gebhart/patrepeval huggingface dataset:
Behavior of Complex Knots in Single DNA Molecules (2003)

We used optical tweezers to tie individual DNA molecules in knots. Although these knots become highly localized under tension, they remain surprisingly mobile and undergo thermal diffusion with classical random walk statistics. The diffusion constants of knots with different complexities correlate with theoretical calculations of knot sizes. We show that this correlation can be explained by a simple hydrodynamical model of "self-reptation" of the knot along a polymer.
The risk of withdrawing chronic anticoagulation because of acute GI bleeding. (1996)

We conclude that symptomatic thromboembolism can occur after the transient withdrawal of chronic anticoagulation for acute GI bleeding but that it does not occur frequently.
Evaluation of Sideritis species as agents for food supplements (2022)

According to the World Health Organization, 80% of the general population in developed countries use supplements to support specific physiological functions. Natural products are a rich source of molecules that can be effectively used in dietary supplements, as a means of promoting health, relieve and prevent [1], [2]. The current study aims to investigate the chemical content of three Sideritis water extracts, specifically S. scardica, S. perfoliata and S. raeseri and evaluate their potential to be used in food supplements. The samples were treated according to predefined conditions. The plant materials were dried, pulverized and water extracts were prepared. HPLC-DAD, HPTLC, and LC-HRMS were used for analysis and chemical markers were identified. The extracts showed many similarities concerning their chemical profile and most differences were quantitative. Phenolic acids, like 5-caffeoylquinic acid and p-coumaric acid 4-O-glucoside and phenylethanoid glycosides, like forsythoside B and verbascoside were detected. The major metabolites of the extracts were acetylated flavonoids glycosides, such as isoscutellarein 7-O-[6′′′-O-acetyl]-allosyl(1 → 2)glucoside, 4′-O-methylhypolaetin 7-O-[6′′′-O-acetyl]-allosyl(1 → 2)glucoside and isoscutellarein 7-O-[6′′′-O-acetyl]-allosyl(1 → 2)-[6′′-O-acetyl]-glucoside. The extracts were fractionated and purified with preparative column chromatography and prep-HPLC and the structures of the isolated compounds were identified with NMR. The extracts were evaluated for their antioxidant activity, showing IC50 values in the DPPH assay less than 50 µg/ml. In conclusion, Sideritis species provide water extracts rich in bioactive constituents that can be used in the production of food supplements.
Development of an Efficient Synthesis of the Pyrrolquinolone PHA-529311 (2006)

An efficient synthesis of N-(4-chlorobenzyl)-2-(2-hydroxyethyl)-8-(morpholin-4-ylmethyl)-6-oxo-6H-pyrrol[3.2.1-ij]quinoline-5-carboxamide (5) was developed. The route was chosen due to its reasonable length (seven steps), solubility of intermediates, and capabilities of the pilot and production facilities. The critical transformations in this route were the selective iodination of an aniline, formation of the quinolone, and Sonogashira coupling/pyrrole formation. In addition, removal of residual palladium and copper from the penultimate and final products, which was of lower concern during the discovery phase of development, became a difficult process chemistry issue on scale-up.
In vitro assessment of interaction of blood with model surfaces. (1978)

An in vitro system for the assessment of blood compatibility of artificial surfaces is described. Anticoagulated human whole blood was pumped through columns of beads and then analyzed for evidence of platelet retention and the release of platelet constitutents. Platelets were retained on the columns by adhesion to the beads and by aggregation. Experiments were conducted with PVAc, PC, PMA and PS beads to provide data on the reproducibility of the system and the effects of anticoagulants and RBC concentration on platelet adhesion and release. The system is versatile, inexpensive, reproducibile, and also suitable for studies of the effects of pharmacologic agents and other aspects of platelet-artificial surface interaction.
Classical 7-norbornenyl cation. Competition between aryl and alkenyl functions in stabilizing 7-aryl-7-norbornenyl cations (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTClassical 7-norbornenyl cation. Competition between aryl and alkenyl functions in stabilizing 7-aryl-7-norbornenyl cationsHerman G. Richey Jr., James D. Nichols, Paul G. Gassman, Allison F. Fentiman Jr., S. Winstein, M. Brookhart, and Ronald K. LustgartenCite this: J. Am. Chem. Soc. 1970, 92, 12, 3783–3784Publication Date (Print):June 1, 1970Publication History Published online1 May 2002Published inissue 1 June 1970https://pubs.acs.org/doi/10.1021/ja00715a041https://doi.org/10.1021/ja00715a041research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations14LEARN 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
Development of Splice Modulators as Potent Anti-Tumor Therapeutics (2021)

Since its discovery in 1977, the study of alternative RNA splicing has led to its implication as a major factor in the onset of disease. The recent identification of natural product and synthetic modulators of RNA splicing has opened access for a chemical-based interrogation of RNA splicing processes and has provided a new platform for molecular discovery and therapy. While splice modulators have entered clinical trials, limited clinical efficacy in splicing factor mutation driven malignancies, such as acute myeloid leukemia, has remained a challenge. There is a pressing unmet medical need for developing potent small molecule splice modulators (SPLMs) for the treatment of a broad array of malignancies characterized by splicing deregulation. However, the inability to practically access gram scale lead molecules with viable pharmacological properties continues to hinder their application. The dissertation herein details two projects that addresses these issues: 1. A scalable approach to prepare 17S-FD-895, a potent in vivo active splice modulator, that not only provided material to enable clinical translation but also furthered lead validation by expanding the structure-activity relationships that guide splice modulation. 2. Utilizing established synthetic methods and RNA isolation strategies to develop and profile a suite of splice modulator analogues to expand the structure-activity relationships of SPLMs and to gain a clearer understanding of the mechanisms underlying inherent gene selectivity in splicing. \n
An Open-Source, Interoperable Architecture for Generating Real-Time Surgical Team Cognitive Alerts from Heart-Rate Variability Monitoring (2023)

Clinical alarm and decision support systems that lack clinical context may create non-actionable nuisance alarms that are not clinically relevant and can cause distractions during the most difficult moments of a surgery. We present a novel, interoperable, real-time system for adding contextual awareness to clinical systems by monitoring the heart-rate variability (HRV) of clinical team members. We designed an architecture for real-time capture, analysis, and presentation of HRV data from multiple clinicians and implemented this architecture as an application and device interfaces on the open-source OpenICE interoperability platform. In this work, we extend OpenICE with new capabilities to support the needs of the context-aware OR including a modularized data pipeline for simultaneously processing real-time electrocardiographic (ECG) waveforms from multiple clinicians to create estimates of their individual cognitive load. The system is built with standardized interfaces that allow for free interchange of software and hardware components including sensor devices, ECG filtering and beat detection algorithms, HRV metric calculations, and individual and team alerts based on changes in metrics. By integrating contextual cues and team member state into a unified process model, we believe future clinical applications will be able to emulate some of these behaviors to provide context-aware information to improve the safety and quality of surgical interventions.
The Use of Three‐Dimensional Shape and Electrostatic Similarity Searching in the Identification of a Melanin‐Concentrating Hormone Receptor 1 Antagonist (2006)

To aid in the identification of novel melanin-concentrating hormone receptor 1 (MCHr1) antagonists, a unique virtual library of readily synthesized molecules was designed and assembled based on 323 monomer compounds containing reactive moieties in combination with 30 core molecules having diamine functionality. The resulting library of 3,129,870 molecules was searched using three-dimensional shape similarity measures that were complimented with a novel electrostatic distribution similarity-matching algorithm. One of the top scoring hits in this library was synthesized and characterized for MCHr1 antagonism, where it exhibited at least a threefold improvement in binding affinity and cellular potency relative to the parent MCHr1 ligand. This work demonstrates that the use of shape and electrostatic similarity matching in combination with a well-designed virtual library can be used to augment standard medicinal chemistry techniques.
The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices (1989)

One method of obtaining useful information about the physical chemistry of peptide/bilayer interactions is to relate thermodynamic parameters of the interactions to structural parameters obtained by diffraction methods. We report here the results of the application of this approach to interactions of hydrophobic tripeptides of the form Ala-X-Ala-O-tert-butyl with lipid bilayers. The thermodynamic constants (delta Gt, delta Ht, and delta St) for the transfer of the tripeptides from water into DMPC vesicles were determined for X = Leu, Phe, and Trp and found to be consistent with those expected for hydrophobic interactions above the phase transition of DMPC. Combining these results with the earlier ones of Jacobs and White [(1986) Biochemistry 25, 2605-2612], the favorable free energies of transfer with different amino acids in the -X- position increase in the order Gly less than Ala less than Leu less than Phe less than Trp in agreement with the Nozaki and Tanford [(1971) J. Biol. Chem. 246, 2211-2217] hydrophobicity scale. Determination of the location of Ala-[2H5]Trp-Ala-O-tert-butyl in oriented DOPC bilayers by neutron diffraction shows that the most hydrophobic peptide of the series is confined to the bilayer headgroup/water region. Refinement of the diffraction measurements shows that only 13% of the tryptophan is associated with the hydrocarbon core. The distribution of the water tends to mirror that of the peptide. Unlike peptide-free bilayers, 5% of the water penetrates the hydrocarbon, which is about 100-fold greater than expected. A quantitative thermodynamic analysis of the interfacial binding of the peptides suggests that (1) the hydrophobic interactions are 60-70% complete upon binding at the bilayer interface, (2) the interface is likely to play an important role in helix formation and insertion, (3) the hydrogen bond status of amino acid side chains is crucial to insertion, and (4) an a priori lack of knowledge of the status of such bonds could limit the precision of hydrophobicity plots. We introduce an interfacial hydrophobicity scale, IFH(h), with a variable hydrogen bond parameter (h) that permits one to consider explicitly hydrogen bonding in transbilayer helix searches.
Recurrence after endoscopic piecemeal mucosal resection for large sessile colorectal polyps (2010)

EPMR is safe, but should be applied carefully in malignant polyps. Close follow-up endoscopic examinations are necessary for early detection of recurrence.
Efficient diffusion of superdense lithium via atomic channels for dendrite-free lithium–metal batteries (2021)

A novel concept of atomic channels within bulk graphite is proposed for the fast diffusion of multi-layered close-packed Li. The feasibility of bulk-diffusion of superdense Li have been verified in the dendrite-free Li metal batteries.
Benchmarking Monolithic 3D Integration for Compute-in-Memory Accelerators: Overcoming ADC Bottlenecks and Maintaining Scalability to 7nm or Beyond (2020)

This paper presents 3D NeuroSim, a benchmark framework of monolithic 3D (M3D) integrated compute-in-memory (CIM) accelerators. To address the challenges of analog-to-digital converter (ADC) overhead and scaling limitations caused by high write voltage in emerging nonvolatile memory (eNVM), we propose partitioning the circuit modules in hybrid technology nodes across two stacked tiers with massive inter-tier vias. This framework features versatile back-end-of-line (BEOL)-compatible transistors, including laser-recrystallized silicon transistor and oxide transistor, and analyzes the thermal profile for M3D integration. Finally, we benchmark the CIM accelerators for VGG-8 on CIFAR-10 and reveal the substantial benefits in energy efficiency of a hybrid M3D architecture (45nm eNVM array+7nm ADC and logic).
NanoART, NeuroAIDS and CNS Drug Delivery (2009)

A broad range of nanomedicines is being developed to improve drug delivery for CNS disorders. The structure of the blood-brain barrier (BBB), the presence of efflux pumps and the expression of metabolic enzymes pose hurdles for drug-brain entry. Nanoformulations can circumvent the BBB to improve CNS-directed drug delivery by affecting such pumps and enzymes. Alternatively, they can be optimized to affect their size, shape, and protein and lipid coatings to facilitate drug uptake, release and ingress across the barrier. This is important as the brain is a sanctuary for a broad range of pathogens including HIV-1. Improved drug delivery to the CNS would affect pharmacokinetic and drug biodistribution properties. This article focuses on how nanotechnology can serve to improve the delivery of antiretroviral medicines, termed nanoART, across the BBB and affect the biodistribution and clinical benefit for HIV-1 disease.
21.7 Tb/s Field Trial with 22 DP-8QAM/QPSK Optical Superchannels Over 1,503-km of Installed SSMF (2012)

To the best of our knowledge, this is the highest capacity field trial completed to date at 21.7 Tb/s. 22 optical superchannels with flexible modulation formats were transmitted over 1,503 km installed SSMF using digital coherent detection.
Purification of a phosphatidylinositol-glycan-specific phospholipase C from liver plasma membranes: a possible target of insulin action. (1987)

Insulin stimulates the hydrolysis of a phosphatidylinositol-glycan, resulting in the generation of two related inositol phosphate-glycan enzyme modulators and diacylglycerol. A phosphatidylinositol-glycan-specific phospholipase C that catalyzed this reaction was found in the plasma-membrane fraction of rat liver. The enzymatic activity was measured by the release of diacylglycerol from the glycosylated-phosphatidylinositol-membrane-anchored variant surface glycoproteins of African trypanosomes. The enzyme also catalyzed the production of an inositol phosphate-glycan from an insulin-sensitive phosphatidylinositol-glycan precursor. The enzyme was solubilized with neutral nonionic detergent and purified to near homogeneity by anion-exchange chromatography on DEAE-cellulose, followed by hydrophobic chromatography on butyl-agarose. The resulting enzyme preparation was purified approximately 20,000-fold from whole liver and exhibited one major silver-stained band of Mr 52,000 on NaDodSO4/PAGE. Gel permeation chromatography of the purified activity revealed a Stokes radius of 35 A and an apparent molecular weight of 62,000, suggesting that the enzyme was tightly associated with lipid or detergent but existed as a monomer in its active form. The enzyme was specific for glycosylated phosphatidylinositol; no hydrolysis of phosphatidylinositol, phosphatidylinositol 4,5-bisphosphate, or phosphatidylcholine was observed. The enzyme was calcium independent and thiol activated. These data suggest a role for the phosphatidylinositol-glycan-specific phospholipase C as an effector for some of the metabolic actions of insulin.
Message Delays in Repeated-Service Tandem Connections (1981)

One of the inherent complexities associated with queueing models for store and forward data communications networks arises from the fact that messages typically preserve their length as they traverse the system. The interarrival and service sequences at queues internal to the network are thus dependent, making standard methods of analysis realistically inappropriate (except in an approximate sense). In an effort to find methods of dealing with such nonstandard queueing systems, a model for sparsely-connected networks (or network segments) called a message channel has been studied. A message channel is defined as a tandem connection of single server queues in which the successive service times experienced by any particular customer are scaled versions of the same random variable. A number of recent results concerning the delay properties of such systems are presented. These include: ordering relations for the successive waiting times in the channel; characterizations of waiting time properties under extreme conditions (simultaneous arrival of all customers): and, simple bounds on performance parameters for systems with uniformly bounded service processes. A general integral equation for the distribution of the equilibrium cumulative waiting time in <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GI/(G/1)^{M}</tex> queueing systems (which are instances of uniform message channels) is also derived. The solution of this equation for systems with discrete service time distributions and Poisson arrivals is indicated and explicitly exhibited for the case of two discrete levels (corresponding to a message switching system with two packet classes).
UV-Induced Modification of Fluorocarbon Polymer: Effect of Treatment Atmosphere and Aging on Dissolution in Organic Solvent (2012)

In back-end of line (BEOL), the use of fluorocarbon-containing plasmas such as CF 4 and C 4 F 8 for patterning of low-k dielectrics with k-value ~2.3-2.5 can result in the presence of a highly fluorinated layer, deposited on the sidewalls and bottom of the trenches [1,. This polymer layer must be removed prior to subsequent processing steps to achieve good adhesion and coverage of materials (metals) deposited in the etched features. However, it is known that this type of fluorocarbon polymer is chemically inert to many existing wet clean solutions, including aqueous solutions such as fluoride ion-containing or highly alkaline solutions, and solvent mixtures [2]. Exposure of the polymer to UV irradiation (λ 200 nm) with doses 3 J/cm 2 significantly modifies the polymer film, which results in substantial removal ability in a subsequent wet clean process. Polymer film modification was shown to be efficient either by using a narrow band single wavelength source with λ = 254 nm [ or by a broad band UV source with λ~200-300 nm [.
Safety of retained microcatheters: an evaluation of radiofrequency heating in endovascular microcatheters with nitinol, tungsten, and polyetheretherketone braiding at 1.5 T and 3 T (2013)

Substantial heating of nitinol braided microcatheters occurred and was a function of SAR level and geometric considerations. SAR and time limitations on MR scanning are proposed for patients with this microcatheter entrapped in their vasculature. In contrast, tungsten and PEEK braided microcatheters showed potential safe use in MRI.
ChemInform Abstract: The Effect of Fluorine on the Diastereoselectivity of the Addition of α‐Oxyradicals to 3‐Fluoro‐2,3‐dihydro‐1H‐λ6‐thiophene‐1,1‐dione. (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.
Ambient carboxylation on a supported reversible CO2 carrier: ketone to β-keto ester (2011)

A reversible CO2 carrier (RCC) has been developed to perform carboxylation of ketone to β-ketoester under ambient CO2 pressure and temperature. RCC has been synthesized by immobilizing 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) on methylhydrosiloxane support and reacting with CO2 with 100% degree of functionalisation. RCC is found to be recyclable and shows retention of activity in 5 recycles. CO2 absorption under ambient temperature and desorption at 120 °C renders the material suitable for carrying out carboxylation reactions at 25 °C with excellent yields. The yield of the reaction can reach up to 100% with TON 200 in 4 h. The extent of the reaction primarily depends upon enol content of the substrate. β-Ketoacid produced during the reaction can be isolated and converted to its corresponding methyl ester derivative by reacting with methyl iodide.
TCR Vaccines against a Murine T Cell Lymphoma: A Primary Role for Antibodies of the IgG2c Class in Tumor Protection (2004)

Tumor-associated proteins can act as effective immunotherapeutic targets. Immunization with tumor TCR protein conjugated to the immunogenic protein keyhole limpet hemocyanin (KLH) protects mice from tumor challenge with the murine T cell lymphoma C6VL. The immune mechanisms responsible for this tumor protection are of interest for designing more effective vaccine strategies. Previous studies using depletion experiments had suggested a CD8-mediated component of protection induced by TCR-KLH vaccines. In this study we used CD8alpha knockout, micro MT, and FcgammaR knockout mice to investigate the relative roles of CD8+ T cells and Ab in protective immunity induced by TCR-KLH immunization. We found that CD8+ T cells are not required for tumor protection, although they may contribute to protection. Vaccine-induced Abs are sufficient to mediate protection against this murine T cell lymphoma through an FcR-dependent mechanism. This was confirmed with Ab transfers, which protect challenged mice. Additionally, recombinase-activating gene 1(-/-) splenocytes can mediate Ab-dependent cellular cytotoxicity against this tumor in the presence of bound anti-TCR Abs. IFN-gamma knockout mice demonstrated a requirement for IFN-gamma, probably via generation of IgG2c Abs, in vaccine-induced tumor protection. IFN-gamma knockout mice were not protected by immunization and had a severe impairment in IgG2c Ab production in response to immunization. Although mock-depleted anti-TCR Abs could transfer tumor protection, IgG2c-deficient anti-TCR Abs were unable to transfer tumor protection to wild-type mice. These results suggest that TCR-KLH vaccine-induced tumor protection in the C6VL system is primarily attributable to the induction of IgG2c Abs and humoral immunity.