gebhart/patrepeval huggingface dataset:
Failure to farnesylate Rheb protein contributes to the enrichment of G0/G1 phase cells in the Schizosaccharomyces pombe farnesyltransferase mutant (2001)

Protein farnesylation is important for a number of physiological processes, including proliferation and cell morphology. The Schizosaccharomyces pombe mutant, cpp1-, defective in farnesylation, exhibits distinct phenotypes, including morphological changes and sensitivity to the arginine analogue, canavanine. In this work, we report a novel phenotype of this mutant, enrichment of G0/G1 phase cells. This phenotype results mainly from the inability to farnesylate the Rheb G-protein, as normal cell cycle progression can be restored to the mutant by expressing a mutant form of SpRheb (SpRheb-CVIL) that can bypass farnesylation. In contrast, a farnesylation-defective mutant of SpRheb (SpRheb-SVIA) is incapable of restoring the normal cell cycle profile to the cpp1- mutant. Inhibition of SpRheb expression leads to the accumulation of cells at the G0/G1 phase of the cell cycle. This growth arrest phenotype of the sprheb- disruption can be complemented by the introduction of wild-type sprheb+. The complementation is dependent on farnesylation, as the farnesylation-defective SpRheb-SVIA mutant is incapable of complementing the sprheb- disruption. Other mutants of SpRheb, E40K and S20N, are also incapable of complementing the sprheb- disruption. Furthermore, efficient complementation can be obtained by the expression of human Rheb but not Saccharomyces cerevisiae Rheb. Our findings suggest that protein farnesylation is important for cell cycle progression of S. pombe cells and that farnesylated SpRheb is critical in this process.
Impact of Linkage Group in Comb-Like Polymer on Dispersion Properties of Cement Pastes (2013)

The present study aimed to develop a full understanding of the effects of the linkage group type in comb-like polymers on dispersion and dispersion retention of concentrated cement pastes. Two comb-like copolymer dispersants with ester and ether linkage groups were produced. The effects of the linkage group type in the comb-like polymers on the adsorption, dispersion, dispersion retention of the concentrated cement suspensions were investigated systematically. The mechanism of dispersion retention was investigated using isothermal calorimetry measurements and structure stability analysis. The retention of dispersion had a close relationship with the hydration of cement and hydrolysis of side chains.
In Situ Growth and Characterization of Metal Oxide Nanoparticles within Polyelectrolyte Membranes (2016)

Abstract This study describes a novel approach for the in situ synthesis of metal oxide–polyelectrolyte nanocomposites formed via impregnation of hydrated polyelectrolyte films with binary water/alcohol solutions of metal salts and consecutive reactions that convert metal cations into oxide nanoparticles embedded within the polymer matrix. The method is demonstrated drawing on the example of Nafion membranes and a variety of metal oxides with an emphasis placed on zinc oxide. The in situ formation of nanoparticles is controlled by changing the solvent composition and conditions of synthesis that for the first time allows one to tailor not only the size, but also the nanoparticle shape, giving a preference to growth of a particular crystal facet. The high‐resolution TEM, SEM/EDX, UV‐vis and XRD studies confirmed the homogeneous distribution of crystalline nanoparticles of circa 4 nm and their aggregates of 10–20 nm. The produced nanocomposite films are flexible, mechanically robust and have a potential to be employed in sensing, optoelectronics and catalysis.
Adapting the RACER Architecture to Integrate Improved In-ReRAM Logic Primitives (2022)

Modern computing applications based upon machine learning can incur significant data movement overheads in state-of-the-art computers. Resistive-memory-based <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">processing-using-memory</i> (PUM) can mitigate this data movement by instead performing computation <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in situ</i> (i.e., directly within memory cells), but device-level limitations restrict the practicality and/or performance of many PUM architecture proposals. The RACER architecture overcomes these limitations, by proposing efficient peripheral circuitry and the concept of bit-pipelining to enable high-performance, high-efficiency computation using small memory tiles. In this work, we extend RACER to adapt easily to different PUM logic families, by (1) modifying the device access circuitry to support a wide range of logic families, (2) evaluating three logic families proposed by prior work, and (3) proposing and evaluating a new logic family called OSCAR that significantly relaxes the switching voltage constraints required to perform logic with resistive memory devices. We show that the modified RACER architecture, using the OSCAR logic family, can enable practical PUM on real ReRAM devices while improving performance and energy savings by 30% and 37%, respectively, over the original RACER work.
A new radioimmunoassay detecting early stages of colon cancer: a comparison with CEA, AFP, and Ca 19-9. (1992)

A previous study reported the results of a radioimmunoassay that analysed immune complexes (IC) with a specific labeled polyclonal antibody for the detection of the early stages of colon cancer. In order to investigate further the possible clinical use of this assay, a blind study that screened 505 patients referred for colonoscopy, compared their pathology reports with the results of four assays that measure levels of circulating tumor markers. These were CEA, AFP, Ca 19-9, and our previously described radioimmunoassay (RIA). Of the patients with no malignancies, the results that were in the normal range were as follows: CEA-473/495 (95.6 per cent), Ca 19-9-486/495 (98.2 per cent) and our RIA-488/495 (98.6 per cent). AFP levels were in the normal range for all patients in the study. The only assay to identify any Dukes' C and D patients was Ca 19-9, which detected 2/3 (67 per cent). Of the patients with Dukes' A and B colon cancer, CEA only identified 1/7 (14 per cent), AFP and Ca 19-9 0/7 (0 per cent), and our own RIA 5/7 (71 per cent). The positive results of our assay were significantly different from those of the other three assays with p values all less than 0.05. These preliminary results suggest that this RIA, because of its ability to detect the early stages of colon cancer, may be an effective complement to the currently available assays. The combination may provide a more comprehensive evaluation in monitoring colon cancer.
Processing-dependent thermal stability of a prototypical amorphous metal oxide (2018)

Amorphous metal oxides (AMOs) are important candidate materials for fabricating next-generation thin-film transistors. While much attention has been directed toward the synthesis and electrical properties of AMOs, less is known about growth conditions that allow AMOs to retain their desirable amorphous state when subjected to high operating temperatures. Using in situ x-ray scattering and level-set simulations, we explore the time evolution of the crystallization process for a set of amorphous $\mathrm{I}{\mathrm{n}}_{2}{\mathrm{O}}_{3}$ thin films synthesized by pulsed-laser deposition at deposition temperatures (${T}_{d}$) of \ensuremath{-}50, \ensuremath{-}25, and 0 \ifmmode^\circ\else\textdegree\fi{}C. The films were annealed isothermally and the degree of crystallinity was determined by a quantitative analysis of the time-evolved x-ray scattering patterns. As expected, for films grown at the same ${T}_{d}$, an increase in the annealing temperature ${T}_{A}$ led to a shorter delay prior to the onset of crystallization, and a faster crystallization rate. Moreover, when lowering the deposition temperature by 25 \ifmmode^\circ\else\textdegree\fi{}C, a 40 \ifmmode^\circ\else\textdegree\fi{}C increase in annealing temperature is needed to achieve the same time interval for the crystals to grow from 10 to 90% volume fraction of the sample. Films grown at ${T}_{d}=0{\phantom{\rule{0.16em}{0ex}}}^{\ensuremath{\circ}}\mathrm{C}$ exhibited strong cubic texture after crystallization. A level-set method was employed to quantitatively model the texture that develops in the microstructures and to determine key parameters, such as the interface growth velocity, the nucleation density, and the activation energy. The differences observed in the crystallization processes are attributed to the changes in the atomic structure of the oxide and possible nanocrystalline inclusions that formed during the deposition of the amorphous phase.
Transport and Rendering Challenges of Multi-Stream, 3D Tele-Immersion Data (2003)

For over four years, our colleagues at the University of Pennsylvania and we have been developing an experimental 3D tele-immersion testbed with the goal of providing high-fidelity scene reconstruction coupled with lifesize, view-dependent stereo display. The UPenn team has focused on stereo reconstruction algorithms, while UNC has worked on system architecture, network transport, and stereo rendering and display issues. This paper provides an overview of our testbed architecture and details the transport and rendering challenges and solutions we have explored.
Comparison of vertical discretization techniques in finite-difference models of ground-water flow; example from a hypothetical New England setting (1994)

realistic than results from the horizontal grids tested. Further testing of discretization procedures by use of a nonhorizontal-layered model with vertical distortion of model cells showed that vertical distortion is a useful tool in approximating some geologic features.
New strategies for fiber-based femtosecond lasers low-noise microwave generation (2011)

Low-phase-noise and stable microwave signals are of prime importance in a variety of scientific and technological fields, such as, for example, atomic frequency standards1,2, radar and remote sensing, and very long baseline interferometry. The combination of ultra-stable lasers 3 and low noise optical frequency division by use a femtosecond laser presents a possibility to realize extremely low phase noise microwave source with reliable and operational-level technology. We have previously reported phase noise levels at −120 dBc/Hz at 1Hz from a 12 GHz carrier, with white phase noise plateau approaching −140dBc/Hz 4,5,6.
In Praise of Basic Research as a Vehicle to Practical Applications: Palladium‐Catalyzed Coupling to Form Carbon‐Nitrogen Bonds (2020)

Two groups' research initiated to address two very different questions on problems of basic chemical research led, after much effort on catalyst development and studies of reaction mechanism, to the discovery and development of the coupling of amines with aryl halides in a practical fashion.
Permanent Magnetized Generator for Marine Current Power Conversion: Proposed Experimental Setup (2005)

In order to verify the theoretical work considering very low speed permanent magnetized generators for marine current power conversion, an experimental setup is under construction. Earlier 2-dimensional Finite Element Method (FEM) simulations have been performed and in this paper focus is on the practical considerations regarding the rotor construction of the generator as well as the total system configuration with motor, frequency transformer and generator. A rotor configuration with milled grooves for magnet fixation along with a power feedback option with a resistive load is chosen for the first experimental setup.
Frequency response for the conventional parallel resonant converter based on the state-plane diagram (1993)

The small-signal analysis of the conventional parallel resonant converter (PRC) operating in the continuous conduction mode is given. This analysis is based on the state-plane approach that has been successfully used to obtain the steady-state response for resonant converters. Applying perturbation directly to the steady-state trajectory, a discrete small-signal model for the converter can be derived in terms of the input voltage, switching frequency, and the converter state variables. Furthermore, this method can be applied to resonant converters in general, regardless of the order of their resonant tanks. Based on the derived closed-form solution, the frequency responses of input-to-output and control-to-output transfer functions are obtained. Computer simulation and experimental results are reported.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Peptide Regulation of Chondrogenic Stem Cell Differentiation (2023)

The search for innovative ways to treat osteoarthritis (OA) is an urgent task for molecular medicine and biogerontology. OA leads to disability in persons of middle and older age, while safe and effective methods of treating OA have not yet been discovered. The directed differentiation of mesenchymal stem cells (MSCs) into chondrocytes is considered one of the possible methods to treat OA. This review describes the main molecules involved in the chondrogenic differentiation of MSCs. The peptides synthesized on the basis of growth factors' structures (SK2.1, BMP, B2A, and SSPEPS) and components of the extracellular matrix of cartilage tissue (LPP, CFOGER, CMP, RDG, and N-cadherin mimetic peptide) offer the greatest promise for the regulation of the chondrogenic differentiation of MSCs. These peptides regulate the WNT, ERK-p38, and Smad 1/5/8 signaling pathways, gene expression, and the synthesis of chondrogenic differentiation proteins such as COL2, SOX9, ACAN, etc.
Copy number variations on chromosome 12q14 in patients with normal tension glaucoma (2011)

We report identification of a novel genetic locus (GLC1P) for normal tension glaucoma (NTG) on chromosome 12q14 using linkage studies of an African-American pedigree (maximum non-parametric linkage score = 19.7, max LOD score = 2.7). Subsequent comparative genomic hybridization and quantitative polymerase chain reaction (PCR) experiments identified a 780 kbp duplication within the GLC1P locus that is co-inherited with NTG in the pedigree. Real-time PCR studies showed that the genes within this duplication [TBK1 (TANK-binding kinase 1), XPOT, RASSF3 and GNS] are all expressed in the human retina. Cohorts of 478 glaucoma patients (including 152 NTG patients), 100 normal control subjects and 400 age-related macular degeneration patients were subsequently tested for copy number variation in GLC1P. Overlapping duplications were detected in 2 (1.3%) of the 152 NTG subjects, one of which had a strong family history of glaucoma. These duplications defined a 300 kbp critical region of GLC1P that spans two genes (TBK1 and XPOT). Microarray expression experiments and northern blot analysis using RNA obtained from human skin fibroblast cells showed that duplication of chromosome 12q14 results in increased TBK1 and GNS transcription. Finally, immunohistochemistry studies showed that TBK1 is expressed in the ganglion cells, nerve fiber layer and microvasculature of the human retina. Together, these data link the duplication of genes on chromosome 12q14 with familial NTG and suggest that an extra copy of the encompassed TBK1 gene is likely responsible for these cases of glaucoma. However, animal studies will be necessary to rule out a role for the other duplicated or neighboring genes.
Pharmacological Approach to Combat Mosquito Transmitted Malaria (2023)

Effective malaria management also decreases transmission of the disease to other people by decreasing the disease reservoir and by preventing the emergence and spread of resistance to antimalarial drugs. World health organization recommended the use of artemisinin based combination therapy as first line treatment for uncomplicated malaria. Resistance has also been documented to all classes of antimalarial medicines, including the artemisinin derivatives, and it is a major threat to malaria control. The main consequence of antimalarial drug resistance is treatment failure. Widespread inappropriate use of antimalarial drugs exerts a strong selective pressure on malaria parasites to develop high levels of resistance. Resistance can be prevented, or its onset slowed considerably by combining antimalarial drugs with different mechanisms of action and ensuring high cure rates through full adherence to correct dose regimens. Regular monitoring of drug efficacy is needed to inform treatment policies in malaria-endemic countries, and to ensure early detection of, and response to, drug resistance.
Serum Proteomic Changes after Randomized Prolonged Erythropoietin Treatment and/or Endurance Training: Detection of Novel Biomarkers (2015)

ClinicalTrials.gov NCT01320449.
G-quadruplexes as therapeutic targets (2000)

The ends of chromosomes (telomeres) consist of tandem repeats of guanine-rich sequences. In eukaryotics, telomeric DNA is single stranded for the final few hundred bases. These single-stranded sequences can fold into a variety of four-stranded structures (quadruplexes) held together by quartets of hydrogen-bonded guanine bases. The reverse transcriptase enzyme telomerase is responsible for maintaining telomeric DNA length in over 85% of cancer cells by catalyzing the synthesis of further telomeric repeats. Its substrate is the single-stranded 3'-telomeric end. Inhibition of telomere maintenance can be achieved by stabilization of a quadruplex structure for the telomere end. A variety of small molecules have been devised to achieve this, ranging from anthraquinones to porphyrins, acridines, and complex polycyclic systems. Structural and mechanistic aspects of these quadruplex complexes are reviewed here, together with a discussion of the issues of selectivity/potency for quadruplex DNAs vs duplex DNA.
Prototypes for building applications based on thermoplastic composites containing mixed waste plastics (2002)

Abstract Automotive shredder residue (ASR) and a complex residue obtained as a by‐product in the tertiary recycling of nylon‐6 fibers from used carpets were evaluated as potential additives in thermoplastic composites to be used for building applications. Prototype blocks were prepared by the “intrusion” process using various ratios of the waste streams and low‐density polyethylene (LDPE) in the absence of compatibilizers. Hence, product morphologies and corresponding properties were largely controlled through processing. They were evaluated for their short‐term and longterm mechanical properties, flammability, thermal conductivity, and heavy‐metal and total organic carbon leaching characteristics. Encapsulation of the waste feedstock by LDPE during molding in a single‐screw extruder significantly reduced the leachable content. In an effort to further reduce the leachable content, the mixtures were processed in two stages by precompounding in adevolatilizing twin‐screw extruder prior to molding. In comparison to the as‐received wastes, improved homogenization decreased the leachable heavy‐metal content by at least 98%. The carpet residue feedstock consisting of polypropylene, styrene‐butadiene rubber and calcium carbonate appears to be an attractive low‐cost, high‐volume material with consistent properties and could be used as filler in thermoplastic composites. Comparison of their performance characteristics suggested that the carpet residue composites would be favored versus ASR composites as replacement of the wood thermal barrier components in a novel steel‐based stud assembly.
Measurement of the jet mass in highly boosted $${\mathrm{t}}\overline{\mathrm{t}}$$ events from pp collisions at $$\sqrt{s}=8$$ $$\,\text {TeV}$$ (2017)

The first measurement of the jet mass [Formula: see text] of top quark jets produced in [Formula: see text] events from pp collisions at [Formula: see text] [Formula: see text] is reported for the jet with the largest transverse momentum [Formula: see text] in highly boosted hadronic top quark decays. The data sample, collected with the CMS detector, corresponds to an integrated luminosity of 19.7[Formula: see text]. The measurement is performed in the lepton+jets channel in which the products of the semileptonic decay [Formula: see text] with [Formula: see text] where [Formula: see text] is an electron or muon, are used to select [Formula: see text] events with large Lorentz boosts. The products of the fully hadronic decay [Formula: see text] with [Formula: see text] are reconstructed using a single Cambridge-Aachen jet with distance parameter [Formula: see text], and [Formula: see text] [Formula: see text]. The [Formula: see text] cross section as a function of [Formula: see text] is unfolded at the particle level and is used to test the modelling of highly boosted top quark production. The peak position of the [Formula: see text] distribution is sensitive to the top quark mass [Formula: see text], and the data are used to extract a value of [Formula: see text] to assess this sensitivity.
Experimental demonstration of short and long term synaptic plasticity using OxRAM multi k-bit arrays for reliable detection in highly noisy input data (2016)

In this paper, we propose a new circuit architecture and a reading/programming strategy to emulate both Short and Long Term Plasticity (STP, LTP) rules using non-volatile OxRAM cells. For the first time, we show how the intrinsic OxRAM device switching probability at ultra-low power can be exploited to implement STP as well as LTP learning rules. Moreover, we demonstrate the computational power that STP can provide for reliable signal detection in highly noisy input data. A Fully Connected Neural Network incorporating STP and LTP learning rules is used to demonstrate two applications: (i) visual pattern extraction and (ii) decoding of neural signals. A high accuracy is obtained even in presence of significant background noise in the input data.
Zero and Controllable Linewidth Enhancement Factor in p-Doped 1.3 µm Quantum Dot Lasers (2007)

We have studied the effects of δ-p-doping on the operating characteristics of quantum dot (QD) lasers. It is well known that increasing δ-p-doping in a laser core increases both the internal loss and threshold current. For QD lasers however, it has the beneficial effects of increasing differential efficiency and saturated ground state gain. A further consequence of increased δ-p-doping is an ultra low linewidth enhancement factor (LEF) that can be tuned through zero and even made negative with increased doping at low injected current densities.
Sparsifying Transformer Models with Trainable Representation Pooling (2022)

We propose a novel method to sparsify attention in the Transformer model by learning to select the most-informative token representations during the training process, thus focusing on the task-specific parts of an input. A reduction of quadratic time and memory complexity to sublinear was achieved due to a robust trainable top-k operator. Our experiments on a challenging long document summarization task show that even our simple baseline performs comparably to the current SOTA, and with trainable pooling we can retain its top quality, while being 1.8 faster during training, 4.5 faster during inference and up to 13 more computationally efficient in the decoder. 1