gebhart/patrepeval huggingface dataset:
Functional properties and toxin pharmacology of a dorsal root ganglion sodium channel viewed through its voltage sensors (2011)

The voltage-activated sodium (Nav) channel Nav1.9 is expressed in dorsal root ganglion (DRG) neurons where it is believed to play an important role in nociception. Progress in revealing the functional properties and pharmacological sensitivities of this non-canonical Nav channel has been slow because attempts to express this channel in a heterologous expression system have been unsuccessful. Here, we use a protein engineering approach to dissect the contributions of the four Nav1.9 voltage sensors to channel function and pharmacology. We define individual S3b-S4 paddle motifs within each voltage sensor, and show that they can sense changes in membrane voltage and drive voltage sensor activation when transplanted into voltage-activated potassium channels. We also find that the paddle motifs in Nav1.9 are targeted by animal toxins, and that these toxins alter Nav1.9-mediated currents in DRG neurons. Our results demonstrate that slowly activating and inactivating Nav1.9 channels have functional and pharmacological properties in common with canonical Nav channels, but also show distinctive pharmacological sensitivities that can potentially be exploited for developing novel treatments for pain.
PlaNet of the Bayesians: Reconsidering and Improving Deep Planning Network by Incorporating Bayesian Inference (2020)

In the present paper, we propose an extension of the Deep Planning Network (PlaNet), also referred to as PlaNet of the Bayesians (PlaNet-Bayes). There has been a growing demand in model predictive control (MPC) in partially observable environments in which complete information is unavailable because of, for example, lack of expensive sensors. PlaNet is a promising solution to realize such latent MPC, as it is used to train state-space models via model-based reinforcement learning (MBRL) and to conduct planning in the latent space. However, recent state-of-the-art strategies mentioned in MBRR literature, such as involving uncertainty into training and planning, have not been considered, significantly suppressing the training performance. The proposed extension is to make PlaNet uncertainty-aware on the basis of Bayesian inference, in which both model and action uncertainty are incorporated. Uncertainty in latent models is represented using a neural network ensemble to approximately infer model posteriors. The ensemble of optimal action candidates is also employed to capture multimodal uncertainty in the optimality. The concept of the action ensemble relies on a general variational inference MPC (VI-MPC) framework and its instance, probabilistic action ensemble with trajectory sampling (PaETS). In this paper, we extend VI-MPC and PaETS, which have been originally introduced in previous literature, to address partially observable cases. We experimentally compare the performances on continuous control tasks, and conclude that our method can consistently improve the asymptotic performance compared with PlaNet.
FACIAL: Synthesizing Dynamic Talking Face with Implicit Attribute Learning (2021)

In this paper, we propose a talking face generation method that takes an audio signal as input and a short target video clip as reference, and synthesizes a photo-realistic video of the target face with natural lip motions, head poses, and eye blinks that are in-sync with the input audio signal. We note that the synthetic face attributes include not only explicit ones such as lip motions that have high correlations with speech, but also implicit ones such as head poses and eye blinks that have only weak correlation with the input audio. To model such complicated relationships among different face attributes with input audio, we propose a FACe Implicit Attribute Learning Generative Adversarial Network (FACIAL-GAN), which integrates the phonetics-aware, context-aware, and identity-aware information to synthesize the 3D face animation with realistic motions of lips, head poses, and eye blinks. Then, our Rendering-to-Video network takes the rendered face images and the attention map of eye blinks as input to generate the photo-realistic output video frames. Experimental results and user studies show our method can generate realistic talking face videos with not only synchronized lip motions, but also natural head movements and eye blinks, with better qualities than the results of state-of-the-art methods.
Surface functionalisation of bacterial cellulose as the route to produce green polylactide nanocomposites with improved properties (2009)

The effect of surface functionalisation of bacterial cellulose nanofibrils (BC) and their use as reinforcement for polylactide (PLLA) nanocomposites was investigated. BC was functionalised with various organic acids via an esterification reaction. This rendered the otherwise hydrophilic BC hydrophobic and resulted in better compatibility (interfacial adhesion) between PLLA and BC. A direct wetting method, allowing the determination of the contact angle of polymer droplets on a single BC nanofibre, was developed to quantify the interfacial adhesion between PLLA and functionalised BC. It was found that the contact angle between PLLA droplets and functionalised BC decreased with increasing chain lengths of the organic acids used to hydrophobise BC. A novel method to compound BC with PLLA based on thermally induced phase separation (TIPS) to yield a dry form of pre-extrusion composite was also developed. The mechanical properties of the surface functionalised BC reinforced PLLA nanocomposites showed significant improvements when compared to neat PLLA and BC reinforced PLLA. The thermal degradation and viscoelastic behaviour of the nanocomposites were also improved over neat PLLA.
Novel molecular glass photoresist materials for next-generation lithography (2010)

A series of Adamantanephenol derivatives was synthesized from adamantinetriphenol / adamantinetrimethylhydroquinone and vinylether compound. Solubility for resist solvent or alkali developer of those materials and thermal properties were examined. Adamantanetrimethylhydroquinone cross-linked with divinylether (AmHQ-CL) had excellent properties as positive tone resist material. We evaluated lithographic properties of AmHQ-CL with photo acid generator and base. Line and space pattern was formed with EB exposure followed with post exposure bake and alkali development. Pattern of smooth wall surface was obtained by removing high molecular weight component from AmHQ-CL. Line width roughness (LWR) of the pattern AnHQ-CL nMWD was less than 30 nm. It was very small value compared with that of traditional polymer resist.
S3D: Stacking Segmental P3D for Action Quality Assessment (2018)

Action quality assessment is crucial in areas of sports, surgery and assembly line where action skills can be evaluated. In this paper, we propose the Segment-based P3D-fused network S3D built-upon ED-TCN and push the performance on the UNLV-Dive dataset by a significant margin. We verify that segment-aware training performs better than full-video training which turns out to focus on the water spray. We show that temporal segmentation can be embedded with few efforts.
<strong>Deletion in the Bardet-Biedl Syndrome Gene <em>TTC8</em> Results in a Syndromic Retinal Degeneration in Dogs</strong> (2020)

In golden retriever dogs, a 1 bp deletion in the canine TTC8 gene has been shown to cause progressive retinal atrophy (PRA), the canine equivalent of retinitis pigmentosa. In humans, TTC8 is also implicated in Bardet-Biedl syndrome (BBS). To investigate if the affected dogs only exhibit a non-syndromic PRA or develop a syndromic ciliopathy similar to human BBS, we recruited ten affected dogs to the study. The progression of PRA for two of the dogs was followed for two years, and a rigorous clinical characterization allowed a careful comparison with primary and secondary characteristics of human BBS. In addition to PRA, the dogs showed a spectrum of clinical and morphological signs similar to primary and secondary characteristics of human BBS patients, such as obesity, renal anomalies, sperm defects, and anosmia. We used Oxford Nanopore long-read cDNA sequencing to characterize retinal full-length TTC8 transcripts in affected and non-affected dogs, the results of which suggest that three isoforms are transcribed in the retina, and the 1 bp deletion is a loss-of-function mutation, resulting in a canine form of Bardet-Biedl syndrome with heterogeneous clinical signs.
VI4IO/io-500-dev: Zenodo Citation Release (2018)

IO-500 benchmark
TAP peptide transporter-independent presentation of heat-killed Sendai virus antigen on MHC class I molecules by splenic antigen-presenting cells (1997)

Abstract Immunization of C57BL/6 (B6) mice with heat-killed Sendai virus generates a Sendai virus-specific CD8+ T cell response. This suggests that APC have the capacity to take up and present exogenous (nonreplicative) Sendai virus Ag on MHC class I molecules. Little is known about the intracellular requirements for processing of this form of Ag and its presentation on MHC class I. Therefore, we have studied the processing and presentation of heat-killed Sendai virus Ag on MHC class I molecules in splenic APC. Heat-killed Sendai virus Ags were efficiently processed by normal B6 as well as by TAP-1(-/-) splenic APC. Presentation was MHC class I restricted, since no presentation was seen by APC from TAP-1/beta2m-/- mice that lack expression of MHC class I. Presentation occurred even in the presence of brefeldin A, but was blocked by cytochalasin D as well as chloroquine. Finally, B6 as well as TAP-1(-/-) splenic APC, loaded with heat-killed Sendai virus Ag in vitro, primed naive CD8+ T cells in vivo. These studies suggest the existence of a TAP-independent pathway for Ag presentation on MHC class I in normal splenic APC, bearing many similarities with the MHC class II pathway for Ag presentation. The present results are discussed in relation to the events underlying the processing and presentation of exogenous Ag on MHC class I, the molecular basis for CD8+ T cell priming during viral infections, and prospects for vaccine development.
Effect of Deguelin on UVB-Induced Skin Carcinogenesis (2005)

Nonmelanoma skin cancer afflicts more than one million people in the U.S. annually, highlighting the need for more effective preventive regimens. We have investigated the ability of deguelin, a plant-derived rotenoid with cancer chemopreventive activity, to inhibit UVB-induced skin carcinogenesis with the SKh-1 mouse model. Topically-applied deguelin significantly inhibited the multiplicity of UVB-induced skin tumors, indicating potential as a human skin cancer chemopreventive agent. Mechanistic studies to determine the potential of deguelin to block a number of established UVB-induced molecular events yielded negative results [including UVB-induced AP-1 DNA binding, c-fos and TNFalpha mRNA induction, arachidonic acid release and UVB-induced phosphorylation of mTOR (Ser2448), akt (Ser473) and erk (Thr202/Tyr204)]. These results are of interest as they contradict a major hypothesis for the mode of action of deguelin, i.e., a general down regulation of signal transduction based on inhibition of NADH dehydrogenase and depletion of ATP levels. In the current work, however, deguelin was found to activate 5' AMP-activated kinase (AMPK), a protein that acts as a cellular energy sensor. This is the first report of a chemopreventive agent having this effect and suggests a possible role for AMPK in cancer chemoprevention.
Synthesis of β-, γ-, and δ-Lactams via Pd(II)-Catalyzed C−H Activation Reactions (2008)

Pd(II)-catalyzed intramolecular amination of sp2 and sp3 C-H bonds are developed using a combination of CuCl2 and AgOAc as the oxidant. The reaction protocol tolerates the presence of a double bond in the substrates. This catalytic reaction provides practical access to a wide range of beta-, gamma-, and delta-lactams.
Application of the homogenization approximation to rough one-dimensional photonic crystals (2005)

As previously reported [Opt. Lett. 29, 2791 (2004)], one-dimensional photonic crystals exhibit a decrease in their normal reflectivity if their interfaces are not flat. We show that the homogenization approximation accurately predicts this diminished optical response by comparing results with finite-difference time-domain (FDTD) simulations applied to the same roughened structures. Within the parameter range tested (rms roughness < 20% and rms wavelengths < 100% of the photonic crystal periodicity), the homogenization approximation accurately reproduces the reflectivities obtained by the FDTD simulations, which are much more computationally expensive.
Potential Antischistosomal Activities of Some Egyptian Native Plants Using Schistosoma mansoni Worm Killing Assay (2014)

4 Abstract: The present study investigated the potential antischistosomal activity of some Egyptian native plants using the in vitro Schistosoma mansoni worm killing assay. Praziquantel (PZQ) treated worms were used as positive control. Key findings: The bioscreening results revealed 27 extracts out of 90 different extracts from the 65 examined plant species possess reproducible in vitro antischistosomal activity. The LC of latex 50 methanol extract of Calotropis procera was 0.30 µg/ml, while the LC of the latex water extract was 0.59 µg/ml 50 compared to 0.21 µg/ml for PZQ. LC of latex water extract of Calotropis procera increased to 3.22 µg/ml. 50 Phytochemical screening of different extracts was carried out to detect extracts major chemical constituents responsible for activity. Other species from families Fabeace, Asparagaceae, Pittosporaceae, Balanitaceae, Zingiberaceae and Lauraceae showed variable percentages of worm killing activities (10%-100%). Conclusion: The C. procera stem latex (after washing off toxic rubber materials) and flowers of C. procera demonstrate promising antischistosomal activity. These effects could be due to an antioxidant or anti-inflammatory activity of their content of cysteine proteases, tannins, flavonoids, sterols and terpenes.
A Fluorescence and Surface-Enhanced Raman Spectroscopic Dual-Modal Aptasensor for Sensitive Detection of Cyanotoxins (2020)

The ability to detect trace analytes without necessitating solid surface attachment or complicated processing steps would facilitate the translation of sensors for monitoring environmental toxins in the field. To address a critical unmet need in fresh water ecology, we have developed a dual-modal aptamer-based biosensor (aptasensor), featuring fluorescence and surface-enhanced Raman spectroscopy (SERS), for sensitive and selective detection of hepatotoxin microcystin-LR (MC-LR). The rational sensor design is based on the high affinity of the cyanine (Cy3) dye-modified complementary DNA (Cy3-cDNA) strand toward the plasmonic gold nanostars (GNSs) in comparison to the Cy3-cDNA/aptamer duplex. The preferential binding of MC-LR toward the MC-LR-specific aptamer triggers the dissociation of Cy3-cDNA/aptamer duplexes, which switches the Cy3's fluorescence "off" and SERS "on" due to the proximity of Cy3 dye to the GNS surface. Both fluorescence and SERS intensities are observed to vary linearly with the MC-LR concentration over the range of investigation. We have achieved high sensitivity and excellent specificity with the aptasensor toward MC-LR, which can be attributed to the fluorescence quenching effect, significant SERS enhancement by the GNSs, and the high affinity of the aptamer toward the MC-LR analytes. We further demonstrate the applicability of the present aptasensor for detection of MC-LR in a diverse set of real water samples with high accuracy and excellent reproducibility. With further refinement, we believe that the aptamer-driven complementary assembly of the SERS and fluorescence sensing constructs can be applied for rapid, multiplexed, and robust measurements of environmental toxins in the field.
Standard-based virtual infrastructure resource management for distributed and heterogeneous servers (2009)

Virtualization technologies can improve IT resource utilization and increase the flexibility needed to adapt to changing requirements and workloads. And, standard-based management enables a more integrated and cost effective development of the interoperable management solutions. With standard-based virtual infrastructure management, virtualization technologies in the distributed and heterogeneous server environment can be adapted and managed more effectively and easily. In this paper, we propose how to enable multiple physical server system to act as a virtual single server platform. Since it supports policy-based workload management, those resources in the shared pool can dynamically be provisioned whenever needed. VINE 1 which is the standard-based infrastructure virtualization software supports the monitoring, life-cycle management, modification, migration and replication of virtual machines.
Mutagenic activation of benzidine requires prior bacterial acetylation and subsequent conversion by prostaglandin H synthase to 4-nitro-4'-(acetylamino)biphenyl (1992)

We have used the Ames test in combination with prostaglandin H synthase (PHS) to study the bioactivation of benzidine as well as other aromatic amines. Previous investigations established that the formation of benzidine mutagens by PHS is dramatically enhanced in Salmonella typhimurium strains with high levels of acetyl CoA-dependent arylamine N-acetyltransferase/arylhydroxylamine O-acetyltransferase activity despite the fact that acetylation of aromatic amines decreases their susceptibility to oxidation by peroxidases. In this study, we used a new strain (YG1012) that has very high acetylation capability to investigate the metabolism and mutagenicity of benzidine and N-acetylbenzidine catalyzed by PHS (from ram seminal vesicle microsomes) and horseradish peroxidase (HRP). YG1012 bacteria rapidly acetylated benzidine to N-acetylbenzidine and N,N'-diacetylbenzidine. Preincubation of the bacteria with benzidine before addition of PHS increased the mutagenicity. Under conditions identical to those used to assess mutagenicity, PHS metabolized benzidine rapidly, but the substrate was not totally consumed, with about 40% of the original concentration remaining intact. These data suggest that conversion to N-acetylbenzidine may be the initial step in the bioactivation of benzidine in the PHS-mediated Ames assay. N-Acetylbenzidine is a cosubstrate for PHS peroxidase activity as measured by 5-phenyl-4-pentenyl hydroperoxide reduction, spectral changes, and formation of protein adducts. N-Acetylbenzidine was converted to mutagens by PHS but not HRP, with enhanced mutagenicity observed in bacteria with high acetylation activity. We used reverse- phase HPLC to characterize the metabolites of N-acetylbenzidine formed by PHS and HRP.(ABSTRACT TRUNCATED AT 250 WORDS)
ANTIINFLAMMATORY ACTIVITY OF ALCOHOL EXTRACT OF JUSTICIA PROCUMBENS (ACANTHACEAE) (1998)

Alcohol (95%) extract of Justicia procumbens has been screened for in vivo antiinflammatory activity in albino rats. It revealed promising antiinflammatory activity at a dose of 100 mg/kg body weight.
Complete Genome Sequence of Propionibacterium avidum Strain 44067, Isolated from a Human Skin Abscess (2013)

Propionibacterium avidum is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota, colonizing moist areas such as the vestibule of the nose, axilla, and perineum. Here we present the complete genome sequence of P. avidum strain 44067, which was isolated from a carbuncle of the trunk.
Patient‐reported measurements of oral mucositis in head and neck cancer patients treated with radiotherapy with or without chemotherapy (2008)

Mucositis occurs among virtually all patients who are undergoing radiation treatment of head and neck cancers. The detrimental effects on QOL and functional status are significant, and opioid analgesia provides inadequate relief. Preventive rather than symptom palliation measures are needed.
Contact and distributed effects in quantum well infrared photodetectors (1995)

We propose a simple distributed model for intersubband quantum well infrared photodetectors (QWIPs), which explicitly takes into account the injecting properties of the contacts. We show that the QWIP operation with multiple QWs involves the formation of a high-field domain near the emitter, caused by the modulation of the bound electron density in the QWs by applied voltage and infrared radiation. The external characteristics of the QWIP (total current, differential resistance, and quasistatic capacitance) are strong functions of the voltage and radiation intensity.
Reconstruction of the patellar ligament insertion for patella maltracking in total knee replacement (2007)

Objective To summarize the method and operation effect of the reconstruction of patellar ligament insertion in correcting the lateral dislocation tendency of the patella with patellofemoral joint maltracking in total knee replacement. MethodsThe lateral 1/2 insertion of patellar ligament was shifted inward to the medial side of patellar ligament and the patellar ligament insertion was reconstructed in 13 knees with 12 cases managed in total knee replacement, which complicated with patella partial or complete dislocation. The knee joint was not immobilized after operation, and patients were encouraged to take early rehabilitation training according to the knee joint condition. All the cases were followed up for more than half a year,which KSS knee joint score and function score were evaluated. Results The valgus deformity and patella partial or complete dislocation were corrected. Laceration or fragmentation was not found in reconstructed patellar ligaments during rehabilitation. The average KSS knee joint score increased from 33 to 79, and the function score increased from 39 to 83. As compared with preoperative condition, the knee’ s function showed a significant amelioration. Conclusions Long- term valgus abnormity of knee joint could cause tibia external rotation abnormity. Both abnormities make patella partial or complete dislocation. The reconstruction of the patellar ligament in insertion point was a reasonable surgical treatment to to correct the dislocation tendency of the patella in total knee replacement, and this operation did not have adverse effect on the early rehabilitation training of knee joints.
Studie zur Start-Machzahl eines generischen Überschalllufteinlaufs (2015)

Die komplexe Wechselwirkung strömungsphysikalischer Prozesse, die beim Öffnen eines Überschalleinlaufs ablaufen, entscheidet über die minimale Flugmachzahl, ab der eine aus-reichende Sauerstoff-Versorgung des luftatmenden Triebwerks erfolgen kann. Ziel des Vor-habens ist die Entwicklung und Validierung eines vereinfachten Modells zur Berechnung der kritischen Geometrieparameter eines generischen Überschalleinlaufs (Rampen- und Hau-ben-Kompressionswinkel, Vorderkantendicke) bei gegebenen Kontraktionsverhältnis und Flugparametern (Flughöhe und -geschwindigkeit). Die aktuelle Parameterstudie wurde am generischen Einlaufmodell mit Variation der Mach-zahl, des Kontraktionsverhältnisses, sowie der Form und Vorderkantendicke der Abdeck-haube experimentell und numerisch durchgeführt. Die Experimente fanden dabei im Rohr-Windkanal Göttingen (RWG) statt und die numerischen Untersuchungen wurden mit Hilfe des TAU-Codes durchgeführt. Die Vorderkantendicke d der Haube wurde in 5 Schritten zwi-schen 0.0 mm und 0.8 mm variiert bei 3 verschiedenen Hauben-Grundformen (Rampe, Doppelrampe und Kompressionsrampe). Die Grenzen zur Variation der Machzahl Ma (2.25 - 3.00) und des Kontraktionsverhältnisses K (2.0 - 2.3) wurden gewählt um eine Änderung des Strömungszustandes zwischen vollständigem Durchströmen (überkritischer Zustand) und Sperren des Innenkanals (unterkritischer Zustand) hervorzurufen.