gebhart/patrepeval huggingface dataset:
Phosphorylation of protein kinase N by phosphoinositide-dependent protein kinase-1 mediates insulin signals to the actin cytoskeleton (2000)

Growth factors such as insulin regulate phosphatidylinositol 3-kinase-dependent actin cytoskeleton rearrangement in many types of cells. However, the mechanism by which the insulin signal is transmitted to the actin cytoskeleton remains largely unknown. Yeast two-hybrid screening revealed that the phosphatidylinositol 3-kinase downstream effector phosphoinositide-dependent protein kinase-1 (PDK1) interacted with protein kinase N (PKN), a Rho-binding Ser/Thr protein kinase potentially implicated in a variety of cellular events, including phosphorylation of cytoskeletal components. PDK1 and PKN interacted in vitro and in intact cells, and this interaction was mediated by the kinase domain of PDK1 and the carboxyl terminus of PKN. In addition to a direct interaction, PDK1 also phosphorylated Thr(774) in the activation loop and activated PKN. Insulin treatment or ectopic expression of the wild-type PDK1 or PKN, but not protein kinase Czeta, induced actin cytoskeleton reorganization and membrane ruffling in 3T3-L1 fibroblasts and Rat1 cells that stably express the insulin receptor (Rat1-IR). However, the insulin-stimulated actin cytoskeleton reorganization in Rat1-IR cells was prevented by expression of kinase-defective PDK1 or PDK1-phosphorylation site-mutated PKN. Thus, phosphorylation by PDK1 appears to be necessary for PKN to transduce signals from the insulin receptor to the actin cytoskeleton.
Natural Killer cells and monoclonal antibodies: Two partners for successful antibody dependent cytotoxicity against tumor cells (2021)

Monoclonal antibodies targeting tumors are one of the most important discoveries in the field of cancer. Although several effective antibodies have been developed, a relapse may occur. One of their mechanisms of action is Antibody Dependent Cell Cytotoxicity (ADCC), by engaging the Fc γ receptor CD16 expressing Natural Killer cells, innate lymphoid cells involved in cancer immunosurveillance and able to kill tumor cells. A lack of NK cells observed in many cancers may therefore be a cause of the low efficacy of antibodies observed in some clinical situations. Here we review clear evidences of the essential partnership between NK cells and antibodies showed in vitro, in vivo, and in clinical trials in different indications, describe the hurdles and ways to enhance ADCC and the evolution of monoclonal antibody therapy. NK cell adoptive immunotherapy combined with monoclonal antibodies may overcome the resistance to the treatment and enhance their efficacy.
Mechanistic Insights on Azide−Nitrile Cycloadditions: On the Dialkyltin Oxide−Trimethylsilyl Azide Route and a New Vilsmeier−Haack-Type Organocatalyst (2011)

The mechanism of the azide-nitrile cycloaddition mediated by the known dialkylltin oxide-trimethylsilyl azide catalyst system has been addressed through DFT calculations. The catalytic cycle for this tin/silicon complex-based mechanism has been thoroughly examined, disclosing the most plausible intermediates and the energetics involved in the rate enhancement. In addition, a new catalyst, 5-azido-1-methyl-3,4-dihydro-2H-pyrrolium azide, is presented for the formation of tetrazoles by cycloaddition of sodium azide with organic nitriles under neutral conditions. The efficiency of this organocatalyst, generated in situ from N-methyl-2-pyrrolidone (NMP), sodium azide, and trimethylsilyl chloride under reaction conditions, has been examined by preparation of a series of 5-substituted-1H-tetrazoles. The desired target structures were obtained in high yields within 15-25 min employing controlled microwave heating. An in depth computational analysis of the proposed catalytic cycle has also been addressed to understand the nature of the rate acceleration. The computed energy barriers have been compared to the dialkylltin oxide-trimethylsilyl azide metal-based catalyst system. Both the tin/silicon species and the new organocatalyst accelerate the azide-nitrile coupling by activating the nitrile substrate. As compared to the dialkylltin oxide-trimethylsilyl azide method, the organocatalytic system presented herein has the advantage of higher reactivity, in situ generation from inexpensive materials, and low toxicity.
Activity and Diversity of Sulfate-Reducing Bacteria in a Petroleum Hydrocarbon-Contaminated Aquifer (2002)

Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO(4)(2-) reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day(-1) for sulfate reduction and from 0.13 to 0.60 day(-1) for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.
Seamless handover in buildings using HVAC ducts: a new system architecture (2004)

In this paper, we present an innovative solution to the handover problem in multi-story buildings using HVAC ducts for wireless communications. The proposed solution is based on a new system architecture design of the indoor wireless networks that use the heating, ventilation, and air conditioning (HVAC) ducts as a communication channel. Exploiting the system architecture design and the time diversity at the mobile terminal, we show that intra-floor handover can be eliminated, while inter-floor handover can be substantially reduced due to the fact that multiple floors can be served via the same access point. Our results indicate that the mean number of handovers per call achieved in the indoor wireless networks that use HVAC ducts reduces; e.g., by up to a factor of nine for the illustrative example considered in this paper compared to that of indoor wireless networks that do not use HVAC ducts. The improvement; i.e., reduction in the mean number of handovers in multi-story building, depends on the number of access points used.
A CMOS 0.18&#x03BC;m 64&#x00D7;64 single photon image sensor with in-pixel 11b time-to-digital converter (2014)

The design and characterization of a CMOS 64×64 single-photon avalanche-diode (SPAD) array with in-pixel 11b time-to-digital converter (TDC) is presented. It is targeted for time-resolved imaging, in particular 3D imaging. The achieved pixel pitch is 64μm with a fill factor of 3.5%. The chip was fabricated in a 0.18μm standard CMOS technology and implements a double functionality: Time-of-Flight estimation and photon counting. The imager features a programmable time resolution for the array of TDCs from 625ps down to 145ps. The measured accuracy of the minimum time bin is lower than ±1LSB DNL and 1.7LSB INL. The TDC jitter over the full dynamic range is less than 1LSB. Die-to-die process variation and temperature are discarded by auto-calibration. Fast quenching/restore circuit on each pixel lowers the power consumption by limiting the avalanche currents. Time gatedoperation is possible as well.
Testing and analysis of passive decay heat removal in liquid-metal systems (1990)

Natural circulation tests were conducted in sodium to demonstrate passive removal of decay heat and to validate the computer codes that predict decay heat removal. Two types of heat removal systems were tested: (1) direct reactor auxiliary cooling system (DRACS) utilizing an in-reactor-vessel sodium-to-sodium heat exchanger to transfer heat to an external natural draft sodium-to-air heat exchanger and (2) reactor air-cooling system ((RACS)/radiant vessel auxiliary cooling system (RVACS)) that relies on natural-circulation air cooling on the outside of the vessel. The purpose of testing is to produce generic data for the validation of three-dimensional multipurpose codes. Design and licensing of liquid-metal reactors (LMRs) requires validation of these codes by comparison with experimental thermal-hydraulic data. Test results demonstrated the functional capability of both the DRACS and RVACS/RACS passive heat-removal systems. Repeatability of results was consistently verified throughout each test series. Computer code analyses have shown good comparison of predicted results with actual test measurements.
Microbioreactor array for full‐factorial analysis of provision of multiple soluble factors in cellular microenvironments (2009)

We report a scalable microbioreactor architecture which uses nested dilution structures to generate a full-factorial array of cell culture conditions. The proof-of-concept microbioreactor array produces all combinations of three concentration levels of two soluble factors (3(2) = 9 unique conditions in total). The full-factorial design is especially useful in optimizing soluble factor treatments and elucidating interaction effects between factors which are otherwise difficult to deconvolute. By nesting hierarchical levels of dilution structures, and designing the device purely by resistive flow (no valves are required), suitable diffusive mixing of growth factors up to 40 kDa is achieved such that the nine culture conditions can be generated and maintained from a minimal number of stock solutions.
Effects of prenatal marijuana exposure on neuropsychological outcomes in children aged 1‐11 years: A systematic review (2018)

The specific effects of prenatal marijuana exposure remain unclear and warrant further research. The larger number of neuropsychological domains that exhibit decreased versus increased psychological and behavioural functions suggests that exposure to marijuana may be harmful for brain development and function.
Photocurable polymer gate dielectrics for cylindrical organic field-effect transistors with high bending stability (2011)

Here we describe the use of photocurable poly(vinyl cinnamate) (PVCN) as a gate dielectric in high-performance cylindrical organic field-effect transistors (OFETs) with high bending stability. A smooth-surface metallic fiber (Al wire) was employed as a cylindrical substrate, and polymer dielectrics (PVCN and poly(4-vinyl phenol) (PVP)) were formed viadip-coating. The PVCN and PVP dielectrics deposited on the Al wire and respectively cross-linked via UV irradiation and thermal heating were found to be very smooth and uniform over the entire coated area. Pentacene-based cylindrical OFETs with the polymer dielectrics exhibited high-performance hysteresis-free operation. Devices made with the PVCN dielectric showed superior bending stability than devices made with PVP dielectrics or previously reported cylindrical OFETs due to the good flexibility of the PVCN dielectric. The devices maintained their excellent performance under bending at a bending radius comparable to the lowest value reported for planar OFETs.
Transplanting carbon nanotubes (2004)

Current efforts of guided growth of carbon nanotubes alone cannot make large-scale and directed assembly of them. The nanopelleting concept overcomes this limitation by embedding carbon nanotubes in microscale pellets that can be transplanted readily. This technique includes vertical growth of carbon nanotubes, pellet casting, planarization, pellet separation, and transplantation. A specific manufacturing process is developed and tested with favorable results. This technology will enable directed assembly of carbon nanotubes in a long-range order.
Duration and Spread of an Entomopathogenic Fungus, Beauveria bassiana (Deuteromycota: Hyphomycetes), Used to Treat Varroa Mites (Acari: Varroidae) in Honey Bee (Hymenoptera: Apidae) Hives (2007)

Journal Article Duration and Spread of an Entomopathogenic Fungus, Beauveria bassiana (Deuteromycota: Hyphomycetes), Used to Treat Varroa Mites (Acari: Varroidae) in Honey Bee (Hymenoptera: Apidae) Hives Get access W. G. Meikle, W. G. Meikle Search for other works by this author on: Oxford Academic PubMed Google Scholar G. Mercadier, G. Mercadier Search for other works by this author on: Oxford Academic PubMed Google Scholar N. Holst, N. Holst Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Nansen, C. Nansen Search for other works by this author on: Oxford Academic PubMed Google Scholar V. Girod V. Girod Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 100, Issue 1, 1 February 2007, Pages 1–10, https://doi.org/10.1093/jee/100.1.1 Published: 01 February 2007
Mapping the locus of autosomal dominant polycystic kidney disease: diagnostic application. (1989)

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common autosomal dominant disorders affecting humans. The recent identification of a number of restriction fragment length polymorphisms linked to ADPKD now offers a method for diagnosis in families that are large enough for linkage and phase of linkage to be established. Initial studies of greater than 50 families with the disease localized all disease-producing mutations to the short arm of chromosome 16. Recently, however, families have been identified in which linkage to 16p markers cannot be detected. Such genetic heterogeneity of linkage limits the value of diagnostic methods based on linkage analysis and focuses attention on the need for direct diagnosis of disease-producing mutations. This in turn requires the isolation, cloning, and characterization of ADPKD genes. A refined map of the region around the PKD1 gene, the ADPKD gene localized on chromosome 16p, is presented.
Recovering reflectance and illumination in a world of painted polyhedra (2002)

To be immune to variations in illumination, a vision system needs to be able to decompose images into their illumination and surface reflectance components. Most computational studies thus far have been concerned with strategies for solving the problem in the restricted domain of 2-D Mondrians. This domain has the simplifying characteristic of permitting discontinuities only in the reflectance distribution while the illumination distribution is constrained to vary smoothly. Such approaches prove inadequate in a 3-D world of painted polyhedra which allows for the existence of discontinuities in both the reflectance and illumination distributions. The authors propose a two-stage computational strategy for interpreting images acquired in such a domain. The first stage attempts to use simple local gray-level junction analysis to classify the observed image edges into the illumination or reflectance categories. Subsequent processing verifies the global consistency of these local inferences while also reasoning about the 3-D structure of the object and the illumination source direction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Kinin B<sub>1</sub>Receptor Expression and Function on Human Brain Endothelial Cells (2000)

The kinin B1 receptor is an inducible receptor expressed in response to inflammatory mediators. We sought to determine whether kinin B1 receptor can be expressed on human brain endothelial cells (HBECs) in vitro and whether signaling via this receptor can regulate permeability and chemokine production properties of these cells. Multiplex RT-PCR amplification and western blot techniques were used to evaluate B1 receptor expression by HBECs. Although B1 receptor mRNA and protein could not be detected on resting HBECs, interferon-gamma induced a dose- and time-dependent up-regulation of B1 receptor mRNA and protein on HBECs. Stimulation of interferon-gamma-treated HBECs with the selective B1 agonist R-838 (Sar [D-Phe8] des Arg9-BK) induced a dose- and time-dependent increase in the production of inositol 3,4,5 tri-phosphate and nitric oxide. Permeability of the HBECs monolayer, as measured by BSA diffusion, was significantly increased by application of the B1 agonist. This biological effect of R-838 could be prevented by R-715, a B1 receptor antagonist and by L-NAME, a nitric oxide synthase blocker. R-838 also inhibited interleukin-8 release from HBECs. We demonstrate that B1 receptors can be up regulated on the surface of HBECs by molecules released during inflammatory response and that signaling via this receptor can regulate BBB permeability and chemokine production in vitro.
A 3.6 GHz 16-Core SPARC SoC Processor in 28 nm (2013)

The 3.6 GHz SPARC T5 processor is Oracle's next generation CMT SoC processor implemented in TSMC's 28 nm process with 1.5 billion transistors. Significant performance improvements were made by doubling the previous generations number of cores to 16 and L3 cache size to 8 MB while increasing bandwidth by nearly 3×. Power efficiency was improved through features like DVFS, core-pair cycle skipping and SerDes power scaling. The SPARC T5 processor has been designed to fit in systems that can scale from 1 to 8 sockets, or 128 to 1024 threads, in glueless fashion. The diverse system-level bandwidth requirements of up to 5.65 TB/sec in these systems are met by advanced SERDES design that handles up to 30 dB loss in an area and power efficient manner. The different thermal envelopes of these systems are addressed by power management features that span software, system and chip design.
Otitis-prone Children Have Immunologic Deficiencies in Naturally Acquired Nasopharyngeal Mucosal Antibody Response after Streptococcus pneumoniae Colonization (2015)

sOP children experience significantly higher colonization rates with Spn, develop lower naturally acquired NP mucosal antibody responses to pneumococcal vaccine candidate proteins pneumococcal histidine triad protein D, PcpA and pneumolysin D1 after colonization by Spn, and suffer greater frequency of AOM if they do not generate high mucosal antibody to the studied proteins.
Importance of ROS1 fene fusions in non-small cell lung cancer (2023)

Targeted therapy has become one of the standards of care for advanced lung cancer. More than 10 genetic aberrations have been discovered that are actionable and several tyrosine kinase inhibitors (TKIs) have been approved to target each of them. Among several genetic aberrations that are actionable in non-small cell lung cancer (NSCLC), <i>ROS1</i> translocations also known as gene fusion proteins, are found in only 1%-2% of the patient population. <i>ROS1</i> mutations can usually be detected using a combination of techniques such as immunohistochemistry (IHC), Fluorescence in-situ testing (FISH), polymerase chain reaction (PCR), and next-generation sequencing (NGS). However, RNA NGS and ctDNA NGS (liquid biopsies) also contribute to the diagnosis. There are currently numerous FDA-approved agents for these tumors, including crizotinib and entrectinib; however, there is in-vitro sensitivity data and clinical data documenting responses to ceritinib and lorlatinib. Clinical responses and survival rates with these agents are frequently among the best compared to other TKIs with genetic aberrations; however, intrinsic or extrinsic mechanisms of resistance may develop, necessitating research for alternative treatment modalities. To combat the mechanisms of resistance, novel agents such as repotrectenib, cabozantinib, talotrectinib, and others are being developed. In this article, we examine the literature pertaining to patients with <i>ROS1</i> tumors, including epidemiology, clinical outcomes, resistance mechanisms, and treatment options.
Human Immunodeficiency Virus Type 1 Virological Synapse Formation in T Cells Requires Lipid Raft Integrity (2005)

Human immunodeficiency virus type 1 (HIV-1) can spread directly between T cells by forming a supramolecular structure termed a virological synapse (VS). HIV-1 envelope glycoproteins (Env) are required for VS assembly, but their mode of recruitment is unclear. We investigated the distribution of GM1-rich lipid rafts in HIV-1-infected (effector) T cells and observed Env colocalization with polarized raft markers GM1 and CD59 but not with the transferrin receptor that is excluded from lipid rafts. In conjugates of effector T cells and target CD4+ T cells, GM1, Env, and Gag relocated to the cell-cell interface. The depletion of cholesterol in the infected cell dispersed Env and GM1 within the plasma membrane, eliminated Gag clustering at the site of cell-cell contact, and abolished assembly of the VS. Raft integrity is therefore critical for Env and Gag co-clustering and VS assembly in T-cell conjugates.
Past HBV Viral Load as Predictor of Mortality and Morbidity from HCC and Chronic Liver Disease in a Prospective Study (2006)

In this prospective study, viral load is associated with increased mortality from HCC and CLD in HBV-infected subjects. Viral load may be a useful prognostic tool in HBV infection, and interventions aimed at its reduction should be explored.