gebhart/patrepeval huggingface dataset:
Brain Glucose Hypometabolism and Oxidative Stress in Preclinical Alzheimer's Disease (2008)

One of the main features of Alzheimer's disease (AD) is the severe reduction of the cerebral metabolic rate for glucose (CMRglc). In vivo imaging using positron emission tomography with 2-[(18)F]fluoro-2-deoxy-D-glucose (FDG-PET) demonstrates consistent and progressive CMRglc reductions in AD patients, the extent and topography of which correlate with symptom severity. Increasing evidence suggests that CMRglc reductions occur at the preclinical stages of AD. CMRglc reductions were observed on FDG-PET before the onset of disease in several groups of at-risk individuals, including patients with mild cognitive impairment (MCI), often a prodrome to AD; presymptomatic individuals carrying mutations responsible for early-onset familial AD; cognitively normal elderly individuals followed for several years until they declined to MCI and eventually to AD; normal, middle-aged individuals who expressed subjective memory complaints and were carriers of the apolipoprotein E epsilon-4 allele, a strong genetic risk factor for late-onset AD. However, the causes of the early metabolic dysfunction forerunning the onset of AD are not known. An increasing body of evidence indicates a deficient or altered energy metabolism that could change the overall oxidative microenvironment for neurons during the pathogenesis and progression of AD, leading to alterations in mitochondrial enzymes and in glucose metabolism in AD brain tissue. The present paper reviews findings that implicate hypometabolism and oxidative stress as crucial players in the initiation and progression of synaptic pathology in AD.
Biocompatible, Luminescent Silver@Phenol Formaldehyde Resin Core/Shell Nanospheres: Large‐Scale Synthesis and Application for In Vivo Bioimaging (2008)

Abstract Biocompatible and green luminescent monodisperse silver/phenol formaldehyde resin core/shell spheres with controllable sizes, in the range of 180 to 1000 nm, and interesting architectures (centric, eccentric, and coenocytic core/shell spheres) have been synthesized by a facile one‐step hydrothermal approach. These spheres can be used as bioimaging labels for human lung cancer H1299 cells. The results demonstrate that the nanoparticles can be internalized into cells and exhibit no cytotoxic effects, showing that such novel biocompatible core/shell structures can potentially be used as in vivo bioimaging labels. This facile one‐pot polymerization and encapsulation technique may provide a useful tool to synthesize other core/shell particles that have potential application in biotechnology.
Double-decker Yttrium(III) Complexes with Phthalocyaninato and Porphyrinato Ligands (1999)

A series of new yttrium(III) double-decker complexes with the same and different phthalocyaninato and porphyrinato ligands has been prepared. The homoleptic complexes Y ( P ) 2 ( P = Pc *(C 7 H 15 ) 8 , Pc *( OC 5 H 11 ) 8 ; Pc * = 2,3,9,10,16,17,23,24-octasubstituted phthalocyaninate) have been synthesized by treating yttrium(III) acetylacetonate ( Y ( acac ) 3 · H 2 O ) with the phthalonitriles C 6 H 2 R 2 ( CN ) 2 ( R = C 7 H 15 , OC 5 H 11 ) in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). The heteroleptic analogues Y ( P )( Pc ) ( P = Pc *( C 7 H 15 ) 8 , Pc *( OC 5 H 11 ) 8 ; Pc = unsubstituted phthalocyaninate) and Y ( P )( Por ) ( P = Pc , Pc *( C 7 H 15 ) 8 ; Por = meso-tetraphenylporphyrinate (TPP), meso-tetra(4-pyridyl)porphyrinate (TPyP)) have been prepared by the base-catalysed tetramerization of the corresponding phthalonitriles using Y ( P )( acac ) ( P = Pc , TPP , TPyP ) as templates. The syntheses along with the spectroscopic and electrochemical properties of these novel double-deckers are described.
Dendritic Cells Infiltrating Human Non-Small Cell Lung Cancer Are Blocked at Immature Stage (2007)

The efficacy of immune response to control human cancer remains controversial. It is particularly debated whether and to what extent the capacity of tumor-infiltrating dendritic cells (DC) to drive immunization can be turned off by transformed cells, leading to tumor-specific tolerance rather than immunization. To address this issue, we have characterized the DC isolated from human non-small cell lung cancer (NSCLC). These biopsy specimens contained CD11c(high) myeloid DC (mDC), but also CD11c(-) plasmacytoid DC (pDC) and a third DC subset expressing intermediate level of CD11c. Compared with peripheral blood, CD11c(high) tumor-infiltrating DC (TIDC) displayed a "semi-mature" phenotype, and TLR4 or TLR8 stimulation drove them to mature partially and to secrete limited amounts of cytokines. In contrast, most tumor-infiltrating pDC were immature but underwent partial maturation after TLR7 activation, whereas TLR9 ligation triggered low secretion of IFN-alpha. CD11c(int) mDC represented approximately 25% of total DC in tumoral and peritumoral tissues and expressed low levels of costimulatory molecules contrasting with high levels of the immunoinhibitory molecule B7-H1. Finally, the poor APC function of total TIDC even after TLR stimulation and the migratory response of both tumor-infiltrating mDC and pDC toward CCL21 and SDF-1 in vitro suggested their ability to compromise the tumor-specific immune response in draining lymph nodes in vivo. Further studies will be required to establish the specific role of the three TIDC subsets in tumor immunity and to draw conclusions for the design of therapeutic strategies.
Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice (2021)

Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2-RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD-immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2-RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses.
Isolation of cDNA Coding for the Major Mite Allergen <i>Der </i><i>p</i> II by IgE Plaque Immunoassay (1990)

A lambda gt11 library made with cDNA from the house dust mite Dermatophagoides pteronyssinus was screened with human allergic serum by IgE plaque radioimmunoassay. This resulted in the isolation of clones coding for the major allergen Der p II. The cDNA coded for a 129-residue protein of 14,131 daltons with no N-glycosylation sites. No sequence homology with other proteins was evident. The Der p II expressed in Escherichia coli reacted with IgE in 14 of 17 sera from mite-allergic patients giving clonal evidence for its designation as a major allergen. This, along with previous work, has resulted in the cloning of the two major mite allergens.
Indexing Semistructured Data (1998)

This paper describes techniques for building and exploiting indexes on semistructured data: data that may not have a fixed schema and that may be irregular or incomplete. We first present a general framework for indexing values in the presence of automatic type coercion. Then based on Lore, a DBMS for semistructured data, we introduce four types of indexes and illustrate how they are used during query processing. Our techniques and indexing structures are fully implemented and integrated into the Lore prototype. 1 Introduction We call data that is irregular or that exhibits type and structural heterogeneity semistructured, since it may not conform to a rigid, predefined schema. Such data arises frequently on the Web, or when integrating information from heterogeneous sources. In general, semistructured data can be neither stored nor queried in relational or object-oriented database management systems easily and efficiently. We are developing Lore 1 , a database management system d...
A Continuum of Anionic Charge: Structures and Functions ofd-Alanyl-Teichoic Acids in Gram-Positive Bacteria (2003)

Teichoic acids (TAs) are major wall and membrane components of most gram-positive bacteria. With few exceptions, they are polymers of glycerol-phosphate or ribitol-phosphate to which are attached glycosyl and D-alanyl ester residues. Wall TA is attached to peptidoglycan via a linkage unit, whereas lipoteichoic acid is attached to glycolipid intercalated in the membrane. Together with peptidoglycan, these polymers make up a polyanionic matrix that functions in (i) cation homeostasis; (ii) trafficking of ions, nutrients, proteins, and antibiotics; (iii) regulation of autolysins; and (iv) presentation of envelope proteins. The esterification of TAs with D-alanyl esters provides a means of modulating the net anionic charge, determining the cationic binding capacity, and displaying cations in the wall. This review addresses the structures and functions of D-alanyl-TAs, the D-alanylation system encoded by the dlt operon, and the roles of TAs in cell growth. The importance of dlt in the physiology of many organisms is illustrated by the variety of mutant phenotypes. In addition, advances in our understanding of D-alanyl ester function in virulence and host-mediated responses have been made possible through targeted mutagenesis of dlt. Studies of the mechanism of D-alanylation have identified two potential targets of antibacterial action and provided possible screening reactions for designing novel agents targeted to D-alanyl-TA synthesis.
Anti-Clumping Factor A Immunoglobulin Reduces the Duration of Methicillin-ResistantStaphylococcus aureusBacteremia in an Experimental Model of Infective Endocarditis (2003)

SA-IGIV is a human polyclonal immunoglobulin containing elevated levels of antibodies specific for the fibrinogen-binding MSCRAMM protein clumping factor A (ClfA). In vitro, SA-IGIV specifically recognized ClfA that was expressed on the surface of Staphylococcus aureus and inhibited bacterial adherence to immobilized human fibrinogen by >95%. Moreover, SA-IGIV efficiently opsonized ClfA-coated fluorescent beads and facilitated phagocytosis by human polymorphonuclear leukocytes. To determine its potential therapeutic efficacy, SA-IGIV was evaluated in combination with vancomycin in a rabbit model of catheter-induced aortic valve infective endocarditis (IE) caused by methicillin-resistant S. aureus (MRSA). The combination therapy was more effective than vancomycin alone in sterilizing all valvular vegetations when used therapeutically during early (12-h) IE. The combination therapy resulted in clearance of bacteremia that was significantly faster than that of vancomycin alone in animals with well-established (24-h) IE. Therefore, in both early and well-established MRSA IE, the addition of SA-IGIV to a standard antibiotic regimen (vancomycin) increased bacterial clearance from the bloodstream and/or vegetations.
TRECVID 2017: Evaluating Ad-hoc and Instance Video Search, Events Detection, Video Captioning, and Hyperlinking (2017)

International audience
Epitaxial oxide thin films on Si(001) (2000)

Over the years, the development of epitaxial oxides on silicon has been a great technological challenge. Amorphous silicon oxide layer forms quickly at the interface when the Si surface is exposed to oxygen, making the intended oxide heteroepitaxy on Si substrate extremely difficult. Epitaxial oxides such as BaTiO3 (BTO) and SrTiO3 (STO) integrated with Si are highly desirable for future generation transistor gate dielectric and ferroelectric memory cell applications. In this article, we review the recent progress in the heteroepitaxy of oxide thin films on Si(001) substrate by using the molecular beam epitaxy technique at Motorola Labs. Structural, interfacial and electrical properties of the oxide thin films on Si have been characterized using in situ reflection high energy electron diffraction, x-ray diffraction, spectroscopic ellipsometry, atomic force microscopy, Auger electron spectroscopy, x-ray photoelectron spectroscopy, high-resolution transmission electron microscopy, high-resolution transmission electron energy loss spectroscopy, capacitance–voltage and current–voltage measurement. We also present the transistor results and address the impact of the epitaxial oxide films on future generation metal-oxide-semiconductor field effect transistors.
Progress of particle therapy in Japan (2001)

The starting time in particle therapy in Japan was not so early compared to other western countries, but the recent development of medical applications using accelerator beams has been outstanding. After 15 years experience in proton therapy at University of Tsukuba and especially the promising results of recent years in heavy ion therapy at HIMAC, many projects of charged particle therapy are promoted at various places. In this paper, the present status of these projects and ongoing clinical results are described.
Nonhormonal Alternatives for the Treatment of Hot Flashes (2004)

Clonidine, venlafaxine, paroxetine, fluoxetine, and gabapentin are nonhormonal agents that have demonstrated efficacy in small controlled and uncontrolled trials in reducing hot flashes and should be considered in patients unwilling or unable to take hormonal therapies.
Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma (2014)

These findings define a genetic basis for benefit from CTLA-4 blockade in melanoma and provide a rationale for examining exomes of patients for whom anti-CTLA-4 agents are being considered. (Funded by the Frederick Adler Fund and others.).
Role of the intracellular domains of CXCR4 in SDF-1–mediated signaling (2002)

The CXCR4 chemokine receptor is a G(i) protein-coupled receptor that triggers multiple intracellular signals in response to stromal cell-derived factor 1 (SDF-1), including calcium mobilization and p44/42 extracellular signal-regulated kinases (ERK1/2). Transduced signals lead to cell chemotaxis and are terminated through receptor internalization depending on phosphorylation of the C terminus part of CXCR4. Receptor endocytosis is also required for some receptors to stimulate ERK1/2 and to migrate through a chemokine gradient. In this study, we explored the role played by the 3 intracellular loops (ICL1-3) and the C terminus domain of CXCR4 in SDF-1-mediated signaling by using human embryonic kidney (HEK)-293 cells stably expressing wild-type or mutated forms of CXCR4. ICL3 of CXCR4 is specifically involved in G(i)-dependent signals such as calcium mobilization and ERK activation, but does not trigger CXCR4 internalization after SDF-1 binding, indicating that ERK phosphorylation is independent of CXCR4 endocytosis. Surprisingly, ICL2, with or without the aspartic acid, arginine, and tyrosine (DRY) motif, is dispensable for G(i) signaling. However, ICL2 and ICL3, as well as the C terminus part of CXCR4, are needed to transduce SDF-1-mediated chemotaxis, suggesting that this event involves multiple activation pathways and/or cooperation of several cytoplasmic domains of CXCR4.
Myocardial Infarction Redefined: Role of Cardiac Troponin Testing (2001)

As we move into the new Millennium, “the times they are a changin” regarding the diagnostic criteria used to rule in and rule out acute myocardial infarction (AMI) (1). The purpose of this editorial is to comment on the new cardiology guidelines for the redefinition of AMI and unstable angina, as well as to compare them with previously published laboratory medicine recommendations. Some of the new recommendations made by clinical groups may appear to be in conflict with those published previously by laboratory medicine groups; thus, we document the chronology and evolution of all guidelines on the use of cardiac markers.

Consensus documents recently published by the European Society of Cardiology (ESC), the American College of Cardiology (ACC), and the American Heart Association (AHA) make specific recommendations on the use of biomarkers for the detection of myocardial infarction (MI) (2)(3)(4)(5). The redefined criteria used to classify acute coronary syndrome (ACS) patients presenting with ischemic symptoms as acute, evolving, or recent MI are heavily predicated on an increased serum/plasma cardiac troponin (I or T) concentration (2)(3)(4). Furthermore, in the new ACC/AHA guidelines for management of patients with unstable angina and non-ST-segment elevation MI (NSTEMI), an increased cardiac troponin value establishes the diagnosis of NSTEMI, whereas a normal cardiac troponin value establishes the diagnosis of unstable angina in ACS patients with ischemic discomfort (5).

The new guidelines emphasize the following clinical issues. First, increases of cardiac troponins are indicative of myocardial injury but are not synonymous with MI or an ischemic mechanism of injury. If an ischemic mechanism of injury is unlikely, other etiologies of myocardial injury should be pursued. Second, increases in cardiac troponin likely reflect irreversible rather than reversible injury, although there is continuing debate on this issue. Third, …
Incorporation of nisin into a meat binding system to inhibit bacteria on beef surfaces (1998)

In two separate experiments, the bacteriocin, nisin, was incorporated into a commercially available meat binding system (Fibrimex) and applied to meat surfaces as a way of inhibiting the meat spoilage organism, Brochothrix thermosphacta during extended refrigerated storage. In experiment 1, pre-rigor lean beef carcass tissue (BCT) was inoculated with B. thermosphacta, left untreated (U), treated with 10 micrograms ml-1 nisin (N), Fibrimex (F) or Fibrimex containing 10 micrograms ml-1 nisin (FN), held aerobically at 4 degrees C for up to 7 d, and populations of B. thermosphacta and nisin activity determined. Experiment 2 determined the effects of the same treatments but on post-rigor, frozen and thawed lean BCT that was inoculated, vacuum-packaged, and stored at 4 degrees C for up to 14 d. In both experiments, N- and FN-treated tissues exhibited significantly lower populations of B. thermosphacta compared to U- and F-treated tissues, for the duration of refrigerated storage. Nisin activity was detected up to 7 d in N- and FN-treated samples from experiment 1. However, activity was detected only to days 0 and 2 in FN- and N-treated samples, respectively, from experiment 2. These studies indicate that the addition of a bacteriocin to a meat binding system and application to meat surfaces may be useful in reducing undesirable bacteria in restructured meat products.
Vorinostat in advanced prostate cancer patients progressing on prior chemotherapy (National Cancer Institute Trial 6862) (2009)

Vorinostat at this dose was associated with significant toxicities limiting efficacy assessment in this patient population. The significant association between IL-6 levels and removal from the study for toxicities warrants further investigation.
Synthesis of mathematical-modeling software (1993)

Sinapse, a knowledge-based, domain-specific system for synthesizing mathematical-modeling software, is discussed. Sinapse generates Fortran-77, Connection Machine Fortran, or C programs from specifications of mathematical equations and numerical methods. The synthesis process is divided into phases of refinement that attempt to duplicate the users' problem-solving processes in the design, implementation, and evolution states of mathematical modeling. These phases, with automated implementation, help modelers increase their productivity because they can write concise specifications and quickly experiment with variations on their models and algorithms by modifying specifications rather than implementations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solid-phase assembly of cow colostrum trypsin inhibitor gene (1987)

A gene for cow colostrum trypsin inhibitor (CTI) was constructed from synthetic oligonucleotides using a novel method of solid-phase gene assembly. In the first step an anchor oligonucleotide was covalently bound to the CNBr-activated Sephacryl S-500 support. Next, triads or tetrads of separately annealed oligonucleotides were stepwise hybridized to the immobilized complementary sequence, with washing after each step. In the last step a linearized vector molecule was ligated to the assembled gene. The whole construct was released from the solid support with a restriction enzyme, circularized, and used for transformation, with a high yield of recombinant clones being obtained. The method represents a generally applicable approach to rapid and efficient assembly of extended DNA duplexes.
Design, Synthesis, and Sequence Selective DNA Cleavage of Functional Models of Bleomycin. 1. Hybrids Incorporating a Simple Metal-Complexing Moiety of Bleomycin and Lexitropsin Carriers (1995)

The syntheses of functional models for bleomycin, which are composed of a simple analog of the metal-complexing moiety of bleomycin and oligo-N-methylpyrrole peptide DNA-binding moieties, are described. The extent and the relative rate of their cleavage of DNA in the presence of reductants were determined independently by an ethidium binding assay and by agarose gel electrophoresis experiments. The rate of DNA cleavage increases with the number of N-methylpyrrole units in the carrier moiety. The sequence selectivity of DNA cleavage was demonstrated by polyacrylamide sequencing gel electrophoresis of cleavage reactions on two 5'-32P labeled restriction fragments: a 158 bp GC-rich fragment from pBR322 and a 241 bp AT-rich fragment fragment from SV40. Comparison of the sequence selectivity with that of bleomycin A2 indicates that the poly-N-methylpyrrole moiety directs the hybrid compounds to AT-rich sequences of DNA. High-resolution denaturing gel electrophoresis of DNA cleaved by the model compounds reveals that 3' phosphate is produced exclusively, indicating that the chemistry of DNA cleavage differs from that of bleomycin.
Detection of hepatitis C virus RNA by a two-stage polymerase chain reaction with two pairs of primers deduced from the 5'-noncoding region. (1990)

The 5'-noncoding region of hepatitis C virus (HCV) genomes is highly conserved. A two-stage polymerase chain reaction (PCR), involving two pairs of primers deduced from the 5'-noncoding region of the HCV genome, was developed for a sensitive and specific detection of HCV RNA. The first stage of PCR was performed for 35 cycles with primers capable of multiplying fragments of 221 base pairs. PCR products in samples negative for HCV RNA were subjected to the second stage of PCR for 30 cycles with primers located internal to those employed in the first stage of PCR. The two-stage PCR detected up to 10 chimpanzee infectious doses/ml of HCV, and HCV RNA in 11 (92%) of 12 sera from patients with chronic non-A, non-B hepatitis without detectable antibodies to HCV by a commercial assay kit. Primers from the 5'-noncoding region of the HCV genome would be suitable for detecting HCV RNA by PCR, since the other regions of the HCV genome diverge extensively in sequence because of its nature as an RNA virus.