gebhart/patrepeval huggingface dataset:
Asymmetric Aldol Reaction Catalyzed by the Anion of an Ionic Liquid (2012)

Herein we report the synthesis of a chiral imidazolium salt derived from trans-L-hydroxyproline and its applications as a catalyst for the asymmetric aldol reaction. By performing the aldol reaction in [Bmim]NTf(2) as a solvent, we report excellent isolated yields of the aldol product (up to 99%), as well as modest to excellent selectivities (dr superior to 99:1. ee up to 89%). Mechanistic insights and the origins of the selectivity of the aldol reaction are discussed on the basis of the results obtained with two catalytic imidazolium salts having different H-bonding potential.
Complexes between Activated Protein C and Protein C Inhibitor Measured with a New Method (2001)

A first clinical evaluation has been made of the performance of a newly devised immunofluorometric assay for measuring plasma concentrations of activated protein C (APC) in complex with protein C inhibitor (PCI). The method was compared with testing for other markers of hypercoagulability in a case-control study comprising 123 patients with clinical suspicion of deep vein thrombosis (DVT). The diagnosis was confirmed by ascending phlebography, and the thrombotic burden estimated with a newly developed scoring system. Receiver operating characteristics (ROC) curves calculated to demonstrate the discriminatory capacity of the methods, showed the area under the curves (AUCs) to be similar for the APC-PCI and D-dimer methods. However, in contrast to the D-dimer method, the APC-PCI method measures a well-defined analyte, a prerequisite for reliable comparisons of future clinical studies. The APC-PCI method appears to be particularly useful as a marker for detection of recently developed proximal thrombi.
Locator/ID Separation Protocol Delegated Database Tree (LISP-DDT) (2017)

This document describes the Locator/ID Separation Protocol Delegated
Database Tree (LISP-DDT), a hierarchical distributed database that
embodies the delegation of authority to provide mappings from LISP
Endpoint Identifiers (EIDs) to Routing Locators (RLOCs). It is a
statically defined distribution of the EID namespace among a set of
LISP-speaking servers called nodes. Each DDT node is configured
as authoritative for one or more EID-prefixes, along with the set of
RLOCs for Map-Servers or child DDT nodes to which more-specific EID-
prefixes are delegated.
Association of Variants in the<i>LIPC</i>and<i>ABCA1</i>Genes with Intermediate and Large Drusen and Advanced Age-Related Macular Degeneration (2011)

LIPC and ABCA1 are related to intermediate and large drusen, as well as advanced AMD. CFH, C3, C2, and ARMS2/HTRA1 are associated with large drusen and advanced AMD. Genes may have varying effects on different stages of AMD.
Estradiol gel (2006)

Estradiol gel can effectively reduce menopause symptoms with minimal side effects. Long-term safety data of estradiol gel are required.
High-Efficiency Reverse (5′→3′) Synthesis of Complex DNA Microarrays (2018)

DNA microarrays are important analytical tools in genetics and have recently found multiple new biotechnological roles in applications requiring free 3' terminal hydroxyl groups, particularly as a starting point for enzymatic extension via DNA or RNA polymerases. Here we demonstrate the highly efficient reverse synthesis of complex DNA arrays using a photolithographic approach. The method is analogous to conventional solid phase synthesis but makes use of phosphoramidites with the benzoyl-2-(2-nitrophenyl)-propoxycarbonyl (BzNPPOC) photolabile protecting group on the 3'-hydroxyl group. The use of BzNPPOC, with more than twice the photolytic efficiency of the 2-(2-nitrophenyl)-propoxycarbonyl (NPPOC) previously used for 5'→3' synthesis, combined with additional optimizations to the coupling and oxidation reactions results in an approximately 3-fold improvement in the reverse synthesis efficiency of complex arrays of DNA oligonucleotides. The coupling efficiencies of the reverse phosphoramidites are as good as those of regular phosphoramidites, resulting in comparable yields. Microarrays of DNA surface tethered on the 5' end and with free 3' hydroxyl termini can be synthesized quickly and with similarly high stepwise coupling efficiency as microarrays using conventional 3'→5' synthesis.
Reducing waiting times in diagnosing patients with endometrial cancer (2005)

The NHS Cancer Plan (2000) is a five-year policy framework for improving cancer outcomes and patients’ experiences of cancer care in England. It contains a series of ambitious targets for reducing the length of time patients wait for diagnosis and treatment, and the government expects the NHS to meet these targets in full by the end of this year. This article describes an award-winning nurse-led service developed to improve waiting times for endometrial cancer.
Phylogenetic basis for a taxonomic dissection of the genus<i>Clostridium</i> (1999)

The 16S rDNA-based phylogenetic analysis of the genus Clostridium has been completed by determination of the phylogenetic position of the type strains of 15 species and two non-validated species. These strains are members of phylogenetic clusters I, III, IV, V, IX, XIVa and XVIII as defined previously by Collins et al. [Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Members of the genus Clostridium span a large evolutionary distance and the genus is not a phylogenetically coherent taxon but is intermixed with members of different genera, exhibiting a combination of Clostridium- and non-Clostridium-type properties. Anaerobacter polyendosporus, Syntrophococcus sucromutans and Acetivibrio multivorans also cluster within the radiation of Clostridium species. Although several taxa have been described for former Clostridium species with distinct phenotypic properties, the majority of Clostridium species, which are not members of the core cluster I, can at present not be reclassified as long as taxon-specific, phenotypic properties are not available.
Interferon Regulatory Factor-Two Restricts Expression of Interferon-Stimulated Genes to the Endometrial Stroma and Glandular Epithelium of the Ovine Uterus1 (2001)

Interferon tau (IFNtau) is the signal for maternal recognition of pregnancy in ruminants. The positive effects of IFNtau on IFN-stimulated gene (ISG) expression are mediated by ISG factor 3 (ISGF3), which is composed of signal transducer and activator of transcription (Stat) 1, Stat 2, and IFN regulatory factor-9 (IRF-9), and by gamma-activated factor (GAF), which is a Stat 1 homodimer. Induction of ISGs, such as ISG17 and 2',5'-oligoadenylate synthetase, by IFNtau during pregnancy is limited to the endometrial stroma (S) and glandular epithelium (GE) of the ovine uterus. The IRF-2, a potent transcriptional repressor of ISG expression, is expressed in the luminal epithelium (LE). This study determined effects of the estrous cycle, pregnancy, and IFNtau on expression of Stat 1, Stat 2, IRF-9, IRF-1, and IRF-2 genes in the ovine endometrium. In cyclic ewes, Stat 1, Stat 2, IRF-1, and IRF-9 mRNA and protein were detected at low levels in the S and GE. During pregnancy, expression of these genes increased only in the S and GE. Expression of IRF-2 was detected only in the LE and superficial GE (sGE) of both cyclic and pregnant ewes. In cyclic ewes, intrauterine administration of IFNtau stimulated Stat 1, Stat 2, IRF-9, and IRF-1 expression in the endometrium. Ovine IRF-2 repressed transcriptional activity driven by IFN-stimulated response elements that bind ISGF3, but not by gamma-activation sequences that bind GAF. These results suggest that IRF-2 in the LE and sGE restricts IFNtau induction of ISGs to the S and GE. In the S and GE, IFNtau hyperactivation of ISG expression likely involves formation and actions of the transcription factors ISGF3 and, perhaps, IRF-1.
Antimutagenic Activity of Gigantol from <i>Dendrobium nobile</i> (1997)

A methanol extract from Dendrobium nobile showed a suppressive effect on umu gene expression of the SOS response in Salmonella typhimurium TA1535/pSK1002 against the mutagen 2-(2-furyl)-3-(5-nitro-2-furyl)acrylamide (furylfuramide). The methanol extract from D. nobile was re-extracted with n-hexane, dichloromethane, 1-butanol, and water, respectively. A suppressive compound in the n-hexane extract fraction was isolated by SiO2 column chromatography and chemical fractionation and was identified as gigantol by EI-MS and 1H and 13C NMR spectroscopy. Gigantol suppressed the SOS-inducing activity of furylfuramide in the umu test. Gene expression was suppressed 90% at <0.73 μmol/mL, and the ID50 value was 0.35 μmol/mL. Gigantol was also assayed with the mutagen 3-amino-1,4-dimethyl-5H-pyrido[4,3b]indole (Trp-P-1), which requires liver metabolizing enzymes, and it suppressed the SOS-inducing activity of Trp-P-1 in the umu test. Gene expression was suppressed 91% at <0.73 μmol/mL, and the ID50 value was 0.32 μmol/mL. In addition, gigantol was assayed for suppressive effect on UV irradiation in the umu test, where it showed suppression of the SOS-inducing activity caused by UV irradiation. Gene expression was suppressed 84% at <0.36 μmol/mL, and the ID50 value was 0.17 μmol/mL. The antimutagenic activities of gigantol against furylfuramide and Trp-P-1 were assayed by an Ames test using S. typhimurium TA100, which indicated that gigantol suppressed each of the mutagens. Keywords: Dendrobium nobile; gigantol; Orchidaceae; antimutagenic activity; umu test; Ames test
Early infection and progression of cystic fibrosis lung disease (2002)

Chronic Pseudomonas aeruginosa infection is the major limitation in overall survival of patients with cystic fibrosis, and elective bronchoscopy shows that infection with this organism starts at a very early age. Early infection with nonmucoid P. aeruginosa gradually develops into chronic infection, characterized by the presence of microcolonies of alginate-producing (mucoid) P. aeruginosa in the bronchial tree. Chronic infection cannot be cured, but aggressive antimicrobial treatment will prolong life expectancy and decrease morbidity. It has, however, over the last decade become evident that early antimicrobial treatment of the initial infection with nonmucoid strains can prevent or at least postpone transition into chronic (mucoid) infection. This treatment strategy is likely to dramatically improve the prognosis of patients with cystic fibrosis in the immediate future.
Documenting and treating acute pain in children (2011)

Pain management for children in emergency departments is often inconsistent or inadequate due to a lack of appropriate protocols. This article discusses the development of such a protocol in an ED in Sydney, Australia, and how its implementation led to a huge improvement in documentation of pain scores and in the appropriateness of pain relief given.
Thermofluid analysis of staggered and inline pin fin heat sinks (2002)

A numerical study is performed of relative thermal and hydrodynamic efficiency of staggered and inline pin fin heat sinks. Advantages of the staggered over the inline design from the standpoint of cooling efficiency (under the same flow conditions) are evident. However, the staggered design has greater airflow resistance, leading to less airflow through the heat sink and a decrease in thermal efficiency. In this study we analyzed two sample pin fin heat sinks using the commercial CFD software Coolit. The heat sinks were placed on the bottom wall of a rectangular duct with thermally insulated walls. A heat source was located at the base of the heat sink. The major parameters of the process were the inlet velocity and the extent of shrouding defined by the distance from the heat sink to the duct walls. Both were varied to account for a wide range of flow conditions. The maximum temperature rise and the pressure drop over the heat sink were monitored. The main conclusion of this study was that the inline design is thermally superior to the staggered design for all but the fully-shrouded heat sinks. Another finding is that in a given geometry the non-dimensional pressure drop over a heat sink is almost constant, which indicates small viscous drag. Finally, the three-dimensional flow patterns and temperature fields obtained in the course of computations give insight into the complex heat sink airflow and heat transfer phenomena and suggest design improvements.
Intermodulation distortion elimination for analog photonics link based on integrated dual-parallel Mach-Zehnder modulator (2014)

We report a total third-order intermodulation distortion elimination method for analog photonics link based on integrated dual-parallel Mach-Zehnder modulator. Theoretical analysis and experiment verification of 33.57 dB suppression are both carried out.
Multi-armed bandit problems with dependent arms (2007)

We provide a framework to exploit dependencies among arms in multi-armed bandit problems, when the dependencies are in the form of a generative model on clusters of arms. We find an optimal MDP-based policy for the discounted reward case, and also give an approximation of it with formal error guarantee. We discuss lower bounds on regret in the undiscounted reward scenario, and propose a general two-level bandit policy for it. We propose three different instantiations of our general policy and provide theoretical justifications of how the regret of the instantiated policies depend on the characteristics of the clusters. Finally, we empirically demonstrate the efficacy of our policies on large-scale real-world and synthetic data, and show that they significantly outperform classical policies designed for bandits with independent arms.
Large scale production of high aspect ratio graphite nanoplatelets with tunable oxygen functionality (2011)

High aspect ratio graphite nanoplatelets with tunable oxygen functionality are prepared using a two-step scalable process consisting of expansion by thermal plasma processing followed by exfoliation with ultrasonic processing. The result of this process is graphite nanoplatelets in high yield with an average particle size distribution ranging from monolayer graphene up to 10 nm in thickness, 1 to 30 μm in length/width, and a tunable carbon to oxygen (C/O) ratio from 50 to 200 without requiring any special separation or isolation techniques such as sedimentation or centrifugation. It has been demonstrated for the first time that an intermediate level of oxygen functionalization improves the ability to exfoliate expanded graphite without having a detrimental effect on electrical conductivity.
Androstenediol in Canine Spermatic Vein Blood and Its Significance in Testosterone Biosynthesis<i>in Vivo</i> (1968)

A change in androgen content of spermatic vein blood of anesthetized dogs after luteinizing hormone (LH: NIH-LH-B3) administration was studied using gas-liquid chromatography. A definite increase in content of androstenediol as well as testosterone, androstenedione and dehydroepiandrosterone was noted. Androstenediol was identified by several chromatographic procedures and by infrared spectroanalysis. In situ and in vivo perfusion study revealed the conversion of dehydroepiandrosterone-4-11C to androstenediol-14C and testosterone-14C, and that of androstenediol-3H to testosterone-3H by the dog testis. Perfusion of androstenedione-4-14C or testosterone-4-14C via the spermatic artery produced no demonstrable androstenediol-14C in canine spermatic vein blood. These findings strongly support the view that androstenediol is one of the important intermediates in testosterone biosynthesis by dog testis. (Endocrinology83: 992, 1968)
Blood-Brain Barrier Permeability Is Increased After Acute Adult Stroke But Not Neonatal Stroke in the Rat (2012)

The immaturity of the CNS at birth greatly affects injury after stroke but the contribution of the blood-brain barrier (BBB) to the differential response to stroke in adults and neonates is poorly understood. We asked whether the structure and function of the BBB is disrupted differently in neonatal and adult rats by transient middle cerebral artery occlusion. In adult rats, albumin leakage into injured regions was markedly increased during 2-24 h reperfusion but leakage remained low in the neonates. Functional assays employing intravascular tracers in the neonates showed that BBB permeability to both large (70 kDa dextran) and small (3 kDa dextran), gadolinium (III)-diethyltriaminepentaacetic acid tracers remained largely undisturbed 24 h after reperfusion. The profoundly different functional integrity of the BBB was associated with the largely nonoverlapping patterns of regulated genes in endothelial cells purified from injured and uninjured adult and neonatal brain at 24 h (endothelial transcriptome, 31,042 total probe sets). Within significantly regulated 1266 probe sets in injured adults and 361 probe sets in neonates, changes in the gene expression of the basal lamina components, adhesion molecules, the tight junction protein occludin, and matrix metalloproteinase-9 were among the key differences. The protein expression of collagen-IV, laminin, claudin-5, occludin, and zonula occludens protein 1 was also better preserved in neonatal rats. Neutrophil infiltration remained low in acutely injured neonates but neutralization of cytokine-induced neutrophil chemoattractant-1 in the systemic circulation enhanced neutrophil infiltration, BBB permeability, and injury. The markedly more integrant BBB in neonatal brain than in adult brain after acute stroke may have major implications for the treatment of neonatal stroke.
CRD: Fast Co-clustering on Large Datasets Utilizing Sampling-Based Matrix Decomposition. (2008)

The problem of simultaneously clustering columns and rows (co-clustering) arises in important applications, such as text data mining, microarray analysis, and recommendation system analysis. Compared with the classical clustering algorithms, co-clustering algorithms have been shown to be more effective in discovering hidden clustering structures in the data matrix. The complexity of previous co-clustering algorithms is usually O(m × n), where m and n are the numbers of rows and columns in the data matrix respectively. This limits their applicability to data matrices involving a large number of columns and rows. Moreover, some huge datasets can not be entirely held in main memory during co-clustering which violates the assumption made by the previous algorithms. In this paper, we propose a general framework for fast co-clustering large datasets, CRD. By utilizing recently developed sampling-based matrix decomposition methods, CRD achieves an execution time linear in m and n. Also, CRD does not require the whole data matrix be in the main memory. We conducted extensive experiments on both real and synthetic data. Compared with previous co-clustering algorithms, CRD achieves competitive accuracy but with much less computational cost.
Process integration of single-wafer technology in a 300-mm fab, realizing drastic cycle time reduction with high yield and excellent reliability (2003)

In this paper, we discuss a new technology implemented with single-wafer processing for a 300-mm fab. Newly developed equipment and chemicals reduce the process time and provide cost savings. The combination of fully automated systems and single-wafer processing significantly reduces queuing time. The process has been re-integrated to eliminate long time processes and make it suitable for single-wafer technologies. As a result, a very aggressive cycle time (0.25 days/layer) with high yield, in double-polysilicon, sextuple-metal, 0.18-/spl mu/m logic process has been demonstrated. High-performance devices with excellent reliability are also obtained. A new methodology for detecting parametric errors effectively in the early stages of production is implemented for quick yield ramp up.
Surface plasmon resonance (SPR) spectrometry as a tool to analyze nucleic acid-protein interactions in crude cellular extracts. (2011)

This study presents proof-of-principle application showing that label-free affinity enrichment surface plasmon resonance (SPR) biosensor binding is able to semiquantitatively detect molecular DNA-protein interactions in crude cellular extracts in a real-time ligand fishing analysis study. Crude cell extracts obtained from a confluent HT-28 human adenocarcinoma cell line, synchronized to the G(0)/G(1) phase of the cell cycle, were extracted in a chaotropic medium and cryopreserved in liquid nitrogen. Various immunoprecipitation antibodies were used against defective human excision and mismatch repair genes, hDDB2 and hMSH2, respectively, which theoretically allow for protein binding to DNA ligands in their native conformation. A set of biotinylated DNA target sequence heteroduplexes were also utilized for binding hDDB2 and hMSH2, prepared by heating a biotinylated oligonucleotide strand with an equimolar amount of the complementary strand to form a DNA duplex for hMSH2; a UV-irradiated duplex was employed for hDDB2 instead of an irradiated single-strand DNA to enhance binding. SDS was used to regenerate heteroduplex-modified chips that were used in a BIAcore 2000 SPR instrument at 25°C. Results showed that hMSH2 does not bind preferentially to the heteroduplex-complementary pair. In contrast, hDDB2 was found to bind preferentially to the UV-irradiated version of the heteroduplex-complementary pair. It is concluded that the choice of antibodies with appropriate epitopes is crucial to the success of these SPR binding studies because of enhanced specificity.
Cytokine profiles in seronegative volunteers immunized with a recombinant canarypox and gp120 prime-boost HIV-1 vaccine (2000)

These data indicate that this vaccination regimen was inducing both Th1- and Th2-type responses to HIV-1 envelope antigens. This prime-boost vaccination approach elicited T cell help for the generation of cytotoxic T lymphocyte responses as well as help for antibody production and so promises to generate a broad HIV-1-specific immune response.
“New Methods of Statistical Economics,” revisited: Short versus long tails and Gaussian versus power‐law distributions (2008)

Abstract The standard “Brownian” model of competitive markets asserts that the increments of price (or of its logarithm) are statistically independent and Gaussian, implying that price itself is a continuous function of time. This model arose in 1900, at an immediately high level of perfection, in the work of L. Bachelier. In many fields of science it became a classic. But for financial prices it is sharply—even overwhelmingly—contradicted by conspicuous and strong symptoms of non‐independence, nonGaussianity, and discontinuity. Since 1963, the author has been tackling those symptoms one by one: first, by incorporating strongly non‐Gaussian marginal distributions (1963), then by incorporating strong long‐term dependence (1965), and finally by combining those two features by introducing the new notion of multifractality (1968 and since). The goal of this article is modest: largely borrowing from the author's previous articles and books, much of it collects and adapts a few brief “teasers” or “appetizers” meant to promote and assist the future development of a framework for a realistic description of actual financial fluctuations. © 2008 Wiley Periodicals, Inc. Complexity, 2009