gebhart/patrepeval huggingface dataset:
Phase Ib trial of trastuzumab emtansine (TE) in combination with lapatinib (L) plus nab-paclitaxel in metastatic HER2-neu overexpressed breast cancer patients: STELA trial. (2014)

TPS669 Background: Therapies directed at HER2 establish a successful treatment paradigm, but de novo and acquired resistance exist. Multiple large randomized clinical trials have demonstrated that dual HER2 targeted therapies are synergistic and result in improved efficacy. We hypothesize that dual targeted therapy with trastuzumab-emtansine and lapatinib will affect both PI3K and ERK1,2 MAPK pathways. This trial was designed to determine the maximum tolerated dose (MTD) and dose limiting toxicities (DLTs) of trastuzumab-emtansine (TE) and lapatinib (L), together with Nab paclitaxel (A). Methods: Eligible patients have stage IV HER2 positive breast cancer, normal LVEF, and Peripheral neuropathy < grade 2. Phase IB planned for up to 9 patients in a standard 3+3 dose de-escalation design. Starting dose level of TE 3.6mg/kg, Lapatinib 750mg and Abraxane(A) 80 mg/m2. DLTs were defined as ≥ grade 3 non hematological toxicity attributed to the study drugs. Currently, our lead cohort has three patients with manageable toxicities and we will start expansion cohort soon. The secondary endpoint includes the description of DLT and other toxicities, document anti-tumor activity as assessed by RECIST 1:1 criteria as well as plasma pharmacokinetics and pharmacodynamics of TE in combination of L and A as well as potential biomarkers of response including HER2 expression levels, PTEN, PI3K and others.
FEN1 Ensures Telomere Stability by Facilitating Replication Fork Re-initiation (2010)

Telomeres are terminal repetitive DNA sequences whose stability requires the coordinated actions of telomere-binding proteins and the DNA replication and repair machinery. Recently, we demonstrated that the DNA replication and repair protein Flap endonuclease 1 (FEN1) is required for replication of lagging strand telomeres. Here, we demonstrate for the first time that FEN1 is required for efficient re-initiation of stalled replication forks. At the telomere, we find that FEN1 depletion results in replicative stress as evidenced by fragile telomere expression and sister telomere loss. We show that FEN1 participation in Okazaki fragment processing is not required for efficient telomere replication. Instead we find that FEN1 gap endonuclease activity, which processes DNA structures resembling stalled replication forks, and the FEN1 interaction with the RecQ helicases are vital for telomere stability. Finally, we find that FEN1 depletion neither impacts cell cycle progression nor in vitro DNA replication through non-telomeric sequences. Our finding that FEN1 is required for efficient replication fork re-initiation strongly suggests that the fragile telomere expression and sister telomere losses observed upon FEN1 depletion are the direct result of replication fork collapse. Together, these findings suggest that other nucleases compensate for FEN1 loss throughout the genome during DNA replication but fail to do so at the telomere. We propose that FEN1 maintains stable telomeres by facilitating replication through the G-rich lagging strand telomere, thereby ensuring high fidelity telomere replication.
Enhancement of Well Log Data Interpretation with Digital Rock Technology (2017)

Abstract Micro-computed X-ray tomography (micro-CT) allows visualization and quantification of pore space, minerals, and the calculation of rock properties at micron-scale. The technology is particularly useful in complex reservoirs where subtle changes in the fabric lead to variations in pore connectivity and fluid flow. Internal rock fabric and physical properties can be calculated with a relatively short turnaround time compared to conventional laboratory techniques. In 2015, Saudi Aramco established a micro-CT laboratory within its Exploration Core Facility to test the feasibility of moving micro-CT analysis from "R&amp;D" to "routine" operational support for exploration and development drilling programs. After the successful completion of this trial, Saudi Aramco is deploying into full production a digital rock physics laboratory utilizing state-of-the-art micro-CT equipment. The objective of this paper is to describe the establishment of the micro-CT lab, a workflow and its application for enhancement of well log data interpretation. Digital rock physics is a multidisciplinary field that requires expertise in 3D imaging, image processing, numerical modeling, computational physics, and petrophysics. A typical workflow integrates micro-CT images, thin sections, mercury injection capillary pressure data, backscattered electron scanning electronic microscopy - energy dispersive spectroscopy results used for digital image analysis to characterize heterogeneities, pore classes, porosity types, mineralogy, and rock properties. Micro-CT images are acquired, processed, and analyzed with resolutions up to 2.5 microns. The following study is focused on the characterization of isolated porosity in carbonates, where the fluids are isolated in moldic pores and may not be contacted by electrical currents of resistivity logging tools, making it difficult to consistently identify saturation. This can lead to erroneous hydrocarbon saturation estimates from wireline logs. Micro-CT analysis of the conductivity, cementation exponent, and formation resistivity factor provided constraints for the petrophysical input parameters of hydrocarbon saturation analysis. The micro-CT analysis of ten carbonate core plug samples resulted in an improved conductivity model that took into account electrical properties of the rock with isolated porosity. This provided a better match between oil saturation calculations from wireline logs and well tests/production data. Comparison of existing standard log analysis results with modified log-derived saturations from micro-CT analysis gave a more reliable estimate of hydrocarbon saturation.
A refined gamma MAP SAR speckle filter with improved geometrical adaptivity (1995)

A modified version of the refined gamma maximum-a-posteriori (RGMAP) speckle filter, which is found in the literature, is presented. The traditional RGMAP speckle filter first defects contours belonging to step edges and thin linear structures, then applies the RGMAP filter to local statistics extracted from rectangular masks that do not cross image contours. The proposed modified RGMAP (MRGMAP) filter first exploits local operators belonging to the odd-symmetric filter category employed by RGMAP to detect image segments, then it computes local statistics over areas that are not necessarily rectangular, but are subsets of the image segments having any possible shape. Therefore, MRGMAP enhances the RGMAP ability in exploiting shape adaptive windowing near image contours, where speckle is not fully developed. The MRGMAP computation time is estimated to be of the same magnitude of that of the original RGMAP, the latter depending on the number of filter categories being employed. The qualitative and quantitative results of the MRGMAP filter applied to real SAR images are satisfactory as the filter seems to be effective in speckle removal whereas it retains edge sharpness and subtle details. However, tests on simulated SAR images must still be performed in order to provide definitive evidence supporting MRGMAP effectiveness. Since MRGMAP typically removes image structures featuring a constant reflectivity gradient, this filter is not particularly suitable for image enhancement in human photo-interpretation. MRGMAP can be rather employed as a preprocessing module in a computer-based SAR image classification procedure based on segment mean value analysis.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
La morgue : voir l'irreprésentable (2009)

Le verbe « morguer » signifie « regarder avec hauteur ». La Morgue a été l’un des monuments parisiens les plus visités du siècle. À partir de l’enseignement freudien sur les « théories sexuelles infantiles », on peut penser que l’enfant vient là pour se former une théorie sexuelle : voir, c’est comprendre. Le corps dans sa nudité et sa crudité est à portée de regard. La pulsion scopique qui pousse un très large public à « venir voir » participe d’une articulation entre la violence, le sexe et la mort. Le scandale qu’a suscité cette institution est à la hauteur de ce qu’elle montre : scandale du corps écorché, nu, morcelé, devant lequel le regard se fait « exercice de cruauté ». Scandale d’une monstration dans laquelle la nudité intrique de façon innommable l’horreur et la fascination.
A Facile and Convenient Method for the Synthesis of Nitro Phenols and Chloropyridinols (2004)

Abstract An efficient, simple, and practical method of preparation of nitro phenols and chloropyridinols has been reported by the active chlorine displacement of chloro nitro benzenes and poly chloro pyridines in the presence of alkali metal hydroxide in low polarity solvent with very good yields. Keywords: Nitro phenolsChloropyridinolsAlkali metal hydroxideTertiary butanol Additional informationNotes on contributorsU. T. Bhalerao Former Director, IICT, Hyderabad, 500 007, India.
FLIPC: a low latency messaging system for distributed real time environments (1996)

FLIPC is a new messaging system intended to support distributed real time applications on high performance communication hardware. Application messaging systems designed for high performance computing environments are not well suited to other environments because they lack support for the complex application structures involving multiple processes, threads, and classes of message traffic found in environments such as distributed real time. These messaging systems also have not been optimized for medium size messages found in important classes of real time applications. FLIPC includes additional features to support applications outside the high performance computing domain. For medium size messages, our system significantly outperforms other messaging systems on the Intel Paragon. An explicit design focus on programmable communication hardware and the resulting use of wait-free synchronization was a key factor in achieving this level of performance. The implementation of FLIPC was accelerated by our use of PC clusters connected by ethernet or by a SCSI bus as development platforms to reduce the need for Paragon time.
A polyimide derivative containing different carbonyl groups for flexible lithium ion batteries (2015)

A novel polyimide derivative is prepared by condensation polymerization and carbonyl groups on different repeating units contribute to the capacity.
Crystal Structure of a Chimeric Receptor Binding Protein Constructed from Two Lactococcal Phages (2009)

Lactococcus lactis, a gram-positive bacterium widely used by the dairy industry to manufacture cheeses, is subject to infection by a diverse population of virulent phages. We have previously determined the structures of three receptor binding proteins (RBPs) from lactococcal phages TP901-1, p2, and bIL170, each of them having a distinct host range. Virulent phages p2 and bIL170 are classified within the 936 group, while the temperate phage TP901-1 is a member of the genetically distinct P335 polythetic group. These RBPs comprise three domains: the N-terminal domain, binding to the virion particle; a beta-helical linker domain; and the C-terminal domain, bearing the receptor binding site used for host recognition. Here, we have designed, expressed, and determined the structure of an RBP chimera in which the N-terminal and linker RBP domains of phage TP901-1 (P335) are fused to the C-terminal RBP domain of phage p2 (936). This chimera exhibits a stable structure that closely resembles the parental structures, while a slight displacement of the linker made RBP domain adaptation efficient. The receptor binding site is structurally indistinguishable from that of native p2 RBP and binds glycerol with excellent affinity.
Nanoantennas for uncooled, double‐band, CMOS compatible, high‐speed infrared sensors (2004)

Abstract Nanoantennas for double‐band uncooled sensors are proposed for infrared focal plane arrays (FPA). Metal‐oxide‐metal tunnel diodes integrated with the nanoantennas are square‐law detectors for currents induced in the antennas by incident infrared radiation. The sensors that operate in the long‐wave infrared band are CMOS compatible and facilitate high‐speed processing exceeding 1000 frames per second. Double‐band sensors are proposed for each pixel of the FPA. The double‐band character of the sensor's responsivity is insured by the design of the antenna geometry. The frequency dependence of the insulator material is taken into account. Simulations of the proposed design are promising. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Direct observation of catalytically active species in reaction solution by X-ray absorption spectroscopy (XAS) (2019)

Abstract Solution V, Nb K-edge XANES (X-ray absorption near edge structure) analysis of molecular catalysis, high oxidation state vanadium(V), niobium(V) complexes containing both imido ligands (possessing metal–nitrogen double bond, NR) and mono anionic ancillary donor ligands (L) of type, M(NR)(L)X 2 (X = Cl, Me), which catalyze ethylene dimerization/polymerization in the presence of Al cocatalysts, has been explored. The analysis method is highly useful to obtain the direct information of the active species (oxidation state, basic framework around the centered metal) in solution (in situ), and should thus become a powerful tool for better understanding the catalysis mechanism, basic coordination and organometallic chemistry.
Unraveling Quasiperiodic Relaxations of Transport Barriers with Gyrokinetic Simulations of Tokamak Plasmas (2013)

The generation and dynamics of transport barriers governed by sheared poloidal flows are analyzed in flux-driven 5D gyrokinetic simulations of ion temperature gradient driven turbulence in tokamak plasmas. The transport barrier is triggered by a vorticity source that polarizes the system. The chosen source captures characteristic features of some experimental scenarios, namely, the generation of a sheared electric field coupled to anisotropic heating. For sufficiently large shearing rates, turbulent transport is suppressed and a transport barrier builds up, in agreement with the common understanding of transport barriers. The vorticity source also governs a secondary instability--driven by the temperature anisotropy (T(∥)≠T(⊥)). Turbulence and its associated zonal flows are generated in the vicinity of the barrier, destroying the latter due to the screening of the polarization source by the zonal flows. These barrier relaxations occur quasiperiodically, and generically result from the decoupling between the dynamics of the barrier generation, triggered by the source driven sheared flow, and that of the crash, triggered by the secondary instability. This result underlines that barriers triggered by sheared flows are prone to relaxations whenever secondary instabilities come into play.
Electrochemically Nanopatterned Conducting Coronas of a Conjugated Polymer Precursor:  SPM Parameters and Polymer Composition (2006)

Here we describe the formation of precisely controlled corona-type nanopatterns on electroactive polymer precursor films using scanning probe microscopy (SPM) methods. The binary composition of electroactive groups in the polymer triggers the formation of corona-type nanopatterns at particular voltages and tip writing speeds through the electrooxidation of the polymer precursor film. Various parameters such as tip speed and applied bias were explored in the nanopatterning process, and the formation of a conductive nanopattern was investigated using conducting atomic force microscopy (C-AFM). The formation of the nanopattern was attributed to the flow of electrons from the AFM tip to the polymer film in a controlled electric field distribution. We also report a new method to distinguish the polymer composition and distribution of a polymer blend film by characterizing biasing differences in the patterning of a polymer film.
Respiratory Tract Infections in Inflammatory Bowel Disease Patients Taking Vedolizumab: A Systematic Review and Meta-Analysis of Randomized Controlled Trials (2021)

The ongoing COVID-19 pandemic has raised concerns about the risk of SARS-CoV-2 infection in patients with Crohn's disease (CD) and patients with ulcerative colitis (UC) taking immunosuppressants or biologics. We conducted a systematic review and meta-analysis to assess the risk of respiratory infections in patients with inflammatory bowel disease (IBD) treated with vedolizumab. We searched PubMed, EMBASE and Scopus to identify randomized controlled trials (RCT) comparing vedolizumab to placebo in patients with IBD. Outcomes were the rate of respiratory tract infections (RTI), upper respiratory tract infections (URTI) and lower respiratory tract infections (LRTI) among patients receiving vedolizumab as compared with placebo. Pooled rates were reported as Odds Ratios (OR) with 95% Confidence Interval (CI). Eight RCT involving 3,287 patients (1873 CD and 1415 UC) were analyzed; 2,493 patients received vedolizumab and 794 received placebo. The rates of RTI and URTI were statistically higher in vedolizumab-treated patients compared to placebo [OR = 1.63; 95% CI (1.07-2.49); OR = 1.64 95% CI (1.07-2.53) respectively]. UC patients, but not CD patients, receiving vedolizumab had a higher risk to develop RTI and URTI [OR = 1.98; 95% CI (1.41-2.77); OR = 2.02; 95% CI (1.42-2.87)] compared to placebo-treated patients. The number of LRTI was small in both treatment groups. Data confirm the good safety profile of vedolizumab even though RTI were more frequent in patients receiving vedolizumab and the risk of URTIs was significantly higher in patients with UC.
The resonant III-nitride grating reflector (2011)

We report here on the fabrication of a guided-mode resonant III-nitride grating reflector on a silicon substrate. In addition to compensating the residual stress of III-nitride layers, hafnium oxide (HfO2) film also serves as a hard mask during inductively coupled plasma reactive ion etching of III-nitride layers. The silicon substrate underneath the III-nitride gratings is etched and thus the III-nitride gratings are released and freely suspended with air as low refractive index materials on the top and bottom. The guided-mode resonances that are affected by the grating period, duty ratio, polarization and effective refractive index are experimentally characterized in the reflectance measurements. These works open the possibility of fabricating resonant III-nitride structures on the silicon substrate for further tunable III-nitride optical devices and integrated optics.
Capturing long‐tailed individual tree diversity using an airborne imaging and a multi‐temporal hierarchical model (2023)

Abstract Measuring forest biodiversity using terrestrial surveys is expensive and can only capture common species abundance in large heterogeneous landscapes. In contrast, combining airborne imagery with computer vision can generate individual tree data at the scales of hundreds of thousands of trees. To train computer vision models, ground‐based species labels are combined with airborne reflectance data. Due to the difficulty of finding rare species in a large landscape, many classification models only include the most abundant species, leading to biased predictions at broad scales. For example, if only common species are used to train the model, this assumes that these samples are representative across the entire landscape. Extending classification models to include rare species requires targeted data collection and algorithmic improvements to overcome large data imbalances between dominant and rare taxa. We use a targeted sampling workflow to the Ordway Swisher Biological Station within the US National Ecological Observatory Network (NEON), where traditional forestry plots had identified six canopy tree species with more than 10 individuals at the site. Combining iterative model development with rare species sampling, we extend a training dataset to include 14 species. Using a multi‐temporal hierarchical model, we demonstrate the ability to include species predicted at &lt;1% frequency in landscape without losing performance on the dominant species. The final model has over 75% accuracy for 14 species with improved rare species classification compared to 61% accuracy of a baseline deep learning model. After filtering out dead trees, we generate landscape species maps of individual crowns for over 670 000 individual trees. We find distinct patches of forest composed of rarer species at the full‐site scale, highlighting the importance of capturing species diversity in training data. We estimate the relative abundance of 14 species within the landscape and provide three measures of uncertainty to generate a range of counts for each species. For example, we estimate that the dominant species, Pinus palustris accounts for c. 28% of predicted stems, with models predicting a range of counts between 160 000 and 210 000 individuals. These maps provide the first estimates of canopy tree diversity within a NEON site to include rare species and provide a blueprint for capturing tree diversity using airborne computer vision at broad scales.
Optical gratings embedded in photosensitive glass by photochemical reaction using a femtosecond laser (2003)

We describe a new approach to the internal refractive index modification of glass by a femtosecond (fs) laser. The glass we used is a photosensitive glass Foturan which contains trace amounts of silver. Silver nanoparticles, which is responsible for the refractive index change, can be formed in the glass after exposed to the fs laser and then postbaked at an appropriate temperature between 500 degrees C and 550 degrees C. In this work, latent images of grating structures are first inscribed into the photosensitive glass by photochemical reaction of a tightly focused fs laser beam with an intensity much lower than the threshold of optical breakdown. After this step, no measurable diffraction can be observed by irradiating the gratings with a He-Ne laser beam. The samples are then baked at 520 degrees C for various durations from 3h to 18h. Diffraction of the optical grating embedded in the glass can now be observed, and the diffraction efficiency increases with postbaking duration, indicating that a refractive index change occurs in the modified regions. The relationship between the refractive index change and the postbaking duration is systematically investigated.
An Automated Cyclic Particle Extractor (2009)

Based on diffusion mechanism, a program-controlled cyclic particle extraction on an integrated PDMS microfluidic platform is presented. The platform comprises on-chip pneumatic peristaltic pumps and valves connected to a PC-based relay board, hence allowing programmable manipulations. The main concept is cycling a sample stream along with an extraction stream multiple times to enhance the particle separation. A sample solution containing 3-μm and 0.5-μm particles was utilized to demonstrate the process. The average flow rate was 4.75 mm/s and the extraction channel length was 84.3 mm. The relatively accumulative concentration for the 0.5-μm particle was 7.52% at the 1st cycle and became 37.99% at the 10th cycle. The result shows an expected improvement of particle concentration after the cyclic extraction. Higher efficiency can be achieved with more cycles.