gebhart/patrepeval huggingface dataset:
Assessing transneuronal dysfunction utilizing manganese‐enhanced MRI (MEMRI) (2008)

In this study we utilized manganese-enhanced MRI (MEMRI) to evaluate the in vivo transneuronal efficiency of manganese ion (Mn(2+)) movement as a means to assess overall changes in neuronal function. We designated this extension the manganese transfer index (MTI) value. To evaluate the MTI value as an index of transneuronal physiology we examined both pharmacological agents and different mouse models of neuronal dysfunction. We found that treatment with isoflurane, which attenuates synaptic vesicle release, or memantine, which attenuates postsynaptic uptake of Ca(2+) as well as Mn(2+), resulted in a decrease in the MTI value. Furthermore, we evaluated if changes in the MTI value can be detected in three knockout mice with altered brain function accompanied either with or without neurodegeneration. Our data demonstrate that the MTI values either decreased or increased in response to different functional as well as anatomical changes. These results demonstrate the potential utility of the MTI value as an in vivo index for the detection of changes in neuronal function in animal models of human disease.
Microvascular Changes in the Cystic Lesion of Branch Retinal Vein Occlusion Imaged by Swept-Source Optical Coherence Tomography Angiography (2022)

Vascular structure in the cystic lesions was unpreserved compared to the other lesions in BRVO. These findings may help in understanding the pathophysiology of retinal edema in BRVO.
Self-reference line-dispersion interferometric microscopy (2017)

We have developed a line-scanning interferometric microscope capable of measuring the quantitative phase over a wide continuous spectrum. The sample is illuminated with a spatially coherent broadband light source shaped into a line beam that interferes with itself in a Michelson configuration, coupled with a grating-based spectrometer. The spatial modulation of the interference pattern in the direction orthogonal to the wavelength axis in the spectrograph image plane allows obtaining the spectral quantitative phase along the line illumination in a single measurement. We show the feasibility of the technique by quantifying the refractive index of polystyrene beads immersed in oil and the dispersive properties of live cells over the visible spectrum.
Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood (2019)

Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.
22q11.2 deletion carriers and schizophrenia-associated novel variants (2014)

The penetrance of schizophrenia risk in carriers of the 22q11.2 deletion is high but incomplete, suggesting the possibility of additional genetic defects. We performed whole exome sequencing on two individuals with 22q11.2 deletion, one with schizophrenia and the other who was psychosis-free. The results revealed novel genetic variants related to neuronal function exclusively in the person with schizophrenia (frameshift: KAT8, APOH and SNX31; nonsense: EFCAB11 and CLVS2). This study paves the way towards a more complete understanding of variant dose and genetic architecture in schizophrenia.
Role of Nano-Porosity in Plasma Enhanced Chemical Vapor Deposition of Hermetic low-k a-SiOCN:H Dielectric Barrier Materials (2013)

Critical thresholds for the diffusion of water through low-k a-SiOCN:H dielectrics were investigated using a combination of x-ray reflectivity (XRR) mass density and positronium annihilation lifetime spectroscopy (PALS) pore size metrologies. It was observed that hermetic low-k a-SiOCN:H dielectrics were achieved only at mass densities &gt; 2.2 g/cm3 and when the PALS pore size is less than or equivalent to the molecular diameter of water.
Nucleophilic Substitution Reactions of 4,5-Dichloro-2-methyl-6-nitro-2H-pyridazin-3-one (2001)

4,5-Dichloro-2-methyl-6-nitro-2H-pyridazin-3-one (1) reacts with various substituted phenols and 2-mercaptopyrimidine in the presence of NaH or K 2 CO 3 to give 3(2H)-pyridazinones (4, 5a-9a, 5b-9b, and 7c) in high yields.The regiochemistry was confirmed by X-Ray analysis and nOe experiments.Since the discovery that pyrrolo [2,3-d]pyrimidine or pyrrolo[2,3-c]pyridazine exhibited antiproliferative activity and/or antiviral activity, much attention has been paid to the development of convenient and efficient routes for synthesis of heterocyclic bases. 1 As a modification of heterocyclic base, we reported recently the results for the synthesis of new N-acyclonucleosides containing pyrrolo[2,3-c]pyridazine skeleton utilizing 4,5-dichloro-2-methyl-6-nitro-2H-pyridazin-3-one (1). 2 Then, the nitro group at 6position of compound (1) is essential for the synthesis of fused-heterocycles containing pyridazinone and various trisubstituted pyridazin-3-ones.In connection with nucleophilic substitution reaction of halogens using various trisubstituted pyridazin-3-ones, 3 we reported that the methoxylation of compound (1) under the K 2 CO 3 /MeOH system gave 4-methoxylated pyridazinone (2) as a major product and 5-methoxylated pyridazinone (3) as a minor product in 62 and 28% yields, respectively (Scheme 1). 4 In order to examine the substitution reaction toward nucleophiles and further synthetic application, we investigated in detail the substitution reaction of 4,5-dichloro-2-methyl-6-nitro-2H-pyridazin-3-one (1) with various substituted phenols and mercaptopyrimidine in the presence of NaH or K 2 CO 3 .
Confinement of Silver Triangles in Silver Nanoplates Templated by Duplex DNA (2008)

The use of DNA as a molecular tool in developing novel nanostructures is based on its ability to form self-organizing three-dimensional structures. In the current report the palindromic DNA dodecamer d(CGTAGATCTACG) was employed as a scaffold to fabricate silver nanostructures. The utility of DNA dodecamer to self-assembly into closed pack monolayers and thereby control the formation of silver nanoplates and the consequent confinement is reported.
Comparison of Vertical, Slanted, and Horizontal Wells Productivity in Layered Gas-Condensate Reservoirs (2007)

Abstract The performance of a horizontal (highly slanted) well (HW) or a slanted well (SW), is generally believed to be better than that of a vertical well (VW) due to its greater exposure to the reservoir. However, the costs of drilling and completion are more and the options for monitoring, control and intervention often limited. Gas-condensate reservoirs are increasingly considered as suitable candidates for drilling SWs or HWs. These reservoirs pose special challenges selecting one type or the other due to the complex nature of fluid flow in porous media exhibited by these low interfacial tension systems, which are different from those of conventional gas-oil systems. In this study we have investigated the performances of SW, HW and VW in both single-layer homogenous and layered gas-condensate reservoirs. ECLIPSE 300 compositional reservoir simulator, which includes our inhouse relative permeability (kr) correlation accounting for the coupling (increase in kr by an increase in velocity and interfacial tension) and inertial (decrease in kr by an increase in velocity) effects, has been used to conduct a series of sensitivity analysis on a single-well model resulting in some important practical guidelines. The effect of fluid properties and that of reservoir anisotropy (vertical to horizontal permeability ratio, kv/kh) have also been studied. For homogenous systems, HW and SW have higher productivities. The improvement due to increase in lateral reach is less pronounced at lower kv/kh values especially for SW. In the case of layered reservoirs, the productivity of SW is adversely affected by the extended cross flow from low permeability to high permeability layers. In this case the impact of position of layers and that of kv/kh is more pronounced for SW and both at lower kv/kh. The decrease in velocity around the wellbore of HW decreases the impact of kr velocity dependency on production.
Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin (2019)

Microbial conversion offers a promising strategy for overcoming the intrinsic heterogeneity of the plant biopolymer, lignin. Soil microbes that natively harbour aromatic-catabolic pathways are natural choices for chassis strains, and Pseudomonas putida KT2440 has emerged as a viable whole-cell biocatalyst for funnelling lignin-derived compounds to value-added products, including its native carbon storage product, medium-chain-length polyhydroxyalkanoates (mcl-PHA). In this work, a series of metabolic engineering targets to improve mcl-PHA production are combined in the P. putida chromosome and evaluated in strains growing in a model aromatic compound, p-coumaric acid, and in lignin streams. Specifically, the PHA depolymerase gene phaZ was knocked out, and the genes involved in β-oxidation (fadBA1 and fadBA2) were deleted. Additionally, to increase carbon flux into mcl-PHA biosynthesis, phaG, alkK, phaC1 and phaC2 were overexpressed. The best performing strain - which contains all the genetic modifications detailed above - demonstrated a 53% and 200% increase in mcl-PHA titre (g l<sup>-1</sup> ) and a 20% and 100% increase in yield (g mcl-PHA per g cell dry weight) from p-coumaric acid and lignin, respectively, compared with the wild type strain. Overall, these results present a promising strain to be employed in further process development for enhancing mcl-PHA production from aromatic compounds and lignin.
High‐Pressure Entry into Platencin (2008)

Bacteria under pressure! An efficient synthesis of the enantiopure tricyclic core of a recently discovered antibiotic, platencin, has been developed. This synthesis highlights a novel high-pressure Diels–Alder reaction of the flavoring agent (S)-(−)-perillaldehyde and an efficient SmI2-mediated pinacol cyclization for the construction of the bicyclo[2.2.2]octane framework (see scheme).
Synthetic studies on histrionicotoxins. I. Stereocontrolled synthesis of (+-)-perhydrohistrionicotoxin (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic studies on histrionicotoxins. I. Stereocontrolled synthesis of (+-)-perhydrohistrionicotoxinM. Aratani, L. V. Dunkerton, T. Fukuyama, Y. Kishi, H. Kakoi, S. Sugiura, and S. InoueCite this: J. Org. Chem. 1975, 40, 13, 2009–2011Publication Date (Print):June 1, 1975Publication History Published online1 May 2002Published inissue 1 June 1975https://pubs.acs.org/doi/10.1021/jo00901a037https://doi.org/10.1021/jo00901a037research-articleACS PublicationsRequest reuse permissionsArticle Views384Altmetric-Citations69LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Quantitative Genetic Analysis of the Retinal Vascular Caliber (2009)

Research into the genetic effects and specific genes associated with retinal vascular caliber, a risk marker of cardiovascular diseases, may provide new insights into the genetic contribution of early microvascular disease. A combined 374 monozygotic and 536 dizygotic twin pairs and 322 siblings from the Twins Eye Study in Tasmania and the Brisbane Adolescent Twin Study underwent complete ophthalmic examinations, including retinal photography, and bilateral retinal vascular caliber was measured. Structural equation modeling was used to estimate the heritability. Genome-wide linkage analysis was conducted on 836 individuals from 381 Brisbane Adolescent Twin Study families, with adjustments for age, sex, and other covariates. The heritabilities for the retinal arteriolar caliber were 59.4% (95% CI: 53.2% to 64.7%) and 56.5% (95% CI: 50.1% to 61.9%) in the Twins Eye Study in Tasmania and the Brisbane Adolescent Twin Study, respectively, and for venular caliber they were 61.7% (95% CI: 55.6% to 67.0%) and 64.2% (95% CI: 58.7% to 68.8%), respectively, after adjusting for age, sex, and body mass index. Two multipoint peaks detected on chromosomes 3p12.3 and 8p23.1 for retinal arteriolar caliber had suggestive linkage, with the highest multipoint peak logarithm of odds score of 2.24 on chromosome 8p23.1 (genome-wide P=7.0 x 10(-4)). Two suggestive logarithm of odds scores for venular caliber were identified on chromosomes 2p14 and 9q21.13. The largest multipoint logarithm of odds score was 2.69 on chromosome 2p14 (genome-wide P=2.0 x 10(-4)). In this large twin population, genetic factors appear to play a significant role in the variation of retinal vascular caliber. Several putative loci were identified for the retinal vascular caliber.
Farview: Disaggregated Memory with Operator Off-loading for Database\n Engines (2021)

Cloud deployments disaggregate storage from compute, providing more\nflexibility to both the storage and compute layers. In this paper, we explore\ndisaggregation by taking it one step further and applying it to memory (DRAM).\nDisaggregated memory uses network attached DRAM as a way to decouple memory\nfrom CPU. In the context of databases, such a design offers significant\nadvantages in terms of making a larger memory capacity available as a central\npool to a collection of smaller processing nodes. To explore these\npossibilities, we have implemented Farview, a disaggregated memory solution for\ndatabases, operating as a remote buffer cache with operator offloading\ncapabilities. Farview is implemented as an FPGA-based smart NIC making DRAM\navailable as a disaggregated, network attached memory module capable of\nperforming data processing at line rate over data streams to/from disaggregated\nmemory. Farview supports query offloading using operators such as selection,\nprojection, aggregation, regular expression matching and encryption. In this\npaper we focus on analytical queries and demonstrate the viability of the idea\nthrough an extensive experimental evaluation of Farview under different\nworkloads. Farview is competitive with a local buffer cache solution for all\nthe workloads and outperforms it in a number of cases, proving that a smart\ndisaggregated memory can be a viable alternative for databases deployed in\ncloud environments.\n
Completely Surface-Potential-Based Compact Model of the Fully Depleted SOI-MOSFET Including Short-Channel Effects (2006)

The reported circuit simulation model Hiroshima University semiconductor technology academic research center IGFET model silicon-on-insulator (HiSIM-SOI) for the fully depleted SOI-MOSFET is based on a complete surface-potential description. Not only the surface potential in the MOSFET channel, but also the potentials at both surfaces of the buried oxide are solved iteratively, which allows including of all relevant device features of the SOI-MOSFET explicitly and in a physically correct way. In particular, an additional parasitic electric field, induced by the surface-potential distribution at the buried oxide, has to be included for accurate modeling of the short-channel effects. The total iteration time for surface potential calculation with HiSIM-SOI is under most bias conditions only a factor 2.0 (up to a factor 3.0 for some bias conditions) longer than for the bulk-MOSFET HiSIM model, where just the channel surface potential is involved. It is verified that HiSIM-SOI reproduces measured current-voltage (I-V) and 1/f noise characteristics of a 250-nm fully depleted SOI technology in the complete operating range with an average error of 1% and 15%, respectively. Stable convergence of HiSIM-SOI in the circuit simulation is confirmed
In vitro transcription of normal, mutant, and truncated mouse alpha-globin genes. (1980)

We have transcribed various alpha-globin gene-containing templates by using a simplified in vitro system and have shown that the 5' end of each of the RNA polymerase II-specific transcripts corresponds to that of authentic alpha-globin mRNA. Using a truncated alpha-globin gene fragment, we then localized the promotor region of the adult alpha-globin gene to a 138-base-pair fragment of alpha-globin DNA, 141 nucleotides of which precede the initiation site. In contrast, when two naturally occurring alpha-globin gene mutants were tested as templates, no RNA polymerase II-dependent initiation was detected. Comparison of the nucleotide sequences of the normal and mutant alpha-globin genes has allowed us to focus upon nucleotide positions that might be essential for promoter activity.
Online Sample Conditioning for Portable Breath Analyzers (2012)

Various innovative chemical sensors have been developed in recent years to sense dangerous substances in air and trace biomarkers in breath. However, in order to solve real world problems, the sensors must be equipped with efficient sample conditioning that can, e.g., control the humidity, which is discussed much less in the literature. To meet the demand, a miniaturized mouthpiece was developed for personal breath analyzers. A key function of the mouthpiece is to condition the humidity in real breath samples without changing the analyte concentrations and introducing substantial backpressure, which is achieved with optimized packing of desiccant particles. Numerical simulations were carried out to determine the performance of the mouthpiece in terms of various controllable parameters, such as the size, density, and geometry of the packing. Mouthpieces with different configurations were built and tested, and the experimental data validated the simulation findings. A mouthpiece with optimized performance reducing relative humidity from 95% (27,000 ppmV) to 29% (8000 ppmV) whereas retaining 92% nitric oxide (50 ppbV to 46 ppbV) was built and integrated into a hand-held exhaled nitric oxide sensor, and the performance of exhaled nitric oxide measurement was in good agreement with the gold standard chemiluminescence technique. Acetone, carbon dioxide, oxygen, and ammonia samples were also measured after passing through the desiccant mouthpiece using commercial sensors to examine wide applicability of this breath conditioning approach.
Larc 20-Year Center Revitalization Plan (2013)

LaRC has developed a 20-Year Center Revitalization Plan. The objective of this plan is to assure that the center infrastructure is sustainable for the long-term and that the center will have the essential facilities and laboratories to execute the future NASA mission. The plan was developed by a centerwide team, VITAL, and was approved by the Center Leadership Council (CLC) in March 2012. The revitalization plan will be implemented through the Center Master Planning process.
ChemInform Abstract: A New Regioselective Synthesis of 1,2,5‐Trisubstituted 1H‐Imidazoles and Its Application to the Development of Eprosartan. (1998)

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.
Inhibition of nuclear export restores nuclear localization and residual tumor suppressor function of truncated SMARCB1/INI1 protein in a molecular subset of atypical teratoid/rhabdoid tumors (2021)

Loss of nuclear SMARCB1 (INI1/hSNF5/BAF47) protein expression due to biallelic mutations of the SMARCB1 tumor suppressor gene is a hallmark of atypical teratoid/rhabdoid tumors (ATRT), but the presence of cytoplasmic SMARCB1 protein in these tumors has not yet been described. In a series of 102 primary ATRT, distinct cytoplasmic SMARCB1 staining on immunohistochemistry was encountered in 19 cases (19%) and was highly over-represented in cases showing pathogenic sequence variants leading to truncation or mutation of the C-terminal part of SMARCB1 (15/19 vs. 4/83; Chi-square: 56.04, p = 1.0E-10) and, related to this, in tumors of the molecular subgroup ATRT-TYR (16/36 vs. 3/66; Chi-square: 24.47, p = 7.6E-7). Previous reports have indicated that while SMARCB1 lacks a bona fide nuclear localization signal, it harbors a masked nuclear export signal (NES) and that truncation of the C-terminal region results in unmasking of this NES leading to cytoplasmic localization. To determine if cytoplasmic localization found in ATRT is due to unmasking of NES, we generated GFP fusions of one of the SMARCB1 truncating mutations (p.Q318X) found in the tumors along with a p.L266A mutation, which was shown to disrupt the interaction of SMARCB1-NES with exportin-1. We found that while the GFP-SMARCB1(Q318X) mutant localized to the cytoplasm, the double mutant GFP-SMARCB1(Q318X;L266A) localized to the nucleus, confirming NES requirement for cytoplasmic localization. Furthermore, cytoplasmic SMARCB1(Q318X) was unable to cause senescence as determined by morphological observations and by senescence-associated β-galactosidase assay, while nuclear SMARCB1(Q318X;L266A) mutant regained this function. Selinexor, a selective exportin-1 inhibitor, was effective in inhibiting the nuclear export of SMARCB1(Q318X) and caused rapid cell death in rhabdoid tumor cells. In conclusion, inhibition of nuclear export restores nuclear localization and residual tumor suppressor function of truncated SMARCB1. Therapies aimed at preventing nuclear export of mutant SMARCB1 protein may represent a promising targeted therapy in ATRT harboring truncating C-terminal SMARCB1 mutations.
Transport measurement across single and coupled dopants implanted in a CMOS channel (2012)

We access properties of single dopants embedded in ultra-scaled MOSFET. In such nanostructures, the ionization energy of a single dopant is enhanced. We establish a new method to determine the energy spectrum of a single dopant by connecting two dopants in series and using one dopant as an energy probe for the second one. Gigahertz microwave driving of this double donor system reveals coherent charge transfert in this ultimate “atomic” transistor.