gebhart/patrepeval huggingface dataset:
Graded-Index Integrated Photonics (2012)

Lead by the theory of Transformation Optics and developments in metamaterials, the field of complex structures is growing in importance in the scientific community. In optics, those concepts add design flexibility to graded-index devices, but fabrication of high refractive index contrasts at the nanometer scale is still challenging. In this presentation we propose three fabrication techniques for high contrast graded-index integrated photonics using only dielectric materials. By avoiding metals and resonant nano-structures we are capable of broad wavelength ranges of operation. Using our fabrication platforms we show how graded-index media can be used to improve existing nanophotonic devices and enable new features in optical systems. Three devices are demonstrated: first, an invisibility cloak that hides a region of space from any external observer. It is implemented with the help of effective material theory and it is composed of nanometer-size silicon pillars. Second, we show that by using a graded-index Luneburg lens to mediate the coupling between optical fibers and highly confined channel waveguides, we can decrease the sensitivity to misalignment in fiber-to-chip couplers. Finally, an optimization algorithm tailored to Transformation Optics in dielectric-only graded media is developed and used to design a multimode waveguide bend with minimal mode conversion. Fabricated via grayscale electron beam lithography, this demonstration enables the utilization of multimode waveguides for integrated photonics and leverages their advantages over single mode waveguides, such as lower propagation loss and higher numerical aperture, without the issue of modal dispersion. Low modal conversion also points towards the possibility of mode multiplexing in future optical interconnects, a path to increase the bandwidth of conventional wavelength-multiplexed systems by folds.
Structural Analysis of Triacylglycerols by Using a MALDI-TOF/TOF System with Monoisotopic Precursor Selection (2012)

A new MALDI-TOF/TOF system with monoisotopic precursor selection was applied to the analysis of triacylglycerols in an olive oil sample. Monoisotopic precursor selection made it possible to obtain product-ion mass spectra without interference from species that differed by a single double bond. Complete structure determination of all triacylglycerols, including structural isomers, was made possible by interpreting the charge-remote fragmentation resulting from high-energy collision-induced dissociation (CID) of the sodiated triacylglycerols.
Optimal display of the coronary arterial tree with an upscan 1,023‐line video display system (1989)

Differences of opinion exist as to whether visualization of the coronary arterial tree is better with 525-line or 1,023-line video imaging systems. The 1,023-line acquisition has been associated with image degradation; 525-line display, however, has prominent raster lines that may also degrade the image. For evaluation of this issue, identical coronary arterial images were obtained with 525-line acquisition and then displayed with either 525-line or 1,023-line display. The 525-line acquisition with digital upscan 1,023-line display had superior image quality compared with 525-line display. With the use of 525-line acquisition and 1,023-line display, video images were similar to or slightly better than the identical cineangiographic images.
Heteroclitic CD33 Peptide With Enhanced Anti-Acute Myeloid Leukemic Immunogenicity (2004)

The goal of these studies was to engineer a synthetic CD33 peptide with enhanced immunogenicity for the induction of acute myeloid leukemia (AML)-specific CTLs. Eight modified CD33 peptides YLISGDSPV, YIGSGDSPV, YIIIGDSPV, YIILGDSPV, YIISGISPV, YIISGDLPV, YIISGDSWV and YIISGDSPL were designed for increased HLA-A2.1 or T cell receptor affinity and compared with the native CD33(65-73) peptide, AIISGDSPV, for enhanced immunogenicity. The YLISGDSPV peptide was found to be the most immunogenic epitope producing highly cytolytic CTLs against AML target cells. The CTLs generated withYLISGDSPV peptide showed CD33 peptide-specificity through targeting of both native (AIISGDSPV) and modified (YLISGDSPV) peptide presenting EBV-BLCL. The CTL cultures displayed a distinct phenotype consisting of a high percentage of activated memory (CD69(+)/CD45RO(+))-CD8(+)and a low percentage of naive (CD45RA(+)/CCR7(+))-CD8(+)cells. In addition, T-cell clones specific to the YLISGDSPV peptide were isolated and characterized to target AML cells. The clones exhibited both HLA-A2.1-restricted and AML cell-specific cytotoxicity that was mediated through a granule-dependent pathway. More importantly, the CTL clones did not lyse or inhibit the proliferation of normal CD34(+) progenitor cells. In conclusion, we report on the identification of a highly immunogenic heteroclitic YLISGDSPV CD33 epitope that is a promising candidate for immunotherapy targeting AML.
Integration of a Micro-Chip Amino Acid Chirality Detector into the MOD Instrument Concept (2004)

The MOD (Mars Organic Detector) instrument concept consists of a sublimation apparatus for organic compound isolation connected to a microfabricated microfluidic analyzer containing a sipper, pumps and a separation channel for organic compound characterization. The target organic compounds are amino acids and polycyclic aromatic hydrocarbons (PAHs). Solid samples are placed within the sublimation apparatus and heated to release organic compounds which sublime onto a cold finger. Half of the cold finger is coated with fluorescamine. which reacts with amino acids and other primary amines to generate an intense fluorescent derivative while the other half is uncoated and is used to directly detect PAH fluorescence, A capillary sipper is then used to dissolve and sample the labeled amino acids and integrated microfabricated pumps transport the labeled amino acids to the chip for analysis. The sample is separated using capillary zone electrophoresis (CZE) together with chiral dextrins to determine amino acid composition and chirality. During the grant period, the following steps have been completed toward the development of a robust instrument and chemistry.
A passive terahertz video camera based on lumped element kinetic inductance detectors (2016)

We have developed a passive 350 GHz (850 μm) video-camera to demonstrate lumped element kinetic inductance detectors (LEKIDs)--designed originally for far-infrared astronomy--as an option for general purpose terrestrial terahertz imaging applications. The camera currently operates at a quasi-video frame rate of 2 Hz with a noise equivalent temperature difference per frame of ∼0.1 K, which is close to the background limit. The 152 element superconducting LEKID array is fabricated from a simple 40 nm aluminum film on a silicon dielectric substrate and is read out through a single microwave feedline with a cryogenic low noise amplifier and room temperature frequency domain multiplexing electronics.
Iron oxide nanoparticles induce cytokine secretion in a complement-dependent manner in a human whole blood model (2017)

Iron oxide nanoparticles (IONPs) are promising nanomaterials for biomedical applications. However, their inflammatory potential has not been fully established. Here, we used a lepirudin anti-coagulated human whole blood model to evaluate the potential of 10 nm IONPs to activate the complement system and induce cytokine production. Reactive oxygen species and cell death were also assessed. The IONPs activated complement, as measured by C3a, C5a and sC5b-9, and induced the production of pro-inflammatory cytokines in a particle-dose dependent manner, with the strongest response at 10 µg/mL IONPs. Complement inhibitors at C3 (compstatin analog Cp40) and C5 (eculizumab) levels completely inhibited complement activation and secretion of inflammatory mediators induced by the IONPs. Additionally, blockade of complement receptors C3aR and C5aR1 significantly reduced the levels of various cytokines, indicating that the particle-induced secretion of inflammatory mediators is mainly C5a and C3a mediated. The IONPs did not induce cell death or reactive oxygen species, which further suggests that complement activation alone was responsible for most of the particle-induced cytokines. These data suggest that the lepirudin anti-coagulated human whole blood model is a valuable ex vivo system to study the inflammatory potential of IONPs. We conclude that IONPs induce complement-mediated cytokine secretion in human whole blood.
Symbolic dynamics approach in the analysis of heart rate in premature babies at high risk for sudden infant death syndrome (SIDS) (2002)

The aim of this study is to evaluate how far the nonlinear symbolic dynamics approach helps to characterize the nonlinear properties of heart rate regulation in high risk infants. The symbolic dynamics calculations were performed on sleep stage classified heart rate (IHR) data. Differences were found in histogram properties of symbol sequences between the risk and the control groups. The results of the analysis suggest that the nonlinear symbolic dynamics approach is helpful in risk stratification of newborns.
The utility of a two‐color fluorescence electrophoretic mobility shift assay procedure for the analysis of DNA replication complexes (2004)

Protein-DNA and protein-protein interactions play essential roles in many biologic processes such as transcription, replication, recombination, and DNA repair. One of the most popular approaches to investigate specific protein-nucleic acid interactions is the electrophoretic mobility shift assay (EMSA). We have developed a new nonradioactive method to detect both nucleotides and protein in EMSA. Nucleic acids are detected with SYBR Green EMSA dye, while proteins are subsequently detected with SYPRO Ruby EMSA dye. All fluorescent staining steps are performed after the entire gel-shift experiment is completed, so there is no need to prelabel either the nucleic acids or the protein. The two-color fluorescence dye staining procedure is fast, simple, and allows independent quantitative determination of either free or bound nucleic acids and protein. The interactions between lac repressor-operator, and among the T4 primase-helicase, primase-DNA, helicase-DNA, and within T4 [ssDNA-primase-helicase6] primosome, were used to demonstrate the advantages of this two-color fluorescence detection EMSA method.
Epoxidation and Oxygen Insertion Into Alkane Ch Bonds by Dioxirane Do Not Involve Detectable Radical Pathways (1997)

Abstract The dimethyldioxirane oxidation of α‐methylstyrene, trans ‐cyclo‐octene, and 1‐vinyl‐2,2‐diphenylcyclopropane gave, under all reaction conditions employed, the corresponding epoxides in high yields. No radical products from allylic oxidation, from trans/cis isomerization, or from cyclopropylcarbinyl rearrangement (radical clock) were observed. Even for these alkenes, which are prone to radical reactions, the previously established electrophilic concerted mechanism applies, rather than the recently proposed radical mechanism. The selective hydroxylation of (–)‐2–phenylbutane by dimethyldioxirane gave only (– )‐2–phenylbutan‐2‐ol with complete retention of configuration and no loss of optical purity. Thus, a radical‐chain oxidation is also discounted in the oxygen insertion into hydrocarbon C‐H bonds for dioxiranes.
Investigation of unusual mobile ion effects in thermally grown SiO2 on 4H-SiC(0001) at high temperatures (2012)

Generation and elimination of mobile ions in thermally grown SiO2 on 4H-SiC(0001) were systematically investigated by electrical measurements of MOS capacitors. In contrast to a SiO2/Si system, intrinsic positive mobile ions were found to exist in as-oxidized SiO2/SiC structures, leading to significant instability of SiC-MOS devices. Post-oxidation annealing in Ar ambient mostly eliminates the mobile ions, but they are generated again by subsequent high-temperature hydrogen annealing despite the improved interface quality. The density of the mobile ions was estimated to be several 1012 cm−2. Possible physical origins of the mobile ions are discussed on the basis of the experimental findings.
The Effects of Fluid Hammer Tools on the Efficiencies of Coiled Tubing Plug Milling - A Comparative Best Practices Study (2011)

Abstract Horizontal fracture stimulated completions remain the de facto method of producing from shale formations. The vast majority of wells are completed using the "Plug and Perf’ fracturing technique which later requires either a drill string or coiled tubing (CT) with a positive displacement motor (PDM) to remove the composite plugs. An estimated 6,000 to 8,000 wells are completed each year, with between 100,000 to 140,000 composite plugs installed in them in the U.S. alone. In extended reach horizontal completions, plug removal using CT becomes less efficient since end load forces transmitted to the PDM from the coiled tubing decrease as well depth increases. Currently many operators rely on ‘word of mouth’ to design and perform extended reach CT jobs, resulting in ‘non-engineered’ and poorly executed plug milling operations. However, one new method to extend the operating envelope of efficient coiled tubing plug milling utilizing a water hammer tool has gained significant momentum. Several water hammer tools are in common use and there is significant anecdotal evidence that their application has improved job efficiencies. This paper reviews plug milling efficiencies and general best practices from milling operations conducted in shale formations across the US (Eagle Ford, Bakken, Haynesville, Barnett and the Marcellus). The scope will cover operations completed with three different fluid hammer tools and base cases conducted without these tools. The paper will also discuss milling efficiencies, number of stalls, stuck pipe incidents, speed and frequency of wiper trips and fluid selection associated with plug milling operations. The authors believe that the information presented in this paper will provide relevant analytical data to assist operators in improving the overall efficiency of the completion process.
ASN Presidential Address 2013: innovation and individualization--the path forward for nephrology (2014)

Welcome to the 47th Annual Meeting of the American Society of Nephrology (ASN)—Kidney Week 2013. Thank you for helping to lead the fight against kidney disease in the United States and across the globe. As ASN President, I would like to thank you for the opportunity to lead this outstanding
Figure S2 from Autocrine Adenosine Regulates Tumor Polyfunctional CD73<sup>+</sup>CD4<sup>+</sup> Effector T Cells Devoid of Immune Checkpoints (2023)

&lt;p&gt;Impact of rh-ADA on Ado-mediated inhibition of CD73+ or CD73neg CD4+ Teff based on the proliferation marker profiles (Cell Trace Violet or CFSE)&lt;/p&gt;
Warop Deformation and Residual Stresses of Two Layered Laminated Bodies Consisted of Metal and Thermosetting Resin. (1994)

LSIプラスチックパッケージを構成する熱硬化性樹脂であるLSI封止用レジンとFe-Ni合金である42アロイリードフレームからなる二層積層体を冷却した場合に発生する反り変形量と残留応力について, 粘弾性解析, 弾性解析, および実験解析を行った. その結果, 粘弾性解析は材料物性の時間および温度依存性を考慮した厳密な解析法であり, 解析結果は実験値とほぼよく一致する. また, 材料物性の温度依存性を考慮すれば汎用の弾性解析でも実用上問題がない場合がある. さらに, 積層体の反り変形や残留応力は, 基本的にレジンの粘弾性挙動と積層体の剛性の両者が複雑に関係しあって生じることがわかった.
The AIM Photonics MPW: A Highly Accessible Cutting Edge Technology for Rapid Prototyping of Photonic Integrated Circuits (2019)

Silicon photonics has been heralded for a number of high technology fields, but access to a high quality technology has been limited to vertically integrated design/fabrication companies, or fabless companies with significant resources to engage high volume fabs. More recently, research and development hubs have developed and released process design kits and multi-project wafer programs to lower the barrier. We present the first silicon photonics multi-project wafer (MPW) service produced in a state-of-the-art 300 mm fabrication facility. The MPW service is enabled by a best-in-class process design kit (PDK) which allows designers to layout and obtain photonic integrated circuits (PICs) that work properly on the first run. The fabrication of these circuits is carried out at the SUNY Polytechnic Institute which operates a world class 300 mm cleanroom that, besides silicon photonics, develops sub-7 nm CMOS architectures. The industrial-level management of this facility and its equipment provides high quality photonic devices which are repeatable from run-to-run along with rapid turnaround time. The devices that are available to designers via the process design kit are produced by Analog Photonics and have been verified on actual runs. The performance of these devices is comparable to the state-of-the-art and enables a wide variety of silicon photonic applications.
Sequence‐Specific Manipulation of DNA (1999)

In this chapter various methods are described that take advantage of the specific recognition of DNA sequences to allow analytical or preparative procedures to be carried out on a selected fraction of a complex DNA sample. For example, one can design chemical or enzymatic schemes to cut at extremely specific DNA sites, to purify specific DNA sequences, or to isolate selected classes of DNA sequences.
The Amelia-1 study: A phase 1b/2 trial of evexomostat (SDX-7320) plus fulvestrant and alpelisib in patients with advanced breast cancer at risk for alpelisib-induced hyperglycemia. (2023)

TPS1129 Background: Alpelisib, a selective PI3K p110a inhibitor, was approved for breast cancer patients with PIK3CA mutations. An on-target toxicity of alpelisib is hyperglycemia and patients with baseline insulin resistance/elevated HbA1c are at greater risk of developing grade 3,4 hyperglycemia after receiving alpelisib. Restoring insulin sensitivity and reducing systemic insulin levels improved the efficacy of alpelisib in animal models of breast cancer. Evexomostat is a polymer-drug conjugate of a novel small molecule methionine aminopeptidase 2 (MetAP2) inhibitor. In normal mice, it reduced alpelisib-induced hyperglycemia/hyperinsulinemia and in an animal model of breast cancer synergized with alpelisib to regress tumor growth. In a Phase 1 trial, evexomostat improved insulin resistance in patients with elevated baseline insulin, reduced angiogenic factors in patients with elevated baseline levels, increased the insulin-sensitizing adipokine adiponectin and showed anti-metastatic effects in patients with advanced solid tumors. Methods: This is a phase 1b/2, open-label, single-arm pilot study (NCT05455619) in postmenopausal women with HR+, HER2- metastatic breast cancer with a PIK3CA mutation who progressed following treatment with endocrine therapy plus a CDK4/6 inhibitor and who are at risk for hyperglycemia (HbA1c between 5.5 and 6.4%inclusive). The primary goal is to determine the safety of evexomostat plus alpelisib and fulvestrant (the ‘triplet therapy’), including the severity and number of hyperglycemic events, as well as anti-tumor benefit. The starting dose of evexomostat in the triplet therapy is 36 mg/m 2 (n=6; one dose below the monotherapy MTD of 49 mg/m 2 ). Once the MTD of evexomostat in the triplet therapy has been defined, up to 20 patients will be enrolled at that dose. An additional 20 patients may be enrolled to further characterize the safety and anti-tumor effect of the triplet therapy (up to 52 patients). This trial is open to accrual at multiple sites in the USA. Safety analysis includes the type, frequency, and severity of treatment-emergent adverse events (TEAEs) per NCI CTCAE, v5, and the number and proportion of patients with grade 3 or 4 hyperglycemia during the first 2 cycles of therapy, with an estimate of the exact upper one-sided 97.5% confidence bound. Efficacy analyses include objective response rate (ORR, consisting of complete response (CR) and partial response (PR)). The number of patients without disease progression six months from the start of the triplet therapy will be assessed. The CBR of CRs, PRs plus stable disease ≥24 weeks from C1D1 will be calculated. Overall survival data will be summarized as available. QoL will be analyzed according to functional scores and recommendations in the EORTC scoring manual. ECOG performance status and change from baseline will be summarized. Clinical trial information: NCT05455619 .
Transformation of a cloning vector, pUB110, intoBacillus anthracis (1987)

A kanamycin-resistance plasmid, pUB110, was introduced into Bacillus anthracis by a newly devised method of transformation. The transformation frequency was ca. 1 × 103 cells/1 μg DNA.
The Negative Solvatochromism of Reichardt‘s Dye B30 – A Complementary Study (2022)

The UV/Vis spectra of a hypothetical negative solvatochromic dye in a solvent are theoretically calculated assuming the classical damped harmonic oscillator model and the Lorentz-Lorenz relation. For the simulations, the oscillator strength of the solvent was varied, while for the solute all oscillator parameters were kept constant. As a result, a simple change of the oscillator strength of the solute can explain the redshift and intensity increase of the UV/Vis band of the solute. Simulated results are compared with measured UV/Vis spectroscopic data of 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate B30 (Reichardt's dye) Significant correlations of the absorption energy (1/λ<sub>max</sub> ) with the molar absorption coefficient ϵ as function of solvent polarity are demonstrated for several derivatives of B30. The approach presented is only applicable to negative solvatochromism. Therefore, while the approach is vital to fully understand solvatochromism, it needs to be complemented by other approaches, e. g., to describe the changes of the chemical interactions based on the nature of the solvent, to explain all its various aspects.
Ectopic Hepcidin Production in Anemia of Cancer (2008)

Anemia is a frequent manifestation of almost all cancers. In some cases, the etiology of the anemia is clear (bleeding, bone marrow infiltration, or chemotherapy). When none of these factors are present, the anemia is referred to as anemia of cancer (AC). Hepcidin is a hormone synthesized in the liver that inhibits iron absorption from the diet and iron release from stores. In 2 patients with hepcidin secreting hepatic adenomas, AC resolved when the tumors were removed (Weinstein et al, Blood, 2002). However, it is unclear whether tumors not of hepatic origin can make hepcidin or whether this mechanism contributes to AC. We created two models of metastatic lung cancer by injecting two syngeneic lung cancer cell lines (TC‐1 and LCC) into the peritoneal cavities of C57Bl6 mice. Our data shows that hepcidin production is increased in both the liver and the tumor from TC‐1 injected mice. Inflammatory markers, SAA‐1 and FGN‐ã, are also elevated, indicating that the rise in hepatic hepcidin is likely due to inflammation. LLC‐injected mice developed less severe anemia and the increase in hepcidin mRNA was not significant. LLC tumors expressed measurable amounts of hepcidin but significantly less than TC‐1 tumors or control livers. Inflammatory induction of hepcidin likely plays an important role in AC. Some tumors express hepcidin, which could contributing to AC.
Plipastatins: New inhibitors of phospholipase A2, produced by Bacillus cereus BMG302-fF67. I. Taxonomy, production, isolation and preliminary characterization. (1986)

Plipastatins have been isolated as part of a program designed to find inhibitors of porcine pancreatic phospholipase A2. They were purified from fermentation broth of Bacillus cereus BMG302-fF67 and finally separated into four fractions by reverse phase HPLC. The respective fractions were designated as plipastatins A1, A2, B1 and B2. Plipastatins also inhibited phospholipases C and D.