gebhart/patrepeval huggingface dataset:
HIV-1 and Its Resistance to Peptidic Carbohydrate-Binding Agents (CBAs): An Overview (2014)

The glycoproteins on the surfaces of enveloped viruses, such as HIV, can be considered as a unique target for antiviral therapy. Different carbohydrate-binding agents (CBAs) target specific glycans present on viral glycoproteins of enveloped viruses. It has been shown that long-term CBA pressure in vitro can result in mutant HIV-1 isolates with several N-linked glycan deletions on gp120. These studies demonstrated that mainly high-mannose type glycans are deleted. However, interestingly, N241, N262 and N356 on gp120 have never been found to be affected after prolonged CBA exposure. Here, we review the mutation and (cross)-resistance profiles of eleven specific generated CBA-resistant HIV-1 strains. We observed that the broad-neutralizing anti-carbohydrate binding mAb 2G12 became completely inactive against all the generated CBA-resistant HIV-1 clade B isolates. In addition, all of the CBAs discussed in this review, with the exception of NICTABA, interfered with the binding of 2G12 mAb to gp120 expressed on HIV-1-infected T cells. The cross-resistance profiles of mutant HIV-1 strains are varying from increased susceptibility to very high resistance levels, even among different classes of CBAs with dissimilar sugar specificities or binding moieties [e.g., α(1,3), α(1,2), α(1,6)]. Recent studies demonstrated promising results in non-topical formulations (e.g., intranasally or subcutaneously), highlighting their potential for prevention (microbicides) and antiviral therapy.
Reliable Breathing Tracking With Wearable Mask Device (2020)

Breathing tracking is critical for the assessment of lung functions, exercise physiologies, and energy expenditure. Conventional methods require using a face mask or mouthpiece that is connected to a stationary equipment through a tube, restricting the location, movement, or even the posture. To obtain accurate breathing physiology parameters that represent the true state of the patient during different scenarios, a wearable technology that has less intervention to patient's activities in free-living conditions is highly preferred. Here, we propose a miniaturized, reliable, and wide-dynamic ranged flow sensing technology that is immune to orientation, movement, and noise. As far as we know, this is the first work of introducing a fully integrated mask device focusing on breath tracking in free-living conditions. There are two key challenges for achieving this goal: miniaturized flow sensing and motion-induced artifacts elimination. To address these challenges, we come up with two technical innovations: 1) in hardware wise, we have designed an integrated flow sensing technique based on differential pressure Pneumotach approach and motion sensing; 2) in software wise, we have developed comprehensive algorithms based baseline tracking and orientation and motion compensation. The effectiveness of the proposed technology has been proven by the experiments. Experimental results from simulator and real breath conditions show high correlation (R<sup>2</sup> = 0.9994 and 0.9964 respectively) and mean error within 2.5% for Minute Volume (VE), when compared to values computed from reference methods. These results show that the proposed method is accurate and reliable to track the key breath parameters in free-living conditions.
ATXN2‐AS, a gene antisense to ATXN2, is associated with spinocerebellar ataxia type 2 and amyotrophic lateral sclerosis (2016)

These results suggest that ATXN2-AS has a role in SCA2 and possibly ALS pathogenesis, and may therefore provide a novel therapeutic target for these diseases. Ann Neurol 2016;80:600-615.
(Invited) Study of HfO2-Based High-k Gate Insulators for GaN Power Device (2021)

We discussed about usefulness of HfO2-based high dielectric constant (High-k) materials such as HfO2, HfSiOx and HfAlOx as gate insulator for GaN power device. Here, we systematically studied characteristics of Hf0.55Al0.45Ox gate insulator which fabricated by plasma-enhanced atomic layer deposition and post-deposition annealing (PDA) at 800°C in N2 ambient. The Hf0.55Al0.45Ox film had an amorphous structure but Ga diffusion into Hf0.55Al0.45Ox film was observed after PDA. The k-value of the Hf0.55Al0.45Ox film was 17.2, which was larger than that of HfSiOx (13.5). The Hf0.55Al0.45Ox also showed superior electrical properties such as a minimal flatband voltage (Vfb) hysteresis ( +10 mV) and a relatively small Vfb shift ( £ -0.95 V), as well as a low interface state density (~ 1 ´ 1011 cm-2eV-1 at Ec-E=0.25 eV), and a high breakdown electric field (8.6 MVcm-1). Based on these experimental data and previous our research of HfO2 and HfSiOx films, we concluded the HfSiOx and HfAlOx had candidate materials as gate insulator for GaN power device.
Theoretical considerations on efficiency degradation due to thermal effect in a planar GaN-based LED with a GaN substrate (2014)

In this paper, using a fully-coupled, three-dimensional electro-thermal device simulator, we study the mechanism of efficiency degradation at high current operation in planar GaN-based light emitting diodes (LED). In particular, the improvement of the efficiency degradation using thicker conductive GaN substrates has been demonstrated. First, it is found that local Joule heating inside thin conductive GaN substrates degrades internal quantum efficiency (IQE) and increases the series resistance. Then, we introduced thicker conductive GaN substrates and simulated distributions of the current density and temperature inside the substrate. It is found that the maximum current density inside the GaN substrate decreases by about six times for a 100-µm-thick substrate compared to that for a 5-µm-thick substrate. Therefore, the maximum junction temperature decreases, and then IQE and the driving voltage are improved. The present study proves that thick GaN substrates are effective to improve the properties of planar LEDs at high current operation.
Supplementary Movie 3 from Tivantinib (ARQ 197) Exhibits Antitumor Activity by Directly Interacting with Tubulin and Overcomes ABC Transporter–Mediated Drug Resistance (2023)

&lt;p&gt;Crizotinib treated (EBC-1 Fucci).&lt;/p&gt;
Visually Optimized Two-Pass Rate Control for Video Coding Using the Low-Complexity XPSNR Model (2021)

Two-pass rate control (RC) schemes have proven useful for generating low-bitrate video-on-demand or streaming catalogs. Visually optimized encoding particularly using latest-generation coding standards like Versatile Video Coding (VVC), however, is still a subject of intensive study. This paper describes the two-pass RC method integrated into version 1 of VVenC, an open VVC encoding software. The RC design is based on a novel two-step rate-quantization parameter (R-QP) model to derive the second-pass coding parameters, and it uses the low-complexity XPSNR visual distortion measure to provide numerically as well as visually stable, perceptually R-D optimized encoding results. Random-access evaluation experiments confirm the improved objective as well as subjective performance of our RC solution.
Circulating microRNAs in Sera Correlate with Soluble Biomarkers of Immune Activation but Do Not Predict Mortality in ART Treated Individuals with HIV-1 Infection: A Case Control Study (2015)

No associations with mortality were found with any circulating miRNA studied. These results cast doubt onto the effectiveness of circulating miRNA as early predictors of mortality or the major underlying diseases that contribute to mortality in participants treated for HIV-1 infection.
ATetrahymenaintron nucleotide connected to the GTP/arginine site (1989)

We have substituted all nucleotides at intron nucleotide 260 (N260) in transcripts related to the self-splicing Tetrahymena rRNA. Substitution slightly affects the binding and reaction of GTP with this group I catalytic center; kcat/Km varies over a three-fold range. The base of N260 therefore communicates with the rG site, but is unlikely to bond directly to GTP. Different nucleotides at this position also alter the binding of L-arginine to the intron, measured by inhibition of the reaction with GTP. Effects of similar small magnitude on interaction of RNA with both GTP and L-arginine support the previous argument from kinetic and structural comparison (Yarus, M. (1988) Science 240, 1751) that placed the two ligands of the RNA in the same binding site. G260 RNA shows the greatest affinity for both D- and L-arginine, but uniquely lacks stereoselectivity for the amino acid. Therefore G260 alters spatial relations within the G site, otherwise conserved in C260, U260, and A260 RNA's. Guanyl urea was used as a probe for the G/guanidino H-bonding part of the rG/arginine site. G260 RNA's dissociation constant for guanyl urea is similar to that of the other RNA's, suggesting that G260 RNA is unaltered at the G/guanidino end of the rG/arginine binding site. To account for all observations, we suggest that the G260 substitution alters the relative location of the RNA backbone near the 5' exon-intron junction, making this location more flexible and closer to the alpha-NH3+'s of L- and D-arginine.
Exploring omega‐3 fatty acids, enzymes and biodiesel producing thraustochytrids from Australian and Indian marine biodiversity (2015)

The marine environment harbours a vast diversity of microorganisms, many of which are unique, and have potential to produce commercially useful materials. Therefore, marine biodiversity from Australian and Indian habitat has been explored to produce novel bioactives, and enzymes. Among these, thraustochytrids collected from Indian habitats were shown to be rich in saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs), together constituting 51-76% of total fatty acids (TFA). Indian and Australian thraustochytrids occupy separate positions in the dendrogram, showing significant differences exist in the fatty acid profiles in these two sets of thraustochytrid strains. In general, Australian strains had a higher docosahexaenoic acid (DHA) content than Indian strains with DHA at 17-31% of TFA. A range of enzyme activities were observed in the strains, with Australian strains showing overall higher levels of enzyme activity, with the exception of one Indian strain (DBTIOC-1). Comparative analysis of the fatty acid profile of 34 strains revealed that Indian thraustochytrids are more suitable for biodiesel production since these strains have higher fatty acids content for biodiesel (FAB, 76%) production than Australian thraustochytrids, while the Australian strains are more suitable for omega-3 (40%) production.
Fabrication of Circular Grating Distributed Feedback Dye Laser by Nanoimprint Lithography (2011)

Within recent years the development of polymer dye lasers has progressed to higher levels of performance and functionality. The most attractive advantages of polymer dye lasers include low-cost processing, wide choice of emission wavelengths, and easy fabrication on flexible substrates. Several waveguide dye lasers have been studied with emission wavelengths ranging from ultraviolet to near infrared (Y. Oki et al., 2002). By simply changing the fluorophore doped in the polymer, these lasers can be used as the tunable sources for various applications, such as spectroscopy (Y. Oki et al., 2002) and fluorescence excitation source Furthermore, microlaser array with multiwavelength emissions can be achieved Currently the integration of miniaturized active light sources such as lasers into microfluidic systems becomes an attractive approach for biological and chemical processes (D. Psaltis et al., 2006). A majority of microfluidic systems are based on external light sources. However, the coupling of optical signals in and out of the devices, typically by optical fibers, remains one of the major challenges in integrated optics. By making on-chip light sources, we can eliminate the optics alignment, which greatly reduces the complexity of the system (E. For applications in biochemical analysis in microfluidic systems, a surface emitting laser would appear to be more useful than other lasers because of its stacked substrate structure. Therefore, we choose a circular grating structure as the laser resonator design to produce low-threshold surface emitting lasing. The laser operating characteristics can be significantly improved by the two-dimensional nature of the resonator structure, and they are suitable to serve as low-threshold, surface-emitting coherent light source in microfluidic networks. The 1-D distributed feedback (DFB) structure is a widely employed resonator geometry, and has been previously demonstrated for polymer lasers (Y. Oki et al., 2002). However, operating characteristics can be significantly improved within 2-D structures. Here, we choose a circular grating distributed feedback structure to obtain low threshold operation, a well-defined output beam, and vertical emission perpendicular to the device plane.
Reconstruction of the lower limb bones from digitised anatomical landmarks using statistical shape modelling (2020)

These results indicate that SSM reconstructions can be used to increase the accuracy in obtaining bone shapes from surface digitised experimental data acquired in motion lab environments.
Optimal T-support anchoring for bar-type BAW resonators (2011)

This paper reports on an optimal support anchoring for bar-type BAW resonators. We demonstrate both theoretically and experimentally the implementation of long (in terms of acoustic wavelength) T-supports without compromising neither on the Q-factor nor on the electromechanical (pull-in) stability of the resonator. Compared to the more common straight supports, these long T-supports provide rigidity for displacements in one direction combined with low stiffness in the other two directions, thus offering more freedom in the structural design, as well as potential for thermal “manipulation”, e.g., insulation.
Per-cluster-prediction based sparse channel estimation for multicarrier underwater acoustic communications (2011)

In this paper, we present a sparse channel estimator for zero-padded orthogonal frequency division multiplexing (ZP-OFDM) modulation in clustered sparse underwater acoustic (UWA) channels. The proposed channel estimator consists of two stages. In the first stage, channel prediction from the previous block to the current block is carried out to generate artificial measurements on OFDM subcarriers. One key innovation is to allow different clusters of channel paths to vary differently across the blocks, where the delay, amplitude and phase variations of the clusters are determined based on the channel estimate of the previous block and the measurements on pilot subcarriers of the current block. In the second stage, a sparse channel estimation is performed based on both the artificially generated measurements and the real measurements of the current block, accounting for their different reliabilities. Experimental results demonstrate that the proposed channel estimator considerably outperforms the conventional channel estimator without cluster-based adaptation.
Efficient Low-resolution Character Recognition Using Sub-machine-code Genetic Programming (2003)

The paper describes an approach to low-resolution character recognition for real-time applications based on a set of binary classifiers designed by means of Sub-machine-code Genetic Programming (SmcGP). SmcGP is a type of GP that interprets long integers as bit strings to achieve SIMD processing on traditional sequential computers. The method was tested on an extensive set of very low-resolution binary patterns (of size 13 × 8 pixels) that represent digits from 0 to 9. Ten binary classifiers were designed, each corresponding to a pattern class. In case of no response by any of the classifiers, a reference LVQ classifier was used. The paper compares the resulting classifier with a reference classifier, showing an almost 10-fold improvement in speed, at the price of a slightly lower accuracy.
Classifying soundtracks with audio texture features (2011)

Sound textures may be defined as sounds whose character depends on statistical properties as much as the specific details of each individually-perceived event. Recent work has devised a set of statistics that, when synthetically imposed, allow listeners to identify a wide range of environmental sound textures. In this work, we investigate using these statistics for automatic classification of a set of environmental sound classes defined over a set of web videos depicting "multimedia events". We show that the texture statistics perform as well as our best conventional statistics (based on MFCC covariance). We further examine the relative contributions of the different statistics, showing the importance of modulation spectra and cross-band envelope correlations.
Broad-Spectrum Antiviral Entry Inhibition by Interfacially Active Peptides (2020)

Numerous peptides inhibit the entry of enveloped viruses into cells. Some of these peptides have been shown to inhibit multiple unrelated viruses. We have suggested that such broad-spectrum antiviral peptides share a property called interfacial activity; they are somewhat hydrophobic and amphipathic, with a propensity to interact with the interfacial zones of lipid bilayer membranes. In this study, we further tested the hypothesis that such interfacial activity is a correlate of broad-spectrum antiviral activity. In this study, several families of peptides, selected for the ability to partition into and disrupt membrane integrity but with no known antiviral activity, were tested for the ability to inhibit multiple diverse enveloped viruses. These include Lassa pseudovirus, influenza virus, dengue virus type 2, herpes simplex virus 1, and nonenveloped human adenovirus 5. Various families of interfacially active peptides caused potent inhibition of all enveloped viruses tested at low and submicromolar concentrations, well below the range in which they are toxic to mammalian cells. These membrane-active peptides block uptake and fusion with the host cell by rapidly and directly interacting with virions, destabilizing the viral envelope, and driving virus aggregation and/or intervirion envelope fusion. We speculate that the molecular characteristics shared by these peptides can be exploited to enable the design, optimization, or molecular evolution of novel broad-spectrum antiviral therapeutics.<b>IMPORTANCE</b> New classes of antiviral drugs are needed to treat the ever-changing viral disease landscape. Current antiviral drugs treat only a small number of viral diseases, leaving many patients with established or emerging infections to be treated solely with supportive care. Recent antiviral peptide research has produced numerous membrane-interacting peptides that inhibit diverse enveloped viruses <i>in vitro</i> and <i>in vivo</i> Peptide therapeutics are becoming more common, with over 60 FDA-approved peptides for clinical use. Included in this class of therapeutics is enfuvirtide, a 36-residue peptide drug that inhibits HIV entry/fusion. Due to their broad-spectrum mechanism of action and enormous potential sequence diversity, peptides that inhibit virus entry could potentially fulfill the need for new antiviral therapeutics; however, a better understanding of their mechanism is needed for the optimization or evolution of sequence design to combat the wide landscape of viral disease.
Successful treatment with voriconazole of Aspergillus brain abscess in a boy with medulloblastoma (2005)

Invasive aspergillosis is an increasing problem in immuno-incompetent patients after prolonged steroid therapy, cancer radio-chemotherapy, and bone marrow or solid organ transplantation. Cerebral aspergillosis is a well-described complication of the invasive aspergillosis but only in rare cases, the brain is the sole site of infection. Despite increasing availability of antifungal drugs, the prognosis of cerebral aspergillosis is poor. We report on an 11-year-old boy with medulloblastoma in the area of the fourth ventricle. Following tumor surgery and radio-chemotherapy, several abscess-like structures occurred in the operating field. After incomplete abscess, resection histology and culture confirmed a localized Aspergillus fumigatus infection. The initial treatment of the Aspergillus fumigatus infection with conventional amphotericin B failed, and treatment with the triazole voriconazole was started. Intravenous treatment with voriconazole resulted in a reduction of the Aspergillus fumigatus abscess. After switching to oral ambulatory therapy, the Aspergillus fumigatus abscess increased in size. To improve treatment, voriconazole dosage was adapted to reach drug concentrations in cerebrospinal fluid (CSF) above the minimal fungicidal concentration and plasma specimens. During the concentration-controlled voriconazole therapy for a period of 18 months, a complete response was achieved.
Einige wichtige Cyclisierungen durch pericyclische Reaktionen (1999)

Reaktionen, bei denen zwei oder mehr Bindungen gleichzeitig durch Elektronenverschiebungen geknüpft oder gebrochen werden, sind pericyclische Reaktionen.1 Viele pericyclische Reaktionen führen auf stereochemisch kontrollierte Weise zu den Produkten. Da zwei oder mehr Bindungen auf eine synchrone oder quasisynchrone Weise gebildet oder gebrochen werden, übertragen sich die stereochemischen Eigenschaften der Reaktanden auf die Produkte. Vier der in der organischen Synthese gebräuchlichsten pericyclischen Reaktionen sind: Die Diels-Alder-Reaktionen, [2+2]-Cycloadditionen, elektrocyclische Reaktionen von Trienen und Cope- bzw. Claisen-Reaktionen.
Abstract A29: Bcl-2 overexpression provides short-term resistance to doxorubicin-DNA adducts but does not protect against longer-term treatments in HL-60 cells. (2011)

Abstract The anthracycline anticancer agent doxorubicin functions primarily as a topoisomerase II inhibitor but forms more cytotoxic DNA adducts in the presence of formaldehyde. For this reason, the efficacy of doxorubicin can be greatly enhanced with the co-administration of formaldehyde-releasing prodrugs such as AN-9. The combination of doxorubicin with AN-9 results in DNA adduct formation and synergistic apoptosis in HL-60 leukemic cells after 6 hr. Under the same conditions HL-60 cells overexpressing the anti-apoptotic protein Bcl-2 (HL-60/Bcl-2 cells) are completely resistant to doxorubicin/AN-9 treatments. This resistance can be overcome with the use of the small molecule Bcl-2/Bcl-xL/BCL-W inhibitor ABT-737. While it appears that Bcl-2 overexpression confers resistance and thus may limit the therapeutic potential of doxorubicin-DNA adduct forming treatments, this is shown to be only a short-term effect. The use of a DNA adduct forming doxorubicin-formaldehyde conjugate, doxazolidine, produced similar results to the doxorubicin/AN-9 combination with HL-60/Bcl-2 cells being resistant to the drug after 4 hr treatment. This resistance was maintained up to 12 hr treatment, however, after 18 hr the HL-60/Bcl-2 cells started to display classical hallmarks of apoptosis including DNA fragmentation, and chromatin condensation which increased over time (18–36 hr). These results suggest that the Bcl-2 protection is only short-lived and that over time the resistance is overcome and the cells die via classical apoptosis. The exact mechanisms involved in overcoming this resistance in HL-60/Bcl-2 cells are currently being investigated and may involve changes in expression of Bcl-2 family proteins, or Bcl-2 interactions with pro-apoptotic proteins which tip the balance in favour of apoptosis. These findings imply that the damage caused by these DNA adduct forming compounds may be sufficient to overcome Bcl-2 mediated resistance observed in tumors in vivo. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A29.