gebhart/patrepeval huggingface dataset:
Electron Capture Dissociation (ECD) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Synergy of Immune Checkpoint Blockade with a Novel Synthetic Consensus DNA Vaccine Targeting TERT (2017)

Immune checkpoint blockade antibodies are setting a new standard of care for cancer patients. It is therefore important to assess any new immune-based therapies in the context of immune checkpoint blockade. Here, we evaluate the impact of combining a synthetic consensus TERT DNA vaccine that has improved capacity to break tolerance with immune checkpoint inhibitors. We observed that blockade of CTLA-4 or, to a lesser extent, PD-1 synergized with TERT vaccine, generating more robust anti-tumor activity compared to checkpoint alone or vaccine alone. Despite this anti-tumor synergy, none of these immune checkpoint therapies showed improvement in TERT antigen-specific immune responses in tumor-bearing mice. αCTLA-4 therapy enhanced the frequency of T-bet<sup>+</sup>/CD44<sup>+</sup> effector CD8<sup>+</sup> T cells within the tumor and decreased the frequency of regulatory T cells within the tumor, but not in peripheral blood. CTLA-4 blockade synergized more than Treg depletion with TERT DNA vaccine, suggesting that the effect of CTLA-4 blockade is more likely due to the expansion of effector T cells in the tumor rather than a reduction in the frequency of Tregs. These results suggest that immune checkpoint inhibitors function to alter the immune regulatory environment to synergize with DNA vaccines, rather than boosting antigen-specific responses at the site of vaccination.
A practical approach for the design of nonuniform lapped transforms (2006)

We propose a simple method for the design of lapped transforms with nonuniform frequency resolution and good time localization. The method is a generalization of an approach previously proposed by Princen, where the nonuniform filter bank is obtained by joining uniform cosine-modulated filter banks (CMFBs) using a transition filter. We use several transition filters to obtain a near perfect-reconstruction (PR) nonuniform lapped transform with significantly reduced overall distortion. The main advantage of the proposed method is in reducing the length of the transition filters, which leads to a reduction in processing delay that can be useful for applications such as real-time audio coding.
The relationship of myocardial contraction and electrical excitation—the correlation between scintigraphic phase image analysis and electrophysiologic mapping (2009)

A noninvasive method to accurately determine the sequence of contraction may serve as a surrogate for the associated electrical activation sequence or be applied to identify their differences.
Hyperimmune cow colostrum reduces diarrhoea due to rotavirus: a double‐blind, controlled clinical trial (1995)

The therapeutic efficacy of hyperimmune bovine colostrum (HBC) from cows immunized with four serotypes of human rotavirus was evaluated in a double-blind, randomized trial in 75 boys, aged 6-24 months, infected with rotavirus diarrhoea. The treatment group received 100 ml of HBC three times a day for 3 consecutive days, while the controls received the same amount of bovine colostrum from significantly shorter duration of diarrhoea than the controls (median 56 versus 72 h (p<0.001); confidence interval of median difference (CI) 8-32 h). Total stool output (g/kg) between admission and cessation of diarrhoea was reduced by 29% in the HBC-treated group compared with controls (median 205 versus 290 g (p=0.04); CI = 1-154 g). In 50% of the children in the study group, diarrhoea stopped by 48 h, whereas 100% of the controls were still suffering from diarrhoea. No untoward effects were noted in either group. Colostrum from cows immunized with rotavirus antigen is clinically effective in reducing the duration and severity of childhood diarrhoea due to rotavirus.
Designing beacon mobility to improve target localization from range measurements (2010)

Traditionally, multiple fixed beacons are required to localize a target node using methods such as trilateration. Under this scenario, localization accuracy can be greatly affected by the geometric configuration of the beacons. In this paper, the fixed beacons are replaced by a single mobile beacon that takes range measurements from multiple locations in order to localize a stationary target. The mobility pattern of the beacon thus replaces geometric configuration as one of the major factors affecting localization accuracy. The mobility pattern can either be predetermined to minimize average localization error or the pattern can be determined during the localization process.
Complete polarization conversion using anisotropic temporal slabs (2021)

It is well known that control over the polarization of electromagnetic waves can be achieved by utilizing artificial anisotropic media such as metamaterials. However, most of the related research has been focused on time-invariant systems. Inspired by the concept of temporal boundaries, we propose a method to realize polarization conversion in real time by employing time-variant materials, whose permittivity or permeability switches between isotropic and anisotropic values. The criteria for complete polarization conversion are studied for several polarization angles, both analytically and numerically.
Ontologizing semantic relations (2006)

Many algorithms have been developed to harvest lexical semantic resources, however few have linked the mined knowledge into formal knowledge repositories. In this paper, we propose two algorithms for automatically ontologizing (attaching) semantic relations into WordNet. We present an empirical evaluation on the task of attaching partof and causation relations, showing an improvement on F-score over a baseline model.
Close−Open−Close Evolution of Holes at the Tips of Conical Graphenes of Single-Wall Carbon Nanohorns (2008)

We previously reported that holes opened at the tips of conical single-graphenes of single-wall carbon nanohorns were closed during heat treatment at 1200 °C in an argon atmosphere. Here, we report phenomena related to the behavior of these holes: the holes closed quickly at first, then reopened, and then slowly closed again as the heat treatment period increased. This close−open−close evolution occurred only when the initial hole size was medium (0.7−0.9 nm). Smaller and larger holes did not reopen after they thermally closed. We discuss the close−open−close mechanism by considering the functions of oxygenated groups existing at the edges of the holes.
Association of structural variation with cardiometabolic traits in Finns (2021)

The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47&amp;nbsp;× 10-54) and is also associated with increased levels of total cholesterol (p = 1.22&amp;nbsp;× 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81&amp;nbsp;× 10-21) and alanine (p = 6.14&amp;nbsp;× 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24&amp;nbsp;× 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53&amp;nbsp;× 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.
Prism-Based DGTD With a Simplified Periodic Boundary Condition to Analyze FSS With D2nSymmetry in a Rectangular Array Under Normal Incidence (2019)

In this letter, we develop a prism-based discontinuous Galerkin time-domain (DGTD) algorithm with simplified periodic boundary conditions (PBCs) to analyze infinite doubly periodic frequency selective surfaces (FSS). Most FSS structures contain patterned planar conductive layers and supporting dielectric layers. These layers are very thin compared to the wavelength. Therefore, general tetrahedral discretization of space will unnecessarily increase the number of mesh elements, as well as the number of unknowns. Instead, we propose using prismatic elements, which are more optimal for planar structures, resulting in less unknowns, less memory usage, and higher efficiency. The accuracy of the proposed prism-based DGTD method is verified by numerical examples compared with commercial software packages. Moreover, the CPU and memory costs are also compared, demonstrating clear advantages of the proposed prism-based DGTD method.
Assembly process integration challenges and reliability assessment of multiple 28nm FPGAs assembled on a Large 65nm passive interposer (2012)

Stacked die packaging has been gaining traction in recent years due to cost and manufacturing issues associated transistor scaling. 3D die stacking architecture with through silicon vias offers a unique combination of low power and high bandwidth per watt without increasing the cost significantly. For Xilinx's FPGAs (Field Programmable Gate Array), due to its repetitive and unique structures, Stacked Silicon Integration (SSI) technology becomes a perfect fit to provide a cost effective solution to build large programmable logic devices with very high logic cell count. In the current configuration, four separate 28nm FPGA die were connected to each other through a 65nm passive silicon interposer. Arrays of more than 10k micro-bumps (ubumps) stitched these four dies together through the silicon interposer. This paper describes the technical and reliability challenges associated with 3D integration of 100um thin interposer and FPGA die on to a single package.
New Routes to Synthesizing an Ordered Perovskite CaCu3Fe2Sb2O12 and Its Magnetic Structure by Neutron Powder Diffraction (2014)

The search for new double-perovskite oxides has grown rapidly in recent years because of their interesting physical properties like ferroelectricity, magnetism, and multiferroics. The synthesis of double perovskites, especially the A-site-ordered perovskites, in most cases needs to be made under high pressure, which is a drawback for applying these materials. Here we have demonstrated synthetic routes at ambient pressure by which we have obtained a high-quality duo-sites-ordered double perovskite, CaCu3Fe2Sb2O12, which has been previously synthesized under high pressure. The availability of a large quantity of the powder sample allows us to determine the crystal and magnetic structures by neutron powder diffraction (NPD) at 300 and 1.3 K. Measurements of the magnetization and heat capacity showed a ferrimagnetic transition at 160 K. A ferrimagnetic structure consisting of the uncompensated antiferromagnetic coupling between neighboring collinear copper and iron spins has been resolved from the low-temperature NPD data.
Hypoxia-Inducible Factor 1α in Clear Cell Renal Cell Carcinoma (2007)

HIF-1 alpha is an important independent prognostic factor for patients with metastatic clear cell RCC. Because HIF-1 alpha and CAIX are independently and differentially regulated in metastatic clear cell RCC, both tumor markers can be complementary in predicting prognosis.
Multi‐Electrode Printed Bioelectronic Patches for Long‐Term Electrophysiological Monitoring (2022)

Abstract A novel architecture of materials and fabrication techniques is proposed that serves as a universal method for implementation of thin‐film biostickers for high resolution electrophysiological monitoring. Unlike the existing wearable patches, the presented solution can be worn for several days, and is not affected by daily routines such as physical exercise or taking bath. A printable biphasic liquid metal silver composite is used, both as the electrical interconnects and the electrodes. This allows combining advantages of dry electrodes, i.e., printability and non‐smearing behavior, with benefits of wet electrodes, i.e., high‐quality signal. A human subject study showed that these biphasic printed electrodes benefit from a lower electrode‐skin impedance compared to clinical grade Ag/AgCl electrodes. Digital printing enables autonomous fabrication of biostickers that are taylor‐made for each user and each application. A universal miniaturized electronic system for biopotential acquisition and wireless communication is develpoed, and demonstrated multiple biopotential acquisition cases, including electrocardiography, electroencephalography, electromyography, and electrooculography.
Back Cover: Alcohol‐Enhanced Cu‐Mediated Radiofluorination (Chem. Eur. J. 14/2017) (2017)

Alcohol
Broad Spectrum Chemokine Inhibitors Related to NR58-3.14.3 (2005)

The chemokine family consists of more than 50 structurally-related small proteins which signal through type 1 G-protein coupled receptors (GPCRs) to regulate a range of immune functions, with particular focus on regulating leukocyte trafficking. They have been implicated both in normal physiological leukocyte traffic, and in recruitment of leukocytes to sites of pathological inflammation. As a result, chemokine inhibitors may have useful anti-inflammatory therapeutic properties in vivo. Compounds with chemokine-inhibitory properties that have been described to date, fall into two broad categories: receptor-specific antagonists which block the action of one or a small number of related chemokines, and broad-spectrum chemokine inhibitors (BSCIs) which block leukocyte migration in response to many, if not all, chemokines simultaneously. Since many chemokines apparently show functional redundancy in vivo, the BSCI class are attractive candidates for development as anti-inflammatory therapies. Here, we review the development of BSCIs, with particular focus on the design and characterisation of non-peptide compounds. The key structural requirements for BSCI activity are discussed, together with their implications for the mechanism of BSCI action.
Rapid prototyping of force/pressure sensors using 3D- and inkjet-printing (2018)

This work reports on inkjet- and 3D-printed force/pressure sensing devices. The employed printing processes can enable cost- and resource-efficient, fast and flexible designs compared to solid-state technology which is used as a reference design. The pressure sensing devices are realized as either 3D-printed steel or 3D-printed ceramic diaphragms. Both designs thus withstand harsh environmental conditions and elevated temperatures. Additionally, the increased size guarantees less sensitivity to dirt or moisture due to the larger diameter of the diaphragms. The hardware used for the capacitive sensor read-out is based on a shunt measurement system and subsequent demodulation. This architecture enables long cabling, allowing for large parasitic capacitances, without significant loss of transferred signal power, due to the employed power matching to the transmission line. Physical analyses such as contact angle measurements, profilometer measurements, and focused ion beam analysis are done to characterize the resulting printed surfaces. Then, the response of both designs is evaluated by applying force on the diaphragms surface using a moveable load cell. The gathered results are also compared to finite element method simulations.
Innate and adaptive immunotherapy: An orchestration of immunogenic cell death by overcoming immune suppression and activating NK and T cell therapy in patients with third line or greater metastatic pancreatic cancer. (2019)

e15787 Background: Pancreatic cancer has multiple mechanisms to prevent immune recognition that lead to the creation of an immune suppressive tumor microenvironment. We hypothesize that sustained response against pancreatic cancer requires a coordinated approach that: 1. reverses the immune-suppressive tumor microenvironment, 2. induces immunogenic tumor cell death and 3. reengages NK and T-cell tumor response against a 4. cascade of tumor antigens. To test this hypothesis, we have developed a temporospatial approach that combines metronomic low-dose chemotherapy, SBRT, cryopreserved allogeneic NK cells, yeast and adenoviral tumor-associated antigen vaccines, an IL-15RαFc superagonist, and checkpoint inhibition. Methods: A phase 1b trial in patients with recurrent metastatic pancreatic cancer was initiated. Treatment occurred in 3-week cycles of low-dose chemotherapy (aldoxorubicin, cyclophosphamide, oxaliplatin, nab-paclitaxel, 5-FU/L), antiangiogenic therapy (bevacizumab), SBRT, allogeneic CD16 NK-92 cells (haNK), IL-15RαFc (N-803), adenoviral CEA vaccine, yeast Ras vaccine, and an IgG1 PD-L1 inhibitor, avelumab. The primary endpoint is incidence of treatment-related adverse events (TRAEs). Secondary endpoints include ORR, DCR, PFS, and OS. Results: 12 subjects with 3rd-line or greater metastatic pancreatic cancer were treated. All treatment was administered in an outpatient setting. AEs were primarily hematologic and managed by planned chemo dose reduction. Grade ≥3 TRAEs were observed in 9 out of 12 subjects, predominately chemotherapy-related neutropenia. 9 out of 12 subjects (75%) had a best response of stable disease (≥ 8 weeks). Median PFS is 7.1 months (4.4 – 8.8) and median OS is 8.2 months (5.7 – 9.7) with 1 subject continuing treatment. Conclusions: These preliminary data suggest that low-dose chemo-radiation combined with innate and adaptive immunotherapy can be administered safely in an outpatient setting. Preliminary OS of 8.2 months is encouraging for this heavily-pretreated population. Clinical trial information: NCT03586869.
An optical switch-based self-restored WDM-PON architecture against fiber faults (2010)

We demonstrate a self-restored WDM-PON architecture by only adding an optical switch in each ONU. Moreover, the performance of proposed protection PON is also discussed and analyzed.
Performance Prediction in Dynamic Clouds using Transfer Learning (2019)

Learning a performance model for a cloud service is challenging since its operational environment changes during execution, which requires re-training of the model in order to maintain prediction accuracy. Training a new model from scratch generally involves extensive new measurements and often generates a data-collection overhead that negatively affects the service performance.In this paper, we investigate an approach for re-training neural-network models, which is based on transfer learning. Under this approach, a limited number of neural-network layers are re-trained while others remain unchanged. We study the accuracy of the re-trained model and the efficiency of the method with respect to the number of re-trained layers and the number of new measurements. The evaluation is performed using traces collected from a testbed that runs a Video-on-Demand service and a Key-Value Store under various load conditions. We study model re-training after changes in load pattern, infrastructure configuration, service configuration, and target metric. We find that our method significantly reduces the number of new measurements required to compute a new model after a change. The reduction exceeds an order of magnitude in most cases.
Effect of ion diffusion on switching voltage of solid-electrolyte nanometer switch (2005)

A solid electrolyte switch turns on or off when a metallic bridge is formed or dissolved respectively in the solid electrolyte (here we use Cu2-αS). For logic applications, the switching voltage (<0.3 V) should be larger than the operating voltage of the logic circuit (about 1 V). We reveal that the switching voltage is mainly affected by Cu+ ionic transport in Cu2-αS and that a solid electrolyte with an ion diffusion coefficient smaller than that of Cu2-αS by several tens of orders of magnitude makes it possible to increase the switching voltage to 1 V.
Three dimensional integration and on-wafer packaging of signal centric sensors for ultra wideband systems (2007)

Future military and commercial communication systems and sensors will require a new generation of circuits with cognitive, deployable, agile, versatile, survivable and sustainable capabilities. The requirement to accommodate arbitrary-bandwidth signals, poses significant challenges to traditional time-invariant matching networks because of the gain-bandwidth restrictions and their inability to ensure a linear phase response for broadband pulse-based inputs (Bode, 1945). To address this need we propose in this paper a time-variant matching network particularly suited for pulse-based systems that is capable of accommodating high-Q RC loads.
PHYSIOLOGICAL EFFECTS OF STROBILURIN FUNGICIDES ON PLANTS (2003)

The interference of plant diseases results in significant losses in the productivity and quality of products obtained. This situation is growing and progressing due to plant breeding aimed at increasing productivity, and the increase of agricultural borders, thus providing food that is more susceptivel to phytopathogens during all seasons of the year. As a result of this action of microorganisms, man is obligated to take steps to neutralize this negative effect, combining other available techniques with the fungicides. Until recently, the fungicides focused on control of phytopathogens with the sole purpose of reducing inoculum. After the launching of strobilurins, and with the evolution of this group of chemical products, the concept of disease control gained new perspectives, especially when considering the advantages obtained by the action of positive physiological effects on these plants. During the last decade of intense research on the fungicidal properties of strobilurins, the evidences of their direct influence in physiological processes of plants not infected or threatened by pathogens were strengthened. This activity was named “physiological effect”. The physiological effects of pyraclostrobin, a new molecule of strobilurin, were reviewed under several levels of complexity, from the greening effect frequently mentioned and the enhancement of stress factors in field and under controlled conditions, to the influence of hormonal regulation and assimilation of carbon and nitrogen by the plant.  Key words: pyraclostrobin, F500, physiological effects, chemical control