gebhart/patrepeval huggingface dataset:
Biomarker analyses from an open-label study of erlotinib in advanced non-small-cell lung cancer (NSCLC) (2008)

19012 Background: The global open-label TRUST study of erlotinib in NSCLC provides a valuable opportunity to assess biomarker hypotheses in a large patient (pt) population. A biomarker analysis of German TRUST pts was reported at ASCO 2007. Here we report data from non-German centers. Methods: Eligibility criteria: pts with stage IIIB/IV NSCLC who had previously failed on or were unsuitable for chemo-/radiotherapy. Erlotinib 150 mg/d p.o. was given until disease progression or unacceptable toxicity. Retrospectively-obtained tumor samples were analyzed by immunohistochemistry (IHC; EGFR expression), fluorescent in-situ hybridization (FISH; EGFR gene copy number) and DNA sequencing (EGFR, KRAS gene mutations). Results: 171 pts were included in this analysis. Baseline characteristics (%): male/female 60/40; Caucasian/other 71/29; adenocarcinoma/squamous-cell/other 56/27/17; never-smoker/ever-smoker 30/70; erlotinib 1st/2nd/3rd-line 9/53/38. Of 155 pts with response data, 13% had CR/PR and 57% had SD; disease control rate = 70%. Median progression-free survival (PFS) was 17.3 wks. EGFR IHC+ pts (≥10% membrane staining; 99/135; 73%) tended to have longer overall survival (OS) and PFS than IHC- pts (36/135; 27%); HR 0.73 in both cases, not significant (ns). OS tended to be greater in EGFR FISH+ (Cappuzzo scoring; 32/56; 57%) vs FISH- (24/56; 43%) pts (HR 0.75; ns), but PFS was similar in these two groups (HR 0.91; ns). OS and PFS were significantly greater in pts with EGFR mutations (11/75; 15%) vs pts with wild-type EGFR (64/75; 85%); HR 0.32 (p=0.013) and 0.43 (p=0.016), respectively. All pts with EGFR mutations achieved PR/SD; the response rate was significantly higher in pts with mutations (46% vs 7% for wild-type; p=0.00043). Pts with KRAS mutations (14/92; 15%) had shorter OS and PFS vs wild-type KRAS (78/92; 85%); HR 1.73 and 1.37, respectively (ns). Interestingly, 3 pts with KRAS mutations had PR. Conclusions: Pts with EGFR mutation+, EGFR IHC+ or EGFR FISH+ tumors tend to have better outcomes on erlotinib therapy. However, the single-arm design of TRUST precludes conclusions on the predictive vs prognostic value of these biomarkers, and their predictive value is being assessed prospectively in a randomized phase III study of erlotinib (SATURN). Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Lilly, Roche Lilly
SiCl4/Cl2 plasmas: A new chemistry to etch high-k materials selectively to Si-based materials (2012)

Plasma etching of ultrathin layers of high-k materials is one critical step in the fabrication of gate transistors. The main challenge in this process is to achieve an infinite etching selectively between the high-k and the Si (or SiO2 covered silicon) substrate to prevent damaging the source and drain regions of the transistor. State of the art high-k etching plasmas use BCl3 chemistries, sometime at high wafer temperature. However, the process window in which an infinite high-k/Si selectivity can be achieved is very narrow and several issues remain associated with these processes. In this work, we introduced a new high-k plasma etching chemistry: SiCl4/Cl2. It can be used to etch Hf-based and Al-based high-k materials with an infinite selectivity towards Si, SiO2 and SiON, and with a much wider process window than BCl3 plasmas. XPS analyses indicate that the selectivity mechanism relies on the formation of a SiClx deposit selectively on Si-containing materials, which prevent them from being etched. By contrast SiClx radicals and ions are directly involved in the etching of the metallic oxide layer by forming volatile products (most probably SiOClx and HfClx). This new chemistry may replace valuably BCl3-based plasmas for future high-k etching processes and it may also be interesting for other applications.
Architecture Transformations of Ultrahigh Areal Capacity Air Cathodes for Lithium‐Oxygen Batteries (2020)

Abstract Lithium‐oxygen (Li−O 2 ) batteries have the highest known theoretical energy density but are still not practical for use in most applications. A key aspect that has been largely overlooked in the field is how to improve the reversible areal capacity of the air cathode to a competitive level (&gt;5–10 mAh cm −2 ). For carbon‐based air cathodes, increase of areal capacity requires a corresponding increase of carbon mass loading. As a result, the electrode thickness also increases which impedes the mass transport of Li ions and O 2 needed for battery reactions. It is therefore imperative to investigate not only the air cathode composition, but also its dimensional architecture, for the effective function of high areal capacity Li−O 2 batteries. Herein, we present the use of several representative additives of carbon‐based nanomaterials, including carbon black, two different diameters of multi‐walled carbon nanotubes, and graphene materials from two sources, into a high mass loading (10 mg cm −2 ), ultrathick (∼100 μm) air cathode architectural platform matrix based on dry‐compressed holey graphene. The performances of these all‐carbon composite air cathodes differ from that of the neat holey graphene, but not by a simple addition or subtraction effect. In addition, the additive effects to full discharge and curtailed cycling experiments are significantly different. The presented results strongly suggest that the architectural volume expandability is critical for the full discharge properties. However, the cycling performance depends more upon the resilience of the air cathode architecture (“breathability”), which does not necessarily correlate with its expandability.
State switched transducers: A new approach to high-power, low-frequency, underwater projectors (1998)

In order to produce high-amplitude, low-frequency signals, an underwater transducer must generate a relatively large volume displacement. Since water exerts a large reaction force back on the transducer, “conventional wisdom” dictates that such a transducer would have to be a high Q resonant device and thus not be broadband. However, a transducer does not have to be broadband in the conventional sense to meet the requirements of communication and sonar systems. A transducer that is capable of instantaneously switching between two discrete frequencies is adequate for communication and transmission of coded signals; one that is capable of switching among several frequencies could produce the chirp signals commonly used in active sonars. Ordinarily, a broadband transducer is needed to accomplish the frequency switching rapidly. A way around this difficulty is the “state-switched” source concept originally proposed by Walter Munk in 1980 which permits instantaneous frequency switching of a high Q resonant transducer while always maintaining the resonance state. The objective of this research has been to investigate this novel approach to the design of high-power, low-frequency, broadband transducers for use in long-range underwater communication, active sonar, and underwater research applications. This paper presents a practical realization of a “state-switched” source.
Majority-Based Tracking Forecast Memories for Stochastic LDPC Decoding (2010)

This paper proposes majority-based tracking forecast memories (MTFMs) for area efficient high throughput ASIC implementation of stochastic Low-Density Parity-Check (LDPC) decoders. The proposed method is applied for ASIC implementation of a fully parallel stochastic decoder that decodes the (2048, 1723) LDPC code from the IEEE 802.3an (10GBASE-T) standard. The decoder occupies a silicon core area of 6.38 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\hbox {mm}}^{2}$</tex></formula> in CMOS 90 nm technology, achieves a maximum clock frequency of 500 MHz, and provides a maximum core throughput of 61.3 Gb/s. The decoder also has good decoding performance and error-floor behavior and provides a bit error rate (BER) of about <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$4\times 10^{-13}$</tex></formula> at <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$E_{b}/N_{0}={\hbox {5.15\ dB}}$</tex></formula> . To the best of our knowledge, the implemented decoder is the most area efficient fully parallel soft -decision LDPC decoder reported in the literature.
Biomedical Applications of Recombinant Silk‐Based Materials (2018)

Silk is mostly known as a luxurious textile, which originates from silkworms first cultivated in China. A deeper look into the variety of silk reveals that it can be used for much more, in nature and by humanity. For medical purposes, natural silks were recognized early as a potential biomaterial for surgical threads or wound dressings; however, as biomedical engineering advances, the demand for high-performance, naturally derived biomaterials becomes more pressing and stringent. A common problem of natural materials is their large batch-to-batch variation, the quantity available, their potentially high immunogenicity, and their fast biodegradation. Some of these common problems also apply to silk; therefore, recombinant approaches for producing silk proteins have been developed. There are several research groups which study and utilize various recombinantly produced silk proteins, and many of these have also investigated their products for biomedical applications. This review gives a critical overview over of the results for applications of recombinant silk proteins in biomedical engineering.
State-of-the-art graphene transistors on hexagonal boron nitride, high-k, and polymeric films for GHz flexible analog nanoelectronics (2012)

We report graphene field-effect transistors on hexagonal boron nitride, high-k, and polymeric films featuring state-of-the-art electrical and mechanical properties on flexible substrates. The record electrical performance includes the highest ON current (~0.3mA/μm), the first demonstration of current saturation on flexible films and intrinsic gain, and the highest conversion gain flexible graphene frequency doubler. Extrinsic transit frequency of 2.23GHz, and maximum frequency of 1.15GHz are also achieved. In addition, robust electrical response down to 0.7mm mechanical bending radius is realized.
Impacts of Blended Bombyx mori Silk Fibroin and Recombinant Spider Silk Fibroin Hydrogels on Cell Growth (2021)

Binary-blended hydrogels fabricated from <i>Bombyx mori</i> silk fibroin (SF) and recombinant spider silk protein eADF4(C16) were developed and investigated concerning gelation and cellular interactions in vitro. With an increasing concentration of eADF4(C16), the gelation time of SF was shortened from typically one week to less than 48 h depending on the blending ratio. The biological tests with primary cells and two cell lines revealed that the cells cannot adhere and preferably formed cell aggregates on eADF4(C16) hydrogels, due to the polyanionic properties of eADF4(C16). Mixing SF in the blends ameliorated the cellular activities, as the proliferation of L929 fibroblasts and SaOS-2 osteoblast-like cells increased with an increase of SF content. The blended SF:eADF4(C16) hydrogels attained the advantages as well as overcame the limitations of each individual material, underlining the utilization of the hydrogels in several biomedical applications.
Surface activation of cobalt oxide nanoparticles for photocatalytic carbon dioxide reduction to methane (2019)

Surface treatment of cobalt oxide nanoparticles with <italic>N</italic>-bromosuccinimide and sulfur resulted in high photocatalytic efficiency of CO<sub>2</sub> reduction into methane.
4.1 22nm Next-generation IBM System z microprocessor (2015)

The next-generation System z design introduces a new microprocessor chip (CP) and a system controller chip (SC) aimed at providing a substantial boost to maximum system capacity and performance compared to the previous zEC12 design in 32nm [1,2]. As shown in the die photo, the CP chip includes 8 high-frequency processor cores, 64MB of eDRAM L3 cache, interface IOs (“XBUS”) to connect to two other processor chips and the L4 cache chip, along with memory interfaces, 2 PCIe Gen3 interfaces, and an I/O bus controller (GX). The design is implemented on a 678 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> die with 4.0 billion transistors and 17 levels of metal interconnect in IBM's high-performance 22nm high-x CMOS SOI technology [3]. The SC chip is also a 678 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> die, with 7.1 billion transistors, running at half the clock frequency of the CP chip, in the same 22nm technology, but with 15 levels of metal. It provides 480 MB of eDRAM L4 cache, an increase of more than 2× from zEC12 [1,2], and contains an 18 MB eDRAM L4 directory, along with multi-processor cache control/coherency logic to manage inter-processor and system-level communications. Both the CP and SC chips incorporate significant logical, physical, and electrical design innovations.
Molecular Engineering of Insulin Icodec, the First Acylated Insulin Analog for Once-Weekly Administration in Humans (2021)

Here, we describe the molecular engineering of insulin icodec to achieve a plasma half-life of 196 h in humans, suitable for once-weekly subcutaneously administration. Insulin icodec is based on re-engineering of the ultra-long oral basal insulin OI338 with a plasma half-life of 70 h in humans. This systematic re-engineering was accomplished by (1) further increasing the albumin binding by changing the fatty diacid from a 1,18-octadecanedioic acid (C18) to a 1,20-icosanedioic acid (C20) and (2) further reducing the insulin receptor affinity by the B16Tyr → His substitution. Insulin icodec was selected by screening for long intravenous plasma half-life in dogs while ensuring glucose-lowering potency following subcutaneous administration in rats. The ensuing structure–activity relationship resulted in insulin icodec. In phase-2 clinical trial, once-weekly insulin icodec provided safe and efficacious glycemic control comparable to once-daily insulin glargine in type 2 diabetes patients. The structure–activity relationship study leading to insulin icodec is presented here.
Polypyrrolones for membrane gas separations. II. Activation energies and heats of sorption (1999)

The temperature dependence of the gas permeability and sorption coefficients of a series of ladder-type polypyrrolones, 6FDA–TAB and 6FDA/PMDA–TAB copolymers, is reported at temperatures up to 80°C. Knowledge of gas transport and sorption behavior at higher temperatures provides insights into these unusual systematically varied high-performance polymers. Activation energies for permeation and diffusion as well as heats of sorption for He, CO2, O2, N2, and CH4 are reported for the four polypyrrolones. These gas transport properties are interpreted in terms of the polypyrrolone structures, which possess different average interchain spacings. In addition, the activation energy for diffusion is shown to be dominant in influencing the activation energy for permeation. The so-called “dual mode” sorption behavior, especially of highly sorbing gases like CO2, is shown to affect the calculation of the apparent heat of sorption. The individual heats of sorption associated with the Henry's law and Langmuir environments provide a more complete description of the temperature dependence of sorption in these glassy materials. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 1251–1265, 1999
Pro-inflammatory S100 proteins are associated with glomerulonephritis and anti-dsDNA antibodies in systemic lupus erythematosus (2016)

Objectives Systemic lupus erythematosus (SLE) is associated with elevated levels of S100A8/A9, pro-inflammatory proteins mainly secreted by activated polymorphonuclear neutrophils (PMNs). The underlying mechanisms for increased S100A8/A9 levels and their relation to the clinical phenotype have not been carefully investigated. We assessed S100A8/A9 and S100A12 levels in SLE patient sera in relation to disease activity, clinical phenotype, presence of anti-dsDNA antibodies and ability to promote phagocytosis of necrotic cells (NCs) by PMNs. Methods Serum levels of S100A8/A9 and S100A12 were measured by ELISA in paired samples of 100 SLE patients at time points of higher and lower disease activity. Serum-mediated phagocytosis of NCs by PMNs was analysed by flow cytometry. Clinical data were recorded at time points of blood sampling. Results Serum levels of S100A8/A9 and S100A12 were increased in SLE patients with high disease activity compared to paired samples at low disease activity ( p = 0.01 and p = 0.008, respectively). Elevated levels of S100A8/A9 were particularly seen in patients with anti-dsDNA antibodies ( p = 0.01) and glomerulonephritis before treatment ( p = 0.02). Immunosuppressive therapy was associated with a reduction of S100A8/A9 serum levels ( p = 0.002). The ability of serum to support phagocytosis of NCs by PMNs was related to increased S100A8/A9 levels ( p = 0.01). Conclusions Elevated serum levels of S100A8/A9 may be used to monitor disease activity and response to treatment in SLE patients, especially in patients with glomerulonephritis. S100A12 may be a marker of disease activity in SLE. Increased S100A8/A9 levels may reflect immune-pathological processes involving phagocytosis of immune complexes by PMNs.
His-tag ELISA for the Detection of Humoral Tumor-Specific Immunity (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: Immune Monitoring
Theoretical Study of the Thermal Decomposition of Carboxylic Acids at Pyrolysis Temperature (2013)

Carboxylic acids are important in the processing of biomass into renewable fuels and chemicals. They are formed from the pretreatment and pyrolysis of hemicellulose biopolymers and are released from the decomposition of sugars. They result from the deconstruction of polyhydroxyalkanoates (bacterial carbon storage polymers) from fatty acids derived from algae, bacteria, and oil crops. The thermal deoxygenation of carboxylic acids is an important step in the conversion of biomass into aliphatic hydrocarbons suitable for use in renewable biofuels and as petrochemical replacements. Decarboxylation, a primary decomposition pathway under pyrolysis conditions, represents an ideal conversion process, because it eliminates two atoms of oxygen for every carbon atom removed. Problematically, additional deoxygenation processes exist (e.g. dehydration) that are in direct competition with decarboxylation and result in the formation of reactive and more fragmented end products. To better understand the competition between decarboxylation and other deoxygenation processes and to gain insight into possible catalysts that would favor decarboxylation, we have investigated the mechanisms and thermochemistry of the various unimolecular and bimolecular deoxygenation pathways for a family of C1-C4 organic acids using electronic structure calculations at the M06-2X/6-311++G(2df,p) level of theory.
Referring-expression generation using a transformation-based learning approach (2006)

A natural language generation system must generate expressions that allow a reader to identify the entities to which they refer. This paper describes the creation of referring-expression (RE) generation models developed using a transformation-based learning approach. We present an evaluation of the learned models and compare their performance to the performance of a baseline system, which always generates full noun phrase REs. When compared to the baseline system, the learned models produce REs that lead to more coherent natural language documents and are more accurate and closer in length to those that people use.
Structure and Energetics of Thin Film Water (2011)

We present a molecular dynamics (MD) simulation study of the structure and energetics of thin films of water adsorbed on solid substrates at 240 K. By considering crystalline silica as a model hydrophilic surface, we systematically investigate the effect of film thickness on the hydrogen bonding, density, molecular orientation, and energy of adsorbed water films over a broad surface coverage range (δ). At the lowest coverage investigated (δ = 1 monolayer, ML), >90% of water molecules form three hydrogen bonds (H-bonds) with surface silanol groups and none with other water molecules; when δ = 1 ML, the most probable molecular orientation is characterized by both the molecular dipole and the OH vectors being parallel to the surface. As δ increases, water−water and water−surface interactions compete, leading to the appearance of an orientational structure near the solid−liquid interface characterized by the dipole moment pointing toward the silica surface. We find that the water−surface H-bond connectivity and energetics of the molecular layer nearest to the solid−liquid interface do not change as δ increases. Interfacial water molecules, therefore, are able to reorient and form water−water H-bonds without compromising water−surface interactions. The surface-induced modifications to the orientational structure of the adsorbed film propagate up to ∼1.4 nm from the solid−liquid interface when δ = 15.1 ML (a film that is ∼2.3 nm thick). For the thinner adsorbed films (δ ≤ 4.3 ML, thickness ≤0.8 nm) orientational correlations imposed by the solid−liquid and liquid−vapor interfaces are observed throughout.
Strong-Form Collocation Method for Solidification and Mechanical Analysis of Polycrystalline Materials (2019)

Materials engineering problems related to polycrystalline solids often require the prediction of grain growth and the stress analysis of polycrystalline materials. This study presents the particle difference method (PDM) as a reliable computational method applicable to this class of engineering problems. The PDM is a meshfree collocation method that directly discretizes the strong form of the governing partial differential equations based on Taylor series approximation and the moving least-squares approach. The PDM was applied to polycrystalline solids in the context of two-dimensional grain growth solidification and stress analysis of the resulting polycrystalline morphology. First, the PDM was used to predict grain growth during the solidification process of polycrystalline materials using a multiphase field model. Then the resulting morphology of the polycrystalline solids was adopted for successive stress analysis of the polycrystalline solids. Results from these analyses were compared with the results from the conventional finite-element method to verify the accuracy and efficacy of the PDM.
Thermomechanical distortions of advanced optical reticles during exposure (1999)

If optical lithography is to be extended into the 157 nm regime, controlling mask-related distortions will be a necessity. Thermomechanical distortions during exposure could be a major source of pattern placement error, especially if alternative materials such as CaF<SUB>2</SUB> or MgF<SUB>2</SUB> are employed. Full 3D finite element heat transfer and structural models have been developed to simulate the response of the reticle during both full-field and scanning exposure systems. Transient and periodic steady-state temperature distributions have been determined for typical exposure duty cycles. Corresponding in-plane and out-of- plane thermal distortions have been identified for both fused silica and calcium fluoride substrates. Under equivalent exposure conditions, the distortions in the CaF<SUB>2</SUB> are significantly higher.
3D visualization of the apoptotic Jurkat T cells (2019)

The rotational view of ROCK inhibitor treated apoptotic Jurkat T cells with internal structures delineated from groupings of refractive index values.