gebhart/patrepeval huggingface dataset:
Return-to-site of an AUV using terrain-relative navigation: Field trials (2014)

This paper presents the results from recent field trials in Monterey Bay, CA which demonstrate the use of Terrain-Relative Navigation (TRN) to perform return-to-site missions using a 53cm diameter Dorado-class Autonomous Underwater Vehicle (AUV). For these tests, a series of targets were identified on a bathymetry map that were recognizable features (e.g. large boulders and outcroppings), and a trajectory was constructed for the AUV to fly over those targets (i.e. the latitudes and longitudes as defined on the map). Multiple missions were flown using a real-time TRN algorithm to identify and correct for georeferencing errors in the bathymetry map. The results were repeatable. They demonstrated that there was a 20m georeferencing error in the map. Without TRN, the targets were missed. With TRN, the AUV flew directly over the targets. Performance was independently validated using acoustic imagery from an on-board mapping multibeam sonar. These field results are presented and described. The TRN algorithm is also discussed.
The Host Protein Staufen1 Participates in Human Immunodeficiency Virus Type 1 Assembly in Live Cells by Influencing pr55 Gag Multimerization (2007)

Human immunodeficiency virus type 1 (HIV-1) requires the sequential activities of virus-encoded proteins during replication. The activities of several host cell proteins and machineries are also critical to the completion of virus assembly and the release of infectious virus particles from cells. One of these proteins, the double-stranded RNA-binding protein Staufen1 (Stau1), selectively associates with the HIV-1 genomic RNA and the viral precursor Gag protein, pr55Gag. In this report, we tested whether Stau1 modulates pr55Gag assembly using a new and specific pr55Gag oligomerization assay based on bioluminescence resonance energy transfer (BRET) in both live cells and extracts after cell fractionation. Our results show that both the overexpression and knockdown of Stau1 increase the pr55Gag-pr55Gag BRET levels, suggesting a role for Stau1 in regulating pr55Gag oligomerization during assembly. This effect of Stau1 on pr55Gag oligomerization was observed only in membranes, a cellular compartment in which pr55Gag assembly primarily occurs. Consistently, expression of Stau1 harboring a vSrc myristylation signal led to a 6.5-fold enrichment of Stau1 in membranes and a corresponding enhancement in the Stau1-mediated effect on pr55Gag-pr55Gag BRET, demonstrating that Stau1 acts on assembly when targeted to membranes. A role for Stau1 in the formation of particles is further supported by the detection of membrane-associated detergent-resistant pr55Gag complexes and the increase of virus-like particle release when Stau1 expression levels are modulated. Our results indicate that Stau1 influences HIV-1 assembly by modulating pr55Gag-pr55Gag interactions, as shown in a live cell interaction assay. This likely occurs when Stau1 interacts with membrane-associated assembly intermediates.
Generation of a functional, semisynthetic [FeFe]-hydrogenase in a photosynthetic microorganism (2018)

[FeFe]-Hydrogenases are hydrogen producing metalloenzymes with excellent catalytic capacities, highly relevant in the context of a future hydrogen economy. Here we demonstrate the synthetic activation of a heterologously expressed [FeFe]-hydrogenase in living cells of <i>Synechocystis</i> PCC 6803, a photoautotrophic microbial chassis with high potential for biotechnological energy applications. H<sub>2</sub>-Evolution assays clearly show that the non-native, semi-synthetic enzyme links to the native metabolism in living cells.
Determining the Noninfectious Complications of Indwelling Urethral Catheters (2013)

Little is known about noninfectious complications resulting from urethral catheter use. This systematic review and meta-analysis examined studies describing such complications and pooled data to es...
Data and Technology for Impact Hiring (2019)

This chapter presents two experiments that explored private sector applications of data and technology to drive positive outcomes for “opportunity youth”, a term used to describe the nearly six million young Americans between the ages of 16 and 24 who are out of work and out of school. Experiment 1 describes a partnership between The Rockefeller Foundation, Incandescent, and HMSHost to analyze retention data and increase tenure for young, entry-level workers that include opportunity youth. Experiment 2 describes a partnership between The Rockefeller Foundation, Incandescent, and Knack to use gamified assessments as a recruitment tool for entry-level hiring. Frontline interviews and observations at locations with average and above-average retention outcomes helped us identify the manager behaviors that matter most for associate engagement. Exemplary managers were often more creative in helping their people, for example, by creating learning moments with their associates. Employers routinely use educational level as a proxy for performance when making hiring decisions.
Advancements in the Geotechnical Design of Energy Piles (2013)

All kinds of ground-embedded structures, such as tunnel anchors and linings, slabs, piles and diaphragm walls, can be used to exchange heat with the ground. A system of pipes installed within concrete structures, with a heat carrier fluid that circulates through it, can extract heat from the ground to satisfy the need for heat during the winter and can expel excess heat during the summer, based on the concept of shallow geothermics. Since energy geostructures are becoming more and more common, there is a need for improved scientific knowledge of their behaviour. A part of the recent advancements related to this topic are illustrated in this work, including mainly the effects of seasonally cyclic thermal loading on the soil and pile-soil interface response, with the consequent effects in terms of stresses and displacements induced in an energy piles foundation.
Towards a wave-extraction method for numerical relativity. IV. Testing the quasi-Kinnersley method in the Bondi-Sachs framework (2006)

We present a numerical study of the evolution of a nonlinearly disturbed black hole described by the Bondi-Sachs metric, for which the outgoing gravitational waves can readily be found using the news function. We compare the gravitational-wave output obtained with the use of the news function in the Bondi-Sachs framework, with that obtained from the Weyl scalars, where the latter are evaluated in a quasi-Kinnersley tetrad. The latter method has the advantage of being applicable to any formulation of Einstein's equations---including the ADM formulation and its various descendants---in addition to being robust. Using the nonlinearly disturbed Bondi-Sachs black hole as a test bed, we show that the two approaches give wave-extraction results which are in very good agreement. When wave extraction through the Weyl scalars is done in a non-quasi-Kinnersley tetrad, the results are markedly different from those obtained using the news function.
Short-term fish oil supplementation applied in presymptomatic stage of Alzheimer's disease enhances microglial/macrophage barrier and prevents neuritic dystrophy in parietal cortex of 5xFAD mouse model (2019)

Dystrophic neurites and activated microglia are one of the main neuropathological characteristics of Alzheimer's disease (AD). Although the use of supplements with omega-3 fatty acids has been associated with reduced risk and lessened AD pathology, it still remains elusive whether such a treatment could affect dystrophic neurites (DNs) formation and microglia/macrophage behavior in the early phase of disease. We analyzed the effects of short-term (3 weeks) fish oil supplementation on DNs formation, tau hyperphosphorylation, Amyloid-beta peptide 1-42 (Aβ42) levels and microglial/macrophage response to AD pathology in the parietal cortex of 4-month-old 5xFAD mice, a mouse model of AD. The present study shows for the first time that short-term FO supplementation applied in presymptomatic stage of AD, alters the behaviour of microglia/macrophages prompting them to establish a physical barrier around amyloid plaques. This barrier significantly suppresses DNs formation through the reduction of both Aβ content and tau hyperphosphorylation. Moreover, the short-term FO treatment neither suppresses inflammation nor enhances phagocytic properties of microglia/macrophages in the response to Aβ pathology, the effects most commonly attributed to the fish oil supplementation. Our findings suggest that fish oil consumption may play an important role in modulating microglial/macrophage response and ameliorating the AD pathology in presymptomatic stage of Alzheimer's disease.
Pilot Comparison of 68Ga-RM2 PET and 68Ga-PSMA-11 PET in Patients with Biochemically Recurrent Prostate Cancer (2015)

(68)Ga-PSMA-11 and (68)Ga-RM2 had distinct biodistributions in this small cohort of patients with biochemically recurrent prostate cancer. Additional work is needed to understand the expression of PSMA and gastrin-releasing peptide receptors in different types of prostate cancer.
Core−Shell Latex Particles Containing a Fluorinated Polymer in the Shell. 2. Internal Structure Studied by Fluorescence Nonradiative Energy Transfer (1997)

The internal structure of core−shell latex particles, containing a fluoropolymer in the shell, was determined by the fluorescence nonradiative direct energy transfer (NRET) technique. Contrast was achieved by labeling the core and the shell with fluorescent dyes, a donor and an acceptor, respectively and inversely. Donor fluorescence emission intensity was recorded in dilute latex dispersions. Analysis of donor fluorescence decay was carried out by choosing a donor concentration profile within the particles. The analysis revealed the absence of a sharp boundary between the core and the shell, but rather a diffuse interface, which was quantified to within a few tens of nanometers for our ca. 230 nm diameter particles. The scale of this interface was changed by varying the compatibility between the core and the shell.
Alkaloids (2010)

Abstract The article contains sections titled: 1. Introduction 2. Alkaloids Derived from Polyketides and the Amino Acids Ornithine and Lysine 2.1. Alkaloids Derived by the Insertion of Nitrogen into a Polyketide 2.1.1. ( S )‐(+)‐Coniine, γ‐Coniceine and Related Alkaloids 2.1.2. Solenopsin Family (Fire Ant Alkaloids) 2.1.3. Perhydroazaphenalenes: Defensive Alkaloids of the Coccinellidae 2.1.4. Cyanobacteria Alkaloids 2.1.5. Additional Polyketide‐Derived Alkaloids 2.2. Alkaloids Derived from Ornithine and/or Arginine 2.2.1. Tropane Alkaloids 2.2.2. Pyrrolizidine Alkaloids 2.3. Alkaloids Derived from Ornithine (and/or Arginine) and Nicotinic Acid 2.4. Alkaloids Derived from Lysine (Lys, K) and Nicotinic Acid 2.5. Purine Alkaloids 2.6. Imidazole Alkaloids 2.7. Pepper Alkaloids 3. Alkaloids Derived from the Shikimate Pathway 3.1. Alkaloids Derived from Anthranilate 3.2. Alkaloids Derived from Phenylalanine and Tyrosine 3.2.1. Biosynthesis of Dopamine, Mescaline and Capsaicin 3.2.2. Biosynthesis of Tetrahydroisoquinoline Alkaloids 3.2.3. Cryptostyline (Orchidaceae) and Alkaloids of the Amaryllidaceae 3.2.4. Ephedra Alkaloids 3.3. Alkaloids Derived from Tyrosine 3.4. Alkaloids Derived from Tryptophan and/or Tryptamine (Indole Alkaloids) 3.4.1. Alkaloids Derived from Tryptamine and an Unrearranged Monoterpene Unit 3.4.2. Mold Metabolites 3.4.3. Ergot Alkaloids 3.4.4. Corynantheine–Heteroyohimbine Structural Types 3.4.5. Corynantheine‐Type Alkaloids 3.4.6. Ajmalicine‐Type Alkaloids 3.4.7. Heteroyohimbine Oxindole Type 3.4.8. Glucoalkaloids 3.4.9. Yohimbine–Reserpine Structural Types 3.4.10. Akuammidine–Quebrachidine–Ervatamine–Gelsemine–Akuammiline Structural Types 3.4.11. Uleine–Ellipticine–Vallesamine–Ngouniensine Structural Types 3.5. The Cinchona Structural Type 3.6. The Camptothecin Structural Type 3.7. Terpene, Sesquiterpene, Diterpene and Steroidal Alkaloids (→ ((anchor interlink a26_205.xml Terpenes))) 3.7.1. Overview of Terpenoid Biosynthesis 3.7.2. Monoterpene Alkaloids 3.7.3. Sesquiterpene Alkaloids 3.7.4. Diterpene Alkaloids 3.7.5. Sesterterpene and Triterpene Alkaloids 3.7.6. Steroidal Alkaloids 4. Summary
Evaluation of a New Harpin Product on Microbial Quality and Shelf Life of Minimally Processed Lettuce (2005)

The effect of pre-harvest application of Extend®, a newly developed second generation harpin product, on shelf life of fresh-cut lettuce was investigated. The lettuces were grown in locations A: Watsonville, CA; B: Cedarville, NJ; and C: Yuma, AZ, and treated five days before harvest at 30, 60 and 90 ppm (2,4 and 6 oz/acre in 50 gal/acre). Lettuce processed and bagged was stored at 34-37°F and evaluated for quality for 20 days. Lettuce from trial A treated with 60-90 ppm harpin consistently had a better overall quality and lower microbial population than the control. Results from trial B showed no differences among treatments. In trial C, microbial population was lower and visual quality higher in lettuce treated at 60 ppm than the control during early stages of storage. Overall results are mixed but it was revealed that a field application of harpin can improve quality of fresh-cut lettuce under conditions that need to be determined.
Rectal dose to prostate cancer patients treated with proton therapy with or without rectal spacer (2016)

The purpose of this study was to evaluate whether a spacer inserted in the prerectal space could reduce modeled rectal dose and toxicity rates for patients with prostate cancer treated in silico with pencil beam scanning (PBS) proton therapy. A total of 20 patients were included in this study who received photon therapy (12 with rectal spacer (DuraSeal™ gel) and 8 without). Two PBS treatment plans were retrospectively created for each patient using the following beam arrangements: (1) lateral-opposed (LAT) fields and (2) left and right anterior oblique (LAO/RAO) fields. Dose volume histograms (DVH) were generated for the prostate, rectum, bladder, and right and left femoral heads. The normal tissue complication probability (NTCP) for ≥grade 2 rectal toxicity was calculated using the Lyman-Kutcher-Burman model and compared between patients with and without the rectal spacer. A significantly lower mean rectal DVH was achieved in patients with rectal spacer compared to those without. For LAT plans, the mean rectal V70 with and without rectal spacer was 4.19 and 13.5%, respectively. For LAO/RAO plans, the mean rectal V70 with and without rectal spacer was 5.07 and 13.5%, respectively. No significant differences were found in any rectal dosimetric parameters between the LAT and the LAO/RAO plans generated with the rectal spacers. We found that ≥ 9 mm space resulted in a significant decrease in NTCP modeled for ≥grade 2 rectal toxicity. Rectal spacers can significantly decrease modeled rectal dose and predicted ≥grade 2 rectal toxicity in prostate cancer patients treated in silico with PBS. A minimum of 9 mm separation between the prostate and anterior rectal wall yields the largest benefit.
Real-time synchronized multiple-sensor IR/EO scene generation utilizing the SGI Onyx2 (1998)

An approach to utilize the symmetric multiprocessing environment of the Silicon Graphics Inc.<SUP>R</SUP> (SGI) Onyx2<SUP>TM</SUP> has been developed to support the generation of IR/EO scenes in real-time. This development, supported by the Naval Air Warfare Center Aircraft Division (NAWC/AD), focuses on high frame rate hardware-in-the-loop testing of multiple sensor avionics systems. In the past, real-time IR/EO scene generators have been developed as custom architectures that were often expensive and difficult to maintain. Previous COTS scene generation systems, designed and optimized for visual simulation, could not be adapted for accurate IR/EO sensor stimulation. The new Onyx2 connection mesh architecture made it possible to develop a more economical system while maintaining the fidelity needed to stimulate actual sensors. An SGI based Real-time IR/EO Scene Simulator (RISS) system was developed to utilize the Onyx2's fast multiprocessing hardware to perform real-time IR/EO scene radiance calculations. During real-time scene simulation, the multiprocessors are used to update polygon vertex locations and compute radiometrically accurate floating point radiance values. The output of this process can be utilized to drive a variety of scene rendering engines. Recent advancements in COTS graphics systems, such as the Silicon Graphics InfiniteReality<SUP>R</SUP> make a total COTS solution possible for some classes of sensors. This paper will discuss the critical technologies that apply to infrared scene generation and hardware-in-the-loop testing using SGI compatible hardware. Specifically, the application of RISS high-fidelity real-time radiance algorithms on the SGI Onyx2's multiprocessing hardware will be discussed. Also, issues relating to external real-time control of multiple synchronized scene generation channels will be addressed.
Bursae and abscess cavities communicating with the hip. Diagnosis using arthrography and CT. (1985)

Bursae or abscess cavities communicating with the hip joint were demonstrated by hip arthrography or by computed tomography (CT) in 40 cases. The bursae or abscess cavities were associated with underlying abnormalities in the hip, including painful hip prostheses, infection, and inflammatory or degenerative arthritis. Structures communicating with the joint capsule included iliopsoas bursae (13 cases), bursae associated with the greater trochanter (21 cases), ischiotrochanteric bursae created by abnormal articulation between the ischium and lesser trochanter (two cases), and abscess cavities not associated with a bursa (four cases). Symptoms may be produced directly as a result of infection or indirectly as a result of inflammation or pressure on adjacent structures. In cases of suspected infection, direct puncture and aspiration of the bursa or abscess cavity, in addition to joint aspiration, may be necessary to obtain organisms for culture as joint aspiration may not yield fluid. Hip arthrography can confirm a diagnosis of bursae and abscess cavities communicating with the hip joint in patients with hip pain or soft-tissue masses around the groin. Differentiation of enlarged bursae from other abnormalities is important to avoid unnecessary or incorrect surgery.
Thermotoga neapolitana bgIB gene, upstream of lamA, encodes a highly thermostable β-glucosidase that is a laminaribiase (1997)

The gene for thermostable 1,3-beta-glucosidase BglB was cloned from the chromosome of Thermotoga neapolitana and its primary sequence was determined. The purified recombinant beta-glucosidase B had a monomer molecular mass of 81 kDa in accordance with the amino acid sequence predicted from the nucleotide sequence of clone pTT51. It was a member of glycosylhydrolase family 3 and belonged to enzyme class EC 3.2.1.21. beta-Glucosidase B had a specific activity of 255 U mg-1 on 4-nitrophenyl(PNP)-beta-glucoside at the optima of pH (5.5) and temperature (90 degrees C), and K(m) values of 0.1, 10 and 50 mM for PNP-beta-glucoside, laminaribiose and cellobiose, respectively. The gene bglB was located immediately upstream of the laminarinase gene lamA. Both genes were transcribed from the same DNA strand and were not separated by a palindromic transcription terminator. The two purified enzymes 1,3-beta-glucosidase BglB (laminaribiase) and 1,3-beta-glucanase LamA (laminarinase) were together capable of completely degrading laminarin to glucose.
Determinisms of plant and microbiome interactions : a multidisciplinary approach involving high-throughput phenotyping (2021)

International audience
Intra-mitochondrial reaction for cancer cell imaging and anti-cancer therapy by aggregation-induced emission (2020)

Controlled intracellular chemical reactions to regulate cellular functions remain a challenge in biology mimetic systems. Herein, we developed an intra-mitochondrial bio-orthogonal reaction to induce aggregation induced emission. <i>In situ</i> carbonyl ligation inside mitochondria drives the molecules to form nano-aggregates with green fluorescence, which leads to depolarization of the mitochondrial membrane, generation of ROS, and subsequently mitochondrial dysfunction. This intra-mitochondrial carbonyl ligation shows great potential for anticancer treatment in various cancer cell lines.
Metabolic Syndrome and the Risk of Mild Cognitive Impairment and Progression to Dementia (2016)

The MetS was associated with an increased incidence of MCI and progression to dementia. Identifying individuals with diabetes mellitus or the MetS with or without MCI is a promising approach in early interventions to prevent or slow progression to dementia.
Communicating efficiently on cluster based grids with MPICH-VMI (2005)

Emerging infrastructure of computational grids composed of clusters-of-clusters (CoC) interlinked through high throughput channels promises unprecedented raw compute power for terascale applications. Projects such as the NSF Teragrid and EU Datagrid deploy CoCs across multiple geographical sites providing tens ofteraflops. Efficient scaling of terascale applications on these grids poses a challenge due to the heterogeneous nature of the resources (operating systems and SANs) present at each site that makes interoperability among multiple clusters difficult. In addition, due to the enormous disparity in latency and throughput of the channels within the SAN and those interlinking multiple clusters, these CoC grids contain deep communication hierarchies that prohibit efficient scaling of tightly-coupled applications. We present a design of a grid-enabled MPI called MPICH-VMI for running terascale applications over CoC based computational grids. MPICH- VMI is based on MPICH implementation of MPI 1.1 standard and utilizes a middleware messaging library called the virtual machine interface (VMI). VM enables MPICH- VMI to communicate over heterogeneous networks common in CoC based grid. MPICH-VMI also features novel optimizations for hiding communication hierarchies present in CoC based grids. We also present some preliminary results with MPICH-VMI running on the TeraGridfor MPl benchmarks and applications.
Fecal Polyomavirus Excretion in Infancy (2014)

Qualitative polymerase chain reaction (PCR) was used to determine the prevalence of fecal excretion of BK virus, JC virus, and simian virus 40 in 1-year-old infants. Overall, 17.8% of 321 specimens from 64.1% of 39 infants were polyomavirus positive. These data suggest that the gastrointestinal tract may be a site of polyomavirus persistence in humans.
Rhodium(III)-Catalyzed Redox-Neutral C–H Arylation via Rearomatization (2014)

Rhodium(III)-catalyzed arylation of arenes bearing a chelating group has been realized via a redox-economy process using 4-hydroxycyclohexa-2,5-dienones as the arylating reagents, leading to the synthesis of 3-arylated phenols. This redox-neutral process proceeds via a C-H activation pathway with rearomatization being the driving force.