gebhart/patrepeval huggingface dataset:
Correlation of constitutive activation of raf-1 with morphological transformation and abrogation of tyrosine phosphorylation of distinct sets of proteins in human squamous carcinoma cells (1997)

We and others have reported an association between raf-1 protein serine/threonine kinase activity and transformation of mammalian cells. Because constitutive tyrosine phosphorylation of specific polypeptides is, in general, indicative of the transformed state of cells, we investigated the effect of activation of raf-1 on phosphotyrosine-containing proteins in a human head and neck squamous cell carcinoma-derived cell line, PCI-06A. raf-1 expression and activity were modulated in PCI-06A cells by means of stable DNA transfection of either the entire coding domain of the human c-raf-1 cDNA (in the sense or antisense orientation) or a fragment of c-raf-1 cDNA coding for the kinase domain of raf-1. Our data showed that constitutive activation of raf-1 correlated with morphological transformation, whereas the inhibition of raf-1 expression and activity had no detectable effect on cell morphology as compared with the untransfected cells. Immunoprecipitation of whole-cell lysates with anti-phosphotyrosine antibody followed by anti-phosphotyrosine immunoblotting revealed four phosphotyrosine-containing proteins of approximately 129, 120, 110, and 63 kDa (I-IV, respectively) in the antisense c-raf-1 cDNA-transfected cells showing relatively diminished raf-1 activity but not in the transfectants expressing activated raf. We concluded that tyrosine phosphorylation of I-IV proteins is abrogated in PCI-06A squamous carcinoma cells transformed with constitutively active raf-1 protein kinase.
A neuro-emulator with learning and virtual emulation capabilities (1996)

In this paper we present and evaluate a novel neuro-emulator. The architecture of this neuro-emulator provides support for learning as well as handling large neural networks in virtual mode. We have identified a set of computational, communication and storage requirements for learning in artificial neural networks. These requirements are representative of a wide variety of algorithms for different styles of learning. The proposed novel neuro-emulator provides the computational ability for the stated requirements. While meeting all the identified requirements the new architecture maintains a high utilization of the machine's resources during learning. To show the capabilities of the proposed machine we present four diverse learning algorithms. We include an evaluation of the machine performance as well as a comparison with other architectures. It is shown that with a modest amount of hardware the proposed architecture yields an extremely high number of connections per second.
Bristle Motion, Forces, and Related Vertical Translation for a Novel Electric Toothbrush Design (2020)

This paper presents a combination of theoretical and experimental techniques applied to characterize the bristle motion, forces, and related vertical translation for a novel electric toothbrush design with a linear drive system. Results of the theoretical description, based on a single filament, were successfully compared with laboratory-based investigations: force measurements and high-speed video analysis, and tracking the toothbrush motion. This work describes the vertical translation induced in the toothbrush head, of up to 250 μm, when the toothbrush bristles are applied against a contact surface at brushing loads of approximately 1 N to 2.5 N. Using these techniques, including Fast-Fourier transform analysis, it is shown that the vertical motion of the head is composed of the driving frequency and its harmonics.
Protecting Group Strategies Toward Glycofuranoses (2018)

This chapter focuses on protecting group strategies used for furanoses and furanosides. It describes the first reactions that allow the synthesis of five-membered rings and then the main acyl, acetal, and silyl protections. Regioselective protection and deprotection are also addressed, according to chemical or chemoenzymatic approaches.
Systematic profiling of C aenorhabditis elegans locomotive behaviors reveals additional components in G-protein Gαq signaling (2013)

Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the application of an automatic imaging system to conduct a quantitative screen for genes regulating the locomotive behavior in Caenorhabditis elegans. Two hundred twenty-seven neuronal signaling genes with viable homozygous mutants were selected for this study. We tracked and recorded each animal for 4 min and analyzed over 4,400 animals of 239 genotypes to obtain a quantitative, 10-parameter behavioral profile for each genotype. We discovered 87 genes whose inactivation causes movement defects, including 50 genes that had never been associated with locomotive defects. Computational analysis of the high-content behavioral profiles predicted 370 genetic interactions among these genes. Network partition revealed several functional modules regulating locomotive behaviors, including sensory genes that detect environmental conditions, genes that function in multiple types of excitable cells, and genes in the signaling pathway of the G protein Gαq, a protein that is essential for animal life and behavior. We developed quantitative epistasis analysis methods to analyze the locomotive profiles and validated the prediction of the γ isoform of phospholipase C as a component in the Gαq pathway. These results provided a system-level understanding of how neuronal signaling genes coordinate locomotive behaviors. This study also demonstrated the power of quantitative approaches in genetic studies.
A Synthesis of α‐Lithiated Enol Ethers from α‐Arenesulfinyl Enol Ethers: Ni(0)‐ and Pd(0)‐Catalyzed Coupling of Enol Triflates and Phosphates Derived from Lactones with Sodium Arenethiolates Gives α‐Arenesulfanyl Enol Ethers. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Production of solar-grade silicon by the SiF<inf>4</inf> and Mg reaction (2016)

Because crystalline Si substrate still accounts for a significant portion of the total cost of solar cells, substantial efforts have been invested in the development of new processes that can significantly lower the production cost of solar-grade silicon. At SRI International, we developed a low-cost process of producing solar-grade silicon based upon the SiF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> -Na reaction. This process has now been scaled up to pilot-plant level, and solar cells obtained using such silicon feedstock reached > 18% efficiencies. Due to continuing increases in demand and production capacity and the simultaneous drop in price of Mg metal, we decided to explore its potential as a reducing agent instead of Na metal. Experimental conditions for obtaining a fast and complete metallothermic reaction between SiF4 and Mg are identified and aspects of the reaction mechanism are discussed. The reaction involves both a heterogeneous liquid-gas phase reaction and a homogeneous gas-gas phase reaction. The separation of the products, Si and MgF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , is described. When pure Mg was used, Si obtained after melt separation had the potential to be suitable for solar cell applications.
Abstract 1393: Automated adeno/squamous-cell NSCLC classification from diagnostic slide images: A deep-learning framework utilizing cell-density maps (2019)

Abstract Background: The most common form of lung cancer, non-small cell lung cancer (NSCLC), is further categorized into two major histopathological subtypes: ~40% Adenocarcinoma (LUAD), and ~30% squamous cell carcinoma (LUSC). Classifying patients accurately is important for prognosis and therapy decisions, but requires costly pathologist review. Here we present an automated algorithm to differentiate LUAD and LUSC diagnostic whole slide images (WSIs). Methods: 488 subtyped NSCLC high-resolution diagnostic WSIs were obtained from TCGA sources. Adjacent normal regions were identified and excluded from analysis. Cancer cell-density maps were created based on cell counts within discrete patches. These maps were then binned into ten ranges of cell counts (20-30 cells per patch, 30-40, etc. up to &amp;gt;110 cells per patch). 2D color patches were transformed into 1D descriptive vectors using the inception v3 deep learning framework. Samples were randomly split into 70% training and 30% testing sets. Ten LUAD/LUSC linear SVM classifiers (one for each cell-density bin) were trained on such transformed data. Subtype prediction in unseen testing samples was achieved by averaging subtype predictions from the 10 subsequent models. Results: 338 TCGA diagnostic WSIs (164 LUAD and 174 LUSC) were used to train, and 150 (71 LUAD and 79 LUSC) were used to test. The proposed system achieved an AUC of 0.9068 in test samples, corresponding to a classification accuracy of 83.33%. The (heretofore excluded) adjacent normal regions were classified correctly almost as accurately as tumor regions (74.7%). Conclusions: This fully-automated histopathology subtyping method generates maps of regions-of-interest within WSIs, providing novel spatial information on tumoral organization. For example, our results on test data show tumor patches of size 100 square microns with 60 to 100 cells distinguish LUAD from LUSC better than other cell-density ranges. Moreover, adjacent normal tissue may provide additional insights into tumorigenesis mechanisms. Citation Format: Mustafa I. Jaber, Liudmila Beziaeva, Christopher W. Szeto, John Elshimali, Shahrooz Rabizadeh, Bing Song. Automated adeno/squamous-cell NSCLC classification from diagnostic slide images: A deep-learning framework utilizing cell-density maps [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1393.
Effects of Dilation on Electronic-ETDRS Visual Acuity in Diabetic Patients (2009)

In an optimized clinical trial setting, there is a decline in best corrected EVA after dilation in diabetic subjects. The large range and magnitude of VA change preclude using postdilation EVA as a surrogate for undilated VA.
Drugging the Undruggable Ras — Immunotherapy to the Rescue? (2016)

Metastatic gastrointestinal cancers that express products of mutant KRAS genes have one of the most dismal outcomes of all solid tumors and present an unsolved problem in cancer medicine. An activating point mutation in one of genes encoding Ras was the first somatic point mutation identified in a human cancer, and its discovery established the role of somatic mutations as the common driver of oncogenesis.1,2 The presence of a T-cell immune infiltrate in surgical specimens at the time of diagnosis is more prognostic of survival than anatomic Dukes staging,3 which suggests that natural immune surveillance can have a powerful . . .
Characteristics of patients with neovascular age-related macular degeneration who are non-responders to intravitreal aflibercept (2018)

Intravitreal aflibercept is effective for treating eye pathology in most naïve AMD cases. However, non-responsiveness may occur in small subgroup of patients with choroidal vascular hyperpermeability.
Performance of simulcast wireless techniques for personal communication systems (1996)

Broadband analog transport facilities using fiber or fiber/coax cable can play a significant role in the evolution of the network infrastructure for personal communications services (PCSs). Low-power PCS systems require a dense grid of radio ports to provide connectivity to the telephone network. Analog transport has a number of important advantages over digital transmission facilities, including the flexibility to support a variety of air interface formats, shared infrastructure cost with other services such as video distribution, and centralized call processing allowing the use of low cost and simple radio ports. A simulcast technique can be used in such systems to permit low rates of handoff (no handoff within each simulcast area) and sharing of hardware resources among multiple radio ports. This paper provides a detailed model and a simulation analysis of the cochannel interference and noise performance as well as the resource sharing benefit of a simulcast PCS system. Several potential PCS air interfaces are considered, including time division multiple access (TDMA) and code division multiple access (CDMA) techniques. Our investigation shows that the impact of multiple antenna noise in a simulcast system is offset by the improved signal-to-interference (SIR) ratio brought about by distributed antennas. Even with distributed antennas, multiple antenna noise places a limit on the maximum number of radio ports that can be assigned to each simulcast group. This limit, however, is shown to have little impact on the achievable resource sharing benefit of simulcasting (i.e., grouping beyond this limit has diminishing returns). A saving of 40% to 60%, in terms of the required central hardware resources, is typical for both TDMA and CDMA systems in suburban environments.
A 3bit/cell 32Gb NAND flash memory at 34nm with 6MB/s program throughput and with dynamic 2b/cell blocks configuration mode for a program throughput increase up to 13MB/s (2010)

A 3.3V 32Gb NAND-Flash memory with 3b/cell is demonstrated in 34nm technology. The device features a programming throughput of 6MB/s on blocks configured as 3b/cell mode and can dynamically switch up to 13MB/s in 2b/cell mode. A new quad-plane architecture and an optimized programming algorithm are adopted to achieve the design targets.
Hydrogel micro-arrays for multi-analyte detection (2007)

Fluorescent microarrays have the ability to detect and monitor multiple analytes simultaneously and noninvasively, following initial placement. This versatility is advantageous for several biological applications including drug discovery, biohazard detection, transplant organ preservation and cell culture monitoring. In this work, poly(ethylene glycol) hydrogel microarrays are described that can be used to measure multiple analytes, including H+ and dissolved oxygen. The array elements are created by filling micro-channels with a hydrogel precursor solution containing analyte specific fluorescent sensors. A photomask is used to create the microarray through UV polymerization of the PEG precursor solution. A compact imaging system composed of a CCD camera, high powered LED, and two optical filters is used to measure the change in fluorescence emission corresponding to analyte concentration. The proposed system was tested in aqueous solution by altering relevant analyte concentrations across their biological ranges.
Double-layer Photonic Devices Based on Transfer Printing of Silicon Nanomembranes for Three-dimensional Photonics (2012)

We present a novel platform for three dimensional (3D) photonics. A double layer 1×12 multimode interference (MMI) coupler is fabricated using transfer printing of silicon nanomembranes. Optical tests confirm low insertion loss and uniform outputs.
A Groebner-bases approach to syndrome-based fast Chase decoding of\n Reed--Solomon codes (2020)

We present a simple syndrome-based fast Chase decoding algorithm for\nReed--Solomon (RS) codes. Such an algorithm was initially presented by Wu (IEEE\nTrans. IT, Jan. 2012), building on properties of the Berlekamp--Massey (BM)\nalgorithm. Wu devised a fast polynomial-update algorithm to construct the\nerror-locator polynomial (ELP) as the solution of a certain linear-feedback\nshift register (LFSR) synthesis problem. This results in a conceptually\ncomplicated algorithm, divided into $8$ subtly different cases. Moreover, Wu's\npolynomial-update algorithm is not immediately suitable for working with\nvectors of evaluations. Therefore, complicated modifications were required in\norder to achieve a true "one-pass" Chase decoding algorithm, that is, a Chase\ndecoding algorithm requiring $O(n)$ operations per modified coordinate, where\n$n$ is the RS code length.\n The main result of the current paper is a conceptually simple syndrome-based\nfast Chase decoding of RS codes. Instead of developing a theory from scratch,\nwe use the well-established theory of Groebner bases for modules over\n$\\mathbb{F}_q[X]$ (where $\\mathbb{F}_q$ is the finite field of $q$ elements,\nfor $q$ a prime power). The basic observation is that instead of Wu's LFSR\nsynthesis problem, it is much simpler to consider "the right" minimization\nproblem over a module. The solution to this minimization problem is a simple\npolynomial-update algorithm that avoids syndrome updates and works seamlessly\nwith vectors of evaluations. As a result, we obtain a conceptually simple\nalgorithm for one-pass Chase decoding of RS codes. Our algorithm is general\nenough to work with any algorithm that finds a Groebner basis for the solution\nmodule of the key equation as the initial algorithm (including the Euclidean\nalgorithm), and it is not tied only to the BM algorithm.\n
Serine racemase is associated with schizophrenia susceptibility in humans and in a mouse model (2009)

Abnormal N-methyl-d-aspartate receptor (NMDAR) function has been implicated in the pathophysiology of schizophrenia. d-serine is an important NMDAR modulator, and to elucidate the role of the d-serine synthesis enzyme serine racemase (Srr) in schizophrenia, we identified and characterized mice with an ENU-induced mutation that results in a complete loss of Srr activity and dramatically reduced d-serine levels. Mutant mice displayed behaviors relevant to schizophrenia, including impairments in prepulse inhibition, sociability and spatial discrimination. Behavioral deficits were exacerbated by an NMDAR antagonist and ameliorated by d-serine or the atypical antipsychotic clozapine. Expression profiling revealed that the Srr mutation influenced several genes that have been linked to schizophrenia and cognitive ability. Transcript levels altered by the Srr mutation were also normalized by d-serine or clozapine treatment. Furthermore, analysis of SRR genetic variants in humans identified a robust association with schizophrenia. This study demonstrates that aberrant Srr function and diminished d-serine may contribute to schizophrenia pathogenesis.
Controlling Infectious Diseases through Vaccination (2014)

Infectious diseases continue to cause significant morbidity and mortality in both animals and humans. Indeed, every year infectious diseases cost the global economy billions of dollars in losses and are responsible for approximately one-third of all human deaths. These deaths occur from routine infections, hospital acquired infections (approximately 100,000 deaths occur annually in North America due to hospital-acquired infections), occasional pandemics or regional outbreaks. The most recent regional outbreak is Ebola in West Africa. This infection has caused significant challenges for the regional health care commu nity and has had a global impact. The challenge in the control of infectious diseases is not only due to routine infections but also to the continued emergence and re-emergence of infectious diseases. These new threats occur on a regular basis with approximately thirty new emerging or re-emerging diseases recorded in the last thirty years. The majority of these emerging diseases are zoonotic (over 70%) causing even greater challenges to their control in humans and animals.
Gastric Cancer Presenting as Gastropericardial Fistula in a Patient With Familial Adenomatous Polyposis Syndrome (2004)

Chinnaiyan, Kavitha M. MD; Ali, M. Ishti MD; Gunaratnam, Naresh T. MD Author Information
From Model Complexes to Metalloprotein Inhibition: A Synergistic Approach to Structure‐Based Drug Discovery (2003)

A happy marriage: The combination of synthetic model chemistry with computational conformational analysis has revealed the binding of an inhibitor to a medically important metalloenzyme. [(TpPh,Me)Zn(mbt)] (TpPh,Me=hydrotris(3,5-phenylmethylpyrazolyl)borate, mbt=2-methoxybenzenethiol) was used to template the conformation of a known inhibitor in the active site of the metalloenzyme, as shown by the green ligand inside the active site of the protein (the ZnII ion is shown in purple).
Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3 (2009)

Changes in gene expression that normally occur during culture under conditions that support L3 development and molting are prevented or delayed by radiation. This may explain the enhanced immunogenicity of L3ir. Gene Ontology and KEGG analyses revealed altered pathways between L3 types. Energy and "immune pathways" are up-regulated and may be needed for L3i invasion and survival, while growth and development are priorities for L3c. This study has improved our understanding of molecules involved in parasite invasion and immune evasion, potential targets of protective immunity, and molecules required for parasite growth and development.
Determination of In-Situ Thermal Conductivity, Thermal Diffusivity, Volumetric Specific Heat and Isobaric Specific Heat of Selected Foods Under Pressure (2010)

Thermal conductivity, thermal diffusivity, volumetric specific heat, and isobaric specific heat of tomato puree, soy protein isolate, soybean oil, guacamole, honey, cream cheese, and sucrose solution under pressure was determined using a dual needle probe from 0.1 to 600 MPa at 25°C. Thermal conductivity and thermal diffusivity of tested materials increased with applied pressure, while the isobaric specific heat decreased with pressure. The maximum combined uncertainty in the measurement of thermal conductivity, thermal diffusivity, volumetric specific heat, and isobaric specific heat were 3.1, 6.8, 6.6, and 6.9%, respectively. The data generated will be useful for the high pressure equipment design and process optimization.
Inlay Autogeneic Bone Grafting of Tibial Defects in Primary Total Knee Arthroplasty (1989)

Reinforcement of the proximal tibia with autogeneic bone grafts preserves an area of subchondral bone essential for optimal thickness of cement and fixation of the implants. Bone grafts reduce the need for custom implants and may prevent fragmentation of large amounts of eccentrically placed methylmethacrylate and implant failure.
Epitaxial film growth and optoelectrical properties of layered semiconductors, LaMnXO (X=P, As, and Sb) (2009)

Thin films of LaMnXO (X=P, As, and Sb), which are isostructural compounds of the newly discovered superconductor, LaFeAsO, were grown epitaxially on MgO (001) substrates at ∼680 °C by pulsed laser deposition. Postdeposition thermal annealing at 1000 °C in evacuated silica glass ampoules improved the crystallinity and orientation for the LaMnPO and LaMnAsO films, but it led to the phase segregation of the LaMnSbO film. Thermopower and optical absorption measurements revealed that all the films are p-type semiconductors with indirect bandgaps from 1.0 to 1.4 eV, which are supported by density functional calculations with the GGA+U approximation.
10-Gb/s transmission of NRZ over 10000 km and solitons over 13500 km error-free in the same dispersion-managed system (1997)

A dispersion management scheme that is capable of supporting both dispersion-managed solitons and nonreturn-to-zero (NRZ) data formats as well as intermediate formats is demonstrated for error-free long-haul transmission at 10 Gb/s in excess of 9500 km. This experimental tool ran be used to directly compare the different data formats. Our results suggest that a format between standard solitons and standard NRZ, such as dispersion-managed solitons or phase-modulated NRZ, may have significant advantages.