gebhart/patrepeval huggingface dataset:
Illuminating the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family using computational metabolomics (2022)

Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse sub-class of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC-MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using Nuclear Magnetic Resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus - the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.
Integrated reliability in EEPROM nonvolatile memory cell design (2005)

We propose a new way to design new memory cells assisted with a physical model taking into account reliability. First, we study the coupling ratio impact on the electric field and its consequences on cell hardness. The choice of coupling ratio in a new cell design should result from a compromise between a high K/sub e/ value in order to use low supply voltages and reduce the charge pump area, and low K/sub e/ value to increase the cell's endurance. Secondly, we investigate the Fowler-Nordheim parameters evolution with operating cycling stress. The experimental measurements necessary to extract these parameters turn out to be more stressing than the operating stress. We propose a new extraction process based on a two-point nonstressing measurement method. At last, the best way to design a robust cell should be to include this degradation effect in the model.
Growth hormone radioimmunoassay using monoclonal antibodies: a useful method to avoid human chorionic somatomammotropin interference in serum samples. (1984)

The suitability of several monoclonal antibodies for specific radioimmunoassay of serum human growth hormone was tested. Sera from pregnant women with high human chorionic somatomammotropin levels were used. From both theoretical and experimental considerations, some specifications were recommended in order to select appropriate monoclonal antibodies for clinical determinations.
An Ontology-Based Conversation System for Knowledge Bases (2020)

Domain-specific knowledge bases (KB), carefully curated from various data sources, provide an invaluable reference for professionals. Conversation systems make these KBs easily accessible to professionals and are gaining popularity due to recent advances in natural language understanding and AI. Despite the increasing use of various conversation systems in open-domain applications, the requirements of a domain-specific conversation system are quite different and challenging. In this paper, we propose an ontology-based conversation system for domain-specific KBs. In particular, we exploit the domain knowledge inherent in the domain ontology to identify user intents, and the corresponding entities to bootstrap the conversation space. We incorporate the feedback from domain experts to further refine these patterns, and use them to generate training samples for the conversation model, lifting the heavy burden from the conversation designers. We have incorporated our innovations into a conversation agent focused on healthcare as a feature of the IBM Micromedex product.
ChemInform Abstract: Sensitization of TiO2 in the Visible Light Region Using Zinc Porphyrins. (1987)

Abstract In acidic solution, a significant enhancement of the photoelectrochemical response of a TiO 2 electrode for visible light irradiation is achieved by coating the electrode with a film of (tetrakis(4‐carboxyphenyl)porphyrinato)Zn(II).
Synthesis of epoxy resins based on bisphenol‐S and its derivatives (1992)

Abstract Bisphenol‐S derivatives of five kinds such as bis[4‐(β‐hydroxyethoxy)‐phenyl]sulfone (HEPS), bis[4‐(β‐hydroxy(iso)propoxy)‐phenyl]sulfone (HPPS), 3,3′,5,5′‐tetrabromobisphenol‐S (TBS), bis[3,5‐dibromo‐4‐(β‐hydroxyethoxy)‐phenyl]sulfone (HEETBS) and bis[3,5‐dibromo‐4‐(β‐hydroxy(iso)propoxy)‐phenyl]sulfone (HPETBS) were successfully prepared by the reaction of bisphenol‐S with ethylene carbonate, 1,2‐propylene carbonate or bromine, respectively. Several sulfone‐containing epoxy resins were obtained by alkaline condensation of bisphenol‐S (bis(4‐hydroxyphenyl)‐sulfone) or its derivatives with epichlorohydrin using sodium hydroxide. The epoxy resins thus obtained were characterized by elemental analysis, IR and 13 C‐NMR spectra. All epoxy resins are solid products except HPPS epoxy which contains oxypropylene units. The melting points (T m ) and glass transition temperatures (T g ) of epoxy resins which have flexible oxyethylene or oxypropylene units were lower than that of epoxy resin derived directly from bisphenol‐S. The increase of melting point which has been observed in brominated epoxy resins is attributed to the bulky bromine atom. The molar‐mass distributions of epoxy resins made by the direct addition of epichlorohydrin to bisphenol‐S (so‐called “taffy” process) or by the reaction of epoxy resin of low molar mass and of which the main constituent is the diglycidyl ether of bisphenol‐S in melt (so‐called “advancement” process) have also been compared. The “taffy” process leads to products containing both odd‐ and even‐numbered diepoxide oligomers in contrast to the “advancement” process which leads to products containing predominantly even‐numbered diepoxide oligomers. Epoxy equivalent and melt viscosity of epoxy resins increased with increasing amount of bisphenol‐S. This result is in accordance with the theoretical distribution calculated according to Flory statistics.
Frontispiece: Heteroatom‐Doped Carbon Materials for Electrocatalysis (2017)

Recent developments and challenges on the most critical and controversial fundamental issues involving metal-free and noble metal-free carbon-based electrocatalysts composed of earth elements are discussed in the Concept article by T. Asefa and X. Huang on page 10703 ff.
Characterization of the hardened single line of sight camera at the National Ignition Facility (2022)

The hardened single line of sight camera has been recently characterized in preparation for its deployment on the National Ignition Facility. The latest creation based on the pulse-dilation technology leads to many new features and improvements over the previous-generation cameras to provide better quality measurements of inertial confinement fusion experiments, including during high neutron yield implosions. Here, we present the characterization data that illustrate the main performance features of this instrument, such as extended dynamic range and adjustable internal magnification, leading to improved spatial resolution.
Predictive modeling targets thymidylate synthase ThyX in Mycobacterium tuberculosis (2016)

There is an urgent need to identify new treatments for tuberculosis (TB), a major infectious disease caused by Mycobacterium tuberculosis (Mtb), which results in 1.5 million deaths each year. We have targeted two essential enzymes in this organism that are promising for antibacterial therapy and reported to be inhibited by naphthoquinones. ThyX is an essential thymidylate synthase that is mechanistically and structurally unrelated to the human enzyme. DNA gyrase is a DNA topoisomerase present in bacteria and plants but not animals. The current study set out to understand the structure-activity relationships of these targets in Mtb using a combination of cheminformatics and in vitro screening. Here, we report the identification of new Mtb ThyX inhibitors, 2-chloro-3-(4-methanesulfonylpiperazin-1-yl)-1,4-dihydronaphthalene-1,4-dione) and idebenone, which show modest whole-cell activity and appear to act, at least in part, by targeting ThyX in Mtb.
Imaging of a targeted PDT drug with fluorescence tomography (2009)

We constructed a whole-body fluorescence tomography instrument to monitor novel bifunctional phototherapeutic drugs (e.g., HPPH-Cyanine dye conjugate) in small animals. The instrument allows dense source and detector sampling with a fast galvo scanner and a CCD detector for improved resolution and sensitivity (Patwardhan et al., 2005). Here we report tissue phantom measurements to evaluate the imaging performance with a newly constructed tomography instrument. Phantom measurements showed that strong fluorescence generated by HPPH-Cyanine dye (HPPH-CD), having high fluorescence quantum yield and long wavelength fluorescence emission, allowed deep tissue imaging. We also report in vivo fluorescence measurements of the conjugate in Nude mice bearing A549 human non-small cell lung carcinoma (NSCLC) tumors at 24 hr post injection to evaluate tumor detection ability of the conjugate. Our results indicate that the HPPH-CD shows preferential uptake in tumors compared to surrounding normal tissue at 24 hr post injection. This study demonstrates a potential use of HPPH-CD in detection (fluorescence imaging) and treatment (PDT) of deeply seated tumors.
Some Extremes in Conventional Lens Design (2013)

Computational imaging is changing the landscape in many dimensions. This work will present some of the extremes in lens systems and examples of potential simplifications when combined with computational methods that extend depth of focus.
Free convection in vertical eccentric annuli with a uniformly heated boundary (1998)

The paper utilizes a boundary‐layer model in bipolar coordinates to study the developing laminar free convection in vertical open‐ended eccentric annuli with one of the boundaries uniformly heated while the other boundary is cooled and kept isothermal at the ambient temperature. This model has been solved numerically using finite‐difference techniques. Results not available in the literature are presented for a fluid of Prandtl number 0.7 in an annulus of radius ratio 0.5 for three values of the dimensionless eccentricity, namely, 0.1, 0.5 and 0.7. These results include the developing velocity profiles and the pressure along the annulus, the channel heights required to naturally induce different flow rates and the variation of the total heat absorbed by the fluid with the channel height.
Multihop Routing for Energy Efficiency in Wireless Sensor Networks (2012)

Wireless sensor networks (WSNs) are attracting increasing research attention, due to their wide spectrum of applications, including military purposes for monitoring, tracking and surveillance of borders, intelligent transportation systems for monitoring traffic density and road conditions, and environmental applications to monitor, for example, atmospheric pollution, water quality, agriculture, etc. [26].
The myth of modularity in rule-based systems (1986)

In this paper, we examine the concept of modularity, an often cited advantage of the ruled-based representation methodology. We argue that the notion of modularity consists of two distinct concepts which we call syntactic modularity and semantic modularity. We argue that when reasoning under uncertainty, it is reasonable to regard the rule-based approach as both syntactically and semantically modular. However, we argue that in the case of plausible reasoning, rules are syntactically modular but are rarely semantically modular. To illustrate this point, we examine a particular approach for managing uncertainty in rule-based systems called the MYCIN certainty factor model. We formally define the concept of semantic modularity with respect to the certainty factor model and discuss logical consequences of the definition. We show that the assumption of semantic modularity imposes strong restrictions on rules in a knowledge base; we argue that such restrictions are rarely valid in practical applications. Finally, we suggest how the concept of semantic modularity can be relaxed in a manner that makes it appropriate for plausible reasoning.
108-Ch (12-Core×9-WDM) Self-Homodyne Transmission Using Only a Single Laser for 8.64-Tb/s Short-Reach Optical Links (2023)

We demonstrate 108-ch (12-core×9-WDM) frequency comb-based self-homodyne multi-core transmission with a net bit rate of 8.64-Tb/s. This demonstration shows the feasibility of high-capacity short-reach SDM/WDM systems using only a single laser.
Research data supporting "A vibrating beam MEMS accelerometer for gravity and seismic measurements" (2020)

The data provided here corresponds to the data presented in Figures 2-5 in the manuscript.The file "ZippedData.zip" consists of all the datasets used to construct the PSD and Allan Deviation plots in Figure 2. Two files are provided for each record -- one corresponding to the raw data and the other corresponding to the data corrected for linear drift. Measurements were carried out at the Cambridge University Nanoscience Centre (labelled by NSC) laboratory and at a seismic vault operated by the BGS in Eskdalemuir (labelled by BGS), Scotland. The files labelled with the wording "........EarthTides.zip" provide the time series data for the plots in Figures 3 and 4 in the manuscript demonstrating the tracking of the response to Earth tides in two different locations. The locations (either BGS or NSC) where measurements have been conducted are provided in the file name. There are two files included for each set one consisting of the raw datafiles including the output frequencies of the two resonators and the differential frequencies, while the other provides the corrected time-stamped gravity readings in microGal. The theoretical values for this period as generated by the software TSoft are also included. The time stamp is referenced to UTC. An excel spreadsheet is provided for the data underlying Figure 5 acquired at the University of Bristol Nanoscience and Quantum Information Lab 2017 Chiapas, Mexico, Earthquake (Mw 8.2) on September 8, 2017. The time-series data (in "g" units) from the MEMS device is provided together with the time-series data from a macroscopic seismometer located in Swindon, UK as part of the BGS monitoring network. An additional file provides the time-series data acquired (timestamp, output frequencies of two resonators, differential frequency, accelerometer output) at NSC on February 16, 2018 corresponding to the 16th February 2018 earthquake in Oaxaca state, Mexico. This dataset is reported in the Supplemental manuscript included with the main paper.
Retrieval of 3D information in X-ray dark-field imaging with a large field of view (2021)

X-ray dark-field imaging is a widely researched imaging technique, with many studies on samples of very different dimensions and at very different resolutions. However, retrieval of three-dimensional (3D) information for human thorax sized objects has not yet been demonstrated. We present a method, similar to classic tomography and tomosynthesis, to obtain 3D information in X-ray dark-field imaging. Here, the sample is moved through the divergent beam of a Talbot-Lau interferometer. Projections of features at different distances from the source seemingly move with different velocities over the detector, due to the cone beam geometry. The reconstruction of different focal planes exploits this effect. We imaged a chest phantom and were able to locate different features in the sample (e.g. the ribs, and two sample vials filled with water and air and placed in the phantom) to corresponding focal planes. Furthermore, we found that image quality and detectability of features is sufficient for image reconstruction with a dose of 68 μSv at an effective pixel size of [Formula: see text]. Therefore, we successfully demonstrated that the presented method is able to retrieve 3D information in X-ray dark-field imaging.
Rituximab Added to an Intensified Salvage Chemotherapy Program Followed by Autologous Stem Cell Transplantation Improve in Relapsed and Refractory Aggressive Non-Hodgkin-Lymphoma. (2005)

Abstract Background We investigated the addition of rituximab to an intensified salvage program followed by a myeloablative course with autologous stem cell transplantation (ASCT) in patients with relapsed or refractory aggressive NHL. Methods Patients with relapsed or progressive aggressive NHL were treated with two cycles of conventional salvage chemotherapy followed by high-dose sequential chemotherapy and a final myeloablative course with ASCT. Rituximab (375mg/m2) was administered at each treatment cycle. This cohort was compared with a historical control group of patients treated with the same chemotherapy but without rituximab. Patients from both treatment groups were matched according to age, duration of first remission, lactate dehydrogenase (LDH) serum level and B symptoms at relapse/progress. Results 22 patients were treated with immunochemotherapy and 57 patients with chemotherapy. The overall response rates (ORR) at the final evaluation were 71% (65% CR and 6% PR) for the immunochemotherapy group compared to 65% (59% CR and 6% PR) for the chemotherapy group. In the historical controlled analysis freedom from second failure (FF2F) at two years in the immunochemotherapy group was 64% and overall survival 77%. Within the chemotherapy group FF2F was 25% (p=0,0185) and OS 44% (p=0,0159). In the matched-pair analysis FF2F was 64% in the immunochemotherapy group, compared to 47% in the chemotherapy group (p=0,7274). OS was 82% vs. 70% respectively (p=0,4854). The toxicity was tolerable and comparable in both groups. Conclusions The addition of rituximab to an intensified salvage chemotherapy regimen seems to improve the prognosis. However, only prospective randomized trial can offer sufficient data of the value of rituximab in relapsed and refractory aggressive NHL.
Analyzing a new mechanism of air holes to suppress micro-bending loss (2012)

A new functionality of air holes, reduction of micro-bending loss, was analyzed and discussed. The optimum air-hole diameter arranged around the fiber edge to minimize microbending loss was also investigated.
Cervical Cancer Immunotherapy: Facts and Hopes (2021)

It is a sad fact that despite being almost completely preventable through human papillomavirus (HPV) vaccination and screening, cervical cancer remains the fourth most common cancer to affect women worldwide. Persistent high-risk HPV (hrHPV) infection is the primary etiologic factor for cervical cancer. Upward of 70% of cases are driven by HPV types 16 and 18, with a dozen other hrHPVs associated with the remainder of cases. Current standard-of-care treatments include radiotherapy, chemotherapy, and/or surgical resection. However, they have significant side effects and limited efficacy against advanced disease. There are a few treatment options for recurrent or metastatic cases. Immunotherapy offers new hope, as demonstrated by the recent approval of programmed cell death protein 1-blocking antibody for recurrent or metastatic disease. This might be augmented by combination with antigen-specific immunotherapy approaches, such as vaccines or adoptive cell transfer, to enhance the host cellular immune response targeting HPV-positive cancer cells. As cervical cancer progresses, it can foster an immunosuppressive microenvironment and counteract host anticancer immunity. Thus, approaches to reverse suppressive immune environments and bolster effector T-cell functioning are likely to enhance the success of such cervical cancer immunotherapy. The success of nonspecific immunostimulants like imiquimod against genital warts also suggest the possibility of utilizing these immunotherapeutic strategies in cervical cancer prevention to treat precursor lesions (cervical intraepithelial neoplasia) and persistent hrHPV infections against which the licensed prophylactic HPV vaccines have no efficacy. Here, we review the progress and challenges in the development of immunotherapeutic approaches for the prevention and treatment of cervical cancer.
Microarray Detection of Duplex and Triplex DNA Binders with DNA-Modified Gold Nanoparticles (2007)

We have designed a chip-based assay, using microarray technology, for determining the relative binding affinities of duplex and triplex DNA binders. This assay combines the high discrimination capabilities afforded by DNA-modified Au nanoparticles with the high-throughput capabilities of DNA microarrays. The detection and screening of duplex DNA binders are important because these molecules, in many cases, are potential anticancer agents as well as toxins. Triplex DNA binders are also promising drug candidates. These molecules, in conjunction with triplex-forming oligonucleotides, could potentially be used to achieve control of gene expression by interfering with transcription factors that bind to DNA. Therefore, the ability to screen for these molecules in a high-throughput fashion could dramatically improve the drug screening process. The assay reported here provides excellent discrimination between strong, intermediate, and weak duplex and triplex DNA binders in a high-throughput fashion.
ChemInform Abstract: Practical New Silyloxy‐Based Alkyne Metathesis Catalysts with Optimized Activity and Selectivity Profiles. (2010)

Abstract Chiral centers next to an enolizable carbonyl group are not racemized and sensitive protection groups remain intact.
End-User Development in the Internet of Things Era (2015)

The paradigm of end-user development enables ordinary end-users of computer systems to engage in the modification, extension and even creation of software artifacts. Technology, organization and context are all important aspects that influence end-users' decisions to engage in end-user development. With this workshop, we invite researchers and practitioners to discuss and exchange their experiences on the role of these aspects for end-user development across various domains.
Phase Conjugation and Negative Refraction using Nonlinear Active Metamaterials (2010)

We present an experimental demonstration of phase conjugation using nonlinear metamaterial elements. Active split-ring resonators loaded with varactor diodes are demonstrated theoretically to act as phase-conjugating or time-reversing discrete elements when parametrically pumped and illuminated with appropriate frequencies. The metamaterial elements were fabricated and shown experimentally to produce a time-reversed signal. Measurements confirm that a discrete array of phase-conjugating elements act as a negatively refracting time-reversal rf lens only 0.12λ thick.