gebhart/patrepeval huggingface dataset:
Increased interleukin-1β gene expression in peripheral blood leukocytes is associated with increased pain and predicts risk for progression of symptomatic knee osteoarthritis (2011)

PBLs from patients with symptomatic knee OA display a characteristic transcriptome profile. Moreover, increased expression of IL-1β identifies a subset of patients with OA who have increased pain and are at higher risk of radiographic progression of OA.
The Pseudomonas Toxin Pyocyanin Inhibits the Dual Oxidase-Based Antimicrobial System as It Imposes Oxidative Stress on Airway Epithelial Cells (2008)

The dual oxidase-thiocyanate-lactoperoxidase (Duox/SCN(-)/LPO) system generates the microbicidal oxidant hypothiocyanite in the airway surface liquid by using LPO, thiocyanate, and Duox-derived hydrogen peroxide released from the apical surface of the airway epithelium. This system is effective against several microorganisms that infect airways of cystic fibrosis and other immunocompromised patients. We show herein that exposure of airway epithelial cells to Pseudomonas aeruginosa obtained from long-term cultures inhibits Duox1-dependent hydrogen peroxide release, suggesting that some microbial factor suppresses Duox activity. These inhibitory effects are not seen with the pyocyanin-deficient P. aeruginosa strain PA14 Phz1/2. We show that purified pyocyanin, a redox-active virulence factor produced by P. aeruginosa, inhibits human airway cell Duox activity by depleting intracellular stores of NADPH, as it generates intracellular superoxide. Long-term exposure of human airway (primary normal human bronchial and NCI-H292) cells to pyocyanin also blocks induction of Duox1 by Th2 cytokines (IL-4, IL-13), which was prevented by the antioxidants glutathione and N-acetylcysteine. Furthermore, we showed that low concentrations of pyocyanin blocked killing of wild-type P. aeruginosa by the Duox/SCN(-)/LPO system on primary normal human bronchial epithelial cells. Thus, pyocyanin can subvert Pseudomonas killing by the Duox-based system as it imposes oxidative stress on the host. We also show that lactoperoxidase can oxidize pyocyanin, thereby diminishing its cytotoxicity. These data establish a novel role for pyocyanin in the survival of P. aeruginosa in human airways through competitive redox-based reactions between the pathogen and host.
Personal Deductions – An "Ideal" or Just Another "Deal"? (2002)

The allowance of many personal deductions, such as the deduction for medical expenses or charitable contributions, has been criticized on the contention that such deductions are not appropriate elements of an income tax system, but rather are merely devices by which Congress has expended federal funds to further some nontax program or other goal. The tax revenues that are not collected because of these provisions have been characterized as “subsidies” or as camouflaged direct expenditures of the government. This view has attained such prominence that Congress requires the federal government to publish annually a “budget” that lists those tax provisions that the issuing department concludes are so-called “tax expenditures.” The premise of these tax expenditure budgets is that the provisions listed in them do not implement the principles that justify using income measurement as the basis for allocating the federal tax burden among the populace. This view rests on a notion that there are immutable principles that underlie the adoption of an income tax system and that some agreement can be reached as to the identification of those principles. The adoption of the tax expenditure concept has had enormous effect on the inclusion and deletion of provisions in the tax law. This article examines four personal deductions that have been characterized in the publication of “budgets” by several government agencies as tax expenditures, and therefore as not conforming to income tax principles. The four deduction are: medical expenses, theft and casualty losses, charitable contributions, and the interest deduction for mortgages on a personal residence. The thesis of this article is that all of those deductions, in fact, do conform to progressive income tax principles and therefore cannot properly by characterized as governmental expenditures. In other words, each of those deductions performs a useful task in the proper measurement of income for tax allocation purposes when the entire structure of the income tax and the principles that underlie it are taken into account. While the determination of whether the deductions discussed in this article are expenditures is not conclusive of the issue of their survival in the tax law, it can have a significant impact on their survival or on the terms on which they might survive. Moreover, the validity and usefulness of the entire tax expenditure concept is open to question, and a demonstration that a number of items have been wrongly identified as expenditures by the government agencies that list those items weakens whatever confidence one might otherwise still have in the concept.
Die Keimbildung bei der Ausscheidung in metallischen Mischkristallen (1938)

Abstract Unter der Annahme, daß die Energie eines Mischkristalls durch einfache Addition von Nachbarbindungen berechnet werden darf, wird die Keimbildungsarbeit für die Ausscheidung in einem übersättigten binären Mischkristall berechnet. Daraus läßt sich die Häufigkeit der Keimbildung bestimmen. Aus der Durchrechnung eines Zahlenbeispiels ergibt sich für diejenige Unterkühlung, bei welcher die Keimbildungshäufigkeit ihr Maximum erreicht, eine befriedigende Übereinstimmung mit vorliegenden Messungen über die Geschwindigkeit der Ausscheidung.
Apoptosis-inducing effect of erlotinib is potentiated by 3,3′-diindolylmethane in vitro and in vivo using an orthotopic model of pancreatic cancer (2008)

Blockade of epidermal growth factor receptor (EGFR) by EGFR tyrosine kinase inhibitors is insufficient for effective antitumor activity because of independently activated survival pathways. A multitargeted approach may therefore improve the outcome of anti-EGFR therapies. In the present study, we determined the effects of 3,3'-diindolylmethane (Bioresponse BR-DIM referred to as B-DIM), a formulated DIM with greater bioavailability on cell viability and apoptosis with erlotinib in vitro and in vivo using an orthotopic animal tumor model. BxPC-3 and MIAPaCa cells with varying levels of EGFR and nuclear factor-kappaB (NF-kappaB) DNA-binding activity were treated with B-DIM (20 micromol/L), erlotinib (2 micromol/L), and the combination. Cell survival and apoptosis was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and histone-DNA ELISA. Electrophoretic mobility shift assay was used to evaluate NF-kappaB DNA-binding activity. We found significant reduction in cell viability by both 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and clonogenic assays, induction of apoptosis, down-regulation of EGFR phosphorylation, NF-kappaB DNA-binding activity, and expression of antiapoptotic genes in BxPC-3 cells when treated with the combination of erlotinib and B-DIM compared with either agent alone. In contrast, no such effect was observed in MIAPaCa cells by similar treatment. Most importantly, these in vitro results were recapitulated in animal model showing that B-DIM in combination with erlotinib was much more effective as an antitumor agent compared with either agent alone. These results suggest that the utilization of B-DIM could be a useful strategy for achieving better treatment outcome in patients with activated status of EGFR and NF-kappaB in their tumors.
Sterility, Stability and Potency Medications Administered by Carers in Home-based Palliative Care (2008)

Nurses providing palliative care to people at end-of-life in the community sometimes prepare and leave single doses of medications in a client's refrigerator. The client's carer, who is usually a relative, will administer the injectable medications subcutaneously (SC), as prescribed, in order to alleviate the palliative care client's symptoms.
Thyroglobulin (Tg) Recovery Testing with Quantitative Tg Antibody Measurement for Determining Interference in Serum Tg Assays in Differentiated Thyroid Carcinoma (2006)

The Nichols Advantage TgR assay is a valuable complementary method to overcome the technical problem of interference by TgAbs or HAMAs in TgAb assays. Further studies are needed to confirm the potential added value of this TgR assay.
Particle Enhanced Light Scattering Immunoassay (1992)

Particle enhanced immunoassays have been in use since the 1920s. In 1925 Jules Freund published an article demonstrating that, if soluble proteins were adsorbed onto the surfaces of small particles they would agglutinate when mixed with antisera raised against the protein.! Freund used tubercle bacteria for his particle and was then followed by several other workers.v' What were probably the first synthetic particles were reported in the 1920s by Loeb, who used collodion, a form of nitrocellulose.' Their use became more widespread following the work of Cannon and Marshall in the 1940s 6 who demonstrated the usefulness of coupling antigen to particles as a rapid means of evaluating the titre of antisera, particularly in the development of a test for anti-tuberculin sera. In 1943 Cavelti explored some of the characteristics of collodion particles that were important in enabling specific antibody mediated aggregations to occur. 7 From these earliest days workers became aware of one of the major problems of particle based assays, that of non-specific aggregation, a problem that still requires careful attention today.
Distance metric learning with eigenvalue optimization (2012)

The main theme of this paper is to develop a novel eigenvalue optimization framework for learning a Mahalanobis metric. Within this context, we introduce a novel metric learning approach called DML-eig which is shown to be equivalent to a well-known eigenvalue optimization problem called minimizing the maximal eigenvalue of a symmetric matrix (Overton, 1988; Lewis and Overton, 1996). Moreover, we formulate LMNN (Weinberger et al., 2005), one of the state-of-the-art metric learning methods, as a similar eigenvalue optimization problem. This novel framework not only provides new insights into metric learning but also opens new avenues to the design of efficient metric learning algorithms. Indeed, first-order algorithms are developed for DML-eig and LMNN which only need the computation of the largest eigenvector of a matrix per iteration. Their convergence characteristics are rigorously established. Various experiments on benchmark data sets show the competitive performance of our new approaches. In addition, we report an encouraging result on a difficult and challenging face verification data set called Labeled Faces in the Wild (LFW).
Nano-Bioelectronics (2015)

Nano-bioelectronics represents a rapidly expanding interdisciplinary field that combines nanomaterials with biology and electronics and, in so doing, offers the potential to overcome existing challenges in bioelectronics. In particular, shrinking electronic transducer dimensions to the nanoscale and making their properties appear more biological can yield significant improvements in the sensitivity and biocompatibility and thereby open up opportunities in fundamental biology and healthcare. This review emphasizes recent advances in nano-bioelectronics enabled with semiconductor nanostructures, including silicon nanowires, carbon nanotubes, and graphene. First, the synthesis and electrical properties of these nanomaterials are discussed in the context of bioelectronics. Second, affinity-based nano-bioelectronic sensors for highly sensitive analysis of biomolecules are reviewed. In these studies, semiconductor nanostructures as transistor-based biosensors are discussed from fundamental device behavior through sensing applications and future challenges. Third, the complex interface between nanoelectronics and living biological systems, from single cells to live animals, is reviewed. This discussion focuses on representative advances in electrophysiology enabled using semiconductor nanostructures and their nanoelectronic devices for cellular measurements through emerging work where arrays of nanoelectronic devices are incorporated within three-dimensional cell networks that define synthetic and natural tissues. Last, some challenges and exciting future opportunities are discussed.
The Malmo platform for artificial intelligence experimentation (2016)

We present Project Malmo - an AI experimentation platform built on top of the popular computer game Minecraft, and designed to support fundamental research in artificial intelligence. As the AI research community pushes for artificial general intelligence (AGI), experimentation platforms are needed that support the development of flexible agents that learn to solve diverse tasks in complex environments. Minecraft is an ideal foundation for such a platform, as it exposes agents to complex 3D worlds, coupled with infinitely varied game-play.

Project Malmo provides a sophisticated abstraction layer on top of Minecraft that supports a wide range of experimentation scenarios, ranging from navigation and survival to collaboration and problem solving tasks. In this demo we present the Malmo platform and its capabilities. The platform is publicly released as open source software at IJCAI, to support openness and collaboration in AI research.
Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties (2005)

We have recently sequenced the genome of a novel thermophilic bacteriophage designated as TS2126 that infects the thermophilic eubacterium Thermus scotoductus. One of the annotated open reading frames (ORFs) shows homology to T4 RNA ligase 1, an enzyme of great importance in molecular biology, owing to its ability to ligate single-stranded nucleic acids. The ORF was cloned, and recombinant protein was expressed, purified and characterized. The recombinant enzyme ligates single-stranded nucleic acids in an ATP-dependent manner and is moderately thermostable. The recombinant enzyme exhibits extremely high activity and high ligation efficiency. It can be used for various molecular biology applications including RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE). The TS2126 RNA ligase catalyzed both inter- and intra-molecular single-stranded DNA ligation to >50% completion in a matter of hours at an elevated temperature, although favoring intra-molecular ligation on RNA and single-stranded DNA substrates. The properties of TS2126 RNA ligase 1 makes it very attractive for processes like adaptor ligation, and single-stranded solid phase gene synthesis.
Lidocaine Toxicity from Topical Mucosal Application (1983)

A case is reported of an infant who experienced seizures while being treated with a topical lidocaine 2% solution (Xylocaine 2% Viscous) for teething. The pharmacology of lidocaine is reviewed to alert physicians to the potential dangers of topical mucosal application of these preparations.
Dentin Permeability: Determinants of Hydraulic Conductance (1978)

A technique is described which permits measurements of the ease with which fluid permeates dentin. This value, the hydraulic conductance of dentin, increased as surface area increases and/or as dentin thickness decreases. It increased 32-fold when dentin was acid etched due to removal of surface debris occluding the tubules.
Marine Animal Biosynthetic Constituents For Cancer Chemotherapy (1981)

A fifteen year investigation of marine animal components as sources for new and potentially useful cancer chemotherapeutic drugs has led to our discovery of a number of such valuable substance. The especially productive Indian Ocean sea hare Dolabella auricularia has yielded (100 kg leads to or approximately 1 mg each) a series of very potent cell growth inhibitory substances designated dolastatins 1-9. The first member of this new series, dolastatin 1, may represent the most potent anticancer agent so far uncovered with, e.g., a curative response (33%) using a dose of 11 microgram/kg (T/C 240, to T/C 139 at 1.37 microgram/kg) in the National Cancer Institute's murine B16 melanoma. Structural elucidation of the new antineoplastic agents is underway, and recent progress is illustrated with peptide dolastatin 3 (P388 ED 50 2.7 x 10(-7) microgram/ml).
The Meaning of Intonational Contours in the Interpretation of Discourse (1990)

Recent investigations of the contribution that intonation makes to overall utterance and discourse interpretation promise new sources of information for the investigation of long-time concerns in NLP. In Hirschberg &amp; Pierrehumber 1986 we proposed that intonational features such as phrasing, accent placement, pitch range, and tune represent important sources of information about the attentional and intentional structures of discourse. In this paper we examine the particular contribution of choice of tune, or intonational contour, to discourse interpretation.
Redesign of the substrate specificity ofescherichia coliaspartate aminotransferase to that ofescherichia colityrosine aminotransferase by homology modeling and site-directed mutagenesis (1995)

Although several high-resolution X-ray crystallographic structures have been determined for Escherichia coli aspartate aminotransferase (eAATase), efforts to crystallize E. coli tyrosine aminotransferase (eTATase) have been unsuccessful. Sequence alignment analyses of eTATase and eAATase show 43% sequence identity and 72% sequence similarity, allowing for conservative substitutions. The high similarity of the two sequences indicates that both enzymes must have similar secondary and tertiary structures. Six active site residues of eAATase were targeted by homology modeling as being important for aromatic amino acid reactivity with eTATase. Two of these positions (Thr 109 and Asn 297) are invariant in all known aspartate aminotransferase enzymes, but differ in eTATase (Ser 109 and Ser 297). The other four positions (Val 39, Lys 41, Thr 47, and Asn 69) line the active site pocket of eAATase and are replaced by amino acids with more hydrophobic side chains in eTATase (Leu 39, Tyr 41, Ile 47, and Leu 69). These six positions in eAATase were mutated by site-directed mutagenesis to the corresponding amino acids found in eTATase in an attempt to redesign the substrate specificity of eAATase to that of eTATase. Five combinations of the individual mutations were obtained from mutagenesis reactions. The redesigned eAATase mutant containing all six mutations (Hex) displays second-order rate constants for the transamination of aspartate and phenylalanine that are within an order of magnitude of those observed for eTATase. Thus, the reactivity of eAATase with phenylalanine was increased by over three orders of magnitude without sacrificing the high transamination activity with aspartate observed for both enzymes.(ABSTRACT TRUNCATED AT 250 WORDS)
Modulation of murine systemic lupus erythematosus with peptides based on complementarity determining regions of a pathogenic anti-DNA monoclonal antibody (1997)

Experimental systemic lupus erythematosus (SLE) can be induced in naive mice by immunization with a murine monoclonal anti-DNA antibody (mAb), 5G12, that bears a major idiotype designated 16/6 Id. Strain-dependent differences were observed in the proliferative responses of lymph node cells of mice immunized with two peptides based on the sequences of the complementarity determining region (CDR) 1 and 3 of mAb 5G12. The capacity of the peptides to bind to major histocompatibility complex class II molecules correlated with the proliferative responses. Immunization of high responder strains with the CDR-based peptides led to production of autoantibodies and clinical manifestations characteristic to experimental SLE. The CDR-based peptides could prevent autoantibody production in neonatal mice that were immunized later either with the peptide or with the pathogenic autoantibody. Furthermore, the peptides inhibited specific proliferation of lymph node cells of mice immunized with the same peptide, with mAb 5G12 or with the human mAb anti-DNA, 16/6 Id. Thus, the CDR-based peptides are potential candidates for therapy of SLE.
High Level Power Estimation and Reduction Techniques for Power Aware Hardware Design (2010)

The unabated continuation of the Moore's law has allowed the doubling of the number of transistors per unit area of a silicon die every 2 years or so. At the same time, an increasing demand on consumer electronics and computing equipments to run sophisticated applications has led to an unprecedented complexity of hardware designs. These factors have necessitated the abstraction level of design-entry of hardware systems to be raised beyond the Register-Transfer-Level (RTL) to Electronic System Level (ESL). However, power envelope on the designs due to packaging and other thermal limitations, and the energy envelope due to battery life-time considerations have also created a need for power/energy efficient design. The confluence of these two technological issues has created an urgent need for solving two problems: (i) How do we enable a power-aware design flow with a design entry point at the Electronic System Level? (ii) How do we enable power aware High Level Synthesis to automatically synthesize RTL implementation from ESL? This dissertation distinguishes itself by addressing the following two issues: (i) Since power/energy consumption of electronic systems largely depends on implementation details, and high-level models abstract away from such details, power/energy estimation at such levels has not been addressed thoroughly. (ii) A lot of work has been done in applying various techniques on control-data-flow graphs (CDFG) to find power/area/latency pareto points during behavioral synthesis. However, high level C-based functional models of various compute-intensive components, which could be easily synthesized as co-processors, have many opportunities to reduce power. Some of these savings opportunities are traditional such as clock-gating, operand-isolation etc. The exploration of alternate granularities of these techniques with target applications in mind, opens the door for traditional power reduction opportunities at the high-level. This work therefore concentrates on the aforementioned two areas of inadequacy of hardware design methodologies. Our proposed solutions include utilizing ESL simulation traces and mapping those to lower abstraction levels for power estimation, derivation of statistical power models using regression based learning for power estimation at early design stages, etc. On the HLS front, techniques that insert the power saving features during the synthesis process using exploration of granularity and scope of clock-gating, sequential clock-gating are proposed. Finally, this work shows how to marry two domains, that is estimation and reduction. In this regard, a power model is proposed, which helps in predicting power savings obtained using clock-gating and further guiding HLS to selectively insert clock-gating.