gebhart/patrepeval huggingface dataset:
An application of scalable massive model interaction using shared-memory systems (2006)

During the end-to-end digital design of a commerical airliner, a massive amount of geometric data is produced. This data can be used for inspection or maintenance throughout the life of the aircraft. Massive model interactive ray tracing can provide maintenance personnel with the capability to easily visualize the entire aircraft at once. This paper describes the design of the renderer used to demonstrate the feasibility of integrating interactive ray tracing in a commerical aircraft inspection and maintenance scenario. We describe the feasibility demonstration involving actual personnel performing real-world tasks and the scalable architecture of the parallel shared memory renderer.
Integrative epigenomic analyses of small cell lung cancer cells demonstrates the clinical translational relevance of gene body methylation (2022)

DNA methylation is a key regulator of gene expression and a clinical therapeutic predictor. We examined global DNA methylation beyond the generally used promoter areas in human small cell lung cancer (SCLC) and find that gene body methylation is a robust positive predictor of gene expression. Combining promoter and gene body methylation better predicts gene expression than promoter methylation alone including genes involved in the neuroendocrine classification of SCLC and the expression of therapeutically relevant genes including <i>MGMT</i>, <i>SLFN11,</i> and <i>DLL3</i>. Importantly, for super-enhancer (SE) covered genes such as <i>NEUROD1</i> or <i>MYC</i>, using H3K27ac and NEUROD1, ASCL1, and POU2F3 ChIP-seq data, we show that genic methylation is inversely proportional to expression, thus providing a new approach to identify potential SE regulated genes involved in SCLC pathogenesis. To advance SCLC transitional research, these data are integrated into our web portal (https://discover.nci.nih.gov/SclcCellMinerCDB/) for open and easy access to basic and clinical investigators.
Treatment-related survival associations of claudin-2 expression in fibroblasts of colorectal cancer (2017)

Claudin-2 is a trans-membrane protein—component of tight junctions in epithelial cells. Elevated claudin-2 expression has been reported in colorectal cancer (CRC). The aim of this study was to investigate the expression patterns of claudin-2 in human CRC samples and analyze its association with clinical characteristics and treatment outcome. TMAs of primary tumors from two cohorts of metastatic CRC (mCRC) were used. Claudin-2 IHC staining was evaluated in a semi-quantitative manner in different regions and cell types. Claudin-2 expression was also analyzed by immunofluorescence in primary cultures of human CRC cancer-associated fibroblasts (CAFs). Initial analyses identified previously unrecognized expression patterns of claudin-2 in CAFs of human CRC. Claudin-2 expression in CAFs of the invasive margin was associated with shorter progression-free survival. Subgroup analyses demonstrated that the survival associations occurred among cases that received 5-FU+oxaliplatin combination treatment, but not in patients receiving 5-FU±irinotecan. The finding was validated by analyses of the independent cohort. In summary, previously unreported stromal expression of claudin-2 in CAFs of human CRC was detected together with significant association between high claudin-2 expression in CAFs and shorter survival in 5-FU+oxaliplatin-treated mCRC patients.
Preparation and Properties of Composite PAN/PANI Membranes (2017)

The methods of modifying PAN membranes have been known and used for many years. An interesting solution seems to be to give the sensory properties to this type of membranes. This paper presents the results of research on the method of obtaining PAN/PANI membranes using phase inversion method from a solution in DMF, following two methods: (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mn fontstyle="italic">1</mml:mn></mml:mrow></mml:math>) dissolving both polymers (PAN and PANI) and then coagulating in water or in an aqueous solution of CSA and (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:mn fontstyle="italic">2</mml:mn></mml:mrow></mml:math>) forming the membranes from polyacrylonitrile solution and coagulation in water, followed by coating of CSA with a solution of TFE. The membranes obtained as a result of the experiment were tested for physical and chemical properties, transport properties, surface morphology, degree of dispersion of composite components, and sensitivity to the presence of dilute acids and bases. FTIR microspectroscopy and scanning electron microscopy were used to study the surface morphology. The sensory properties of membranes that are inherently colored were determined visually and by UV-Vis spectrophotometry. Furthermore, when choosing the method of membrane forming, we can obtain membranes with good physical and chemical and transport properties or ones characterized by high sensitivity to the pH of the solution.
PyRanges: efficient comparison of genomic intervals in Python (2019)

Supplementary data are available at Bioinformatics online.
Examination of various dissolution methods for the quantitative analysis of Ir-based alloys. (2002)

It is well known that Ir is a chemically stable element that is difficult to dissolve even in a strong acid. Furthermore, when transition metals are added to it, Ir becomes more difficult to dissolve in acid. To solve this problem, we tried to dissolve Ir alloys including several transition metals using a fusion method at 800°C in sodium peroxide. We found that, when the powder size of a sample was sufficiently small, under 75 μm, Ir alloys could be dissolved. We also showed that it is possible to analyze the composition of Ir alloys using the solution with ICP-AES.
Human antibody reactivity against xenogeneic N‐glycolylneuraminic acid and galactose‐α‐1,3‐galactose antigen (2016)

We showed that IgG-mediated CDC was detected in Neu5Gc-overexpressed HEK293 cells incubated with human sera; however, this antibody reactivity to Neu5Gc was highly variable among individuals. Our results suggest that additional modifications to the CMAH gene should be considered for widespread use of pig organs for human transplants.
Confinement-Induced Transition between Wavelike Collective Cell Migration Modes (2019)

The structural and functional organization of biological tissues relies on the intricate interplay between chemical and mechanical signaling. Whereas the role of constant and transient mechanical perturbations is generally accepted, several studies recently highlighted the existence of long-range mechanical excitations (i.e., waves) at the supracellular level. Here, we confine epithelial cell monolayers to quasi-one-dimensional geometries, to force the establishment of tissue-level waves of well-defined wavelength and period. Numerical simulations based on a self-propelled Voronoi model reproduce the observed waves and exhibit a phase transition between a global and a multinodal wave, controlled by the confinement size. We confirm experimentally the existence of such a phase transition, and show that wavelength and period are independent of the confinement length. Together, these results demonstrate the intrinsic origin of tissue oscillations, which could provide cells with a mechanism to accurately measure distances at the supracellular level.
Supplementary Table 2 from <i>HOXB13</i> G84E Mutation in Finland: Population-Based Analysis of Prostate, Breast, and Colorectal Cancer Risk (2023)

&lt;p&gt;PDF file - 47K, Presentation of segregation analysis.&lt;/p&gt;
Editorial board page for “Catalysis Reviews—Science and Engineering”, Volume 35, Number 3 (1993)

TEST 02 - Elsevier's Scopus, the largest abstract and citation database of peer-reviewed literature. Search and access research from the science, technology, medicine, social sciences and arts and humanities fields.
NiO films on sapphire as potential antiferromagnetic pinning layers (2017)

Epitaxial NiO thin films were grown on single crystal substrates of m-plane (101¯0), a-plane (1¯1¯20), c-plane (0001), and r-plane (11¯02) sapphires by ion beam sputtering of a Ni metal target in a mixed argon and oxygen atmosphere. X-ray measurements indicate that the NiO grows epitaxially on all substrates, with its orientation dependent on the cut of the sapphire substrate. The growth mode is the Stranski–Krastanov mode. (110)-oriented NiO grows on m-plane sapphire, while (111)-oriented NiO films are found on both the a-plane and c-plane sapphire. The orientation of NiO found on r-plane sapphire is found to be surface and temperature dependent but is mainly given by (110)-oriented grains. Thus, thin NiO films on c-plane and a-plane substrates are best suited to serve as antiferromagnetic pinning layers in magneto-electronic devices.
Quantifying the effectiveness of testing via efficient residual path profiling (2007)

Software testing is extensively used for uncovering bugs in large, complex software. Testing relies on well designed regression test suites that anticipate all reasonable software usage scenarios. Unfortunately, testers today have no way of knowing how much of real-world software usage was untested by their regression suite. Recent advances in low-overhead path profiling provide the opportunity to rectify this deficiency and perform residual path profiling on deployed software. Residual path profiling identifies all paths executed by deployed software that were untested during software development. We extend prior research to perform low-overhead interprocedural path profiling. We demonstrate experimentally that low-overhead path profiling, both intraprocedural and interprocedural, provides valuable quantitative information on testing effectiveness. We also show that residual edge profiling is inadequate as a significant number of untested paths include no new untested edges.
A systematic design of microstrip-to-CPS transition for 60-GHz package applications (2011)

This paper discusses a systematic design of a MS-to-CPS transition (or balun) that has good impedance match and low insertion loss, and maintains phase and amplitude balance, which are important for many mmWave applications. Phase and amplitude balance are not discussed in previous MS-to-CPS transition studies.
Final technical report (2004)

This project sought to develop new means of creating variation in the structure of starch that accumulates in maize seeds, through manipulation of the enzyme starch synthase III (SSIII). The central hypothesis was that SSIII is responsible for construction of certain lengths of linear glucan chains within the major starch component amylopectin, and that manipulation of this enzyme could create new varieties of starch that might have novel utilities as a renewable resource. The hypothesis was proven to be true through analysis of the effects of maize du1- mutations, which affect the structure and function of SSIII. SSIII was found to be required for the formation for two distinct groups of chain lengths in maize amylopectin, specifically those containing 7-9 glucose units and those containing 37-55 glucose units. Decrease in the frequency of these chains, as compared to wild type, is accompanied by an increase in chains of 11-15 glucose units. A hypothesis consistent with these data is that one of the other SS isoforms produces chains in the range of 11-15 units, and these are then elongated by SSIII to the range of 37-55 units. In order to try to manipulate the activity of SSIII in novel ways, transgenic maize plants were constructed in which the presumed regulatory part of the protein was detached from the known catalytic region responsible for synthesis of linear glucan chains within starch. Three different transgenes were introduced into maize, each containing different truncated versions of SSIII. Transgenic plants were followed over several generations, and their structure of their starches were analyzed. Novel structures were in fact observed. Specifically, there was a large increase in the frequency of chains containing 9-15 glucose units as compared two wild type maize starch, and a decrease in the frequency of those with 18-30 units. These structures of starch are distinct from those that caused by null mutations that eliminate SSIII, indicated a novel functional effect on starch synthesis in the transgenic plants. The novel starches produced by this method can now be tested for any advantageous functional properties.
Distributed stochastic learning for continuous power control in wireless networks (2012)

In this paper, we develop a distributed stochastic learning framework for seeking Nash equilibria under state dependent payoff functions. Most of the existing works assumes that a closed form expression of the reward is available at the nodes. We consider here a realistic assumption that the nodes have only a numerical realization of the reward at each time and develop a discrete time stochastic learning using sinus perturbation. We examine the convergence of our discrete time algorithm to a limiting trajectory defined by an Ordinary Differential Equation (ODE). Finally, we conduct a stability analysis and apply the proposed scheme in a generic power control problem in wireless networks.
Evaluating structure in thin block copolymer films with soft x-rays (Conference Presentation) (2017)

The semiconductor industry is evaluating a variety of approaches for the cost efficient production of future processing and memory generations. Amongst the technologies being explored are multiple patterning steps, extreme ultraviolet (EUV) lithography, multiple-beam electron beam lithography and the directed self-assembly (DSA) of block copolymers (BCPs). BCP DSA utilizes a chemical or topographical template to induce long range order in a thin film of BCP which enhances the resolution of the original pattern. The characterization of buried structure within a DSA BCP film is challenging due to the lack of contrast between the organic materials. Critical-dimension small angle x-ray scattering (CDSAXS) measurements were performed on DSA BCP films, using soft X-rays to tune the contrast, in order to understand the relationship between template structure and film morphology.1 The results of these measurements show that as the width of the guiding stripe widens the arrangement of the BCP on the guiding stripe inverts, shifting from the A block being centered on the guiding stripe to the B block being centered on the guiding stripe. The initial results of integration of mean field simulations into the analysis of scattering data will also be discussed. In addition to examining the BCP structure with CDSAXS, soft X-ray reflectivity2 measurements were performed on BCP to better understand the relationship between interface width for systems with alternative architectures (triblocks) and additives (polymers/ionic liquids). The addition of a selectively associating additive increases the interaction parameter between the two blocks, resulting in the reduction of the interface width and access to smaller pitches. The use of soft X-ray reflectivity allows the evaluation of the distribution of the additive. (1) Sunday, D. F.; Hammond, M. R.; Wang, C.; Wu, W.; Delongchamp, D. M.; Tjio, M.; Cheng, J. Y.; Kline, R. J.; Pitera, J. W. Determination of the Internal Morphology of Nanostructures Patterned by Directed Self Assembly. ACS Nano 2014, 8, 8426–8437. (2) Sunday, D. F.; Kline, R. J. Reducing Block Copolymer Interfacial Widths through Polymer Additives. Macromolecules 2015, 48, 679–686.
Aluminum-induced neurofibrillary degeneration disrupts acquisition of the rabbit's classically conditioned nictitating membrane response. (1988)

Rabbits received intraventricular injections of aluminum chloride, hydrochloric acid, or served as unoperated controls. On the 6th day postsurgery, they underwent 4 days (100 trials per day) of classical conditioning of the nictitating membrane response (NMR) to a tone conditioned stimulus and an air-puff unconditioned stimulus. Unoperated and hydrochloric acid control animals readily acquired the conditioned response. Aluminum intoxicated rabbits, in contrast, did not acquire the conditioned response over the 4 days of testing. This disruption of conditioning in aluminum-treated rabbits could not be attributed to deficits in sensory or motor processes or to illness. Neuropathological analysis revealed widespread neurofibrillary tangle formation in aluminum-treated animals. Furthermore, the degree of neurofibrillary degeneration was significantly negatively correlated with the degree of conditioning. The results are considered in the context of using the rabbit NMR preparation as a model system for studying age-related conditioning disorders.
Building Bing Developer Assistant MSR-TR-2015-36 (2015)

Software developers heavily rely on code snippets and API usage examples searched on the Internet. This paper presents Bing Code Search, a Visual Studio extension that allows developers to write, within an IDE, free-form natural language questions, and get C# code snippets answering those questions. Bing Code Search automatically adapts the suggested snippets into the user’s programming context via variable renaming, and records users’ interactions to improve its suggestions. Compared to prior related research, Bing Code Search provides a complete automation of the full search-paste-adapt process. Three weeks after we released this free extension, more than 20,000 users downloaded it; and they issue on average 3,000 queries per day. We believe that Bing Code Search is the most widely used tool in its category. In the following, we fully describe our framework, and draw clear empirical evidence of the benefits of Bing Code Search: (1) From our evaluation benchmark, compared with Bing’s result, Bing Code Search delivers more relevant snippet solutions. (2) In a controlled experiment, it was able to save developers 28% of time on completing API related tasks. (3) Telemetries collected from thousands of users show some users already built up the habit of using the tool: they issue multiple queries to solve a complex task, or use it as a fast auto-completion.
Aza-Riley Oxidation of Ugi-Azide and Ugi-3CR Products toward Vicinal Tricarbonyl Amides: Two-Step MCR-Oxidation Methodology Accessing Functionalized α,β-Diketoamides and α,β-Diketotetrazoles (2018)

Direct oxidative deamination of glyoxal-derived Ugi-azide and Ugi three-component reaction products readily affords vicinal tricarbonyls (α,β-diketoamides) and α,β-diketotetrazoles with two diversity elements. This significant extension of our previously described multicomponent reaction-oxidative deamination methodology is proposed to proceed through a mechanistically distinct SeO<sub>2</sub>-mediated C-N oxidation derived from an active enol of α-amino-β-ketone systems, effectively an aza-Riley oxidation. This methodology accesses diverse VTC systems from prototypical amines, glyoxaldehydes, and isocyanide building blocks in a mere two steps.
Genome sequence ofAspergillus luchuensisNBRC 4314 (2016)

Awamori is a traditional distilled beverage made from steamed Thai-Indica rice in Okinawa, Japan. For brewing the liquor, two microbes, local kuro (black) koji mold Aspergillus luchuensis and awamori yeast Saccharomyces cerevisiae are involved. In contrast, that yeasts are used for ethanol fermentation throughout the world, a characteristic of Japanese fermentation industries is the use of Aspergillus molds as a source of enzymes for the maceration and saccharification of raw materials. Here we report the draft genome of a kuro (black) koji mold, A. luchuensis NBRC 4314 (RIB 2604). The total length of nonredundant sequences was nearly 34.7 Mb, comprising approximately 2,300 contigs with 16 telomere-like sequences. In total, 11,691 genes were predicted to encode proteins. Most of the housekeeping genes, such as transcription factors and N-and O-glycosylation system, were conserved with respect to Aspergillus niger and Aspergillus oryzae An alternative oxidase and acid-stable α-amylase regarding citric acid production and fermentation at a low pH as well as a unique glutamic peptidase were also found in the genome. Furthermore, key biosynthetic gene clusters of ochratoxin A and fumonisin B were absent when compared with A. niger genome, showing the safety of A. luchuensis for food and beverage production. This genome information will facilitate not only comparative genomics with industrial kuro-koji molds, but also molecular breeding of the molds in improvements of awamori fermentation.
A New Short and Efficient Synthetic Route to C8-N-Acetylarylamine 2′-Deoxyguanosine Phosphoramidites (2007)

In addition to their C8-NH-arylamine-dG counterparts, C8-N-acetylarylamine adducts of 2′-deoxyguanosine (2′-dG) play an important role in the possible induction of chemical carcinogenesis. A new synthetic pathway of this adduct type using different aromatic amines has been developed following most probably an electrophilic amination reaction. These adducts can be converted into the corresponding phosphoramidites for incorporation into oligonucleotides.
GS0506 Influencing Factors on Fatigue Properties of Stainless Steels in High Pressure Gaseous Hydrogen (2008)

鋼管状試験片を用いた外圧または内圧疲労試験により,最高85MPa高圧水素ガス環境下におけるステンレス鋼の疲労特性に及ぼす各種因子の影響を調査した.安定オーステナイト系ステンレス鋼SUS316L,準安定オーステナイト系ステンレス鋼SUS304を対象に,最長600s/cycleでの長周期疲労試験,室温または-40℃での疲労試験,溶接継手の疲労試験などを実施した.SUS304の場合,高圧水素ガス環境下における疲労特性はサイクルタイム,試験温度,溶接施工などの影響を受ける,一方,SUS316Lの場合にはこれらの因子の影響はSUS304の場合より小さい.
Single and low order mode interrogation of a multimode sapphire fiber Bragg grating sensor with tapered fibers (2005)

Multimode sapphire fiber Bragg gratings (SFBG) made with an IR femtosecond laser and a phase mask were probed using tapered single mode fibers of different taper diameters producing single and low order mode reflection/transmission responses. A configuration made of an input single mode tapered fiber and multimode silica fiber used for output coupling was also tested and has delivered a filtered multimode transmission spectrum. The tapered coupling improved the spectral resolution of the SFBG as compared to its multimode responses previously reported. Such improvements facilitate the utilization of the SFBG as a high temperature sensor. Wavelength shifts of the single mode response were monitored as a function of temperature up to 1500 °C and were consistent with the measurement obtained from the multimode response published previously.
High-Temperature Thermoelectric Characterization of III–V Semiconductor Thin Films by Oxide Bonding (2010)

A device fabrication and measurement method utilizing a SiO2–SiO2 covalent bonding technique is presented for high-temperature thermoelectric characterization of thin-film III–V semiconductor materials that suffer from the side-effect of substrate conduction at high temperatures. The proposed method includes complete substrate removal, high-temperature surface passivation, and metallization with a Ti-W-N diffusion barrier. A thermoelectric material, thin-film ErAs:InGaAlAs metal/semiconductor nanocomposite grown on a lattice-matched InP substrate by molecular beam epitaxy, was transferred onto a sapphire substrate using the oxide bonding technique at 300°C, and its original InP substrate, which is conductive at high temperatures, was removed. Electrical conductivities and Seebeck coefficients were measured from room temperature to 840 K for this material on both the InP and sapphire substrates, and the measurement results clearly show that the InP substrate effect was eliminated for the sample on the sapphire substrate. A strain experiment has been conducted to investigate the effect of strain on electrical conductivity.