gebhart/patrepeval huggingface dataset:
Figure S5_1 from Integrative Kinome Profiling Identifies mTORC1/2 Inhibition as Treatment Strategy in Ovarian Clear Cell Carcinoma (2023)

&lt;p&gt;Supplementary Figure 5 | Clustering (n=106) and survival analysis (n=70) on kinome mutations and CNA. (A) Disease-specific survival of patients (n=70) grouped on ARID1A status, (B) PIK3CA status and (C) ARID1A + PIK3CA status. (D) Consensus clustering, with maximum group count set to 10 and clustering optimization with 1000 repetitions maximum, shows adding of tumors (n=106) as consensus index (horizontally) and empirical cumulative distribution (vertically) for 1-10 clusters. (E) Area under the curve plot of decrease in friction from 1-10 clusters. (F) Heatmap distribution of tumors in 8 clusters. (G) Disease-specific survival of patients (n=70) in 8 clusters, (H) cluster 3 vs. other clusters. (I) Disease-specific survival in advanced stage OCCC patients (FIGO 2C-4), Log rank (Mantel-Cox) was used for statistical analysis. (J) Nonsynonymous mutation distribution in genes involved in the frequently mutated PI3K/AKT/mTOR (blue) and MAPK pathway (yellow), ERBB family of receptor tyrosine kinases (green) and DNA repair pathway (red) as well as ARID1A and PALB2 are shown with OncoPrint. CNA in each mutated gene are added. The 106 OCCC tumors that were both kinome sequenced and SNP arrayed are shown on the horizontal axis grouped on tumor clusters and ordered on total event frequency in the subsequently altered pathways. (K) Oncoprint from advanced stage patients in cluster 3 vs. other clusters, shown on the horizontal axis grouped on tumor clusters and ordered on total event frequency in the subsequent altered pathways, ordered as aforementioned.&lt;/p&gt;
Ultrahigh Power Efficiency Thermally Activated Delayed Fluorescent OLEDs by the Strategic Use of Electron‐Transport Materials (2018)

Abstract Thermally activated delayed fluorescent (TADF) emitters are one of the most promising candidates for developing low‐cost organic light‐emitting devices (OLEDs) that can achieve an internal quantum efficiency of 100%. However, the power efficiency values are still significantly lower than that of their phosphorescent counterparts. To achieve high power efficiency, both a high external quantum efficiency and low drive voltage are required. Here, TADF OLEDs with an ultrahigh power efficiency of 133 lm W −1 and an unprecedented low turn‐on voltage of 2.22 V are successfully developed via the strategic use of electron‐transport materials (ETMs). 9‐[4‐(4,6‐Diphenyl‐1,3,5‐triazin‐2‐yl)phenyl]‐ N,N,N′,N ′‐tetraphenyl‐9H‐carbazole‐3,6‐diamine as a TADF emitter is used. A series of green TADF OLEDs are fabricated using two different types of pyrimidine‐based ETMs as an exciplex host partner and electron‐transport layer to minimize the drive voltages. The optimized device shows an external quantum efficiency of 29.2% and maximum power efficiency of 133.2 lm W −1 without any light‐outcoupling enhancement. The device also shows 124.0 lm W −1 at 100 cd m −2 and 95.2 lm W −1 at a high brightness of 1000 cd m −2 . The drive voltages are 2.48 V at 100 cd m −2 and 2.88 V at 1000 cd m −2 .
Current and Future Potential Impact of COVID-19 on Kratom (Mitragyna speciosa Korth.) Supply and Use (2020)

Kratom (<i>Mitragyna speciosa</i> Korth., Rubiaceae) is native to and has traditional use in Southeast Asia. The number of kratom users outside of Southeast Asia has increased significantly in recent decades with use spreading to the Unites States (US) and Europe. Because of its reputed opioid-like psychoactive effects at higher doses, kratom has been regulated in several countries and is subject to an import ban by the US Food and Drug Administration. Nonetheless, in the US it is estimated that 10-15 million people consume kratom primarily for the self-treatment of pain, psychiatric disorders, to mitigate withdrawal from or dependence on opioids, and to self-treat opioid use disorder or other substance use disorders (SUDs). Due to the global COVID-19 pandemic, a shortage in the supply of kratom products may place unexpected burdens on kratom users, potentially influencing some who use kratom for SUD self-treatment to regress to harmful drug use, hence increasing the likelihood of adverse outcomes, including overdose. Inadequate treatment, treatment barriers, and increases in the sales of adulterated kratom products on the internet or in convenience stores could exacerbate circumstances further. Although there are currently no verified indications of kratom scarcity, researchers and clinicians should be aware of and remain vigilant to this unanticipated possibility.
Targeting SxIP-EB1 interaction: An integrated approach to the discovery of small molecule modulators of dynamic binding sites (2017)

End binding protein 1 (EB1) is a key element in the complex network of protein-protein interactions at microtubule (MT) growing ends, which has a fundamental role in MT polymerisation. EB1 is an important protein target as it is involved in regulating MT dynamic behaviour, and has been associated with several disease states, such as cancer and neuronal diseases. Diverse EB1 binding partners are recognised through a conserved four amino acid motif, (serine-X-isoleucine-proline) which exists within an intrinsically disordered region. Here we report the use of a multidisciplinary computational and experimental approach for the discovery of the first small molecule scaffold which targets the EB1 recruiting domain. This approach includes virtual screening (structure- and ligand-based design) and multiparameter compound selection. Subsequent studies on the selected compounds enabled the elucidation of the NMR structures of the C-terminal domain of EB1 in the free form and complexed with a small molecule. These structures show that the binding site is not preformed in solution, and ligand binding is fundamental for the binding site formation. This work is a successful demonstration of the combination of modelling and experimental methods to enable the discovery of compounds which bind to these challenging systems.
Shot-Noise Limited Single-Molecule FRET Histograms:  Comparison between Theory and Experiments (2006)

We describe a simple approach and present a straightforward numerical algorithm to compute the best fit shot-noise limited proximity ratio histogram (PRH) in single-molecule fluorescence resonant energy transfer diffusion experiments. The key ingredient is the use of the experimental burst size distribution, as obtained after burst search through the photon data streams. We show how the use of an alternated laser excitation scheme and a correspondingly optimized burst search algorithm eliminates several potential artifacts affecting the calculation of the best fit shot-noise limited PRH. This algorithm is tested extensively on simulations and simple experimental systems. We find that dsDNA data exhibit a wider PRH than expected from shot noise only and hypothetically account for it by assuming a small Gaussian distribution of distances with an average standard deviation of 1.6 A. Finally, we briefly mention the results of a future publication and illustrate them with a simple two-state model system (DNA hairpin), for which the kinetic transition rates between the open and closed conformations are extracted.
Non-vacuum deposition of aqueous-based CuIn<inf>x</inf>Ga<inf>1&#x2212;x</inf>Se<inf>2</inf> (CIGS) nanoparticles for solar applications (2011)

CuIn <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> Ga <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1−x</inf> Se <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> (CIGS) as an absorber material in solar cells is already known to present a less toxic alternative to current solar cells based on toxic elements such as CdTe. CIGS developed as nanoparticles in solution are ideal for non-vacuum deposition methods which help achieve lower-cost solar cells, compared to high vacuum deposition methods. This study investigates deposition, processing, and characterization of aqueous-based CIGS nanoparticles. The films are deposited via sono-deposition, spin coating method, and drop cast method. The as-deposited thin films are characterized via X-Ray Diffraction (XRD), Optical Microscope, and Scanning Electron Microscopy (SEM, and STEM). The films are then annealed via Pulsed Thermal Processing (PTP) technique, and post-PTP characterization shows change in the morphology of CIGS nanoparticles.
Design and characterization of thermosetting polyimide structural adhesive and composite matrix systems (1997)

Fully cyclized, organo soluble, phenylethynyl-terminated, ether-imide oligomers of 2–10,000 g/mol (Mn) were prepared by the reaction of 2,2′-bis[4-(3,4-dicarboxyphenoxy)phenyl]-propane dianhydride (bisphenol-A dianhydride, BPADA) with a stoichiometric excess of either para, meta, or isomeric mixtures of phenylene diamine and phenylethynylphthalic anhydride (4-PEPA) endcapper. High para-containing oligomers produced semicrystalline powders, but the all meta isomer was completely amorphous. The lower molecular weight oligomers displayed an attractive low viscosity melt and were cured to very high gel content networks at 350–380°C for 30–90 min. The cured 3000 g/mol oligomers showed a (DSC) glass transition temperature (Tg) of 267°C and produced tough, solvent-resistant films. Excellent adhesion to surface-treated titanium alloys was achieved, as judged by single-lap shear measurements. Resin infusion molding was conducted, which permitted low-void, graphite-fabric composite panels to be prepared. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 2943–2954, 1997
Adaptive-robust friction compensation in a hybrid brake-by-wire actuator (2013)

This work focuses on the development of a pressure-loop controller for a hybrid brake-by-wire system, composed of a hydraulic link and an electro-mechanical actuator. Towards this goal, we will start by constructing a reduced model that is capable of capturing the fundamental dynamics of the actuator, which is particularly useful for control design purposes. Motivated by the large friction disturbances that affect the system, we also investigate linear-in-the-parameter models suitable for (online) model-based friction compensation. More specifically, results from the theory of function approximation, together with optimization techniques, are explored to approximate the Stribeck friction model through a linear-in-the-parameter model. This new linear-in-the-parameter model is then employed in the design of a control law for tracking the braking pressure of the hybrid brake-by-wire. The main features of this controller are the robustness to parametric uncertainties, thanks to the inclusion of a switching- σ adaptive mechanism, and the attenuation of non-parametric disturbances with a continuous sliding mode action. The stability and robustness properties of the closed-loop system are investigated with the help of the Lyapunov method. Finally, experimental tests demonstrate the effectiveness of the proposed approach and its ability to handle disturbances.
B302 Gait Analysis and Accuracy Verification Using Wearable Measurement System (2015)

In human gait motion analysis, which is one useful method for efficient physical rehabilitation, ground reaction forces, kinetic and kinematic parameters are measured. For obtaining these data as the unrestrained gait measurement, a novel gait motion analysis system using mobile force plate and attitude sensor has been developed. However, it has been used at only specially-cleaned experimental laboratory. In this study, ground reaction forces and joint position applied on the lower limb of healthy subjects are measured by two measurement methods. One is a traditional way: a combination of force sensor based on ground and motion capture system. And the other is wearable measurement system composed of mobile force plate and attitude sensor. By compering this two measured results, we can evaluate the accuracy of the wearable measurement system. As a result of the experiments, vertical component of ground reaction force and knee joint angle are measured with a high degree of accuracy. On the other hand, antenior-postenior and medial-lateral components of the force and ankle and hip joint angles showed different results. The data measured by wearable system are mostly larger. Precision placement of attitude sensor is very difficult as the figure of lower limbs is different one by one, and this may be the reason. Future subject is structuring a new algorithm to set off a declination of attitude sensor position.
Murine Notch Homologs (N1–4) Undergo Presenilin-dependent Proteolysis (2001)

Oncogenic forms of Notch1, Notch2, and Notch4 appear to mimic signaling intermediates of Notch1 and suggest that the role of proteolysis in Notch signaling has been conserved. Here we demonstrate that extracellularly truncated Notch homologs are substrates for a presenilin-dependent gamma-secretase activity. Despite minimal conservation within the transmembrane domain, the requirement for a specific amino acid (P1' valine) and its position at the cleavage site relative to the cytosolic border of the transmembrane domain are preserved. Cleaved, untethered Notch intracellular domains from each receptor translocate to the nucleus and interact with the transcriptional regulatory protein CSL. All four Notch proteins display presenilin-dependent transactivating potential on a minimal promoter reporter. Thus, this study increases the number of biochemically characterized gamma-secretase substrates from two to five. Despite a high degree of structural homology and the presenilin-dependent activity of truncated Notch proteins, the extent that this reflects functional redundancy is unknown.
Altered Neuronal Mitochondrial Coenzyme A Synthesis in Neurodegeneration with Brain Iron Accumulation Caused by Abnormal Processing, Stability, and Catalytic Activity of Mutant Pantothenate Kinase 2 (2005)

Mutations in the pantothenate kinase 2 (PANK2) gene have been identified in patients with neurodegeneration with brain iron accumulation (NBIA; formerly Hallervorden-Spatz disease). However, the mechanisms by which these mutations cause neurodegeneration are unclear, especially given the existence of multiple pantothenate kinase genes in humans and multiple PanK2 transcripts with potentially different subcellular localizations. We demonstrate that PanK2 protein is localized to mitochondria of neurons in human brain, distinguishing it from other pantothenate kinases that do not possess mitochondrial-targeting sequences. PanK2 protein translated from the most 5' start site is sequentially cleaved at two sites by the mitochondrial processing peptidase, generating a long-lived 48 kDa mature protein identical to that found in human brain extracts. The mature protein catalyzes the initial step in coenzyme A (CoA) synthesis but displays feedback inhibition in response to species of acyl CoA rather than CoA itself. Some, but not all disease-associated point mutations result in significantly reduced catalytic activity. The most common mutation, G521R, results in marked instability of the intermediate PanK2 isoform and reduced production of the mature isoform. These results suggest that NBIA is caused by altered neuronal mitochondrial lipid metabolism caused by mutations disrupting PanK2 protein levels and catalytic activity.
New DVB‐S2X constellations for improved performance on the satellite channel (2015)

Summary Digital Video Broadcasting via satellite second generation has experienced worldwide adoption because of its revolutionary and yet practical physical layer technology and its flexibility. Recently, the standard has been updated with several new features without changing its fundamental structure. This paper provides a high‐level discussion on several of the most important additions to the new standard with particular emphasis on some of the new signal constellations. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Building an insurance against modern pandemics. (2010)

The response to the first influenza pandemic of the 21st century benefited from the extensive preparation for an avian influenza pandemic and the mild nature of the 2009 A/H1N1 swine influenza virus. However, the pandemic demonstrated the limited ability to predict influenza pandemics, to anticipate levels of cross-protection, and to deliver vaccines in a timely manner, particularly to low income countries. The lessons learned from the 2009 H1N1 pandemic are of paramount importance to develop more effective preparations against future pandemics.
Breaking the Far-Field Diffraction Limit in Optical Nanopatterning via Repeated Photochemical and Electrochemical Transitions in Photochromic Molecules (2011)

By saturating a photochromic transition with a nodal illumination (wavelength, λ), one isomeric form of a small molecule is spatially localized to a region smaller than the far-field diffraction limit. A selective oxidation step effectively locks this pattern allowing repeated patterning. Using this approach and a two-beam interferometer, we demonstrate isolated lines as narrow as λ/8 (78 nm) and spacing between features as narrow as λ/4 (153 nm). This is considerably smaller than the minimum far-field diffraction limit of λ/2. Most significantly, nanopatterning is achieved via single-photon reactions and at low light levels, which in turn allow for high throughput.
Proceedings of the 13th ACM International Symposium on Mobility Management and Wireless Access (2015)

On behalf of the organizing committees, it is our great pleasure to welcome you to the 13th ACM International Symposium on Mobility Management and Wireless Access -- MobiWac 2015. Previous editions of this symposium took place in Dallas/Fort Worth (TX, USA), Philadelphia (PA), Maui (Hawaii), Torremolinos (Spain), Chania (Greece), Vancouver (Canada), Tenerife (Spain), Bodrum (Turkey), Miami (FL, USA), Paphos (Cyprus), Barcelona (Spain) and Montreal (Canada). This year MobiWac takes place in Cancun, Mexico, and continues its successful track record of being a forum where researchers from academy and industry gather to discuss novel advances in mobility, wireless access and related topics, aiming at advancing knowledge and identifying new directions for future research and development. The call for papers attracted 37 submissions from Africa, America, Asia and Europe. From these works, the program committee accepted 12 as regular papers and 2 more as short papers, which represents an acceptance rate of 37.8%. Accepted works cover a wide variety of topics, including mobility management and medium access, MANET networking, tracking, quality of service, security and applications. The accepted papers come from 10 countries (Brazil, Canada, Germany, Greece, Japan, Luxemburg, Mexico, Sweden, Tunisia and USA), which reflects the international nature of the symposium.
Supplementary Text from Tumor Promotion by Intratumoral Plasmacytoid Dendritic Cells Is Reversed by TLR7 Ligand Treatment (2023)

&lt;p&gt;Supplementary Text - PDF file 132K, Supplementary Material and methods, and Supplementary figure legends&lt;/p&gt;
Versatile microbial communities rapidly assimilate ammonium hydroxide-treated plastic waste (2023)

Waste plastic presently accumulates in landfills or the environment. While natural microbial metabolisms can degrade plastic polymers, biodegradation of plastic is very slow. This study demonstrates that chemical deconstruction of polyethylene terephthalate (PET) with ammonium hydroxide can replace the rate limiting step (depolymerization) and by producing plastic-derived terephthalic acid and terephthalic acid monoamide. The deconstructed PET (DCPET) is neutralized with phosphoric acid prior to bioprocessing, resulting in a product containing biologically accessible nitrogen and phosphorus from the process reactants. Three microbial consortia obtained from compost and sediment degraded DCPET in ultrapure water and scavenged river water without addition of nutrients. No statistically significant difference was observed in growth rate compared to communities grown on DCPET in minimal culture medium. The consortia were dominated by Rhodococcus spp., Hydrogenophaga spp., and many lower abundance genera. All taxa were related to species known to degrade aromatic compounds. Microbial consortia are known to confer flexibility in processing diverse substrates. To highlight this, we also demonstrate that two microbial consortia can grow on similarly deconstructed polyesters, polyamides, and polyurethanes in water instead of medium. Our findings suggest that microbial communities may enable flexible bioprocessing of mixed plastic wastes when coupled with chemical deconstruction.
Differential cross-section measurements for the electroweak production of dijets in association with a Z boson in proton–proton collisions at ATLAS (2021)

Abstract Differential cross-section measurements are presented for the electroweak production of two jets in association with a Z boson. These measurements are sensitive to the vector-boson fusion production mechanism and provide a fundamental test of the gauge structure of the Standard Model. The analysis is performed using proton–proton collision data collected by ATLAS at $$\sqrt{s}=13\ \hbox {TeV}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>13</mml:mn> <mml:mspace/> <mml:mtext>TeV</mml:mtext> </mml:mrow> </mml:math> and with an integrated luminosity of $$139\ \hbox {fb}^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mn>139</mml:mn> <mml:mspace/> <mml:msup> <mml:mtext>fb</mml:mtext> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:mrow> </mml:math> . The differential cross-sections are measured in the $$Z\rightarrow \ell ^+\ell ^-$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>Z</mml:mi> <mml:mo>→</mml:mo> <mml:msup> <mml:mi>ℓ</mml:mi> <mml:mo>+</mml:mo> </mml:msup> <mml:msup> <mml:mi>ℓ</mml:mi> <mml:mo>-</mml:mo> </mml:msup> </mml:mrow> </mml:math> decay channel ( $$\ell =e,\mu $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>ℓ</mml:mi> <mml:mo>=</mml:mo> <mml:mi>e</mml:mi> <mml:mo>,</mml:mo> <mml:mi>μ</mml:mi> </mml:mrow> </mml:math> ) as a function of four observables: the dijet invariant mass, the rapidity interval spanned by the two jets, the signed azimuthal angle between the two jets, and the transverse momentum of the dilepton pair. The data are corrected for the effects of detector inefficiency and resolution and are sufficiently precise to distinguish between different state-of-the-art theoretical predictions calculated using Powheg+Pythia8 , Herwig7+Vbfnlo and Sherpa 2.2. The differential cross-sections are used to search for anomalous weak-boson self-interactions using a dimension-six effective field theory. The measurement of the signed azimuthal angle between the two jets is found to be particularly sensitive to the interference between the Standard Model and dimension-six scattering amplitudes and provides a direct test of charge-conjugation and parity invariance in the weak-boson self-interactions.
Effectiveness of adaptive supply voltage and body bias for reducing impact of parameter variations in low power and high performance microprocessors (2003)

Test chip measurements show that adaptive V/sub CC/ is useful for reducing impacts of parameter variations on frequency, active power and leakage power of microprocessors. Using adaptive V/sub CC/ together with adaptive V/sub BS/ or WID-V/sub BS/ is much more effective than using any of them individually.