gebhart/patrepeval huggingface dataset:
Double Strand RNA Absorption in Citrus Trees for Delivery to Asian Citrus Psyllids, &lt;em&gt;Diaphorina citri&lt;/em&gt; (Hemiptera: Liviidae). (2021)

RNA interference, RNAi, continues to be a leading tool in functional genomics studies and in crop plants, for the management of viral pathogens, insect pests, and improving plant traits. However, there are still questions concerning consistent delivery into plants when using topically applied RNAi. RNAi products have the potential to reduce psyllid vector populations by disrupting nymph survival, which may provide an effective strategy in the disruption of Candidatus Liberibacter asiaticus transmission throughout citrus trees. This study examined factors that may affect dsRNA absorption and systemic movement in citrus trees and the subsequent delivery into the hemipteran, Diaphorina citri, the Asian citrus psyllid.
Prevalence of Pulmonary Embolism After Total Elbow Arthroplasty (2007)

Background: Although numerous articles have addressed the risk of pulmonary embolism following total knee and total hip arthroplasty, we were unable to find comparable information for the risk following elbow arthroplasty. We therefore sought to determine the prevalence of pulmonary embolism after total elbow arthroplasty. Methods: We conducted a retrospective review of the medical records of consecutive patients who had undergone primary elbow arthroplasty (816 procedures) or revision total elbow arthroplasty (260 procedures) at our tertiary-care academic medical institution between June 1981 and June 2001. Our purpose was to identify all patients in whom a pulmonary embolism developed after the surgery. Results: Three patients had a pulmonary embolism and one died as a result of the complication during the twenty-year study period. Because of a low index of suspicion, the presenting symptoms of the pulmonary embolus were originally attributed to other causes of respiratory distress in two of the three patients. Conclusions: These findings suggest that pulmonary embolism after total elbow arthroplasty is a rare but potentially fatal complication. Surgeons should consider this diagnosis when a patient exhibits respiratory distress after total elbow arthroplasty. Level of Evidence: Therapeutic Level IV. See Instructions to Authors for a complete description of levels of evidence.
Simulation of a Self-Excited Power Generation System for Dielectric Elastomer Generation (2019)

In recent years, global warming is a serious international problem. We focused on dielectric elastomer power generation to solve the problem. The dielectric elastomer generation has characteristics such as compactness and flexibility. The dielectric elastomer generation can harvest electric energy from renewable energy sources such as sea wave, wind, and human motion. However, the dielectric elastomer generation has a weakness dependent on an external power supply. In this paper, we proposed a self-excited dielectric elastomer generation circuit using piezoelectric elements. As a circuit verification method, circuit simulations are performed using MATLAB / Simulink, and the circuit behavior is confirmed from the results. From results, it is considered that dielectric elastomer generation can be performed without using the external power supply.
Clinical characterization of rare EGFR mutations in non-small cell lung cancer and in silico prediction of drug sensitivity (2018)

Background: Recent genome scale characterization of cancers identified overwhelming numbers of novel, rare and uncharacterized somatic mutations, variance of unknown significance (VUS), in non-small cell lung cancer (NSCLC). In order to make these VUS data clinically useful, further functional and biological characterization of each mutation is mandatory. In addition, development of novel strategies to overcome mutation diversity of lung cancer is needed. Methods: Using the large-scale prospective cohort data of the LC-SCRUM-Japan, nationwide lung cancer clinical and the genomic characterization network in Japan, we characterized the frequency and distribution of rare EGFR mutations in NSCLC and the clinical course of the patients harboring these mutations. In addition, to perform functional and biological characterization of each mutation, we created a Ba/F3 EGFR minor mutation library. Furthermore, the in silico sensitivity prediction model has been developed to demonstrate binding affinity of protein and drug compound and applied to EGFR tyrosine kinase inhibitor with mutated EGFR. Results: Of the 2164 NSCLC patients examined by LC-SCRUM-Japan, 113 (5.2%) harbored rare EGFR mutations. We found the diverse distribution of EGFR mutations throughout the gene, the most frequent group included EGFR exon 20 insertion mutations (52 cases). We clarified the sensitivity profile of the VUS to EGFR tyrosine kinase inhibitors. Binding affinities calculated by the in silico sensitivity prediction model showed statistically significant correlation (R2: 0.7425, p < 0.05) with the experimentally observed IC50 values. Conclusions: These data may help in choosing or predicting the appropriate inhibitor for lung cancer with VUS in EGFR, thereby contributing to the further development of precision medicine. Here, we clarified the diversity of VUS in EGFR and provide novel insights, via supercomputer utilized drug sensitivity prediction, in the cancer field. Legal entity responsible for the study: Keio University School of Medicine. Funding: Grants-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. Disclosure: All authors have declared no conflicts of interest.
Syntheses and Structural Properties of Severely Distorted Porphyrins: N-Methyl Derivatives (1997)

Syntheses and characterization of a series of N-methylated derivatives of sterically distorted porphyrins are reported; the work includes the first example of a tetra-N-methylated porphyrin obtained by methylation of an intact porphyrin.
Measurement Quantum Cellular Automata and Anomalies in Floquet Codes (2023)

We investigate the evolution of quantum information under Pauli measurement circuits. We focus on the case of one- and two-dimensional systems, which are relevant to the recently introduced Floquet topological codes. We define local reversibility in context of measurement circuits, which allows us to treat finite depth measurement circuits on a similar footing to finite depth unitary circuits. In contrast to the unitary case, a finite depth locally reversible measurement circuit can implement a translation in one dimension. A locally reversible measurement circuit in two dimensions may also induce a flow of logical information along the boundary. We introduce "measurement quantum cellular automata" which unifies these ideas and define an index in one dimension to characterize the flow of logical operators. We find a $\mathbb{Z}_2$ bulk invariant for two-dimensional Floquet topological codes which indicates an obstruction to having a trivial boundary. We prove that the Hastings-Haah honeycomb code belongs to a class with such obstruction, which means that any boundary must have either nonlocal dynamics, period doubled, or admits anomalous boundary flow of quantum information.
Organic Computing - Design of Self-Organizing Systems (2011)

This report documents the program and the outcomes of Dagstuhl Seminar 11181 “Organic Computing ‐ Design of Self-Organizing Systems”. Seminar 1.‐6. May, 2011 ‐ www.dagstuhl.de/11181 1998 ACM Subject Classification F.1.1 Models of computation.
A distributed control law for optimum sensor placement for source localization (2014)

We formulate a nonlinear distributed control law that guides the motion a group of sensors to achieve a configuration that permits them to optimally localize a hazardous source they must keep a prescribed distance from. Earlier work shows that such a configuration involves the sensors being placed in an equispaced manner on a prescribed circle. The nonlinear control law we propose assumes that each sensor resides and moves on the prescribed circle, by accessing only the states of its two immediate clockwise and counterclockwise neighbors. We theoretically prove and verify through simulations, that the law allows the sensors to achieve the desired configuration while avoiding collisions.
Extracting a Knowledge Base of Mechanisms from COVID-19 Papers (2021)

Tom Hope, Aida Amini, David Wadden, Madeleine van Zuylen, Sravanthi Parasa, Eric Horvitz, Daniel Weld, Roy Schwartz, Hannaneh Hajishirzi. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2021.
Imbalance entanglement: Symmetry decomposition of negativity (2018)

In the presence of symmetry, entanglement measures of quantum many-body states can be decomposed into contributions from distinct symmetry sectors. Here we investigate the decomposability of negativity, a measure of entanglement between two parts of a generally open system in a mixed state. While the entanglement entropy of a subsystem within a closed system can be resolved according to its total preserved charge, we find that negativity of two subsystems may be decomposed into contributions associated with their charge imbalance. We show that this charge-imbalance decomposition of the negativity may be measured by employing existing techniques based on creation and manipulation of many-body twin or triple states in cold atomic setups. Next, using a geometrical construction in terms of an Aharonov-Bohm-like flux inserted in a Riemann geometry, we compute this decomposed negativity in critical one-dimensional systems described by conformal field theory. We show that it shares the same distribution as the charge-imbalance between the two subsystems. We numerically confirm our field theory results via exact calculations for noninteracting particles based on a double-Gaussian representation of the partially transposed density matrix.
Association Between Fatty Acid Binding Protein 3 Gene Variants and Essential Hypertension in Humans (2008)

We found an association between FABP3 gene polymorphisms and EH in a Japanese population, thereby suggesting that FABP3 is a susceptibility locus for EH.
Perioperative Complications of Cervical Spine Surgery: Analysis of a Prospectively Gathered Database through the Association for Collaborative Spinal Research (2015)

<b>Study Design</b> Retrospective review of prospectively gathered data. <b>Objective</b> To report the rate and impact of perioperative complications in cervical spine surgery. To our knowledge, no prior study of the cervical spine has analyzed a large prospectively gathered data set for adverse events, based on surgical subgroup. <b>Methods</b> The ProSTOS database features prospectively documented perioperative adverse events for 1,269 patients who had cervical spine surgery at multiple centers in North America between 2008 and 2011. We subgrouped patients by approach, whether surgery was a primary or revision operation, and by the number of levels involved. Multivariate analysis with stepwise logistic regression was used to relate complication rates to gender, age, smoking status, body mass index, approach, revision status, and number of levels involved. Follow-up was 41%. <b>Results</b> Adverse events occurred significantly more frequently in posterior and combined procedures than in anterior procedures. Revision surgery had significantly more complications than primary surgery. For patients who had anterior surgery, those who had one, two, and three or more levels operated had no significant difference in complication rates. Patients who had posterior surgery had significantly more complications if they had two or more levels operated compared with one level. The lowest rates of complications were for one-level primary surgery (<5%), and multilevel posterior, revision posterior, and revision combined surgery had complication rates over 6 times higher (>28%). Patients who had complications were significantly older than patients who did not. The most common adverse events were dysphagia and cardiac complications. The most severe morbid complications, in terms of increased treatment needs and hospital stay, were paraparesis and seizure. <b>Conclusions</b> Perioperative complication rates in cervical spine surgery are significantly lower in younger patients, surgery performed through an anterior approach (compared with a posterior or combined approach), with fewer levels involved (particularly in posterior surgery), and in primary (compared with revision) procedures.
MS-k NN: protein function prediction by integrating multiple data sources (2013)

Based on our results, we have several useful insights: (1) the k-nearest neighbor algorithm is an efficient and effective model for protein function prediction; (2) it is beneficial to transfer functions across a wide range of organisms; (3) it is helpful to integrate multiple sources of protein information.
Graph Extraction from Color Images (2001)

Abstract. An approach to symbolic contour extraction will be described that consists of three stages: enhancement, detection, and extraction of edges and corners. Edges and corners are enhanced by models of monkey cortical complex and end-stopped cells. Detection of corners and local edge maxima is performed by selection of local maxima in both edge and corner enhanced images. These maxima form the anchor points of a greedy contour following algorithm that extracts the edges. This algorithm is based on an idea of spatially linking neurons along the edge that will fire in synchrony to indicate an extracted edge. The extracted edges and detected corners represent the symbolic representation of the image. The advantage of the proposed model over other models is that the same low constant thresholds for corner and local edge maxima detection are used for different images. Closed contours are guaranteed by the contour following algorithm to yield a fully symbolic representation which is more suitable for reasoning and recognition. In this respect our methodology is unique, and clearly different from the standard edge detection methods. 1
Comparison of signal collection abilities of different classes of imaging spectrometers (2002)

Although the throughput and multiplex advantages of Fourier transform spectrometry were established in the early 1950's (by Jacquinot and Fellgett , respectively) confusion and debate arise when these advantages are cited in reference to imaging spectrometry. In non-imaging spectrometry the terms throughput and spectral bandwidth clearly refer to the throughput of the entire field-of-view (FOV), and the spectral bandwidth of the entire FOV, but in imaging spectrometry these terms may refer to either the entire FOV or to a single element in the FOV. The continued development of new and fundamentally different types of imaging spectrometers also adds to the complexity of predictions of signal and comparisons of signal collection abilities. Imaging spectrometers used for remote sensing may be divided into classes according to how they relate the object space coordinates of cross-track position, along-track position, and wavelength (or wavenumber) to the image space coordinates of column number, row number, and exposure number for the detector array. This transformation must be taken into account when predicting the signal or comparing the signal collection abilities of different classes of imaging spectrometer. The invariance of radiance in an imaging system allows the calculation of signal to be performed at any space in the system, from the object space to the final image space. Our calculations of signal - performed at several different spaces in several different classes of imaging spectrometer - show an interesting result: regardless of the plane in which the calculation is performed, interferometric (Fourier transform) spectrometers have a dramatic advantage in signal, but the term in the signal equation from which the advantage results depends upon the space in which the calculation is performed. In image space, the advantage results from the spectral term in the signal equation, suggesting that this could be referred to as the multiplex (Fellgett) advantage. In an intermediate image plane the advantage results from a difference in a spatial term, while for the exit pupil plane it results from the angular term, both of which suggest the throughput (Jacquinot) advantage. When the calculation is performed in object coordinates the advantage results from differences in the temporal term.
Program manipulation via interactive transformations (2003)

Systematic large-scale modification of source code is tedious and error-prone, because developers use authoring and editing tools poorly suited to the program maintenance task. We combine the results from psychology of programming, software visualization, program analysis, and program transformation fields to create a novel environment that lets the programmers express operations on program source code at a level above text-oriented editing.
First Experimental Demonstration of Orchestration of Optical Transport, RAN and Cloud based on SDN (2015)

We design and experimentally demonstrate the first resource orchestration across DWDM optical transport, radio access networks (RANs) and cloud domains based on SDN. The orchestration enables agile service creation and optimized resource allocation.
A Dual-Mode Nested Rectifier for Ambient Wireless Powering in CMOS Technology (2020)

This article proposes a dual-mode (DM) nested radio frequency (RF) rectifier for ambient wireless powering. The proposed architecture utilizes a DM nested feedback circuit to enhance the conductivity of the rectifier at low power while reducing the reverse leakage current at high power by generating supply voltages at the gates of the pMOS rectifying transistors. The proposed rectifier is fabricated in a 65-nm CMOS technology and occupies an area of 6480 μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The measurement results show a peak power conversion efficiency of 86%, 10.1-dB dynamic range, and -19.2-dBm 1-V sensitivity when operating with a 100-kΩ load at the industrial, scientific, and medical band 433 MHz. Moreover, the enhanced low-power performance is achieved by reducing the effective threshold voltage of the rectifier by about 37%, compared with a low-threshold transistor in the 65-nm technology. This reduction in the threshold voltage allows the rectifier to operate with efficiency exceeding 10% for input power ≥ -40 dBm.
The Role of the Epigenome in Gene Expression Control and the Epimark Changes in Response to the Environment (2014)

Our knowledge base involving the biochemical participants of epigenetic control has expanded greatly over the last decade. The role of epigenetic marks to DNA and histones controlled by non-coding RNAs is one of the most intensely studied areas of biology today. This review covers many of the mechanisms that non-coding RNAs and other molecules use to control gene expression and eventually affect responses to the environment. In the first part of the review, we discuss the array of covalent modifications to the genome that constitute the epigenome, which consists of the histone variants, covalent modifications, and post-translational modifications that result in gene expression changes. How the histone variants and post-translational modifications including, acetylation, methylation, phosphorylation, ubiquitination and sumoylation help form the epigenome is also summarized. Our eventual understanding of how the environment controls these modifications will open incredible opportunities in agriculture, medicine and the development of practical tools for biology. In the second part of this review we discuss the growing list of environmentally-mediated epigenetic modifications, and examples of transgenerational epigenetic inheritance events, that may begin to change our views of adaptive responses to the environment and evolution.
Boron and high-k dielectrics: Possible fourth etch stop colors for multipattern optical lithography processing (2017)

In a companion article, the etch characteristics of materials within the Si-C-O-N-H system were surveyed using two common fluorinated plasma etches used to etch SiO2 interlayer dielectrics and SiN:H etch stop layers (CHF3 and CF4/O2, respectively) with the goal of identifying new materials or “colors” to assist in the simplification of advanced multipass optical lithography. In this study, the authors investigate additional materials outside the traditional Si-C-O-N-H phase diagram with the hope of identifying potential third or fourth color pattern-assist materials. The specific materials investigated include a series of high-k dielectrics commonly used in the industry (Al2O3, AlN, and HfO2) and boron-based solids (a-B:H, a-BxN:H, a-BxP:H, and a-BxC:H) that have been previously identified as potential hard mask, polish stop, and/or low-k dielectric materials. The high-k dielectrics were all found to exhibit low to unmeasureable etch rates in both fluorinated etches. In contrast, the boron-based solids all exhibited etch rates in the CF4/O2 etch up to an order of magnitude or more higher than those of silicon-based materials while still exhibiting comparable etch rates in the CHF3 interlayer dielectric etch. The high-k dielectrics thus appear to be potential third or fourth color materials, provided etch chemistries capable of selectively etching these relative to other silicon- and carbon-based materials can be identified. The results for the boron-based solids suggest more immediate applications in patterning silicon-based materials. A more detailed examination of the B-C-H system also suggests that significant optimization of the etch selectivity can be achieved via compositional tuning for a-BxC:H and other boron-based dielectric materials.
Gas phase hydrogen/deuterium exchange reactions of peptide ions in a quadrupole ion trap mass spectrometer (1997)

Hydrogen/deuterium exchange reactions of protonated and sodium cationized peptide molecules have been studied in the gas phase with a MALDI/quadrupole ion trap mass spectrometer. Unit-mass selected precursor ions were allowed to react with deuterated ammonia introduced into the trap cell by a pulsed valve. The reactant gas pressure, reaction time, and degree of the internal excitation of reactant ions were varied to explore the kinetics of the gas phase isotope exchange. Protonated peptide molecules exhibited a high degree of reactivity, some showing complete exchange of all labile hydrogen atoms. On the contrary, peptide molecules cationized with sodium exhibited only very limited reactivity, indicating a vast difference between the gas phase structures of the two ions. © 1997 Wiley-Liss Inc.
Antagonists of the Human A2A Adenosine Receptor. 4. Design, Synthesis, and Preclinical Evaluation of 7-Aryltriazolo[4,5-d]pyrimidines (2008)

Antagonism of the human A(2A) receptor has been implicated as a point of therapeutic intervention in the alleviation of the symptoms associated with Parkinson's disease. This is thought to occur, at least in part, by increasing the sensitivity of the dopaminergic neurons to the residual, depleted levels of striatal dopamine. We herein describe a novel series of functionalized triazolo[4,5-d]pyrimidine derivatives that display functional antagonism of the A(2A) receptor. Optimization of these compounds has resulted in improvements in potency, selectivity, and the pharmacokinetic properties of key derivatives. These efforts have led to the discovery of 60 (V2006/BIIB014), which demonstrates strong oral activity in commonly used models of Parkinson's disease. Furthermore, this derivative has shown excellent preclinical pharmacokinetics and has successfully completed phase I clinical studies. This compound is presently undergoing further clinical evaluation in collaboration with Biogen Idec.