gebhart/patrepeval huggingface dataset:
Noninvasive molecular subtyping and risk stratification of DLBCL. (2016)

7554 Background: Clinically distinct DLBCL subsets can be stratified using gene expression profiles (GEP), allowing prognostic classification based on cell-of-origin (COO) with potential therapeutic implications. Current methods for COO assessment either rely on adequate tumor tissue or are limited by low accuracy and reproducibility. Circulating tumor DNA (ctDNA) is a noninvasive biomarker for tumor detection with potential for DLBCL disease monitoring. Here, we explored the utility of ctDNA for tumor subtyping and risk stratification. Methods: Using a training cohort originally classified by mRNA GEP (n = 142), webuilt a novel COO classifier based on somatic variants detected by tumor DNA genotyping. COO classifier performance was then assessed on 76 tumor and 41 plasma samples using CAPP-Seq, a highly sensitive method for ctDNA detection and noninvasive plasma genotyping for all major somatic mutation classes (Newman et al., Nat. Med. 2014). COO classifier results were compared against the Hans algorithm. Additionally, associations between ctDNA and clinical indices for noninvasive risk stratification were assessed by Pearson correlation, Mann-Whitney test and Cox regression. Results: CAPP-Seq genotyping allowed COO assessment in 100% of patients using tumor tissue. Tumor COO classification with CAPP-Seq (GCB = 45 / Non-GCB = 31) was highly concordant with plasma-based COO classification (88% - 93% depending on ctDNA levels) and showed 84% concordance with the Hans algorithm. COO classification by CAPP-Seq from either tissue or plasma samples significantly predicted PFS (P = 0.008 and 0.02, respectively), while classification by Hans criteria showed no significant difference (P = 0.29). Pretreatment ctDNA levels were significantly correlated with LDH (r = 0.94), PET/CT metabolic tumor volume (r = 0.67), stage (P = 0.0003) and IPI (P < 0.0001). High ctDNA concentrations at diagnosis were strongly associated with PFS (P < 0.0001), with assessment of independent prognostic value ongoing in a larger validation cohort. Conclusions: CAPP-Seq ctDNA profiling allows accurate noninvasive DLBCL COO subtyping and clinical risk stratification. Further investigation is required to characterize its potential role in guiding therapy decisions.
Multi-Signal Characterization of Biological Structures at Low-Voltage Using STEM-in-SEM (2022)

Journal Article Multi-Signal Characterization of Biological Structures at Low-Voltage Using STEM-in-SEM Get access Kelly Parker, Kelly Parker Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Abhalaxmi Singh, Abhalaxmi Singh Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, United States Search for other works by this author on: Oxford Academic Google Scholar Vinayak P Dravid Vinayak P Dravid Department of Materials Science and Engineering, Northwestern University, Evanston, IL, United StatesNorthwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL, United States Corresponding author: v-dravid@northwestern.edu Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 28, Issue S1, 1 August 2022, Pages 1108–1110, https://doi.org/10.1017/S1431927622004688 Published: 01 August 2022
Synthesis of Cyclosporine. Part II. Synthesis of Boc‐D‐Ala‐MeLeu‐MeLeu‐MeVal‐OH, a part of the peptide sequence of cyclosporine, by different strategic ways and synthesis of its isomers Boc‐D‐Ala‐MeLeu‐D‐MeLeu‐MeVal‐OH, Boc‐D‐MeLeu‐DMeVal‐OH, and Boc‐D‐Ala‐MeLeu‐MeLeu‐D‐MeVal‐OH as reference compounds (1983)

Abstract Boc‐ D ‐Ala‐MeLeu‐MeLeu‐MeVal‐OH ( DLLL ) and its isomers DLDL, DLDD and DLLD were synthesized using several different strategic approaches and a modification of the mixed pivalic anhydride method for carboxyl activation. Alternatively, the tert ‐butoxy‐carbonyl (Boc) or benzyloxycarbonyl (Z) amino‐protecting groups and the benzyloxy (OBzl) or tert ‐butoxy ( Ot Bu) carboxyl‐protecting groups were used to protect the reacting peptides. By monitoring the reaction temperature, it was possible to synthesize, starting from the tripeptide DLL as peptide model, either the tetrapeptide DLLL (−20°) or the tetrapeptide DLDL (+20°), selectively. Using 1 H‐NMR spectroscopy to follow the mixed pivalic anhydride formation of the DLL ‐ and DLD ‐tripeptides, it could be shown that anhydride formation is strongly dependent on the temperature. It is slow at −20° (several hours) and fast at +20° (20 to 40min). The isomerization of the DLL ‐anhydride to the more stable DLD ‐anhydride can be reduced to a minimum by working at −20°, while this isomerization proceeds to near completion at +20°.
Vitronectin is produced in the lung upon infection by respiratory pathogens, and is utilized to evade the innate immunity (2017)

Bacterial extracellular vesicles (EVs) are shed during growth by the respiratory pathogens Pseudomonas aeruginosa and Haemophilus influenzae. Vesicles trigger release of antimicrobial compounds and proteins of the complement, which are partly regulated by vitronectin. We hypothesized that vitronectin is elevated in the lungs during pneumonia, that respiratory epithelial cells produce vitronectin upon bacterial stimulation and that vitronectin is utilized by bacteria for increased virulence. Vitronectin-concentrations were measured by ELISA in bronchoalveolar lavage fluid (BALF) from patients with pneumonia (n=8) and from healthy volunteers (n=13) with or without pulmonary endotoxin instillation. Elevated vitronectin concentrations were found in BALF collected during pneumonia compared to healthy individuals (p=0.0063) and in endotoxin-challenged pulmonary segments compared to control segments (after 12h: p=0.031; 48h: p=0.016). Flow cytometry revealed that bacteria captured vitronectin from BALF onto their surface and subsequently became less sensitive to killing by serum compared to controls (P. aeruginosa p=0.016, H. influenzae p=0.011). Increased levels of VTN mRNA after one hour (p=0.022) and increased surface bound vitronectin after 24h (p<0.001) were observed with type II bronchial alveolar epithelial cells (A549) after stimulation with EVs. In conclusion, elevated vitronectin concentrations were found in BALF from patients with pneumonia and in healthy volunteers after pulmonary endotoxin instillation. Cellular experiments confirmed vitronectin production upon EV stimulation in vitro. Bacteria captured vitronectin from BALF on their surface to evade lysis by complement in serum. Hence, vitronectin is produced by epithelial cells upon bacterial infection and utilized by respiratory pathogens to persist in the respiratory tract.
Heterogeneous Cation–Lattice Interaction and Dynamics in Triple-Cation Perovskites Revealed by Infrared Vibrational Nanoscopy (2020)

Hybrid organic–inorganic perovskites exhibit extraordinary photovoltaic performance. This is believed to arise from almost liquid-like low-energy interactions among lattice ions and charge carriers. While spatial variations have recently been identified over multiple length scales in the optoelectronic response of perovskites, the relationship between the heterogeneity and the soft cation–lattice interactions has remained elusive. Here, we apply multivariate infrared vibrational nanoimaging to a formamidinium (FA)–methylammonium (MA)–cesium triple-cation perovskite by using the FA vibrational resonance as a sensitive probe of its local chemical environment. The derived correlation among nanoscale composition, cation–lattice coupling, and associated few-picosecond vibrational dynamics implies a heterogeneous reaction field and lattice contraction that we attribute to a spatially nonuniform distribution of cesium cations. The associated spatial variation in elasticity of the lattice leads to disorder in charge–phonon coupling and related polaron formation—the control of which is central to improving perovskite photovoltaics.
Data Processing at the INTEGRAL Science Data Centre (2004)

INTEGRAL, the INTErnational Gamma Ray Astrophysics Laboratory of the European Space Agency, was launched on October 17, 2002. INTEGRAL operations are performed very successfully and the instruments provide data of good quality. These data are routed to the INTEGRAL Science Data Centre (ISDC), where they are processed, archived and finally distributed to the science community. In this paper we present the organisation of the centre and its software development. Some details of the data flow are given along with a description of the core ISDC software libraries.
Computational camera (2006)

Article Share on Computational camera: convergence of optics and software Author: Shree K. Nayar Columbia University Columbia UniversityView Profile Authors Info & Claims SIGGRAPH '06: ACM SIGGRAPH 2006 CoursesJuly 2006 Pages 6–eshttps://doi.org/10.1145/1185657.1185737Online:30 July 2006Publication History 0citation16DownloadsMetricsTotal Citations0Total Downloads16Last 12 Months2Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Numerical and experimental studies of the flow in the nip region of a partially intermeshing co‐rotating twin‐screw extruder (1990)

Abstract The flow pattern within a partially intermeshing co‐rotating twin‐screw extruder is three dimensional and extremely complex. In order to simplify the problem, a slice perpendicular to the axis of the twin‐screw extruder has been considered for flow analysis as a two‐dimensional or a quasi‐three‐dimensional problem. The flow in this slice may be considered to consist of a nip region (located between the two screws) and a translation region in which the movement of the material is very similar to the one found in single‐screw extruders. The flow in these two regions have been studied separately. This paper presents the numerical and experimental results of the nip region study. The flow division in the nip region has been quantified and results are presented in terms of a flow division ratio X f . The flow field patterns have also been obtained. Newtonian as well as non‐Newtonian behavior has been investigated. The influences of such factors as (i) the geometry (the radius of the barrel, radius of the screw, distance between the two screws), (ii) the material properties (the power‐law index for shear rate dependent viscosity), and (iii) processing conditions (the screw speed), have also been studied.
Surface potential measurements of vacuum ultraviolet irradiated Al/sub 2/O/sub 3/, Si/sub 3/N/sub 4/, and SiO/sub 2/ (2005)

Vacuum ultraviolet radiation (VUV), generated during plasma processing of semiconductors devices can induce charge on dielectric materials. By exposing dielectric coated wafers to synchrotron radiation of varying energy, it is possible to separate the photoemission and photoconductive effects, both of which result in an increase in the surface potential of the dielectric. Maps of the surface potential induced on the dielectrics by VUV can be obtained by the use of a Kelvin probe.
Abstract 1434: Uncovering the mechanism of adaptive resistance to RET inhibitors in RET rearranged thyroid cancer (2021)

Abstract Kinase inhibitors are a critical tool for cancer treatment, but their efficacy is limited by resistance mechanisms. In thyroid and lung cancer RET gene rearrangements result in constitutive MAPK pathway activation and drive malignancy. While treatment with new selective RET inhibitors has been associated with significant clinical responses, a majority of patients experience a partial response or disease stabilization as their best clinical outcome. Resistance to RET inhibitors has emerged as a clinical problem requiring new treatment strategies. Using a combination of drug screening, proteomic, and biochemical profiling we identified a strategy to overcome adaptive resistance to RET inhibitors in human thyroid cancer cell lines and vertebrate animal models. The identification of alternative signaling pathways that reactivates ERK signaling as a mechanism of resistance to RET inhibitors provides an opportunity to anticipate resistance to selective RET inhibitors and use combination therapy that leads to more significant and durable anti-tumor responses in patients with RET rearranged cancers. Citation Format: Renuka Raman, Jacques Villefranc, Timothy Ullmann, Jessica Thiesmeyer, Viviana Anelli, Chantal Pauli, Rohan Bareja, Kenneth Wha Eng, Princesca Dorsaint, David Wilkes, Shaham Beg, Reid Shaw, Michael Churchill, Naveen Gumpeni, Theresa Scognamiglio, Mark Rubin, Carla Grandori, Juan Mosquera, Juan Mosquera, Juan Mosquera, Noah Dephoure, Andrea Sboner, Olivier Elemento, Yariv Houvras. Uncovering the mechanism of adaptive resistance to RET inhibitors in RET rearranged thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1434.
ChemInform Abstract: Trichlorosilane‐Mediated Stereoselective Reduction of C=N Bonds (2011)

Abstract Review: 52 refs.
Reduction of calcium flux from the extracellular region and endoplasmic reticulum by amorphous nano-silica particles owing to carboxy group addition on their surface (2017)

Several studies have reported that amorphous nano-silica particles (nano-SPs) modulate calcium flux, although the mechanism remains incompletely understood. We thus analyzed the relationship between calcium flux and particle surface properties and determined the calcium flux route. Treatment of Balb/c 3T3 fibroblasts with nano-SPs with a diameter of 70 nm (nSP70) increased cytosolic calcium concentration, but that with SPs with a diameter of 300 or 1000 nm did not. Surface modification of nSP70 with a carboxy group also did not modulate calcium flux. Pretreatment with a general calcium entry blocker almost completely suppressed calcium flux by nSP70. Preconditioning by emptying the endoplasmic reticulum (ER) calcium stores slightly suppressed calcium flux by nSP70. These results indicate that nSP70 mainly modulates calcium flux across plasma membrane calcium channels, with subsequent activation of the ER calcium pump, and that the potential of calcium flux by nano-SPs is determined by the particle surface charge.
Synthesis, Spectroscopic, and in Vitro Photosensitizing Efficacy of Ketobacteriochlorins Derived from Ring-B and Ring-D Reduced Chlorins via Pinacol–Pinacolone Rearrangement (2011)

In this report, we present a regioselective oxidation of a series bacteriochlorins, which on reacting with either ferric chloride (FeCl(3)) or 2,3-dichloro-5,6-dicyanobenzoquinone (DDQ) yielded the corresponding ring-B or ring-D reduced chlorins. The effect of the number of electron-withdrawing groups present at the peripheral position, with or without a fused isocyclic ring (ring-E), did not make any significant difference in regioselective oxidation of the pyrrole rings. However, depending on the nature of substituents, the intermediate bis-dihydroxy bacteriochlorins on subjecting to pinacol-pinacolone reaction conditions gave various ketochlorins. The introduction of the keto-group at a particular position in the molecule possibly depends on the stability of the intermediate carbocation species. The newly synthesized bacteriochlorins show strong long-wavelength absorption and produced significant in vitro (Colon26 cells) photosensitizing ability. Among the compounds tested, the bacteriochlorins containing a keto-group at position 7 of ring-B with cleaved five-member isocyclic ring showed the best efficacy.
A Key 6G Challenge and Opportunity—Connecting the Base of the Pyramid: A Survey on Rural Connectivity (2020)

Providing connectivity to around half of the world population living in rural or underprivileged areas is a tremendous challenge, but, at the same time, a unique opportunity. Access to the Internet would provide the population living in these areas a possibility to progress on the educational, health, environment, and business levels. In this article, a survey of technologies for providing connectivity to rural areas, which can help address this challenge, is provided. Although access/fronthaul and backhaul techniques are discussed in this article, it is noted that the major limitation for providing connectivity to rural and underprivileged areas is the cost of backhaul deployment. In addition, energy requirements and cost-efficiency of the studied technologies are analyzed. In fact, the challenges faced for deploying an electricity network, as a prerequisite for deploying communication networks, are huge in these areas, and they are granted an important share of the discussions in this article. Furthermore, typical application scenarios in rural areas are discussed, and several country-specific use cases are surveyed. The main initiatives by key international players aiming to provide rural connectivity are also described. Moreover, directions for the future evolution of rural connectivity are outlined in this article. Although there is no single solution that can solve all rural connectivity problems, building gradually on the current achievements in order to reach ubiquitous connectivity, while taking into account the particularities of each region and tailoring the solution accordingly, seems to be the most suitable path to follow.
RTPORT: the 5G-based Model-Driven real Time Module for General Cargo Management (2019)

Major maritime carriers are globally demanding improvements in the efficiency of port operations. Cargo carried by ships must be loaded and unloaded quickly with minimal stopover time in the port. This is driving the implementation of more efficient processes and the reorganization of technologies at the terminals: connected platforms, cloud-based services, service-oriented architectures (SOA), sensors and other IoT technologies (M2M), augmented/virtual reality (AR/VR), autonomous transportation, next generation mobile networks (5G) and blockchain-based technology. RTPORT, the 5G-based Model-Driven Real Time Module, will allow a better management of general cargo resulting in faster throughput compared to traditional human-driven communications. A full reorganized mobile network (5G), connecting smart sensors with cloud resources will be used in order decrease environmental impacts by optimizing trucks movements in the port area as well as improving workers’ safety and enhance their skills with digital tools. The effectiveness of RTPORT will be evaluated in the Port of Livorno for EU Horizon 2020-funded Capacity with a Positive<br> Environmental and Societal Footprint - Ports in the Future (COREALIS) project and it represents the starting point for the deployment of the Physical Internet.<br>
Studies on Pyrrolopyrimidines as Selective Inhibitors of Multidrug-Resistance- Associated Protein in Multidrug Resistance (2004)

Multidrug resistance mediated by P-glycoprotein (Pgp) or multidrug-resistance-associated protein (MRP) remains a major obstacle for successful treatment of cancer. Inhibition of Pgp and MRP transport is important for high efficacy of anticancer drugs. While several Pgp inhibitors have entered clinical trials, the development of specific MRP1 inhibitors is still in its infancy. In our screening program, we have identified a pyrrolopyrimidine (4) as a novel and selective MRP1 inhibitor. Subsequent SAR work on the 4-position of the template revealed the phenethylpiperazine side chain as a potent replacement of the benzylthio group of the lead molecule. Introduction of groups at the 2-position seems to have no detrimental effect on activity. Modifications to the nitrile group at the 7-position resulted in the identification of analogues with groups, such as amides, with superior pharmacokinetic profiles. In vivo efficacy has been demonstrated by xenograft studies on selected compounds.
Demonstration of microwave frequency shifting by use of a highly chirped mode-locked fiber laser (1998)

We report an experimental demonstration of a photonic microwave shifter using a highly chirped mode-locked fiber laser. The system is based on dispersive compression or expansion of highly chirped optical pulses that are amplitude modulated by the microwave signal. Using this technique, we demonstrated frequency shifting of a microwave signal from 10 GHz down to 5 GHz and up to 25 GHz.
Study of the secondary structure of the luteinizing hormone releasing factor using intramolecular charge transfer complexes (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudy of the secondary structure of the luteinizing hormone releasing factor using intramolecular charge transfer complexesBernard Donzel, Jean Rivier, and Murray GoodmanCite this: Biochemistry 1977, 16, 12, 2611–2618Publication Date (Print):June 14, 1977Publication History Published online1 May 2002Published inissue 14 June 1977https://pubs.acs.org/doi/10.1021/bi00631a006https://doi.org/10.1021/bi00631a006research-articleACS PublicationsRequest reuse permissionsArticle Views18Altmetric-Citations13LEARN 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
Sparse R-CNN: End-to-End Object Detection with Learnable Proposals (2021)

We present Sparse R-CNN, a purely sparse method for object detection in images. Existing works on object detection heavily rely on dense object candidates, such as k anchor boxes pre-defined on all grids of image feature map of size H × W. In our method, however, a fixed sparse set of learned object proposals, total length of N, are provided to object recognition head to perform classification and location. By eliminating HWk (up to hundreds of thousands) hand-designed object candidates to N (e.g. 100) learnable proposals, Sparse R-CNN completely avoids all efforts related to object candidates design and many-to-one label assignment. More importantly, final predictions are directly output without non-maximum suppression post-procedure. Sparse R-CNN demonstrates accuracy, run-time and training convergence performance on par with the well-established detector baselines on the challenging COCO dataset, e.g., achieving 45.0 AP in standard 3× training schedule and running at 22 fps using ResNet-50 FPN model. We hope our work could inspire re-thinking the convention of dense prior in object detectors. The code is available at: https://github.com/PeizeSun/SparseR-CNN.