gebhart/patrepeval huggingface dataset:
Validation of GWAS-Identified Variants for Anti-TNF Drug Response in Rheumatoid Arthritis: A Meta-Analysis of Two Large Cohorts (2021)

We aimed to validate the association of 28 GWAS-identified genetic variants for response to TNF inhibitors (TNFi) in a discovery cohort of 1361 rheumatoid arthritis (RA) patients monitored in routine care and ascertained through the REPAIR consortium and DANBIO registry. We genotyped selected markers and evaluated their association with response to TNFi after 6 months of treatment according to the change in disease activity score 28 (ΔDAS28). Next, we confirmed the most interesting results through meta-analysis of our data with those from the DREAM cohort that included 706 RA patients treated with TNFi. The meta-analysis of the discovery cohort and DREAM registry including 2067 RA patients revealed an overall association of the <i>LINC02549</i><sub>rs7767069</sub> SNP with a lower improvement in DAS28 that remained significant after correction for multiple testing (per-allele OR<sub>Meta</sub>=0.83, <i>P</i><sub>Meta</sub>=0.000077; <i>P</i><sub>Het</sub>=0.61). In addition, we found that each copy of the <i>LRRC55</i><sub>rs717117G</sub> allele was significantly associated with lower improvement in DAS28 in rheumatoid factor (RF)-positive patients (per-allele OR<sub>Meta</sub>=0.67, <i>P</i>=0.00058; <i>P</i><sub>Het</sub>=0.06) whereas an opposite but not significant effect was detected in RF-negative subjects (per-allele OR<sub>Meta</sub>=1.38, <i>P</i>=0.10; <i>P</i><sub>Het</sub>=0.45; <i>P</i><sub>Interaction</sub>=0.00028). Interestingly, although the identified associations did not survive multiple testing correction, the meta-analysis also showed overall and RF-specific associations for the <i>MAFB</i><sub>rs6071980</sub> and <i>CNTN5</i><sub>rs1813443</sub> SNPs with decreased changes in DAS28 (per-allele OR<sub>Meta_rs6071980</sub> = 0.85, <i>P</i>=0.0059; <i>P</i><sub>Het</sub>=0.63 and OR<sub>Meta_rs1813443_RF+</sub>=0.81, <i>P</i>=0.0059; <i>P</i><sub>Het</sub>=0.69 and OR<sub>Meta_rs1813443_RF-</sub>=1.00, <i>P</i>=0.99; <i>P</i><sub>Het</sub>=0.12; <i>P</i><sub>Interaction</sub>=0.032). Mechanistically, we found that subjects carrying the <i>LINC02549</i><sub>rs7767069T</sub> allele had significantly increased numbers of CD45RO+CD45RA+ T cells (<i>P</i>=0.000025) whereas carriers of the <i>LINC02549</i><sub>rs7767069T/T</sub> genotype showed significantly increased levels of soluble scavengers CD5 and CD6 in serum (<i>P</i>=0.00037 and <i>P</i>=0.00041). In addition, carriers of the <i>LRRC55</i><sub>rs717117G</sub> allele showed decreased production of IL6 after stimulation of PBMCs with <i>B burgdorferi</i> and <i>E coli</i> bacteria (<i>P</i>=0.00046 and <i>P</i>=0.00044), which suggested a reduced IL6-mediated anti-inflammatory effect of this marker to worsen the response to TNFi. In conclusion, this study confirmed the influence of the <i>LINC02549</i> and <i>LRRC55</i> loci to determine the response to TNFi in RA patients and suggested a weak effect of the <i>MAFB and CNTN5</i> loci that need to be further investigated.
Lactococcus lactis subsp. lactis MA83 Suşunda Aktif Bir Faj Dirençlilik Sisteminin Genetik ve Biyokimyasal Doğası (2015)

Lactococcus lactis subsp. lactis MA83 susunda fajlann adsorbsiyonu, bu bakteride 32.7 kb büyüklükteki plazmidin varlığında üretilen ekzopolisakkarit materyal tarafından engellendi. Kimyasal analizler sonucunda bu ekzopolisakkarit materyalin ana bileşenlerinin galaktoz, galaktozamin, ramnoz ve fosfat olduğu belirlendi. Ayrıca, L. lactis subsp. lactis MA83 susunda Øla2, Øp78, Ør4 ve Øp81 fajlannın almaç bölgelerinin protein yapıda olduğu saptandı.
Coupled aerothermal-mechanical analysis in single crystal double wall transpiration cooled gas turbine blades with a large film hole density (2022)

The ambition for increasing gas turbine efficiency beyond current levels through the elevation of gas temperatures demands substantial progress in turbine blade cooling technology. Double wall transpiration cooling (DWTC) is an emerging technology which offers enhanced thermal protection at only modest coolant flows, thanks to a combination of impingement jets and densely packed arrays of film cooling holes. This paper presents a coupled aerothermal-mechanical investigation of a transpiration cooled double wall turbine blade design, by employing Computational Fluid Dynamics (CFD), heat transfer theory as well as stress analysis based on plate theory and Finite Element (FE) analysis. In comparison to previously explored systems with modest outer wall porosity, a system with high porosity is found to display enhanced cooling effectiveness and to reduce the temperature difference across the two walls that drives thermal stresses. This difference can be decreased further by reducing the wall spacing, H, or the inner-outer wall thickness ratio, tc/th, at the cost of higher overall metal temperatures. A lower bound for H should be used to avoid undesirable poor coolant flow distribution and hot gas ingestion effects, whereas the tc/th ratio does not impose any aerothermal constraints. Thermal stresses associated with a fixed temperature field are invariant with H but they vary drastically with tc/th. From a design perspective, the above suggest that H is primarily determined by aerothermal requirements, whereas tc/th by the mechanical performance. The single crystal orientation and elastic anisotropy of Nickel alloys are shown to have a profound impact on the stress concentration around cooling holes, with secondary crystallographic directions, such as 〈110〉 and 〈111〉, playing a prominent role in the local stress state. Our study provides a framework for optimising the aerothermal and mechanical performance in a range of high temperature components and highlights key areas where more elaborate analysis is needed.
Bioremediation of Benzophenone by Glycosylation with Immobilized Marine Microalga Chrysocampanulla spinifera and Amphidinium crassum (2011)

Reduction and glycosylation of benzophenone, which is an endocrine disrupting chemical, were investigated using immobilized marine microalga and plant cells from the viewpoint of bioremediation of benzophenone. Immobilized marine microalga of Chrysocampanulla spinifera reduced benzophenone to diphenylmethanol. Immobilized marine microalga of Amphidinium crassum glucosylated diphenylmethanol to the corresponding glucoside. The sequential biotransformation with C. spinifera and A. crassum effectively converted benzophenone into diphenylmethyl glucoside. On the other hand, immobilized plant cells of Catharanthus roseus transformed benzophenone to diphenylmethanol, diphenylmethyl glucoside, and diphenylmethyl primeveroside, which was a new compound, by one-step biotransformation.
Plasma pigment epithelium-derived factor is positively associated with obesity in Caucasian subjects, in particular with the visceral fat depot (2008)

We conclude that the plasma SERPINF1 level is strongly associated with body adiposity, in particular with the visceral fat depot in the non-diabetic general population. This association may (partly) explain the relationship between SERPINF1 and metabolic syndrome in this population.
Ultraviolet radiation-induced murine tumors produced in the absence of ultraviolet radiation-induced systemic tumor immunosuppression. (1991)

Using micro-UV-irradiation versus whole-dorsal irradiation for inducing cutaneous carcinomas in Skh:HRI mice and an assay for UV radiation (UVR)-induced systemic tumor immunosuppression, the dependence upon systemic immunosuppression for the growth of UVR-induced carcinomas was examined. Squamous cell carcinomas were produced by repeated microirradiation of 0.8-cm2 middorsal skin with xenon are solar-simulated UVR. These tumors were excised from tumor-bearing animals who 7 days later were inoculated ventrally with a cloned UVR-induced squamous cell carcinoma cell line, the T51/6. This cell line only grows in UVR-induced immunosuppressed Skh:HRI mice. In two separate experiments T51/6 inocula failed to grow significantly in the previously tumor-bearing animals (1 of 13) and in unirradiated mice (0 of 19), whereas it grew in 100% (15 of 15) of animals given a whole-dorsal subcarcinogenic UVR dose from a filtered fluorescent tube solar simulator. No sinecomitant immune response to the T51/6 was found in previously UVR-induced tumor-bearing animals. In contrast to whole-dorsal UVR-induced tumors, microirradiation-induced squamous cell carcinomas, whose original growth environment lacked UVR-induced systemic tumor immunosuppression, did not grow preferentially in mice given an immunosuppressive dose of UVR. However both the whole-dorsal and microirradiation-induced tumors were shown to be poorly antigenic, since they lacked preferential growth in athymic nude mice. These observations provide evidence that UVR-induced systemic tumor immunosuppression is not necessary for the production of UVR-induced tumors. However, it does cause a positive selection pressure during tumor formation, independent of the carcinogenic effect of UVR, which affects the transplantation biology of a tumor.
TDM EPON Fronthaul Upstream Capacity Improvement via Traffic Classification and Sifting (2017)

Mobile Fronthaul (MF) is defined as the connection between Remote Radio Head (RRH) and Baseband Processing Unit (BBU) in a Cloud Radio Access Network (C-RAN). Dedicated MF connections between RRH and BBU would be very costly. Thus, Time Division Multiplexing Ethernet Passive Optical Network (TDM EPON) is a promising solution to reduce cost as it can enable multiplexing gain. Note that, even though mobile users transmit intermittently, in the upstream channel RRH is sampling radio signal all the time, limiting the achievable multiplexing gain. Our study enhances the conventional TDM EPON architecture by introducing traffic classification, sifting of useless data to avoid the transmission of unnecessary EPON frames, and hence increasing the multiplexing gain in the upstream channel. We also propose a Hybrid Bandwidth Allocation (HBA) scheme to exploit the traffic usefulness classification information. Simulation results show significant improvements in terms of load and number of connected RRHs that can be supported by same EPON, while keeping the end-to-end delay under 100 μs.
The behavior of poly(amino acids) containing l‐cysteine and their block copolymers with poly(ethylene glycol) on gold surfaces (2013)

ABSTRACT Poly(ethylene glycol) (PEG) is often used to biocompatibilize surfaces of implantable biomedical devices. Here, block copolymers consisting of PEG and l ‐cysteine‐containing poly(amino acid)s (PAA's) were synthesized as polymeric multianchor systems for the covalent attachment to gold surfaces or surfaces decorated with gold nanoparticles. Amino‐terminated PEG was used as macroinitiator in the ring‐opening polymerization, (ROP), of respective amino acid N ‐carboxyanhydrides (NCA's) of l ‐cysteine ( l ‐Cys), l ‐glutamate ( l ‐Glu), and l ‐lysine ( l ‐Lys). The resulting block copolymers formed either diblock copolymers, PEG‐ b ‐p( l ‐Glu x ‐ co ‐ l ‐Cys y ) or triblock copolymers, PEG‐ b ‐p( l ‐Glu) x ‐ b ‐p( l ‐Cys) y . The monomer feed ratio matches the actual copolymer composition, which, together with high yields and a low polydispersity, indicates that the NCA ROP follows a living mechanism. The l ‐Cys repeat units act as anchors to the gold surface or the gold nanoparticles and the l ‐Glu repeat units act as spacers for the reactive l ‐Cys units. Surface analysis by atomic force microscopy revealed that all block copolymers formed homogenous and pin‐hole free surface coatings and the phase separation of mutually immiscible PEG and PAA blocks was observed. A different concept for the biocompatibilization of surfaces was followed when thiol‐terminated p( l ‐Lys) homopolymer was first grafted to the surface and then covalently decorated with HOOC‐CH 2 ‐PEG‐ b ‐p(Bz‐ l ‐Glu) polymeric micelles. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52 , 248–257
Identification of tumor epithelium and stroma in tissue microarrays using texture analysis (2012)

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/4123422336534537.
Fusion of Huntingtin Interacting Protein 1 to Platelet-Derived Growth Factor β Receptor (PDGFβR) in Chronic Myelomonocytic Leukemia With t(5;7)(q33;q11.2) (1998)

Abstract We report the fusion of the Huntingtin interactin protein 1(HIP1) gene to the platelet-derived growth factor βreceptor (PDGFβR) gene in a patient with chronic myelomonocytic leukemia (CMML) with a t(5;7)(q33;q11.2) translocation. Southern blot analysis of patient bone marrow cells with a PDGFβR gene probe demonstrated rearrangement of the PDGFβR gene. Anchored polymerase chain reaction using PDGFβRprimers identified a chimeric transcript containing the HIP1gene located at 7q11.2 fused to the PDGFβR gene on 5q33. HIP1 is a 116-kD protein recently cloned by yeast two-hybrid screening for proteins that interact with Huntingtin, the mutated protein in Huntington's disease. The consequence of t(5;7)(q33;q11.2) is an HIP1/PDGFβR fusion gene that encodes amino acids 1 to 950 of HIP1 joined in-frame to the transmembrane and tyrosine kinase domains of the PDGFβR. The reciprocalPDGFβR/HIP1 transcript is not expressed. HIP1/PDGFβR is a 180-kD protein when expressed in the murine hematopoietic cell line, Ba/F3, and is constitutively tyrosine phosphorylated. Furthermore, HIP1/PDGFβR transforms the Ba/F3 cells to interleukin-3–independent growth. These data are consistent with an alternative mechanism for activation of PDGFβR tyrosine kinase activity by fusion with HIP1, leading to transformation of hematopoietic cells, and may implicate Huntingtin or HIP1 in the pathogenesis of hematopoietic malignancies.
The new architecture of medical education (2007)

It will be much more than just another glittering multi-million dollar facility in booming Wild Rose Country. In fact, proponents believe the new $900 million state-of-the-art Edmonton Clinic, scheduled to open in 2011, will embody a revolutionary experiment in medical education: an attempt to
Experimental Combination Chemotherapy: Intracarotid versus Intravenous Administration of Aziridinylbenzoquinone, BCNU, and Cisplatin in Dogs (1987)

Sixteen adult beagles (10-12 kg) were used to evaluate combinations of 2,5-diaziridinyl-3,6-biscarboethoxyamino-1,4-benzoquinone (AZQ, aziridinylbenzoquinone), 1,3-bis-2-chloroethyl-1-nitrosourea (BCNU, carmustine), and cis-dichlorodiammineplatinum(II) (CDDP, cisplatin) administered by intravenous or intracarotid infusion. Moderate to severe systemic toxicities resulted from all drug infusions, but no histopathologic changes were found in the central nervous system (CNS) of any of the dogs. Results indicated that the toxicities were not dependent on the route of administration or the recipient's gender, and they were reversible in most cases with intravenous supportive therapy. Cisplatin seemed to have an additive effect when administered in combination with AZQ and/or BCNU.
Primary versus secondary contributions to particle number concentrations in the European boundary layer (2011)

Abstract. It is important to understand the relative contribution of primary and secondary particles to regional and global aerosol so that models can attribute aerosol radiative forcing to different sources. In large-scale models, there is considerable uncertainty associated with treatments of particle formation (nucleation) in the boundary layer (BL) and in the size distribution of emitted primary particles, leading to uncertainties in predicted cloud condensation nuclei (CCN) concentrations. Here we quantify how primary particle emissions and secondary particle formation influence size-resolved particle number concentrations in the BL using a global aerosol microphysics model and aircraft and ground site observations made during the May 2008 campaign of the European Integrated Project on Aerosol Cloud Climate Air Quality Interactions (EUCAARI). We tested four different parameterisations for BL nucleation and two assumptions for the emission size distribution of anthropogenic and wildfire carbonaceous particles. When we emit carbonaceous particles at small sizes (as recommended by the Aerosol Intercomparison project, AEROCOM), the spatial distributions of campaign-mean number concentrations of particles with diameter &gt;50 nm (N50) and &gt;100 nm (N100) were well captured by the model (R2≥0.8) and the normalised mean bias (NMB) was also small (−18% for N50 and −1% for N100). Emission of carbonaceous particles at larger sizes, which we consider to be more realistic for low spatial resolution global models, results in equally good correlation but larger bias (R2≥0.8, NMB = −52% and −29%), which could be partly but not entirely compensated by BL nucleation. Within the uncertainty of the observations and accounting for the uncertainty in the size of emitted primary particles, BL nucleation makes a statistically significant contribution to CCN-sized particles at less than a quarter of the ground sites. Our results show that a major source of uncertainty in CCN-sized particles in polluted European air is the emitted size of primary carbonaceous particles. New information is required not just from direct observations, but also to determine the "effective emission size" and composition of primary particles appropriate for different resolution models.
Dynamic power reduction through process and design optimizations on CMOS 80 nm embedded non-volatile memories technology (2014)

This paper describes different solutions to decrease dynamic consumption of circuits processed on an embedded non-volatile memories CMOS 80 nm technology. Up to 25 % in dynamic power reduction is demonstrated without degrading performances and static leakages of devices and above all, with full DMR compliancy. Ring oscillator designs are used to estimate the dynamic power gain, comparing new development process (B) to reference process (A) currently in use in manufacturing.
A Mechanical Leech for Transverse Rectus Abdominis Musculocutaneous Flaps (1993)

Venous congestion in the intraoperative and postoperative period can be a problem with some transverse rectus abdominis musculocutaneous flaps. We evolved a technique to allow us the ability to bleed the congested flap in a controlled manner both intra- and postoperatively. Arteriotomy cannulae are placed within the lumens of the deep inferior epigastric artery (DIEA) and vein (DIEV) and they are brought out on the lateral aspect of the reconstructed breast. We believe that intermittent venous bleeding from the DIEV allows a congested flap time to improve venous outflow and adapt to the new reversed blood circulation. When laser Doppler flow meter is simultaneously used as a monitor, bleeding from the DIEV or DIEA can improve balance between arterial and venous pressure in the flap.
Observations on the Effect of Pressure Ratio and Upstream Flow Configuration on the Acoustical Response of Closed Pipes (1971)

The frequency response of a closed flue pipe as a function of blowing pressure is examined. It is hypothesized that the turbulence level in the air jet is the controlling factor in fixing the frequency of oscillation. Modifications are made in the flue pipe to reduce turbulence in order to test the hypothesis. Consequences of the turbulence-driven oscillation with regard to the use of such oscillators as temperature sensors are discussed.
Adult Survivorship of the Dengue Mosquito Aedes aegypti Varies Seasonally in Central Vietnam (2014)

The survival characteristics of the mosquito Aedes aegypti affect transmission rates of dengue because transmission requires infected mosquitoes to survive long enough for the virus to infect the salivary glands. Mosquito survival is assumed to be high in tropical, dengue endemic, countries like Vietnam. However, the survival rates of wild populations of mosquitoes are seldom measured due the difficulty of predicting mosquito age. Hon Mieu Island in central Vietnam is the site of a pilot release of Ae. aegypti infected with a strain of Wolbachia pipientis bacteria (wMelPop) that induces virus interference and mosquito life-shortening. We used the most accurate mosquito age grading approach, transcriptional profiling, to establish the survival patterns of the mosquito population from the population age structure. Furthermore, estimations were validated on mosquitoes released into a large semi-field environment consisting of an enclosed house, garden and yard to incorporate natural environmental variability. Mosquito survival was highest during the dry/cool (January-April) and dry/hot (May-August) seasons, when 92 and 64% of Hon Mieu mosquitoes had survived to an age that they were able to transmit dengue (12 d), respectively. This was reduced to 29% during the wet/cool season from September to December. The presence of Ae. aegypti older than 12 d during each season is likely to facilitate the observed continuity of dengue transmission in the region. We provide season specific Ae. aegypti survival models for improved dengue epidemiology and evaluation of mosquito control strategies that aim to reduce mosquito survival to break the dengue transmission cycle.
Long‐term clinical outcomes following drug‐eluting stent implantation for unprotected distal trifurcation left main disease: The Milan‐New Tokyo (MITO) registry (2013)

PCI with DES for ULMT stenosis is feasible with a high procedural success rate and no definite/probable ST reported at follow-up. A true trifurcation lesion is associated with enhanced risk of MACE mainly driven by TLR.
An experimental Mosaic interface to scientific information systems (2005)

The NASA Earth Observing System (EOS) information system, EOSDIS, is a key component for disseminating EOS instrument data. Within EOSDIS the Information Management System (IMS) provides access to products maintained at data archives distributed throughout the country. At the heart of the IMS graphical user interface is the widely accepted X11 display protocol. An important feature of X11 that has facilitated IMS prototyping is that it allows users to separate the host computer on which an application program runs from the host where the output is displayed. Running remote X11 applications in this manner is appealing to organizations that for one reason or another do not want to distribute and support software packages or release the source code for their applications. The drawback is the X11 network message traffic generated when an application is run remotely. The authors' work investigates the feasibility of eliminating X11 network traffic by using HTML+ and Mosaic to configure interfaces to information systems such as the NASA IMS. This approach offers advantages to both the information supplier and consumer. To the information consumer the system provides a single X11 software package which can communicate with any World Wide Web (WWW) information supplier. For the information supplier the approach will eliminate the need for X11 programming.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>