gebhart/patrepeval huggingface dataset:
Validation of a Low-Cost on-Demand Compact Ozone Covid-19 Sterilization Chamber (2021)

The COVID-19 pandemic has resulted in limited availability of N95 masks and other personal protective equipment (PPE). The sterilization and re-use of PPE can be of immediate benefit to help alleviate shortages and offer peace of mind to healthcare workers. Also, an inexpensive, precise, and portable sterilizer will have many applications beyond the current health crisis in a variety of field disaster relief operations. The sterilization of PPE and medical or other instruments will reduce costs, improve safety, and reduce waste. The portable sterilizer can also be utilized by individuals and businesses outside of the health care sector with similar benefits. Ozone sterilization does not require chemical consumables, uses ambient oxygen to generate ozone on site, and results in no toxic residuals. KWJ Engineering led the development of a small benchtop sterilizer with on board ozone generation controlled by feedback from an electrochemical sensor module and complete with an ozone destruct cycle for safety. Relative humidity as well as temperature and O 3 concentration are also continuously recorded and can be maintained at the most effective levels for sterilization. Validation of the ozone sterilization protocol for deactivation of surrogate viruses on N95 masks has been demonstrated using TLS, an E. coli bacteriophage (bacteria-infecting virus), to provide a measure of effectiveness for variables such as time, ozone and viral concentrations, temperature, relative humidity, and virus-contaminated substrate. Additional organisms and conditions of sterilization are reported in this study to provide further analysis of efficacy of equipment and procedures as well as deleterious effects, if any, on PPE. The experiments with bacteriophage indicate that there is 99.99% inactivation of the robust bacteriophage when placed on N95 mask material with a one-hour treatment at 200 ppm ozone as compared to a 0-ppm control. The inactivation was shown to be 99.8% with only 50 ppm ozone. These ozone levels are easily achieved with a low power source and the entire system is operated using 12 VDC from a charger or battery. This sterilization effect is highly dependent on humidity, and the higher inactivation rates require higher relative humidity. The inactivation was demonstrated on multiple types of substrates with and without prior drying of the deposited phage. We expect the covid19 to be easier to inactivate than the bacteriophage and will test the system on SARS-CoV2 in a separate series of experiments. The sterilizer apparatus is simple and low cost and can be constructed from readily available parts and software for automated control is open sourced by KWJ.
A Structure-Function Analysis Revealed Histidine in the Transmembrane Domain of Human Thrombopoietin Receptor Is Essential for a Novel Non-Peptidyl Thromobopoietin Mimetics, NIP-004, To Induce Signaling for Cellular Proliferation. (2005)

Abstract NIP-004 is a novel synthetic compound that displays human (Hu) thrombopoietin receptor (Mpl) agonistic activity. NIP-004 stimulated proliferation of HuMpl-expressing cell lines such as UT-7/EPO-HuMpl and Ba/F3-HuMpl, but not murine (Mu) Mpl-expressing cell lines such as UT-7/EPO-MuMpl and Ba/F3-MuMpl. NIP-004 or its derivative compound stimulated colony formation of CD41a+ megakaryocytes from human bone marrow (BM)-derived CD34+ hematopoietic progenitor cells, but not from murine BM cells or cynomolgus or rhesus monkey BM-derived CD34+ cells. These results indicated that NIP-004 has strict species specificity. To identify a molecular basis for the species specificity displayed by NIP-004, we analyzed the amino acid sequence of Mpl from two non-human primates, cynomolgus and rhesus. Cynomolgus Mpl displayed the highest level of sequence homology, 96% identical to HuMpl, with only 22 amino-acids differing between the two species, and 14 residues in the 22 amino-acids of HuMpl differed from rhesus Mpl. Comparison of these 14 amino-acid residues as either hydrophobic or hydrophilic and either electrically charged or uncharged revealed distinguishing features of an amino acid residue. Histidine (His) at position 499 from the N-terminal residue in the transmembrane domain of HuMpl is specific for humans. We thus performed site-directed mutagenesis this residue in HuMpl and MuMpl, and analyzed STAT5 activation via each receptor in the Hek293 human embryonic kidney cell line using STAT-reporter gene assay. Wild-type HuMpl, but not MuMpl, activated STAT5 after stimulation with NIP-004. HuMpl with His499 mutated to Leu (HuMplH499L) failed to induce STAT5 activation via NIP-004 stimulation. Conversely, when MuMpl was engineered to contain His490 (MuMplL490H), it was then capable of activating STAT5. Furthermore, NIP-004 stimulated proliferation of Ba/F3-MuMplL490H cells, but not Ba/F3-HuMplH499L cells. Western blotting analysis revealed that NIP-004 induced phosphorylation of STAT5 proteins in Ba/F3-HuMpl and Ba/F3-MuMplL490H cells, but not Ba/F3-MuMpl and Ba/F3-HuMplH499L cells. All Ba/F3 transfectants expressing these Mpl constructs responded to TPO stimulation. These observations indicate that His in the transmembrane domain of Mpl is an essential residue for the ability of NIP-004 to act as an Mpl agonist. We also found none of other experimental animals such as common marmoset, squirrel monkey, beagle dog, Japanese White rabbit, Syrian hamster, Hartley guinea pig and Wistar rat with His in the transmembrane of Mpl. Although His exists in the transmembrane domain of human G-CSFR, NIP-004 failed to stimulate the proliferation of Ba/F3 cells expressing human G-CSFR. In conclusion, a novel non-peptidyl synthetic compound, NIP-004, displays Mpl agonistic activity with strict species specificity via His in the transmembrane domain of Mpl.
Coupled Methyl Group Epimerization and Reduction by Polyketide Synthase Ketoreductase Domains. Ketoreductase-Catalyzed Equilibrium Isotope Exchange (2013)

Incubation of [2-(2)H]-(2S,3R)-2-methyl-3-hydroxypentanoyl-SACP ([2-(2)H]-1a) with the epimerizing ketoreductase domain EryKR1 in the presence of a catalytic amount NADP(+) (0.05 equiv) resulted in time- and cofactor-dependent washout of deuterium from 1a, as a result of equilibrium isotope exchange of transiently generated [2-(2)H]-2-methyl-3-ketopentanoyl-ACP. Incubations of [2-(2)H]-(2S,3S)-2-methyl-3-hydroxy-pentanoyl-SACP with RifKR7 and with NysKR1 also resulted in time-dependent loss of deuterium. By contrast, incubations of [2-(2)H]-(2R,3S)-2-methyl-3-hydroxypentanoyl-SACP and [2-(2)H]-(2R,3R)-2-methyl-3-hydroxypentanoyl-SACP with the non-epimerizing ketoreductase domains EryKR6 and TylKR1, respectively, did not result in any significant washout of deuterium. The isotope exchange assay directly establishes that specific polyketide synthase ketoreductase domains also have an intrinsic epimerase activity, thus enabling mechanistic analysis of a key determinant of polyketide stereocomplexity.
T-cell Receptor Specificity Maintained by Altered Thermodynamics (2013)

The T-cell receptor (TCR) recognizes peptides bound to major histocompatibility molecules (MHC) and allows T-cells to interrogate the cellular proteome for internal anomalies from the cell surface. The TCR contacts both MHC and peptide in an interaction characterized by weak affinity (KD = 100 nM to 270 μM). We used phage-display to produce a melanoma-specific TCR (α24β17) with a 30,000-fold enhanced binding affinity (KD = 0.6 nM) to aid our exploration of the molecular mechanisms utilized to maintain peptide specificity. Remarkably, although the enhanced affinity was mediated primarily through new TCR-MHC contacts, α24β17 remained acutely sensitive to modifications at every position along the peptide backbone, mimicking the specificity of the wild type TCR. Thermodynamic analyses revealed an important role for solvation in directing peptide specificity. These findings advance our understanding of the molecular mechanisms that can govern the exquisite peptide specificity characteristic of TCR recognition.
High structural quality InN∕In0.75Ga0.25N multiple quantum wells grown by molecular beam epitaxy (2006)

In N ∕ In 0.75 Ga 0.25 N multiple quantum wells (MQWs) were grown by rf plasma-assisted molecular beam epitaxy. The high-resolution transmission electron microscope and x-ray diffraction measurements showed evidence of growth of atomically smooth and sharp interface and good periodicity. Room-temperature photoluminescence emissions from InN quantum wells were observed at the wavelength range from 1.59to1.95μm by changing the well thickness. The unstrained valence band offset of InN∕GaN was estimated to be ΔEv=0.9eV by comparing the experimental transition wavelengths of the MQWs and a theoretical calculation considering strain effects and built-in, mainly piezoelectric, fields.
A World-to-Digital Microfluidic Interface for Whole Blood RNA Preparation. (2013)

Abstract not provided.
Polymyxin B/Surfactant-Gemische reduzieren das Wachstum von E. coli in Mekoniumsuspensionen (2004)

Fragestellung: E. coli oder B-Streptokokken (GBS) gehören zu den häufigsten Erregern neonataler Infektionen. Im Rahmen des Mekoniumaspirationssyndrom kommt es zu einer pulmonalen Entzündungsreaktion, die sowohl chemisch ("steril") als auch bakteriell bedingt sein kann. Das antimikrobielle Peptid Polymyxin B erhöht durch Verbindung von Lipidmembranen ("cross linking") die Resistenz von Surfactant gegenüber einer Inhibition durch Mekonium. In dieser Studie sollte untersucht werden, ob Surfactant/PxB-Gemische neben einer biophysikalischen auch eine antimikrobielle Wirkung auf E. Coli und GBS in einem mekoniumhaltigen Medium ausüben.
Generating Skeletal Diversity and Complexity from Boron‐Substituted 1,3‐Dienes and Enophiles (2020)

Boron‐substituted 1,3‐dienes participate in ene reactions to afford new functionalized synthetic intermediates. After evaluating several enophiles as partners, the resulting products have been engaged in multistep sequences involving first a Diels Alder/allylboration process. A variety of skeletally diverse and complex polycyclic heterocycles were thus synthesized, such as tetrahydro‐1 H ‐isoindole‐1,3( 2H )‐diones, eight‐membered lactones or tricyclic spiro compounds.
Suspended Carbon Nanotubes for Humidity Sensing (2018)

A room temperature microfabrication technique using SU8, an epoxy-based highly functional photoresist as a sacrificial layer, is developed to obtain suspended aligned carbon nanotube beams. The humidity-sensing characteristics of aligned suspended single-walled carbon nanotube films are studied. A comparative study between suspended and non-suspended architectures is done by recording the resistance change in the nanotubes under humidity. For the tests, the humidity was varied from 15% to 98% RH. A comparative study between suspended and non-suspended devices shows that the response and recovery times of the suspended devices was found to be almost 3 times shorter than the non-suspended devices. The suspended devices also showed minimal hysteresis even after 10 humidity cycles, and also exhibit enhanced sensitivity. Repeatability tests were performed by subjecting the sensors to continuous humidification cycles. All tests reported here have been performed using pristine non-functionalized nanotubes.
C-Axis Oriented YBa2Cu3O6.8 Films on Amorphous Silicate Glasses Using Laser Deposition (1991)

In situ laser deposition was used to fabricate YBa 2 Cu 3 O 6.8 (YBCO) films on amorphous glasses. Yttrium stabilized zirconia (YSZ) and conducting indium-tin-oxide (ITO) were used as the buffer layers to improve the transport properties of YBCO films. There was negligible interdiffusion occurring at the interfaces. YBCO films were strongly c -axis oriented normal to the substrate. However, those films were randomly oriented in the a-b plane. T c ′ s of 81 K and 72 K were achieved for YBCO films, with a YSZ buffer and an ITO buffer, respectively. Also, the resistivity of the ITO buffer fabricated by laser deposition was in the order of 10 -4 Ω·cm.
Observation of critical gate oxide thickness for substrate-defect related oxide failure (1999)

The presence of crystal originated particles in silicon substrates leads to gate oxide failures in metal–oxide–semiconductor devices. A nonlinear relationship is known to exist between the oxide defect density and the oxide thickness, but the mechanism behind this remains unclear. In this work, we evaluate the gate oxide integrity for oxide thicknesses ranging from 2.5 to 26.5 nm. The results show no appreciable oxide degradation below an oxide thickness of approximately 5 nm; above this threshold value, the defect density depends strongly on the presence of crystal originated particles. Oxide thinning is unlikely to be responsible for this behavior.
Negatives between Chamic and Bahnaric (2015)

The paper deals with the verb embracing double negation found in both Chamic and&#13;\nBahnaric languages and with the question how it developed. We propose both an internal&#13;\nand external explanation. The former relates to what is called a ‘Jespersen Cycle’, a&#13;\nhypothesis about the renewal of single negation out of double negation, itself developing&#13;\nout of another single negation. The latter is language interference from Chamic to&#13;\nBahnaric. We argue that the Jespersen Cycle hypothesis is more plausible for Chamic,&#13;\nthus revisiting Lee (1996), and that the language contact hypothesis makes more sense&#13;\nfor Bahnaric, thus supporting a more general hypothesis about the direction of&#13;\ninterference between the two families (Sidwell 2008: 261, 265).
Electrical properties and Tc of CaLaBaCu3Ox at pressures up to 9 GPa (1990)

Abstract By means of a four-point resistivity method the critical temperature (Tc) of the tetragonal high temperature super-conductor CaLaBaCu3Ox was studied for pressures up to 9 GPa. The pressure dependence of Tc is small and negative, dTc/dp = - 0.77 K/GPa, and agrees with the general trend observed in previous data.
Clinical significance and predictors of oncologic outcome after radical prostatectomy for invisible prostate cancer on multiparametric MRI (2018)

In our results, cases of iPCa had clinically significant PCa, and AP and poor prognosis were also observed in some. Additionally, we found that PSA is the most clinically reliable predictor of oncologic outcome. We suggest that active treatment and diagnosis should be considered for patients with iPCa with PSA > 6.2 ng/ml.
Receptor mimicking TGF-β1 binding peptide for targeting TGF-β1 signaling (2020)

Prolonged and elevated transforming growth factor-β1 (TGF-β1) signaling can lead to undesired scar formation during tissue repair and fibrosis that is often a result of chronic inflammation in the lung, kidney, liver, heart, skin, and joints. We report new TGF-β1 binding peptides that interfere with TGF-β1 binding to its cognate receptors and thus attenuate its biological activity. We identified TGF-β1 binding peptides from the TGF-β1 binding domains of TGF-β receptors and engineered their sequences to facilitate chemical conjugation to biomaterials using molecular docking simulations. The in vitro binding studies and cell-based assays showed that RIPΔ, which was derived from TGF-β type I receptor, bound TGF-β1 in a sequence-specific manner and reduced the biological activity of TGF-β1 when the peptide was presented either in soluble form or conjugated to a commonly used synthetic biomaterial. This approach may have implications for clinical applications such as treatment of various fibrotic diseases and soft tissue repair and offer a design strategy for peptide antibodies based on the biomimicry of ligand-receptor interactions.
An experimental study and model determination of the stiffness of paper folds (2015)

International audience
Mechanical properties of plasma membrane vesicles correlate with lipid order and viscosity and depend on cell density (2019)

Abstract Plasma membranes dynamically respond to external cues and changing environment. Quantitative measurements of these adaptations can elucidate the mechanism that cells exploit to survive, adapt and function. However, cell-based assays are affected by active processes while measurements on synthetic models suffer from compositional limitations. Here, as a model system we employ giant plasma membrane vesicles (GPMVs), which largely preserve the plasma membrane lipidome and proteome. From analysis of fluorescence emission and lifetime of environment-sensitive dyes, and membrane shape fluctuations, we investigate how plasma membrane order, viscosity and bending rigidity are affected by different stimuli such as cell seeding density in three different cell models. Our studies reveal that bending rigidity of plasma membranes vary with lipid order and microviscosity in a highly correlated fashion. Thus, readouts from polarity- and viscosity-sensitive probes represent a promising indicator of membrane mechanical properties. Quantitative analysis of the data allows for comparison to synthetic lipid membranes as plasma membrane mimetics.
von Willebrand factor and retinal circulation in early-stage retinopathy of type 1 diabetes. (2000)

Increased vWF was associated with a prolonged retinal circulation time and reduced retinal blood flow in early-stage retinopathy of type 1 diabetes. Reduced blood flow associated with increased vWF levels may promote stasis in the retinal circulation and lead to local hypoxemia. These changes might contribute to the microvascular complications of diabetes. Whether the vWF levels predict retinal complications deserves further investigation.
Complete, Programmable Decoding of Oxidized 5-Methylcytosine Nucleobases in DNA by Chemoselective Blockage of Universal Transcription-Activator-Like Effector Repeats (2018)

5-Methylcytosine (5mC) and its oxidized derivatives are regulatory elements of mammalian genomes involved in development and disease. These nucleobases do not selectively modulate Watson-Crick pairing, preventing their programmable targeting and analysis by traditional hybridization probes. Transcription-activator-like effectors (TALEs) can be engineered for use as programmable probes with epigenetic nucleobase selectivity. However, only partial selectivities for oxidized 5mC have been achieved so far, preventing unambiguous target binding. We overcome this limitation by destroying and re-inducing nucleobase selectivity in TALEs via protein engineering and chemoselective nucleobase blocking. We engineer cavities in TALE repeats and identify a cavity that accommodates all eight human DNA nucleobases. We then introduce substituents with varying size, flexibility, and branching degree at each oxidized 5mC. Depending on the nucleobase, substituents with distinct properties effectively block TALE-binding and induce full nucleobase selectivity in the universal repeat. Successful transfer to affinity enrichment in a human genome background indicates that this approach enables the fully selective detection of each oxidized 5mC in complex DNA by programmable probes.
Activation of specific interneurons improves V1 feature selectivity and visual perception (2012)

Inhibitory interneurons are essential components of the neural circuits underlying various brain functions. In the neocortex, a large diversity of GABA (γ-aminobutyric acid) interneurons has been identified on the basis of their morphology, molecular markers, biophysical properties and innervation pattern. However, how the activity of each subtype of interneurons contributes to sensory processing remains unclear. Here we show that optogenetic activation of parvalbumin-positive (PV+) interneurons in the mouse primary visual cortex (V1) sharpens neuronal feature selectivity and improves perceptual discrimination. Using multichannel recording with silicon probes and channelrhodopsin-2 (ChR2)-mediated optical activation, we found that increased spiking of PV+ interneurons markedly sharpened orientation tuning and enhanced direction selectivity of nearby neurons. These effects were caused by the activation of inhibitory neurons rather than a decreased spiking of excitatory neurons, as archaerhodopsin-3 (Arch)-mediated optical silencing of calcium/calmodulin-dependent protein kinase IIα (CAMKIIα)-positive excitatory neurons caused no significant change in V1 stimulus selectivity. Moreover, the improved selectivity specifically required PV+ neuron activation, as activating somatostatin or vasointestinal peptide interneurons had no significant effect. Notably, PV+ neuron activation in awake mice caused a significant improvement in their orientation discrimination, mirroring the sharpened V1 orientation tuning. Together, these results provide the first demonstration that visual coding and perception can be improved by increased spiking of a specific subtype of cortical inhibitory interneurons.
DNA-based Fish Species Identification Protocol (2010)

We have developed a fast, simple, and accurate DNA-based screening method to identify the fish species present in fresh and processed seafood samples. This versatile method employs PCR amplification of genomic DNA extracted from fish samples, followed by restriction fragment length polymorphism (RFLP) analysis to generate fragment patterns that can be resolved on the Agilent 2100 Bioanalyzer and matched to the correct species using RFLP pattern matching software. The fish identification method uses a simple, reliable, spin column- based protocol to isolate DNA from fish samples. The samples are treated with proteinase K to release the nucleic acids into solution. DNA is then isolated by suspending the sample in binding buffer and loading onto a micro- spin cup containing a silica- based fiber matrix. The nucleic acids in the sample bind to the fiber matrix. The immobilized nucleic acids are washed to remove contaminants, and total DNA is recovered in a final volume of 100 mul. The isolated DNA is ready for PCR amplification with the provided primers that bind to sequences found in all fish genomes. The PCR products are then digested with three different restriction enzymes and resolved on the Agilent 2100 Bioanalyzer. The fragment lengths produced in the digestion reactions can be used to determine the species of fish from which the DNA sample was prepared, using the RFLP pattern matching software containing a database of experimentally- derived RFLP patterns from commercially relevant fish species.
Broadband continuous mode power amplifier with on‐board harmonic injection (2019)

This study presents the design of a broadband continuous mode power amplifier (PA) with an active harmonic injection (HI). Since the injected harmonic signal is generated on‐board using a frequency doubler, this design has a single radio frequency input. The generated second harmonic is injected at the drain terminal of a gallium nitride high‐electron‐mobility transistor used in designing continuous class B/J PA. A design space in terms of amplitude and phase of the injected harmonic signal is analysed to obtain the loads that operate the PA in the continuous class B/J mode at the current generator reference plane. The proposed design strategy is verified by designing a prototype with a frequency doubler and a PA using 10 and 15 W gallium nitride high‐electron‐mobility transistors, respectively. The measured drain efficiency of 60.04–70.96% and output power of 40.17–42.6 dBm is obtained from 1 to 1.9 GHz. This corresponds to a broadband operation of 900 MHz with 62% fractional bandwidth. The designed HI–PA is also tested with a 20 MHz long‐term evolution signal whose corresponding adjacent channel power ratio is better than −47.76 dBc in the overall band after applying digital predistortion.