gebhart/patrepeval huggingface dataset:
Additions and Corrections - Optimized Intermolecular Potential Functions for Amides and Peptides. Hydration of Amides. (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdditions and Corrections - Optimized Intermolecular Potential Functions for Amides and Peptides. Hydration of Amides.William Jorgensen and Carol SwensonCite this: J. Am. Chem. Soc. 1985, 107, 17, 5025Publication Date (Print):August 1, 1985Publication History Published online31 March 2004Published inissue 1 August 1985https://pubs.acs.org/doi/10.1021/ja00303a603https://doi.org/10.1021/ja00303a603research-articleACS PublicationsRequest reuse permissionsArticle Views35Altmetric-Citations-LEARN 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
Magnetic Nanoparticles: general discussion (2014)

Oliver Reiser opened the discussion of the paper by Peter Dobson: Is a size of below 20 nm critical to achieve cell penetration by nanoparticles? Peter Dobson responded: No, I chose this as a typical size. I believe that the most important point is the surface chemistry and that
TIGIT and PD-1 Mark Intratumoral T Cells with Reduced Effector Function in B-cell Non-Hodgkin Lymphoma (2019)

Checkpoint blockade can reverse T-cell exhaustion and promote antitumor responses. Although blocking the PD-1 pathway has been successful in Hodgkin lymphoma, response rates have been modest in B-cell non-Hodgkin lymphoma (NHL). Coblockade of checkpoint receptors may therefore be necessary to optimize antitumor T-cell responses. Here, characterization of coinhibitory receptor expression in intratumoral T cells from different NHL types identified TIGIT and PD-1 as frequently expressed coinhibitory receptors. Tumors from NHL patients were enriched in CD8<sup>+</sup> and CD4<sup>+</sup> T effector memory cells that displayed high coexpression of TIGIT and PD-1, and coexpression of these checkpoint receptors identified T cells with reduced production of IFNγ, TNFα, and IL2. The suppressed cytokine production could be improved upon <i>in vitro</i> culture in the absence of ligands. Whereas PD-L1 was expressed by macrophages, the TIGIT ligands CD155 and CD112 were expressed by lymphoma cells in 39% and 50% of DLBCL cases and in some mantle cell lymphoma cases, as well as by endothelium and follicular dendritic cells in all NHLs investigated. Collectively, our results show that TIGIT and PD-1 mark dysfunctional T cells and suggest that TIGIT and PD-1 coblockade should be further explored to elicit potent antitumor responses in patients with NHL.
The maize premature senesence2 encodes for PHYTOCHROME‐DEPENDENT LATE‐FLOWERING and its expression modulation improves agronomic traits under abiotic stresses (2020)

Among the various abiotic stresses, water and nitrogen are major stress factors that limit crop productivity worldwide. Since leaf nutrients remobilization during leaf senescence might impact response to abiotic stress in crops, we undertook a forward screen of the <i>Mutator</i>-active approach to identify <i>premature senescence</i> loci in maize. A mutant line isolated from a cross between a Pioneer Brand elite line and a public <i>Mutator</i>-active material, designated <i>premature senescence2</i> (<i>pre2</i>), expressed leaf senescence during flower initiation. The <i>Pre2</i> gene encodes PHYTOCHROME-DEPENDENT LATE-FLOWERING (PHL) protein, a nuclear receptor coactivator. The <i>pre2-1</i> mutant allele was not a null mutation but produced a functional wild-type transcript along with multiple mRNA species of varying lengths resulting from the alternate splicing of the <i>Pre2</i> gene. The PHL accelerates flowering by suppressing the inhibitory effect of <i>phyB</i> on flowering in Arabidopsis (Endo et al., 2013). The ZmPRE2 polypeptide is highly conserved in plant species and has two identifiable motifs namely SPT20 and MED15. The Spt20 domain, which is a part of the SAGA (Spt-Ada-Gcn5 acetyltransferase) complex, is involved in histone deacetylation and MED15 proteins have nuclear functions in mediating DNA Pol II transcription. The differential spliced mature transcripts in both the <i>pre2</i> alleles, as a result of transposon interference, were producing truncated proteins that lacked polyglutamine (Q) tract near the C-terminus and might be causative of the premature senescence phenotype in maize. Endogenous gene suppression of <i>ZmPre2</i> by RNAi improves maize agronomic performance under both water stress and suboptimal nitrogen conditions. The homozygous T-DNA knockout of the <i>pre2</i> homolog in Arabidopsis (At1G72390; the same insertional allele used by Endo et al., 2013) results in higher biomass, delayed maturity, enhanced tolerance to drought, and improved nitrogen utilization efficiency. The Arabidopsis mutant also showed hypersensitive response to 1 µM ABA (abscisic acid) concentration. These results indicate that the PHL protein plays a direct or indirect role in ABA-dependent drought and N signaling pathways.
Antigenic Properties of Experimental Leukemias. II. Immunological Studies <italic>In Vivo</italic> With C57BL/6 Radiation-Induced Leukemias<xref ref-type="fn" rid="FN2">2</xref> (1963)

The serum of C57BL/6 mice immunized against an A strain TL+(thymus leukemia antigen) spontaneous leukemia was highly cytotoxic for the cells of several C57BL/6 leukemias. Paradoxically, this was not associated with resistance in vivo to the inoculation of 2 TL+ C57BL/6 radiation-induced leukemias highly sensitive to TL antisera in vitro. Leukemia cells recovered after their outgrowth in immunized C57BL/6 mice lost their sensitivity to TL antisera in vitro and their ability to absorb specific cytotoxic activity from TL antisera. A single further passage of these cells in normal untreated C57BL/6 hosts was accompanied by complete restoration of sensitivity, even after 3 consecutive passages in immunized hosts. Immunoselection, inadequate complementation, or interference by blocking antibody might account for the outgrowth of TL+ leukemia cells in immunized hosts, but the present evidence does not favor these interpretations. More probably the temporary changes in antigenicity reflect an adaptational alteration affecting the entire population of leukemia cells.
Why are mitochondria involved in apoptosis? Permeability transition pores and apoptosis as selective mechanisms to eliminate superoxide‐producing mitochondria and cell (1996)

Petit and co-authors have recently summarized results of their studies on the involvement of mitochondria in apoptosis [Petit et al. (1996) FEBS Lett. 396, 7-13]. The mechanism consists in the release to the cytosol of a protein (presumably a protease) that is normally sequestered in the intermembrane space of mitochondria. This protein, when added to isolated nuclei, caused typical apoptotic changes. Its release from mitochondria was shown to occur as a result of disruption of the outer mitochondrial membrane due to swelling of mitochondria caused by opening of so-called permeability transition pores in their inner membranes. Increase in the level of products of the one-electron reduction of O2 (reactive oxygen species, ROS) is known to induce the mitochondrial pores. The hypothesis described here assumes that pore formation and apoptosis are involved in the organization of a defense system preventing ROS formation. It is proposed that ROS-induced pore opening lowers ROS production due to (a) maximal stimulation of mitochondrial O2 consumption and, hence, intracellular [O2] lowering and (b) complete dissipation of mitochondrial membrane potentials and, as a consequence, maximal oxidation of such respiratory chain carriers as CoQ.- which serve as one-electron O2 reductants. ROS decrease allows pore closure. If, nevertheless, ROS are still accumulating in a mitochondrion, long-lived pores cause degradation of the organelle which cannot import and synthesize proteins due to the absence of the membrane potential. In this way, ROS-producing mitochondria can be eliminated (mitochondrial selection). Another result of the long-lived pores is mitochondrial swelling. This disrupts the outer mitochondrial membrane and releases the apoptosis-inducing protein. Apoptosis eliminates ROS-producing cells (cell selection).
Automotive vehicle sensors (1995)

This report is an introduction to the field of automotive vehicle sensors. It contains a prototype data base for companies working in automotive vehicle sensors, as well as a prototype data base for automotive vehicle sensors. A market analysis is also included.
Stereoselective α,α′-Annelation Reactions of 1,3-Dioxan-5-ones (2010)

Pyrrolidine enamines derived from three 1,3-dioxan-5-ones undergo α,α'-annelation reactions with methyl α-(bromomethyl)acrylate to produce bridged 2,4-dioxabicyclo[3.3.1]nonane ring systems with complete stereocontrol. Stereochemical outcomes have been rationalized based on steric and stereoelectronic interactions in intermediate boat-like conformations of the 1,3-dioxane ring and subsequent kinetic protonation to set an axial ester group on the cyclohexanone ring. Base-mediated ester epimerization provides the stereochemical array found in the highly oxygenated cyclohexane ring of phyllaemblic acid and glochicoccins B and D.
Supplementary Tables 1, 3 and 4 from <i>BRAF/NRAS</i> Wild-Type Melanomas Have a High Mutation Load Correlating with Histologic and Molecular Signatures of UV Damage (2023)

&lt;p&gt;Supplementary tables 1, 3 and 4 - XLSX file 31K, 1. Performance summary of exome sequencing and capture kit used for each sample 3. List of genes for each melanoma subtype 4. List of potential actionable mutations in BRAF/NRAS wild-type tumors&lt;/p&gt;
Cytostatic activity of pyrazine sorafenib analogues (2015)

Sorafenib je noviji citostatik, inhibitor vise kinaza ukljucenih u stanicnu proliferaciju i preživljavanje (1). Sorafenib inhibira domene tirozin-kinaze dvaju podtipova receptora za VEGF (VEGFR2 i VEGFR3), receptora za trombocitni faktor rasta-β (PDGFR-β), a inhibira i Raf. On je jedini lijek odobren za lijecenje uznapredovalog hepatocelularnog karcinoma, a koristi se i za lijecenje uznapredovalog metastatskog karcinoma bubrežnih stanica (2). Nedostaci sorafeniba (losa fizicko-kemijska svojstva, slabo djelovanje u lijecenju malignog melanoma, toksicnost i rezistencija na terapiju) poticaj su za dizajniranje novih, djelotvornijih i/ili manje toksicnih derivata. U okviru nasih istraživanja sintetizirani su novi analozi sorafeniba koji umjesto piridinskog imaju pirazinski prsten, a međusobno se razlikuju u karbamidnom i amidnom dijelu (3). U ovom radu ispitano je njihovo antitumorsko djelovanje na stanicnu liniju akutne limfoblasticne leukemije (Molt4/C8 i CEM), limfocitne leukemije (L1210), hepatocelularnog karcinoma (HepG2), karcinoma cerviksa (HeLa), kolona (SW 620), dojke (MCF-7) i pluca (A549). Svi ispitivani spojevi pokazali su znacajno antiproliferativno djelovanje na ispitanim stanicnim linijama, a neki su pokazali jace antiproliferativno djelovanje od sorafeniba.
AutoAI (2020)

Automated Artificial Intelligence and Machine Learning (AutoAI / AutoML) can now automate every step of the end-to-end AI Lifecycle, from data cleaning, to algorithm selection, and to model deployment and monitoring in the machine learning workflow. AutoAI technologies, initially aimed to save data scientists from the low level coding tasks, also has great potential to serve non-technical users such as domain experts and business users to build and deploy machine learning models. Researchers coined it as "democratizing AI", where non-technical users are empowered by AutoAI technologies to create and adopt AI models. To realize such promise, AutoAI needs to translate and incorporate the real-world business logic and requirements into the automation. In this Demo, we present a first of its kinds experimental system, IBM AutoAI Playground, that enables non-technical users to define and customize their business goals (e.g., Prediction Time) as constraints. AutoAI then builds models to satisfy those constraints while optimizing for the model performance (e.g., ROC AUC score). This Demo also showcases AutoAIViz, a Conditional Parallel Coordinates visualization feature, and a TrustedAI feature from two accepted IUI'20 papers.
Phenyl vs Alkyl Polythiophene: A Solar Cell Comparison Using a Vinazene Derivative as Acceptor (2010)

The solar cell performance of poly[3-(4-n-octyl)-phenylthiophene] (POPT) and poly(3-hexylthiophene) (P3HT) are compared in devices using 4,7-bis(2-(1-(2-ethylhexyl)-4,5-dicyanoimidazol-2-yl)vinyl)benzo[c][1,2,5]-thiadiazole (EV-BT) as the electron acceptor. Despite their reduced light absorption, POPT:EV-BT devices generate higher photocurrents in both bilayer and bulk heterojunction (BHJ) architectures than analogous P3HT:EV-BT devices. Optimized POPT:EV-BT BHJ devices achieve 1.4% average efficiency, whereas the analogous P3HT devices only reach 1.1%. Morphology does not account for the large difference in performance as AFM studies of the active layer suggest comparable levels of phase separation in the two systems. Reverse bias analysis demonstrates that P3HT devices have a higher maximum potential than POPT devices, but P3HT devices appear to be more severely limited by recombination losses under standard operating conditions. A possible explanation for the superior performance in POPT devices is that the pendant phenyl ring in POPT can twist out-of-plane and increase the separation distance with the acceptor molecule. A larger donor/acceptor separation distance can destabilize the geminate pair and lead to more efficient charge separation in POPT:EV-BT devices. Our results emphasize the importance of donor/acceptor pair interactions and its effect on charge separation processes in polymer solar cells.
ANALYSIS AND TOOLS FOR THE DESIGN OF VLIW EMBEDDED SYSTEMS IN A MULTI-OBJECTIVE SCENARIO (2007)

The use of Application-Specific Instruction-set Processors (ASIP) in embedded systems is a solution to the problem of increasing complexity in the functions these systems have to implement. Architectures based on Very Long Instruction Word (VLIW) have found fertile ground in multimedia electronic appliances thanks to their ability to exploit high degrees of Instruction Level Parallelism (ILP) with a reasonable trade-off in complexity and silicon costs. In this case the ASIP specialization involves a complex interaction between hardware- and software-related issues. In this paper we propose tools and methodologies to cope efficiently with this complexity from a multi-objective perspective. We present EPIC-Explorer, an open platform for estimation and system-level exploration of an EPIC/VLIW architecture. We first analyze the possible design objectives, showing that it is necessary, given the fundamental role played by the VLIW compiler in instruction scheduling, to evaluate the appropriateness of ILP-oriented compilation on a case-by-case basis. Then, in the architecture exploration phase, we will use a multi-objective genetic approach to obtain a set of Pareto-optimal configurations. Finally, by clustering the configurations thus obtained, we extract those representing possible trade-offs between the objectives, which are used as a starting point for evaluation via more accurate estimation models at a subsequent stage in the design flow.
Substituent effect of Ru(ii)-based sensitizers bearing a terpyridine anchor and a pyridyl azolate ancillary for dye sensitized solar cells (2015)

Sensitizer <bold>PRT-tBu</bold> is the best candidate for fabrication of DSC devices after taking into the consideration the relative performances, device stability and scaled-up production capability.
Prodrugs of Ara-CMP and Ara-AMP with aS-Acyl-2-thioethyl (SATE) Biolabile Phosphate Protecting Group: Synthesis and Biological Evaluation (1999)

The bis(S-pivaloyl-2-thioethyl) phosphotriesters of Ara-C and Ara-A were synthesized as potential bioreversible mononucleotide prodrugs. Some N- and O-acylated derivatives were also prepared with the aim to modify the lipophilicity of the title pronucleotides. Compounds were tested for their antitumor/antiviral activity against a variety of tumor cells and viruses.
Abstract IA08: Systematic interrogation of cancer dependencies (2017)

Abstract Although we now have a draft view of the genetic alterations that occur in human cancer, the number of mutations found at low frequency and the molecular heterogeneity of most cancers makes identifying genes that contribute to cancer phenotypes challenging. Determining the function of genes altered in cancer genomes is essential to develop new therapeutic approaches. To complement these genome characterization studies, we have used genome scale gain and loss of function approaches to identify genes required for cell survival and transformation. Specifically, we have performed systematic studies to interrogate rare alleles found altered in cancer genomes and used advances in synthetic gene synthesis to prospectively interrogate all possible alleles of known cancer genes. In parallel, we have performed both genome scale RNAi and CRISRP-Cas9 screens in more than 500 cell lines to identify differentially essential genes and the context that specifies gene dependency. This approach now permits us to identify and classify cancer dependencies. These studies allow us to begin to define a global cancer dependencies map. Citation Format: William C. Hahn. Systematic interrogation of cancer dependencies [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr IA08.
Impact of the fiber type and nonlinear management over the performance of a 16×40 Gb/s DWDM transmission system (2004)

We examine impact of the fiber type as well as nonlinear management over the performance of a 16×40 Gb/s DWDM NRZ transmission system. The line is constituted of 3×100 km of G.652 or G.655 fiber with periodic dispersion compensation and hybrid Raman-EDFA amplification scheme.
Oncogenic Kit signalling on the Golgi is suppressed by blocking secretory trafficking with M-COPA in gastrointestinal stromal tumours (2017)

Most gastrointestinal stromal tumours (GISTs) are caused by constitutively active mutations in Kit tyrosine kinase. The drug imatinib, a specific Kit inhibitor, improves the prognosis of metastatic GIST patients, but these patients become resistant to the drug by acquiring secondary mutations in the Kit kinase domain. We recently reported that a Kit mutant causes oncogenic signals only on the Golgi apparatus in GISTs. In this study, we show that in GIST, 2-methylcoprophilinamide (M-COPA, also known as "AMF-26"), an inhibitor of biosynthetic protein trafficking from the endoplasmic reticulum (ER) to the Golgi, suppresses Kit autophosphorylation at Y703/Y721/Y730/Y936, resulting in blockade of oncogenic signalling. Results of our M-COPA treatment assay show that Kit Y703/Y730/Y936 in the ER are dephosphorylated by protein tyrosine phosphatases (PTPs), thus the ER-retained Kit is unable to activate downstream molecules. ER-localized Kit Y721 is not phosphorylated, but not due to PTPs. Importantly, M-COPA can inhibit the activation of the Kit kinase domain mutant, resulting in suppression of imatinib-resistant GIST proliferation. Our study demonstrates that Kit autophosphorylation is spatio-temporally regulated and may offer a new strategy for treating imatinib-resistant GISTs.
Carrier and Time Synchronization (2021)

Mismatch in both time and frequency between communication sides is inevitable, and the receiver must be synchronized with the transmitter; otherwise, the performance of the system is degraded severely if it operates at all. This chapter addresses carrier and time synchronizations and advances the conventional receiver structure further to include those functionalities. It discusses signal modeling and the effects of impairments. The main target of this chapter is synchronization for lab equipment, i.e. software defined radio equipment, and since the processed signals given to and returned by these devices are baseband signals, the focus is on the baseband signal modeling. The chapter addresses carrier phase error where feedback and feedforward compensation techniques are presented. Time synchronization is considered, where both frame edge detection and downsampling problems are addressed. For downsampling, both feedback and feedforward methods are shown.
Home energy management as a service over networking platforms (2015)

About 40% of the U.S. primary energy is consumed in the buildings. Therefore, to manage the energy consumption and its usages pattern, for instance, the U.S. state of California mandated Zero Net Energy buildings by 2020 for the residential sector (22% of the U.S. primary energy). Moreover, towards this goal, U.S. Department of Energy, Building Technologies Office is trying to develop techniques to improve the efficiency of buildings. Home Energy Management (HEM) may be used to improve the energy consumption in the residential buildings. However, the cost, scalability, and flexibility of the software and hardware architectures available, have increased the time-to-market and have made HEMs hard to penetrate the consumer market. To solve these limitations, in this paper, we have presented a novel HEM platform, which utilizes a low power IEEE 802.15.4 standard to monitor and control all the appliances in a house. Moreover, it utilizes Service-Oriented Architecture and Devices Profile for Web Services to implement the monitoring and controlling algorithms and therefore may significantly improve the scalability and flexibility of the platform. Also, some other features like: plug-n-play capability, remote access feature, and open source architecture are implemented in this platform. Finally, a table-top prototype of the HEM platform is demonstrated in the paper.