gebhart/patrepeval huggingface dataset:
Expanding the Toolbox of Photoswitches for DNA Nanotechnology Using Arylazopyrazoles (2017)

Photoregulation is among the most promising tools for development of dynamic DNA nanosystems, due to its high spatiotemporal precision, biocompatibility, and ease of use. So far, azobenzene and its derivatives have shown high potential in photocontrolling DNA duplex hybridization by light-dependent photoisomerization. Despite many recent advances, obtaining sufficiently high photoswitching efficiency under conditions more suitable for work with DNA nanostructures are challenging. Here we introduce a pair of arylazopyrazoles as new photoswitches for efficient and reversible control of DNA hybridization achieved even at room temperature with a low number of required modifications. Their photophysical properties in the native state and in DNA strands result in near-quantitative isomerization rates by irradiation with UV and orange light. To demonstrate the applicability of these photoswitches, we have successfully applied one of them to open and close a DNA hairpin by light at room temperature.
Nicotinylalanine Increases the Formation of Kynurenic Acid in the Brain and Antagonizes Convulsions (1992)

Kynurenic acid (KYNA) was quantified in the extracellular spaces of the rat hippocampus using microdialysis and HPLC (fluorimetric detection) to study the possible role of this tryptophan metabolite in the modulation of the function of the N-methyl-D-aspartate (NMDA) receptor. Addition of probenecid (1 mM), which is an inhibitor of the organic acid transport system, to the Ringer's solution perfusing the dialysis probe increased the KYNA concentration in the dialysate from 10.4 +/- 0.9 to 48 +/- 6 nM. Addition of 2 mM aminooxyacetic acid, a nonspecific inhibitor of KYNA synthesis, reduced this concentration by 50%. These data suggest that KYNA is continuously synthesized in the rat hippocampus. Nicotinylalanine (NAL), 200-400 mg/kg i.p., an analogue of kynurenine that is able to direct the flow of tryptophan metabolites toward the synthesis of KYNA, significantly increased the KYNA concentration in the hippocampal dialysate and significantly potentiated the effect of tryptophan on the accumulation of KYNA in the brain and other organs. This increase resulted in pharmacological actions compatible with an antagonism of the NMDA receptors. In fact, NAL antagonized sound-induced seizures and prevented death in DBA/2 mice. Pretreatment of the mice with D-serine (100 micrograms intracerebroventricularly), a glycine agonist and a competitive antagonist of KYNA, completely prevented the anticonvulsive action of NAL. These data suggest that changes in the extracellular concentration of KYNA in the brain are associated with a modulation of NMDA receptor function.
P1‐400: TAU AND ALPHA‐SYNUCLEIN SELECTIVE BINDING COMPOUNDS DERIVED FROM APRINOIA THERAPEUTIC'S PM‐PBB3 BINDING‐SITE FOCUSED COMPOUND COLLECTION (2018)

18F-PM-PBB3 is unique among known Tau imaging agents as it has been shown to be useful for PET imaging of Tau lesions in both AD (3R + 4R) and progressive supranuclear palsy (4R) pathologies. Aprinoia, in collaborating with QST, has initiated global clinical studies with 18F-PM-PBB3 in the US, China, Japan and Taiwan. Aprinoia's development of the next generation PM-PBB3 binding-site focused tracer has led to the generation of a ∼1000 compound CNS-biased collection. This collection has been screened against other protein aggregates and targets to generate selective new leads. Here, we describe the screen of both tau and alpha-synuclein (aSyn) selective binding compounds via in vitro generated aSyn and Tau aggregated proteins. Our goal is to provide a single imaging compound able to image multi-isoforms of Tau across various tauopathies. Additionally, we hope to leverage our compound collection to generate tracers for other protein aggregates such as alpha-synuclein, TDP-43 etc., to help facilitate diagnosis, track progression and assist clinical trials.
Antibacterial and Solubility Optimization of Thiomuracin A (2016)

Synthetic studies of the antimicrobial secondary metabolite thiomuracin A (1) provided access to analogues in the Northern region (C2-C10). Selective hydrolysis of the C10 amide of lead compound 2 and subsequent derivatization led to novel carbon- and nitrogen-linked analogues (e.g., 3) which improved antibacterial potency across a panel of Gram-positive organisms. In addition, congeners with improved physicochemical properties were identified which proved efficacious in murine sepsis and hamster C. difficile models of disease. Optimal efficacy in the hamster model of C. difficile was achieved with compounds that possessed both potent antibacterial activity and high aqueous solubility.
Block polymers from isocyanate‐terminated intermediates. IV. Properties of cured butadiene–ε‐caprolactam block polymers (1975)

Abstract Butadiene–ε‐caprolactam block polymers containing a high proporation of 1,2 units in the butadiene‐segments were synthesized and physical properties were measured on the cured copolymers. Flexural strength and impact resistance both increase regularly with increasing ε‐caprolactam content in peroxide cured copolymers. This behavior is explained by the higher values of flexural modulus and impact resistance for poly(ε‐caprolactam) compared with peroxide‐cured polybutadiene resins. Copolymers reinforced with silica showed higher heat distortion temperatures but lower impact resistance than corresponding unfilled samples. Arrhenius plots of flexural properties at various test temperatures were linear. Both flexural modulus and strength decreased regularly with increasing test temperature. Flexural properties of filled copolymers were relatively unaffected by heat aging up to 204°C for several weeks, however, dramatic decreases in these properties were noted in a matter of days when heat aging was done at 260–316°C. These results are explained by the rapid degradation of poly(ε‐caprolactam) above its melting point. Block polymers whose butadiene segments contained a high proportion of 1,4 units were also synthesized. These copolymers were elastomeric when cured with either sulfur or peroxide.
Delineating Diseases by IMS-MS Profiling of Serum N-linked Glycans (2011)

Altered branching and aberrant expression of N-linked glycans is known to be associated with disease states such as cancer. However, the complexity of determining such variations hinders the development of specific glycomic approaches for assessing disease states. Here, we examine a combination of ion mobility spectrometry (IMS) and mass spectrometry (MS) measurements, with principal component analysis (PCA) for characterizing serum N-linked glycans from 81 individuals: 28 with cirrhosis of the liver, 25 with liver cancer, and 28 apparently healthy. Supervised PCA of combined ion-mobility profiles for several, to as many as 10 different mass-to-charge ratios for glycan ions, improves the delineation of diseased states. This extends an earlier study [J. Proteome Res.2008, 7, 1109-1117] of isomers associated with a single glycan (S(1)H(5)N(4)) in which PCA analysis of the IMS profiles appeared to differentiate the liver cancer group from the other samples. Although performed on a limited number of test subjects, the combination of IMS-MS for different combinations of ions and multivariate PCA analysis shows promise for characterizing disease states.
Photostrictive effect in a polyvinylidene fluoride-trifluoroethylene copolymer (2011)

We present an extensive characterization and modeling of the use of a polyvinylidene fluoride trifluoroethylene copolymer P(VDF-TrFE) as a photo activated actuator. P(VDF-TrFE) copolymers are very appealing for applications because, on the opposite of the PVDF homopolymer, which requires a drawing or stretching followed by annealing and poling process to show ferroelectric properties, they spontaneously crystallize to beta phase. Based on the measurement of the bending of P(VDF-TrFE) strips under illumination, we extrapolated a model of the role of temperature, piezoelectric effect, and photostrictive components.
A 50 &#x00B5;W, 2.1 mdeg/s/&#x221A;Hz frequency-to-digital converter for frequency-output MEMS gyroscopes (2014)

Frequency-modulated operation of MEMS gyroscopes promises numerous benefits, including inherently accurate scale factor, improved bias stability, high dynamic range, and low power dissipation. An FM demodulator based on sigma-delta frequency-to-digital conversion decouples dynamic range from power dissipation to achieve a resolution of 41.1μHz in a 50 Hz bandwidth for a 30 kHz signal (2.1 mdeg/s/√Hz) with a maximum input range of 2000 deg/s while consuming 27.6μA at 1.8V. The high performance and low power consumption of this circuit enable the development of high performance, ultra-low-power, frequency-output gyroscopes and other frequency-output MEMS sensors.
Fully Integrated 94-GHz Dual-Polarized TX and RX Phased Array Chipset in SiGe BiCMOS Operating up to 105 °C (2018)

94-GHz dual-polarized phased array transmitter and receiver ICs in 130 nm BiCMOS technology are reported. The transmitter IC integrates 16 transmitter front ends with two independent outputs, a 1-to-16 power splitter, and an intermediate frequency (IF)-to-RF up-converter. The receiver IC integrates 32 front ends, two separate 16-to-1 power combiners, and two RF-to-IF down-converters, which can either support a 32-element phased array or a 16-element polarimetric phased array if connected to 16 dual-polarized antennas. Both transmitter and receiver ICs include IF/baseband circuitry, a frequency synthesizer with continuous lock detection, a temperature sensor, and digital circuitry, including serial interface and front-end memory. On-wafer TX measurements at 94 GHz taken at 25°C show an IF-to-RF conversion gain of 35 dB, oP1dB of 4 dBm, P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SAT</sub> of 7.8 dBm per channel with a total power consumption of 3 W. On-wafer RX measurements at 94 GHz and 25°C show a maximum RF-to-IF array conversion gain of 40 dB and an noise figure (NF) of 6 dB. The total RX power consumption varies from 3 to 4.6 W as it is configured from its minimum to its maximum RF front-end gain settings. RF phase shifting elements used in both TX and RX demonstrate a 1.6° phase resolution with 360° tuning range and gain variation (rms) lower than 0.5 dB. Phase-invariant gain tunability in TX and RX front ends has been achieved for independent tapering and beam steering, demonstrating the measured phase variation within ±0.5° for 10-dB gain tuning. Both TX and RX ICs are functional up to 105°C, maintaining P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SAT</sub> > 6.5 dBm per channel in TX and NF <; 12 dB in RX. The TX and RX ICs each have a chip size of 6.7 mm × 5.6 mm.
Query size estimation by adaptive sampling (extended abstract) (1990)

We present an adaptive, random sampling algorithm for estimating the size of general queries. The algorithm can be used for any query Q over a database D such that 1) for some n, the answer to Q can be partitioned into n disjoint subsets Q1, Q2, …, Qn, and 2) for 1 ≤ i ≤ n, the size of Qi is bounded by some function b(D, Q), and 3) there is some algorithm by which we can compute the size of Qi, where i is chosen randomly. We consider the performance of the algorithm on three special cases of the algorithm: join queries, transitive closure queries, and general recursive Datalog queries.
A Case Report of Traumatic Perineal Degloving Injury (2017)

Introduction: Degloving injuries are most commonly caused by road traffic accidents and industrial accidents. They result from of a large rotational force, which avulses the skin and subcutaneous tissue from the underlying fascia. The majority of such injuries involve the lower extremities. Perineal degloving injury is seldom reported in the literature. Presentation of case: In this case report, we present the case of a 22 year old male pedestrian involved in a motor vehicle accident. He sustained an open perineal degloving injury. Discussion: The management of perineal degloving injuries involves resuscitation and early identification of bony fractures, urogenital or anorectal injuries. Multiple wound irrigation with staged debridement can salvage potentially viable degloved segments. The degloved skin flaps should be secured to the wound bed without tension for the first 5 days. We utilized negative pressure wound therapy as a temporary wound dressing to facilitate wound healing. We opted for a diverting colostomy to minimize infective complications as our patient sustained an extensive perineal injury adjacent to the anus. The patient was nursed on a differential air-loss mattress to minimize pressure necrosis. Delayed wound closure was performed on day 8 of injury after full demarcation has occurred. Conclusion: We managed a specific presentation of an open perineal degloving injury which achieved a favorable outcome. With our approach, we were able to minimize tissue loss, minimize septic complications and reduce patient’s morbidity.
Playing Vivaldi in Hyperbolic Space (2006)

Internet coordinate systems have emerged as an efficient method to estimate the latency between pairs of nodes without any communication between them. They avoid the cost of explicit measurements by placing each node in a finite coordinate space and estimating the latency between two nodes as the distance between their positions in the space. In this paper, we adapt the Vivaldi algorithm to use the Hyperbolic space for embedding. Researchers have found promise in Hyperbolic space due to its mathematical elegance and its ability to model the structure of the Internet. We attempt to combine the elegance of the Hyperbolic space with the practical, decentralized Vivaldi algorithm. We evaluate both Euclidean and Hyperbolic Vivaldi on three sets of real-world latencies. Contrary to what we expected, we find that the performance of the two versions of Vivaldi varies with each data set. Furthermore, we show that the Hyperbolic coordinates have the tendency to underestimate large latencies (&amp;gt; 100 ms) but behave better when estimating short distances. Finally, we propose two distributed heuristics that help nodes decide whether to choose Euclidean or Hyperbolic coordinates when estimating distances to their peers. This is the first comparison of Euclidean and Hyperbolic embeddings using the same distributed solver and using a data set with more than 200 nodes. 1
Comparison of Various Converter Topologies for Bipolar Switched Reluctance Motor Drives (2006)

Switched reluctance (SR) drives manifest an effective integration of electromechanical energy conversion devices and modern power electronics technology. Although SR drives can be operated using a unidirectional inverter, recent studies have shown that a bipolar excitation, in which a short flux path between two adjacent phases is maintained, can provide superior performance under multi-phase excitation scenarios. In order to provide bipolar excitation to a SRM drive, a new series of inverter topologies have been introduced. In this paper, the primary focus has been given to circuit topologies that can provide flexibility in control, versatility in operation, and survivability. A four phase, 2.1 kW, 42 V SRM has been used in this investigation
Enhanced Coupling Structures for Wireless Power Transfer Using the Circuit Approach and the Effective Medium Constants (Metamaterials) (2012)

Enhanced Coupling Structures for Wireless Power Transfer Using the Circuit Approach and the Effective Medium Constants (Metamaterials)
ChemInform Abstract: Structure—Function Relationships in Peptoids: Recent Advances Toward Deciphering the Structural Requirements for Biological Function (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Week 1 Changes in Bowel and Abdominal Symptoms Following Linaclotide Treatment: Results from Two Phase 3 Trials in Chronic Constipation Patients (2010)

Purpose: Linaclotide, a first-in-class, minimally-absorbed, guanylate cyclase type-C receptor agonist, statistically significantly improved bowel and abdominal symptoms, and patient global assessments in chronic constipation (CC) and irritable bowel syndrome with constipation patients in Phase 2b trials. Two recent, randomized, double-blind, Phase 3 trials (MD-01 and 103-303) in patients with CC demonstrated statistically significant improvements in bowel and abdominal symptoms. The aim of this analysis is to determine the time to onset of symptom changes following treatment initiation in both Phase 3 trials. Methods: 1272 patients who met modified Rome II criteria for CC, and had <3 complete spontaneous bowel movements (CSBM) per week and ≤6 SBMs per week during a 2-week baseline period were randomized to oral once-daily 133 or 266μg linaclotide or placebo for 12 weeks. Results: In pooled analyses, 67% and 57% of linaclotide 133 and 266 μg patients had an SBM within 24 hours following initial study drug dosing, vs. 39% for placebo (both P<0.0001); for CSBM results, 31% and 28% of Linaclotide 133 and 266μg patients had a CSBM vs. 12% for placebo (both p<0.0001). Results by study for bowel symptoms and weekly constipation severity were also statistically significantly improved for linaclotide vs. placebo (p<0.0001) after 1 week of treatment (Table). Statistically significant improvements in bloating and abdominal discomfort were obtained at Week 1 and Week 2 of treatment, respectively. Bowel and abdominal symptom improvements were seen throughout the 12-week treatment period. The week 1 incidence of diarrhea across both studies was 8%, 8%, and 1% for the 133μg, 266μg, and placebo groups, respectively. Conclusion: Once daily doses of linaclotide resulted in early and sustained statistically significant improvements in bowel and abdominal symptoms during treatment of patients with CC. Diarrhea was the most common adverse event.Table: [1303] Week 1 change from baseline in CC symptoms, by doseDisclosure: A. Lembo - Paid Consultant: Ironwood Pharmaceuticals. H. Schneier and S. Shiff - Employees: Forest Research Institute and owner of stock/stock options in Forest Labs. B. Lavins, J. MacDougall, C. Kurtz, O'Dea, M. Currie, and J. Johnston - Employees of and owners of stock/stock options in Ironwood Pharmaceuticals. Disclosure: Funded by Ironwood Pharmaceuticals and Forest Laboratories.
GDNF, CDNF and MANF have divergent effects on nigrostriatal dopamine neurochemistry in rats (2018)

Background
Simultaneous Estimation of Bias and Resolution in PET Images with a Long-Lived “Pocket” Phantom System (2018)

A challenge in multicenter trials that use quantitative positron emission tomography (PET) imaging is the often unknown variability in PET image values, typically measured as standardized uptake values, introduced by intersite differences in global and resolution-dependent biases. We present a method for the simultaneous monitoring of scanner calibration and reconstructed image resolution on a per-scan basis using a PET/computed tomography (CT) "pocket" phantom. We use simulation and phantom studies to optimize the design and construction of the PET/CT pocket phantom (120 × 30 × 30 mm). We then evaluate the performance of the PET/CT pocket phantom and accompanying software used alongside an anthropomorphic phantom when known variations in global bias (±20%, ±40%) and resolution (3-, 6-, and 12-mm postreconstruction filters) are introduced. The resulting prototype PET/CT pocket phantom design uses 3 long-lived sources (15-mm diameter) containing germanium-68 and a CT contrast agent in an epoxy matrix. Activity concentrations varied from 30 to 190 kBq/mL. The pocket phantom software can accurately estimate global bias and can detect changes in resolution in measured phantom images. The pocket phantom is small enough to be scanned with patients and can potentially be used on a per-scan basis for quality assurance for clinical trials and quantitative PET imaging in general. Further studies are being performed to evaluate its performance under variations in clinical conditions that occur in practice.
Identification and Localization of Toxic Elements in Normal Human Lung Macrophages (1981)

The elemental content of pulmonary macrophages obtained by bronchopulmonary lavage from 13 healthy adult volunteers was assessed. Subcellular localization of elements was accomplished using energy-dispersive X-ray analysis in the scanning transmission microscope. Silicon, aluminum, iron, and sulfur were identified and localized to subcellular particles. These observations indicate that the elemental content of alveolar macrophages lavaged from living individuals can be determined by microanalysis and that the alveolar macrophages of normal persons retain potentially toxic elements.
A paradigm shift in verification methodology (2016)

Todays SoCs are driving unprecedented verification complexity. The combination of billions of gates, system-level functionality on a chip, complex design methodologies like asynchronous clock domains and an explosion of untimed paths on a chip, interacting dynamic power domains, aggressive reset schemes etcetera could have been the perfect storm to staunch productivity. Instead it has turned out to be the mother of all necessities that has driven significant innovation in verification and brought about a paradigm shift. Static sign-off has proven to be a pillar in this new paradigm. This talk will discuss the template for what has made static techniques successful in verifying modern SoCs. The recent successes are, in no small part, due to the FMCAD community that has pursued formal methods doggedly for decades despite glacial practical adoption. Complementing the efforts of the research community has been the equally determined pursuit in the EDA community to bring structure and automation into the verification process. Through this partnership, we have been able to bring about an analysis framework within which a combination of semantic analysis and formal methods enables a systematic verification process that leads to sign-off level confidence for important failure modes. It will be gratifying for the FMCAD audience to realize that SAT, model checking, functional abstraction, QBF etcetera have become essential in being able to tape out some of the most complex chips in the world on time and within budget. The adoption of IC3/PDR into the verification process was almost immediate. The recent successes represent a strong debut for static methods. What is the vision to extend the promise into bigger slices of the verification pie? System-level verification continues to be an art-form with very little of the automation, process and problem-framing that have proven successful in other domains. May be the FMCAD community should adopt that as its next major challenge.
Efforts Toward the Direct Experimental Characterization of Enzyme Microenvironments: Tyrosine100 in Dihydrofolate Reductase (2009)

Abstract Eine ortsspezifische Deuterierung und FTIR‐Studien belegen, dass Tyr100 in der Katalyse durch Dihydrofolat‐Reduktase eine wichtige Rolle zufällt, weil dieser Aminosäurerest mit der Ladung, die im Übergangszustand des Hydridtransfers entsteht, stark elektrostatisch gekoppelt ist (siehe Bild: NADP + violett, Tyr100 grün). Allerdings könnten auch korrelierte Bewegungen, die von entfernten Stellen im Protein an den Hydriddonor weitergegeben werden, die Katalyse erleichtern. magnified image