gebhart/patrepeval huggingface dataset:
Role of β-Oxidation Enzymes in γ-Decalactone Production by the Yeast Yarrowia lipolytica (2001)

Some microorganisms can transform methyl ricinoleate into gamma-decalactone, a valuable aroma compound, but yields of the bioconversion are low due to (i) incomplete conversion of ricinoleate (C(18)) to the C(10) precursor of gamma-decalactone, (ii) accumulation of other lactones (3-hydroxy-gamma-decalactone and 2- and 3-decen-4-olide), and (iii) gamma-decalactone reconsumption. We evaluated acyl coenzyme A (acyl-CoA) oxidase activity (encoded by the POX1 through POX5 genes) in Yarrowia lipolytica in lactone accumulation and gamma-decalactone reconsumption in POX mutants. Mutants with no acyl-CoA oxidase activity could not reconsume gamma-decalactone, and mutants with a disruption of pox3, which encodes the short-chain acyl-CoA oxidase, reconsumed it more slowly. 3-Hydroxy-gamma-decalactone accumulation during transformation of methyl ricinoleate suggests that, in wild-type strains, beta-oxidation is controlled by 3-hydroxyacyl-CoA dehydrogenase. In mutants with low acyl-CoA oxidase activity, however, the acyl-CoA oxidase controls the beta-oxidation flux. We also identified mutant strains that produced 26 times more gamma-decalactone than the wild-type parents.
Adaptive high-speed and ultra-low power optical interconnect for data center communications (2017)

In this paper, two basic methods for a performance and power adaptivity on system and component level in optical interconnects for data center communications are introduced and explained. The approaches are investigated in the EC FP7 project ADDAPT (Adaptive Data and Power Aware Transceivers for Optical Communications) which targets significant power savings in optical interconnects. First, a rapid link on/off switching is investigated when idle symbols are present in the data stream. For active data, a rapid on-switching in less than 20 ns at data rate of 56 Gb/s is achieved, which is almost one order of magnitude faster than in current systems. To evaluate power savings potential in links with multiple lanes, network analyses were performed and several packet statistics were investigated. As a result, up to 80% power savings can be achieved at 10% link utilization. Second, dynamic speed adaptation allows scaling down the performance of individual link system according to varying network traffic load. By this adaptive tuning, a reduction of the nominal power consumption by up to 80% is estimated when tuning down the link data rate from 56 Gb/s to 7 Gb/s.
Laparoscopic Versus Open Right Posterior Sectionectomy for Hepatocellular Carcinoma in a High‐Volume Center: A Propensity Score Matched Analysis (2018)

In HCC, LRPS can be performed safely compared to ORPS, regarding the operative outcome, patient recovery, and oncological outcomes.
PI3 Kinase Pathway Mutations in Human Cancers (2016)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
Temporal soliton generated in a micro-resonator directly with a diode laser (2018)

A single-soliton state is generated in a micro-resonator using a customized low-noise diode laser. This demonstration greatly simplifies the soliton generation setup and represents a significant step forward to a fully integrated soliton comb system.
Electrical Properties of Carbon Nanotubes: Spectroscopy Localization and Electrical Breakdown (2005)

Perfect carbon nanotubes (NTs) are predicted to have rather unique electrical properties. This expectation is one of the main reasons for the interest in these systems. The resistance of a perfect NT should be quantized, and carrier transport can be ballistic with little energy dissipation along the NT. Of course nanotubes, like any other material, are rarely perfect. They can have structural defects, they can be bent or twisted, or contaminated by impurities. In order to evaluate the potential of nanotubes for applications in nanoelectronics, one has to examine the properties of real materials and determine the nature of the deviations from ideal behavior. Here we summarize some of our work on the electronic structure and electrical properties of both single-walled (SWNTs) and multiwalled (MWNTs) nanotubes. Specifically, in order to obtain insight into the transport mechanism in SWNTs we prepare and perform magneto-resistance (MR) measurements on nanotube rings composed of coils of SWNTs. This configuration allows us to determine the coherence length of the carriers in the SWNTs as a function of temperature. The negative MR observed and the temperature dependence of the resistance indicate that the SWNT rings are in a state of weak localization over a wide temperature range. The dominant dephasing mechanism at low temperatures is found to involve electron-electron interactions. Strong electron-electron interactions can lead to the development of a Fermi level singularity. Indeed, we find such a singularity at low temperatures. At the state of the SWNTs changes from weak to strong localization characterized by activated conduction. Below a weak positive MR is observed at low magnetic fields turning into negative MR at high fields. Scattering mechanisms that may be responsible for the “antilocalization” behavior are discussed. We then explore briefly the transport and electrical breakdown characteristics of MWNTs over a large range of applied voltage. Scanning tunneling spectroscopy (STS) and transport studies are used to obtain information on the character of the carriers in semiconducting tubes. Evidence is found of not only charge
Alignment Monitor for Free-Space Optical Links in the Presence of Turbulence using the Beating of Opposite-Order Orbital-Angular-Momentum Beams on Two Different Wavelengths (2020)

We experimentally demonstrate an approach for monitoring misalignment between transmitter and receiver for free space optical links under turbulence effects using the beating of two opposite-order orbital-angular-momentum beams on two different wavelengths.
Adenosine Kinase Inhibitors. 3. Synthesis, SAR, and Antiinflammatory Activity of a Series of l-Lyxofuranosyl Nucleosides (2003)

Chronic inflammatory diseases, such as arthritis and rheumatoid arthritis, remain major health problems worldwide. We previously demonstrated that adenosine kinase inhibitors (AKIs) exhibit antiinflammatory effects by inhibiting TNF-alpha production, neutrophil accumulation, and edema formation. Although adenosine receptor agonists produce similar effects, AKIs showed the antiinflammatory activity without the cardiovascular side effects that prevented the development of adenosine receptor specific agonists. However, previously described potent AKIs, such as 5-iodotubercidin, are nucleosides which have the potential to undergo in vivo 5'-O-phosphorylation and therefore produce cytotoxicity. In an effort to eliminate toxicities produced by phosphorylated nucleosides, l-lyxofuranosyl analogues of tubercidin were tested as potential AKIs since the opposite stereochemical orientation of the CH(2)OH was expected to eliminate intracellular phosphorylation. Described herein are the discovery of a new series of AKIs based on alpha-l-lyxofuranosyl nucleosides, their SAR, as well as the antiinflammatory activity of the lead compound GP790 (IC(50) = 0.47 nM, 47% inhibition of paw swelling at 10 mg/kg in rat carrageenan paw edema model). In addition, a study showing that in the skin lesion model the antiinflammatory activity is reversed by an A2 selective adenosine receptor antagonist 3,7-dimethyl-1-propargyl xanthine [correction of propylxanthine] (DMPX) is also described.
P3A-1 Directional Fusion-based Multi-Volume Rendering Technique for 3D Color Doppler Imaging (2006)

We present a new multi-volume rendering technique (i.e., directional fusion) to integrate 3D anatomical structure from B-mode imaging with flow information from color Doppler imaging. In this technique, negative and positive flows are separated and independently rendered, and then these two rendered frames are merged with the rendered B-mode frame using alpha blending to generate a final 3D color Doppler image. Due to its independent rendering in separately handling negative and positive flows, this directional fusion method can preserve the directionality in the flow, unlike the conventional multi-volume rendering method where two directional flows are rendered together. To evaluate the feasibility of directional fusion, we have implemented the proposed rendering technique on a programmable ultrasound machine with four digital signal processors running at 450 MHz. For 128 times 128 times 128 B-mode and color Doppler volumes, the proposed method takes 141 ms, which corresponds to 7.1 volumes/s. In addition, we have evaluated the proposed directional fusion-based multi-volume technique on in vivo liver data acquired using a commercial ultrasound machine (i.e., EUB-8500, Hitachi Medical Corporation, Japan). The proposed fusion technique can clearly visualize the fused tissue structures and vascularity while preserving directionality in the flow. These preliminary results indicate that although it takes more computation due to the additional rendering pipeline, it can still be implemented in real time on modern ultrasound systems with 3D imaging capability while providing improved vascularity and tissue structure visualization
Two-dimensional orthogonal and symmetrical wavelets and filter-banks (2002)

Two-dimensional compactly supported, symmetric, orthogonal wavelets and filter-banks are presented. Two cases are discussed, filters with two-fold symmetry (centrosymmetric), and filters with four-fold symmetry that are symmetric (or anti-symmetric) about the vertical and horizontal axes. We show that imposing the requirement of symmetry (linear phase) in the case of factorable wavelets and filter-banks, imposes a simple constraint on each of its polynomial degree-1 factors. We thus obtain a simple and complete method of constructing orthogonal factorable filter-banks with linear phase. This method is exemplified by design in the case of four-band separable sampling. An interesting result is obtained, similar to the one well known in the case of 1D, orthogonal factorable wavelets can not be both continuous and have four-fold symmetry.
2D AND 3D dose verification at The Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital using EPIDs (2010)

A review is given of the clinical use of EPID dosimetry in the Department of Radiation Oncology of The Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital. All curative plans (almost all IMRT or VMAT) are verified with EPID dosimetry, mostly in vivo. The 2D approach for IMRT verification and the 3D method for VMAT verification are elucidated and their clinical implementation described. It has been shown that EPID dosimetry plays an important role in the total chain of verification procedures that are implemented in our department. It provides a safety net for advanced treatments such as IMRT and VMAT, as well as a full account of the dose delivered.
Room-temperature continuous-wave operation of GaInNmultiquantum well laser diodes with low indium content (1999)

Based on the indium content dependence of optical gain in a GaInN multiquantum well (MQW) structure, room-temperature continuous-wave operation of GaInN MQW laser diodes is demonstrated. Amplified spontaneous emission spectra for Ga1–xInxN (x = 0.07 – 0.11) MQWs suggest that lower indium content leads to smaller bandgap inhomogeneity and an improvement in the laser performance. Ga0.93In0.07N MQW laser diodes were operated with a threshold current density of 11 kA/cm2.
Discovery of antibodies and cognate surface targets for ovarian cancer by surface profiling (2022)

Although antibodies targeting specific tumor-expressed antigens are the standard of care for some cancers, the identification of cancer-specific targets amenable to antibody binding has remained a bottleneck in development of new therapeutics. To overcome this challenge, we developed a high-throughput platform that allows for the unbiased, simultaneous discovery of antibodies and targets based on phenotypic binding profiles. Applying this platform to ovarian cancer, we identified a wide diversity of cancer targets including receptor tyrosine kinases, adhesion and migration proteins, proteases and proteins regulating angiogenesis in a single round of screening using genomics, flow cytometry, and mass spectrometry. In particular, we identified BCAM as a promising candidate for targeted therapy in high-grade serous ovarian cancers. More generally, this approach provides a rapid and flexible framework to identify cancer targets and antibodies.
Overcoming the Domain Gap in Contrastive Learning of Neural Action Representations (2021)

A fundamental goal in neuroscience is to understand the relationship between neural activity and behavior. For example, the ability to extract behavioral intentions from neural data, or neural decoding, is critical for developing effective brain machine interfaces. Although simple linear models have been applied to this challenge, they cannot identify important non-linear relationships. Thus, a self-supervised means of identifying non-linear relationships between neural dynamics and behavior, in order to compute neural representations, remains an important open problem. To address this challenge, we generated a new multimodal dataset consisting of the spontaneous behaviors generated by fruit flies, Drosophila melanogaster -- a popular model organism in neuroscience research. The dataset includes 3D markerless motion capture data from six camera views of the animal generating spontaneous actions, as well as synchronously acquired two-photon microscope images capturing the activity of descending neuron populations that are thought to drive actions. Standard contrastive learning and unsupervised domain adaptation techniques struggle to learn neural action representations (embeddings computed from the neural data describing action labels) due to large inter-animal differences in both neural and behavioral modalities. To overcome this deficiency, we developed simple yet effective augmentations that close the inter-animal domain gap, allowing us to extract behaviorally relevant, yet domain agnostic, information from neural data. This multimodal dataset and our new set of augmentations promise to accelerate the application of self-supervised learning methods in neuroscience.
Vestibulo-spinal Control Differs in Patients with Reduced Versus Distorted Vestibular Function (1983)

Abnormal vestibular function disrupts a subject's reference to gravity (earth) vertical, and prevents resolution of conflicting or inaccurate visual and somatosensory spatial references. However, errors which patients make when attempting to resolve conflicting visual and somatosensory orientation inputs during upright stance differed markedly in patients with (1) symmetric or asymmetric reduced vestibular function, (2) benign paroxysmal positional nystagmus and vertigo, and (3) a combination of distorted and reduced function. Objective characterization of spatial orientation systems and compensatory strategies under altered sensory conditions is an essential first step toward identifying optimal treatment methods for each of these three types of vestibular deficient patients.
Color Electroluminescent Devices Prepared by Metal Organic Chemical Vapor Deposition (1987)

This paper discusses the preparation of AC thin film ZnS:Tb (green), Sm (red) and Tm (blue) color electroluminescent devices by metal organic chemical vapor deposition, using dimethylzinc and H 2 S as source gases. A new doping method for luminescent centers was used. This was accomplished by evaporating TbF 3 , SmF 3 SmCl 3 and TmF 3 after they had been heated to their melting points during the growth of ZnS in a MOCVD reactor. The maximum brightnesses of ZnS:TbF 3 , ZnS:SmCl 3 and ZnS:TmF 3 are 5000, 1000 and 10 cd/m 2 . The ZnS:SmCl 3 EL devices showed a deeper red chromaticity than the ZnS:SmF 3 EL ones.
Data from Myeloid Expression of Adenosine A<sub>2A</sub> Receptor Suppresses T and NK Cell Responses in the Solid Tumor Microenvironment (2023)

&lt;div&gt;Abstract&lt;p&gt;High concentrations of adenosine in tumor microenvironments inhibit antitumor cytotoxic lymphocyte responses. Although T cells express inhibitory adenosine A&lt;sub&gt;2A&lt;/sub&gt; receptors (A&lt;sub&gt;2A&lt;/sub&gt;R) that suppress their activation and inhibit immune killing of tumors, a role for myeloid cell A&lt;sub&gt;2A&lt;/sub&gt;Rs in suppressing the immune response to tumors has yet to be investigated. In this study, we show that the growth of transplanted syngeneic B16F10 melanoma or Lewis lung carcinoma cells is slowed in &lt;i&gt;Adora2a&lt;sup&gt;f/f&lt;/sup&gt;–&lt;/i&gt;LysM&lt;i&gt;Cre&lt;/i&gt;&lt;sup&gt;+/−&lt;/sup&gt; mice, which selectively lack myeloid A&lt;sub&gt;2A&lt;/sub&gt;Rs. Reduced melanoma growth is associated with significant increases in MHCII and IL12 expression in tumor-associated macrophages and with &gt;90% reductions in IL10 expression in tumor-associated macrophages, dendritic cells (DC), and Ly6C&lt;sup&gt;+&lt;/sup&gt; or Ly6G&lt;sup&gt;+&lt;/sup&gt; myeloid-derived suppressor cells (MDSC). Myeloid deletion of A&lt;sub&gt;2A&lt;/sub&gt;Rs significantly increases CD44 expression on tumor-associated T cells and natural killer (NK) cells. Depletion of CD8&lt;sup&gt;+&lt;/sup&gt; T cells or NK cells in tumor-bearing mice indicates that both cell types initially contribute to slowing melanoma growth in mice lacking myeloid A&lt;sub&gt;2A&lt;/sub&gt; receptors, but tumor suppression mediated by CD8&lt;sup&gt;+&lt;/sup&gt; T cells is more persistent. Myeloid-selective A&lt;sub&gt;2A&lt;/sub&gt;R deletion significantly reduces lung metastasis of melanomas that express luciferase (for &lt;i&gt;in vivo&lt;/i&gt; tracking) and ovalbumin (as a model antigen). Reduced metastasis is associated with increased numbers and activation of NK cells and antigen-specific CD8&lt;sup&gt;+&lt;/sup&gt; T cells in lung infiltrates. Overall, the findings indicate that myeloid cell A&lt;sub&gt;2A&lt;/sub&gt;Rs have direct myelosuppressive effects that indirectly contribute to the suppression of T cells and NK cells in primary and metastatic tumor microenvironments. The results indicate that tumor-associated myeloid cells, including macrophages, DCs, and MDSCs all express immunosuppressive A&lt;sub&gt;2A&lt;/sub&gt;Rs that are potential targets of adenosine receptor blockers to enhance immune killing of tumors. &lt;i&gt;Cancer Res; 74(24); 7250–9. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Interplay between the Hepatitis B Virus and Innate Immunity: From an Understanding to the Development of Therapeutic Concepts (2017)

The hepatitis B virus (HBV) infects hepatocytes, which are the main cell type composing a human liver. However, the liver is enriched with immune cells, particularly innate cells (e.g., myeloid cells, natural killer and natural killer T-cells (NK/NKT), dendritic cells (DCs)), in resting condition. Hence, the study of the interaction between HBV and innate immune cells is instrumental to: (1) better understand the conditions of establishment and maintenance of HBV infections in this secondary lymphoid organ; (2) define the role of these innate immune cells in treatment failure and pathogenesis; and (3) design novel immune-therapeutic concepts based on the activation/restoration of innate cell functions and/or innate effectors. This review will summarize and discuss the current knowledge we have on this interplay between HBV and liver innate immunity.
Multidrug Adaptive Resistance of Pseudomonas aeruginosa Swarming Cells (2019)

Swarming surface motility is a complex adaptation leading to multidrug antibiotic resistance and virulence factor production in <i>Pseudomonas aeruginosa</i> Here, we expanded previous studies to demonstrate that under swarming conditions, <i>P. aeruginosa</i> PA14 is more resistant to multiple antibiotics, including aminoglycosides, β-lactams, chloramphenicol, ciprofloxacin, tetracycline, trimethoprim, and macrolides, than swimming cells, but is not more resistant to polymyxin B. We investigated the mechanism(s) of swarming-mediated antibiotic resistance by examining the transcriptomes of swarming cells and swarming cells treated with tobramycin by transcriptomics (RNA-Seq) and reverse transcriptase quantitative PCR (qRT-PCR). RNA-Seq of swarming cells (versus swimming) revealed 1,581 dysregulated genes, including 104 transcriptional regulators, two-component systems, and sigma factors, numerous upregulated virulence and iron acquisition factors, and downregulated ribosomal genes. Strain PA14 mutants in resistome genes that were dysregulated under swarming conditions were tested for their ability to swarm in the presence of tobramycin. In total, 41 mutants in genes dysregulated under swarming conditions were shown to be more resistant to tobramycin under swarming conditions, indicating that swarming-mediated tobramycin resistance was multideterminant. Focusing on two genes downregulated under swarming conditions, both <i>prtN</i> and <i>wbpW</i> mutants were more resistant to tobramycin, while the <i>prtN</i> mutant was additionally resistant to trimethoprim under swarming conditions; complementation of these mutants restored susceptibility. RNA-Seq of swarming cells treated with subinhibitory concentrations of tobramycin revealed the upregulation of the multidrug efflux pump MexXY and downregulation of virulence factors.
Nonuniform grid time domain (NGTD) algorithm for fast evaluation of transient wave fields (2006)

A novel algorithm to efficiently compute transient wave fields produced by known three-dimensional source constellations is proposed. The algorithm uses domain decomposition concepts and comprises two steps to be repeated for each subdomain considered. In the first step, delay- and amplitude- compensated fields, produced by sources residing inside each subdomain are computed at a sparse set of points surrounding the observation domain. In the second step, total fields in the observer domain are evaluated by interpolation, delay and amplitude restoration, and aggregation of subdomain fields. The proposed scheme is well-suited to accelerate the solution of time domain integral equations by marching on in time, to carry out time domain physical optics calculations, and to realize near- to far-field transformations of transients. Moreover, the scheme automatically adapts to, and takes advantage of, special geometrical features of the source-observer constellation studied, a key benefit when analyzing quasi-planar configurations. In addition, it realizes a seamless transition from the dynamic to the quasi-static regime, thus facilitating a unified treatment of electrically large and small problems. Last but not least, the scheme is remarkably simple to implement.