gebhart/patrepeval huggingface dataset:
High <i>T</i> <i>c</i> superconducting NbN films deposited at room temperature (1985)

Thin films of niobium nitride with superconducting transition temperature (Tc ) of 15.7 K have been deposited on a variety of amorphous as well as crystalline substrates including glass, glazed ceramic, fused quartz, and sapphire, maintained at room temperature, by dc reactive magnetron sputtering in a mixture of Ar and N2 gases. The effects of the deposition conditions, particularly the carrier gas pressure and composition, on the film crystal structure, orientation, and resistivity have been studied in an effort to maximize the superconducting transition temperature. A study of the variation of nitrogen consumption with nitrogen injection pressures for constant background argon pressures is conducted and found to be an absolute indicator of the NbN formation systematics. Initially, the consumption increases linearly with the injection pressure but beyond a certain threshold, it shows a distinct drop. The desired high Tc NbN with B1 crystal structure is formed in the vicinity of this turning point of the reactive gas consumption-injection characteristic. High Tc films possess B1 (fcc, NaCl-type) crystal structure as revealed by their x-ray diffraction patterns. An initial increase in the injection pressure of the reactive gas (N2) results in a remarkable increase in the (111) diffraction line intensity along with an increase in the film Tc. This trend continues up to the turning point of consumption-injection characteristic, beyond which the crystal structure distorts into the substoichiometric tetragonal phase with a consequent reduction in the transition temperature. A general protocol for studying the formation systematics of transition metal nitrides has thus emerged.
Increasing quantitation in spatial single-cell metabolomics by using fluorescence as ground truth (2022)

Abstract Imaging mass spectrometry (MS) is becoming increasingly applied for single-cell analyses. Multiple methods for imaging MS-based single-cell metabolomics were proposed, including our recent method SpaceM. An important step in imaging MS-based single-cell metabolomics is the assignment of MS intensities from individual pixels to single cells. In this process, referred to as pixel-cell deconvolution, the MS intensities of regions sampled by the imaging MS laser are assigned to the segmented single cells. The complexity of the contributions from multiple cells and the background, as well as lack of full understanding of how input from molecularly-heterogeneous areas translates into mass spectrometry intensities make the cell-pixel deconvolution a challenging problem. Here, we propose a novel approach to evaluate pixel-cell deconvolution methods by using a molecule detectable both by mass spectrometry and fluorescent microscopy, namely fluorescein diacetate (FDA). FDA is a cell-permeable small molecule that becomes fluorescent after internalisation in the cell and subsequent cleavage of the acetate groups. Intracellular fluorescein can be easily imaged using fluorescence microscopy. Additionally, it is detectable by matrix-assisted laser desorption/ionisation (MALDI) imaging MS. The key idea of our approach is to use the fluorescent levels of fluorescein as the ground truth to evaluate the impact of using various pixel-cell deconvolution methods onto single-cell fluorescein intensities obtained by the SpaceM method. Following this approach, we evaluated multiple pixel-cell deconvolution methods, the ‘weighted average’ method originally proposed in the SpaceM method as well as the novel ‘linear inverse modelling’ method. Despite the potential of the latter method in resolving contributions from individual cells, this method was outperformed by the weighted average approach. Using the ground truth approach, we demonstrate the extent of the ion suppression effect which considerably worsens the pixel-cell deconvolution quality. For compensating the ion suppression, we propose a novel data-driven approach. We show that compensating the ion suppression effect in a single-cell metabolomics dataset of co-cultured HeLa and NIH3T3 cells considerably improved the separation between both cell types. Finally, using the same ground truth, we evaluate the impact of drop-outs in the measurements and discuss the optimal filtering parameters of SpaceM processing steps before pixel-cell deconvolution.
Oxidation‐reduction chemistry of chromium: Relevance to the regulation and remediation of chromate‐contaminated soils (1997)

Developing health‐protective clean‐up standards and remediation strategies for chromium‐contaminated soils based on the hexavalent forms of this heavy metal is a complex and controversial issue, because certain forms of Cr(III) can oxidize to Cr(VI) and Cr(VI) can be reduced to Cr(III) under diverse soil conditions. The extent of oxidation of Cr(III) in soils amended with wastes is based on four interacting parameters: (1) solubility and form of Cr(III) related to oxidation (waste oxidation potential, or WOP), (2) reactive soil Mn(III,IV) (hydr)oxide levels (soil oxidation potential for Cr(III), or SOP), (3) soil potential for Cr(VI) reduction (soil reduction potential, or SRP), and (4) soil‐waste pH as a modifier of the first three parameters (pH modification value, or PMV). Each of these four parameters can be quantified with laboratory tests and ranked numerically; the sum of which is the Potential Chromium Oxidation Score (PCOS) for assessing the relative hazard of a waste‐soil combination. The PCOS value is proposed as the basis for setting acceptable maximum limits for Cr(III)‐containing wastes in particular soil environments to maintain Cr(VI) levels at or below health‐based limits. Adjusting and controlling the PCOS parameters will allow practitioners to design remediation strategies and regulators to establish Cr clean‐up standards under soil conditions that minimize Cr(III) oxidation and maximize Cr(VI) reduction. Effective remediation of Cr(VI)‐Contaminated soils by reduction depends on three principles: (1) reduction of Cr(VI) to forms of Cr(III) that are inert toward re‐ oxidation, (2) the absence of undesirable reaction products (e.g., the oxidized forms of certain reducing agents), and (3) establishment or maintenance of soil pH and Eh conditions that favor reduction of Cr(VI) and disfavor the oxidation of Cr(III). This article focuses on the importance of understanding the waste forms of Cr and the redox‐related properties of Cr‐contaminated soils in the design of remedial goals to protect human health and ecological function.
A microrod-resonator Brillouin laser with 240 Hz absolute linewidth (2016)

Wedemonstrate an ultralow-noise microrod-resonator based laser that oscillates on the gain supplied by the stimulated Brillouin scattering optical nonlinearity. Microresonator Brillouin lasers are known to offer an outstanding frequency noise floor, which is limited by fundamental thermal fluctuations. Here, we show experimental evidence that thermal effects also dominate the close-to-carrier frequency fluctuations. The 6mmdiameter microrod resonator used in our experiments has a large\noptical mode area of∼100 μm2, and hence its 10 ms thermal time constant filters the close-to-carrier optical frequency noise. The result is an absolute laser linewidth of 240 Hz with a corresponding white-frequency noise floor of 0.1 Hz2 Hz−1.We explain the steady-state performance of this laser by measurements of its operation state and of its mode detuning and lineshape. Our results highlight a mechanism for noise that is common to many microresonator devices due to the inherent coupling between intracavity power and mode frequency.Wedemonstrate the ability to reduce this noise through a feedback loop that stabilizes the intracavity power.
Nanopatterned Optical Fiber Tip for Guided Mode Resonance and Application to Gas Sensing (2017)

This paper reports on an efficient and convenient method of patterning nanostructures on the cleaved facet of an optical fiber to realize a high-performance fiber-optic gas sensor. The fabrication method utilizes an ultraviolet assisted nanoimprint lithography to transfer nanoscale patterns from a pre-formed stamp to the fiber tip. The novelty of this paper lies in utilizing simpler fabrication steps with better control over angle of contact at the fiber tip, which leads to rapid and precise formation of nanostructures with well-defined features. A periodic array of polymer nanoposts are formed at the fiber tip and coated with titanium dioxide to serve as a guided mode resonant (GMR) device. A gas sensor is realized by coating the GMR structure with a thin layer of graphene oxide (GO) nanosheets. We have utilized the resonance sensitivity of the nanopatterned fiber-tip gas sensor to surrounding refractive index. The abundant functional groups available at GO provides an effective adsorption surface for gas molecules. Microscopic imaging and spectroscopic studies are conducted to illustrate the structural and optical properties, and gas-sensing performance of the sensor. Volatile organic compounds, such as ethylene and methanol, associated with crop plant health, are detected by the sensor. The sensor provides sensitivities of 0.92 and 1.37 pm/ppm for ethylene and methanol vapors, respectively, with a three-fold enhancement in sensitivity and 50% reduction in response time compared with the non-GO coated counterpart. In addition, the sensor demonstrates good stability and reproducibility, thus having a great potential in fiber-optic remote sensing applications.
Frequent Mutations of Chromatin Remodeling Gene <i>ARID1A</i> in Ovarian Clear Cell Carcinoma (2010)

Ovarian clear cell carcinoma (OCCC) is an aggressive human cancer that is generally resistant to therapy. To explore the genetic origin of OCCC, we determined the exomic sequences of eight tumors after immunoaffinity purification of cancer cells. Through comparative analyses of normal cells from the same patients, we identified four genes that were mutated in at least two tumors. PIK3CA, which encodes a subunit of phosphatidylinositol-3 kinase, and KRAS, which encodes a well-known oncoprotein, had previously been implicated in OCCC. The other two mutated genes were previously unknown to be involved in OCCC: PPP2R1A encodes a regulatory subunit of serine/threonine phosphatase 2, and ARID1A encodes adenine-thymine (AT)-rich interactive domain-containing protein 1A, which participates in chromatin remodeling. The nature and pattern of the mutations suggest that PPP2R1A functions as an oncogene and ARID1A as a tumor-suppressor gene. In a total of 42 OCCCs, 7% had mutations in PPP2R1A and 57% had mutations in ARID1A. These results suggest that aberrant chromatin remodeling contributes to the pathogenesis of OCCC.
A high-resolution mixed field immersion lens attachment for conventional scanning electron microscopes (2002)

This article deals with a compact mixed field add-on lens attachment for conventional scanning electron microscopes (SEMs). By immersing the specimen in a mixed electric–magnetic field combination, the add-on lens is able to provide high image resolution at relatively low landing energies (&lt;1 keV). Experimental results show that the add-on lens unit enables a tungsten gun SEM to acquire images with a resolution of better than 4 nm at a landing energy of 600 eV, which lies close to simulation predictions. Normally, this type of SEM would only be able to provide this kind of resolution at high voltages (30 kV).
Synthesis and Antibacterial Activity of Novel Pyrido[1,2,3-<i>de</i>][1,4]benzoxazine-6-carboxylic Acid Derivatives Carrying the 3-Cyclopropylaminomethyl-4-substituted-1-pyrrolidinyl Group as a C-10 Substituent (2008)

Novel pyrido[1,2,3- de][1,4]benzoxazine-6-carboxylic acid derivatives 5- 9 carrying a 3-cyclopropylaminomethyl-4-substituted-1-pyrrolidinyl moiety at the C-10 position were synthesized and their in vitro antibacterial activity, intravenous single-dose toxicity, convulsion inductive ability, and phototoxicity were evaluated. It appeared evident that compounds 5a, 6a, 8a, and 9a, which have a cis-oriented 4-methyl or 4-fluoro-3-cyclopropylaminomethyl-1-pyrrolidinyl moiety at the C-10 position, exhibited 2- to 16-fold more potent in vitro antibacterial activity than clinafloxacin against quinolone-resistant Gram-positive clinical isolates. Furthermore, it was obvious that introduction of a fluorine atom to the C-4 position of the 3-cyclopropylaminomethyl-1-pyrrolidinyl moiety reduced intraveneous single-dose acute toxicity and the convulsion inductive ability, and introduction of a fluorine atom to the C-3 methyl group of the pyridobenzoxazine nucleus eliminated the phototoxicity.
Synthesis of cyclic carbonates using monometallic, and helical bimetallic, aluminium complexes (2012)

The aluminium complexes of a series of bis(pyrazol-1-yl)methane derived ligands were investigated as catalysts for the synthesis of cyclic carbonates from carbon dioxide and epoxides. A bimetallic, helical, heteroscorpionate complex displayed significantly higher catalytic activity than the corresponding monometallic complexes. The optimal reaction conditions were found to involve the use of 5 mol% of the bimetallic complex and 5 mol% of tetrabutylammonium bromide under solvent free conditions in the presence of 10 bar of wet carbon dioxide. Under these conditions, eleven monosubstituted epoxides were converted into the corresponding cyclic carbonates in 51–91% yield. A kinetic study showed that the reactions were first order in epoxide, catalyst and tetrabutylammonium bromide and allowed a catalytic cycle to be proposed.
Integrated optical tamper sensor (1991)

This invention consists of an monolithic optical tamper sensor, comprising an optical emitter and detector, connected by an optical waveguide and placed into the critical entry plane of an enclosed sensitive region, the tamper sensor having a myriad of scraps of a material optically absorbent at the wavelength of interest, such that when the absorbent material is in place on the waveguide, an unique optical signature can be recorded, but when entry is attempted into the enclosed sensitive region, the scraps of absorbent material will be displaced and the optical/electrical signature of the tamper sensor will change and that change can be recorded.
Distributed Research Teams: Meeting Asynchronously in Virtual Space (2006)

As computer networks improve, more social and work interactions are carried out “virtually” by geographically separated group members. In this paper we discuss the design of a tool, PAVE, to support remote work interactions among colleagues in different time zones. PAVE extends a 2D graphical MOO and supports synchronous and asynchronous interactions. PAVE logs and indexes activities in the space. This capture facility enables playback and augmentation of meeting interactions by non-collocated group members. Thus, members can participate asynchronously in meetings they could not attend in real time, not just review them.
Large-Field Contextual Feature Learning for Glass Detection (2022)

Glass is very common in our daily life. Existing computer vision systems neglect it and thus may have severe consequences, e.g., a robot may crash into a glass wall. However, sensing the presence of glass is not straightforward. The key challenge is that arbitrary objects/scenes can appear behind the glass. In this paper, we propose an important problem of detecting glass surfaces from a single RGB image. To address this problem, we construct the first large-scale glass detection dataset (GDD) and propose a novel glass detection network, called GDNet-B, which explores abundant contextual cues in a large field-of-view via a novel large-field contextual feature integration (LCFI) module and integrates both high-level and low-level boundary features with a boundary feature enhancement (BFE) module. Extensive experiments demonstrate that our GDNet-B achieves satisfying glass detection results on the images within and beyond the GDD testing set. We further validate the effectiveness and generalization capability of our proposed GDNet-B by applying it to other vision tasks, including mirror segmentation and salient object detection. Finally, we show the potential applications of glass detection and discuss possible future research directions.
Biomechanical properties of an implanted engineered tubular gut-sphincter complex (2016)

Neuromuscular diseases of the gut alter the normal motility patterns. Although surgical intervention remains the standard treatment, preservation of the sphincter attached to the rest of the gut is challenging. The present study aimed to evaluate a bioengineered gut-sphincter complex following its subcutaneous implantation for 4 weeks in rats. Engineered innervated human smooth muscle sheets and innervated human sphincters with a predefined alignment were placed around tubular scaffolds to create a gut-sphincter complex. The engineered complex was subcutaneously implanted in the abdomen of the rats for 4 weeks. The implanted tissues were vascularized. In vivo manometry revealed luminal pressure at the gut and the sphincter zone. Tensile strength, elongation at break and Young's modulus of the engineered complexes were similar to those of native rat intestine. Histological and immunofluorescence assays showed maintenance of smooth muscle circular alignment in the engineered tissue, maintenance of smooth muscle contractile phenotype and innervation of the smooth muscle. Electrical field stimulation induced relaxation of the smooth muscle of both the sphincter and the gut parts. Relaxation was partly inhibited by nitric oxide inhibitor indicating nitrergic contribution to relaxation. The present study has demonstrated for the first time a successfully developed and subcutaneously implanted a tubular human-derived gut-sphincter complex. The sphincteric part of Tubular Gut-Sphincter Complex (TGSC) maintained the basal tone characteristic of a native sphincter. The gut part also maintained its specific neuromuscular characteristics. The results of this study provide a promising therapeutic approach to restore gut continuity and motility. Copyright © 2016 John Wiley & Sons, Ltd.
Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis (2019)

<b>Rationale:</b> Idiopathic pulmonary fibrosis (IPF) is a complex lung disease characterized by scarring of the lung that is believed to result from an atypical response to injury of the epithelium. Genome-wide association studies have reported signals of association implicating multiple pathways including host defense, telomere maintenance, signaling, and cell-cell adhesion.<b>Objectives:</b> To improve our understanding of factors that increase IPF susceptibility by identifying previously unreported genetic associations.<b>Methods:</b> We conducted genome-wide analyses across three independent studies and meta-analyzed these results to generate the largest genome-wide association study of IPF to date (2,668 IPF cases and 8,591 controls). We performed replication in two independent studies (1,456 IPF cases and 11,874 controls) and functional analyses (including statistical fine-mapping, investigations into gene expression, and testing for enrichment of IPF susceptibility signals in regulatory regions) to determine putatively causal genes. Polygenic risk scores were used to assess the collective effect of variants not reported as associated with IPF.<b>Measurements and Main Results:</b> We identified and replicated three new genome-wide significant (<i>P</i> < 5 × 10<sup>-8</sup>) signals of association with IPF susceptibility (associated with altered gene expression of <i>KIF15</i>, <i>MAD1L1</i>, and <i>DEPTOR</i>) and confirmed associations at 11 previously reported loci. Polygenic risk score analyses showed that the combined effect of many thousands of as yet unreported IPF susceptibility variants contribute to IPF susceptibility.<b>Conclusions:</b> The observation that decreased <i>DEPTOR</i> expression associates with increased susceptibility to IPF supports recent studies demonstrating the importance of mTOR signaling in lung fibrosis. New signals of association implicating <i>KIF15</i> and <i>MAD1L1</i> suggest a possible role of mitotic spindle-assembly genes in IPF susceptibility.
Fibre optic pressure and temperature sensor for geothermal wells (2010)

In this paper a fibre optic sensor is developed and tested to measure pressure and temperature under simulated wellbore conditions. The sensor consists of a miniature all-silica fibre optic Extrinsic Fabry-Perot Interferometer (EFPI) sensor which has a novel embedded Fibre Bragg Grating (FBG) reference sensor element to determine both pressure and temperature at the point of measurement. The sensor head is completely fabricated from fused-silica components, i.e. completely made of glass, utilizing a 200μm outer diameter silica glass fibre, a silica glass capillary and a Single-Mode FBG. All silica-glass components were spliced together using a conventional fusion splicer to obtain a robust sensor structure.
iXora: exact haplotype inferencing and trait association (2013)

iXora provides detailed resolution in parental inheritance, along with the capability of handling very large populations, which allows for accurate haplotype extraction and trait association. iXora is available for non-commercial use from http://researcher.ibm.com/project/3430.
Synthesis and Fungicidal Activity of Alicyclic Diamines (1996)

As part of an ongoing program of work on polyamine analogues, a number of alicyclic diamines were synthesized and examined for fungicidal activity. The alicyclic diamine 1,2-bis(aminomethyl)-4,5-dimethylcyclohexa-1,4-diene (BAD), synthesized as the dihydrochloride salt, controlled the important crop pathogen Erysiphe graminis f.sp hordei. Greatest control of E. graminis was achieved when BAD was applied 2 days postinoculation. The alicyclic diamines trans-4,5-bis(aminomethyl)-1,2-dimethylcyclohex-1-ene (trans-BAD) and the cis-isomer (cis-BAD), as well as 1,2-bis(aminomethyl)cyclopentene (BACP) and trans-1,2-bis(dimethylaminomethyl)cyclobutane (TCCBM), were also synthesized as their dihydrochloride salts. trans-BAD was found to possess greater fungicidal activity than the cis-isomer against E. graminis, while BACP and TCCBM both gave >80% control of powdery mildew infection. Since the powdery mildew fungus cannot be grown axenically, the effects of the alicyclic diamines on polyamine metabolism were examined using the oat leaf stripe pathogen, Pyrenophora avenae. BAD and derivatives had little effect on polyamine metabolism in the fungal pathogen P. avenae. It seems clear, therefore, that the antifungal activity of these derivatives may not be associated with altered polyamine metabolism. Keywords: Polyamines; alicyclic diamines; fungicide; powdery mildew
Molecular cloning and in vivo evaluation of canine granulocyte- macrophage colony-stimulating factor (1991)

Abstract Canine granulocyte-macrophage colony-stimulating factor (caGM-CSF) was cloned and expressed to allow further investigation of GM-CSF in a large animal model. The cDNA is 850 base pairs (bp) long and encodes a peptide of 144 amino acids. The nucleotide and amino acid sequence homology between caGM-CSF and human GM-CSF (hGM-CSF) is 80% and 70%, respectively. A mammalian expression vector pCMV/CAGM was constructed and used to transfect COS cells for expression of caGM-CSF. Supernatant from transfected COS cells enriched with caGM-CSF was shown to have significant stimulating activity in granulocyte-macrophage colony forming unit (CFU-GM) assays of canine marrow. caGM-CSF, expressed from bacteria, was used to treat seven dogs at varying doses twice daily subcutaneously (sc) for 14 to 16 days. Circulating blood neutrophils and monocytes increased significantly. The increase in circulating eosinophils was variable. Thrombocytopenia developed during administration of caGM-CSF but corrected rapidly after cessation of treatment. Evaluation of survival times of 51Cr-labeled autologous platelets suggested increased consumption as the primary reason for thrombocytopenia. A species-specific GM-CSF will be a useful tool for hematologic or immunologic studies in dogs.