gebhart/patrepeval huggingface dataset:
Supplement method and figures from A Small-Molecule Antagonist of HIF2α Is Efficacious in Preclinical Models of Renal Cell Carcinoma (2023)

&lt;p&gt;Supplementary method includes detailed experimental procedure for the synthesis of PT2385. Supplementary Figures 1-7 - Lack of cytotoxicity of PT2385 in cultured 786-O and A498 cells (1); PT2385 pharmacokinetics in CD-1 mice (2); Inhibition of HIF-2ï�¡ gene expression and circulating hVEGFa in A498 mouse xenograft model after treatment with PT2385 (3); HIF-2ï�¡ mRNA and protein levels in 786-O cells in vitro after treatment with PT2385 (4); Levels of HIF-1ï�¡ and HIF-2ï�¡ in patient-derived xenograft tumors (5); Body weight of mice in efficacy studies treated with either vehicle, PT2385 or sunitinib (6); Binding of PT2385 to rat HIF-2ï�¡ as determined by ITC and inhibition of mouse kidney EPO gene expression with PT2385 treatment (7).&lt;/p&gt;
FBMC and L-DACS Performance for Future Air-to-Ground Communication Systems (2016)

Recently, two different L-band digital aeronautical communication systems (L-DACS), i.e., L-DACS1 and L-DACS2, have been proposed as two future communication infrastructure candidates for air-to-ground (AG) communication systems, with L-DACS1 selected as the best candidate. In this paper, we describe a filter bank multicarrier (FBMC)-based communication system and show its advantages over the L-DACS systems. We provide simulation results for all three communication systems to fairly compare their power spectral density, peak-to-average power ratio (PAPR), and bit error ratio (BER) performance. We show that in a measurement-based AG communication channel model, FBMC has better performance (and spectral containment) than the L-DACS schemes, and this is particularly true in the presence of actual interfering signals from distance measuring equipment (DME). Simulation results show that FBMC can substantially reduce the out-of-band power and can suppress DME interference by at least 19.5 dB, due to its well-localized subcarrier prototype filters. FBMC can also increase throughput and spectral efficiency by reducing the number of guard-band subcarriers and removal of the cyclic prefix, postfix, as well as windowing techniques used in L-DACS1. These results show that an FBMC-based communication system can be an appealing candidate for future AG communication systems.
Pressure dependence of the electronic spectra of quasi-one-dimensional Pt2X semiconductors (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPressure dependence of the electronic spectra of quasi-one-dimensional Pt2X semiconductorsMary Ann Stroud, Harry G. Drickamer, Miriam Heinrichs Zietlow, Harry B. Gray, and Basil I. SwansonCite this: J. Am. Chem. Soc. 1989, 111, 1, 66–72Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/ja00183a012https://doi.org/10.1021/ja00183a012research-articleACS PublicationsRequest reuse permissionsArticle Views101Altmetric-Citations26LEARN 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
Malachite green‐conjugated microtubules as mobile bioprobes selective for malachite green aptamers with capturing/releasing ability (2006)

We have developed a novel mobile bioprobe using a conjugate of a kinesin-driven microtubule (MT) and malachite green (MG) as a platform for capturing MG RNA aptamers. The fluorescence of MG increases when it is bound to an MG aptamer, allowing MT-MG conjugates to work as sensors of RNA transcripts containing the MG aptamer sequence. Kinesin motor proteins provide an effective driving force to create mobile bioprobes without any manipulation. Although the fluorescence of a small number of MG-binding aptamers is low, the self-organization of tubulins into MTs enables the microscopic observation of the bound aptamers by collecting them on MTs. We demonstrate that MT-MG conjugates can select target aptamers from a transcription mixture and transport them without losing their inherent motility. Because the MG aptamer binds MG in a reversible manner, MT-MG conjugates can conditionally load and unload the target aptamers. This is one advantage of this system over the molecular probes developed previously in which reversible unloading is impossible due to high-affinity binding, such as between avidin and biotin. Furthermore, an MT-MG conjugate can be used as a platform for other MG aptameric sensors with recognition regions for various target analytes optimized by further selection procedures. This is the first step to applying living systems to in vitro devices. This technique could provide a new paradigm of mobile bioprobes establishing high-throughput in vitro selection systems using microfluidic devices operating in parallel.
Prolonged Cold Ischemic Time Is a Risk Factor for Biliary Strictures in Duct-to-Duct Biliary Reconstruction in Living Donor Liver Transplantation (2008)

Background. Duct-to-duct (DD) anastomosis is an accepted procedure for biliary reconstruction in living donor liver transplantation (LDLT). However, biliary complication rates in LDLT recipients have been reported to be as high as 20% to 30% or more. In this study, we examined various potential risk factors for biliary stricture (BS) that occurs in the context of DD reconstruction in a single-active transplant center. Methods. Enrolled in this study were adults who underwent their first LDLT with DD reconstruction between August 2002 and May 2007 (n=283). BSs were defined as anastomotic strictures that required interventions or operative procedures to be corrected. We reviewed retrospectively the medical records of recipients, including medical history, surgical procedures, and progress, and analyzed risk factors of BS with the Kaplan-Meier method. Results. BS occurred in 58 of the 283 recipients (20.5%). The mean follow-up period was 24.4 months posttransplant (SD=16.5). The univariate analysis revealed that recipient age (P=0.032), bile duct size (P=0.003), biliary reconstruction surgeon (P=0.023), perfusion solution (P=0.001), cold ischemic time (CIT) (P<0.001), and biliary leakage history (P<0.001) were significant risk factors. In the multivariable analysis, CIT (P=0.001), biliary leakage history (P=0.002), bile duct size (P=0.021), and recipient age (P=0.036) were significant risk factors for BS. And, a CIT cutoff value of 71 min was calculated using the minimum P value approach with correction by the Miller and Siegmund method (P=0.0186). Conclusions. In this study, prolonged CIT is identified as a risk factor for BS in DD biliary reconstruction in LDLT.
Identification of an N-terminal domain of eukaryotic DNA topoisomerase I dispensable for catalytic activity but essential for in vivo function. (1992)

We have found that deletion of a 70-amino acid domain, spanning from position 141 to 210 in the N-terminal part of human topoisomerase I, has no effect on the catalytic activity of the enzyme in vitro but suppresses the lethal consequence of overexpressing human topoisomerase I in a rad52 top1 Saccharomyces cerevisiae strain. By immunostaining, the 70-amino acid domain is shown to be necessary for nuclear location of topoisomerase I. We demonstrate that the nuclear localization signal from the SV40 large T antigen can substitute for the 70-amino acid domain, restoring both the lethal effect of overexpression and the correct subcellular localization of topoisomerase I. Thus, we have identified a domain in the N-terminal part of human topoisomerase I, nonessential for catalytic activity in vitro but serving an in vivo function by directing the enzyme to the nucleus. Based on sequence comparisons, we suggest that this domain is a conserved element in the apparently non-homologous N-terminal parts of yeast and human topoisomerase I.
Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence (2020)

Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.
Deep ultraviolet emission from multiple quantum wells on flat N-polar AlN templates fabricated using periodical pulsed H 2 etching (2021)

Abstract In a previous study, we successfully grew flat N-polar AlN layers on a c -plane sapphire substrate with a misorientation angle of 2.0° by metal-organic vapor phase epitaxy. However, its surface had undulations due to step bunching, and therefore further improvement of the surface flatness is required. In this study, we employed pulsed H 2 etching during the growth of N-polar AlN layers to improve the surface flatness. Atomic force microscopy results indicated that the surface flatness was significantly improved, exhibiting a root mean square value of 0.4 nm. Further, the deep ultraviolet emission from AlGaN-based multiple quantum wells (MQWs) on the N-polar AlN layers was characterized, and the effect of the surface flatness on the optical characteristics was investigated. The surface flatness was found to play a crucial role in improving the optical characteristics of MQWs on N-polar AlN layers.
Analysis of GHG Reduction Potential on Road Transportation Sector using the LEAP Model - Low Carbon Car Collaboration Fund, Fuel Efficiency, Improving Driving Behavior - (2016)

This study the efficiency of greenhouse gas reduction of ‘low carbon car collaboration fund’ and its alternative ‘control of average fuel efficiency and greenhouse gas’, and ‘improving driving behavior’ were analyzed by using LEAP, long term energy analysis model.BR Total 4 scenarios were set, baseline scenario, without energy-saving activity, ‘low carbon car collaboration fund’ scenario, ‘fuel efficiency improving scenario’, and ‘improving driving behavior’ scenario. The contents of analysis were forecast of energy demand by scenario and application as well as reduction of greenhouse gas emission volume, and the period taken for analysis was every 1 year during 2015∼2030.BR Baseline scenario, greenhouse gas emission volume in 2015 would be 7,935,697 M/T and 13,081,986 M/T in 2030, increased 64.8%. The analysis result was average annual increase rate of 3.4%. The expected average annual increase rate of other scenarios was, ‘low carbon car collaboration fund’ scenario 1.7%, ‘fuel efficiency improving’ scenario 3.0%. and ‘improving driving behavior’ scenario 3.4%. and these were each 1.7%, 0.3%. 0.3% reduce from baseline scenario. The largest reduction was ‘low carbon car collaboration fund’ scenario, and there after were ‘fuel efficiency improving scenario’, and ‘improving driving behavior’ scenario.
Supplementary Table 1 from An Epithelial–Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance (2023)

&lt;p&gt;PDF file - 214K, The EMT signature genes&lt;/p&gt;
Ex vivo impact of human milk oligosaccharides and lactose on microbiome in infants with cow's milk protein allergy (2023)

Cow’s milk protein allergy (CMPA) is the most common food allergy in infancy. CMPA is associated with gut microbial dysbiosis, characterized by low Bifidobacteriaceae levels. This study investigated the impact of a human milk oligosaccharide (HMO) mixture of 2’-fucosyllactose (2’-FL) and lacto- N -neotetraose (LNnT), as well as lactose (L), on the fecal microbiome of infants with clinically diagnosed CMPA (n=12), using the ex vivo intestinal fermentation SIFR technology. The fecal microbiota displayed considerable heterogeneity, with low abundances of Bifidobacteriaceae found in most infants, except two breastfed infants. HMO and lactose both enriched Bifidobacteriaceae via stimulation of Operational Taxonomic Units (OTUs) related to B. breve , B. longum , B. pseudocatenulatum and, for HMO+L, also B. bifidum . All supplementations significantly boosted the production of acetate, propionate, aromatic lactic acids and N-acetylated amino acids, with additive effects observed for combining HMO+L. Additional contributors to HMO fermentation were OTUs related to Bacteroides fragilis, Blautia obeum/wexlerae and Ruminococcus gnavus, while OTUs related to Escherichia coli and Veillonella parvula were involved in lactose fermentation, suggesting involvement of substrate-specific fermentation pathways. In conclusion, the observed bifidogenic effect of HMO confirms the potential of 2’-FL and LNnT to ameliorate CMPA-associated dysbiosis, with additive effects found for the abundance of B. bifidum and bifidobacterial metabolite levels. The clinical significance of the partial reversal of fecal microbial dysbiosis and enhanced production of beneficial metabolites on the clinical course of CMPA requires further investigation.
Face Recognition via Active Annotation and Learning (2016)

In this paper, we introduce an active annotation and learning framework for the face recognition task. Starting with an initial label deficient face image training set, we iteratively train a deep neural network and use this model to choose the examples for further manual annotation. We follow the active learning strategy and derive the Value of Information criterion to actively select candidate annotation images. During these iterations, the deep neural network is incrementally updated. Experimental results conducted on LFW benchmark and MS-Celeb-1M challenge demonstrate the effectiveness of our proposed framework.
8C-4 Active and Passive Muscle Properties Assessed by Ultrasound Techniques (2007)

The non invasive and in vivo assessment of the active and passive properties of the musculoskeletal system remains today a great challenge for the understanding of muscular diseases. In a previous paper, we showed that the transient contraction of a muscle fiber bundle triggered by electrostimulation can be followed in space and time by an ultrafast ultrasound system. On the one hand, this experiment is generalized to measure the three dimensional (3D) velocity fields allowing a much easier localization of the contracting fibers bundle. On the other hand, the supersonic shear imaging technique is applied to assess viscoelastic properties of the biceps brachii in different conditions. By combining in vivo imaging of both passive and active muscle activity, this study aims to provide new potential ultrasonic tools for muscle diseases diagnosis and monitoring. In order to image the contraction, which is a very quick phenomenon, an ultrasound scanner able to take up to 5000 frames/s was used. Tissue velocities were obtained from conventional speckle tracking techniques. The probe, positioned perpendicularly to the arm in a water tank, was moved with a linear motor. For each position, the imaging system was set to trigger an electrostimulation firing the contraction. A second experiment for the assessment of passive muscle elastic properties in different positions of the arm and contraction levels is then performed using the same probe in the supersonic shear imaging (SSI) mode. Generated by the radiation force induced by a focused ultrasound beam, shear waves propagate in the medium and are imaged by an ultrafast ultrasound scanner allowing the reconstruction of viscoelastic properties. The localization of the contracting fibers bundle and the resolution of its main temporal and spatial behavior are demonstrated. Paving the way to a clinical protocol on muscle diseases, viscoelastic parameters are measured in different conditions and reproducibility is discussed. These two complementary ultrasound techniques offer new perspectives for muscle diagnosis both as an active contractile tissue and as a passive tissue.
ChemInform Abstract: Trisubstituted Pyrimidine Derivatives from Tetrafluoropyrimidine. (2010)

Abstract The method includes three sequential reactions with nucleophiles as amines and sodium alkoxides.
Dual Regulation of Ligand Binding by CD11b I Domain (1998)

The role of coagulation factor X as a ligand for CD11b/CD18 (Mac-1, alphaMbeta2) in leukocyte adhesion was investigated. A factor X peptide, (G)L238YQAKRFKV246(G), blocked ligand binding to CD11b/CD18 and prevented monocyte procoagulant activity. This peptide also inhibited monocytic THP-1 cell adhesion to tumor necrosis factor alpha-stimulated endothelium and blocked neutrophil migration through tumor necrosis factor alpha-activated endothelial cell monolayers. In contrast, other factor X-derived peptides were ineffective. Radiolabeled peptide (G)LYQAKRFKV(G) bound specifically and saturably to isolated recombinant CD11b I domain. Functionally, the factor X sequence (G)LYQAKRFKV(G) dose-dependently inhibited THP-1 cell attachment to intercellular adhesion molecule 1 (ICAM-1) transfectants (IC50 = approximately 50 microg/ml), indistinguishably from anti-CD18 monoclonal antibodies 60.3 and IB4. In contrast, peptide (G)LYQAKRFKV(G) failed to reduce binding of 125I-fibrinogen to immobilized CD11b I domain, which was abolished by the fibrinogen-derived peptide KYG190WTVFQKRLDGSV202. By Lineweaver-Burke analysis, peptide (G)LYQAKRFKV(G) inhibited factor X binding to CD11b/CD18 in a noncompetitive fashion, and intact factor X did not reduce monocyte-endothelial cell interaction. These data suggest that the factor X sequence (G)LYQAKRFKV(G) defines an ICAM-1-binding site on CD11b I domain physically distinct from and nonoverlapping with the fibrinogen interacting region(s). Engagement of this site induces a conformational change in the holoreceptor, which disrupts a distant factor X-binding site required for monocyte procoagulant activity. These observations demonstrate a dual regulatory role of CD11b I domain in ligand binding and provide a molecular basis for the recently reported anti-inflammatory properties of factor X homologous sequences in vivo.
Oxygen Transport Through Electronically Conductive Polyanilines (1999)

Emeraldine base of polyaniline was synthesized by a chemical oxidation polymerization technique. The resulting emeraldine base film was treated with 4M HC1,1M NH4OH, and subsequently with varying dopant HC1 concentrations. The oxygen and nitrogen permeabilities through the doped polyanilines decreased with their doping level, while their oxygen selectivity over nitrogen increased up to 12.2 when doped with 0.0150 M HC1 solution. When doped with 0.0175 M HC1, the membrane selectivity is expected to be higher but immeasurable because of extremely low permeability of nitrogen. The origin of such high selectivity is explored in terms of the facilitated transport and free volume change upon doping. Because the polarons generated upon doping react with oxygen molecules specifically and reversibly, these polarons can act as oxygen carriers and thereby facilitate oxygen transport. It is, therefore, expected that the oxygen permeability increases with the polaron (carrier) concentration. However, permeability for oxygen in these materials decreased with the increase in polaron concentration. Instead, the permeability correlated well with the d-spacing or free volume, measured via x-ray diffraction. It is found that although facilitated oxygen transport may occur, its contribution to oxygen permeability is insignificant. The free volume change upon doping seems to play a major role in determining gas permeation.
Deep Multi-Emitter Spectrum Occupancy Mapping that is Robust to the Number of Sensors, Noise and Threshold (2022)

One of the primary goals in spectrum occupancy mapping is to create a system that is robust to assumptions about the number of sensors, occupancy threshold (in dBm), sensor noise, number of emitters and the propagation environment. We show that such a system may be designed with neural networks using a process of aggregation to allow a variable number of sensors during training and testing. This process transforms the variable number of measurements into approximate log-likelihood ratios (LLRs), which are fed as a fixed-resolution image into a neural network. The use of LLR's provides robustness to the effects of noise and occupancy threshold. In other words, a system may be trained for a nominal number of sensors, threshold and noise levels, and still operate well at various other levels without retraining. Our system operates without knowledge of the number of emitters and does not explicitly attempt to estimate their number or power. Receiver operating curves with realistic propagation environments using topographic maps with commercial network design tools show how performance of the neural network varies with the environment. The use of very low-resolution sensors in this system can still yield good performance.
ChemInform Abstract: Simple, Efficient Catalyst System for the Palladium‐Catalyzed Amination of Aryl Chlorides, Bromides, and Triflates. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.