gebhart/patrepeval huggingface dataset:
Quantum Simulation via Filtered Hamiltonian Engineering: Application to Perfect Quantum Transport in Spin Networks (2013)

We propose a method for Hamiltonian engineering that requires no local control but only relies on collective qubit rotations and field gradients. The technique achieves a spatial modulation of the coupling strengths via a dynamical construction of a weighting function combined with a Bragg grating. As an example, we demonstrate how to generate the ideal Hamiltonian for perfect quantum information transport between two separated nodes of a large spin network. We engineer a spin chain with optimal couplings starting from a large spin network, such as one naturally occurring in crystals, while decoupling all unwanted interactions. For realistic experimental parameters, our method can be used to drive almost perfect quantum information transport at room temperature. The Hamiltonian engineering method can be made more robust under decoherence and coupling disorder by a novel apodization scheme. Thus, the method is quite general and can be used to engineer the Hamiltonian of many complex spin lattices with different topologies and interactions.
Evaluation of phase‐sensitive versus magnitude reconstructed inversion recovery imaging for the assessment of myocardial infarction in mice with a clinical magnetic resonance scanner (2012)

The PSIR technique provides stable and consistent contrast between hyperenhanced and remote myocardium independent of the selected inversion time (TI) and proved to be a robust, fast, and accurate tool for the assessment of MI in mice.
Transcriptome Analysis Revealed Plant Hormone Biosynthesis and Response Pathway Modification by Epichloëgansuensis in Achnatheruminebrians under Different Soil Moisture Availability (2021)

The present study was designed to explore the effects of the endophyte <i>Epichloë gansuensis</i> on gene expression related to plant hormone biosynthesis and response pathways and the content of salicylic acid (SA) and jasmonic acid (JA) hormones of <i>Achnatherum inebrians</i>, under different moisture conditions. Through a pot experiment and transcriptome analysis, we found a total of 51 differentially expressed genes (DEGs) related to hormone biosynthesis and response pathways, including 12 auxin related genes, 8 cytokinin (CTK) related genes, 3 gibberellin (GA) related genes, 7 abscisic acid (ABA) related genes, 7 ethylene (ET) related genes, 12 JA related genes and 4 SA related genes. Furthermore, key genes of JA and SA biosynthesis and response pathways, such as <i>LOX2S</i>, <i>AOS</i>, <i>OPR</i>, <i>ACX</i>, <i>JMT</i>, <i>JAZ</i>, <i>PAL</i>, <i>NPR1</i>, <i>TGA</i> and <i>PR-1</i>, showed different degrees of upregulation or downregulation. Under 60% soil moisture content, the JA content of endophyte-free (EF) <i>A. inebrians</i> was significantly (<i>p</i> < 0.05) higher than that of endophyte-infected (EI) <i>A. inebrians</i>. Under 30% and 60% soil moisture content, the SA content of EF <i>A. inebrians</i> was significantly (<i>p</i> < 0.05) higher than that of EI <i>A. inebrians</i>. SA content of EI <i>A. inebrians</i> under 30% and 60% soil moisture content was significantly (<i>p</i> < 0.05) higher than that under 15% soil moisture content. With both EI and EF plants, the SA and JA levels, respectively, are very similar at 15% soil moisture content. This study has revealed that <i>E. gansuensis</i> differentially activated plant hormone synthesis and signal transduction pathways of <i>A. inebrians</i> plants under different soil moisture availability.
Direct Selection of DNA-Encoded Libraries for Biased Agonists of GPCRs on Live Cells (2023)

G protein-coupled receptors (GPCRs) are the largest superfamily of human membrane target proteins for approved drugs. GPCR ligands can have a complex array of pharmacological activities. Among these activities, biased agonists have potential to serve as both chemical probes to understand specific aspects of receptor signaling and therapeutic leads with more specific, desired activity. Challenges exist, however, in the development of new biased activators due, in part, to the low throughput of traditional screening approaches. DNA-encoded chemical libraries (DELs) dramatically improve the throughput of drug discovery by allowing a collective selection, rather than discrete screening, of large compound libraries. The use of DELs has been largely limited to affinity-based selections against purified protein targets, which identify binders only. Herein, we report a split protein complementation approach that allows direct identification of DNA-linked molecules that induce the dimerization of two proteins. We used this selection with a DEL against opioid receptor GPCRs on living cells for the identification of small molecules that possess the specific function of activation of either β-arrestin or G protein signaling pathways. This approach was applied to δ-, μ-, and κ-opioid receptors and enabled the discovery of compound [66,66], a selective, G-protein-biased agonist of the κ-opioid receptor (EC<sub>50</sub> = 100 nM, <i>E</i> <sub>max</sub> = 82%, G<sub>i</sub> bias factor = 6.6). This approach should be generally applicable for the direct selection of chemical inducers of dimerization from DELs and expand the utility of DELs to enrich molecules with a specific and desired biochemical function.
Prediction and analysis of human thoracic impact responses and injuries in cadaver impacts using a full human body finite element model (2003)

Human thoracic dynamic responses and injuries associated with frontal impact, side impact, and belt loading were investigated and predicted using a complete human body finite element model for an average adult male. The human body model was developed to study the impact biomechanics of a vehicular occupant. Its geometry was based on the Visible Human Project (National Library of Medicine) and the topographies from human body anatomical texts. The data was then scaled to an average adult male according to available biomechanical data from the literature. The model includes details of the head, neck, ribcage, abdomen, thoracic and lumbar spine, internal organs of the chest and abdomen, pelvis, and the upper and lower extremities. The present study is focused on the dynamic response and injuries of the thorax. The model was validated at various impact speeds by comparing predicted responses with available experimental cadaver data in frontal and side pendulum impacts, as well as belt loading. Model responses were compared with similar individual cadaver tests instead of using cadaver corridors because the large differences between the upper and lower bounds of the corridors may confound the model validation. The validated model was then used to study thorax dynamic responses and injuries in various simulated impact conditions. Parameters that could induce injuries such as force, deflection, and stress were computed from model simulations and were compared with previously proposed thoracic injury criteria to assess injury potential for the thorax. It has been shown that the model exhibited speed sensitive impact characteristics, and the compressibility of the internal organs significantly influenced the overall impact response in the simulated impact conditions. This study demonstrates that the development of a validated FE human body model could be useful for injury assessment in various cadaveric impacts reported in the literature. Internal organ injuries, which are difficult to detect in experimental studies with human cadavers, can be more easily identified with a validated finite element model through stress-strain analysis, especially in conjunction with experimental studies.
Generation of Personal Sound Zones With Physical Meaningful Constraints and Conjugate Gradient Method (2021)

Personal sound zones provide users to experience independent listening and quiet areas in the same acoustic environment using multiple loudspeakers. The generalized eigenvalue decomposition (GEVD) has been proposed for sound zones generation, allowing user to control the trade-off between acoustic contrast and signal distortion by adjusting some parameters. Unfortunately, these parameters are not physically meaningful, and the user has to tune them for different source materials and acoustic environments. Moreover, performing a high dimensional GEVD is computational complex. In this article, we first propose various strategies to control the reproduced sound zones as precisely and accurately as possible by reformulating the problem using physically meaningful constraints using regularization approach. Then, a hybrid approach of combining the conjugate gradient method and GEVD is proposed to reduce the computational complexity and signal distortion when the subspace dimension is small. The proposed methods show precise control over the reproduced sound zone via extensive numerical simulations in reverberant environments for different physically meaningful constraints.
Quantitative analysis of the giant magnetoresistance effect at microwave frequencies (2011)

The high-frequency analog of giant magnetoresistance (GMR) in the microwave reflection and transmission coefficients of spin valves was measured and quantified. The relative change in transmission is nearly a factor of 2 larger than the electrical transport GMR effect. The change in reflection is of opposite sign and an order of magnitude smaller. A calculation of the reflection and transmission coefficients, considering the interfaces and the decay of the fields within the layers, provides a quantitative relationship to the transport GMR with no free parameters.
Supplementary Material for: Electrophysiological Evidence of the Basilar-Membrane Travelling Wave and Frequency Place Coding of Sound in Cochlear Implant Recipients (2017)

<i>Aim:</i> To obtain direct evidence for the cochlear travelling wave in humans by performing electrocochleography from within the cochlea in subjects implanted with an auditory prosthesis. <i>Background:</i> Sound induces a travelling wave that propagates along the basilar membrane, exhibiting cochleotopic tuning with a frequency-dependent phase delay. To date, evoked potentials and psychophysical experiments have supported the presence of the travelling wave in humans, but direct measurements have not been made. <i>Methods:</i> Electrical potentials in response to rarefaction and condensation acoustic tone bursts were recorded from multiple sites along the human cochlea, directly from a cochlear implant electrode during, and immediately after, its insertion. These recordings were made from individuals with residual hearing. <i>Results:</i> Electrocochleography was recorded from 11 intracochlear electrodes in 7 ears from 6 subjects, with detectable responses on all electrodes in 5 ears. Cochleotopic tuning and frequency-dependent phase delay of the cochlear microphonic were demonstrated. The response latencies were slightly shorter than those anticipated which we attribute to the subjects' hearing loss. <i>Conclusions:</i> Direct evidence for the travelling wave was observed. Electrocochleography from cochlear implant electrodes provides site-specific information on hair cell and neural function of the cochlea with potential diagnostic value.
Characterization Of Commonly Encountered Explosives Using Highfield Asymmetric Waveform Ion Mobility Spectrometry Coupled With Mass Spectrometry (2007)

The goal of this research was to characterize explosive compounds using high-field asymmetric waveform ion mobility spectrometry (FAIMS) as an ion separation device interface to a mass spectrometer (MS). FAIMS is a relatively recently developed technology that is promising adding a dimension of separation. This method was employed in such a way as to be conducive to possible future development of field instruments (e.g., use of atmospheric pressure chemical ionization (APCI)). In addition, several experiments were conducted with the application of this method, mainly dealing with optimization of the instrument parameters. These experiments led to the development of a new method: high-resolution FAIMS. An ion mobility spectrometer was used as a desolvation and ion focusing device to drastically improve FAIMS resolution. This allowed for the separation of mixtures that otherwise could not have been separated. The resolution was high enough that isomers of the same explosive were successfully resolved. This can be beneficial to forensics studies.
Comparison of scar signal quantification using phase corrected and conventional magnitude inversion recovery delayed enhancement imaging in patients with ischemic and non-ischemic cardiomyopathy (2013)

Background Myocardial scar volume quantification has been shown to predict response to medical, surgical, and device therapy. Phase sensitive inversion recovery (PSIR)-based Late Gadolinium Enhancement (LGE) image reconstruction is clinically attractive for its reduced dependence on accurate prescription of the Time from Inversion (TI time), and is becoming a preferred approach for many centers. However, while an efficient approach for the visual interpretation of myocardial injury, the influence of this approach on signal-threshold based scar volume quantification has been poorly explored. Methods A total of 80 patients with obvious myocardial scar by LGE imaging (40 ischemic, 40 non-ischemic) underwent blinded evaluations of total scar volume (%LV mass) using matched MIR and PSIR short axis images. Analysis was performed using the Signal Threshold Versus Reference Myocardium (STRM) technique at ≥2, ≥3, and ≥5 SD thresholds. In those with ischemic scar the Full Width at Half Maximum (FWHM) approach was incrementally evaluated. Linear regression and BlandAltman analyses comparing MIR verses PSIR-based scar quantification was performed. Results Linear regression analysis demonstrated an excellent correlation between PSIR and MIR-based STRM scar volumes at all 3 STRM-based thresholds for both ischemic scar (r=0.96, 0.95, and 0.88, respectively) and non-ischemic scar (r=0.86, 0.89, 0.90, respectively). FWHM analysis showed good correlation in ischemic scar (r=0.83). Bland-Altman analysis of STRM analysis showed a systematic bias with lower scar volumes produced by PSIR reconstruction images for both ischemic and non-ischemic scar. These differences were modest using STRM for ischemic scar (-3.3, -4.0 and -4.9%,
Peri-implant fracture after dual-plating knee arthrodesis for failed total knee arthroplasty: case series (2019)

Knee arthrodesis is an option in the setting of failed total knee arthroplasty. Dual-plate fixation is a described technique to obtain knee fusion in this scenario. Literature on the complications of knee arthrodesis with dual-plate constructs is limited. We present 3 cases who underwent dual-plate knee arthrodesis complicated by peri-implant femur fracture.
Hollow MXene Spheres and 3D Macroporous MXene Frameworks for Na‐Ion Storage (2017)

2D transition metal carbides and nitrides, named MXenes, are attracting increasing attentions and showing competitive performance in energy storage devices including electrochemical capacitors, lithium- and sodium-ion batteries, and lithium-sulfur batteries. However, similar to other 2D materials, MXene nanosheets are inclined to stack together, limiting the device performance. In order to fully utilize MXenes' electrochemical energy storage capability, here, processing of 2D MXene flakes into hollow spheres and 3D architectures via a template method is reported. The MXene hollow spheres are stable and can be easily dispersed in solvents such as water and ethanol, demonstrating their potential applications in environmental and biomedical fields as well. The 3D macroporous MXene films are free-standing, flexible, and highly conductive due to good contacts between spheres and metallic conductivity of MXenes. When used as anodes for sodium-ion storage, these 3D MXene films exhibit much improved performances compared to multilayer MXenes and MXene/carbon nanotube hybrid architectures in terms of capacity, rate capability, and cycling stability. This work demonstrates the importance of MXene electrode architecture on the electrochemical performance and can guide future work on designing high-performance MXene-based materials for energy storage, catalysis, environmental, and biomedical applications.
Temporal RVL: A Depth Stream Compression Method (2020)

The advent of depth cameras has led to new opportunities, but at the same time has led to new challenges in the form of larger network bandwidth. To address this problem, we propose a lossy compression method Temporal RVL, which results in better compression with little loss of depth information. Temporal RVL adds a preprocessing step to RVL and effectively utilizes the similarities across frames, while maintaining important depth information such as edges. For the default settings, Temporal RVL achieves a compression ratio of 20.1 (4.2 times higher than RVL) while at the same time facilitating faster decompression.
Simulation, registration, and reconstruction of digital holograms of arbitrary objects by means of liquid crystal on silicon spatial light modulator (2005)

Each hologram: optical, digital and computer generated represents the phase and amplitude of an object. Therefore the process of object reconstruction may rely on one of two alternative procedures: optoelectronic direct reconstruction of hologram, which is represented by diffractive structure intensity, and recombining of object phase and amplitude as calculated from wavefront propagation process (here the method is based on singular wave component that is derived from a rigorous Sommerfeld's solution) or numerical reconstruction of digital hologram. In the paper we present the comparison of these two ways of optoelectronic reconstruction. The pros and cons for application of these procedures from image quality point of view are given. The experimental systems based on a Twyman-Green interferometer with two phase and amplitude LCOS or on a single digital hologram or computer generated hologram reconstruction setup are presented. The conclusions of these experiments will be utilized for optimizing of the process of production of security holograms with use of LCOS modulators.
Physiology of Na+/H+ Exchangers in the Male Reproductive Tract: Relevance for Male Fertility1 (2014)

The maintenance of pH homeostasis in the male reproductive tract is kept through the involvement of several mechanisms, among which is included the transmembranous movement of H(+) ions. Na(+)-H(+) exchangers (SLC9, solute carrier 9 family members) are among the membrane transporters known to participate in intracellular and extracellular pH regulation but also have important roles in salt and water absorption across epithelia and in the regulation of cell volume. The presence of several Na(+)-H(+) exchangers has been reported in the male reproductive tract. Their involvement in the processes that ensure the correct pursuance of the spermatogenetic event and spermatozoa maturation has been suggested. Indeed, the formation of mature spermatozoa is highly dependent on the maintenance of adequate ductal luminal milieu pH and ionic balance. Perturbations in these processes result in reduced male reproductive potential and consequently male subfertility and/or infertility. Thus, it is imperative to understand H(+) transport dynamics in order to identify and counteract possible alterations associated with reduced male fertility caused by pathological conditions. Herein, we will discuss the expression pattern and physiological roles of SLC9 family members in the cells of the male reproductive tract as well as the molecular basis of H(+) transport and its involvement in male reproductive potential.
Sensitivity enhancement of a mode-locked ring laser gyroscope by giant intracavity dispersion (2018)

It has been theoretically predicted that giant intracavity dispersion can significantly alter the response of a ring laser gyroscope. We demonstrate this effect experimentally in a mode-locked ring laser. Group velocity dispersion of this magnitude can only be the resonant dispersion due to the Kramers-Kronig relation. Although the bandwidth of this large dispersion is rather small, inserting a Fabry-Perot interferometer into the cavity provides positive dispersion (resulting in ”slow light”) to all components of the frequency comb. We show that this is due to the the Fabry-Perot comb coupling to the laser resonator comb. Increasing the sensitivity of the gyroscope would require a large negative dispersion (resulting in ”fast light”) in the cavity. This can be achieved using a Gires-Tournois-interferometer.
Antisense suppression of the lignin biosynthetic enzyme, caffeate <i>O</i> -methyltransferase, improves <i>in vitro</i> digestibility of the tropical pasture legume, <i>Stylosanthes humilis</i> (2001)

The high lignin content of tropical forage plants reduces digestibility and voluntary feed intake by ruminants. We have used antisense technology to suppress caffeate O -methyltransferase (COMT EC, 2.1.1.68), a lignin biosynthetic enzyme in the tropical forage legume, Stylosanthes humilis Kunth. Plants were transformed using a Ti binary vector containing an antisense COMT construct under the control of the CaMV 35S promoter. From 50 transgenic plants, five were selected on the basis of normal morphology, high levels of antisense gene expression and altered lignin histochemistry. No plants with altered lignin were observed in a population of 20 transgenic plants derived using a binary vector that lacked the COMT cDNA insert. The progeny of lignin-altered plants were analysed for COMT enzyme activity and lignin histochemistry. A variety of COMT and lignin phenotypes was observed. In several T1 plants, COMT activity was specifically suppressed by more than 95% compared to controls. In these plants, expression of antisense mRNA was high while sense mRNA could not be detected on northern blots. The overall lignin content of these plants was unchanged but histochemical tests showed abnormally low levels of the syringyl component, mimicking the pattern of young tissue. Digestibility of these transgenic plants was assessed by incubation of stem material with rumen fluid and acid pepsin in vitro . The digestibility of the antisense material was increased dramatically compared to that of equivalent samples from control transformed plants (72 vs 62%).