gebhart/patrepeval huggingface dataset:
Conformational Changes of Calmodulin on Calcium and Peptide Binding Monitored by Film Bulk Acoustic Resonators (2011)

Film bulk acoustic resonators (FBAR) are mass sensitive, label-free biosensors that allow monitoring of the interaction between biomolecules. In this paper we use the FBAR to measure the binding of calcium and the CaMKII peptide to calmodulin. Because the mass of the calcium is too small to be detected, the conformational change caused by the binding process is measured by monitoring the resonant frequency and the motional resistance of the FBAR. The resonant frequency is a measure for the amount of mass coupled to the sensor while the motional resistance is influenced by the viscoelastic properties of the adsorbent. The measured frequency shift during the calcium adsorptions was found to be strongly dependent on the surface concentration of the immobilized calmodulin, which indicates that the measured signal is significantly influenced by the amount of water inside the calmodulin layer. By plotting the measured motional resistance against the frequency shift, a mass adsorption can be distinguished from processes involving measurable conformational changes. With this method three serial processes were identified during the peptide binding. The results show that the FBAR is a promising technology for the label-free measurement of conformational changes.
Single-Cell CRISPR-Based Lineage Tracing in Mice (2019)

[Image: see text]
Activation of Cell-Penetrating Peptides with Ionpair−π Interactions and Fluorophiles (2016)

In this report, we elaborate on two new concepts to activate arginine-rich cell-penetrating peptides (CPPs). Early on, we have argued that repulsion-driven ion-pairing interactions with anionic lipids account for their ability to move across hydrophobic cell membranes and that hydrophobic anions such as pyrenebutyrate can accelerate this process to kinetically outcompete endosomal capture. The original explanation that the high activity of pyrenebutyrate might originate from ionpair-π interactions between CPP and activator implied that replacement of the π-basic pyrene with polarized push-pull aromatics should afford more powerful CPP activators. To elaborate on this hypothesis, we prepared a small collection of anionic amphiphiles that could recognize cations by ionpair-π interactions. Consistent with theoretical predictions, we find that parallel but not antiparallel ionpair-π interactions afford operational CPP activators in model membranes and cells. The alternative suggestion that the high activity of pyrenebutyrate might originate from self-assembly in membranes was explored with perfluorinated fatty acids. Their fluorophilicity was expected to promote self-assembly in membranes, while their high acidity should prevent charge neutralization in response to self-assembly, i.e., generate repulsion-driven ion-pairing interactions. Consistent with these expectations, we find that perfluorinated fatty acids are powerful CPP activators in HeLa cells but not in model membranes. These findings support parallel ionpair-π interactions and repulsion-driven ion pairing with self-assembled fluorophiles as innovative concepts to activate CPPs. These results also add much corroborative support for counterion-mediated uptake as the productive mode of action of arginine-rich CPPs.
Identification of an Integrin α6‐Targeted Peptide for Nasopharyngeal Carcinoma‐Specific Nanotherapeutics (2019)

Abstract Integrin α6 emerges as an attractive cancer therapeutic target. Here, the authors present for the first‐time, that integrin α6 is overexpressed in nasopharyngeal carcinoma (NPC) and serves as a prognostic predictor and a cancer stem cell (CSC) biomarker. An NPC‐targeted peptide CRWYDENAC (dubbed RWY) with high specificity and affinity for integrin α6 is identified, and an integrin α6‐targeted nanotherapeutic against NPC is developed by encapsulating a cisplatin prodrug Pt(IV) with RWY‐grafted polymeric nanoparticles (dubbed RWY‐NP/Pt(IV)). The delivery of cisplatin prodrug Pt(IV) by RWY‐NP/Pt(IV) results in an approximately 100‐fold increase in cytotoxicity over free cisplatin, as well as a 5‐fold increase over Scramble‐NP/Pt(IV) control. RWY‐NP/Pt(IV) suppresses NPC tumor growth with an inhibition rate of around 78%, compared with the 44% and 41% achieved by free cisplatin and Scramble‐NP/Pt(IV) treatment. Loss of body weight is observed in free cisplatin treated mice but not in RWY‐NP/Pt(IV) treated mice. Taken together, RWY‐NP/Pt(IV) enhances the therapeutic efficacy of cisplatin treatment and reduces deleterious side effects, suggesting the potential application of the integrin α6‐targeted RWY peptide for nanotherapeutics against NPC.
Active disk paxos with infinitely many processes (2002)

We present an improvement to the Disk Paxos protocol by Gafni and Lamport which utilizes extended functionality and flexibility provided by Active Disks and supports unmediated concurrent data access by an unlimited number of processes. The solution facilitates coordination by an infinite number of clients using finite shared memory. It is based on a collection of read-modify-write objects with faults, that emulate a new, reliable shared memory abstraction called a ranked register. The required read-modify-write objects are readily available in Active Disks and in Object Storage Device controllers, making our solution suitable for state-of-the-art Storage Area Network (SAN) environments.
Surgical Treatment for Lung Metastases from Colorectal Cancer. (1996)

大腸癌の肺転移は大腸癌手術症例の2.4%が切除対象であり, overallの5年生存率は50%, 10年生存率は43%であった. 根治切除58例の5年生存率は53%であるのに対し, 姑息3例や非切除19例の50%生存期間はそれぞれ1年3カ月, 1年と予後不良であった (p<0.01). 予後因子としては, 術前血清CEA値, 肺転移の個数, 胸腔内洗浄細胞診, 縦隔リンパ節転移があげられた. 診断方法として, ヘリカル胸部CTによる転移巣の数と部位の診断向上があり, 切除方法としては, 特にYAG-Laserを用いた部分切除が有用で, 残肺再切除や肝・肺切除等適応拡大に寄与していると考えられた.
Nonlinearity aware bisection-based sphere shaping for optical digital subcarrier multiplexing systems (2022)

In this paper, a nonlinearity-tolerant sphere shaping is proposed based on the parallel bisection structure. Compared to enumerative sphere shaping (ESS), the bisection-based sphere shaping (BS-SS) can achieve a lower average energy and rate loss at the same blocklength by selecting all preferential sequences. The nonlinearity-tolerant BS-SS (BS-SS-NLI) can mitigate the fiber nonlinearity by reducing the energy variation, which is demonstrated in the simulations with probabilistically shaped, single channel, dual-polarization 64-ary quadrature amplitude modulation (DP-64QAM) for a multi-span long-haul transmission over 2500 km of standard single-mode fiber (SSMF) applying digital subcarrier multiplexing (SCM), comparing with recent literature kurtosis-limited ESS (K-ESS) and list-encoding constant composition distribution matching (L-CCDM). The BS-SS-NLI can provide 0.25 dB effective signal-to-noise ratio (SNR) gain over ESS and 0.39 dB gain over L-CCDM. The achievable information rate (AIR) can be improved ∼0.1 bits/4D-symbol by BS-SS-NLI over ESS.
Resolution-Directed Optimization-based Distributed Sensing (2015)

In this paper we study the problem of optimal zone coverage, using distributed sensing, i.e. a group of collaborating sensors. We formulate the problem as an optimization problem with time-varying cost function. We examine the case where a group of elevated imaging sensors look down to and form the map of a 2-dimensional environment at a pre-specified resolution. The sensors solve an optimization problem that attempts to optimize a time-varying cost function. The cost at any time instance measures the distance between the desired resolution function and the achieved resolution until the previous time instant. We discuss the numerical implementation challenges of this approach and demonstrate its performance on a numerical example.
Heart transplantation Michael A Acker and David Zeltsman (2004)

The technique of the orthotopic cardiac transplantation was developed and popularized by Richard Lower and Norman Shumway. The authors used moderate hypothermia, cardiopulmonary bypass, and an atrial ‘cuff ’ anastomosis, a technique that became the standard for cardiac transplant. The world’s first successful human-to-human heart transplant was performed on 3 December 1967 in South Africa by Christian Barnard. However, over the next several years, poor early clinical results led to few heart transplantation attempts, and only the most dedicated centers continued experimental and clinical work in the field. The introduction of cyclosporine for the management of immune reactions and rejection episodes greatly facilitated heart transplantation. The number of transplants dramatically increased from only 106 in 1980 to over 4000 cases in 2002 worldwide.
Neural Ranking Models with Multiple Document Fields (2017)

Deep neural networks have recently shown promise in the ad-hoc retrieval task. However, such models have often been based on one field of the document, for example considering document title only or document body only. Since in practice documents typically have multiple fields, and given that non-neural ranking models such as BM25F have been developed to take advantage of document structure, this paper investigates how neural models can deal with multiple document fields. We introduce a model that can consume short text fields such as document title and long text fields such as document body. It can also handle multi-instance fields with variable number of instances, for example where each document has zero or more instances of incoming anchor text. Since fields vary in coverage and quality, we introduce a masking method to handle missing field instances, as well as a field-level dropout method to avoid relying too much on any one field. As in the studies of non-neural field weighting, we find it is better for the ranker to score the whole document jointly, rather than generate a per-field score and aggregate. We find that different document fields may match different aspects of the query and therefore benefit from comparing with separate representations of the query text. The combination of techniques introduced here leads to a neural ranker that can take advantage of full document structure, including multiple instance and missing instance data, of variable length. The techniques significantly enhance the performance of the ranker, and also outperform a learning to rank baseline with hand-crafted features.
Motilin and OHM-11526 activate a calcium current in human and canine jejunal circular smooth muscle (1997)

Motilin is a potent agonist for gastrointestinal smooth muscle contraction and has been proposed to regulate the onset of phase III of the migrating motor complex in dogs and humans. The effects of motilin and OHM-11526, a motilin antagonist in rabbit smooth muscle strips, were examined in isolated canine and human jejunal circular smooth muscle cells using whole cell patch-clamp techniques with Ba2+ as the charge carrier. Effects of both drugs on inward current through L-type Ca2+ channels (ICaL) in both canine and human cells were first observed at 10(-3) M. At 10(-6) M, motilin increased ICaL in canine and human jejunal circular smooth muscle cells by 43 +/- 20 and 45 +/- 11%, respectively, and OHM-11526 increased ICaL by 54 +/- 8 and 54 +/- 14%, respectively. The increase in inward current was blocked by nifedipine and by guanosine 5'-O-(2-thiodiphosphate) but not by pertussis toxin. Washout of both drugs resulted in a further increase in ICaL. These data suggest that both motilin and OHM-11526 activate and ICaL in human and canine jejunal circular smooth muscle cells through a G protein-coupled mechanism.
Visual environment for designing sequence control program with AI planning (2002)

A visual environment for designing sequence control program with AI planning is described. In order to increase productivity and improve the quality and reliability of the control specifications, the authors have been developing a planning-based Visual Programming System for Sequence Control Program Specification Design (VIPS/S-SFCD). VIPS/S-SFCD features an example-based programming technique in which designers specify the initial states and goal states of machines using visual representations, and generates control specification by AI planning. To overcome the difficulty of dealing with complex data/knowledge of the planner, VIPS/S-SFCD analyzes and confirms user intention using context-dependent valence theory and case grammar. They used VIPS/S-SFCD to experimentally generate control program specifications for actually existing steel plants. The experimental results showed that visual representation with dynamic, intuitional icons, the coverage of the grammar rule, and generating time of control specification are practical.
Temperature Dependence of Grating-Assisted Coupling to Small Silicon Waveguides (2007)

Coupling optical fibres with small silicon waveguides can present a challenge due to a large difference in retractive index and dimensions between the two. Here we investigate the temperature influence on a grating-assisted directional coupler.
Deep Neural Networks-Based Weight Approximation and Computation Reuse for 2-D Image Classification (2022)

Deep Neural Networks (DNNs) are computationally and memory intensive, which present a big challenge for hardware, especially for resource-constrained devices such as Internet-of-Things (IoT) nodes. This paper introduces a new method to improve DNNs performance by fusing approximate computing with data reuse techniques for image recognition applications. First, starting from the pre-trained network, then the DNNs weights are approximated based on the linear and quadratic approximation methods during the retraining phase to reduce the DNN model size and number of arithmetic operations. Then, the DNNs weights are replaced with the linear/quadratic coefficients to execute the inference so that different DNNs weights can be computed using the same coefficients. That leads to a repetition of the weights, which enables the reuse of the DNN sub-computations (computational reuse) and leverages the same data (data reuse) to reduce DNNs computations memory accesses, and improve energy efficiency, albeit at the cost of increased training time. Complete analysis for MNIST, Fashion MNIST, CIFAR 10, CIFAR 100, and tiny ImageNet datasets is presented for image recognition, where different DNN models are used, including LeNet, ResNet, AlexNet, and VGG16. Our results show that the linear approximation achieves <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1211.3\times $ </tex-math></inline-formula> , <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$21.8\times $ </tex-math></inline-formula> , <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$700\times $ </tex-math></inline-formula> , and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$19.3\times $ </tex-math></inline-formula> on LeNet-5 MNIST, LeNet Fashion MNIST, VGG16 and ResNet-20. respectively, with small accuracy loss. Compared to the state-of-the-art Row Stationary (RS) method, the proposed architecture saved 54% of the total number of adders and multipliers needed. Overall, the proposed approach is suitable for IoT edge devices as it reduces computing complexity, memory size, and memory access with a small impact on accuracy.
Compressibility and pressure-induced phase transformation of Ti3GeC2 (2004)

In order to explore the large shear-strain-induced polymorph, α-Ti3GeC2 polycrystals were investigated by using a synchrotron radiation source to 64GPa under nonhydrostatic state. Upon compression to 26.6GPa, α-Ti3GeC2 starts to transform to β-Ti3GeC2. As compared to α-Ti3GeC2, the cell parameter a of β-Ti3GeC2 is slightly shorter, and both c and c∕a larger. These two polymorphs exhibit similar compressibility. The bulk modulus is calculated to be 179(±10)GPa at a fixed K′=4.0. This is lower than that of Ti3SiC2, and close to that of Ti3Si0.5Ge0.5C2. The compressibilities of these two Ti3GeC2 polymorphs do not display an apparent anisotropy, and differ from the large anisotropies observed from Ti3SiC2 and Ti3Si0.5Ge0.5C2.
Power Loop Busbars Design and Experimental Validation of 1 kV, 5 kA Solid-State Circuit Breaker Using Parallel Connected RB-IGCTs (2021)

This article investigates the design of a 1 kV, 5 kA solid-state circuit breaker by using parallel connection of reverse blocking IGCTs (RB-IGCT). The presented breaker topology is based on the parallel connection of low conduction loss RB-IGCTs which delivers efficiency as high as 99.9%. The focus of this article is on the power loop design and experimental validation of parallel connection of two and three RB-IGCTs with emphasis on current sharing during dynamic events such as short-circuits. A 3-D CAD-based design of power loop busbars was verified by several simulation test cases to represent dynamic current sharing under variations in RB-IGCT package impedances. An optimized busbar design approach and its tradeoffs are also discussed with simulation verification. The experimental results confirm that the parallel topology is able to perform current interruption during overload and short-circuit situations up to 10 kA for two devices in parallel and up to 14 kA for three devices in parallel - with current deviation from the mean as little as 6%.
Study on influence of gypsum upon adsorption of new polycarboxylate superplasticizer on cement surface (2009)

The influence of sulfate ion on adsorption of polycarboxylate superplasticizer on cement surface was investigated by adjusting the content and forms of gypsum. The test results show that,with the content of gypsum increases,the absorption amount and ratio of superplasticizer on cement decrease gradually. The form of gypsum has certain influence on absorption behavior. Adding anhydrous gypsum make polycarboxylate superplasticizer increase adsorption rate on cement;Same form (dihydrate gypsum) but different kinds of gypsum have different adsorption rate and the adsorption rate of phosphogypsum is even higher. It is proposed to change the amount of adsorption between cement and polycarboxylate superplasticizer by increase or reduce the amount of sulfate ion.
Biomarker Profiles in Heart Failure Patients With Preserved and Reduced Ejection Fraction (2017)

In HFpEF, inflammation and angiogenesis-mediated interactions are predominantly observed, while stretch-mediated interactions are found in HFrEF. The remodeling marker osteopontin and the angiogenesis marker neuropilin predicted outcome in HFpEF, but not in HFrEF.
Elevated Serum Metal Levels from Vitamin Supplementation (2013)

Cooper, H. John MD; Jacobs, Joshua J. MD; Leikin, Jerrold B. MD; Barden, Regina M. RN, BSN; Rosenberg, Aaron G. MD Author Information
A Simple Synthesis of 5-Amino-3-(2-dimethylaminoethyl) indole [5-Amino-N,N-dimethyltryptamine] (1993)

Abstract A short (three step) synthesis of 5-amino-3-(2-dimethylaminoethyl)indole [5-amino-N, N-dimethyltryptamine, 4] from commercially available starting materials is presented. Reaction of 5-nitroindole with oxalyl chloride followed by dimethylamine afforded N,N-dimethyl 5-nitroindole-3-glyoxamide (1), which was reduced by diborane to 5-nitro-3-(2-dimethylaminoethyl)indole (3). Catalytic reduction of (3) afforded the title compound in 19% overall yield from 5-nitroindole.
TGFβ pathway is required for viable gestation of Fanconi anemia embryos (2022)

Overexpression of the TGFβ pathway impairs the proliferation of the hematopoietic stem and progenitor cells (HSPCs) pool in Fanconi anemia (FA). TGFβ promotes the expression of NHEJ genes, known to function in a low-fidelity DNA repair pathway, and pharmacological inhibition of TGFβ signaling rescues FA HSPCs. Here, we demonstrate that genetic disruption of Smad3, a transducer of the canonical TGFβ pathway, modifies the phenotype of FA mouse models deficient for Fancd2. We observed that the TGFβ and NHEJ pathway genes are overexpressed during the embryogenesis of Fancd2-/- mice and that the Fancd2-/-Smad3-/- double knockout (DKO) mice undergo high levels of embryonic lethality due to loss of the TGFβ-NHEJ axis. Fancd2-deficient embryos acquire extensive genomic instability during gestation which is not reversed by Smad3 inactivation. Strikingly, the few DKO survivors have activated the non-canonical TGFβ-ERK pathway, ensuring expression of NHEJ genes during embryogenesis and improved survival. Activation of the TGFβ-NHEJ axis was critical for the survival of the few Fancd2-/-Smad3-/- DKO newborn mice but had detrimental consequences for these surviving mice, such as enhanced genomic instability and ineffective hematopoiesis.
Additions, Annotations, and Marginalia (2013)

The rising importance of manuscript contexts to the study of Old English goes hand in hand with the increasing attention devoted to marginalized - if not always marginal - Old English texts. Some manuscripts preserve incidental records - some additional, some Original. Colophons are forms of direct address to the book's readers that frequently reveal some details of the book's production, especially the names of scribes. Many of the less substantial pieces of Old English that can be found scattered about Anglo-Saxon manuscripts are too brief and too diverse, or simply too obscure, to categorize very easily, but a pronounced interest in folkloristic texts, including pseudo-historical, apotropaic, and cryptographic ones, emerges from a survey of these materials. Notes on Christian lore or notes of general religious interest have a presence in Old English marginalia and additions to Anglo-Saxon manuscripts.
Infrared Transmission for Intervehicle Ranging and Vehicle-To-Roadside Communication Systems Using Spread-Spectrum Technique (2004)

In this paper, an infrared intervehicle ranging and vehicle-to-roadside communication systems are studied. A direct-sequence spread-spectrum (DS-SS) technology is employed to obtain the robustness against multiuser interference and ambient light noise. We compare the correlation properties for various optical spreading codes such as an optical orthogonal code (OOC), a prime code, an extended prime code, and a modified m-sequence. The performance of the infrared DS-SS ranging and communication system is evaluated by computer simulation over a channel in consideration of multipath dispersion, multiuser interference, and a background light noise. The infrared DS-SS intervehicle ranging system using an OOC has lower ranging error rate (RER) than ranging systems using a prime code, an extended prime code, and modified m-sequences even if there is the interference from other users and lightwave dispersion. In the infrared DS-SS vehicle-to-roadside communication system, L-ary pulse position modulation (L-PPM) is used as a modulation scheme due to high average power efficiency. It is shown that the proposed system achieves smaller BER performance as the modulation order L increases and the proposed system with a (361,6,1,1) OOC has a smaller BER than that with a (181,6,1,1) OOC.