gebhart/patrepeval huggingface dataset:
Maximizing binary interactome mapping with a minimal number of assays (2019)

Complementary assays are required to comprehensively map complex biological entities such as genomes, proteomes and interactome networks. However, how various assays can be optimally combined to approach completeness while maintaining high precision often remains unclear. Here, we propose a framework for binary protein-protein interaction (PPI) mapping based on optimally combining assays and/or assay versions to maximize detection of true positive interactions, while avoiding detection of random protein pairs. We have engineered a novel NanoLuc two-hybrid (N2H) system that integrates 12 different versions, differing by protein expression systems and tagging configurations. The resulting union of N2H versions recovers as many PPIs as 10 distinct assays combined. Thus, to further improve PPI mapping, developing alternative versions of existing assays might be as productive as designing completely new assays. Our findings should be applicable to systematic mapping of other biological landscapes.
Compositions for Treatment of Cancer and Inflammation (2008)

Celecoxib (Celebrex, Pfizer, NY, USA) is a worldwide top branded COX-2-specific inhibitor. It was shown to provide relief of arthritic pain and inflammation and has recently been under investigation for the prevention and treatment of cancer. However, recent studies showed that long term use of high doses of celecoxib is associated with an increased cardiovascular toxicity. We discovered that the addition of curcumin, a natural COX-2 inhibitor, to celecoxib synergistically (up to 1000%) augments the growth inhibitory effects of celecoxib in in-vitro and in-vivo models of arthritis and cancer, thus rendering effective action of the drug at up to tenfold lower dose. This may pave the way for a novel strategy to treat arthritis and cancer because its effect [1] can be achieved in the serum of patients receiving standard anti inflammatory or anti-neoplastic dosages of celecoxib, and [2] involves a regimen with a very low profile of side effects. Preliminary data suggest that the combination is not limited only to celecoxib and that addition of curcumin to other NSAIDs such as sulindac, synergistically augments neoplastic cell growth inhibition. Based on these finding we received an IRB approval to evaluate celecoxib+curcumin in patients with osteoarthritis, pancreatic cancer and metastatic CRC. We hope to complete these novel human clinical trials, in 12-18 months.
P‐177: Engineering Host Materials for High Efficiency and Long Operational Lifetime in Blue Phosphorescent Organic Light‐emitting Diodes (2018)

Two host materials for blue phosphorescent organic light emitting diodes (PhOLEDs) were developed to exhibit high external quantum efficiency (EQE) and long device lifetime, By substituting strong electron deficient CN moiety in different positions, the highest occupied molecular orbital and the lowest unoccupied molecular orbital energy levels were controlled. Although the CN substitution position is different between the two hosts, both of the host materials showed high triplet energy of 2.98 eV. The CN modification in dibenzothiophene was effective to improve electron injection and high EQE. The new host materials also showed long device operational lifetime when CN modified phenylimidazole ligand based blue phosphorescent emitter was used as a blue triplet emitter.
On the disjointess of sources in music using different time-frequency representations (2011)

This paper studies the disjointness of the time-frequency representations of simultaneously playing musical instruments. As a measure of disjointness, we use the approximate W-disjoint orthogonality as proposed by Yilmaz and Rickard [1], which (loosely speaking) measures the degree of overlap of different sources in the time-frequency domain. The motivation for this study is to find a maximally disjoint representation in order to facilitate the separation and recognition of musical instruments in mixture signals. The transforms investigated in this paper include the short-time Fourier transform (STFT), constant-Q transform, modified discrete cosine transform (MDCT), and pitch-synchronous lapped orthogonal transforms. Simulation results are reported for a database of polyphonic music where the multitrack data (instrument signals before mixing) were available. Absolute performance varies depending on the instrument source in question, but on the average MDCT with 93 ms frame size performed best.
Optical Micromechanical Amplification and Damping in a Waveguide Microcavity (2010)

We demonstrate resonant amplification and damping in an integrated micromechanical resonator coupled to a waveguide Fabry-Perot microcavity. By varying the laser power and wavelength, the effective mechanical Q-factor (Q0 =2.5×104) is varied from 9.8×103 to 4.9×105.
Evaluating Material Properties to Optimize Wood Strands for Wind Erosion Control (2006)

Wind erosion is a widespread problem in much of the western United States due to aridconditions and persistent winds. Fugitive dust from eroding land poses a risk to both environmentalquality and human health. Since the advent of the Clean Air Act in 1971, ambient air qualitystandards have been set regulating particulate matter in the atmosphere. Agricultural straw hasbeen widely used for erosion control, but there are numerous drawbacks to its use. In addition to thefact that it is a lightweight material and lacks stability during high wind events, there is growingconcern over the introduction of noxious weeds to wildlands, chemical residues from pesticides, andrisks associated with dust particles liberated from the shattering of straw elements during the application process. The efficacy of a wood strand material, a wood analog to straw, for winderosion mitigation was investigated during this study. A series of wind tunnel tests were conductedto evaluate material properties of wood strands in terms of reducing total sediment loss andmaintaining air quality. Results indicate that wood strands are stable at wind speeds of up to 18 m/s,while wheat straw is only stable at wind speeds of up to 6.5 m/s. At a wind velocity of 18 m/s, thestraw, due to its instability, did not reduce soil loss; however, wood strands reduced total sedimentloss and peak dust emissions by over 90% when compared to a bare soil.
A prospective, randomized, double‐blind, multicentre, parallel‐group, active controlled study to compare efficacy and safety of biosimilar adalimumab (Exemptia;ZRC‐3197) and adalimumab (Humira) in patients with rheumatoid arthritis (2015)

The results demonstrated biosimilarity with respect to efficacy, tolerability and safety of test adalimumab (Exemptia) and reference adalimumab (Humira) in patients with moderate to severe RA.
Solutions to mitigate parasitic NPN bipolar action in high voltage analog technologies (2010)

This is a study of the parasitic NPN premature turn-on for high voltage BiCMOS technologies. In this work, we will investigate several methods to suppress its turn-on. Using TCAD and TLP we will investigate solutions based on increased well spacing, offset of wells, self-protection and beta reduction through highly doped base implant. We will also investigate the limitations associated with each of these solutions.
The tragedy of the commons and the comedy of community: The commons in history (1986)

Hardin's (1968) tragedy of the commons model has been implicated in projections of growing resource crises, an eventual threat to quality of life, and the extinction of civilization. The commons parable is explored in light of the open-field commons system that characterized European agricultural village communities for as many as 1,000 years. This system enabled carrying capacity to increase, not to be exceeded. The essential role of community organization and group solidarity is highlighted, and some suggestions for commons' beneficial use in community are presented. Comedy as a worldview for community is contrasted with tragedy.
ChemInform Abstract: Tactics and Strategies in Solid Phase Peptide Synthesis: New Directions, Methods and Applications (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Meeting the Challenge of Multiple Threshold Voltages in Highly Scaled Undoped FinFETs (2013)

Undoped FinFETs are of significant technological interest as they mitigate variation from random discrete dopant effects and provide for density and voltage scaling. A key requirement for undoped FinFETs for VLSI system application is the ability to obtain multiple threshold voltages on chip. This brief discusses options to obtain one logic and one SRAM threshold for both NFETs and PFETs in highly scaled undoped fins and shows that achieving such dual thresholds is challenging and requires new solutions such as more than two metal-gate work functions, dual fin thicknesses, or dual channel materials.
Experimental techniques in the determination of aetiology of acute infantile gastroenteritis. (1976)

Techniques used in the research laboratory for the microbiological diagnosis of infantile gastroenteritis are described. These techniques are in essence experimental models of the three pathogenetic mechanisms of bacterial diarrhoea. From the clinical bacteriological standpoint, although there is little difficulty with the identification of enteropathic bacteria such as Salmonella and Shigella, the differentiation of enteropathic strains of Escherichia coli from commensal strains is not possible with present routine bacteriological procedures. Possible adaptations of these experimental techniques to the routine laboratory are discussed. At present, negative-staining electron microscopy is the only way in which reoviruslike particles, the most important viral pathogen in infantile gastroenteritis, may be detected. Because of its relative simplicity this examination is strongly recommended in all cases of infantile gastroenteritis.
Quantification of the Brain Proteome in Alzheimer’s Disease Using Multiplexed Mass Spectrometry (2014)

We have compared the brain proteome in the temporal neocortex between Alzheimer's disease (AD) patients and non-AD individuals by using shotgun mass spectrometry based on a stable isotope dimethyl labeling. A total of 827 unique proteins were identified and quantitated. Of these, 227 proteins were found in at least 9 out of 10 AD/control pairs and were further subjected to statistical analysis. A total of 69 proteins showed different levels (p-value < 0.05) in AD versus control brain samples. Of these proteins, 37 were increased and 32 were decreased as compared to the non-AD subjects. Twenty-three proteins comprise novel proteins that have not previously been reported as related to AD, e.g., neuronal-specific septin-3, septin-2, septin-5, dihydropteridine reductase, and clathrin heavy chain 1. The proteins with altered levels in the AD brain represent a wide variety of pathways suggested to be involved in the disease pathogenesis, including energy metabolism, glycolysis, oxidative stress, apoptosis, signal transduction, and synaptic functioning. Apart from leading to new insights into the molecular mechanisms in AD, the findings provide us with possible novel candidates for future diagnostic and prognostic disease markers.
Persistent Equine Arteritis Virus Infection in HeLa Cells (2008)

The horse-adapted virulent Bucyrus (VB) strain of equine arteritis virus (EAV) established persistent infection in high-passage-number human cervix cells (HeLa-H cells; passages 170 to 221) but not in low-passage-number human cervix cells (HeLa-L cells; passages 95 to 115) or in several other cell lines that were evaluated. However, virus recovered from the 80th passage of the persistently infected HeLa-H cells (HeLa-H-EAVP80) readily established persistent infection in HeLa-L cells. Comparative sequence analysis of the entire genomes of the VB and HeLa-H-EAVP80 viruses identified 16 amino acid substitutions, including 4 in the replicase (nsp1, nsp2, nsp7, and nsp9) and 12 in the structural proteins (E, GP2, GP3, GP4, and GP5). Reverse genetic studies clearly showed that substitutions in the structural proteins but not the replicase were responsible for the establishment of persistent infection in HeLa-L cells by the HeLa-H-EAVP80 virus. It was further demonstrated that recombinant viruses with substitutions in the minor structural proteins E and GP2 or GP3 and GP4 were unable to establish persistent infection in HeLa-L cells but that recombinant viruses with combined substitutions in the E (Ser53-->Cys and Val55-->Ala), GP2 (Leu15-->Ser, Trp31-->Arg, Val87-->Leu, and Ala112-->Thr), GP3 (Ser115-->Gly and Leu135-->Pro), and GP4 (Tyr4-->His and Ile109-->Phe) proteins or with a single point mutation in the GP5 protein (Pro98-->Leu) were able to establish persistent infection in HeLa-L cells. In summary, an in vitro model of EAV persistence in cell culture was established for the first time. This system can provide a valuable model for studying virus-host cell interactions, especially virus-receptor interactions.
Integration of tolerances in Computer-aided Assembly Planning (1995)

info:eu-repo/semantics/published
Resolution of disulfide heterogeneity in Nogo receptor 1 fusion proteins by molecular engineering (2010)

NgRI (Nogo-66 receptor) is part of a signalling complex that inhibits axon regeneration in the central nervous system. Truncated soluble versions of NgRI have been used successfully to promote axon regeneration in animal models of spinal-cord injury, raising interest in this protein as a potential therapeutic target. The LRR (leucine-rich repeat) regions in NgRI are flanked by N- and C-terminal disulfide-containing 'cap' domains (LRRNT and LRRCT respectively). In the present work we show that, although functionally active, the NgRI(310)-Fc fusion protein contains mislinked and heterogeneous disulfide patterns in the LRRCT domain, and we report the generation of a series of variant molecules specifically designed to prevent this heterogeneity. Using these variants we explored the effects of modifying the NgRI truncation site or the spacing between the NgRI and Fc domains, or replacing cysteines within the NgRI or IgG hinge regions. One variant, which incorporates replacements of Cys²⁶⁶ and Cys³⁰⁹ with alanine residues, completely eliminated disulfide scrambling while maintaining functional in vitro and in vivo efficacy. This modified NgRI-Fc molecule represents a significantly improved candidate for further pharmaceutical development, and may serve as a useful model for the optimization of other IgG fusion proteins made from LRR proteins.
To alloy or not to alloy? Cr modified Pt/C catalysts for PEM fuel cells (2008)

The cathode electrocatalysts for proton exchange membrane (PEM) fuel cells are commonly platinum and platinum based alloy nanoparticles dispersed on a carbon support. Control over the particle size and composition has, historically, been attained empirically, making systematic studies of the effects of various structural parameters difficult. The controlled surface modification methodology used in this work has enabled the controlled modification of carbon supported Pt nanoparticles by Cr so as to yield nanoalloy particles with defined compositions. Subsequent heat treatment in 5% H-2 in N-2 resulted in the formation of a distinct Pt3Cr alloy phase which was either restricted to the surface of the particles or present throughout the bulk of the particle structure. Measurement of the oxygen reduction activity of the catalysts was accomplished using the rotating thin film electrode method and the activities obtained were related to the structure of the nanoalloy catalyst particles, largely determined using Cr K edge and Pt L-3 edge XAS.
Disentangled Adversarial Autoencoder for Subject-Invariant Physiological Feature Extraction (2020)

Recent developments in biosignal processing have enabled users to exploit their physiological status for manipulating devices in a reliable and safe manner. One major challenge of physiological sensing lies in the variability of biosignals across different users and tasks. To address this issue, we propose an adversarial feature extractor for transfer learning to exploit disentangled universal representations. We consider the trade-off between task-relevant features and user-discriminative information by introducing additional adversary and nuisance networks in order to manipulate the latent representations such that the learned feature extractor is applicable to unknown users and various tasks. Results on cross-subject transfer evaluations exhibit the benefits of the proposed framework, with up to 8.8% improvement in average accuracy of classification, and demonstrate adaptability to a broader range of subjects.
The 3′-Azido Group Is Not the Primary Determinant of 3′-Azido-3′-deoxythymidine (AZT) Responsible for the Excision Phenotype of AZT-resistant HIV-1 (2005)

The mechanism of human immunodeficiency virus (HIV) 1 resistance to 3'-azido-3'-deoxythymidine (AZT) involves reverse transcriptase (RT)-catalyzed phosphorolytic excision of the chain-terminating AZT-5'-monophosphate (AZTMP). Primers terminated with AZTMP are generally better substrates for this reaction than those terminated with 2',3'-dideoxynucleoside-5'-monophosphate (2',3'-ddNMP) analogs that lack a 3'-azido moiety. This led to the hypothesis that the 3'-azido group is a major structural determinant for maintaining the primer terminus in the appropriate site for phosphorolytic excision of AZTMP by AZT-resistant (AZT(R)) RT. To test this hypothesis, we evaluated the incorporation, phosphorolytic excision, and antiviral activity of a panel of 3'-azido-2',3'-ddN including 3'-azido-2',3'-ddA (AZddA), 3'-azido-2',3'-ddC (AZddC), 3'-azido-2',3'-ddG (AZddG), AZT, and 3'-azido-2',3'-ddU (AZddU). The results indicate that mutations correlated with resistance to AZT (D67N/K70R/T215F/K219Q) confer resistance to the 3'-azidopyrimidine nucleosides (AZddC, AZT, and AZddU) but not to the 3'-azidopurine nucleosides (AZddA and AZddG). The data suggest that the presence of a 3'-azido group on the 3'-terminal nucleotide of the primer does not confer increased phosphorolytic excision by AZT(R) RT for all 3'-azido-ddNMP analogs. Thus, the 3'-azido group cannot be the only structural determinant important for the enhanced phosphorolytic excision of AZTMP associated with HIV resistance to AZT. Other structural components, such as the base, must play a role in defining the specificity of the excision phenotype arising from AZT resistance mutations.
Continuous and Ultra-Fast Sars-Cov-2 Monitoring of Indoor Air (2021)

With the COVID-19 pandemic extending over a year now, it has become even more important to detect the SARS-CoV-2 virus as early as possible. Detecting the virus is of utmost importance to ensure safe return to schools, offices, public places, etc. Continuous monitoring of classrooms, workspaces has thus become the need of the hour. For this purpose, there is a pressing need for real-time sensors that can detect and warn the presence of SARS-CoV-2 virus in air. As a remedy to this problem, we have developed an ultra-fast electrochemical sensor device that detects the SARS-CoV-2 virus present in air. The SARS-CoV-2 viral proteins interact with a Ni-based electrode at an alkaline pH to produce a positive current difference compared to a baseline solution devoid of any viral proteins. The mechanism of detection is hypothesized to be analogous to the binding mechanism of SARS-CoV-2 on human body surfaces. As a result of such a mechanism, it is believed that local pH changes occur at the electric double layer and are captured as current signatures by the sensor. Our sensor device has selectively detected SARS-CoV-2 when tested in the presence of H1N1 Influenza A, SARS-CoV, and Human CoV OC43. Moreover, the use of electrochemical technique has rendered a very low detection limit for the sensor. Using continuous monitoring devices such as this ultra-fast COVID-19 diagnostic sensor for monitoring the air surrounding us would be the way forward for ensuring safe return to normalcy post-pandemic.
Novel synthetic approach for accessing drug–dye conjugates for targeted tumour therapy (2022)

The use of heptamethine cyanine dyes (HMCD) as a vehicle for targeted delivery of drugs to cancer tissues shows promise. The synthesis of drug–dye conjugates is hampered by scalability and purification issues. Herein we disclose synthetic procedure to procure such drug–dye conjugates that avoid the formation of undesired side products. This novel procedure also avoids the use of HPLC, thereby improving the yield and scalability of such drug–dye conjugates. Improving the atom-efficient coupling of drugs to HMCDs, will facilitate the clinical translation of HMCDs as a drug-delivery system for targeted tumour therapies.
Fluidymation: Stylizing Animations Using Natural Dynamics of Artistic Media (2021)

Abstract We present Fluidymation—a new example‐based approach to stylizing animation that employs the natural dynamics of artistic media to convey a prescribed motion. In contrast to previous stylization techniques that transfer the hand‐painted appearance of a static style exemplar and then try to enforce temporal coherence, we use moving exemplars that capture the artistic medium's inherent dynamic properties, and transfer both movement and appearance to reproduce natural‐looking transitions between individual animation frames. Our approach can synthetically generate stylized sequences that look as if actual paint is diffusing across a canvas in the direction and speed of the target motion.
A real time 4×4 MIMO-OFDM SDR for wireless networking research (2007)

A real time, 2 Mbps to 150 Mbps portable SDR unit with MIMO and sensing capability which exposes all the PHY parameters to the higher layers will help advance experimental cognitive radio (CR), and wireless networking research. The current SDR implements a slight variant of the 802.11n draft specification, with the entire baseband implemented on a single Xilinx Virtex II 8000 device using commercial boards from Nallatech. A fully self contained PHY solution, this SDR is capable of over 300 unique modes of operation all under direct control of the MAC, and features a robust MAC API through which all PHY parameters can be controlled on a per-packet basis. The same API will allow the PHY to communicate channel state information, SNR, and RSSI measurements back to the MAC. In this paper we provide an overview of the SDR and its development.