gebhart/patrepeval huggingface dataset:
Total Synthesis of 11‐Azasteroids. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Siderophore-Mediated Iron Uptake inAlcaligenes eutrophus CH34 and Identification ofaleBEncoding the Ferric Iron-Alcaligin E Receptor (1996)

erophore-deficient A. eutrophus mutants under iron-restricted conditions and promoted 59 Fe uptake by ironlimited cells. However, the growth of the Sid 2 mutant AE1152, which was obtained from CH34 by Tn5-Tc mutagenesis,wascompletelyinhibitedbytheadditionofalcaliginE.AE1152alsoshowedstronglyreduced 59 Fe uptakeinthepresenceofalcaliginE.Thisindicatesthatagene,designatedaleB,whichisinvolvedintransport of ferric iron-alcaligin E across the membrane is inactivated. ThealeBgene was cloned, and its putative amino acid sequence showed strong similarity to those of ferric iron-siderophore receptor proteins. Both wild-type strain CH34 and aleB mutant AE1152 were able to use the same heterologous siderophores, indicating that AleB is involved only in ferric iron-alcaligin E uptake. Interestingly, no utilization of pyochelin, which is also a phenolate-type siderophore, was observed forA. eutrophusCH34. Genetic studies of different Sid 2 mutants, obtained after transposon mutagenesis, showed that the genes involved in alcaligin E and ferric iron-alcaligin E receptor biosynthesis are clustered in a 20-kb region on theA. eutrophusCH34 chromosome in the proximity of thecys-232locus.
Stark-induced adiabatic Raman passage examined through the preparation of D2 (v = 2, j = 0) and D2 (v = 2, j = 2, m = 0) (2019)

We study the conditions that must be met for successful preparation of a large ensemble in a specific target quantum state using Stark-induced adiabatic Raman passage (SARP). In particular, we show that the threshold condition depends on the relative magnitudes of the Raman polarizability (r<sub>0v</sub>) and the difference of the optical polarizabilities (Δα<sub>00→vj</sub>) of the initial (v = 0, j = 0) and the target (v, j) rovibrational levels. Here, v and j are the vibrational and rotational quantum numbers, respectively. To illustrate how the operation of SARP is controlled by these two parameters, we experimentally prepared D<sub>2</sub> (v = 2, j = 0) and D<sub>2</sub> (v = 2, j = 2, m = 0) in a beam of D<sub>2</sub> (v = 0, j = 0) molecules using a sequence of partially overlapping pump and Stokes laser pulses. By comparing theory and experiment, we were able to determine the Raman polarizability r<sub>02</sub> ≈ 0.3 × 10<sup>-41</sup> Cm/(V/m) and the difference polarizabilities Δα<sub>00→20</sub> ≈ 1.4 × 10<sup>-41</sup> Cm/(V/m) and Δα<sub>00→22</sub> ≈ 3.4 × 10<sup>-41</sup> Cm/(V/m) for the two Raman transitions. Our experimental data and theoretical calculations show that because the ratio r/Δα is larger for the (0,0) → (2,0) transition than the (0,0) → (2,2) transition, much less optical power is required to transfer a large population to the (v = 2, j = 0) level. Nonetheless, our experiment demonstrates that substantial population transfer to both the D<sub>2</sub> (v = 2, j = 0) and D<sub>2</sub> (v = 2, j = 2, m = 0) is achieved using appropriate laser fluences. Our derived threshold condition demonstrates that with increasing vibrational quantum number, it becomes more difficult to achieve large amounts of population transfer.
Limiting racemization and aspartimide formation in microwave‐enhanced Fmoc solid phase peptide synthesis (2006)

Microwave energy represents an efficient manner to accelerate both the deprotection and coupling reactions in 9-fluorenylmethyloxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS). Typical SPPS side reactions including racemization and aspartimide formation can occur with microwave energy but can easily be controlled by routine use of optimized methods. Cysteine, histidine, and aspartic acid were susceptible to racemization during microwave SPPS of a model 20mer peptide containing all 20 natural amino acids. Lowering the microwave coupling temperature from 80 degrees C to 50 degrees C limited racemization of histidine and cysteine. Additionally, coupling of both histidine and cysteine can be performed conventionally while the rest of the peptide is synthesized using microwave without any deleterious effect, as racemization during the coupling reaction was limited to the activated ester state of the amino acids up to 80 degrees C. Use of the hindered amine, collidine, in the coupling reaction also minimized formation of D-cysteine. Aspartimide formation and subsequent racemization of aspartic acid was reduced by the addition of HOBt to the deprotection solution and/or use of piperazine in place of piperidine.
Association of Structural Variation with Cardiometabolic Traits in Finns (2020)

Abstract The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low frequency SVs for association with 116 quantitative traits, and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including two novel loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB gene promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p=1.47×10 −54 ), and is also associated with increased levels of total cholesterol (p=1.22×10 −28 ) and 14 additional cholesterol-related traits, and (2) a multiallelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p=4.81×10 −21 ) and alanine (p=6.14×10 −12 ) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs), and one linking recurrent HP gene deletion and cholesterol levels (p=6.24×10 −10 ), which was also found to be strongly associated with increased glycoprotein level (p=3.53×10 −35 ). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.
Compact fiber laser system for 589 nm laser guide star generation (2004)

Laser guided adaptive optics for astronomy can significantly improve the resolution of ground-based telescopes. We are developing an all-fiber 589nm laser system for this application by sum-frequency mixing 1583nm Er/Yb:doped and 938nm Nd:silica fiber lasers in a periodically poled crystal. Both CW and pulsed formats are under development.
Multi - Fpga Processor For Gray-Scale Morphology (1998)

Publication in the conference proceedings of EUSIPCO, Rhodes, Greece, 1998
DeepCEST: 9.4 T Chemical Exchange Saturation Transfer MRI contrast\n predicted from 3 T data - a proof of concept study (2018)

Purpose: Separation of different CEST signals in the Z-spectrum is a\nchallenge especially at low field strengths where amide, amine, and NOE peaks\ncoalesce with each other or with the water peak. The purpose of this work is to\ninvestigate if the information in 3T spectra can be extracted by a deep\nlearning approach trained by 9.4T human brain target data. Methods:\nHighly-spectrally-resolved Z-spectra from the same volunteer were acquired by\n3D-snapshot CEST MRI at 3 T and 9.4 T with similar saturation schemes. The\nvolume-registered 3 T Z-spectra-stack was then used as input data for a 3-layer\ndeep neural network with the volume-registered 9.4 T fitted parameter stack as\ntarget data. The neural network was optimized and applied to training data, to\nunseen data from a different volunteer, and as well to a tumor patient data\nset. Results: A useful neural net architecture could be found and verified in\nhealthy volunteers. The principle gray-/white matter contrast of the different\nCEST effects was predicted with only small deviations. The 9.4 T prediction was\nless noisy compared to the directly measured CEST maps, however at the cost of\nslightly lower tissue contrast. Application to a tumor patient measured at 3 T\nand 9.4 T revealed that tumorous tissue Z-spectra and corresponding\nhyper/hypo-intensities of different CEST effects can also be predicted.\nConclusion: Deep learning might be a powerful tool for CEST data processing and\ndeepCEST could bring the benefits and insights of the few ultra-high field\nsites to a broader clinical use. Vice versa deepCEST might help for determining\nwhich subjects are good candidates to measure additionally at UHF.\n
A 9.4T human fMRI study reveals differential laminar responses for visual motion in eye- and world-centered reference frames in area V3A (2016)

Neural mechanisms underlying a stable perception of the world during pursuit eye movements are not fully understood. Both, perceptual stability as well as perception of real-world motion are the product of multi-modal integration between retinal motion (visual motion signals) and efference copies of eye movements (non-visual motion signals). The comparison between these two signals allows differentiating between self-induced motion and external, real-world motion. Recently, pursuit-paradigms revealed that human area V3A responds to motion predominantly in a world-centered rather than in a retina-centered reference frame (Fischer et al., 2012). This indicates that V3A integrates retinal motion with non-retinal eye-movement signals. In this study we combined ultra-high-field (9.4T) human fMRI, state of the art pulse sequences, and laminar analysis to find out if there is a differential involvement of cortical layers in the processing of real world motion compared to retinal motion in area V3A. We used a 2D GE EPI sequence with 0.8 mm isotropic resolution to measure BOLD signal at different cortical depths while subjects performed a visual pursuit task. The paradigm involved a 2x2 design containing real motion and visual pursuit, which allowed separating responses to retinal and real motion while fully controlling for pursuit-related effects. A laminar surface-based analysis method was used to study the relationship between spatial localization and activation strength as a function of cortical depth by sampling the BOLD signal from the superficial, middle, or deep cortical lamina in area V3A. The results show that signals related to retinal motion were evenly spread across layers with a bias towards deep layers of V3A while real-motion responses had a gradient with a peak in superficial layers. The differential laminar response profile is compatible with differential local processing for the two motion types. The stronger involvement of superficial layers during real motion processing may be indicative of feedback related processing, possibly through mediation of efference-copy related signals from higher-level regions such as parietal cortex or smooth pursuit fields of the frontal eye fields with which V3A has direct connections. Future studies are needed to clarify the reasons for differential laminar responses and to identify communication pathways leading to V3A.
The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients (2018)

<b>Purpose:</b> Cell-free DNA (cfDNA) sequencing provides a noninvasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants.<b>Experimental Design:</b> We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types. To facilitate interpretation of the genomic complexity of circulating tumor DNA in advanced, treated cancer patients, we developed methods to identify cfDNA copy-number driver alterations and cfDNA clonality.<b>Results:</b> Patterns and prevalence of cfDNA alterations in major driver genes for non-small cell lung, breast, and colorectal cancer largely recapitulated those from tumor tissue sequencing compendia (The Cancer Genome Atlas and COSMIC; <i>r</i> = 0.90-0.99), with the principal differences in alteration prevalence being due to patient treatment. This highly sensitive cfDNA sequencing assay revealed numerous subclonal tumor-derived alterations, expected as a result of clonal evolution, but leading to an apparent departure from mutual exclusivity in treatment-naïve tumors. Upon applying novel cfDNA clonality and copy-number driver identification methods, robust mutual exclusivity was observed among predicted truncal driver cfDNA alterations (FDR = 5 × 10<sup>-7</sup> for <i>EGFR</i> and <i>ERBB2</i>), in effect distinguishing tumor-initiating alterations from secondary alterations. Treatment-associated resistance, including both novel alterations and parallel evolution, was common in the cfDNA cohort and was enriched in patients with targetable driver alterations (>18.6% patients).<b>Conclusions:</b> Together, these retrospective analyses of a large cfDNA sequencing data set reveal subclonal structures and emerging resistance in advanced solid tumors. <i>Clin Cancer Res; 24(15); 3528-38. ©2018 AACR</i>.
1200dpi thin film LED array by silicon photonics technology (2008)

Higher density single crystal thin film light emitting diode (LED) arrays have been studied. Bonding of epitaxial thin film (epifilm) LEDs of about 2 mum in thickness has been achieved on CMOS IC drivers and other dissimilar material substrates by intermolecular force ("Epi Film Bonding (EFB)" technology). The epifilm LED array provides good enough characteristics to apply in LED printheads (small variation of emitted light power (< plusmn 5%) and long lifetime (>1000 h)). Fabrication test of two dimensional (2D) epifilm LED arrays shows that 2D 1200 dpi epifilm LED arrays (a small light emitting region of 10 mum times 10 mum and a fine array pitch of 21.2 mum) achieves good performance to display characters. Bonding of 1200 dpi epifilm LED arrays on diamond-like carbon (DLC) thin films having high thermal conductivity has been tested for the first time. The test result shows that good bonding of small epifilms (10 mum times 10 mum) on the DLC thin film can be achieved. The LED array that is bonded on the DLC thin film formed on the Si substrate shows higher thermal conduction character; rough estimation of LED temperature suggests about 50 degrees centigrade even at a very high LED current density of 20 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Fiber optic system for remote spectroscopy in the mid-infrared using chalcogenide fiber (1996)

We have developed a system for remote spectroscopic measurements in the mid-infrared wavelength range (2-6µm) using chalcogenide fibers for in- situ detection (≤200ppm) of hydrocarbon contamination in soils.
A Quadrupole Ion Trap as Low-Energy Cluster Ion Beam Source (2003)

Kinetic energy distribution of ion beams was measured by a retarding field energy analyzer for a mass-selective cluster ion beam deposition system that uses a quadrupole ion trap as a cluster ion beam source. The results indicated that the system delivers a cluster-ion beam with energy distribution of ∼2 eV, which corresponded well to the calculation results of the trapping potentials in the ion trap. Using this deposition system, mass-selected hydrogenated Si cluster ions SinHx+ were actually deposited on Si(111)-(7×7) surfaces at impact kinetic energy Ed of 3–30 eV. Observation by using a scanning tunneling microscope (STM) demonstrated that Si6Hx+ cluster ions landed on the surface without decomposition at Ed=3 eV, while the deposition was destructive at Ed≧18 eV.
Nasal Continuous Positive Airway Pressure Reduces Sleep-induced Blood Pressure Increments In Preeclampsia (2000)

Abstract Preeclampsia is the predominant cause of admissions to neonatal intensive care. The diurnal blood pressure pattern is flattened or reversed in preeclampsia. We hypothesized that snoring and partial upper airway obstruction contribute to nocturnal rises in blood pressure. We tested this hypothesis by controlling sleep- induced upper airway flow limitation and snoring with nasal positive pressure. Eleven women with preeclampsia underwent two consecutive polygraphic sleep studies with simultaneous beat-to-beat blood pressure monitoring. Average blood pressure for the night overall and in each sleep stage was calculated. Sleep architecture was similar on the two study nights. Sleep-induced partial upper airway flow limitation occurred in all patients in the initial study. Autosetting nasal continuous positive airway pressure (CPAP) applied at a mean maximal pressure of 6 ± 1 cm H2O eliminated flow limitation throughout sleep on the treatment night. Blood pressure was markedly reduced on the treatment night [(128 ± 3)/(73 ± 3)] when compared with the initial nontreatment study night [(146 ± 6)/(92 ± 4)], p = (0.007)/(0.002). We conclude that partial upper airway obstruction during sleep in women with preeclampsia is associated with increments in blood pressure, which can be eliminated with the use of nasal CPAP.
Constant Envelope Pilot-Based Low-Complexity CFO Estimation in Massive\n MU-MIMO Systems (2016)

In this paper we consider a constant envelope pilot signal based carrier\nfrequency offset (CFO) estimation in massive multiple-input multiple-output\n(MIMO) systems. The proposed algorithm performs spatial averaging on the\nperiodogram of the received pilots across the base station (BS) antennas. Our\nstudy reveals that the proposed algorithm has complexity only linear in $M$\n(the number of BS antennas). Further our analysis and numerical simulations\nalso reveal that with fixed number of users and a fixed pilot length, the\nminimum required transmit pilot power decreases as $\\frac{1}{\\sqrt{M}}$ with\nincreasing $M$, while maintaining a fixed desired mean squared error (MSE) of\nCFO estimation.\n
MMSE receivers for multirate DS-CDMA systems (2001)

Minimum-mean squared error (MMSE) receivers are designed and analyzed for multiple data rate direct-sequence code-division multiple-access (DS-CDMA) systems. The inherent cyclostationarity of the DS-CDMA signal is exploited to construct receivers for asynchronous multipath channels. Multiple- and single-bandwidth access are treated for both single and multicarrier scenarios. In general, the optimal receiver is periodically time-varying. When the period of the optimal receiver is large, suboptimal receivers are proposed to achieve a lower complexity implementation; the receivers are designed as a function of the cyclic statistics of the signals. In multiple chipping rate systems, the complexity of receivers for smaller bandwidth users can also be controlled by changing their front-end filter bandwidth. The effect of front-end filter bandwidth on receiver performance and system capacity is quantified for a variable chipping rate system. Analysis and simulation show that significant performance gains are realized by the periodically time-varying MMSE receivers over their time-invariant counterparts.
Oxidative Stress in Chronic Renal Allograft Nephropathy in Rats: Effects of Long-term Treatment with Carvedilol, BM 91.0228, or Alpha-tocopherol (2003)

Oxidative stress is markedly increased after kidney transplantation and may participate in the development and/or progression of chronic renal allograft nephropathy. In the present study we sought to assess the nephroprotective potential of antioxidative treatment in renal allograft recipients. Experiments were performed in the Fisher-Lewis rat model of chronic renal allograft nephropathy, with isografted Lewis rats serving as controls. Allografted rats were orally treated with carvedilol, an antihypertensive drug with antioxidative properties (25 mg/kg/d), its purely antioxidative derivative BM 91.0228 (5 mg/kg/d), alpha-tocopherol (100 mg/kg/d), a combination of propranolol/doxazosine (10/5 mg/kg/d), or vehicle for 24 weeks. At the end of the study, oxidative status and influence of antioxidative treatment were assessed in transplanted animals. Chronic allograft nephropathy was characterized by a marked increase of markers for oxidative stress (increased plasma and kidney levels of malondialdehyde, reduced glutathione, and tocopherol levels in renal allografts). Treatment with carvedilol, BM 91.0228, and tocopherol significantly improved antioxidative status of allograft kidney recipients. In addition, carvedilol reduced elevated blood pressure in allografted rats. However none of the drugs had a beneficial influence on functional and morphologic renal changes. Our data thus demonstrate that long-term treatment with the antioxidants carvedilol, BM 91.0228, or alpha-tocopherol does not prevent development of chronic transplant nephropathy, despite an improvement of antioxidative status.
What do healthcare professionals need to turn risk models for type 2 diabetes into usable computerized clinical decision support systems? Lessons learned from the MOSAIC project (2019)

By using a holistic approach, we have been able to understand user needs, behaviours and interactions and give new insights in the definition of effective Decision Support Systems to deal with the complexity of T2D care.
ChemInform Abstract: Synthetic Silicate Zeolites: Diverse Materials Accessible Through Geoinspiration (2011)

Abstract Review: 250 refs.
The use of dielectric coatings in capacitive power transfer systems (2014)

Capacitive power transfer (CPT) is emerging as a competitive alternative to inductive power transfer (IPT) for non-contact applications over short distances. One distinct advantage CPT has is that the electric field is mostly contained between the coupling plates. These plates are in or near contact with each other but are galvanically isolated by an insulating coating. This paper discusses the function dielectric coating have in CPT and gives insight to their design. Ceramic coatings are presented as a viable option given their durability, high permittivity, dielectric strength and ease of application. Specifically, titanium dioxide is identified as a ceramic coating ideally suited for CPT applications. Titanium dioxide is coated on both aluminum and stainless steel substrates via relatively new sol-gel process. This process is documented step by step with the thickness and chemical composition of the coating verified by scanning electron microscope. The effective permittivity and dielectric breakdown strength of the titanium dioxide coatings are measured.