gebhart/patrepeval huggingface dataset:
Optimal selection of markers for validation or replication from genome‐wide association studies (2007)

With reductions in genotyping costs and the fast pace of improvements in genotyping technology, it is not uncommon for the individuals in a single study to undergo genotyping using several different platforms, where each platform may contain different numbers of markers selected via different criteria. For example, a set of cases and controls may be genotyped at markers in a small set of carefully selected candidate genes, and shortly thereafter, the same cases and controls may be used for a genome-wide single nucleotide polymorphism (SNP) association study. After such initial investigations, often, a subset of "interesting" markers is selected for validation or replication. Specifically, by validation, we refer to the investigation of associations between the selected subset of markers and the disease in independent data. However, it is not obvious how to choose the best set of markers for this validation. There may be a prior expectation that some sets of genotyping data are more likely to contain real associations. For example, it may be more likely for markers in plausible candidate genes to show disease associations than markers in a genome-wide scan. Hence, it would be desirable to select proportionally more markers from the candidate gene set. When a fixed number of markers are selected for validation, we propose an approach for identifying an optimal marker-selection configuration by basing the approach on minimizing the stratified false discovery rate. We illustrate this approach using a case-control study of colorectal cancer from Ontario, Canada, and we show that this approach leads to substantial reductions in the estimated false discovery rates in the Ontario dataset for the selected markers, as well as reductions in the expected false discovery rates for the proposed validation dataset.
MEMBRANE EXPRESSION OF NK RECEPTOR KIR3DL2 CONTRIBUTES TO DELINEATE THE ACUTE‐TYPE AND IS A THERAPEUTIC TARGET IN ADULT T‐CELL LEUKEMIA/LYMPHOMA (2019)

Introduction: Adult T-cell leukemia/lymphoma (ATL) is a lymphoid neoplasm of CD4+ T lymphocytes caused by the human T-cell leukemia virus type I (HTLV-1), which is classified into 4 clinical subtypes (ie, smoldering, chronic, acute, and lymphoma). Natural killer receptors (NKRs) were previously identified on T-cell lymphoma. Methods: NKRs expression was assessed by flow-cytometry and immunohistochemistry on peripheral blood samples (n = 55) and biopsies (n = 21) obtained from 50 ATL patients. Array-based analysis of genomic DNA methylation patterns of KIR3DL2 promoter was assessed. To explore the role of HTLV-1 on KIR3DL2 expression, KIR3DL2 and TAX mRNA expressions were assessed on primary ATL cells and on activated CD4+ T cells that were infected with HTLV-1 in-vitro. Ex-vivo autologous antibody dependent cell cytotoxicity (ADCC) was performed on sorted primary ATL cells with IPH4102, a monoclonal anti-KIR3DL2 antibody that has shown robust clinical activity in Phase I in patients with relapsed Sézary Syndrome (NCT02593045). Results: KIR3DL2 was the only detected NKR, mainly expressed on acute- compared to lymphoma- and chronic-types ATL (28/30 vs. 2/8 and 2/12 respectively; p = 0.001). KIR3DL2 expression correlated with the demethylation status in its promoter, and treatment by 5-Aza increased its expression from a positive basal state. TAX mRNA and KIR3DL2 expressions were correlated on primary ATL cells. HTLV-1 infection triggered KIR3DL2 protein expression by CD4+ cells. However, Tax alone is not sufficient to induce KIR3DL2 mRNA expression. Treatment with IPH4102 can selectively kill human KIR3DL2+ primary ATL cells ex-vivothrough ADCC with autologous NK cells. Conclusion: KIR3DL2 expression is mainly associated with acute-type ATL, the most frequent subtype with the poorest prognosis. Induction of KIR3DL2 gene transcription may be triggered by HTLV-1 infection followed by transcription maintenance due to DNA hypomethylation of the gene promoter. The benefit of targeting KIR3DL2 by IPH4102 should be further investigated in ATL patients. Keywords: human T-lymphotropic virus (HTLV); monoclonal antibodies (MoAb); peripheral T-cell lymphomas (PTCL). Disclosures: Cheminant, M: Research Funding: yes. Bruneau, J: Research Funding: yes. Sicard, H: Employment Leadership Position: yes; Stock Ownership: yes. Bonnafous, C: Employment Leadership Position: yes; Stock Ownership: yes. Hermine, O: Research Funding: yes.
Digital data sets that describe aquifer characteristics of the alluvial and terrace deposits along the North Canadian River from Canton Lake to Lake Overholser in central Oklahoma (1997)

ARC/INFO export and nonproprietary format files This diskette contains digitized aquifer boundaries and maps of of hydraulic conductivity, recharge, and ground-water level elevation contours for the alluvial and terrace deposits along the alluvial and terrace deposits along the North Canadian River from Canton Lake to Lake Overholser in central Oklahoma. Ground water in approximately 400 square miles of Quaternary-age alluvial and terrace aquifer is an important source of water for irrigation, industrial, municipal, stock, and domestic supplies. The aquifer consists of clay, silt, sand, and gravel. Sand-sized sediments dominate the poorly sorted, fine to coarse, unconsolidated quartz grains in the aquifer. The hydraulically connected alluvial and terrace deposits unconformably overlie Permian-age formations. The aquifer is overlain by a layer of wind-blown sand in parts of the area. Most of the lines in the aquifer boundary, hydraulic conductivity, and recharge data sets were extracted from published digital surficial geology data sets based on a scale of 1:250,000. The ground-water elevation contours and some of the lines for the aquifer boundary, hydraulic conductivity, and recharge data sets were digitized from a ground-water modeling report about the aquifer published at a scale of 1:250,000. The hydraulic conductivity values and recharge rates also are from the ground-water modeling report. Ground-water flow models are numerical representations that simplify and aggregate natural systems. Models are not unique; different combinations of aquifer characteristics may produce similar results. Therefore, values of hydraulic conductivity and recharge used in the model and presented in this data set are not precise, but are within a reasonable range when compared to independently collected data.
Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: A model for homology search in homologous genetic recombination (1998)

Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions are essential for homologous genetic recombination in various organisms. From NMR studies, we previously reported a novel deoxyribose-base stacking interaction between adjacent residues on the extended single-stranded DNA bound to RecA protein. In this study, we found that the same DNA structure was induced by the binding to Saccharomyces cerevisiae Rad51 protein, indicating that the unique DNA structure induced by the binding to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of this structure, we have formulated the structure of duplex DNA within filaments formed by RecA protein and its homologs. Two types of molecular structures are presented. One is the duplex structure that has the N-type sugar pucker. Its helical pitch is approximately 95 A (18.6 bp/turn), corresponding to that of an active, or ATP-form of the RecA filament. The other is one that has the S-type sugar pucker. Its helical pitch is approximately 64 A (12.5 bp/turn), corresponding to that of an inactive, or ADP-form of the RecA filament. During this modeling, we found that the interconversion of sugar puckers between the N-type and the S-type rotates bases horizontally, while maintaining the deoxyribose-base stacking interaction. We propose that this base rotation enables base pair switching between double-stranded DNA and single-stranded DNA to take place, facilitating homologous pairing and strand exchange. A possible mechanism for strand exchange involving DNA rotation also is discussed.
How to Garble Arithmetic Circuits (2011)

Yao's garbled circuit construction transforms a boolean circuit C : {0, 1} <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> → {0, 1} <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> into a "garbled circuit" Ĉ along with n pairs of k-bit keys, one for each input bit, such that Ĉ together with the n keys corresponding to an input x reveal C(x) and no additional information about x. The garbled circuit construction is a central tool for constant-round secure computation and has several other applications. Motivated by these applications, we suggest an efficient arithmetic variant of Yao's original construction. Our construction transforms an arithmetic circuit C : ℤ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> → ℤ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> over integers from a bounded (but possibly exponential) range into a garbled circuit Ĉ along with n affine functions L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> : ℤ → ℤ <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sup> such that Ĉ together with the n integer vectors L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> (x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">i</sub> ) reveal C(x) and no additional information about x. The security of our construction relies on the intractability of the learning with errors (LWE) problem.
9,10‐Dihydrophenanthrenes as Phytoalexins of Orchidaceae (1983)

Hydroxy derivatives of 9,10-dihydrophenanthrenes, orchinol and hircinol, were isolated from bulbs of Orchidaceae which had been induced to accumulate phytoalexins. Incorporation of radioactive precursors, L-phenylalanine and various hydroxycinnamic acids, has been investigated by feeding experiments in vivo. m-Coumaric acid and dihydro-m-coumaric acid were found to be efficiently incorporated into the dihydrophenanthrene derivatives. Dihydro-m-coumaric acid was not only converted into the dihydrophenanthrenes but was also formed from L-phenylalanine in the same tissue; it was thus proved to be an intermediate. The role of dihydro-m-coumaric acid was substantiated by studies in vitro. An active stilbene synthase was detected in enzyme preparations from induced orchid bulbs and assayed with different CoA esters. The enzyme, characterized on the basis of its substrate specificity, selectively converted dihydro-m-coumaroyl-CoA plus malonyl-CoA into 3,3',5-trihydroxybibenzyl. The role of 3,3',5-trihydroxybibenzyl as physiological intermediate was further corroborated by investigations with intact plants. Both its formation from phenylpropanoids and its conversion into orchinol was demonstrated. The data provided evidence for a biosynthetic sequence originating from L-phenylalanine and leading to 9,10-dihydrophenanthrenes via m-coumaric acid, dihydro-m-coumaric acid, and 3,3',5-trihydroxybibenzyl.
Novel Therapeutic Strategy Using Interventional Radiology (IVR) for Hepatitis C Virus (HCV)-Related Decompensated Liver Cirrhosis: A Case Report (2019)

BACKGROUND The appearance of direct acting antivirals (DAAs) has produced a major paradigm shift in hepatitis C virus (HCV) infection treatment, and virus elimination has become possible in most patients. Improvement of the model for end-stage liver disease (MELD) score by elimination of HCV has been reported, but for decompensated liver cirrhosis, it is also important to overcome various complications before antiviral treatment. CASE REPORT A 72-year-old male, who had been treated for HCV-related liver cirrhosis was referred to our hospital for treatment of refractory hepatic encephalopathy. At that time, his Child-Pugh score was 10 and class was C. On contrast-enhanced computed tomography (CT), a splenorenal shunt, splenomegaly, and splenic artery aneurysm were noted. The disease was also complicated by cytopenia associated with hypersplenism, and embolization of the splenic artery aneurysm and partial splenic embolization (PSE) were concomitantly performed. One month after the PSE, balloon occluded retrograde transvenous obliteration (BRTO) for refractory hepatic encephalopathy was performed. Hepatic functional reserve improved compared with that at the first examination, and SOF/LDV therapy was initiated. Fortunately, no adverse effect occurred during treatment, and sustained virologic response (SVR) was achieved. Hepatic functional reserve further improved thereafter. At the time of this report, a Child-Pugh A status was being maintained without administration of a branched chain amino acid preparation, drugs for hyperammonemia, or diuretics. CONCLUSIONS We encountered a patient with decompensated liver cirrhosis accompanied by complications of hypersplenism, hepatic encephalopathy, and splenic artery aneurysm. These complications were overcome by treatment with PSE and BRTO, which led to DAAs treatment and a marked improvement of hepatic function.
Palladium-Catalyzed Amination of Aryl Halides on Solid Support (2002)

[reaction: see text] The first examples of the Pd(0)-catalyzed amination of aryl halides using Rink-resins as nitrogen source are described. Pd(2)dba(3)/BINAP/NaO-t-Bu was found to be the most efficient catalyst/base system, while a solvent mixture of dioxane and tert-butyl alcohol was shown to enhance the selectivity toward the desired monoarylation. Moderate to good yields and excellent purities of the amination products were found with electron-poor aryl halides, while electon-rich aryl halides failed to react under these conditions.
Isoflurane delays the development of early brain injury after subarachnoid hemorrhage through sphingosine-related pathway activation in mice* (2012)

Isoflurane posttreatment delays the development of postsubarachnoid hemorrhage early brain injury through antiapoptotic mechanisms including sphingosine-related pathway activation, implying its use for anesthesia during acute aneurysm surgery or intervention.
EXAFS Measurements of Laser-Shocked V and Ti and Crystal Phase Transformation in Ti (2004)

Extended X-Ray Absorption Fine Structure (EXAFS), using a laser-imploded target as a source, can yield the properties of laser-shocked metals on a nanosecond time scale. EXAFS measurements of vanadium shocked to {approx}0.4 Mbar yield the compression and temperature in good agreement with hydrodynamic simulations and shock-speed measurements. In laser-shocked titanium at the same pressure, the EXAFS modulation damping is much higher than warranted by the predicted temperature increase. This is shown to be due to the {alpha}-Ti to {omega}-Ti crystal-phase transformation, known to occur below {approx}0.1 Mbar for slower shock waves. The dynamics of material response to shock loading has been extensively studied in the past [1]. The goal of those studies has been to understand the shock-induced deformation and structural changes at the microscopic level [2]. Laser-generated shocks can be employed to broaden these studies to higher pressures ({approx}1 Mbar) and strain rates ({approx} 10{sup 7}-10{sup 8} s{sup -1}). Recently, laser-shocked materials have been studied with in-situ x-ray diffraction [3,4]. The goal of this work is to examine the use of in-situ EXAFS [5] as a complementary characterization of laser-shocked metals. EXAFS is the modulation in the x-ray absorption above the K edge (or L edge) due to the interference of the photoelectron waves with the waves reflected from neighboring atoms. The frequency of EXAFS modulations is related to the inter-particle distance, hence to the compression. The damping rate of the modulation can yield the lattice temperature, which is not readily available by other methods.
FRACTIONS OXIDIZABLE OF ORGANIC CARBON IN AGROECOLOGICAL BASE SYSTEMS IN PRODUCTION OF BAHIA SEMIARID (2018)

The objective of this study was to quantify the total contents and the organic carbon variation of soil with different degrees of lability in areas under organic fruit production system in the semi-arid Bahia. The study was conducted at Organic Bocaiúva Chacara located in Humble district, Feira de Santana, Bahia. The selected areas under different uses were: (CIT) Cultivation of citrus, (MAR) passion fruit cultivation and (ABA) area under pineapple cultivation. For comparison it was also evaluated an area under native forest system (MN). For each use system soil samples were collected at 0-10 and 10-20 cm in four replications. To obtain the different fractions was used doses of 2.5 and 5 ml of concentrated H2SO4, which corresponded to concentrations of 3 and 6 mol L-1, respectively, while keeping constant the concentration of K2Cr2O7 in 0.167 mol L-1. Total organic carbon was obtained by wet oxidation with an external source of heat. The results show that the organic production systems studied non labile C is the highest percentage in the formation of COT. The SEA area presented organic carbon values in the various fractions and the COT like reference system (MN), which indicates that the system is being handled properly, causing no decrease in the levels of organic matter in the soil
Nanoscale Science of Single Molecules Using Local Probes (1999)

Experiments on individual molecules using scanning probe microscopies have demonstrated an exciting diversity of physical, chemical, mechanical, and electronic phenomena. They have permitted deeper insight into the quantum electronics of molecular systems and have provided unique information on their conformational and mechanical properties. Concomitant developments in experimentation and theory have allowed a diverse range of molecules to be studied, varying in complexity from simple diatomics to biomolecular systems. At the level of an individual molecule, the interplays of mechanical and electronical behavior and chemical properties manifest themselves in an unusually clear manner. In revealing the crucial role of thermal, stochastic, and quantum-tunneling processes, they suggest that dynamics is inescapable and may play a decisive role in the evolution of nanotechnology.
A flexible robot skin for safe physical human robot interaction (2009)

Providing contact sensing on the whole body of a robot is a key feature to increase the safety level of physical human-robot interaction. In this paper, a new robot skin capable of sensing multiple contact locations is presented. The motivation behind the proposed design is to produce a relatively inexpensive skin having the capability to provide the spatial location of collisions and also to add compliance to the robot's external cover. The resulting device is a thin flexible sensor sheet made of polyimide films with electrically conductive ink and a pressure sensitive conductive rubber sheet. The problem of internal wire routing is circumvented by the use of conductive ink and a circuit is proposed to minimize the number of output wires. To provide collision absorption and mechanical robustness, the sensor is embedded in different layers of polyurethane using shape deposition manufacturing (SDM). The paper presents the design and the fabrication process of the skin but also some experimental results on the determination of the mechanical properties of the resulting sensor as well as its potential for increasing human safety during human robot interaction.
NDE using laser generated ultrasound and integrated ultrasonic transducer receivers (2008)

Non-destructive evaluation (NDE) of parts using laser generated ultrasound and integrated ultrasonic transducers (IUTs) as receiver is presented. Pulsed laser represents a versatile ultrasound generation transducer. Sol-gel fabricated thick piezoelectric film IUTs coated directly onto steel, aluminum (Al) and graphite/epoxy (Gr/Ep) composites substrates with planar or curves surfaces serve as efficient ultrasonic receivers without the need of couplant. Ultrasonic NDE of metals and Gr/Ep composite using laser generation in the thermoelastic or ablation regime and IUT receiving in longitudinal bulk waves, symmetric or shear-horizontal plate acoustic waves has been carried out.
SuprimeCam Observation of Sporadic Meteors during Perseids 2004 (2007)

Abstract We report on serendipitous findings of 13 faint meteors and 44 artificial space objects by SuprimeCam imaging observations during 2004 August 11–16. The meteors, at about 100 km altitude, and artificial satellites/debris in orbit, at 500 km altitude or higher, were clearly discriminated by their apparent defocused image sizes. We defined a peak video-rate magnitude by comparing the integrated photon counts from the brightest portion of the track traversed within 33 ms to those from a 0-mag star during the same time duration. The magnitudes thus defined for the meteors, including 1 Perseid, 1 Aquarid, and 11 sporadic meteors, were in the range 4.0 $&amp;lt; V_{\rm vr} &amp;lt;$ 6.4 and 4.1 $&amp;lt; I_{\rm vr} &amp;lt;$ 5.9. Although the spatial resolution is insufficient to resolve the source size of anything smaller than about 1 m, we developed a new estimate of the collisionally excited column diameter of these meteors. A diameter as small as a few mm was derived from their collisionally excited [O I] 5577 photon rates, meteor speed, and the volume density of the oxygen atoms at an altitude of 100 km. The actual column diameter of the radiating zone, however, could be as large as few 100 m because the excited oxygen atoms travel that distance before they emit forbidden lines in 0.7 s of its average lifetime.
<title>Experimental service of 3DTV broadcasting relay in Korea</title> (2002)

This paper introduces 3D HDTV relay broadcasting experiments of 2002 FIFA World Cup Korea/Japan using a terrestrial and satellite network. We have developed 3D HDTV cameras, 3D HDTV video multiplexer/demultiplexer, a 3D HDTV receiver, and a 3D HDTV OB van for field productions. By using a terrestrial and satellite network, we distributed a compressed 3D HDTV signal to predetermined demonstration venues which are approved by host broadcast services (HBS), KirchMedia, and FIFA. In this case, we transmitted a 40Mbps MPEG-2 transport stream (DVB-ASI) over a DS-3 network specified in ITU-T Rec. G.703. The video/audio compression formats are MPEG-2 main-profile, high-level and Dolby Digital AC-3 respectively. Then at venues, the recovered left and right images by the 3D HDTV receiver are displayed on a screen with polarized beam projectors.
Nonlocal effects in magnetization of high-κsuperconductors (2000)

The reversible magnetization $M(T,H)$ in high quality single crystals of $\mathrm{Lu}({\mathrm{Ni}}_{1\ensuremath{-}x}{\mathrm{Co}}_{x}{)}_{2}{\mathrm{B}}_{2}\mathrm{C}$ with $x=0\ensuremath{-}0.09$ is measured in a broad $T,H$ domain and interpreted within London theory corrected for nonlocality of the current -- vector-potential relation. Profound deviations in the data from the standard London result, $M\ensuremath{\propto}\mathrm{ln}{(H}_{c2}/H)$ in intermediate fields ${H}_{c1}\ensuremath{\ll}H\ensuremath{\ll}{H}_{c2},$ are seen in clean samples at low $T$'s.Unlike strongly anisotropic high-${T}_{c}$ compounds, for nearly isotropic borocarbides this behavior cannot be attributed to fluctuations of weakly interacting pancake vortices. We show that the nonlocal London model describes qualitatively and consistently the whole set of $M(T,H)$ data and, in particular, its temperature and the mean-free path dependence. The scaling field ${H}_{0},$ which arises in ${M=M(H/H}_{0})$ due to nonlocality, is found to be nearly proportional to the the field ${H}_{2}$ at which the vortex lattice undergoes the symmetry change (the ``square-to-hex'' transition).