gebhart/patrepeval huggingface dataset:
Engineered Reciprocal Chromosome Translocations Drive High Threshold, Reversible Population Replacement in Drosophila (2018)

Replacement of wild insect populations with transgene-bearing individuals unable to transmit disease or survive under specific environmental conditions using gene drive provides a self-perpetuating method of disease prevention. Mechanisms that require the gene drive element and linked cargo to exceed a high threshold frequency in order for spread to occur are attractive because they offer several points of control: they bring about local, but not global population replacement; and transgenes can be eliminated by reintroducing wildtypes into the population so as to drive the frequency of transgenes below the threshold frequency required for drive. Reciprocal chromosome translocations were proposed as a tool for bringing about high threshold population replacement in 1940 and 1968. However, translocations able to achieve this goal have only been reported once, in the spider mite Tetranychus urticae, a haplo-diploid species in which there is strong selection in haploid males for fit homozygotes. We report the creation of engineered translocation-bearing strains of Drosophila melanogaster, generated through targeted chromosomal breakage and homologous recombination. These strains drive high threshold population replacement in laboratory populations. While it remains to be shown that engineered translocations can bring about population replacement in wild populations, these observations suggest that further exploration of engineered translocations as a tool for controlled population replacement is warranted.
Creation of the first anomeric D/L-sugar kinase by means of directed evolution (2003)

Chemoenzymatic routes toward complex glycoconjugates often depend on the availability of sugar-1-phosphates. Yet the chemical synthesis of these vital components is often tedious, whereas natural enzymes capable of anomeric phosphorylation are known to be specific for one or only a few monosaccharides. Herein we describe the application of directed evolution and a high-throughput multisugar colorimetric screen to enhance the catalytic capabilities of the Escherichia coli galactokinase GalK. From this approach, one particular GalK mutant carrying a single amino acid exchange (Y371H) displayed a surprisingly substantial degree of kinase activity toward sugars as diverse as d-galacturonic acid, d-talose, l-altrose, and l-glucose, all of which failed as wild-type GalK substrates. Furthermore, this mutant provides enhanced turnover of the small pool of sugars converted by the wild-type enzyme. Comparison of this mutation to the recently solved structure of Lactococcus lactis GalK begins to provide a blueprint for further engineering of this vital class of enzyme. In addition, the rapid access to such promiscuous sugar C-1 kinases will significantly enhance accessibility to natural and unnatural sugar-1-phosphates and thereby impact both in vitro and in vivo glycosylation methodologies, such as natural product glycorandomization.
3D Visual Proxemics: Recognizing Human Interactions in 3D from a Single Image (Open Access) (2013)

Abstract : We present a unified framework for detecting and classifying people interactions in unconstrained user generated images. Unlike previous approaches that directly map people/face locations in 2D image space into features for classification, we first estimate camera viewpoint and people positions in 3D space and then extract spatial configuration features from explicit 3D people positions. This approach has several advantages. First, it can accurately estimate relative distances and orientations between people in 3D. Second, it encodes spatial arrangements of people into a richer set of shape descriptors than afforded in 2D. Our 3D shape descriptors are invariant to camera pose variations often seen in web images and videos. The proposed approach also estimates camera pose and uses it to capture the intent of the photo. To achieve accurate 3D people layout estimation, we develop an algorithm that robustly fuses semantic constraints about human interpositions into a linear camera model. This enables our model to handle large variations in people size, heights (e.g. age) and poses. An accurate 3D layout also allows us to construct features informed by Proxemics that improves our semantic classification. To characterize the human interaction space, we introduce visual proxemes; a set of prototypical patterns that represent commonly occurring social interactions in events. We train a discriminative classifier that classifies 3D arrangements of people into visual proxemes and quantitatively evaluate the performance on a large, challenging dataset.
Imaging of Port Wine Stain Lesions Using a Multi-Sensor Photoacoustic Probe (2004)

Successful treatment of port wine stain (PWS) birthmarks in human skin utilizes cryogen spray cooling (CSC) in conjunction with laser treatment. CSC pre-cools the epidermis to protect it from subsequent laser irradiation which raises the temperature of both the epidermis and the deeper PWS. As the epidermal temperature is depressed by cryogen, damage to the skin surface is minimized while the PWS reaches temperatures sufficient to permanently damage the lesion. In order to optimize cooling and laser heating dosages and to properly guide laser therapy, the spatial relationship of epidermal melanin and PWS must be known. Photoacoustic depth profiling of human skin uses low energy, nanosecond pulses of laser light to induce acoustic waves in optically absorbing media, such as blood and melanin. We used a 532 nm Nd:YAG laser to measure total epidermal melanin content in human skin, comparing the results with visible reflectance spectroscopy. Furthermore, we performed numerical simulations of photoacoustic generation in skin, showing that a hemisperical acoustic sensor array could be used to reconstruct the rete pattern of epidermal melanin in the basal layer. Finally, we built a hemispherical probe for use in future experiments for imaging of human skin.
Stress-Compensated Quartz Resonators Having Ultra-Linear Frequency-Temperature Responses (1984)

A new family of stress compensated quartz resonators having cuts exhibiting an ultra-linear frequency vs. temperature characteristic. This family of resonators has an orientation defined with respect to the crystallographic axes by polar angles φ and θ, which angles lie on the locus where the second-order temperature coefficient of frequency is zero between the angles φ=20°±2° and θ=20°±5°, and in close proximity to the locus of zero coefficient of stress. In one preferred embodiment, the resonator comprises a plate whose angles of cut φ and θ are both substantially equal to 20°. In a second preferred embodiment an exact stress compensation is provided where φ is substantially equal to 20.8° and θ is substantially equal to 23.2°, and orientation where the locus of the zero coefficient of stress intersects the locus of the zero of the second-order temperature coefficient.
Optical see-through HMD calibration: a stereo method validated with a video see-through system (2000)

We present initial results from ongoing work to calibrate optical see-through head-mounted displays (HMDs). We have developed a method to calibrate stereoscopic optical see-through HMDs based on the 3D alignment of a target in the physical world with a virtual object in the user's view. This is an extension of the single point active alignment method (SPAAM) (Tuceryan and Navab, 2000) developed for monocular HMDs. Going from the monocular to the stereoscopic optical HMDs for calibration purposes is not straightforward. This is in part due to the perceptual complexity of the stereo fusion process bringing up completely new challenges including the choice of the shape of the virtual object, the physical target and how to display the virtual object without any knowledge of the characteristics of the HMD and eye combination, i.e. the projection model. We have addressed these issues and proposed a solution for the calibration problem which we have validated through experiments on the see-through HMD system described in (Sauer et al., 2000). By experimenting, we have found the appropriate type of virtual objects and physical features to be used in the 3D alignment. Furthermore, we have measured how good the alignment and calibration actually are.
Automatic image retargeting with fisheye-view warping (2005)

Image retargeting is the problem of adapting images for display on devices different than originally intended. This paper presents a method for adapting large images, such as those taken with a digital camera, for a small display, such as a cellular telephone. The method uses a non-linear fisheye-view warp that emphasizes parts of an image while shrinking others. Like previous methods, fisheye-view warping uses image information, such as low-level salience and high-level object recognition to find important regions of the source image. However, unlike prior approaches, a non-linear image warping function emphasizes the important aspects of the image while retaining the surrounding context. The method has advantages in preserving information content, alerting the viewer to missing information and providing robustness.
P‐94: Polymer Cholesteric Liquid Crystal Flakes for Particle Displays (2003)

Abstract Polymer cholesteric liquid crystal (PCLC) flakes suspended in a moderately conductive host fluid reorient in the presence of an AC electric field within a specific frequency range, causing a dramatic change in flake reflectivity. PCLC flakes reflect light of a specific color and (circular) polarization, thereby eliminating the need for backlighting, color filters, and polarizers to attain unique optical effects. Reorientation can be seen in fields as low as several milli‐volts per micron, and reorientation times are on the order of several hundred milliseconds, thereby approaching response times for both nematic liquid crystal displays and other particle displays. Applications for electro‐optic devices, decorative commercial and consumer products, and displays, particularly electronic paper, are envisioned.
Channel Wall Plasma Thermal Loads in Hall Thrusters with Magnetic Shielding (2011)

Computer simulations using Hall2De identified the fundamental physical processes through which magnetic shielding can reduce channel wall erosion by orders of magnitude in Hall thrusters. Because magnetic shielding reduces significantly the energy and flux of the incident plasma a natural question is whether it has also a large effect on Hall thruster thermal design. In particular, if a Hall thruster is designed with magnetic shielding, will it be able to operate at significantly higher power densities than a conventional Hall thruster due to reduced thermal loads to the walls? If magnetically shielded Hall thrusters can operate at higher power densities, then high power Hall thrusters could be made smaller and lighter than present designs. In this paper we use Hall2De simulations of a laboratory thruster with and without magnetic shielding to predict the thermal loads from both ions and electrons including the self-consistently calculated wall sheaths. The formulations are similar to those previously applied in a hollow cathode thermal model. The numerical simulations show that, while magnetic shielding reduces high energy ion bombardment and power deposition in the acceleration zone of the discharge chamber, it has little effect on the total plasma thermal loads to thruster surfaces subject to plasma heating. Higher power densities were calculated on thruster surfaces downstream of the discharge chamber for the magnetic shielding configuration. Still, the reduction in peak plasma heating in the acceleration zone for the magnetic shielding configurations should reduce wall temperatures in this region that may lead to higher power density operation if the power deposition on the downstream surfaces for the magnetic shielded configuration can be mitigated.
Connectivity-aware virtual network embedding (2016)

The problem of ensuring virtual network (VN) connectivity in presence of multiple link failures in the substrate network (SN) is not well investigated in Network Virtualization (NV) literature. We name this problem as Connectivity-aware Virtual Network Embedding (CoViNE). Solving CoViNE will enable a VN operator to perform failure recovery without depending on the SN provider, similar to the IP restoration mechanisms in IP-over-WDM networks. There are two steps in solving CoViNE: i) finding the virtual links that should be embedded disjointly, and ii) finding a substrate resource efficient embedding that ensures the virtual link disjointness constraint. We present two solutions to the CoViNE problem. The first solution uses a heuristic to compute the disjointness constraint, while an optimization model is used for VN embedding. The second solution, in contrast, uses heuristic for both the steps, and thus can solve larger instances of the problem. We compare our solutions with a cut set based approach that ensures VN connectivity for a single substrate link failure. Evaluation results show that our heuristics allocate ∼15% extra resources on average compared to the cut set based optimal solution, and executes two to three orders of magnitude faster on the same problem instances.
Design and implementation of all-optical half adder using cross gain modulation in semiconductor optical amplifiers (2007)

By using only two input signals of A and B, an all-optical half adder that utilizes a cross gain modulation in semiconductor optical amplifiers is demonstrated at 10 Gbps. The half adder utilizes two logic functions of SUM and CARRY, which can be demonstrated by using the XOR gate and the AND gate, respectively. The extinction ratios of SUM and CARRY are approximately 6.1 dB. No additional input beam such as clock signal or continuous wave light, which is required in many other all-optical logic gates, is used in this design concept.
A haptic platform to enable fingertip grasping and manipulation (2011)

\n\t\t\t\t\tHaptic technologies allow human users to haptically interact with virtual environments. Haptics has been employed in many application domains including operator training, virtual exploration and teleoperation. Currently, most commercially available haptic devices focus on a single point of haptic interaction. While single-point haptics have been successfully employed in many applications, they remain limited to particular types of haptic interaction. Multi-point haptic devices are a logical progression and facilitate a far wider range of interactions including object grasping, multi-finger object manipulation and size discrimination. The ability to effectively achieve such interactions offers significant benefits for many applications including virtual training, telesurgery and telemanipulation. In such applications, the ability to use multi-point haptic interactions can provide far more effective user interaction as well improved perception of the virtual environment.\n\t\t\t\t
Synchronous nanoscale topographic and chemical mapping by differential-confocal controlled Raman microscopy (2020)

Confocal Raman microscopy is currently used for label-free optical sensing and imaging within the biological, engineering, and physical sciences as well as in industry. However, currently these methods have limitations, including their low spatial resolution and poor focus stability, that restrict the breadth of new applications. This paper now introduces differential-confocal controlled Raman microscopy as a technique that fuses differential confocal microscopy and Raman spectroscopy, enabling the point-to-point collection of three-dimensional nanoscale topographic information with the simultaneous reconstruction of corresponding chemical information. The microscope collects the scattered Raman light together with the Rayleigh light, both as Rayleigh scattered and reflected light (these are normally filtered out in conventional confocal Raman systems). Inherent in the design of the instrument is a significant improvement in the axial focusing resolution of topographical features in the image (to <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="m1"> <mml:mrow> <mml:mo form="prefix">∼</mml:mo> <mml:mn>1</mml:mn> <mml:mtext> </mml:mtext> <mml:mi>nm</mml:mi> </mml:mrow> </mml:math> ), which, when coupled with super-resolution image restoration, gives a lateral resolution of 220 nm. By using differential confocal imaging for controlling the Raman imaging, the system presents a significant enhancement of the focusing and measurement accuracy, precision, and stability (with an antidrift capability), mitigating against both thermal and vibrational artefacts. We also demonstrate an improved scan speed, arising as a consequence of the nonaxial scanning mode.
Utilizing a handheld electrode array for localized muscle impedance measurements (2012)

These data support the potential use of a handheld array for performing rapid localized surface impedance measurements.
Design of a New Histamine H<sub>3</sub> Receptor Antagonist Chemotype: (3a<i>R</i>,6a<i>R</i>)-5-Alkyl-1-aryl-octahydropyrrolo[3,4-<i>b</i>]pyrroles, Synthesis, and Structure−Activity Relationships (2009)

A new histamine H3 receptor (H3R) antagonist chemotype 1 was designed by combining key pharmacophoric elements from two different precursor structural series and then simplifying and optimizing the resulting combined structural features. First, analogues were made based on a previously identified conessine-based H3R antagonist series. While the first analogues 11 and 15 showed no antagonistic activity to H3R, the mere addition of a key moiety found in the reference compound 7 (ABT-239) elevated the series to high potency at H3R. The hybrid structure (16b) was judged too synthetically demanding to enable an extensive SAR study, thus forcing a strategy to simplify the chemical structure. The resulting (3aR,6aR)-5-alkyl-1-aryl-octahydropyrrolo[3,4-b]pyrrole series proved to be highly potent, as exemplified by 17a having a human H3 K(i) of 0.54 nM, rat H3 K(i) of 4.57 nM, and excellent pharmacokinetics (PK) profile in rats (oral bioavailability of 39% and t(1/2) of 2.4 h).
Triazole Bridged Flavonoid Dimers as Potent, Nontoxic, and Highly Selective Breast Cancer Resistance Protein (BCRP/ABCG2) Inhibitors (2019)

The present work describes the syntheses of diverse triazole bridged flavonoid dimers and identifies potent, nontoxic, and highly selective BCRP inhibitors. A homodimer, <b>Ac22(Az8)</b><sub><b>2</b></sub>, with <i>m</i>-methoxycarbonylbenzyloxy substitution at C-3 of the flavone moieties and a <i>bis-</i>triazole-containing linker (21 atoms between the two flavones) showed low toxicity (IC<sub>50</sub> toward L929, 3T3, and HFF-1 > 100 μM), potent BCRP-inhibitory activity (EC<sub>50</sub> = 1-2 nM), and high BCRP selectivity (BCRP selectivity over MRP1 and P-gp > 455-909). <b>Ac22(Az8)</b><sub><b>2</b></sub> inhibits BCRP-ATPase activity, blocks the drug efflux activity of BCRP, elevates the intracellular drug accumulation, and finally restores the drug sensitivity of BCRP-overexpressing cells. It does not down-regulate the surface BCRP protein expression to enhance the drug retention. Therefore, <b>Ac22(Az8)</b><sub><b>2</b></sub> and similar flavonoid dimers appear to be promising candidates for further development into combination therapy to overcome MDR cancers with BCRP overexpression.
The NPXXY Motif Regulates β-Arrestin Recruitment by the CB1 Cannabinoid Receptor (2022)

<b>Background:</b> Activation of signaling effectors by G-protein coupled receptors (GPCRs) depends on different molecular mechanisms triggered by conserved amino acid residues. Although studies have focused on the G-protein signaling state, the mechanism for β-arrestin signaling by CB1 is not yet well defined. Studies have indicated that transmembrane helix 7 (TMH7) and the highly conserved NPXXY motif can be subject to different conformational changes in response to biased ligands and could therefore participate in a molecular mechanism to trigger β-arrestin recruitment. <b>Objective:</b> To investigate the effect of mutations in the NPXXY motif on different signaling pathways activated by the CB1 receptor. <b>Materials and Methods:</b> Point mutations of the NPXXY motif and associated residues were generated in the CB1 receptor using site-directed mutagenesis and transfection into HEK-293 cells. Signaling by wild-type and mutant receptors was analyzed by quantifying inhibition of cAMP, and by β-arrestin recruitment assays. <b>Results:</b> We found that N7.49 and Y7.53 are essential for β-arrestin recruitment by CB1. N7.49A and Y7.53F impair β-arrestin signaling, with no effect on G-protein signaling. We found a regulatory role for residue I2.43; I2.43 interacts with Y7.53, affecting its positioning. Reducing steric bulk at I2.43 (I2.43A) enhances β-arrestin1 recruitment, while introducing a polar residue (I2.43T) reduces β-arrestin recruitment. <b>Conclusions:</b> These findings point to a novel mechanism for β-arrestin recruitment, implicating amino acids in the NPXXY motif as critical for the putative β-arrestin biased conformational state of Class A GPCRs.
Demonstration of a rib optical waveguide with cutoff mesa isolation (2002)

In conclusion, a new single-mode cutoff mesa GaAs-AlGaAs rib waveguide has been designed and demonstrated. Using the principle of the cutoff slab waveguide, this waveguide provides singlemode performance regardless of any deep etches that might be used for electrical isolation between integrated electrooptic devices. Single mode operation is achievable with a wide range of rib widths and does not require demanding etch depth tolerances.
JALI (2016)

The rich signals we extract from facial expressions imposes high expectations for the science and art of facial animation. While the advent of high-resolution performance capture has greatly improved realism, the utility of procedural animation warrants a prominent place in facial animation workflow. We present a system that, given an input audio soundtrack and speech transcript, automatically generates expressive lip-synchronized facial animation that is amenable to further artistic refinement, and that is comparable with both performance capture and professional animator output. Because of the diversity of ways we produce sound, the mapping from phonemes to visual depictions as visemes is many-valued. We draw from psycholinguistics to capture this variation using two visually distinct anatomical actions: Ja w and L ip, wheresound is primarily controlled by jaw articulation and lower-face muscles, respectively. We describe the construction of a transferable template jali 3D facial rig, built upon the popular facial muscle action unit representation facs. We show that acoustic properties in a speech signal map naturally to the dynamic degree of jaw and lip in visual speech. We provide an array of compelling animation clips, compare against performance capture and existing procedural animation, and report on a brief user study.