gebhart/patrepeval huggingface dataset:
Feature Visualization for 3D Point Cloud Autoencoders (2020)

In order to reduce the dimensionality of 3D point cloud representations, autoencoder architectures generate increasingly abstract, compressed features of the input data. Visualizing these features is central to understanding the learning process, however, while successful visualization techniques exist for neural networks applied to computer vision tasks, similar methods for geometric, especially non-Euclidean, input data are currently lacking. Hence, we propose a first-of-kind method to project the features learned by point cloud autoencoders into a 3D-space augmented with color maps. Our proposal explores the properties of 1D-convolutions, used in state-of-the art point cloud autoencoder architectures to handle the input data, which leads to an intuitive interpretation of the visualized features. Furthermore, we tackle the search for relevant co-activations in the feature space by clustering the input data in the latent space, where we explore the correspondence between network features and geometric characteristics of typical shapes of the clusters. We tested our approach with experiments on a benchmark data set, and with three different configurations of a point cloud autoencoder, where we show that the features learned by the autoencoder correlate with the occupancy of the input space by the training data.
Antioxidants stimulate meiosis resumption, but inhibit mitogen-activated protein kinase phosphorylation and further cell cycle progression in porcine oocytes (2001)

In the present study the effects of two cell-permeant antioxidants, 2(3)-tert-butyl-4-hydroxyanisole (BHA) and nordihydroguaiaretic acid (NDGA), on porcine oocyte meiosis resumption, chromatin behaviour and spindle assembly were investigated. The antioxidants BHA and NDGA stimulated meiosis resumption in a dose-dependent manner in both cumulus-enclosed and denuded porcine oocytes. After in vitro culture for 8 h, few oocytes underwent germinal vesicle breakdown (GVBD) in control groups, whereas GVBD occurred in high percentages of oocytes treated with BHA or NDGA at concentrations that inhibit GVBD in rodent oocytes, although mitogen-activated protein (MAP) kinase was not phosphorylated as revealed by Western immunoblots. Orcein staining and fluorescein isothiocyanate-anti-alpha-tubulin labelling showed that chromosome and spindle formation, respectively, and further meiosis progression were inhibited 20 and 25 h after culture. Instead, chromatin was highly condensed or existed in scattered condensed clusters. Correspondingly, MAP kinase phosphorylation was inhibited by both BHA and NDGA in a dose-dependent manner. The inhibitory effects of BHA on meiosis completion and MAP kinase phosphorylation was reversible. These results suggest that, unlike in rodent oocytes, antioxidants stimulate GVBD in the absence of MAP kinase activation, but inhibit MAP kinase phosphorylation, meiotic apparatus formation and thus the further progression of the meiosis of porcine oocytes.
Characterization of Mechanical Performance of Composites Fabricated Using Innovative Carbon Fiber Wet Laid Process (2020)

Recent innovation in production of optimized nonwoven wet laid (WL) carbon fiber (CF) mats raised the question of optimal translation of the performance and isotropy into composites formed through these dry preforms. This work explores the mechanical behavior of composites produced from WL-CF mats in conjunction with the microstructure predicted through Object Oriented Finite Element Analysis (OOF). The mats used for the composites were prepared in two dispersion regimes using 25.4 mm long CF. The mixing regimes discussed in the author’s previous work, are identified as Method 1 for the traditional processing regime and Method 2 for the innovative regime that provided optimal nonwoven WL-CF mats. Composite panels from Method 2 mats showed a normalized tensile strength increase of 52% over those from Method 1 panels. Reproducibility analysis of composites made from Method 2 mats demonstrated a standard deviation of 2% in fiber weight content, 2% in tensile modulus and 9% in tensile strength, while composites made from Method 1 mats demonstrated a standard deviation of 5% in fiber weight content, 5% in tensile modulus and 17% in tensile strength. Systematic study of the microstructure and its analysis through OOF confirmed the isotropy translation of mats produced through method 2 to the composites. This study validated the hypothesis that optimal nonwoven mats lead to a well-balanced composite with optimal performance and that non-optimal nonwoven mats do not pack into a well-balanced composite.
Developing a model for estimating the activity of colonic microbes after intestinal surgeries (2021)

The mathematical model developed here provides an important framework for describing the effect of clinical interventions on the colon's microorganisms.
ChemInform Abstract: GENERATION OF (η5‐CYCLOPENTADIENYL)DICARBONYLIRON CARBENE COMPLEXES VIA PROTONATION OF THE CORRESPONDING ALKENYL COMPLEXES (1983)

Abstract Die Alkenyl‐Fe‐Komplexe (Ia) werden von Tetrafluoroborsäure unter intermediärerBildung der Alkyliden‐Komplexe (II) protoniert, deren Umsetzung mit den Alkenen (III) zu den Methylcyclopropan‐Derivaten (IV) führt.
P‐4: Electrical Characteristics of Dual‐Gate CAAC‐IGZO FET with Self‐Aligned Top Gate (2016)

We fabricated dual‐gate CAAC‐IGZO FETs with self‐aligned top gates and investigated their electrical characteristics. The drain current was larger than expectedfrom the GI capacitance ratio to single‐gate FETs. Device simulation results suggest that shallow trap states and increase in electron mobility by self‐heating of FETs can explain the large drain current.
Range resolved lidar for long distance ranging with sub-millimeter resolution (2010)

A lidar technique employing temporally stretched, frequency chirped pulses from a 20 MHz mode locked laser is presented. Sub-millimeter resolution at a target range of 10.1 km (in fiber) is observed. A pulse tagging scheme based on phase modulation is demonstrated for range resolved measurements. A carrier to noise ratio of 30 dB is observed at an unambiguous target distance of 30 meters in fiber.
Regulation of cADP-ribose-induced Ca2+ Release by Mg2+ and Inorganic Phosphate (1996)

cADP-ribose (cADPr) has recently been shown to release Ca2+ from an intracellular store of permeabilized T lymphocyte cell lines (Guse, A. H., da Silva, C. P., Emmrich, F., Ashamu, G. A., Potter, B. V. L., and Mayr, G. W. (1995) J. Immunol. 155, 3353-3359). Using permeabilized Jurkat and HPB. ALL T lymphocytes, the effects of varying concentrations of inorganic phosphate and Mg2+ on cADPr-induced Ca2+ release were investigated. cADPr-induced Ca2+ release was dependent on the concentration of inorganic phosphate, showing very low Ca2+ release activity between 0.5 and 2 mM inorganic phosphate. At 4 to 5 mM inorganic phosphate, the cADPr-induced Ca2+ release was much more pronounced, reaching maximal values at 10 mM inorganic phosphate. The underlying mechanism for this stimulatory effect was an increased loading of the cADPr-sensitive Ca2+ store, which was demonstrated by enhanced resequestration of Ca2+ selectively into the cADPr-sensitive Ca2+ store. The free Mg2+ concentration also influenced cADPr-induced Ca2+ release in permeabilized cells: at 0 and 8.58 mM the release was nearly completely abolished, whereas at 1.06 mM maximal Ca2+ release by cADPr was observed. High performance liquid chromatographic analysis of exogenously added cADPr revealed that the catabolism of cADPr at varying Mg2+ and Pi concentrations had only minor relevance for the modulatory effects observed. To correlate the effects of inorganic phosphate and Mg2+ on cADPr-induced Ca2+ release observed in the permeabilized cell preparations, measurements of these ions in intact Jurkat T lymphocytes were carried out. Intact Jurkat T cells stimulated via the T cell receptor middle dotCD3 complex did not respond with significant elevation of the free intracellular Mg2+ concentration. In contrast, stimulation via the T cell receptor middle dotCD3 complex resulted in an increase in the intracellular inorganic phosphate concentration. These data indicate a role for the intracellular inorganic phosphate concentration in the regulation of cADPr-mediated Ca2+ release in T lymphocytes.
Human TRIM71 and Its Nematode Homologue Are Targets of let-7 MicroRNA and Its Zebrafish Orthologue Is Essential for Development (2007)

Animal microRNAs (miRNAs) are short RNAs that function as posttranscriptional regulators of gene expression by binding to the target mRNAs. Noting that some miRNAs are highly conserved in evolution, we explored the possibility of evolutionary conservation of their targets. We identified human orthologues of experimentally verified let-7 miRNA target genes in Caenorhabditis elegans and used the luciferase reporter system to examine whether these human genes are still the targets of let-7 miRNA. We found that in some cases, the miRNA-target relationship has indeed been conserved in human. Interestingly, human TRIM71, an orthologue of C. elegans let-7-target lin-41 gene, can be repressed by hsa-let-7a and hsa-let-7c. This repression was abolished when both predicted let-7 target sites of TRIM71 were mutated. Moreover, the zebrafish lin-41 orthologue was also repressed by let-7 to a similar degree as was TRIM71. When the expression of zebrafish lin-41 orthologue was silenced by microinjection of RNA interference or morpholino into zebrafish zygotes, retarded embryonic development was observed, providing direct evidence for an essential role of lin-41 in zebrafish development. Taken together, our results suggest that the regulation of TRIM71 expression by let-7 has been evolutionarily conserved and that TRIM71 likely plays an important role in development.
Vestibular-autonomic interactions: beyond orthostatic dizziness (2021)

The vestibular-autonomic reflexes affect various sympathetic and parasympathetic functions. Understanding these relationships will provide improved identification of underlying etiology and drive improved patient management.
Total Syntheses of Amphidinolides T1 and T4 via Catalytic, Stereoselective, Reductive Macrocyclizations (2005)

Described in this work are total syntheses of amphidinolides T1 and T4 using two nickel-catalyzed reductive coupling reactions of alkynes, with an epoxide in one case (intermolecular) and with an aldehyde in another (intramolecular). The latter was used to effect a macrocyclization, form a C-C bond, and install a stereogenic center with >10:1 selectivity in both natural product syntheses. Alternative approaches in which intermolecular alkyne-aldehyde reductive coupling reactions would serve to join key fragments were investigated and are also discussed; it was found that macrocyclization (i.e. intramolecular alkyne-aldehyde coupling) was superior in several respects (diastereoselectivity, yield, and length of syntheses). Alkyne-epoxide reductive couplings were instrumental in the construction of key fragments corresponding to approximately half of the molecule of both natural products. In one case (T4 series), the alkyne-epoxide coupling exhibited very high site selectivity in a coupling of a diyne. A model for the stereoselectivity observed in the macrocyclizations is also proposed.
Dimers of d - myo -Inositol 1,4,5-Trisphosphate:  Design, Synthesis, and Interaction with Ins(1,4,5)P 3 Receptors (2004)

The design and synthesis of dimeric versions of the intracellular signaling molecule d-myo-inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)] are reported. Ins(1,4,5)P(3) dimers in a range of sizes were constructed by conjugation of a partially protected 2-O-(2-aminoethyl)-Ins(1,4,5)P(3) intermediate with activated oligo- and poly(ethylene glycol) (PEG) tethers, to give benzyl-protected dimers with amide or carbamate linkages. After deprotection, the resulting water-soluble Ins(1,4,5)P(3) dimers were purified by ion-exchange chromatography. The interaction of the Ins(1,4,5)P(3) dimers with tetrameric Ins(1,4,5)P(3) receptors was explored, using equilibrium [(3)H]Ins(1,4,5)P(3)-binding to membranes from cerebellum, and (45)Ca(2+)-release from permeabilized hepatocytes. The results showed that dimers, even when they incorporate large PEG tethers, interact potently with Ins(1,4,5)P(3) receptors, and that the shorter dimers are more potent than Ins(1,4,5)P(3) itself. A very small dimer, consisting of two Ins(1,4,5)P(3) motifs joined by a short N,N'-diethylurea spacer, was synthesized. Preliminary studies of (45)Ca(2+) release from the intracellular stores of permeabilized hepatocytes showed this shortest dimer to be almost as potent as adenophostin A, the most potent Ins(1,4,5)P(3) receptor ligand known. Possible interpretations of this result are considered in relation to the recently disclosed X-ray crystal structure of the type 1 Ins(1,4,5)P(3) receptor core binding domain.
Comment on acp-2022-598 (2022)

Nitric Acid Trihydrate (NAT) crystal formation in the absence of water ice is important for a subset of Polar Stratospheric Clouds (PSCs) and thereby ozone depletion. It has been suggested that either fragmented meteoroids or meteoric smoke particles (MSPs), or possibly both, are important as heterogeneous nuclei of these crystals. Previous work has focused on the nucleating ability of meteoric material in nitric acid in the absence of sulfuric acid. However, it is known that when immersed in stratospheric sulfuric acid droplets, metal-containing meteoric material particles partially dissolve and components can re-precipitate as silica and alumina that have different morphologies to the original meteoric material. Hence, in this study we experimentally and theoretically explore the relative role that sulfuric acid-processed meteoric smoke and meteoric fragments may play in NAT nucleation in PSCs. We compared meteoric fragments that had been recently prepared (by milling a meteorite sample) to a sample annealed under conditions designed to simulate heating during entry into the Earth’s atmosphere. Whilst the addition of sulfuric acid decreased the nucleating ability of the recently milled meteoric material relative to nucleation in binary nitric acid-water solutions (at similar NAT saturation ratio), the annealed meteoric fragments nucleated NAT with a similar effectiveness in both solutions. However, combining our results with measured fluxes of meteoric material to the Earth, sedimentation modelling and recent experiments on fragmentation of incoming meteoroids, suggests that there are unlikely to be sufficient fragments to contribute to the nucleation of crystalline NAT particles. We then considered silica formed from sulfuric acid processed meteoric smoke particles. Our previous work showed that nano-particulate silica (radius ~6 nm) is a relatively poor promoter of nucleation compared with micron scaled silica particles, which were more effective. Both materials have similar chemical and structural (crystallographically amorphous) properties, indicating size is critical. Here we account for surface curvature of primary grains using Classical Nucleation Theory (CNT) to explore this size dependence. This model is able to explain the discrepancy in nucleation effectiveness of fumed silica and fused quartz, by treating their nucleating activity (contact angle) as equal but with differing particle size (or surface curvature), assuming interfacial energies that are physically reasonable. Here we use this CNT model to present evidence that nucleation of NAT on acid processed MSPs, where the primary grain size is 10s nm, is also effective enough to contribute to NAT crystals in early season PSCs where there is an absence of ice. This study demonstrates that modelling of crystal nucleation in PSCs and resulting ozone depletion relies on accurate understanding of the transport and chemical processing of MSPs. This will affect estimated sensitivity of stratospheric chemistry to rare events such as large volcanic eruptions and long-term forecasting of ozone recovery in a changing climate.
Etifoxine (Stresam®) for chemotherapy-induced pain? (2009)

Institute of Pharmacology and Toxicology, University of Zurich, and Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland. Tel.: +41 44 6355912; fax: +41 44 6355988. E-mail address:[email protected]
Correlated electron states and transport in triangular arrays (2005)

We study correlated electron states in frustrated geometry of a triangular lattice. The interplay of long-range interactions and finite residual entropy of a classical system gives rise to unusual effects in equilibrium ordering as well as in transport. A correlated fluid phase is identified in a wide range of densities and temperatures above freezing into commensurate solid phases. The charge dynamics in the correlated phase is described in terms of a height field, its fluctuations, and topological defects. We demonstrate that the height field fluctuations give rise to a ``free'' charge flow and finite dc conductivity. We show that freezing into the solid phase, controlled by the long-range interactions, manifests itself in singularities of transport properties.
Copeptin, IGFBP-1, and Cardiovascular Prognosis in Patients With Type 2 Diabetes and Acute Myocardial Infarction (2010)

Copeptin is an independent predictor of cardiovascular events and appears to at least partly explain the prognostic impact of IGFBP-1 in patients with type 2 diabetes and myocardial infarction. Copeptin may be a pathogenic factor to address to improve outcome in these patients.
An investigation of the noise figure and conversion efficiency of 0.98 mu m pumped erbium-doped fiber amplifiers under saturated conditions (1992)

The results of an investigation of the noise figure and conversion efficiency or erbium-doped fiber amplifiers for unsaturated, moderately saturated, and heavily saturated operation are reported. Quantum-limited 3 dB noise figures result only for small signal operation of low-gain amplifiers. For high gain, partially saturated amplifiers useful as in-line repeaters, bidirectional pumping results in the best combination of noise performance and conversion efficiency while co-propagation of signal and pump produces the best noise performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Highly Selective Fluorescent Probe for Thiol Bioimaging (2007)

A new fluorescent turn-on probe (3) for the selective sensing and bioimaging of thiols is reported. In aqueous buffer solutions at physiological pH, thiols cleave the 2,4-dinitrobenzenesulfonyl group to release the red-emissive donor-acceptor fluorophore (4). The probe displays excellent immunity to interference from nitrogen and oxygen nucleophiles and the imaging of thiols in living cells is demonstrated.
Influences of secretory activities in rat submandibular glands on tissue kallikrein circulating in the blood (1995)

Changes in serum levels of rat tissue kallikrein (rK1) in venous blood were measured, using a newly developed radioimmunoassay, before and after autonomic nerve stimulations of submandibular salivary secretion. rK1 secreted into saliva under these conditions was measured by radioimmunoassay and by enzymic activity assay, using the fluorogenic peptide substrate D-Val-Leu-Arg-7-amino-4-trifluoromethylcoumarin (AFC). Following an overnight fast, serum rK1 concentration was 30-40 ng ml-1. Unilateral electrical stimulation of the submandibular sympathetic nerve supply (at 50 Hz in bursts of 1 s every 10 s for 60 min) evoked a small flow of saliva with a very high rK1 concentration, resulting in a large output of rK1 of 2104.4 +/- 603.5 micrograms (n = 6). Such stimulation caused a large degranulation of granular duct cells and a corresponding reduction in glandular rK1 content. Unilateral electrical stimulation of the parasympathetic nerve supply (at 5 Hz continuously for 60 min) evoked a copious flow of saliva with a very low rK1 concentration, resulting in a low output of rK1 (18.1 +/- 4.9 micrograms; n = 6). Despite these large differences in salivary outputs of rK1, serum concentrations of rK1 were increased similarly following either sympathetic or parasympathetic stimulation by 48 and 46%, respectively. If the submandibular duct was briefly obstructed during sympathetic stimulation, inducing leakage and glandular oedema, then serum rK1 increased greatly (40-fold); a similar increase to that seen by others in previous studies without deliberate obstruction. Four days after bilateral submandibular-sublingual sialadenectomy serum rK1 concentration was reduced by approximately 50%. The results indicate that submandibular glands normally contribute to circulating levels of rK1 in rats, but this contribution is independent of the amounts of rK1 secreted into saliva by sympathetically induced exocytosis, and is likely to arise from basal vesicular transport. However, if glandular leakage occurs during sympathetic stimulation of submandibular secretion this then causes increases in the circulating levels of rK1 that correlate with the large amounts being secreted into saliva.
Harnessing virtual screening for the targeted discovery of cisplatin adjuvants from marine invertebrates (2012)

Cisplatin is a widely used chemotherapeutic agent that acts by damaging DNA, ultimately leading to apoptosis. However, studies with patient tissues have shown positive correlation between overexpression of the DNA repair enzyme ERCC1 and resistance to cisplatin. In this study, we have used virtual screening (VS) of 3D libraries derived from MarinLit targeting a protein binding pocket critical for recruitment of ERCC1. VS results were used in the chemotaxonomic selection of “prioritized” organisms as a pre-filter to in vitro HTS of marine natural products disrupting this protein-protein interaction. This methodology has provided a validation of the predictive value of the VS, a six-fold reduction of screening burden and a near two-fold increase in validated hit rate relative to “non-prioritized” organisms. We have also identified several potential leads from known compounds to discover disruptors of this DNA repair mediated resistance in cancer.
Welding Mechanism and Failure of Ultrasonic Welds (2017)

Ultrasonic metal welding has been used widely to join battery cell terminals, or tabs (either Al or Cu), with bus bars (Cu) to form assembled battery packs in battery electric vehicles. However, the mechanism of ultrasonic welding for Al/Cu is still not well understood. In this chapter, the microstructures of the ultrasonic welds between three layers of lithium-ion battery tabs (either Al or Cu) and bus bars were studied. From the microstructure analysis, the weld formation mechanism and failure modes were investigated. It was found that the metal inter-mix or interlocking is the main weld formation mechanism among Al tabs, while metallic bonding is the main mechanism for Cu-Cu or Al-Cu joining. Metallographs also indicated that the weld failure is a combination of the interfacial debonding between the innermost tab (either Cu or Al) and the Cu bus bar and the through-thickness fracture of the tabs. This chapter provides better understanding of weld formation and failure, and hence provides insight into ultrasonic welding process toward weld quality improvement. This understanding and insight can be used to develop science-based design guidelines toward selecting the most appropriate materials (including heat treatment and coating), and welding configurations (such as layers of tabs), and welding process parameters.
Response to “Comment on ‘The transition from a TEM-like mode to a plasmonic mode in parallel-plate waveguides’” [Appl. Phys. Lett. 102, 246103 (2013)] (2013)

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