method either directly or in a sequential fashion.
Influenza‐specific IgG1+ memory B‐cell numbers increase upon booster vaccination in healthy adults but not in patients with predominantly antibody deficiency (2020)

We have successfully identified AM15-specific Bmem cells in healthy controls and PAD patients. The presence of antigen-specific Bmem cells could offer an additional diagnostic tool to aid in the clinical diagnosis of PAD. Furthermore, alterations in the number or immunophenotype of HA-specific Bmem cells post-booster vaccination could assist in the evaluation of immune responses in individuals receiving IgRT.
An improved synthesis of the radiolabeled prostate‐specific membrane antigen inhibitor, [18F]DCFPyL (2016)

The radiosynthesis of [(18) F]DCFPyL on 2 distinct automated platforms with full regulatory compliant quality control specifications is described. The radiotracer synthesis was performed on a custom-made radiofluorination module and the Sofie Biosciences ELIXYS. The radiofluorination module synthesis was accomplished in an average of 66 minutes from end of bombardment with an average specific activity at end of synthesis (EOS) of 4.4 TBq/μmol (120 Ci/μmol) and an average radiochemical yield of 30.9% at EOS. The ELIXYS synthesis was completed in an average of 87 minutes with an average specific activity of 2.2 TBq/μmol (59.3 Ci/μmol) and an average radiochemical yield of 19% at EOS. Both synthesis modules produced large millicurie quantities of [(18) F]DCFPyL while conforming to all standard US Pharmacopeia Chapter <823> acceptance testing criteria.
Effect of oral administration of oxytetra cycline on the oxygen uptake of the Indian major carp, Catla catla. (2016)

The Indian major carp, Catla catla is selected to oral administration of low (0.3mg) and high (0.6mg) doses of oxytetracycline at 24 h intervals for 48-h and its impact on the oxygen uptake of the fish
UWB radio deployment challenges (2002)

The challenges related to the deployment of ultrawideband (UWB) radios are posed in terms of interference issues that UWB radio systems will encounter. The problem of coexistence with a Global Positioning System (GPS) receiver is used as an experimental example. Calculation of an upper bound to the UWB transmitter power illustrates the effect of one possible type of regulation for a given UWB antenna system. The interference environment for a UWB receiver is used to lower bound the UWB transmitter power necessary for a given data rate. Sample measurements are provided.
LocusRoute: a parallel global router for standard cells (2003)

A fast and easily parallelizable global routing algorithm for standard cells and its parallel implementation are presented. LocusRoute is meant to be used as the cost function for a placement algorithm, and so this context constrains the structure of the global routing algorithm and its parallel implementation. The router is based on enumerating a subset of all two-bend routes between two points, and results in 16% to 37% fewer total number of tracks than the Timber Wolf global router for standard cells. It is comparable in quality to a maze router and an industrial router, but is ten times or more faster. Three approaches to parallelizing the router are implemented: wire-by-wire parallelism, segment-by-segment and route-by-route. Two of these approaches achieve significant speedup; route-by-route achieves up to 4.6 using eight processors, and wire-by-wire achieves from 5.8 to 7.6 on eight processors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The proteome of methylmalonic acidemia (MMA): the elucidation of altered pathways in patient livers (2015)

Methylmalonic acidemia (MMA) is a heterogeneous and severe autosomal recessive inborn error of metabolism most commonly caused by the deficient activity of the vitamin B12 dependent enzyme, methylmalonyl-CoA mutase (MUT). The main treatment for MMA patients is the dietary restriction of propiogenic amino acids and carnitine supplementation. Despite treatment, the prognosis for vitamin B12 non-responsive patients remains poor and is associated with neonatal lethality, persistent morbidity and decreased life expectancy. While multi-organ pathology is a feature of MMA, the liver is severely impacted by mitochondrial dysfunction which likely underlies the metabolic instability experienced by the patients. Liver and/or combined liver/kidney transplantation is therefore sometimes performed in severely affected patients. Using liver specimens from donors and MMA patients undergoing elective liver transplantation collected under a dedicated natural history protocol (clinicaltrials.gov: NCT00078078), we employed proteomics to characterize the liver pathology and impaired hepatic metabolism observed in the patients. Pathway analysis revealed perturbations of enzymes involved in energy metabolism, gluconeogenesis and Krebs cycle anaplerosis. Our findings identify new pathophysiologic and therapeutic targets that could be valuable for designing alternative therapies to alleviate clinical manifestations seen in this disorder.
Comprehensive scanning mutagenesis of human retrotransposon LINE-1 identifies motifs essential for function (2019)

Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only autonomous active transposable element in the human genome. The L1-encoded proteins ORF1p and ORF2p enable the element to jump from one locus to another via a “copy and paste” mechanism. ORF1p is an RNA-binding protein and ORF2p has endonuclease and reverse transcriptase activities. The huge number of truncated L1 remnants in the human genome suggests that the host has likely evolved mechanisms to prevent full L1 replication and thereby decrease the proliferation of active elements and reduce the mutagenic potential of L1. In turn, L1 appears to have a minimized length to increase the probability of successful full-length replication. This streamlining would be expected to lead to high information density. Here, we describe the construction and initial characterization of a library of 538 consecutive trialanine substitutions that scan along ORF1p and ORF2p to identify functionally important regions. In accordance with the streamlining hypothesis, retrotransposition was overall very sensitive to mutations in ORF1p and ORF2p, only 16% of trialanine mutants retained near-wild-type activity. All ORF1p mutants formed near-wild-type levels of mRNA transcripts and seventy-five percent formed near-wild-type levels of protein. Two ORF1p mutants present a unique nucleolar-relocalization phenotype. Regions of ORF2p that are sensitive to mutagenesis, but lack phylogenetic conservation were also identified. We provide comprehensive information on the regions most critical to retrotransposition. This resource will guide future studies of intermolecular interactions that form with RNA, proteins and target DNA throughout the L1 life cycle.
Genome-Wide Association Study Identifies Single Nucleotide Polymorphism in DYRK1A Associated with Replication of HIV-1 in Monocyte-Derived Macrophages (2011)

These findings suggest that the kinase DYRK1A is involved in the replication of HIV-1, in vitro in macrophages as well as in vivo.
Inductive Transfer for Text Classification using Generalized Reliability Indicators (2003)

Machine-learning researchers face the omnipresent challenge of developing predictive models that converge rapidly in accuracy with increases in the quantity of scarce labeled training data. We introduce Layered Abstraction-Based Ensemble Learning (LABEL), a method that shows promise in improving generalization performance by exploiting additional labeled data drawn from related discrimination tasks within a corpus and from other corpora. LA-BEL first maps the original feature space, targeted at predicting membership in a specific topic, to a new feature space aimed at modeling the reliability of an ensemble of text classifiers. The resulting abstracted representation is invariant across each of the binary discrimination tasks, allowing the data to be pooled. We then construct a context-sensitive combination rule for each task using the pooled data. Thus, we are able to more accurately model domain structure which would not have been possible using only the limited labeled data from each task separately. Using several corpora for an empirical evaluation of topic classification accuracy of text documents, we demonstrate that LABEL can increase the generalization performance across a set of related tasks.
Cognitive changes and modified processing of amyloid precursor protein in the cortical and hippocampal system after cholinergic synapse loss and muscarinic receptor activation (1999)

A number of in vitro studies have shown that activation of muscarinic receptors by cholinergic agonists stimulates the nonamyloidogenic, alpha-secretase-processing pathway of amyloid precursor protein (APP). To determine whether increased cholinergic neurotransmission can modify the APP processing in vivo, we administered a muscarinic receptor agonist (RS86) to normal or aged rats and rats with severe basal forebrain cholinergic deficits (induced by 192 IgG-saporin). The levels of the cell-associated APP in neocortex, hippocampus, and striatum, as well as the secreted form of APP (APPs) in cerebrospinal fluid, were examined by Western blots. Additionally, we investigated the association between the altered APP levels and behavioral deficits caused by cholinergic lesions. We found that treatment with muscarinic receptor agonist resulted in decreased APP levels in neocortex and hippocampus and increased levels of APPs in cerebrospinal fluid. Regulation of APP processing by the muscarinic agonist treatment occurred not only in normal rats, but also in aged and cholinergic denervated rats that model this aspect of Alzheimer's disease. Interestingly, we found that elevation of APP in neocortex correlated with the cognitive deficits in water-maze testing of rats with cholinergic dysfunction. These data indicate that increased cholinergic neurotransmission can enhance nonamyloidogenic APP processing in intact and lesioned rats and that APP may be involved in cognitive performance.