gebhart/patrepeval huggingface dataset:
Distributed I/O with ParaMEDIC: Experiences with a Worldwide Supercomputer (2008)

Achieving high performance for distributed I/O on a wide-area network continues to be an elusive holy grail. Despite enhancements in network hardware as well as software stacks, achieving high-performance remains a challenge. In this paper, our worldwide team took a completely new and non-traditional approach to distributed I/O, called ParaMEDIC: Parallel Metadata Environment for Distributed I/O and Computing, by utilizing application-specific transformation of data to orders-of-magnitude smaller meta-data before performing the actual I/O. Specifically, this paper details our experiences in deploying a large-scale system to facilitate the discovery of missing genes and constructing a genome similarity tree by encapsulating the mpiBLAST sequence-search algorithm into ParaMEDIC. The overall project involved nine different computational sites spread across the U.S. generating more than a petabyte of data, that was “teleported ” to a large-scale facility in Tokyo for storage. Keywords: distributed I/O, bioinformatics, BLAST, grid computing, cluster computing. 1
ChemInform Abstract: Synthesis of Tertiary Phosphine Oxides Mediated by SmCp2 or SmI2 (1996)

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.
The Wolf-Rayet star population in the most massive giant H II regions of M33 (1990)

We have obtained narrow-band images of NGC 604, NGC 595, and NGC 592, the most massive giant H II regions (GHRs) in M33, in order to study their Wolf-Rayet content. These images reveal the presence of nine candidates in NGC 604 (seven WN, two WC), 10 in NGC 595 (nine WN, one WC), and two in NGC 592 (two WN). Precise positions and estimated magnitudes are given for the candidates, half of which have so far been confirmed spectroscopically as genuine W-R stars. The flux in the emission lines of all candidates is comparable to that of normal Galactic W-R stars of similar subtype. A few of the putative "superluminous W-R stars" are shown to be close visual double or multiple stars; their newly estimated luminosities are now more compatible with those of normal W-R stars. NGC 595 seems to be overabundant in W-R stars for its mass compared to other GHRs, while NGC 604 is normal. Factors influencing the W-R/O number ratio in GHRs are discussed: metallicity and age appear to be the most important.
Dynamic uplink-downlink optimization in TDD-based small cell networks (2014)

Dynamic Time-division duplex (TDD) can provide efficient and flexible splitting of the common wireless cellular resources between uplink (UL) and downlink (DL) users. In this paper, the UL/DL optimization problem is formulated as a noncooperative game among the small cell base stations (SCBSs) in which each base station aims at minimizing its total UL and DL flow delays. To solve this game, a self-organizing UL/DL resource configuration scheme for TDD-based small cell networks is proposed. Using the proposed scheme, an SCBS is able to estimate and learn the UL and DL loads autonomously while optimizing its UL/DL configuration accordingly. Simulations results show that the proposed algorithm achieves significant gains in terms of packet throughput in case of asymmetric UL and DL traffic loads. This gain increases as the traffic asymmetry increases, reaching up to 97% and 200% gains relative to random and fixed duplexing schemes respectively. Our results also show that the proposed algorithm is well-adapted to dynamic traffic conditions and different network sizes, and operates efficiently in case of severe cross-link interference in which neighboring cells transmit in opposite directions.
ChemInform Abstract: Oxaziridines and Nitrones as Potential Inhibitors of Bacterial D,D‐Peptidases. (1990)

Abstract The Schiff bases of the acylamino aldehydes (I) are oxidized with a peracid to yield the oxaziridines (III).
Halogen‐substituted triarylpyrazoles: Potential estrogen receptor‐alpha selective radiopharmaceuticals (2001)

Abstract Halogen‐substituted analogs of a pyrazole ligand for the estrogen receptor have been synthesized. These analogs retain much of the affinity preference of the parent ligand for the estrogen receptor alpha subtype (ERα) vs the beta subtype (ERβ).
Full-field singular stresses in a composite laminate weakened by a cylindrical cavity: theory and experiment (2002)

Analytical and experimental investigation of strain fields arising in composite laminates in the vicinity of an open hole and ply interfaces was performed. The singular stress fields, arising at the ply interface and hole edge intersections, were analytically examined by using a novel technique based on superposition of an asymptotic and spline approximation solution. The moiré interferometry technique, providing high spatial resolution and allowing rapid strain variations across a laminate thickness to be recorded, was utilized to experimentally measure the strain distributions throughout the thickness of a [+302/-302/904]3s laminate. The singular solution and the experimentally measured strain showed good agreement for most strain components with some discrepancy for the interlaminar normal strain component.
2-D Tracking Performance Evaluation Using the Cricket Location-Support System (2006)

One of the most interesting applications of sensor networks is the localization and tracking of moving objects. The cricket location-support system (CLS), originally developed at MIT and now distributed by Crossbow Technologies, tracks a moving object using time-difference-of-arrival (TDOA) between radio frequency (RF) and ultrasonic signals. In this work we evaluate the ability of CLS to track people with various levels of mobility within a 2-dimensional space. The results presented here are preliminary results in a larger effort to determine whether or not CLS can be used to track people in a smart assistive technology living space
Linkage Analysis of Alcohol Dependence Symptoms in the Community (2009)

The results support the finding that large community samples can be informative in the study of alcohol-related traits.
Nano-particles transportation using a holographic multiple-vortex tweezer (2009)

Optical vortex tweezers, providing orbital angular momentum to trapped particles, have been successfully demonstrated to sort and deliver micro-particles on a mesoscopic-scale. They used mostly a single vortex, in which a single phase singularity is involved in a wavefront. A multiple-vortex with several phase singularities in a wavefront is potentially capable of controlling several independent optical traps, each with individually specified characteristics, by using a single laser. In this paper, we demonstrate the transport of nano-particles to a specified direction in a mesoscopic field by utilizing three independent vortices with individually specified rotational speed and direction, computer-generated from a single laser beam, for the first time. We call this system a holographic multiple-vortex tweezer. This system, in which many independent vortices with individually specified rotational speed and direction are produced in a mesoscopic field, can thus be adapted to a wide range of applications, including sub-cellular engineering and macromolecular sorting.
Spatial coherence of Nd: glass laser radiation and its second harmonic (1979)

Soft tissue sarcomas are uncommon tumors, and intraduodenal soft tissue sarcoma manifestation is even more rare. Only three cases of intraduodenal sarcomas have been reported in the literature thus far. Here, we report a case of an intraduodenal recurrence of a retroperitoneal sarcoma causing bowel obstruction. This unusual recurrence pattern likely relates to the patient's previous resection and radiation treatment, and highlights the benefits, limitations and follow-up strategies after multimodality treatment.
Residual Urine in an Elderly Female Population: Novel Implications for Oral Estrogen Replacement and Impact on Recurrent Urinary Tract Infection (2004)

Of elderly women those with high PVR were more likely to have recurrent UTIs. Improved bladder function was documented in women receiving oral estrogen replacement therapy.
IMMU-16. PROGRAMMED DEATH LIGAND 1 EXPRESSION AND TUMOR INFILTRATING LYMPHOCYTES IN TUMORS ASSOCIATED WITH NEUROFIBROMATOSIS TYPE 1 AND 2 (2017)

BACKGROUND: Immune checkpoint inhibitors targeting programmed cell death 1 (PD-1) or its ligand (PD-L1) have been shown to be effective in treating subsets of patients with a variety of cancers. Biomarker studies have found positive associations between clinical response rates and PD-L1 expression on tumor cells, as well as the presence of tumor infiltrating lymphocytes (TILs). It is currently unknown whether tumors associated with neurofibromatosis types 1 and 2 (NF1 and NF2) express PD-L1. We hypothesized that NF-associated tumors may express PD-L1 and therefore might be amenable to immunotherapy with immune checkpoint inhibitors. METHODS: We performed immunohistochemistry for PD-L1 (Spring Bioscience, clone SP142), CD3, CD20, CD8, and CD68 in 17 NF1-related tumors (11 dermal neurofibromas and 6 plexiform neurofibromas) and 20 NF2-related tumors (10 meningiomas and 10 schwannomas) using archival formalin-fixed paraffin-embedded tissues. Expression of PD-L1 was considered positive in cases with >5% membranous staining of tumor cells, in accordance with previously published biomarker studies. RESULTS: PD-L1 expression was detected in all tumors, with highest expression levels observed in plexiform neurofibromas and schwannomas. PD-L1 positive tumor cells with >5% membranous staining were observed in 6/6 (100%) of plexiform neurofibromas, 9/11 (82%) of dermal neurofibromas, 7/10 (70%) of schwannomas, and 4/10 (40%) of meningiomas. Sparse to moderate presence of CD68, CD3, or CD8 positive tumor-infiltrating lymphocytes (TILs) was found in 37/37 (100%) of tumor specimens. However, expression of CD20 positive lymphocytes was limited to rare cells detectable in 4/37 (11%) of tumors. CONCLUSION: Our findings indicate that adaptive resistance to cell-mediated immunity plays a major role in the tumor immune environment of NF1 and NF2 associated tumors. Expression of PD-L1 on tumor cells and presence of TILs suggests that these tumors may be responsive to immune therapy with immune checkpoint inhibitors, which should be explored in clinical trials for NF patients.
SMMM-a Secure MultiMedia Mail system (2002)

This paper presents Secure MultiMedia Mail System (SMMM), a secure multimedia electronic mail system that deals with issues related to security, network traffic reduction and storage management of multimedia messages. The composition of M/H (multimedia/hypermedia) messages in SMMM is based on NCM (Nested Context Model), a conceptual model for hypermedia documents. SMMM provides support for multimedia message exchange with security services that can be independently defined for messages and for their contents. SMMM is a platform independent mail system implemented in Java that uses widespread cryptographic mechanisms and is built on top of existing mail transport protocols for interoperability reasons.
Memory Enhancement by Oral Administration of Extract of Eleutherococcus senticosus Leaves and Active Compounds Transferred in the Brain (2019)

The pharmacological properties of <i>Eleutherococcus senticosus</i> leaf have not been clarified although it is taken as a food item. In this study, the effects of water extract of <i>Eleutherococcus senticosus</i> leaves on memory function were investigated in normal mice. Oral administration of the extract for 17 days significantly enhanced object recognition memory. Compounds absorbed in blood and the brain after oral administration of the leaf extract were detected by LC-MS/MS analyses. Primarily detected compounds in plasma and the cerebral cortex were ciwujianoside C3, eleutheroside M, ciwujianoside B, and ciwujianoside A1. Pure compounds except for ciwujianoside A1 were administered orally for 17 days to normal mice. Ciwujianoside C3, eleutheroside M, and ciwujianoside B significantly enhanced object recognition memory. These results demonstrated that oral administration of the leaf extract of <i>E. senticosus</i> enhances memory function, and that active ingredients in the extract, such as ciwujianoside C3, eleutheroside M, and ciwujianoside B, were able to penetrate and work in the brain. Those three compounds as well as the leaf extract had dendrite extension activity against primary cultured cortical neurons. The effect might relate to memory enhancement.
Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh (2003)

A Gram-negative, non-motile, non-spore-forming, moderately halophilic rod (strain SM-1T) was isolated from salt marsh around the junction of the Youngsan River and the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. This organism grew optimally at 37 degrees C and was able to grow at 10 and 45 degrees C. It grew optimally in the presence of 2-3% (w/v) NaCl. The major fatty acids in strain SM-1T were iso-C15:0 and C16:0. Strain SM-1T and Microbulbifer hydrolyticus DSM 11525T were characterized by having ubiquinone-8 as the predominant respiratory lipoquinone. The DNA G+C content of strain SM-1T was 59 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain SM-1T formed a coherent cluster with M. hydrolyticus; this relationship was supported by a bootstrap resampling value of 100%. The level of 16S rDNA identity between strain SM-1T and the type strain of M. hydrolyticus was 98.6%. The mean level of DNA-DNA relatedness between strain SM-1T and the type strain of M. hydrolyticus was 20.6%. Therefore, on the basis of phenotypic properties, phylogeny and genomic data, strain SM-1T should be placed in the genus Microbulbifer as a member of a novel species, for which the name Microbulbifer salipaludis sp. nov. is proposed. The type strain of the novel species is strain SM-1T (=KCCM 41586T =JCM 11542T).
DAP12 Is Required for Macrophage Recruitment to the Lung in Response to Cigarette Smoke and Chemotaxis toward CCL2 (2010)

DAP12 is an adapter protein that associates with several receptors in macrophages. Little is known about the biological role of DAP12 in alveolar macrophages. In genome-wide profiling, we previously found that two DAP12-associated receptors, myeloid DAP12-associated lectin-1 and triggering receptor expressed on myeloid cells 2 (TREM2), were highly induced in alveolar macrophages from habitual smokers. Here, we found that transcript levels for these receptors in alveolar macrophages increased with packs per day of cigarettes smoked and expression of TREM2 protein was increased in lung macrophages of former smokers with emphysema compared with that in controls. In vitro, cigarette smoke directly induced expression of myeloid DAP12-associated lectin-1 and TREM2 and activation of DAP12 signaling in mouse macrophages. To determine whether DAP12 plays a role in cigarette smoke-induced pulmonary inflammation, we exposed wild-type and DAP12-deficient mice to chronic cigarette smoke and found significant reduction in recruitment of alveolar macrophages in DAP12-deficient mice. Because cigarette smoking induces the macrophage chemoattractant CCL2, we tested the chemotactic ability of DAP12-deficient macrophages and found abrogation of chemotaxis toward CCL2 in vitro. Airway administration of CCL2 also resulted in a significant reduction of macrophage recruitment to the lungs of DAP12-deficient mice compared with that in controls. DAP12 was also required for normal macrophage migration in a "scratch" assay. Reconstitution studies revealed that phosphorylation of the DAP12 ITAM was required for normal migration in vitro and association with TREM2 was sufficient for normal migration. These findings indicate that DAP12, possibly through association with TREM2, contributes to alveolar macrophage chemotaxis and recruitment to the lung and may mediate macrophage accumulation in lung diseases such as emphysema.
Vergleichende Wirksamkeitsprüfung neuartiger, auf hauteigenen Ceramidbausteinen basierender kosmetischer Wirkstoffe (2007)

Das Ziel der vorliegenden Arbeit war es, neue kosmetische Wirkstoffe, basierend auf der fermentativ gewonnenen Sphingoidbase Phytosphingosin, zu synthetisieren und ihre Wirksamkeit zu untersuchen. Die Wirksamkeitsuntersuchungen wurden mit Hilfe von zwei verschiedenartigen experimentellen Ansätzen, der DNA-Chiptechnologie und der RT-PCR- Methode, durchgeführt. Bei der DNA-Chiptechnologie wurden die hergestellten Sphingolipidderivate in basalen Modellen (menschliche Keratiniozyten) zu unterschiedlichen Zeitpunkten eingebracht und mittels DNA-Chip-Analyse bewertet. Aus dem Vergleich der Expressionsstärke unter verschiedenen Bedingungen wurden Aussagen zur Wirksamkeit der synthetisierten Verbindungen abgeleitet. Die beobachteten Effekte der Sphingoidderivate bei der DNA-Analyse wurden in komplexen physiologischen Modellen (Hautmodellen) überprüft. Diese Methode berücksichtigt sowohl die topische Applikation der Wirkstoffe, als auch die Barrierefunktion der Epidermis. Die Genexpression wird mittels RT-PCR ermittelt und die Veränderungen der Expressionsstärke von ausgewählten Zielgenen analysiert.
Catalytic enantioselective rearrangements and cycloadditions involving ylides from diazo compounds (2001)

This review summarizes the background and state of the art (as of June 2000) of catalytic enantioselective rearrangements and cycloadditions involving ylides from diazo compounds. The field is still in its infancy, as until a few years ago it was not considered likely that a catalyst, having decomposed a diazo compound to form an ylide, would still be able to exert an influence on subsequent transformations of the ylide. Recent developments have shown this not to be the case and a new era of synthetically important ylide transformations in organic chemistry has begun where appropriate metal–chiral (nonracemic) ligand combinations are starting to be developed to render these transformations enantioselective.
Alginate Materials and Dental Impression Technique: A Current State of the Art and Application to Dental Practice (2018)

Hydrocolloids were the first elastic materials to be used in the dental field. Elastic impression materials include reversible (agar-agar), irreversible (alginate) hydrocolloids and synthetic elastomers (polysulfides, polyethers, silicones). They reproduce an imprint faithfully, providing details of a high definition despite the presence of undercuts. With the removal of the impression, being particularly rich in water, the imprints can deform but later adapt to the original shape due to the elastic properties they possess. The advantages of using alginate include the low cost, a better tolerability on the part of the patient, the ease of manipulation, the short time needed for execution, the instrumentation and the very simple execution technique and possibility of detecting a detailed impression (even in the presence of undercuts) in a single step. A comprehensive review of the current literature was conducted according to the PRISMA guidelines by accessing the NCBI PubMed database. Authors conducted a search of articles in written in English published from 2008 to 2018. All the relevant studies were included in the search with respect to the characteristics and evolution of new marine derived materials. Much progress has been made in the search for new marine derived materials. Conventional impression materials are different, and especially with the advent of digital technology, they have been suffering from a decline in research attention over the last few years. However, this type of impression material, alginates (derived from marine algae), have the advantage of being among the most used in the dental medical field.
Transcriptional Induction of Matrix Metalloproteinase-13 (Collagenase-3) by 1α,25-Dihydroxyvitamin D3 in Mouse Osteoblastic MC3T3-E1 Cells (2001)

The removal of unmineralized matrix from the bone surface is essential for the initiation of osteoclastic bone resorption because osteoclasts cannot attach to the unmineralized osteoid. Matrix metalloproteinases (MMPs) are known to digest bone matrix. We recently reported that among the MMPs expressed in mouse osteoblastic cells, MMP-13 (collagenase-3) was the one most predominantly up-regulated by bone resorbing factors including 1alpha,25-dihydroxyvitamin D3 [1alpha,25(OH)2D3]. In this study, we examined the mechanism of regulation of MMP-13 expression by 1alpha,25(OH)2D3 in mouse osteoblastic MC3T3-E1 cells. 1Alpha,25(OH)2D3 increased steady-state messenger RNA (mRNA) and protein levels of MMP-13. De novo protein synthesis was essential for the induction because cycloheximide (CHX) decreased the effect of 1alpha,25(OH)2D3 on the MMP-13 mRNA level. 1Alpha,25(OH)2D3 did not alter the decay of MMP-13 mRNA in transcriptionally arrested MC3T3-E1 cells; however, it increased the MMP-13 heterogeneous nuclear RNA (hnRNA) level and MMP-13 transcriptional rate. The binding activity of nuclear extracts to the AP-1 binding site, but not to the Cbfa1 binding site, in the MMP-13 promoter region was up-regulated by 1alpha,25(OH)2D3, suggesting the mediation of AP-1 in this transcriptional induction. To determine the contribution of MMPs to bone resorption by 1alpha,25(OH)2D3, the inhibitory effect of BB94, an MMP inhibitor, on resorbed pit formation by mouse crude osteoclastic cells was examined on either an uncoated or collagen-coated dentine slice. BB94 did not prevent resorbed pit formation on uncoated dentine whereas it did on collagen-coated dentine. We therefore propose that the transcriptional induction of MMP-13 in osteoblastic cells may contribute to the degradation of unmineralized matrix on the bone surface as an early step of bone resorption by 1alpha,25(OH)2D3.
Distributed fiber-optic sensing system with OFDR and its applications to structural health monitoring (2009)

In the field of fiber-optic sensing technology, distributed sensors that return a value of the measurand as a function of linear position along an optical fiber are regarded as a promising sensor which can be applied to structural health monitoring (SHM). We have developed a distributed strain sensing technique using long gauge fiber Bragg grating (FBG) based on optical frequency domain reflectometry (OFDR). FBGs functioning as mirrors with wavelengthselective reflectivity have been used as strain or temperature sensors. OFDR is a technique designed to measure backreflections from optical fiber networks and components. In our system, we use a longer gauge FBG whose length is ordinarily more than 100 mm and we can measure strain at an arbitrary position along the FBG. Therefore, we can obtain continuous strain data along the FBG. Furthermore, since the spatial resolution in strain measurements is less than 1 mm, it enables us to measure the strain distribution of stress concentrated area, such as welded and bonded joints, precisely. In this paper, we describe the principle of the distributed sensing technique based on OFDR and the applications to strain monitoring of a bonded joint and a wing box structure.
Chemical Modification of Oligonucleotides: A Novel Approach Towards Gene Targeting (2012)

© 2012 Torigoe and Imanishi, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Chemical Modification of Oligonucleotides: A Novel Approach Towards Gene Targeting