gebhart/patrepeval huggingface dataset:
The C-terminal region of Schizosaccaromyces pombe proliferating cell nuclear antigen is essential for DNA polymerase activity (1999)

Proliferating cell nuclear antigen (PCNA), the processivity factor (sliding clamp) of DNA polymerases (Pols), plays essential roles in DNA metabolism. In this report, we examined the functional role of the C-terminal region of Schizosaccaromyces pombe PCNA both in vitro and in vivo. The deletion or Ala substitution of the last 9 aa (252-260A), as well as Ala replacement of only 4 aa (252-255A) at the C terminus, failed to substitute for the wild-type PCNA protein for cell growth in S. pombe. Two other PCNA mutant proteins, A251V and K253E, exhibited cold-sensitive phenotypes. Several yeast strains harboring mutations, including those at the acidic C-terminal region, showed elevated sensitivity to DNA damage. The ability of the mutant PCNA proteins to stimulate DNA synthesis by Poldelta and Polepsilon also was studied in vitro. The mutant proteins that did not support cell growth and a mutant protein containing a single amino acid substitution at position 252, where Pro is replaced by Ala, stimulated Poldelta and Polepsilon activities poorly. All mutant PCNA proteins, however, were assembled around DNA by the clamp loader, replication factor C, efficiently. Thus, the C-terminal region of PCNA is important for interactions with both Poldelta and Polepsilon and for cell survival after DNA damage. The C terminus of sliding clamps from other organisms has been shown to be important for clamp loading as well as polymerase interactions. The relationship between the conserved sequence in this region in different organisms is discussed.
<title>Rapid chemical agent identification by surface-enhanced Raman spectroscopy</title> (2001)

Although the Chemical Weapons Convention prohibits the development, production, stockpiling, and use of chemical warfare agents (CWAs), the use of these agents persists due to their low cost, simplicity in manufacturing and ease of deployment. These attributes make these weapons especially attractive to low technology countries and terrorists. The military and the public at large require portable, fast, sensitive, and accurate analyzers to provide early warning of the use of chemical weapons. Traditional laboratory analyzers such as the combination of gas chromatography and mass spectroscopy, although sensitive and accurate, are large and require up to an hour per analysis. New, chemical specific analyzers, such as immunoassays and molecular recognition sensors, are portable, fast, and sensitive, but are plagued by false-positives (response to interferents). To overcome these limitations, we have been investigating the potential of surface-enhanced Raman spectroscopy (SERS) to identify and quantify chemical warfare agents in either the gas or liquid phase. The approach is based on the extreme sensitivity of SERS demonstrated by single molecule detection, a new SERS material that we have developed to allow reproducible and reversible measurements, and the molecular specific information provided by Raman spectroscopy. Here we present SER spectra of chemical agent simulants in both the liquid and gas phase, as well as CWA hydrolysis phase.
TOPICS IN DESIGN AND IMPLEMENTATION (2006)

The need for openness in mobile handset platform architectures from an applications development perspective, with a conflicting need for closedness in such platform architectures for security, manageability, and multiprotocol communications processing, has created a need for an overall platform architecture that provides simultaneous support for such features. Platform architectures are suggested that are rooted in hardware along with a trusted platform-aware architecture manager that creates closed partitions to provide cryptographic, communications, and manageability services, as well as open partitions for applications processing. Important and desirable ingredients in such platform architectures include domain separation, hardware rooted mechanisms to establish platform trust, hierarchical key management, secure storage, efficient resource management, and an inherently manageable platform.
Supplementary Tables 1 - 4 from Identification of Alternative Splicing Events Regulated by the Oncogenic Factor SRSF1 in Lung Cancer (2023)

&lt;p&gt;PDF file - 54K, Supplementary Table S1. Characteristics of microarray platforms for the analysis of splicing. Supplementary Table S2. Clinicopathological characteristics of the patients. Supplementary Table S3. List of the top 20 ranked genes selected by ExonPointer from the expression data obtained using Oryzon arrays. Supplementary Table S4. Results of the ExonPointer analysis in genes reported by Karni et al. (2007) as targets of SRSF1.&lt;/p&gt;
Direct Probing of Quantum Dots through Linear and Nonlinear Nano-Optics (2002)

Advances in nanoscopic probing techniques have led to the development of direct spatial and spectroscopic mapping methodologies which have revealed a wealth of information about single quantum dots. These techniques, combined with the favorable properties of naturally formed quantum dots, have allowed us to treat a single exciton confined to a quantum dot as a single solid state quantum absorber in analogy to atomic and molecular systems. Direct measurements on these systems, including absorption and coherent nonlinear spectroscopy, have revealed dipole moments and dynamic time scales of the individual excitations. Combined with microscopy, these probes have revealed global properties of the quantum dot system.
Molecular Encapsulation of Trimeric Chromium Carboxylate Clusters in Metal–Organic Frameworks and Propylene Sorption (2019)

Oxo-bridged trimeric chromium acetate clusters [Cr<sub>3</sub> O(OOCCH<sub>3</sub> )<sub>6</sub> (H<sub>2</sub> O)<sub>3</sub> ]NO<sub>3</sub> have been encapsulated for the first time in the mesoporous cages of the chromium terephthalate MIL-101(Cr). The isolated clusters in MIL-101(Cr) have increased affinity towards propylene compared to propane, due to generation of a new kind of pocket-based propylene-binding site, as supported by DFT calculations.
Activation of p53 protein by telomeric (TTAGGG)n repeats (2001)

Genome instability is a primary factor leading to the activation of the p53 tumor suppressor protein. Telomeric repeat (TR) sequences are also responsible for genome integrity. By capping the termini of the chromosomes, TRs prevent them undergoing nucleolytic degradation, ligation or chromosome fusion. Interestingly, telomere shortening was suggested to activate p53, which in turn may cause primary cells to senesce. In order to elucidate the nature of a possible cross talk between the two, we introduced into cells TRs of defined length and investigated their effect on p53 activation and subsequent cellular response. We found that the introduction of a TR into cells leads to stabilization of the p53 protein. This stabilization was specific to TRs and was not observed in response to exposure of cells to plasmids containing non-TR sequences. p53 stabilization requires the presence of an intact p53 oligomerization domain. TR-activated p53 exhibited enhanced transcriptional activity. Eventually, TRs induced p53-dependent growth suppression, measured as a reduction in colony formation.
Early Detection of Nonalcoholic Steatohepatitis in Patients with Nonalcoholic Fatty Liver Disease by Using MR Elastography (2011)

In patients with NAFLD, hepatic stiffness measurements with MR elastography can help identify individuals with steatohepatitis, even before the onset of fibrosis; NAFLD patients with inflammation but no fibrosis have greater liver stiffness than those with simple steatosis and lower mean stiffness than those with fibrosis.
Single White-Emitting Phosphor (Ba,Sr,Ce)4–mLi(Si,Al)19+2m(O,N)29+m for White LEDs (2023)

A new sialon compound, with the composition (Ba,Ce,Sr)4–mLi(Si,Al)19+2m(O,N)29+m (m = 0.3, n = 1), has been discovered. It crystallizes in the P3m1 space group, with two types of Ba/Sr sites: a ninefold coordinated site located in the cavities of the SiN4 tetrahedral framework and a sixfold coordinated site that is in substitutional disorder with a (Si/Al)2(O,N) group. This interesting structural feature gives rise to a rare occurrence of (Si,Al) atoms in a fivefold trigonal bipyramidal configuration with (O,N) anions, as confirmed by high-resolution solid-state 29Si MAS NMR and 27Al 2D 3QMAS NMR spectroscopy. At high Ce concentrations, the Ce ions substitute on both Ba/Sr sites, resulting in white light emission upon UV light excitation due to a double broad-band emission with peaks around 465 and 625 nm. This is a rare occasion of a single activator white-light-emitting phosphor, and the first Ce-doped sialon-based one to be reported. The new phosphor is promising for UV-excitable white LED applications because a single white-light-emitting phosphor with a single dopant does not rely on energy transfer between different activators or a complicated color balance for RGB phosphors, resulting in a cheaper and easier process to fabricate white LEDs.
The effects of a novel histamine-3 receptor inverse agonist on essential tremor in comparison to stable levels of alcohol (2011)

Essential tremor (ET) is a common movement disorder. Animal studies show that histaminergic modulation may affect the pathological processes involved in the generation of ET. Histamine-3 receptor inverse agonists (H3RIA) have demonstrated attenuating effects on ET in the harmaline rat model. In this double-blind, three-way cross-over, single-dose, double-dummy study the effects of 25 mg of a novel H3RIA (MK-0249) and a stable alcohol level (0.6 g L(-1)) were compared with placebo, in 18 patients with ET. Tremor was evaluated using laboratory tremorography, portable tremorography and a clinical rating scale. The Leeds Sleep Evaluation Questionnaire (LSEQ) and a choice reaction time (CRT) test were performed to evaluate potential effects on sleep and attention, respectively. A steady state of alcohol significantly diminished tremor as assessed by laboratory tremorography, portable tremorography and clinical ratings compared with placebo. A high single MK-0249 dose was not effective in reducing tremor, but caused significant effects on the LSEQ and the CRT test. These results suggest that treatment with a single dose of MK-0249 does not improve tremor in alcohol-responsive patients with ET, whereas stable levels of alcohol as a positive control reproduced the commonly reported tremor-diminishing effects of alcohol.
Recombineering in Vibrio natriegens (2017)

Abstract Here, we show that λ-Red homologs found in the Vibrio -associated SXT mobile element potentiate allelic exchange in V. natriegens by ~10,000-fold. Specifically, we show SXT-Beta (s065), SXT-Exo (s066), and λ-Gam proteins are sufficient to enable recombination of single- and double-stranded DNA with episomal and genomic loci. We characterize and optimize episomal oligonucleotide-mediated recombineering and demonstrate recombineering at genomic loci. We further show targeted genomic deletion of the extracellular nuclease gene dns using a double-stranded DNA cassette. Continued development of this recombination technology will advance high-throughput and large-scale genetic engineering efforts to domesticate V. natriegens and to investigate its rapid growth rate.
14.7 In-situ techniques for in-field sensing of NBTI degradation in an SRAM register file (2015)

SRAM register files have sensitive circuitry and often operate with high switching activity and at high temperature. This makes them particularly vulnerable to aging by negative-bias temperature instability (NBTI) degradation of their PMOS devices. We propose a technique to sense this aging degradation; it is an in-situ technique sensing the threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> ) of PMOSs directly in bitcells, and can operate in-field, thanks to the ability to sense V, robustly across temperature and voltage variations. This technique can be foundational for several dynamic reliability management (DRM) approaches, including: 1) sensing V, values periodically (e.g., every several months) for evaluating the amount and the rate of NBTI degradation; 2) sensing V, differences between two PMOSs in a bitcell to determine their strength skew and to estimate the minimum functional voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MIN</sub> ) degradation; and, 3) using the skew information across bitcells to create recovery vectors, which can be used to recover the aged PMOSs and thereby rebalance the skews. Existing in-situ techniques using ring oscillators or current sensors to sense bitcell reliability and performance cannot support in-field operation, which is a critical issue for DRM since it is impractical to control environmental parameters, particularly temperature, during sensing.
Nonmonotonic Aging and Memory Retention in Disordered Mechanical Systems (2017)

We observe nonmonotonic aging and memory effects, two hallmarks of glassy dynamics, in two disordered mechanical systems: crumpled thin sheets and elastic foams. Under fixed compression, both systems exhibit monotonic nonexponential relaxation. However, when after a certain waiting time the compression is partially reduced, both systems exhibit a nonmonotonic response: the normal force first increases over many minutes or even hours until reaching a peak value, and only then is relaxation resumed. The peak time scales linearly with the waiting time, indicating that these systems retain long-lasting memory of previous conditions. Our results and the measured scaling relations are in good agreement with a theoretical model recently used to describe observations of monotonic aging in several glassy systems, suggesting that the nonmonotonic behavior may be generic and that athermal systems can show genuine glassy behavior.
Measurement of effective refractive index of nematic liquid crystal (2014)

We report a measurement of effective refractive index of a nematic liquid crystal Fabry-Perot etalon according to the applied static electric field intensity. The effective refractive index decreases from 1.67 to 1.51 as the applied electric field intensity is increased.
Discrete-Continuous Gradient Orientation Estimation for Faster Image Segmentation (2014)

The state-of-the-art in image segmentation builds hierarchical segmentation structures based on analyzing local feature cues in spectral settings. Due to their impressive performance, such segmentation approaches have become building blocks in many computer vision applications. Nevertheless, the main bottlenecks are still the computationally demanding processes of local feature processing and spectral analysis. In this paper, we demonstrate that based on a discrete-continuous optimization of oriented gradient signals, we are able to provide segmentation performance competitive to state-of-the-art on BSDS 500 (even without any spectral analysis) while reducing computation time by a factor of 40 and memory demands by a factor of 10.
High-throughput process chain for single electron transistor devices based on field-emission scanning probe lithography and Smart Nanoimprint lithography technology (2019)

Next generation electronic devices like single electron transistors (SETs) operating at room temperature (RT) demand for high-resolution patterning techniques and simultaneously cost-effective, high-throughput manufacturing. Thereby, field-emission scanning probe lithography (FE-SPL) is a direct writing method providing high-resolution and high-quality nanopatterns. SET devices prepared by FE-SPL and plasma etching at cryogenic substrate temperature were shown to operate at RT [C. Lenk et al., Microelectron. Eng. 192, 77 (2018); Z. Durrani, M. Jones, F. Abualnaja, C. Wang, I. W. Rangelow, M. Kaestner, S. Lenk, C. Lenk, and A. Andreev, J. Appl. Phys. 124, 144502 (2018); I. W. Rangelow et al., J. Vac. Sci. Technol. B 34, 06K202 (2016)]. Nevertheless, FE-SPL lacks in writing speed and large area manufacturing capability required for industrial device manufacturing. This can be overcome by combining FE-SPL with nanoimprint lithography (NIL), which enables the replication of high-resolution features on large areas and provides high throughput. In this work, the authors will review a high-throughput process chain for RT-SET fabrication based on reproducing FE-SPL prepared masters by NIL and etching.
Kernel-Based Optimization for Traffic Density Estimation in ITS (2011)

Efficiency of transportation systems is defined as relationship between costs and benefits. Congestion is a phenomena that increase utilization cost in different modes of transportation including the road networks. In this paper, a kernel-based density estimation method is utilized to extract the congestion spots in road networks based on collected position samples with time-stamp from floating car data. A probabilistic framework is developed to find optimized weights of kernels in an approximation function, centered at points-of-interest by minimizing the Cramer-von Mises distance between localized cumulative distributions of mixture of Dirac distributions of position samples and Gaussian mixtures of points-of-interest in a pre-defined time window. The approximation density function by optimized kernels' weights can be used to estimate the mobile vehicles density in a specific time and space. The proposed method can be significantly improved if we have a spatial-temporal model of floating car data.
Comparison of the Anion Inhibition Profiles of the α-CA Isoforms (SpiCA1, SpiCA2 and SpiCA3) from the Scleractinian Coral Stylophora pistillata (2018)

Carbonic anhydrases (CAs, EC 4.2.1.1) are widespread metalloenzymes used by living organisms to accelerate the CO₂ hydration/dehydration reaction at rates dramatically high compared to the uncatalyzed reaction. These enzymes have different isoforms and homologues and can be found in the form of cytoplasmic, secreted or membrane-bound proteins. CAs play a role in numerous physiological processes including biomineralization and symbiosis, as is the case in reef-building corals. Previously, molecular and biochemical data have been obtained at the molecular level in the branching coral <i>Stylophora pistillata</i> for two coral isoforms which differ significantly in their catalytic activity and susceptibility to inhibition with anions and sulfonamides. More recently it has been determined that the genome of <i>S. pistillata</i> encodes for 16 CAs. Here, we cloned, expressed, purified and characterized a novel α-CA, named SpiCA3, which is cytoplasmic and ubiquitously expressed in all the cell layers including the calcifying cells. SpiCA3 is the most effective CA among the coral isoforms investigated and the most efficient catalyst known up to date in Metazoa. We also investigated the inhibition profiles of SpiCA3 and compared it with those obtained for the two other isoforms in the presence of inorganic anions and other small molecules known to interfere with metalloenzymes. These results suggest that <i>S. pistillata</i> has adapted its CA isoforms to achieve the physiological functions in different physicochemical microenvironments.
Whiplash Injury (1999)

Yoganandan, Narayan PhD; Pintar, Frank A. PhD; Kleinberger, Michael PhD Author Information
EVALUATION OF BRIDGE APPROACH RAILS. FINAL REPORT (1992)

A recent study on the performance of guardrail-to-bridge rail transitions revealed that many widely used designs do not meet current safety standards. As a result, the Federal Highway Administration (FHWA) requested that the Arizona Department of Transportation (ADOT) verify the safety performance of its standard transition designs. Three transition designs currently being used by ADOT were evaluated through a combined program of computer simulation and full-scale crash testing. The standard ADOT wood post transition, incorporating a channel rubrail and two different sizes of timber posts at a reduced post spacing near the bridge rail end, was found to be in compliance with National Cooperative Highway Research Program (NCHRP) Report 230 performance criteria. The standard ADOT steel post transition with channel rubrail was also found to be in compliance with NCHRP Report 230 requirements when impacted near the end of the bridge rail. However, the upstream end of the steel post transition required modification to eliminate deficiencies identified during testing. The modified design, which terminated the channel rubrail behind a W6x9 guardrail post, was successfully crash tested. The third transition design evaluated was the standard ADOT steel post system with a 6 in. curb extending along the length of the transition. When tested, this system failed to meet NCHRP Report 230 test criteria. Significant modifications were made to the design including the addition of a rubrail section and tubular steel blockouts near the bridge end. This modified design was successfully tested in accordance with NCHRP Report 230 recommendations. In an effort to assess the risk posed by the current design an additional test on the unmodified system was conducted using impact conditions of 60 mph and 20 degrees. The steel post system with curb successfully passed this crash test, indicating that there is no need to establish a retrofit program. It is recommended that the wood and steel post systems with curb, as well as the steel post system with rubrail and without curb, be retrofit or replaced as they are damaged and reconstructed.
Photoresponsive Slide‐Ring Gel (2007)

Slide-ring topological gels with mobile cross-linking units are a new class of soft materials that exhibit distinct features differing from those of conventional chemically or physically cross-linked gels. Photoresponsive behavior arising from the dynamic nature of the cross-linkers is demonstrated for a slide-ring gel prepared by adding azobenzene units to the mobile α-cyclodextrin units of a poly(ethylene oxide)-based polyrotaxane (see figure).
Restriction of antigen recognition in mouse B lymphocytes by genes mapping within the major histocompatibility complex. (1980)

B cells, like T cells, show genetic restrictions in their interactions with other cells. B cells from (C3H/HeJ X C57BL/6J)F1 mice were stimulated with foreign antigen (sheep erythrocytes, SRBC) in parental-strain irradiated hosts. They could be subsequently activated to antibody formation in vitro by SRBC presented on cells of the same parental type, and much less by SRBC on cells of the other parental type. The restriction was seen whether antigen was presented on macrophages or by activated T cells. Experiments with congenic mice showed that the restriction was controlled by the MHC locus. Restriction of F1 B cells to responsiveness against either parental haplotype was much more readily induced in bone marrow than in splenic populations. This restriction could be broken down by giving the irradiated host a second injection of antigen 3 weeks after the first; this probably reflects "reeducation" of the F1 B cells by SRBC associated with donor, F1-type macrophages. Normal unprimed spleen B cells also showed a strong preference for activation by SRBC in association with syngeneic activated T cells.
Metabolite coupling in genome-scale metabolic networks (2006)

The coupling of metabolites is an important topological property of metabolic networks. By computing coupling quantitatively for the first time in genome-scale metabolic networks, we provide insight into the basic structure of these networks.
Staggered mode MEMS gyroscope (2016)

This paper presents a novel design concept of a MEMS gyroscope comprising a sense mode with a staggered frequency response. Considering a two-degree of freedom sense-mode structure, the bandwidth is enhanced by more than 40%. A post-fabrication electrostatic tuning mechanism based on two tuning electrodes is proposed to achieve resonance frequency trimming. The concept is applied on the design and analysis of fully decoupled gyroscope based on the SOI MUMPS process and operating around a resonance frequency of 5 kHz. The concept is extendable for multi-degree of freedom for wider bandwidth extension.