gebhart/patrepeval huggingface dataset:
Phonon‐polaritonics: enabling powerful capabilities for infrared photonics (2018)

Abstract Here, we review the progress and most recent advances in phonon‐polaritonics, an emerging and growing field that has brought about a range of powerful possibilities for mid‐ to far‐infrared (IR) light. These extraordinary capabilities are enabled by the resonant coupling between the impinging light and the vibrations of the material lattice, known as phonon‐polaritons (PhPs). These PhPs yield a characteristic optical response in certain materials, occurring within an IR spectral window known as the reststrahlen band. In particular, these materials transition in the reststrahlen band from a high‐refractive‐index behavior, to a near‐perfect metal behavior, to a plasmonic behavior – typical of metals at optical frequencies. When anisotropic they may also possess unconventional photonic constitutive properties thought of as possible only with metamaterials. The recent surge in two‐dimensional (2D) material research has also enabled PhP responses with atomically‐thin materials. Such vast and extraordinary photonic responses can be utilized for a plethora of unusual effects for IR light. Examples include sub‐diffraction surface wave guiding, artificial magnetism, exotic photonic dispersions, thermal emission enhancement, perfect absorption and enhanced near‐field heat transfer. Finally, we discuss the tremendous potential impact of these IR functionalities for the advancement of IR sources and sensors, as well as for thermal management and THz‐diagnostic imaging.
Laser-written integrated photonics in glass-ceramics Zerodur (2020)

We demonstrated fabrication of waveguide and directional coupler in bulk glass-ceramics Zerodur, through femtosecond laser direct-writing. Waveguide propagation loss of no more than 1.5 dB/cm was achieved. We expect this will lead to the deployment of Zerodur integrated photonics in fields like space-borne astronomy, quantum technology and fundamental physics, for both economic and technical benefits.
Bromide and Other Halide Ion Removal From Drinking Waters Using Silver‐Amended Coagulation (2018)

High bromide ion concentrations are of concern because of formation of brominated disinfection byproducts in drinking water, which may be more toxic than their chlorinated analogs. Jar tests dosed with alum and silver were performed on several water samples with chloride‐to‐bromide (Cl:Br) ratios ranging from 15 to 866 mg Cl/mg Br. In lower‐chloride waters (15 mg Cl/mg Br), silver‐amended coagulation (SAC) removed 20–90% of the initial bromide. In higher‐chloride water (525 mg Cl/mg Br), a silver dose of 15 mol Ag/mol Br achieved 40% bromide removal. Iodide and chloride removal also occurred during silver addition. SAC did not influence total organic carbon or turbidity removal, and residual silver was below the secondary maximum contaminant level but was successful in decreasing trihalomethane (THM) formation from 44 to 28 μg/L by shifting away from brominated THM species. SAC may only be applicable and cost‐effective in a narrow range of waters with lower Cl:Br ratios, and other technologies should be developed for waters with &gt;300 mg Cl/mg Br.
ChemInform Abstract: PHOTOISOMERIZATION OF BIS(TRIFLUOROMETHYL)THIOPHENES (1984)

Abstract 2,3‐Bis‐trif1uormethyl‐ thiophen (I) liefert bei der Photolyse die Bicyclen (II) und (III) sowie die Bis‐trifluormethyl‐thiophene (IV)‐(VI), wobei (IV) bei längerem Bestrahlen in (V) übergeht.
Disruptin, a cell-penetrating peptide degrader of EGFR (2021)

Disruptin is a cell-permeable decoy peptide designed to destabilize activated EGFR, both by inhibiting Hsp90 chaperoning and dissociating the active asymmetric EGFR dimer, which leads to an increase in engagement of activated EGFR with the proteolytic degradation machinery and subsequent loss from the cells. Disruptin is an N-terminally biotinylated nonadecapeptide, with 8 amino acids from the αC-helix-β4 sheet loop of EGFR (S<sup>767</sup>-C<sup>774</sup>) fused to a TAT undecapeptide. The S<sup>767</sup>-R<sup>775</sup> loop is at the interface with juxtamembrane domains in the active EGFR dimers and is a binding site for Hsp90. Cellular studies in EGFR-activated tumor cells demonstrated that Disruptin causes the disappearance of EGFR protein from cells over a few hours, a growth inhibitory effect, similar but more effective than the EGFR kinase inhibition. Interestingly, cells without activated EGFR remained unaffected. In vivo studies showed that Disruptin slowed the growth of small tumors. Larger tumors responded to intratumoral injections but did not respond to systemic administration at tolerated doses. Investigation of these results revealed that systemic administration of Disruptin has acute toxicities, mainly related to its TAT peptide moiety. Therefore, we conclude that although the efficacy of both in vitro and in vivo intratumoral injection of Disruptin supports the therapeutic strategy of blocking activated EGFR dimerization, Disruptin is not suitable for further development. These studies also highlight the importance of the chosen models and drug-delivery methods for such investigations.
Analysis on Transition between Index- and Bandgap-guided Modes in Photonic Crystal Fiber (2016)

We calculate optical properties of guided modes of a hybrid-guiding photonic crystal fiber. The design and modeling of such hybrid-guiding PCF is made by replacing air holes with inserts of high refractive index material layer by layer in order. The optical properties such as mode intensity profile, mode dispersion, optical birefringence, confinement loss, and chromatic dispersion during transition of the guiding mechanism are analyzed and discussed. The guided modes in the hybrid-guiding region are also compared with those of reference index-guiding and bandgap-guiding photonic crystal fibers.
Deep Circumflex Iliac Artery Perforator Skin Flap: Anatomic Study and Clinical Application (2006)

The groin donor site distinguishes itself among other choices because it is easily concealed and has minimal morbidity. However, the flap has many drawbacks including a short pedicle length and small sized vessels. A perforator skin flap in this region would potentially offer the advantages of an aesthetically favored donor scar, long vascular pedicle, and minimal donor-site morbidity. The purpose of this report was to describe the anatomic basis of the deep circumflex iliac artery (DCIA) perforator skin flap and to report clinical applications.
Mesoporous Titanium Dioxide Nanofibers with a Significantly Enhanced Photocatalytic Activity (2016)

Abstract Mesoporous TiO 2 nanofibers with controlled diameter, crystal size, and anatase versus rutile crystal structures are produced by calcination at 500–700 °C of precursor nanofibers of polyvinylpyrrolidone and titanium isopropoxide, obtained from a scalable gas jet fiber spinning process. These TiO 2 nanofibers are used in the photocatalytic oxidation of gas‐phase ethanol at room temperature on exposure to UV irradiation. The experimental trends are analyzed using electron–hole (e‐h) charge recombination inferred from high‐intensity photoluminescence emission spectra, specific surface area, crystallinity, and the proportions of anatase and rutile phases. The nanofibers show a photocatalytic activity that is up to an order of magnitude higher than that of commercial‐grade P25 TiO 2 nanoparticles because of slower e‐h recombination phenomena in the former. The results show that ethanol undergoes complete oxidation into CO 2 and H 2 O on the nanofibers without the accumulation of the intermediate products acetaldehyde and formic acid.
Antibody attributes that predict the neutralization and effector function of polyclonal responses to SARS-CoV-2 (2022)

Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.
New porphyrin dendrimers with fluorenyl-based connectors: a simple way to improving the optical properties over dendrimers featuring 1,3,5-phenylene connectors (2020)

Dendrimers with new fluorenyl-based connectors have been synthesized and characterized. Their detailed luminescence properties and selected photophysical properties are discussed in the frame of two-photon-induced theranostics.
Flightweight Carbon Nanotube Magnet Technology (2003)

Virtually all plasma-based systems for advanced airborne/spaceborne propulsion and power depend upon the future availability of flightweight magnet technology. Unfortunately, current technology for resistive and superconducting magnets yields system weights that tend to counteract the performance advantages normally associated with advanced plasma-based concepts. The ongoing nanotechnology revolution and the continuing development of carbon nanotubes (CNT), however, may ultimately relieve this limitation in the near future. Projections based on recent research indicate that CNTs may achieve current densities at least three orders of magnitude larger than known superconductors and mechanical strength two orders of magnitude larger than steel. In fact, some published work suggests that CNTs are superconductors. Such attributes imply a dramatic increase in magnet performance-to-weight ratio and offer real hope for the construction of true flightweight magnets. This Technical Publication reviews the technology status of CNTs with respect to potential magnet applications and discusses potential techniques for using CNT wires and ropes as a winding material and as an integral component of the containment structure. The technology shortfalls are identified and a research and technology strategy is described that addresses the following major issues: (1) Investigation and verification of mechanical and electrical properties, (2) development of tools for manipulation and fabrication on the nanoscale, (3) continuum/molecular dynamics analysis of nanotube behavior when exposed to practical bending and twisting loads, and (4) exploration of innovative magnet fabrication techniques that exploit the natural attributes of CNTs.
Supplementary Figure 1 from JAGGED1 Expression Is Associated with Prostate Cancer Metastasis and Recurrence (2023)

Supplementary Figure 1 from JAGGED1 Expression Is Associated with Prostate Cancer Metastasis and Recurrence
Do consanguineous parents of a child affected by an autosomal recessive disease have more DNA identical-by-descent than similarly-related parents with healthy offspring? Design of a case-control study (2010)

This study contains a new approach to risk assessment in consanguineous couples. There is no previous study on the amount of DNA identical-by-descent in consanguineous parents of affected children compared to the consanguineous parents of healthy children. If our hypothesis proves to be correct, further studies are needed to obtain different risk figure estimates for the different proportions of DNA identical-by-descent. With more precise information about their risk status, empowerment of couples can be improved when making reproductive decisions.
MP63-10 IMPACT OF URETERAL ACCESS SHEATH DIAMETER ON THE OUTCOMES OF FLEXIBLE URETEROSCOPIC STONE REMOVAL AS DETERMINED BY THE URETEROSCOPIC STONE EFFICIENCY QUOTIENT (2020)

INTRODUCTION AND OBJECTIVE: The use of a ureteral access sheath (UAS) during flexible ureteroscopy (URS) enhances pressure-flow dynamics within the collecting system, resulting in improved visualization and maintenance of lower intrarenal pressure. As the diameter of the deployed UAS increases, there is a concomitant improvement in irrigant flow and easier removal of larger stone fragments. We evaluated the impact of the largest diameter UAS (i.e. 16 Fr), on post URS computed tomography (CT) stone free rates (SFR) and herein introduce the concept of the ureteroscopic stone efficiency quotient (USEQ). METHODS: We reviewed our prospectively maintained database, and evaluated patients undergoing URS for renal calculi with the use of an 11 Fr, 14 Fr, or 16 Fr UAS. At the outset of each case, passage of a 16 Fr UAS was attempted; if the 16 Fr UAS did not pass easily, then the UAS was downsized to a smaller sheath. Patient demographics, stone parameters, procedure time, and postoperative CT scan results were recorded. SFR was defined as complete absence of stones. The USEQ was defined as: %SFR / operative time (minutes) X 100. We evaluated the outcomes of the three UASs using student’s T test, Chi square test, and logistic regression. RESULTS: Among 110 patients undergoing URS between January 2018 and June 2019, 56 patients with renal stones (65 renal units) had a postoperative CT. Mean aggregate stone size was 15±7 mm, number of stones 2.7±1.6, and stone density 711±430 HU. We deployed 11 Fr, 14 Fr, and 16 Fr UAS in 12%, 29%, and 59% of renal units, respectively. Stone parameters did not differ significantly among the three groups. Median time to patients’ postoperative CT was 39 days. The overall SFR was 55%. Using univariate analysis, the stone-free cohort had smaller aggregate stone size (13 vs. 18 mm, p=0.03) and fewer stones (2.2 vs. 3.2, p=0.01). The SFR for 16 Fr vs. 14 Fr was 58% and 63% (p=0.7) while the SFR for 16 Fr vs. 11 Fr was 58% and 25% (p=0.09). There were 3 (4.6%) UAS-induced high grade ureteral injuries noted as a split in the urothelium (post ureteroscopy lesion scale = 3, based on a 0-5 scoring system); all were treated with a ureteral stent. The use of 16 Fr UAS was associated with shorter operative time (92 minutes) compared to the 14 Fr UAS (139 minutes, p=0.03) and 11 Fr UAS (118 minutes, p=0.53). The USEQ was markedly improved with use of the 16 Fr UAS: 64 vs. 14 Fr: 45 vs. 11 Fr: 21. CONCLUSIONS: Use of a 16 Fr UAS vs. a 14 Fr or 11 Fr UAS reduced operative time without impairment of SFR while markedly augmenting the ureteroscopy stone efficiency quotient. Source of Funding: none
Turnover and Inactivation Mechanisms for (S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase (2021)

The inhibition of human ornithine δ-aminotransferase (<i>h</i>OAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (<i>S</i>)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, <b>6</b>) was identified as a potent mechanism-based inactivator of <i>h</i>OAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of <b>6</b>. A monofluorinated ketone (<b>M10</b>) was identified as the primary metabolite of <b>6</b> in <i>h</i>OAT. By soaking <i>h</i>OAT holoenzyme crystals with <b>6</b>, a precursor to <b>M10</b> was successfully captured. This <i>gem</i>-diamine intermediate, covalently bound to Lys292, observed for the first time in <i>h</i>OAT/ligand crystals, validates the turnover mechanism proposed for <b>6</b>. Co-crystallization yielded <i>h</i>OAT in complex with <b>6</b> and revealed a novel noncovalent inactivation mechanism in <i>h</i>OAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.
ChemInform Abstract: Caesium Trifluoroacetate Displacement of Triflates in the Inversion of Alcohols. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Enhancing Software Traceability by Automatically Expanding Corpora with Relevant Documentation (2013)

Software trace ability is the ability to describe and follow the life of a requirement in both a forward and backward direction by defining relationships to related development artifacts. A plethora of different trace ability recovery approaches use information retrieval techniques, which depend on the quality of the textual information in requirements and software artifacts. Not only is it important that stakeholders use meaningful names in these artifacts, but also it is crucial that the same names are used to specify the same concepts in different artifacts. Unfortunately, the latter is difficult to enforce and as a result, software trace ability approaches are not as efficient and effective as they could be - to the point where it is questionable whether the anticipated economic and quality benefits were indeed achieved. We propose a novel and automatic approach for expanding corpora with relevant documentation that is obtained using external function call documentation and sets of relevant words, which we implemented in Trace Lab. We experimented with three Java applications and we show that using our approach the precision of recovering trace ability links was increased by up to 31% in the best case and by approximately 9% on average.
Structure-activity relationships for unit C pyridyl analogues of the tuberculosis drug bedaquiline (2019)

The ATP-synthase inhibitor bedaquiline is effective against drug-resistant tuberculosis but is extremely lipophilic (clogP 7.25) with a very long plasma half-life. Additionally, inhibition of potassium current through the cardiac hERG channel by bedaquiline, is associated with prolongation of the QT interval, necessitating cardiovascular monitoring. Analogues were prepared where the naphthalene C-unit was replaced with substituted pyridines to produce compounds with reduced lipophilicity, anticipating a reduction in half-life. While there was a direct correlation between in vitro inhibitory activity against M. tuberculosis (MIC<sub>90</sub>) and compound lipophilicity, potency only fell off sharply below a clogP of about 4.0, providing a useful lower bound for analogue design. The bulk of the compounds remained potent inhibitors of the hERG potassium channel, with notable exceptions where IC<sub>50</sub> values were at least 5-fold higher than that of bedaquiline. Many of the compounds had desirably higher rates of clearance than bedaquiline, but this was associated with lower plasma exposures in mice, and similar or higher MICs resulted in lower AUC/MIC ratios than bedaquiline for most compounds. The two compounds with lower potency against hERG exhibited similar clearance to bedaquiline and excellent efficacy in vivo, suggesting further exploration of C-ring pyridyls is worthwhile.
[Co/Ni]-CoFeB hybrid free layer stack materials for high density magnetic random access memory applications (2016)

Alternative free layer materials with high perpendicular anisotropy are researched to provide spin-transfer-torque magnetic random access memory stacks' sufficient thermal stability at critical dimensions of 20 nm and below. We demonstrate a high tunnel magetoresistance (TMR) MgO-based magnetic tunnel junction stack with a hybrid free layer design made of a [Co/Ni] multilayer and CoFeB. The seed material on which the [Co/Ni] multilayer is deposited determines its switching characteristics. When deposited on a Pt seed layer, soft magnetic switching behavior with high squareness is obtained. When deposited on a NiCr seed, the perpendicular anisotropy remains high, but the squareness is low and coercivity exceeds 1000 Oe. Interdiffusion of the seed material with the [Co/Ni] multilayers is found to be responsible for the different switching characteristics. In optimized stacks, a TMR of 165% and low resistance-area (RA) product of 7.0 Ω μm2 are attained for free layers with an effective perpendicular magnetic anisotropy energy of 1.25 erg/cm2, which suggests that the hybrid free layer materials may be a viable candidate for high density magnetic random access memory applications.
Disorders of Vascular Permeability (2016)

The endothelial barrier maintains vascular and tissue homeostasis and modulates many physiological processes, such as angiogenesis. Vascular barrier integrity can be disrupted by a variety of soluble permeability factors, and changes in barrier function can exacerbate tissue damage during disease progression. Understanding endothelial barrier function is critical for vascular homeostasis. Many of the signaling pathways promoting vascular permeability can also be triggered during disease, resulting in prolonged or uncontrolled vascular leak. It is believed that recovery of the normal vasculature requires diminishing this hyperpermeable state. Although the molecular mechanisms governing vascular leak have been studied over the last few decades, recent advances have identified new therapeutic targets that have begun to show preclinical and clinical promise. These approaches have been successfully applied to an increasing number of disease conditions. New perspectives regarding how vascular leak impacts the progression of various diseases are highlighted in this review.
Molecular Mechanism of Ochratoxin A Transport in the Kidney (2010)

The mycotoxin, ochratoxin A (OTA), is thought to be responsible for Balkan endemic nephropathy. OTA accumulates in several tissues, especially in the kidneys and liver. The excretion of OTA into urine is thought to be mainly by tubular secretion, presumably via the organic anion transport system. Recently, several families of multispecific organic anion transporters have been identified: organic anion transporters (OATs), organic anion-transporting polypeptides (OATPs), oligopeptide transporters (PEPTs), and ATP-binding cassette (ABC) transporters, such as MRP2 and BCRP. These renal transporters mediate the transmembrane transport of OTA and play a pivotal role in the development of OTA-induced nephrotoxicity.
Reactions of 3-Hydrazino-5H-1,2,4-triazino[5,6-b]indoles with Trifluoroacetic Anhydride, Acetylacetone, Hexafluoroacetylacetone and Acetophenone (1981)

3-Hydrazin0-5&1.2,4triazino [5,6-b] indole affords a t e t r a c y c l i c r i n g system containing compound: 3-trifluorcm e t h y l -1 0 ~1 , 2 , 4 t r i a z o l o [4',3':2,3] [I ,2,4]triazino[5,6-b] indole with t r i f l u o r o a c e t i c anhydride.3-Hydrazino derivatives, r e a c t with acetylacetone, i n absolute ethanol giving r i s e t o 3-fi-(3,5-dimethylp~azolyl)] -551.2, k t r i a z i n o [5,6-b] indoles while t h e reaction with hexafluoroacetylacetone gives c c r r e s ponding hydrazone instead of expected 3-~-( 3 , 5 -b i s ( t r i f l u o r omethyl)pyrazolyl)] -5&1 , 2 , 4 t r i a z i n o 15,~-blindole. 3 -P i d r azino derivatives also condense with aoetophenone but t h e r e s u l t i n g hydrazone does not produce thiazclidinone with mercaptoacetic acid.A l l t h e synthesized compounds have been characterized on t h e basis of elemental analyses and ir,pmr, 'V