gebhart/patrepeval huggingface dataset:
Photoinhibition of FeFe Hydrogenase (2017)

In the enzyme FeFe hydrogenase, hydrogen oxidation and production occur at the H-cluster, a Fe6S6 active site that bears intrinsic carbonyl and cyanide ligands. This enzyme has been coupled to photosensitizers to design H2 photoproduction systems, and yet, according to earlier reports, the enzyme from Desulfovibrio desulfuricans is “easily destroyed” in “normal laboratory light”. Here we report direct electrochemistry measurements of the effect of light on the activity of the enzymes from Chlamydomonas reinhardtii and Clostridium acetobutylicum, together with TDDFT and DFT calculations of the reactivity of the excited states of the H-cluster. We conclude that visible light does not inhibit these enzymes, but absorption of UVB (280–315 nm) irreversibly damages the H-cluster by triggering the release of an intrinsic CO ligand; the resulting unsaturated species rearranges and protonates to form a stable, inactive dead-end. Answering the question of which particular hydrogenase can resist which particular wavelengths is important regarding solar H2 production, and our results show that some but not all FeFe hydrogenases can actually be combined with photosensitizers that utilize the solar spectrum, provided a UV screen is used. We suggest that further investigations of the compatibility of hydrogenases or hydrogenase mimics with light-harvesting systems should also consider the possibility of irreversible photoinhibition.
Imaged based 3D solid model construction of human arteries for blood flow simulations (2002)

In recent years, the finite element method has been used increasingly by researchers seeking to understand the mechanics of blood flow in the human vascular system. Researchers have made use of averaged, idealized, and patient-specific geometric models of blood vessels as a basis for their numerical simulations. However, in order to determine the exact flow conditions in a given individual's vascular system for clinical diagnoses or surgical planning, models which faithfully represent individual anatomic features and flow conditions are necessary. The creation of such patient-specific models is both error-prone and time consuming. In this paper an interactive software system is described which facilitates the creation of complex 3D patient-specific solid models of vessels for numerical blood flow simulations with Computer Aided Design and Computer Aided Engineering (CAD/CAE) technologies.
Attenuation and fluorescence characteristics of optical signals propagating in an erbium-doped fiber (1993)

For a monochromatic input signal launched into an erbium-doped fiber (EDF), a broadband fluorescence spectrum will be generated with total power approximately 30 dB lower than input signal power. The forward fluorescence power decays slowly at long EDF length due to smaller absorption cross section for wavelength components away from absorption peak. Care must be taken when the conventional cutback method is used to measure the attenuation of the optical signals in an EDF. The backward fluorescence power is saturated to a constant level, and the spectrum does not change for long EDF.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nanoscale Proximity Effect in the High-Temperature SuperconductorBi2Sr2CaCu2O8+δUsing a Scanning Tunneling Microscope (2010)

High-temperature cuprate superconductors exhibit extremely local nanoscale phenomena and strong sensitivity to doping. While other experiments have looked at nanoscale interfaces between layers of different dopings, we focus on the interplay between naturally inhomogeneous nanoscale regions. Using scanning tunneling microscopy to carefully track the same region of the sample as a function of temperature, we show that regions with weak superconductivity can persist to elevated temperatures if bordered by regions of strong superconductivity. This suggests that it may be possible to increase the maximum possible transition temperature by controlling the distribution of dopants.
Could London Dispersion Force Control Regioselective (2 + 2) Cyclodimerizations of Benzynes? YES: Application to the Synthesis of Helical Biphenylenes (2021)

In recent years, London dispersion interactions, which are the attractive component of the van der Waals potential, have been found to play an important role in controlling the regio- and/or stereoselectivity of various reactions. Particularly, the dispersion interactions between substrates and catalysts (or ligands) are dominant in various selective catalyzes. In contrast, repulsive steric interactions, rather than the attractive dispersion interactions, between bulky substituents are predominant in most of the noncatalytic reactions. Herein, we demonstrate the first example of London dispersion-controlled noncatalytic (2 + 2) cyclodimerization of substituted benzynes to selectively afford proximal biphenylenes in high yields and regioselectivities, depending on the extent of dispersion interactions in the substituents. This method can be applied for the synthesis of novel helical biphenylenes, which would be fascinating for chemists as these compounds are potential skeletons for ligands, catalysts, and medicines.
In vivo therapy of malignant melanoma by means of antagonists of αv integrins (2000)

Integrin αvβ3 (vitronectin receptor) has been implicated in human malignant melanoma progression and angiogenesis as a receptor that provides survival signals. However, little is known about the therapeutic potential of antagonists of αvβ3. In this report, we characterize the activities of 2 antagonists of αvβ3 integrins: a human specific monoclonal antibody (MAb), 17E6, and a cyclic RGD peptide that blocked cell adhesion and induced detachment of previously substrate-attached cells in vitro. In vivo, αvβ3 antagonists behaved as anti-tumor drugs in a dose- and time-dependent manner. Moreover, different therapeutic treatments proved to be effective even in the therapy of established macroscopic tumor masses, thus supporting the use of these antagonists in clinical therapy. Using a panel of 6 human melanomas and 5 carcinomas, MAb 17E6 efficiently blocked the in vivo tumor growth of melanomas expressing αvβ3 as xenografts but did not affect the αvβ3-negative (although αv integrin-positive) tumors. This demonstrated that αvβ3 is a pivotal integrin for the growth of human melanomas. Furthermore, since MAb 17E6 does not recognize murine αvβ3, the effect is due only to the direct anti-tumor activity and not to the well-known anti-angiogenic activity of αv-integrin antagonists. Taken together, our results confirm the essential role of αvβ3 integrin in the growth of human malignant melanoma in vivo and provide strong evidence of the therapeutic potential of αv-integrin antagonists for the treatment of such tumors. Int. J. Cancer 87:716–723, 2000. © 2000 Wiley-Liss, Inc.
Generation Mean Analysis for Resistance in Maize to the Corn Leaf Aphid (Homoptera: Aphididae) (1991)

Corn leaf aphids [Rhopalosiphum maidis (Fitch)] can be a serious pest of maize, Zea mays L. Because very little is known about the genetics of corn leaf aphid resistance in maize, a generation mean analysis was conducted on nine generations of maize [P1 B96 (susceptible); P2 Mo17 (resistant); F1; F2; F3; BC1; BC2; BS1; and BS2] to determine the type of gene action involved. The model that included additive and dominant effects explained 64.8% of the total variation among generations, whereas the model that included additive, dominant, and epistatic effects did not significantly improve the fit. The estimate of the additive genetic effects was most important, indicating that several loci contributed resistance to the corn leaf aphid. Dominant genetic effects were significant, but not as important as additive effects. Residuals remaining after fitting for additive and dominance effects were significant, indicating that more complicated genetic mechanisms may be involved.
Hybrid-DIA: Intelligent Data Acquisition for Simultaneous Targeted and Discovery Phosphoproteomics in Single Spheroids (2022)

Abstract Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging when analyzing tiny sample amounts. We present a novel hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem MS scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmarked hybrid-DIA against state-of-the-art targeted MS methods (i.e. SureQuant) using EGF-stimulated HeLa cells and found the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiled the global phosphoproteome. To demonstrate the robustness, sensitivity and potential of hybrid-DIA, we profiled chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluated the difference of cancer cells in 2D vs 3D culture. Altogether, we showed that hybrid-DIA is the way-to-go method in highly sensitive phospho-proteomics experiments.
Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population (2014)

Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10⁻⁸) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P = 1.5×10⁻¹¹⁷). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10⁻⁴), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers.
Organic solar cells: A new look at traditional models (2011)

Traditional inorganic solar cell models, originating with the work of Shockley, are widely used in understanding bulk heterojunction (BHJ) organic solar cell response (organic solar cells are also referred to as organic photovoltaics, or OPVs). While these models can be useful, there are several key points of departure from traditional solar cell behavior. In this Perspective, we discuss three important areas: (1) geminate pair and bimolecular recombination, (2) effects of interfacial layers inserted between the electrodes and active layer, and (3) resistance effects. Since organic solar cell materials typically have large Coulombic exciton binding energies (e.g., ∼0.3–0.5 eV), limited dissociation of photogenerated charge carriers can be a significant limitation in these cells that is not observed in traditional silicon solar cells. Additionally, the active layer morphology of BHJ organic solar cells allows free charge carriers to recombine before extraction from the cell, creating another photocurrent loss mechanism. Interfacial layers serve a unique role in BHJ organic solar cells; in addition to conventional functions such as photon transmission and charge injection, interfacial layers often act as “blocking” layers, ensuring that charge carriers are collected at their respective electrodes (i.e., electrons at the cathode and holes at the anode). Additionally, resistance effects in organic solar cells differ from traditional models in both field and cell area dependencies. Organic semiconductor mobilities and charge densities exhibit significant sensitivity to field strength, with mobility varying by ∼10x over typical cell voltage test ranges (1 V). This creates the need for alternative models to describe cell internal resistance. Finally, resistance losses are also sensitive to cell area, due to the limited conductivities of the transparent electrode materials used. Therefore, accommodation of the above deviations from traditional models is imperative for the design and synthesis of new generation high efficiency organic solar cell materials.
Orbitals Distortion of Carbonyl and Olefin Groups. Unsymmetrization of .PI. Lobes Arising from .PI.-.PI. Orbital Interactions. (1994)

We have detected the unsymmetrical π faces of the carbonyl groups of spiro [cyclopentane] fluorenes and 2-substituted and 3-substituted dibenzobicyclo [2.2.2] octadienones (2-substituted and 3-substituted 9, 10- dihydro-9, 10- (11-ketoethano) anthracenes) and of the olefin groups in spiro [cyclopentene]fluorenes and 2-substituted dibenzobicyclo [2.2.2] octatrienes (2-substituted-9, 10-dihydro-9, 10-ethenoanthracenes), wherein σ-type overlaps of the π orbitals are involved, in a similar manner to spiro and longicyclic conjugations, respectively. An intrinsically nonequivalent substituent at distal positions modulates the epoxidation and dihydroxylation of the olefin group and the reduction of the carbonyl group. Herein we interpret these biases or non-biases in terms of unsymmetrization of π lobes of the olefin and carbonyl π orbitals, arising from nonequivalent π-π interactions rather than from electron-donating or -withdrawing effect.
Impact of torque tube reflection on bifacial photovoltaic single axis tracked system performance (2023)

Among the racking elements of bifacial photovoltaic (PV) single-axis tracked systems, the torque tube (TT) introduces the most shading and reflection, increasing irradiance nonuniformity and electrical mismatch loss. We simulate the impact of TT shading and reflection on the irradiance profiles, electrical mismatch, and energy yield for central bifacial PV modules on one-in-portrait (1P) and two-in-portrait (2P) single-axis trackers. TT reflection increases annual irradiance in 1P and 2P systems by 0.17% and 0.30%, respectively. Overall, TT reflection increases the predicted instantaneous energy yield by up to 0.8% and 0.4%, and the annual energy yield by 0.11% and 0.18% in 1P and 2P systems, respectively.
Ideal Mixing of Paraelectric and Ferroelectric Nematic Phases in Liquid Crystals of Distinct Molecular Species (2021)

The organic mesogens RM734 and DIO are members of separate molecular families featuring distinct molecular structures. These families, at the present time, are the only ones known to exhibit a ferroelectric nematic liquid crystal (LC) phase. Here we present an experimental investigation of the phase diagram and electro-optics of binary mixtures of RM734 and DIO. We observe paraelectric nematic (N) and ferroelectric nematic (NF) phases in both materials, each of which exhibits complete miscibility across the phase diagram, showing that the paraelectric and ferroelectric are the same phases in RM734 as in DIO. Remarkably, these molecules form ideal mixtures with respect to both the paraelectric-ferroelectric nematic phase behavior and the ferroelectric polarization density of the mixtures, the principal order parameter of the transition. Ideal mixing is also manifested in the orientational viscosity, and the onset of glassy dynamics at low temperature. This behavior is attributable in part to the similarity of their overall molecular shape and net longitudinal dipole moment (~ 11 Debye), and to a common tendency for head-to-tail molecular association. In contrast, the significant difference in molecular structures leads to poor solubility in the crystal phases, enhancing the stability of the ferroelectric nematic phase at low temperature in the mixtures and making possible room temperature electro-optic effects. In the mixtures with excess DIO, an intermediate phase appears via an ultraweak, first-order transition from the N phase, in a narrow temperature range between the paraelectric and ferroelectric nematics.
Tuning of a Hard Disk Drive Servo Controller Using Fixed-Structure H∞ Controller Optimization (2000)

As the storage capacity of hard disk drives (HDDs) increases dramatically, the demand for positioning control accuracy of a read/write head of HDD is becoming more stringent. This paper presents a tuning methodology for fixed-structure controllers using the H∞ optimization. The tuning of a PID (Proportional plus Integral plus Derivative) controller for head positioning of an HDD is presented as an application example. The H∞ optimization problem of fixed-structure controllers can be locally solved by using the transformation into an H∞ synthesis problem of static output feedback control. Simulation and experimental results show the effectiveness of the proposed approach as a fine tuning method to improve controller performance without requiring profound knowledge and experiences in manual loop-shaping.
Asynchronous Media Streaming Over Wireless Broadcast Channels (2005)

We consider wireless broadcasting of multimedia content to allow asynchronous media access. Receivers subscribe at any time to the ongoing broadcast session, but are still able to display the media stream from the beginning. A fully scalable broadcasting scheme is presented where the media stream is appropriately segmented and segments are protected by fountain codes. The decoding behavior of rateless codes on wireless as well as on erasure channels is considered within the framework of information collection. Asynchronous data access and full reliability at the same time are achieved. Depending on its receiving conditions the receiver adapts its initial playout delay for high probability of successful playout. Analytical expressions for the failure probability of successful media playout are derived depending on the initial delay and the channel conditions at the receiver.
A SiGe-HBT 2:1 analog multiplexer with more than 67 GHz bandwidth (2017)

This paper presents a 2:1 Analog Multiplexer (AMUX) in a SiGe-HBT technology. The AMUX is used for time interleaving operation of two digital-to-analog converters (DACs) and therefore extends both the sampling rate and the bandwidth compared to a single DAC. The linear AMUX signal path allows for generation of broadband signals with higher order modulation schemes which is essential for raising data rates in optical communication networks. The AMUX provides a differential peak-to-peak output voltage of up to 1 V with linear gain. A signal path 3-dB bandwidth exceeding 67 GHz has been measured. The clock path exhibits a 3-dB bandwidth of 60 GHz. S-parameter measurements are presented. Measured PAM4 eye diagrams at 56 GS/s from the time interleaving operation of two DACs are reported.
Characterization of Stress in Porous Silicon Films Prepared by Reactive Hydrogen Plasma Sputtering Technique (1995)

Hydrogenated porous silicon (P-Si:H) films with columnar structure are prepared by reactive hydrogen plasma sputtering of silicon. Stress in the films is characterized by X-ray diffraction and Raman scattering measurement. Experimental results show that the stress mainly results due to a lattice expansion (Δ a / a 0 ) of Si grains in the films. Δ a / a 0 increases with decrease in Si grain size, and tends towards the limiting value of about 1.2%, both when Si grain size is below 100 Å and when a large amount of amorphous silicon hydrides are present in the films.
Facile and Efficient One-Pot Synthesis of Highly Functionalized Thieno[2,3-<i>b</i>]thiopyran-4-ones from β-Keto ε-Xanthyl Phosphonates (2016)

The one-pot synthesis of various functionalized thieno[2,3-&lt;i&gt;b&lt;/i&gt;]thiopyran-4-ones from readily available β-keto ε-xanthyl phosphonates has been accomplished by combining a Horner−Wadsworth−Emmons olefination with a base-induced intramolecular domino cyclization/thio-Michael addition. The use of cyclic ketones in this transformation allowed a facile access to novel spiro-type thieno[2,3-&lt;i&gt;b&lt;/i&gt;]thiopyran structures.
Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection (2015)

Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations.