gebhart/patrepeval huggingface dataset:
Demonstration of a High Extinction Ratio Monolithic CMOS Integrated Nanophotonic Transmitter and 16 Gb/s Optical Link (2014)

We present a 16-Gb/s transmitter composed of a stacked voltage-mode CMOS driver and periodic-loaded reverse biased pn junction Mach-Zehnder modulator. The transmitter shows 9-dB extinction ratio and 10.3-pJ/bit power consumption and operates with 1.3 μm light. Penalties as low as 0.5 dB were seen as compared to a 25-Gb/s LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> transmitter with both a monolithic metal-semiconductor-metal receiver and a reference receiver at 16-Gb/s operation. We also present an analytic expression for relative transmitter penalty (RTP), which allows one to quickly assess the system impact of design parameters such as peak-to-peak modulator drive voltage, modulator figure of merit, and transmitter extinction ratio to determine the circumstances under which a stacked CMOS cascode driver is desirable.
Rewritable storage channels with limited number of rewrite iterations (2010)

We consider storage channels that admit optional reading and rewriting of the content at a given cost. This is a general class of channels that models many nonvolatile memories. We present recent results on such rewritable channels with constraints on both the maximum and the average number of atomic rewrite iterations. We derive a general lower capacity bound for rewritable storage channels impaired by additive noise. For the special case of uniform noise, we present tight upper and lower capacity bounds and suggest some capacity-achieving coding techniques.
Improved Migration of Arsenic by Bio-Electrokinetics in Soil (2015)

본 연구에서는 비소로 오염된 지역의 토양 및 지하수에 동전기적 기술을 사용하고 배양된 토양 미생물과 배양액을 주입하여 토양 내의 토착 미생물을 활성화하여 비소의 이동도를 상승시키는 것이 주요목표이다. 생물학적 동전기법은 미생물의 전기적 이동을 이용하여 기존의 생물학적 복원에서 문제시 되어온 늦은 분해속도와 낮은 제거효율의 단점을 극복할 수 있었다. 이는 전극의 전해액 대신 토양 미생물과 배양액을 혼합 주입하여 유기물질을 전자 공여체로 이용하는 다양한 토양 미생물이 Fe, Mn 등을 환원하게 된다. 이에 따라 주변의 금속 산화 미생물이 As(III)를 As(V)로 변환시킴으로써 As(III)의 이동도가 증가하게 되고, 이로 인해 As의 이동도가 기존 동전기법의 약 30%에 비해 60 ~ 70%정도로 상승함을 확인하였다. In this study, bio-electrokinetics was used to increase migration of arsenic by activating endemic microorganisms in the soil. In this technology, bio-electrokinetics which the cultured soil microorganisms and nutrients injected combines with biological technology. This technology using electrical movement of microorganisms could overcome the weakness of late degradation speed and low removal efficiency. And, various soil microorganisms reduce ferreous, manganese, etc., using organic matter by as an electron donor by injecting mixture of soil microorganisms and nutrients instead of using electrolyte of the electrode. Accordingly, surrounding metal oxide microorganisms convert arsenic (III) to arsenic (V) to increase migration of arsenic (III), in consequence, migration of arsenic increased in 60 to 70% compared to about 30% of conventional electrokinetics.
Motion Acquisition and Reproduction of Human Hand by Interaction Mode Control (2006)

Recently, skill preservation of an expert has been a serious problem of the medical or production fields. If digital skill preservation as a bilateral database is attained, it may become an innovative solution of the problem. This paper proposes a motion acquisition and reproduction of human motion by the interaction mode control. The proposed interaction mode control can control only the interactions between the systems. The interactions are abstracted by using the quarry matrix. Since the quarry matrix can divide systems into decoupled modes, it is possible to design a controller in the modal space. The order of the quarry matrix corresponds to the number of human finger. Thus the skilled motion by a human is easily obtained and analyzed in the modal space by using the quarry matrix. The experimental results show viability of the proposed method
Exploiting the Kinome to Target Signalling and Cell Cycle Regulation (2007)

CN01-03 Even before the cataloguing of the protein kinase complement of the human genome (the “kinome”), the therapeutic targeting of kinases for cancer treatment was a focus of drug discovery groups in both academia and industry. This was driven by the fact that many of the major oncogenic pathways in cancer cells are controlled by kinase cascades and was in spite of major concerns that ATP competitive inhibitors would lack selectivity. However, the last 10 years have shown that kinase inhibitor selectivity between closely related kinases is achievable. Indeed, the paradigm for new gene product-targeted therapy is the Bcr-Abl tyrosine kinase inhibitor, imatinib which shows selectivity for Bcr-Abl versus other receptor and non-receptor tyrosine kinases. Imatinib also selectively inhibits the growth of Bcr-Abl driven tumours in vivo and is now a registered drug for the treatment of the Bcr-Abl driven chronic myeloid leukaemia. Interestingly, the additional knowledge that it also targets KIT and PDGFR has had therapeutic benefit in for patients with gastrointestinal stromal tumours, which are driven by these oncogenes. This raises the question and now ongoing debate of how selective do you wish your kinase targeted drug to be? Either way, the targeting of kinases for cancer treatment is proving to have clinical benefit for cancer patients.  In addition, the transition away from the earlier principle of screening compound libraries for cellular cytoxicity to identifying and targeting kinases for cancer treatment has also changed the way we think about measuring the activity of these small molecules in a clinical trial. In particular, the development of pharmacodynamic (PD) biomarkers that measure the effects of the drug on the body through analysis of molecular, cellular, histopathological and imaging parameters that are modulated by target inhibiton and may correlate with clinical effects are of vital importance.  During the last decade, signalling pathways and cell cycle regulation have been a major theme of kinase drug development for cancer treatment, with inhibitors of RAF, MEK and the CDKs either in clinical trial or approved. What, therefore, will be the next kinase targeted agents entering the clinic and also potential new ones for cancer drug discovery? Much recent attention has focussed on the PI3 Kinase (PI3K) pathway whilst exploitation of cell cycle checkpoints has also been of interest and in particular of the cell cycle checkpoint kinase CHK1. In this session I will present on current drug discovery programs in these areas and also look forward at potential new kinase targets for cancer drug discovery. An emphasis will also be placed on potential PD biomarkers for drug development and subsequent clinical trials of these molecularly targeted agents and the role they may play in these processes.
Minimizing THD of multilevel inverters with optimal values of DC voltages and switching angles using LSHADE-EpSin algorithm (2017)

Multilevel inverters are mainly used for DC to AC power conversion and these inverters can be classified into types current source inverter (CSI) and voltage source inverter (VSI). Voltage source inverters are more common in power industry to convert lower levels of DC voltages into higher levels of AC voltages. In the process of conversion widely implemented pulse width modulated (PWM) switching technique of DC sources introduces harmonics in inverter output voltage. Total harmonic distortion (THD) is a measure of harmonic pollution in the power system and it is observed that variations in both DC voltages and switching angles of inverter affect the THD of inverter output voltage. Cascaded multilevel symmetric inverters ideally have DC sources all equal and constant. This paper considers inverters where DC sources can be unequal, a justifiable and realistic supposition. Optimal values of DC voltages and switching angles, which minimize THD level, are found using evolutionary algorithm. An advanced form of Differential Evolution (DE), called LSHADE-EpSin, is applied for the optimization problem. SHADE is a success history based parameter adaptation technique of DE. LSHADE improves the performance of SHADE with linearly reducing the population size in successive generations. LSHADE-EpSin introduces an additional adaptation technique for control parameters of the evolutionary algorithm. The algorithm has successfully been implemented for higher levels of inverters considered in the scope of our research study.
Targeting tumor-derived NLRP3 reduces melanoma progression by limiting MDSCs expansion (2021)

Interleukin-1β (IL-1β)-mediated inflammation suppresses antitumor immunity, leading to the generation of a tumor-permissive environment, tumor growth, and progression. Here, we demonstrate that nucleotide-binding domain, leucine-rich containing family, pyrin domain-containing-3 (NLRP3) inflammasome activation in melanoma is linked to IL-1β production, inflammation, and immunosuppression. Analysis of cancer genome datasets (TCGA and GTEx) revealed greater NLRP3 and IL-1β expression in cutaneous melanoma samples (<i>n</i> = 469) compared to normal skin (<i>n</i> = 324), with a highly significant correlation between NLRP3 and IL-1β (<i>P</i> < 0.0001). We show the formation of the NLRP3 inflammasome in biopsies of metastatic melanoma using fluorescent resonance energy transfer analysis for NLRP3 and apoptosis-associated speck-like protein containing a CARD. In vivo, tumor-associated NLRP3/IL-1 signaling induced expansion of myeloid-derived suppressor cells (MDSCs), leading to reduced natural killer and CD8<sup>+</sup> T cell activity concomitant with an increased presence of regulatory T (Treg) cells in the primary tumors. Either genetic or pharmacological inhibition of tumor-derived NLRP3 by dapansutrile (OLT1177) was sufficient to reduce MDSCs expansion and to enhance antitumor immunity, resulting in reduced tumor growth. Additionally, we observed that the combination of NLRP3 inhibition and anti-PD-1 treatment significantly increased the antitumor efficacy of the monotherapy by limiting MDSC-mediated T cell suppression and tumor progression. These data show that NLRP3 activation in melanoma cells is a protumor mechanism, which induces MDSCs expansion and immune evasion. We conclude that inhibition of NLRP3 can augment the efficacy of anti-PD-1 therapy.
Model-Based Integration and Optimization – Gas Cycling Benchmark (2009)

Abstract A benchmark for computational integration of petroleum operations has been constructed. The benchmark consists of two gas-condensate reservoirs producing to a common process facility. A fraction of the processed gas is distributed between the two reservoirs for gas injection. Total project economics are calculated from the produced streams and process related costs. This benchmark may be used to compare different computational integration frameworks, and optimization strategies. The methods of model integration and optimization discussed in this paper are applicable to complex petroleum operations where it is difficult to quantify cause-and-effect without comprehensive model-based integration. A framework for integration of models describing petroleum operations has been developed. An example test problem is described and studied in detail. Substantial gains in full-field development may be achieved by optimizing over the entire production system. All models and data in the benchmark problem are made available so that different software platforms can study the effects of alternative integration methods and optimization solver strategy. The project itself can, and probably should, be extended by others to add more complexity (realism) to the reservoir, process, and economics modeling.
Supplementary Figure 2B from Cancer Immunotherapy Based on Killing of <i>Salmonella</i>-Infected Tumor Cells (2023)

Supplementary Figure 2B from Cancer Immunotherapy Based on Killing of &lt;i&gt;Salmonella&lt;/i&gt;-Infected Tumor Cells
Identification of the Initial Steps in d -Lysine Catabolism in Pseudomonas putida (2007)

Pseudomonas putida uses l-lysine as the sole carbon and nitrogen source which preferentially requires its metabolism through two parallel pathways. In one of the pathways delta-aminovalerate is the key metabolite, whereas in the other l-lysine is racemized to d-lysine, and l-pipecolate and alpha-aminoadipate are the key metabolites. All the genes and enzymes involved in the d-lysine pathway, except for those involved in the conversion of d-lysine into Delta(1)-piperideine-2-carboxylate, have been identified previously (30). In this study we report that the conversion of d-lysine into Delta(1)-piperideine-2-carboxylate can be mediated by a d-lysine aminotransferase (PP3590) and a d-lysine dehydrogenase (PP3596). From a physiological point of view PP3596 plays a major role in the catabolism of d-lysine since its inactivation leads to a marked reduction in the growth rate with l- or d-lysine as the sole carbon and nitrogen source, whereas inactivation of PP3590 leads only to slowed growth. The gene encoding PP3590, called here amaC, forms an operon with dpkA, the gene encoding the enzyme involved in conversion of Delta(1)-piperideine-2-carboxylate to l-pipecolate in the d-lysine catabolic pathway. The gene encoding PP3596, called here amaD, is the fifth gene in an operon made up of seven open reading frames (ORFs) encoding PP3592 through PP3597. The dpkA amaC operon was transcribed divergently from the operon ORF3592 to ORF3597. Both promoters were mapped by primer extension analysis, which showed that the divergent -35 hexamers of these operon promoters were adjacent to each other. Transcription of both operons was induced in response to l- or d-lysine in the culture medium.
Low‐Temperature Atomic Layer Deposition of MoS2 Films (2017)

Abstract Wet chemical screening reveals the very high reactivity of Mo(NMe 2 ) 4 with H 2 S for the low‐temperature synthesis of MoS 2 . This observation motivated an investigation of Mo(NMe 2 ) 4 as a volatile precursor for the atomic layer deposition (ALD) of MoS 2 thin films. Herein we report that Mo(NMe 2 ) 4 enables MoS 2 film growth at record low temperatures—as low as 60 °C. The as‐deposited films are amorphous but can be readily crystallized by annealing. Importantly, the low ALD growth temperature is compatible with photolithographic and lift‐off patterning for the straightforward fabrication of diverse device structures.
LONGITUDINAL GAIT ADAPTATIONS OF ACL-INJURED INDIVIDUALS RECONSTRUCTED WITH THE HAMSTRING GRAFT (1999)

522 Longitudinal gait adaptations of ACL-injured patients reconstructed with the patellar tendon have been described. Gait adaptations that may occur in individuals after semitendinosus-gracilis graft (DLSTG) reconstruction have not been identified despite its wide spread use. The purpose of this study was to compare the joint kinematics and kinetics during walking at 3, 6, 9 and 12 weeks post-surgery in patients reconstructed with the DLSTG technique to a healthy group. Nine DLSTG patients and five healthy subjects walked at self-selected and 1.5 m/s, respectively. Video (60 Hz) and force platform (1200 Hz) data were collected and combined with anthropometrics in an inverse dynamics solution to compute hip and knee joint kinematic and kinetic data. Individual t-tests (p ≤ 0.05) were used to determine gait differences between the reconstructed group and the control group at each session. (Table)TableCompared to normals, early (0-6 wks) adaptations in the DLSTG group were characterized by slower walking velocity, increased stance time, increased hip and knee flexion and extensor angular impulses. Except for average knee position, all gait parameters returned to near normal values at 9 weeks post-reconstruction.
Utilization of Mass Spectrometry in Clinical Chemistry (2008)

This chapter contains sections titled: Introduction Where are Mass Spectrometers Utilized in Clinical Applications? Most Common Analytes Detected by Mass Spectrometers Multianalyte Detection of Clinical Biomarkers, The Real Success Story Quantitative Profiling A Clinical Example of the Use of Mass Spectrometry Demonstrations of Concepts of Quantification in Clinical Chemistry
Selective aromatic chlorination and bromination with N-halogeno amines in acidic solution (1989)

1,2-Dimethoxybenzene and 3,4-dimethoxytoluene are efficiently chlorinated by N-chlorodialkylamines in sulphuric acid. The reaction has a very marked selectivity for monochlorination of the para-position. The chlorination and bromination of monoalkylbenzenes (toluene, ethyl-, and isopropylbenzenes) under the same conditions is much less selective, but the para/ortho ratio can be reversed going from unsubstituted alkyl groups in the N-halogeno amines to alkyl groups substituted at the β-position by electron-withdrawing groups [morpholine, piperazine, bis(cyanoethyl)amine]. m-Xylene is chlorinated with high selectivity at the 4-position. The nature of the chlorinating species is discussed.
Network topology generators (2002)

Following the long-held belief that the Internet is hierarchical, the network topology generators most widely used by the Internet research community, Transit-Stub and Tiers, create networks with a deliberately hierarchical structure. However, in 1999 a seminal paper by Faloutsos et al. revealed that the Internet's degree distribution is a power-law. Because the degree distributions produced by the Transit-Stub and Tiers generators are not power-laws, the research community has largely dismissed them as inadequate and proposed new network generators that attempt to generate graphs with power-law degree distributions.Contrary to much of the current literature on network topology generators, this paper starts with the assumption that it is more important for network generators to accurately model the large-scale structure of the Internet (such as its hierarchical structure) than to faithfully imitate its local properties (such as the degree distribution). The purpose of this paper is to determine, using various topology metrics, which network generators better represent this large-scale structure. We find, much to our surprise, that network generators based on the degree distribution more accurately capture the large-scale structure of measured topologies. We then seek an explanation for this result by examining the nature of hierarchy in the Internet more closely; we find that degree-based generators produce a form of hierarchy that closely resembles the loosely hierarchical nature of the Internet.
State Machine Replication Is More Expensive Than Consensus. (2018)

Consensus and State Machine Replication (SMR) are generally considered to be equivalent problems. In certain system models, indeed, the two problems are computationally equivalent: any solution to the former problem leads to a solution to the latter, and vice versa. In this paper, we study the relation between consensus and SMR from a \emph{complexity} perspective. We find that, surprisingly, completing an SMR command can be more expensive than solving a consensus instance. Specifically, given a synchronous system model where every instance of consensus always terminates in constant time, completing an SMR command does \emph{not} necessarily terminate in constant time. This result naturally extends to partially synchronous models. Besides theoretical interest, our result also corresponds to practical phenomena we identify empirically. We experiment with two well-known SMR implementations (Multi-Paxos and Raft) and show that, indeed, SMR is more expensive than consensus in practice. One important implication of our result is that---even under synchrony conditions---no SMR algorithm can ensure bounded response times.
Replacement of Phosgene with Carbon Dioxide: Synthesis of Alkyl Carbonates (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReplacement of Phosgene with Carbon Dioxide: Synthesis of Alkyl CarbonatesWilliam McGhee and Dennis RileyCite this: J. Org. Chem. 1995, 60, 19, 6205–6207Publication Date (Print):September 1, 1995Publication History Published online1 May 2002Published inissue 1 September 1995https://pubs.acs.org/doi/10.1021/jo00124a044https://doi.org/10.1021/jo00124a044research-articleACS PublicationsRequest reuse permissionsArticle Views1125Altmetric-Citations54LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Tumor Microenvironment Characterization using a Spatial Multiomic Assay to Simultaneously Profile Protein and Gene Expression in FFPE Tumors (2022)

The tumor microenvironment (TME) is composed of highly heterogeneous structures and cell types that dynamically influence and communicate with each other. The constant interaction between a tumor and its microenvironment plays a critical role in how the cancer develops, progresses, and responds to therapies. Traditionally, Hematoxylin and Eosin (H&amp;E) and immunohistochemistry staining have been used to annotate and characterize tissues and associated pathologies. Recent single analyte approaches spatially interrogate targeted or transcriptome‐wide expression of RNA in tissue sections, while others capture phenotypes using a limited number of protein markers. However, for a more comprehensive understanding of the unique characteristics of cell types, cell states, and cell‐cell interactions within the TME, analysis of multiple analytes is necessary. Here we demonstrate a novel, streamlined multiomic spatial assay that integrates histological staining and imaging with simultaneous transcriptome‐wide gene expression and highly multiplexed protein expression profiling from the same formalin‐fixed paraffin embedded (FFPE) tissue section. In short, tissue sections from archived FFPE samples were placed on slides containing arrayed capture oligos with unique positional barcodes. The H&amp;E stained tissues were then imaged, followed by incubation with transcriptome‐wide probes and a high‐plex DNA‐barcoded antibody panel containing intra‐ and extracellular markers. Transcriptome probes and antibody‐barcodes were then spatially captured on the slide and converted into sequencing‐ready libraries. Our data analysis and interactive visualization software enable interrogation of all data layers (H&amp;E morphology, RNA, protein) from the same tissue section. We apply this method to simultaneously measure gene and protein expression within the TME of human breast cancer and melanoma FFPE samples using whole transcriptome probes and an immune‐oncology antibody panel. The data enables comparison and correlation of multiple analytes and their patterns within the same sample section. In addition, this simultaneous detection enables marker‐guided regional selection and differential gene expression analysis on the defined areas. Taken together, our data demonstrates that a spatially resolved, multiomic approach provides a more comprehensive understanding of cellular behavior in and around tumors, yielding new insights into disease progression, predictive biomarkers, drug response and resistance, and therapeutic development.