gebhart/patrepeval huggingface dataset:
VD-BERT: A Unified Vision and Dialog Transformer with BERT (2020)

Visual dialog is a challenging vision-language task, where a dialog agent needs to answer a series of questions through reasoning on the image content and dialog history. Prior work has mostly focused on various attention mechanisms to model such intricate interactions. By contrast, in this work, we propose VD-BERT, a simple yet effective framework of unified vision-dialog Transformer that leverages the pretrained BERT language models for Visual Dialog tasks. The model is unified in that (1) it captures all the interactions between the image and the multi-turn dialog using a single-stream Transformer encoder, and (2) it supports both answer ranking and answer generation seamlessly through the same architecture. More crucially, we adapt BERT for the effective fusion of vision and dialog contents via visually grounded training. Without the need of pretraining on external vision-language data, our model yields new state of the art, achieving the top position in both single-model and ensemble settings (74.54 and 75.35 NDCG scores) on the visual dialog leaderboard. Our code and pretrained models are released at https://github.com/salesforce/VD-BERT.
Cytochrome P450 Limonene Hydroxylases of Mentha Species (1995)

The oxygenation pattern of the monoterpenoids of mint (Mentha) species is determined by regiospecific cytochrome P450-catalyzed hydroxylation of the common olefinic precursor (-)-limonene. In peppermint, C3-allylic hydroxylation leads to (-)-trans-isopiperitenol that ultimately is converted to (-)-menthol, whereas in spearmint, C6-allylic hydroxylation leads to (-)-trans-carveol that is oxidized to (-)-carvone. The limonene-6-hydroxylase and the cytochrome P450 reductase were purified from the oil glands of spearmint, and the system was reconstituted. Amino acid sequences from the purified hydroxylase were utilized to design primers with which a large, non-degenerate PCR product was prepared. This probe was employed to screen a spearmint oil gland cDNA library from which the corresponding full-length cDNA was isolated. This clone provides the tool for isolating the homologous cDNA species from peppermint and related Mentha species.
Objective Quality Control for Colonoscopy (2006)

Purpose: Objective data to explain why a significant number of large polyps and cancers are not detected during colonoscopy do not exist. Here we present a novel, objective approach to automatically extract endoscopic metrics reflecting quality from digital video files created during colonoscopy. Methods: Digital Video Signal Capture. A workstation was developed that digitally captures and stores the complete video file generated during colonoscopy. Quality Control Algorithms. We developed software that automatically extracts 5 metrics from digitized video files created during colonoscopy. Metric 1 measures the overall duration of the insertion phase termed the insertion time. Metric 2 measures the duration of the withdrawal phase termed the withdrawal time. Metric 3 measures the clear withdrawal time defined as the duration of the withdrawal phase without out-of-focus frames. Metric 4 reflects the number of back and forth movements. Metric 5 includes fractions of Metric 3 that are spent on close inspections of the colon wall (off-axial or wall view) or global inspections (axial or lumen view). Results: We created approximately 250 digital video files during colonoscopy. Several critical algorithms were developed that allowed discrimination between clear and out-of-focus frames, forward or backward movement, and presence or abscence of the appendix. The image recognition algorithms that detect out-of-focus frames and movement direction have high sensitivity and specificity (>95%). Appendix recognition on a test dataset had a sensitivity of 90% and a specificity of 86%. Conclusions: We have created novel software that automatically extracts 5 objective quality control metrics from colonoscopy video files. Our method has the potential to provide large scale, continuous quality control for colonoscopy in the day-to-day medical practice setting. Lastly, our method may be useful to assess progress during colonoscopy training, or as part of endoscopic skills assessment evaluations. [figure 1]Figure 1
Photoacoustic microscopy with 7.6-μm axial resolution (2013)

The axial resolution of photoacoustic microscopy (PAM) is much lower than its lateral resolution, which resolves down to the submicron level. Here we achieved so far the highest axial resolution of 7.6 μm by using a commercial 125 MHz ultrasonic transducer for signal detection, followed by the Wiener deconvolution for signal processing. The axial resolution was validated by imaging two layers of red ink in a wedge shape. Melanoma cells were imaged ex vivo with high axial resolution. Compared with a PAM system with a 50 MHz ultrasonic transducer, our high-axial-resolution PAM system resolved the blood vessels in mouse ears in vivo much more clearly in the depth direction.
Unsynchronized structured light (2015)

Various Structured Light (SL) methods are used to capture 3D range images, where a number of binary or continuous light patterns are sequentially projected onto a scene of interest, while a digital camera captures images of the illuminated scene. All existing SL methods require the projector and camera to be hardware or software synchronized, with one image captured per projected pattern. A 3D range image is computed from the captured images. The two synchronization methods have disadvantages, which limit the use of SL methods to niche industrial and low quality consumer applications. Unsynchronized Structured Light (USL) is a novel SL method which does not require synchronization of pattern projection and image capture. The light patterns are projected and the images are captured independently, at constant, but possibly different, frame rates. USL synthesizes new binary images as would be decoded from the images captured by a camera synchronized to the projector, reducing the subsequent computation to standard SL. USL works both with global and rolling shutter cameras. USL enables most burst-mode-capable cameras, such as modern smartphones, tablets, DSLRs, and point-and-shoots, to function as high quality 3D snapshot cameras. Beyond the software, which can run in the devices, a separate SL Flash, able to project the sequence of patterns cyclically, during the acquisition time, is needed to enable the functionality.
Synthesis of 7-O-(2,6-dideoxy-2-fluoro-4-O-(3-fluorotetrahydropyran-2-yl)-.ALPHA.-L-talopyranosyl)daunomycinone. (1992)

7-O-[2,6-Dideoxy-2-fluoro-4-O-(3-fluorotetrahydropyran-2-yl)-alpha -L- talopyranosyl]daunomycinones (7a-7c) have been prepared by condensation of 3'-O-benzoyl derivative of 7-O-(2,6-dideoxy-2-fluoro-alpha-L-talopyranosyl)daunomycinone with 2,3-difluorotetrahydropyran as the key reaction. Antitumor activities of these compounds are described.
Mutation of Serine-39 to Threonine in Thermostable Secondary Alcohol Dehydrogenase from <i>Thermoanaerobacter ethanolicus</i> Changes Enantiospecificity (1998)

The substrate specificity of wild-type and Ser39 → Thr (S39T) secondary alcohol dehydrogenase (SADH) from Thermoanaerobacter ethanolicus was examined. The S39T mutation increases activity for 2-propanol without any significant effect on NADP+ binding. There is no significant effect of the mutation on the primary and secondary alcohol specificity of SADH. However, an effect on the enantiospecificity of SADH by the S39T mutation is demonstrated. Throughout the temperature range from 15 to 55 °C, wild-type SADH exhibits a preference for (S)-2-pentanol. In contrast, a temperature-dependent reversal of enantiospecificity is observed for 2-butanol, with a racemic temperature of 297 K. Throughout the same range of temperatures, S39T SADH exhibits higher enantiospecificity for the (R)-enantiomers of both 2-butanol and 2-pentanol. Examination of individual kcat/Km values for each enantiomer of the chiral alcohols reveals that the effect of the mutation is to decrease (S)-2-butanol specificity, and to preferentially enhance (R)-2-pentanol specificity relative to (S)-2-pentanol. These results are the first step toward expanding the synthetic utility of SADH to allow efficient preparation of a range of (R)-alcohols.
Distortion Product Emissions in Humans (1990)

Distortion product otoacoustic emissions (DPEs) at the 2f1-f2 frequency were recorded from 44 normal ears in response to equilevel primary tones. Detailed testing included the recording of DPE "audiograms" in 100-Hz steps from 1 to 8 kHz at three primary-tone levels (65, 75, and 85 dB sound pressure level [SPL]). In addition, response-growth or input-output (I/O) functions depicting the relationship of the amplitudes of DPEs to primary-tone levels, ranging from 25 to 85 dB SPL in 5-dB steps, were also tested for 11 frequencies distributed at quarter-octave intervals over the identical frequency range. The average DPE "audiogram" illustrating the frequency response of these emissions demonstrated a bilobed contour having a low-frequency maximum at approximately 1.5 kHz and a high-frequency peak that plateaued at about 5.5 kHz. The two maximum regions were separated by a minimum around 2.5 kHz. Depending on the frequency region, the average I/O functions exhibited detection "thresholds" at 3 dB above the noise floor at primary levels between 35 and 45 dB sound pressure level. The dynamic range of the emitted response between detection "threshold" and maximum amplitude varied over a 40-dB extent of the stimulus-level dimension. Approximately one third of the ears exhibited irregular DPE "audiograms" in which emitted responses were significantly reduced in restricted regions tested by low, medium, or high frequencies. When the 44 ears were separated into two groups representing more-normal and less-normal responses, the irregular "normal" ears demonstrated increased variability, especially in high-frequency regions. Mean age did not explain the differences noted between the two types of normally hearing subjects. However, across ears, DPE amplitudes and "thresholds" for the highest frequencies tested were correlated significantly with age in that the oldest individuals showed higher "thresholds" and lower amplitudes.
Microwave Remote Sensing Techniques for Measuring Thin Surface Films (1987)

Microwave techniques for the detection and measurement of thin surface films are described. These are based on comparison of the reflection coefficients of vertically and horizontally polarised signals from the surface under test. The design of two types of instrument is described, one based on polarisation ratio measurement near the pseudo-Brewster angle and one on phase detection by means of an array of receiving aerials.
Pharmacophoric Requirements for the Cannabinoid Side Chain. Probing the Cannabinoid Receptor Subsite at C1‘ (2003)

Earlier work from our laboratories has provided evidence for the existence of a subsite within the CB1 and CB2 cannabinoid receptor binding domain corresponding to substituents at the benzylic side chain position of classical cannabinoids. The existence and stereochemical features of this subsite have now been probed through the synthesis of a novel series of (-)-Delta(8)-tetrahydrocannabinol analogues bearing C1'-ring substituents. Of the compounds described here, those with C1'-dithiolane (1c), C1'-dioxolane (2d), and cyclopentyl (2a) substituents exhibited the highest affinities for CB1 and CB2. We used molecular modeling approaches to better define the stereochemical limits of the putative subsite. In vitro pharmacological testing found 1c to be a potent CB1 agonist.
Automatic vehicle recommendation (2002)

The purpose of this paper is to describe an approach to automated vehicle recommendation (AVR) for the purpose of CAD. For the purpose of this discussion AVR is defined as computer-assisted determination of a set of vehicles which are best suited to respond to an incident based on their AVL-determined geographic proximity to that incident. It is important to differentiate this from routing, which is the process of finding the nearest vehicle to a location. Routing is not the topic of this discussion as it refers to a specific implementation of AVR where a route and set of driving instructions are generated using the topology of the street network. When driving instructions are not required, Trimble's AVR approach is much more efficient in a real-time dispatch application than a conventional routing approach.
Active protection in pulse cavitational ultrasound therapy (histotripsy) (2009)

The overall goal of active protection is to preserve a selected zone (e.g., critical structures) during pulsed cavitational ultrasound therapy (histotripsy) using local suppression of cavitation. A specific application of active protection, focal sharpening, was investigated where a ring area immediately surrounding the focus was selected to be preserved. We have developed a pulse-by-pulse spatial-temporal pulsing strategy for focal sharpening. Treatments in cell-gel phantoms showed that the peripheral damage was substantially suppressed by 77 ± 13 % while desired treatment outcome in the center (i.e., complete fractionation) was maintained. High speed imaging of the bubble clouds showed a significant decrease in the maximum width of bubble clouds by 48 ± 23 % using focal sharpening. Preliminary experiments in ex vivo tissues demonstrated that active focal sharpening produced more confined lesions in real tissues.
Whole-spacecraft vibration isolation for broadband attenuation (2002)

Launch vehicles impart high levels of vibration to spacecraft during launch. The vibration environments are defined over several frequency bands: (1) transient vibration <80 Hz, (2) random vibration 20 to 2000 Hz, and (3) pyrotechnic shock 100 to 10000 Hz. Loads from transient vibration define spacecraft design of primary structures such as spacecraft bus, solar panel and antenna supports, instrument mounts, etc. Loads from random vibration define the design for spacecraft light structures such as antennas and solar panels, and shock loads define the design of electronic components and instruments. The spacecraft must survive the combination of all vibration environments. This requires spacecraft structures, instruments, and components to be designed to minimize vibration across a broad frequency range. Spacecraft are designed for the short launch to orbit, which is well beyond the requirements for on-orbit performance. A better choice is to reduce the magnitude of the high launch loads across all frequency bands and design smaller and less costly spacecraft. SoftRide systems are under development for the first and second OrbitaVSuborbital Program (OSP) launches and for the TaurusNTI launch. Additionally, isolation systems are being designed for larger liquid-fueled launch vehicles. This isolation system technology will greatly further the goal of better, faster, cheaper, and lighter spacecraft.
A Highly Effective African Swine Fever Virus Vaccine Elicits a Memory T Cell Response in Vaccinated Swine (2022)

African Swine Fever Virus (ASFV) is the causative agent of a highly contagious and lethal vector-borne disease in suids. Recently, a live attenuated virus strain, developed using the currently circulating, virulent Georgia strain (ASFV-G) with a single gene deletion (ASFV-G-ΔI177L), resulted in an effective vaccine. Nevertheless, protective immune response mechanisms induced by this candidate are poorly understood. In this study, Yorkshire crossbred swine intramuscularly vaccinated with 10<sup>6</sup> 50% hemadsorption dose (HAD<sub>50</sub>) of ASFV-G-ΔI177L or a vehicle control were challenged at 28 days post-inoculation (dpi) with 10<sup>2</sup> HAD<sub>50</sub> of ASFV-G. Analysis of purified peripheral blood mononuclear cells following inoculation and challenge revealed that CD4+, CD8+ and CD4+CD8+ central memory T cells (CD44+CD25-CD27-CD62L+CCR7+, T<sub>cm</sub>) decreased significantly by 28 dpi in ASFV-G-ΔI177L-vaccinated swine compared to baseline and time-matched controls. Conversely, CD4+, CD8+ and CD4+CD8+ effector memory T cells (CD44+CD25-CD27-CD62-CCR7-, T<sub>em</sub>) increased significantly among ASFV-G-ΔI177L-vaccined swine by 28 dpi compared to baseline and time-matched controls. Additionally, the percentage of natural killer (NK), CD4+ and CD4+CD8+ T<sub>em</sub> and CD8+ T<sub>cm</sub> and T<sub>em</sub> positive for IFNγ increased significantly following inoculation, surpassing that of controls by 28 dpi or earlier. These results suggest that NK and memory T cells play a role in protective immunity and suggest that studying these cell populations may be a surrogate immunity marker in ASF vaccination.
High-power electroabsorption modulator using intra-step-barrier quantum wells (2001)

We propose an efficient high-optical-saturation-power electroabsorption modulator (EAM) using intra-step-barrier quantum wells (IQWs) incorporating a step-barrier inside the well for both the conduction and the valence bands. From the simulation, we show that in the IQW (a) the onset of the redshift of the quantum-confined Stark effect is delayed to a higher electric field; and after the onset, (b) the transition energy and the oscillator strength respond sharply to the electric field. As the screening effect by the photogenerated carriers is reduced at the higher electric field, the optical saturation effect in the IQWs can be significantly reduced. Due to the higher optical power handling capability and better modulation efficiency, the EAM with IQWs is expected to substantially improve the fiber link performance.
AMPA/kainate glutamate receptor antagonists prevent posttraumatic osteoarthritis (2020)

Musculoskeletal disorders represent the third greatest burden in terms of death and disability in the developed world. Osteoarthritis is the single greatest cause of chronic pain, has no cure, and affects 8.5 and 27 million people in the UK and US, respectively. Osteoarthritis is most prevalent in older people, but as it commonly occurs after joint injury, young people with such injuries are also susceptible. Painful joints are often treated with steroid or hyaluronic acid (HA) injections, but treatments to prevent subsequent joint degeneration remain elusive. In animals, joint injury increases glutamate release into the joint, acting on nerves to cause pain, and joint tissues to cause inflammation and degeneration. This study investigated synovial fluid glutamate concentrations and glutamate receptor (GluR) expression in injured human joints and compared the efficacy of GluR antagonists with current treatments in a mouse model of injury-induced osteoarthritis (ACL rupture). GluRs were expressed in the ligaments and meniscus after knee injury, and synovial fluid glutamate concentrations ranged from 19 to 129 μM. Intra-articular injection of NBQX (GluR antagonist) at the time of injury substantially reduced swelling and degeneration in the mouse ACL rupture model. HA had no effect, and Depo-Medrone reduced swelling for 1 day but increased degeneration by 50%. Intra-articular administration of NBQX modified both symptoms and disease to a greater extent than current treatments. There is an opportunity for repurposing related drugs, developed for CNS disorders and with proven safety in humans, to prevent injury-induced osteoarthritis. This could quickly reduce the substantial burden associated with osteoarthritis.
Spin transfer torque switching assisted by thermally induced anisotropy reorientation in perpendicular magnetic tunnel junctions (2011)

A method to switch the magnetization of the free layer in magnetic tunnel junctions with perpendicular anisotropy is demonstrated. It consists in assisting the spin transfer switching of the magnetization by a thermally induced reorientation of the free layer magnetic anisotropy from out-of-plane to in-plane. The junction temperature increase is due to the Joule dissipation around the tunnel barrier produced by the same pulse of current which generates the spin transfer torque. This magnetic reorientation allows the spin transfer torque efficiency to be maximal since the spin polarization of the current is perpendicular to the magnetization of the free layer. Such a thermally assisted switching allows designing highly down-size scalable magnetoresistive random access memory cells with improved write efficiency.
Novel enzymatic single-nucleotide modification of DNA oligomer: prevention of incessant incorporation of nucleotidyl transferase by ribonucleotide-borate complex (2019)

Terminal deoxynucleotidyl transferase (TdT), which mediates template-independent polymerization with low specificity for nucleotides, has been used for nucleotide extension of DNA oligomers. One concern is that it is difficult to control the number of incorporated nucleotides, which is a limitation on the use of TdT for single-nucleotide incorporation of DNA oligomers. Herein, we uncovered an interesting inhibitory effect on TdT when ribonucleotide substrates (rNTPs) were employed in a borate buffer. On the basis of unique inhibitory effects of the ribonucleotide-borate complex, we developed a novel enzymatic method for single-nucleotide incorporation of a DNA oligomer with a modified rNTP by TdT. Single-nucleotide incorporation of a DNA oligomer with various modified rNTPs containing an oxanine, biotin, aminoallyl or N6-propargyl group was achieved with a high yield. The 'TdT in rNTP-borate' method is quite simple and efficient for preparing a single-nucleotide modified DNA oligomer, which is useful for the design of functional DNA-based systems.
Modeling of Hybrid Energy Harvesting Communication Systems (2019)

Energy harvesting is considered as a prominent technology, particularly for low-power wireless nodes. In this paper, we propose the use of hybrid energy harvesting (HEH) utilizing multiple type energy sources and present the modeling of HEH communication systems based on their probabilistic natures. According to our approach, received energy levels of an HEH system for possible combinations of energy arrivals are characterized by using Gaussian mixture models, which are used to determine harvested energy levels. The range of harvested energy is partitioned, and probabilities of partitioning intervals are used to form a finite-state Markov energy channel (FSMEC) model as an energy channel. Similar to the energy arrival, we also include the probabilistic energy consumption of wireless node in this model, depending on multiple application services, by means of the FSMEC model. Thus, we develop an integrated Markov energy model for HEH communication systems corresponding to the energy harvesting and energy consumption profiles. To evaluate the performance of an HEH communication system, we derive the expressions of energy outage, energy shortage, and service loss probabilities analytically. In numerical studies, the derived expressions are verified by matching simulation results, and it is shown that the performance improves significantly with energy source diversity.
Spatial Audio Coding (2007)

This chapter contains sections titled: Introduction Related techniques Binaural Cue Coding (BCC) Coding of low-frequency effects (LFE) audio channels Subjective performance Generalization to spatial audio coding