gebhart/patrepeval huggingface dataset:
A New Magnesium-Catalyzed Doubly Diastereoselective anti-Aldol Reaction Leads to a Highly Efficient Process for the Total Synthesis of Lactacystin in Quantity (1998)

A new process is described for metal-catalyzed doubly diastereoselective Mukaiyama aldol coupling of a chiral tertiary α-amino aldehyde and an achiral silyl enol ether to form selectively an anti-aldol product. The metal requirement is strict, since of several salts tested only MgI2 functions as an effective catalyst. The MgI2-catalyzed aldol greatly facilitates the total synthesis of lactacystin (1) and the corresponding β-lactone (2), microbial products which are potent and selective inhibitors of proteasome function, cell cycle progression, and gene regulation. The method also allows the synthesis of analogues of 1 in which the 7β-methyl group of lactacystin is replaced by higher alkyl or aralkyl groups. Detailed experimental procedures are presented for the optimized synthesis of lactacystin on the scale required to meet the current needs of many hundreds of biological laboratories.
Protein kinase C (1987)

The combined application of protein structural techniques, immunochemistry, and molecular biology has permitted an analysis of the differential expression of the genes for the three related protein kinases, C-alpha, -beta, and gamma. The evidence now suggests that the type of protein kinase C in a cell may govern the nature and mechanisms of functional responses.
Preventing Venous Thromboembolic Disease in Patients Undergoing Elective Hip and Knee Arthroplasty (2011)

This guideline supersedes a prior one from 2007 on a similar topic. The work group evaluated the available literature concerning various aspects of patient screening, risk factor assessment, and prophylactic treatment against venous thromboembolic disease (VTED), as well as the use of postoperative mobilization, neuraxial agents, and vena cava filters. The group recommended further assessment of patients who have had a previous venous thromboembolism but not for other potential risk factors. Patients should be assessed for known bleeding disorders, such as hemophilia, and for the presence of active liver disease. Patients who are not at elevated risk of VTED or for bleeding should receive pharmacologic prophylaxis and mechanical compressive devices for the prevention of VTED. The group did not recommend specific pharmacologic agents and/or mechanical devices. The work group recommends, by consensus opinion, early mobilization for patients following elective hip and knee arthroplasty. The use of neuraxial anesthesia can help limit blood loss but was not found to affect the occurrence of VTED. No clear evidence was established regarding whether inferior vena cava filters can prevent pulmonary embolism in patients who have a contraindication to chemoprophylaxis and/or known VTED.
The CMS tracker operation and performance at the Magnet Test and Cosmic Challenge (2008)

During summer 2006 a fraction of the CMS silicon strip tracker was operated in a comprehensive slice test called the Magnet Test and Cosmic Challenge (MTCC). At the MTCC, cosmic rays detected in the muon chambers were used to trigger the readout of all CMS sub-detectors in the general data acquisition system and in the presence of the 4 T magnetic field produced by the CMS superconducting solenoid. This document describes the operation of the Tracker hardware and software prior, during and after data taking. The performance of the detector as resulting from the MTCC data analysis is also presented.
Optimization of Projected Phase Change Memory for Analog In‐Memory Computing Inference (2023)

Abstract Phase change memory (PCM) is one of the most promising candidates for non‐von Neumann based analog in‐memory computing–particularly for inference of previously‐trained deep neural networks (DNN). It is shown that PCM electrical properties can be tuned systematically using a projection liner, which is designed for resistance drift mitigation, in the manufacturable mushroom PCM. A systematic study of the electrical properties‐including resistance values, memory window, resistance drift, read noise, and their impact on the accuracy of large neural networks of various types and with tens of millions of weights is performed. It is sown that the DNN accuracy can be improved by the PCM with liner for both the short term and long term after programming, due to reduced resistance drift and read noise, respectively, despite the trade‐off of reduced memory window. The liner conductance, PCM device characteristics, and network inference accuracy with PCM memory window and reset state conductance is correlated, which allows us to identify the device optimization space to achieve better short term and long term accuracy for large neural networks.
Growth and Differentiation of C2 Myogenic Cells Are Dependent on Serum Response Factor (1996)

In order to study to what extent and at which stage serum response factor (SRF) is indispensable for myogenesis, we stably transfected C2 myogenic cells with, successively, a glucocorticoid receptor expression vector and a construct allowing for the expression of an SRF antisense RNA under the direction of the mouse mammary tumor virus long terminal repeat. In the clones obtained, SRF synthesis is reversibly down-regulated by induction of SRF antisense RNA expression by dexamethasone, whose effect is antagonized by the anti-hormone RU486. Two kinds of proliferation and differentiation patterns have been obtained in the resulting clones. Some clones with a high level of constitutive SRF antisense RNA expression are unable to differentiate into myotubes; their growth can be blocked by further induction of SRF antisense RNA expression by dexamethasone. Other clones are able to differentiate and are able to synthesize SRF, MyoD, myogenin, and myosin heavy chain at confluency. When SRF antisense RNA expression is induced in proliferating myoblasts by dexamethasone treatment, cell growth is blocked and cyclin A concentration drops. When SRF antisense RNA synthesis is induced in arrested confluent myoblasts cultured in a differentiation medium, cell fusion is blocked and synthesis of not only SRF but also MyoD, myogenin, and myosin heavy chain is inhibited. Our results show, therefore, that SRF synthesis is indispensable for both myoblast proliferation and myogenic differentiation.
Polarization independent microphotonic circuits (2005)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.
Optimizing the mapping of low-density parity check codes on parallel decoding architectures (2002)

We study the problem of optimizing the mapping of LDPC codes on parallel machines to minimize the communication cost. To reduce the search space, the problem is solved in two stages: clustering, and cluster allocation. We propose a simplified clustering technique based on a modified min-cut algorithm that reduces the search complexity from O(n/sup 2/) to O(n). It was found that most of the locality is exploited by the clustering operation, which results in a 40-52% improvement in the total communication cost over random mapping. For large networks, cluster allocation is much more costly and results in only 1-8% additional improvement in unidirectional and bi-directional torus topologies. We compared the performance of two different approaches for cluster allocation. The first one is bused on min-cut algorithm, and the second one is based on a genetic algorithm. It was found that the min-cut based approach is better for small network sizes. For large network sizes with the number of clusters /spl ges/64, the genetic based approach becomes more attractive.
The Capsule of Cryptococcus neoformans Modulates Phagosomal pH through Its Acid-Base Properties (2018)

Phagosomal acidification is a critical cellular mechanism for the inhibition and killing of ingested microbes by phagocytic cells. The acidic environment activates microbicidal proteins and creates an unfavorable environment for the growth of many microbes. Consequently, numerous pathogenic microbes have developed strategies for countering phagosomal acidification through various mechanisms that include interference with phagosome maturation. The human-pathogenic fungus <i>Cryptococcus neoformans</i> resides in acidic phagosomes after macrophage ingestion that actually provides a favorable environment for replication, since the fungus replicates faster at acidic pH. We hypothesized that the glucuronic acid residues in the capsular polysaccharide had the capacity to affect phagosomal acidity through their acid-base properties. A ratiometric fluorescence comparison of imaged phagosomes containing <i>C. neoformans</i> to phagosomes containing beads showed that the latter were significantly more acidic. Similarly, phagosomes containing nonencapsulated <i>C. neoformans</i> cells were more acidic than those containing encapsulated cells. Acid-base titrations of isolated <i>C. neoformans</i> polysaccharide revealed that it behaves as a weak acid with maximal buffering capacity around pH 4 to 5. We interpret these results as indicating that the glucuronic acid residues in the <i>C. neoformans</i> capsular polysaccharide can buffer phagosomal acidification. Interference with phagosomal acidification represents a new function for the cryptococcal capsule in virulence and suggests the importance of considering the acid-base properties of microbial capsules in the host-microbe interaction for other microbes with charged residues in their capsules.<b>IMPORTANCE</b><i>Cryptococcus neoformans</i> is the causative agent of cryptococcosis, a devastating fungal disease that affects thousands of individuals worldwide. This fungus has the capacity to survive inside phagocytic cells, which contributes to persistence of infection and dissemination. One of the major antimicrobial mechanisms of host phagocytes is to acidify the phagosomal compartment after ingestion of microbes. This study shows that the capsule of <i>C. neoformans</i> can interfere with full phagosomal acidification by serving as a buffer.
Sonic Hedgehog-activated engineered blood vessels enhance bone tissue formation (2012)

Large bone defects naturally regenerate via a highly vascularized tissue which progressively remodels into cartilage and bone. Current approaches in bone tissue engineering are restricted by delayed vascularization and fail to recapitulate this stepwise differentiation toward bone tissue. Here, we use the morphogen Sonic Hedgehog (Shh) to induce the in vitro organization of an endothelial capillary network in an artificial tissue. We show that endogenous Hedgehog activity regulates angiogenic genes and the formation of vascular lumens. Exogenous Shh further induces the in vitro development of the vasculature (vascular lumen formation, size, distribution). Upon implantation, the in vitro development of the vasculature improves the in vivo perfusion of the artificial tissue and is necessary to contribute to, and enhance, the formation of de novo mature bone tissue. Similar to the regenerating callus, the artificial tissue undergoes intramembranous and endochondral ossification and forms a trabecular-like bone organ including bone-marrow-like cavities. These findings open the door for new strategies to treat large bone defects by closely mimicking natural endochondral bone repair.
Systemic Therapy of Neuroendocrine Neoplasia: Single Center Experience from a Cohort of 110 Consecutive Cases (2020)

Further prospective studies are warranted to help stratify available options for therapeutic intervention in NEN patients.
Sequence‐Based Design of α/β‐Peptide Foldamers That Mimic BH3 Domains (2008)

Faltung annehmen! Foldamere haben sich als vielseitige Gerüste beim Design funktioneller Makromoleküle bewährt. Bei einem direkten Ansatz wird die Primärsequenz eines natürlichen α-Peptidliganden in einer Weise verändert, dass ein α/β-Peptid mit vergleichbarer Bindungsaffinität für die Zielproteine des α-Peptids resultiert (siehe Schema).
Left Ventricular Pacing Minimizes Diastolic Ventricular Interaction, Allowing Improved Preload-Dependent Systolic Performance (2004)

This study suggests a potentially important mechanism by which LV pacing may produce hemodynamic benefit. LV pacing minimizes external constraint to LV filling, resulting in an increase in effective filling pressure; the consequent increase in LV end-diastolic volume increases stroke volume via the Starling mechanism.
Iron-57 NMR of heme proteins. Chemical shift anisotropy of ferrocytochrome c (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIron-57 NMR of heme proteins. Chemical shift anisotropy of ferrocytochrome cLars BaltzerCite this: J. Am. Chem. Soc. 1987, 109, 11, 3479–3481Publication Date (Print):May 1, 1987Publication History Published online1 May 2002Published inissue 1 May 1987https://pubs.acs.org/doi/10.1021/ja00245a060https://doi.org/10.1021/ja00245a060research-articleACS PublicationsRequest reuse permissionsArticle Views109Altmetric-Citations17LEARN 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
Guidelines for the Application of NAD(P)H Regenerating Glucose Dehydrogenase in Synthetic Processes (2013)

Abstract Glucose dehydrogenase (GDH) is frequently used for the reduction of NAD + and NADP + in bench‐ and industrial‐scale syntheses because the coenzyme regenerating system GDH is easy to apply, robust and relatively inexpensive. To optimize the application of this long known coenzyme regeneration system we investigated the commonly applied Bacillus GDH and characterized this enzyme by its kinetic features in the presence of substrates and products at pH 6.4 and 8.0. Three substrates/products were found to inhibit GDH considerably: (i) the reaction product glucono‐1,5‐lactone, (ii) the reduced coenzyme NAD(P)H and (iii) the oxidized coenzyme NAD(P) + . The inhibition of GDH under several process conditions was modeled using the determined kinetic constants. It was found that the GDH regeneration system is strongly inhibited by the usually applied conditions. This study provides the rate equation of the GDH reaction and simulations of this coenzyme regenerating system leading to an improved prediction and, thus, to a faster scale‐up and increased efficiency of NAD(P)H‐dependent synthetic processes.
Comparison between a Shack-Hartmann and a distorted grating wavefront sensor (2003)

A comparison of the wavefronts recorded simultaneously by a Shack-Hartmann and a Distorted Grating Wavefront Sensor (DGWFS) has been completed. The DGWFS is a phase diversity/wavefront curvature type of sensor using a grating to generate the multiple image planes. Data were collected under simulated propagation conditions using the Advanced Concept Laboratory at Lincoln Laboratory. The sensors were arranged such that both recorded a time varying sample of the wavefront at exactly the same time. Dynamic and static comparisons of the two sensors under conditions that ranged from a benign path, D/r<sub>0</sub> = 2, to a propagation condition with significant scintillation, D/r<sub>0</sub> =50, were completed. The data show that the two techniques measure static, low amplitude, on the order of a few waves, aberrations with little difference. Under conditions where there are significant aberrations, the wavefronts measured by the two sensors show notable differences with the DGWFS exhibiting a smoothed, low passed, rendition of the wavefront. As the aberrations increase to produce scintillated condition the differences become more pronounced.
Glycogen Synthase Kinase-3 (GSK-3) Inhibitory Activity and Structure–Activity Relationship (SAR) Studies of the Manzamine Alkaloids. Potential for Alzheimer’s Disease (2007)

Manzamine A and related derivatives isolated from a common Indonesian sponge, Acanthostrongylophora, have been identified as a new class of GSK-3beta inhibitors. The semisynthesis of new analogues and the first structure-activity relationship studies with GSK-3beta are also reported. Moreover, manzamine A proved to be effective in decreasing tau hyperphosphorylation in human neuroblastoma cell lines, a demonstration of its ability to enter cells and interfere with tau pathology. Inhibition studies of manzamine A against a selected panel of five different kinases related to GSK-3beta, specifically CDK-1, PKA, CDK-5, MAPK, and GSK-3alpha, show the specific inhibition of manzamine A on GSK-3beta and CDK-5, the two kinases involved in tau pathological hyperphosphorylation. These results suggest that manzamine A constitutes a promising scaffold from which more potent and selective GSK-3 inhibitors could be designed as potential therapeutic agents for Alzheimer's disease.
Defects in DNA repair genes and sensitivity to cisplatin based neoadjuvant chemotherapy (NAC) for bladder cancer. (2015)

4514 Background: Cisplatin based NAC prior to cystectomy is standard of care for MIBC, with 40-50% expected to respond with ≤ pT1N0M0. Biomarkers predictive of response are lacking. Methods: MIBC pts who received 3 cycles of cisplatin based NAC on 1 of 2 prospective multicenter clinical trials were included. Pts treated with accelerated methotrexate, vinblastine, doxorubicin + cisplatin (AMVAC) provided the discovery set [n = 34, 15/34 (44%) ≤ pT1N0M0]. Pts treated with dose dense gemcitabine + cisplatin (DDGC) provided the validation set [n = 24, 11/24 (46%) ≤ pT1N0M0]. DNA from pre-treatment tumor tissue underwent sequencing for all coding exons of 287 cancer-related genes and was analyzed for presence of base substitutions, indels, copy number alterations, and selected re-arrangements. The mean number of variants and variant status for each gene were correlated with response using two-sample t-test and Fisher’s exact tests. Variant data were used to create a classification tree to discriminate responders vs. non-responders in the AMVAC discovery cohort. The resulting decision rule was then tested in the independent DDGC validation set. Overall survival analysis was performed using Kaplan-Meier. Results: Pts with pT0 had significantly more alterations than those with residual tumor in both the AMVAC discovery (p = .024) and DDGC validation (p = 0.018) set. In the AMVAC discovery set, alteration in ≥ 1 of the three DNA repair genes ATM, RB1 or FANCC predicted for ≤ pT1N0M0 (p < 0.001, 87% sensitivity, 100% specificity) and improved overall survival (OS) (p = 0.007). This test remained predictive for ≤ pT1N0M0 in the DDGC validation set (p = 0.033), with a trend towards improved OS (p = 0.055) at short median follow up of 16.75 mo. Conclusions: Alterations in ≥ 1 of ATM, RB1 and FANCC predict response to cisplatin based chemotherapy defined as ≤ pT1N0M0 in both our AMVAC discovery and DDGC validation sets. We hypothesize that defects in these genes, which are important for maintenance of chromatin structure and DNA repair, confer sensitivity to DNA damaging chemotherapy and explain the accumulation of alterations seen among pts with pT0. Further validation is planned.
Channel Modeling and Performance Analysis in Watermarking (2006)

Digital watermarking is equivalent to a communication problem, where the embedded message goes through an effective channel consisting of the image interference, noise, and attacks. Understanding and quantifying the performance of watermarking strategies, i.e., bit error rates (BER), under various scenarios is key to the further development of this field. Although a few watermark-specific and attack-specific results do exist, a general framework for performance evaluation of watermarking has not been available to date. Motivated by results in communication theory, we propose a modeling and performance evaluation strategy that uses the concept of intersymbol interference (ISI) channels and applies to a variety of embedding methods as well as various attacks. We first show the applicability of this general approach to several watermarks and attacks. We derive pair wise error probability equations that are used to calculate BER bounds. These bounds are verified by simulations. Finally, we study the use of MMSE detectors in watermarking, and give some results
New Charge-Transfer Mechanism across the Interface between Selenium and Polystyrene Hexylmethacrylate (1979)

Thin-film structures composed of amorphous Se and polystyrene-hexylmethacrylate copolymer sandwiched between two semitransparent Al electrodes have been studied using transient photocurrent techniques. The dependence of the observed "transit time" on the applied voltage showed lengthening as the voltage was increased, contrary to the expected behavior in the time-of-flight experiments! This novel effect has been associated with a rate-limited charge-transfer mechanism across the Se-polymer interface.
Transport challenges facing a next‐generation hybrid satellite Internet (2010)

Abstract This paper considers the transport layer implications by assuming a position where satellite networks form one integrated component of a hybrid Internet architecture. It reviews the key role of transport protocols in providing a reliable and robust end‐to‐end Internet service. A history of TCP protocol evolution from a satellite perspective is followed by focussing on the role of protocol‐enhancing proxies in satellite systems and how these have impacted the introduction of new Internet transport techniques. Current transport research issues are identified and related to two new architectural approaches to highlight the expected performance benefits and derive the implications on the design of geostationary satellite Internet systems as the network evolves toward a next‐generation Internet. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Torsional Piezoresistive Effect in Polysilicon (2010)

This paper presents a microelectromechanical test device and calibration method for finding torsional piezoresistive coefficients for micro sensing applications. The test device consists of a slider-crank connected to two torsional legs. The slider-crank creates torsional stress in the legs which causes a change in the electrical resistance through the legs. A model that predicts the effects of a scissor hinge on the slider-crank is presented. Torsional stresses in the legs are calculated and the legs are discretized into long parallel resistors and the stresses applied to each resistor. Assuming a second-order piezoresistance, an optimization is then done to find the piezoresistive coefficients by changing them until the model prediction fits the test data. These coefficients can be used to predict angular displacement from resistance measurements in fully integrated torsional sensors.