gebhart/patrepeval huggingface dataset:
Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors (2018)

Innate behaviors are genetically encoded, but their underlying molecular mechanisms remain largely unknown. Predator odor 2,4,5-trimethyl-3-thiazoline (TMT) and its potent analog 2-methyl-2-thiazoline (2MT) are believed to activate specific odorant receptors to elicit innate fear/defensive behaviors in naive mice. Here, we conduct a large-scale recessive genetics screen of ethylnitrosourea (ENU)-mutagenized mice. We find that loss of Trpa1, a pungency/irritancy receptor, diminishes TMT/2MT and snake skin-evoked innate fear/defensive responses. Accordingly, Trpa1 <sup>-/-</sup> mice fail to effectively activate known fear/stress brain centers upon 2MT exposure, despite their apparent ability to smell and learn to fear 2MT. Moreover, Trpa1 acts as a chemosensor for 2MT/TMT and Trpa1-expressing trigeminal ganglion neurons contribute critically to 2MT-evoked freezing. Our results indicate that Trpa1-mediated nociception plays a crucial role in predator odor-evoked innate fear/defensive behaviors. The work establishes the first forward genetics screen to uncover the molecular mechanism of innate fear, a basic emotion and evolutionarily conserved survival mechanism.
Rapid liquid-liquid extraction of thallium(III) from succinate media with 2-octylaminopyridine in chloroform as the extractant (2008)

A simple solvent extraction study of thallium(III) was conducted. Selective and quantitative extraction of thallium(III) by 2-octylaminopyridine (2-OAP) in chloroform occurred from aqueous sodium succinate medium (0.0075 M) at pH 3.0. Thallium(III) was back extracted with acetate buffer (pH 4.63). The effect of the concentration of succinate and 2-OAP, the role of various diluents, stripping agents, loading capacity of 2-OAP, equilibrium time and aqueous:organic volume ratio on the extraction of thallium(III) was studied. The stoichiometry of the extracted species was determined based on the slope analysis method and found to be 1: 2: 1 (metal:acid:extractant). The temperature dependence of the extraction equilibrium constant was also examined to estimate the apparent thermodynamic functions ?H, ?G and ?S for the extraction reaction. The method is free from interference of a large number of cations and anions. The method was used for the selective extraction of thallium(III) from its binary mixture with Zn(II), Cd(II), Hg(II), Bi(III), Pb(II), Se(IV), Te(IV), Sb(III), Ga(III), In(III), Al(III), Tl(I) and Fe(III). The proposed method was applied to the synthetic mixtures and alloys. It is simple, selective, rapid and eco-friendly.
Evaluation of the Performances of Two Wearable Systems for Gait Analysis: A Pilot Study (2016)

Wearable sensor systems to perform human motion analysis are receiving increasing attention in different application fields. Among wearable sensors, inertial sensors have promising features. However, before they can be employed routinely in clinical applications, it is important to evaluate their reliability. Gait analysis was performed on one male volunteer: data were simultaneously collected with HGait System, based on magnetic and inertial measurement sensor units system, and with STEP32, a commercial electromechanical system already used in clinics. Spatio temporal parameters and joint kinematics in the sagittal plane obtained with H-Gait and STEP32 are compared. The MIMUs system provides a reliable estimation of spatiotemporal parameters, and acceptable hip and knee kinematic curves, while ankle joint measurements must be improved to be clinically useful.
Supplementary Figure 5 from αvβ6 Integrin Promotes Castrate-Resistant Prostate Cancer through JNK1-Mediated Activation of Androgen Receptor (2023)

&lt;p&gt;alphavbeta6 enhances AR transcriptional activity in LNCaP cells.&lt;/p&gt;
Carbocyclic Amino Ketones by Bredt's Rule‐Arrested Kulinkovich–de Meijere Reaction (2016)

Abstract The Ti II ‐mediated formation of cyclopropylamines from alkenes and amides, the Kulinkovich–de Meijere reaction, involves two carbon–carbon bond‐forming steps. Strategic use of a tricyclic intermediate can arrest the process if the second step requires formation of a bridgehead double bond. Use of this Bredt's rule constraint results in the production of carbocyclic amino ketones, key alkaloid building blocks.
Multilevel fast physical optics algorithm for radiation from non-planar apertures (2005)

A novel multilevel algorithm for computing the radiation patterns of nonplanar aperture antennas over a range of observation angles is presented. The proposed technique is directly applicable to reflector and lens antennas as well as to radomes. The multilevel computational sequence is based on a hierarchical decomposition of the radiating aperture and comprises two main steps. First, computation of the radiation patterns of all subapertures of the finest level over a very coarse angular grid. Second, multilevel aggregation of the radiation patterns of neighboring subapertures into the final pattern of the whole aperture via a phase compensated interpolation. The multilevel algorithm attains computational complexity comparable to that of the fast Fourier transform based techniques while avoiding their limitations.
Rapid assessment of plasma damage effects (1998)

This paper reports the use of a mercury probe with a highly repeatable contact area to monitor the effects of plasma damage on a gate oxide resulting from a PECVD process. The advantage of the mercury probe is that no processing is required to form the gate, allowing measurements to be made on plain oxidized wafers immediately before and after plasma exposure. The Hg probe provides a sensitive and rapid method for monitoring plasma damage without the need for antenna structures.
Plutonium purification cycle in centrifugal extractors: comparative study of flowsheets using uranous nitrate and hydroxylamine nitrate (1998)

The extension of the UP2 plant at La Hague includes a new plutonium purification cycle using multi-stage centrifugal extractors, to replace the present cycle which uses mixer/settler banks. The advantage of this type of extractor is basically the compactness of the equipment and the short residence time, which limits solvent degradation, particularly when reprocessing fuel containing a high proportion of plutonium 238. Two types of reducing agents have been considered for the plutonium stripping operation, uranous nitrate and hydroxylamine nitrate. Uranous nitrate displays a very fast reduction kinetics, ideal for the very short residence time of the phases in the centrifugal extractors. However, its extractability in the organic phase exacerbates the undesirable re-oxidation of plutonium, which is present in high concentration in this stage of the process. The short residence time of the centrifugal extractors is an advantage in as much as it could conceivably be adequate to obtain a sufficient reduction efficiency, while minimizing undesirable re-oxidation mechanisms. Hydroxylamine nitrate helps to minimize undesirable re-oxidation and is the normal choice for this type of operation. However, the plutonium (IV) reduction kinetics obtained is slower than with uranous nitrate, making it necessary to check whether its use is compatible with the very short residence times of centrifugal extractors.This article discusses the feasibility studies employing these two reducing agents. (author)
"Preference space" for parameters of two-channel speech compression (2003)

Speech processed with amplitude compression can maintain high levels of intelligibility over a wide range of compression parameter values. The perceived quality of the speech, however, varies widely over this parameter range, especially in the presence of low-level background noise. The present work provides data showing that both normal-hearing listeners and listeners with impairments prefer low compression ratios and long time constants in two-channel compression processing. In addition, we describe a quantitative model linking the release time and compression ratio of the two-channel compression system to the preference judgments of normal-hearing and hearing impaired listeners.
Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients (2021)

Multiple studies have identified an association between neutrophils and COVID-19 disease severity; however, the mechanistic basis of this association remains incompletely understood. Here we collected 781 longitudinal blood samples from 306 hospitalized COVID-19 <sup>+</sup> patients, 78 COVID-19 <sup>âˆ'</sup> acute respiratory distress syndrome patients, and 8 healthy controls, and performed bulk RNA-sequencing of enriched neutrophils, plasma proteomics, cfDNA measurements and high throughput antibody profiling assays to investigate the relationship between neutrophil states and disease severity or death. We identified dynamic switches between six distinct neutrophil subtypes using non-negative matrix factorization (NMF) clustering. At days 3 and 7 post-hospitalization, patients with severe disease had an enrichment of a granulocytic myeloid derived suppressor cell-like state gene expression signature, while non-severe patients with resolved disease were enriched for a progenitor-like immature neutrophil state signature. Severe disease was associated with gene sets related to neutrophil degranulation, neutrophil extracellular trap (NET) signatures, distinct metabolic signatures, and enhanced neutrophil activation and generation of reactive oxygen species (ROS). We found that the majority of patients had a transient interferon-stimulated gene signature upon presentation to the emergency department (ED) defined here as Day 0, regardless of disease severity, which persisted only in patients who subsequently died. Humoral responses were identified as potential drivers of neutrophil effector functions, as enhanced antibody-dependent neutrophil phagocytosis and reduced NETosis was associated with elevated SARS-CoV-2-specific IgG1-to-IgA1 ratios in plasma of severe patients who survived. <i>In vitro</i> experiments confirmed that while patient-derived IgG antibodies mostly drove neutrophil phagocytosis and ROS production in healthy donor neutrophils, patient-derived IgA antibodies induced a predominant NETosis response. Overall, our study demonstrates neutrophil dysregulation in severe COVID-19 and a potential role for IgA-dominant responses in driving neutrophil effector functions in severe disease and mortality.
Three-dimensional ion transport networks and current collectors for electrochemical cells (2023)

Provided herein are three-dimensional ion transport networks and current collectors for electrodes of electrochemical cells. Exemplary electrodes include interconnected layers and channels including an electrolyte to facilitate ion transport. Exemplary electrodes also include three dimensional current collectors, such as current collectors having electronically conducting rods, electronically conducting layers or a combination thereof.
Supplementary Table 1 from Oncogenic ERG Represses PI3K Signaling through Downregulation of IRS2 (2023)

&lt;p&gt;List of most significantly differentially expressed genes following ERG knock-out.&lt;/p&gt;
The pan-BCL-2-blocker obatoclax (GX15-070) and the PI3-kinase/mTOR-inhibitor BEZ235 produce cooperative growth-inhibitory effects in ALL cells (2017)

Acute lymphoblastic leukemia (ALL) is characterized by leukemic expansion of lymphoid blasts in hematopoietic tissues. Despite improved therapy only a subset of patients can be cured. Therefore, current research is focusing on new drug-targets. Members of the BCL-2 family and components of the PI3-kinase/mTOR pathway are critically involved in the regulation of growth and survival of ALL cells. We examined the effects of the pan-BCL-2 blocker obatoclax and the PI3-kinase/mTOR-inhibitor BEZ235 on growth and survival of ALL cells. In <sup>3</sup>H-thymidine uptake experiments, both drugs suppressed the <i>in vitro</i> proliferation of leukemic cells in all patients with Philadelphia chromosome-positive (Ph<sup>+</sup>) ALL and Ph<sup>-</sup> ALL (obatoclax IC<sub>50</sub>: 0.01-5 μM; BEZ235, IC<sub>50</sub>: 0.01-1 μM). Both drugs were also found to produce growth-inhibitory effects in all Ph<sup>+</sup> and all Ph<sup>-</sup> cell lines tested. Moreover, obatoclax and BEZ235 induced apoptosis in ALL cells. In drug-combination experiments, obatoclax and BEZ235 exerted synergistic growth-inhibitory effects on ALL cells. Finally, we confirmed that ALL cells, including CD34<sup>+</sup>/CD38<sup>-</sup> stem cells and all cell lines express transcripts for PI3-kinase, mTOR, BCL-2, MCL-1, and BCL-xL. Taken together, this data shows that combined targeting of the PI3-kinase/mTOR-pathway and BCL-2 family-members is a potent approach to counteract growth and survival of ALL cells.
Two-Photon Optical Biopsy Of Thick Tissues (1998)

Get PDF Email Share Share with Facebook Share on X Post on reddit Share with LinkedIn Add to Mendeley Add to BibSonomy Share with WeChat Get Citation Copy Citation Text P. T. C. So, B. R. Masters, E. Gratton, and I. E. Kochevar, "Two-Photon Optical Biopsy Of Thick Tissues," in Advances in Optical Imaging and Photon Migration, J. Fujimoto and M. Patterson, eds., Vol. 21 of OSA Trends in Optics and Photonics (Optica Publishing Group, 1998), paper JMA3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Application of GaAs pHEMT technology for efficient high-frequency switching regulators (2010)

The potential of GaAs pHEMT technology for low-voltage high-frequency power switching applications is discussed with a view towards their application for power supplies in portable electronic systems. The design and implementation of a 4.5V-to-3.3V buck converter power IC utilizing an enhancement mode pHEMT high side switch is demonstrated. The fabricated buck circuit is capable of operating at switching frequencies ranging from 100-MHz. While operating from a 4.5V supply a power efficiency of 87% is obtained at 100MHz when the output voltage is 3.3V and current is 500mA.
Rational synthesis and structure of a borosilicate zeolite with intersecting 10- and 11-ring channels (2013)

Rational synthesis and structure of a borosilicate zeolite with intersecting 10- and 11-ring channels
Use of Gammarus fossarum (Amphipoda) embryo for toxicity testing: A case study with cadmium (2017)

The effects of environmental contaminants on arthropod embryo stages have been poorly investigated in ecotoxicology. Moreover, many of these tests used hatching success as the sole metric, although it is possible to detect many more subtle effects. After a detailed description of embryogenesis in Gammarus fossarum, the present study reports on the sublethal effects of cadmium (Cd) exposure during embryonic development in G. fossarum. Embryos were first directly exposed in multiwell plates throughout the entire embryonic cycle (23 d) to increasing Cd concentrations (0, 1.5, and 3.0 μg/L; 120 embryos/concentration). Then, to assess the representativeness of the gammarid embryo assay performed in multiwell plates, embryos were exposed to similar Cd concentrations through the maternal open brood pouch. Next, to pinpoint sensitive periods of development, embryos were directly exposed to 3.0 μg/L of Cd for shorter periods of time: during gastrulation, organogenesis, and hatching. After hatching, the following parameters were measured in the newborn individuals: 1) body mass; 2) activity of the enzyme phenoloxidase, a key enzyme of the arthropod immune system; and 3) locomotor activity. Phenoloxidase activity was strongly inhibited in newborn individuals of embryos exposed (either in multiwell plates or in the maternal brood pouch) to 3.0 μg/L Cd throughout embryonic development. Furthermore, strong detrimental locomotor effects were observed in newborn individuals of embryos directly exposed to 3.0 μg/L. Exposures for shorter periods of time were not sufficient to induce such effects; no sensitive period could be determined. By bringing new insights into a critical time window of exposure, the gammarid embryo assay could provide a novel and interesting addition to existing bioassays in gammarids. Environ Toxicol Chem 2017;36:2436-2443. © 2017 SETAC.
Regioselective Cleavage of O‐Benzyl‐N‐arylamidoximes: Synthesis of N‐Aryl Amidines and Amidoximes. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Additional Information for E-Area Vault Performance Assessment, Appendix I `Suspect Soil Performance` - Results of Modeling the Effects of Organic Matter on the Mobility of Radionuclides as it Relates to the Disposal of Wood Products in E-Area Slit Trenches (1996)

Numerous laboratory and field studies have shown that the chemical form (i.e., speciation) of many metals and radionuclides is affected by the presence of naturally occurring organic matter (OM) and its degradation products. The effects of OM (e.g., wood products) on the speciation and, therefore, the mobility of Am, Bk, Cf, Cm, Cs, Ni, NpO{sub 2}, Rb, Sr. UO{sub 2}, and Zr were estimated through use of geochemical and groundwater flow modeling. Due to the complex mixture nature of naturally occurring OM, the OM system was simplified through use of surrogate compounds (citric acid and ethylenedinitrilotetraacetic acid (EDTA)) to estimate effects of OM on radionuclide mobility. Using this approach, OM was found to have no effect on the inventory limits for Cs, NpO{sub 2}, Rb and Zr. The inventory limits for the isotopes of Am, Bk, Cf, Cm, Ni, Pd, PuO{sub 2}, Sr, and UO{sub 2} calculated in the presence of OM decreased over a range of 26 percent for U-233 to 48 percent for Pu-240. The information in this report will be included in the next revision of the E-Area Vaults Performance Assessment.
Growth Assessment of Bifidobacterium on Glucansucrase-Derived Oligosaccharides (2020)

Prebiotics are dietary supplements used to selectively stimulate the growth of beneficial intestinal bacteria such as Bifidobacterium in humans and animals. Maintenance of beneficial intestinal bacteria may provide ecological-based, health-promoting factors such as disease suppression and improved metabolism. A promising source of potential prebiotic supplements is through enzymatic synthesis of oligosaccharides using microbial glucansucrase enzymes. Glucansucrases can be used to prepare a seemingly endless variety of potential prebiotic oligosaccharides containing various linkage structures and monosaccharide components. In this study, six oligosaccharide products synthesized by bacterial glucansucrase were assessed for ability to support bacterial growth (growth rate, &micro; h-1) and biomass (cell dry weight, mg ml-1) formation using two Bifidobacterium species commonly associated with the gastrointestinal tract of animals. Each growth assessment was performed in triplicate and reported as the mean. Overall, oligosaccharide products Sucromalt (Cargill, Inc) and isomelezitose supported the highest growth rates for B. adolescentis (0.60, 0.69 &micro; h-1) and B. pseudocatenulatum (0.66, 0.52 &micro; h-1) when compared to glucose (0.51, 0.37 &micro; h-1). The raffinose-derived and gentiobiose-derived oligosaccharide products supported the lowest growth rates for the listed species. In addition to growth rate, isomelezitose also supported the highest biomass formation for both Bifidobacterium species (497, 464 mg ml-1) when compared to glucose and the other oligosaccharides. The raffinose-derived product, however, supported the second highest biomass formation for both species (404, 416 mg ml-1) even though the growth rates were lowest indicating a slow but steady metabolism of this supplement by Bifidobacterium. In summary, the Sucromalt, isomelezitose, and raffinose products supported significant growth of intestinal Bifidobacterium and are good candidates for further studies of their prebiotic potential.
Disrupting proteasomal and autophagic degradation systems of misfolded alpha-sarcoglycan protein by bortezomib and givinostat combination (2021)

Background and Purpose: Limb-girdle muscular dystrophy type R3 (LGMD R3) is a rare genetic disorder characterized by a progressive proximal muscle weakness and caused by mutations in the SGCA gene encoding alpha-sarcoglycan (α-SG). Here, we report the results of a mechanistic screening ascertaining the molecular mechanisms involved in the degradation of the most prevalent misfolded R77C-α-SG protein. Experimental Approach: We performed a combinatorial study to identify drugs potentializing the effect of a low dose of the proteasome inhibitor bortezomib on the R77C-α-SG degradation inhibition. Key Results: Analysis of the screening associated to artificial intelligence-based predictive ADMET characterization of the hits led to identification of the HDAC inhibitor givinostat as potential therapeutical candidate. Functional characterization revealed that givinostat effect was related to autophagic pathway inhibition, unveiling new theories concerning degradation pathways of misfolded SG proteins. Conclusion and Implications: Beyond the identification of a new therapeutic option for LGMD R3 patients, our results shed light on the potential repurposing of givinostat for the treatment of other genetic diseases sharing similar protein degradation defects such as LGMD R5 and cystic fibrosis.
Heat transfer and fluid flow during keyhole mode laser welding of tantalum, Ti–6Al–4V, 304L stainless steel and vanadium (2007)

Because of the complexity of several simultaneous physical processes, most heat transfer models of keyhole mode laser welding require some simplifications to make the calculations tractable. The simplifications often limit the applicability of each model to the specific materials systems for which the model is developed. In this work, a rigorous, yet computationally efficient, keyhole model is developed and tested on tantalum, Ti–6Al–4V, 304L stainless steel and vanadium. Unlike previous models, this one combines an existing model to calculate keyhole shape and size with numerical fluid flow and heat transfer calculations in the weld pool. The calculations of the keyhole profile involved a point-by-point heat balance at the keyhole walls considering multiple reflections of the laser beam in the vapour cavity. The equations of conservation of mass, momentum and energy are then solved in three dimensions assuming that the temperatures at the keyhole wall reach the boiling point of the different metals or alloys. A turbulence model based on Prandtl's mixing length hypothesis was used to estimate the effective viscosity and thermal conductivity in the liquid region. The calculated weld cross-sections agreed well with the experimental results for each metal and alloy system examined here. In each case, the weld pool geometry was affected by the thermal diffusivity, absorption coefficient, and the melting and boiling points, among the various physical properties of the alloy. The model was also used to better understand solidification phenomena and calculate the solidification parameters at the trailing edge of the weld pool. These calculations indicate that the solidification structure became less dendritic and coarser with decreasing weld velocities over the range of speeds investigated in this study. Overall, the keyhole weld model provides satisfactory simulations of the weld geometries and solidification sub-structures for diverse engineering metals and alloys.
Fig S1 from <i>Frizzled-7</i> Is Required for Wnt Signaling in Gastric Tumors with and Without <i>Apc</i> Mutations (2023)

&lt;p&gt;Figure S1 shows the relative expression of Fzd receptors in gastric cancer cells.&lt;/p&gt;