gebhart/patrepeval huggingface dataset:
Recent progress in photonic crystals and their applications (2013)

I will report on the recent progresses in 2D and 3D photonic crystals, including 2D high-Q nanocavities-based new phenomena, novel lasers including ultra-compact Si Raman lasers, thermal emission control, and on-demand 3D optical guiding, etc.
A homozygous missense variant in type I keratin <i>KRT25</i> causes autosomal recessive woolly hair (2015)

Our findings implicate a novel gene involved in human hair abnormality, and are consistent with the curled, fragile hair found in mice with Krt25 mutations, and further support the role of IRS-specific type I keratins in hair follicle development and maintenance of hair texture.
Efficient schemes for adaptive optics in high-resolution microscopy (2011)

Specimen-induced aberrations frequently affect image quality in high-resolution microscopes. We develop efficient adaptive optical schemes to correct aberrations in confocal, multiphoton and harmonic generation microscopes. Image resolution and contrast is improved with minimal specimen exposure.
Swiss Cheeses and Their Applications (2014)

Swiss cheese sets have been used in the literature as useful examples in the study of rational approximation and uniform algebras. In this paper, we give a survey of Swiss cheese constructions and related results. We describe some notable examples of Swiss cheese sets in the literature. We explain the various abstract notions of Swiss cheeses, and how they can be manipulated to obtain desirable properties. In particular, we discuss the Feinstein-Heath classicalisation theorem and related results. We conclude with the construction of a new counterexample to a conjecture of S. E. Morris, using a classical Swiss cheese set.
Impaired Cellular Bioenergetics Causes Mitochondrial Calcium Handling Defects in MT-ND5 Mutant Cybrids (2016)

Mutations in mitochondrial DNA (mtDNA) can cause mitochondrial disease, a group of metabolic disorders that affect both children and adults. Interestingly, individual mtDNA mutations can cause very different clinical symptoms, however the factors that determine these phenotypes remain obscure. Defects in mitochondrial oxidative phosphorylation can disrupt cell signaling pathways, which may shape these disease phenotypes. In particular, mitochondria participate closely in cellular calcium signaling, with profound impact on cell function. Here, we examined the effects of a homoplasmic m.13565C>T mutation in MT-ND5 on cellular calcium handling using transmitochondrial cybrids (ND5 mutant cybrids). We found that the oxidation of NADH and mitochondrial membrane potential (Δψm) were significantly reduced in ND5 mutant cybrids. These metabolic defects were associated with a significant decrease in calcium uptake by ND5 mutant mitochondria in response to a calcium transient. Inhibition of glycolysis with 2-deoxy-D-glucose did not affect cytosolic calcium levels in control cybrids, but caused an increase in cytosolic calcium in ND5 mutant cybrids. This suggests that glycolytically-generated ATP is required not only to maintain Δψm in ND5 mutant mitochondria but is also critical for regulating cellular calcium homeostasis. We conclude that the m.13565C>T mutation in MT-ND5 causes defects in both mitochondrial oxidative metabolism and mitochondrial calcium sequestration. This disruption of mitochondrial calcium handling, which leads to defects in cellular calcium homeostasis, may be an important contributor to mitochondrial disease pathogenesis.
On the accuracy of the binomial approximation to the distance distribution of codes (1995)

The binomial distribution is a well-known approximation to the distance spectra of many classes of codes. We derive a lower estimate for the deviation from the binomial approximation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Endogenous zinc nanoparticles in the rat olfactory epithelium are functionally significant (2020)

The role of zinc in neurobiology is rapidly expanding. Zinc is especially essential in olfactory neurobiology. Naturally occurring zinc nanoparticles were detected in olfactory and nasal respiratory epithelia and cilia in animals. The addition of these nanoparticles to a mixture of odorants, including ethyl butyrate, eugenol, and carvone, considerably increased the electrical responses of the olfactory sensory receptors. Studies of these nanoparticles by ransmission electron microscopy (TEM) and selected area electron diffraction revealed metal elemental crystalline zinc nanoparticles 2-4 nm in diameter. These particles did not contain oxidized zinc. The enhancement of the odorant responses induced by the endogenous zinc nanoparticles appears to be similar to the amplification produced by engineered zinc nanoparticles. Zinc nanoparticles produce no odor response but increase odor response if mixed with an odorant. These effects are dose-dependent and reversible. Some other metal nanoparticles, such as copper, silver, gold, and platinum, do not have the effects observed in the case of zinc nanoparticles. The olfactory enhancement was observed in young and mature mouse olfactory epithelium cultures, in the dissected olfactory epithelium of rodents, and in live conscious dogs. The physiological significance of the detected endogenous metal nanoparticles in an animal tissue has been demonstrated for the first time. Overall, our results may advance the understanding of the initial events in olfaction.
C-peptide induced transcription factor ZEB DNA binding and Na,K-ATPase α&lt;sub&gt;1&lt;/sub&gt;-subunit mRNA expression. (2015)

&lt;p&gt;&lt;b&gt;A.&lt;/b&gt; Exposure to 1 nM of C-peptide increased DNA binding activity of ZEB detected by EMSA. &lt;b&gt;B.&lt;/b&gt; The electrophoretic mobility supershift assay with specific antibodies against ZEB. A–B. Experiments were performed at least 5 times and representative images are shown. &lt;b&gt;C.&lt;/b&gt; mRNA expression of Na,K-ATPase α&lt;sub&gt;1&lt;/sub&gt;-subunit. Results are means ± SE for 6 independent experiments. * P&lt;0.05 versus 5 mM glucose without C-peptide.&lt;/p&gt;
Sensor-Based River Monitoring System: A Case for Kikuletwa River Floods in Tanzania (2023)

Reliable and accurate flood prediction is a challenging task in poorly gauged basins due to data scarcity. Data is an essential component of any AI/ML model today, and the performance of such models hugely depends on the availability of sufficient amount of trusted, representative data. However, unlike a few well-studied rivers, most of the rivers in developing countries are still insufficiently monitored, which significantly hinges the design and development of advanced flood prediction models and early warning systems. This paper presents a multi-modal, sensor-based and near-real time river monitoring system to produce a multi-feature data set for the Kikuletwa river in Northern Tanzania, an area that heavily suffers from frequent floods. Our deployed system, which gather information about river depth levels and weather at several locations, aims at widening the ground truth of the river characteristics and eventually improve the accuracy of flood predictions. We provide details on the monitoring system used to gather the data as well as report on the methodology and the nature of the data. Finally, we present the relevance of the data set in the context of flood prediction, discussing the most suitable AI/ML-based forecasting approaches, while also highlighting some applications of the data set beyond flood warning systems.
Osteoinduction by Foamed and 3D-Printed Calcium Phosphate Scaffolds: Effect of Nanostructure and Pore Architecture (2017)

Some biomaterials are osteoinductive, that is, they are able to trigger the osteogenic process by inducing the differentiation of mesenchymal stem cells to the osteogenic lineage. Although the underlying mechanism is still unclear, microporosity and specific surface area (SSA) have been identified as critical factors in material-associated osteoinduction. However, only sintered ceramics, which have a limited range of porosities and SSA, have been analyzed so far. In this work, we were able to extend these ranges to the nanoscale, through the foaming and 3D-printing of biomimetic calcium phosphates, thereby obtaining scaffolds with controlled micro- and nanoporosity and with tailored macropore architectures. Calcium-deficient hydroxyapatite (CDHA) scaffolds were evaluated after 6 and 12 weeks in an ectopic-implantation canine model and compared with two sintered ceramics, biphasic calcium phosphate and β-tricalcium phosphate. Only foams with spherical, concave macropores and not 3D-printed scaffolds with convex, prismatic macropores induced significant ectopic bone formation. Among them, biomimetic nanostructured CDHA produced the highest incidence of ectopic bone and accelerated bone formation when compared with conventional microstructured sintered calcium phosphates with the same macropore architecture. Moreover, they exhibited different bone formation patterns; in CDHA foams, the new ectopic bone progressively replaced the scaffold, whereas in sintered biphasic calcium phosphate scaffolds, bone was deposited on the surface of the material, progressively filling the pore space. In conclusion, this study demonstrates that the high reactivity of nanostructured biomimetic CDHA combined with a spherical, concave macroporosity allows the pushing of the osteoinduction potential beyond the limits of microstructured calcium phosphate ceramics.
Targeting Triple Negative Breast Cancer with a Nucleus-Directed p53 Tetramerization Domain Peptide (2020)

Triple negative breast cancer (TNBC) has no targeted detection or treatment method. Mutant p53 (mtp53) is overexpressed in >80% of TNBCs, and the stability of mtp53 compared to the instability of wild-type p53 (wtp53) in normal cells makes mtp53 a promising TNBC target for diagnostic and theranostic imaging. We generated Cy5p53Tet, a novel nucleus-penetrating mtp53-oligomerization-domain peptide (mtp53ODP) to the tetramerization domain (TD) of mtp53. This mtp53ODP contains the p53 TD sequence conjugated to a Cy5 fluorophore for near-infrared fluorescence imaging (NIRF). In vitro co-immunoprecipitation and glutaraldehyde cross-linking showed a direct interaction between mtp53 and Cy5p53Tet. Confocal microscopy and flow cytometry demonstrated higher uptake of Cy5p53Tet in the nuclei of TNBC MDA-MB-468 cells with mtp53 R273H than in ER-positive MCF7 cells with wtp53. Furthermore, depletion of mtp53 R273H caused a decrease in the uptake of Cy5p53Tet in nuclei. In vivo analysis of the peptide in mice bearing MDA-MB-468 xenografts showed that Cy5p53Tet could be detected in tumor tissue 12 min after injection. In these in vivo experiments, significantly higher uptake of Cy5p53Tet was observed in mtp53-expressing MDA-MB-468 xenografts compared with the wtp53-expressing MCF7 tumors. Cy5p53Tet has clinical potential as an intraoperative imaging agent for fluorescence-guided surgery, and the mtp53ODP scaffold shows promise for modification in the future to enable the delivery of a wide variety of payloads including radionuclides and toxins to mtp53-expressing TNBC tumors.
Resolving the Mechanistic Complexity in Triarylborane-Induced Conjugate Additions (2022)

Previous studies have shown that the catalytically active species in the Lewis acid-catalyzed addition reactions of allyl silanes or silyl enol ethers to carbonyl compounds or Michael acceptors are often silylium-carbonyl adducts rather than the adducts of the carbonyl group with the Lewis acid used for the induction of the reaction. Indirect evidence for such catalyst variations has so far been derived from double-label crossover experiments and comparisons of absolute reaction rates. We have now performed a detailed investigation on the kinetics and mechanism of the triarylborane-initiated conjugate addition reactions of allylsilanes and silyl enol ethers to α,β-unsaturated carbonyl compounds. NMR spectroscopic monitoring of such reactions gave rise to sigmoidal kinetic profiles, allowing us to directly follow the change of the catalytically active Lewis acid from triarylboranes in the induction period to silylium ions during the main part of the reaction. Crossover experiments and the isolation of four- and five-membered cyclic intramolecular trapping products provided further insight into the mechanism. DFT calculations of various mechanistic variants and kinetic modeling elucidated the operation of a complex reaction network, which rationalizes the experimental observations.
Distributed Quantized Detection of Sparse Signals Under Byzantine Attacks (2023)

This paper investigates distributed detection of sparse stochastic signals with quantized measurements under Byzantine attacks. Under this type of attack, sensors in the networks might send falsified data to degrade system performance. The Bernoulli-Gaussian (BG) distribution in terms of the sparsity degree of the stochastic signal is utilized for modeling the sparsity of signals. Several detectors with improved detection performance are proposed by incorporating the estimated attack parameters into the detection process. First, we propose the generalized likelihood ratio test with reference sensors (GLRTRS) and the locally most powerful test with reference sensors (LMPTRS) detectors with adaptive thresholds, given that the sparsity degree and the attack parameters are unknown. Our simulation results show that the LMPTRS and GLRTRS detectors outperform the LMPT and GLRT detectors proposed for an attack-free environment and are more robust against attacks. The proposed detectors can achieve the detection performance close to the benchmark likelihood ratio test (LRT) detector, which has perfect knowledge of the attack parameters and sparsity degree. When the fraction of Byzantine nodes are assumed to be known, we can further improve the system's detection performance. We propose the enhanced LMPTRS (E-LMPTRS) and enhanced GLRTRS (E-GLRTRS) detectors by filtering out potential malicious sensors with the knowledge of the fraction of Byzantine nodes in the network. Simulation results show the superiority of proposed enhanced detectors over LMPTRS and GLRTRS detectors.
Integrated Reservoir Characterization and 3D Modeling of the Monteith Formation: Tight Gas Sandstones in the Western Canada Sedimentary Basin, Alberta, Canada (2014)

Abstract The Monteith Formation is an important tight gas reservoir in the Deep Basin, Alberta, and consists of a progradational succession of shallow marine sediments, non-marine carbonaceous and coaly, coastal plain facies, and coarse-grained fluvial deposits, from base to top, respectively. This study compares rock properties and production performance of the uppermost lithostratigraphic unit ("Monteith A") and the lowermost portion ("Monteith C") of the Monteith Formation in the Western Canada Sedimentary Basin (WCSB) in Alberta. The study is based on multi-scale description and characterization techniques using cores and drill cuttings, including multiple laboratory measurements of key reservoir parameters such as porosity and permeability. A second stage of the study involves the use of laboratory measurements obtained from cores and drill cuttings and their integration with well logs to produce a numerical 3D model of the study area. The 3D model is used to history match gas production, and forecast performance of new wells in those areas where the geologic model indicates potential for gas production. The ultimate goal is to provide a better understanding of the distribution of reservoir properties in the study area, for developing drilling prospects and their production potential. In addition to that, the reservoir modeling stage is carried out by implementing a recently developed methodology that integrates a Variable Shape Distribution (VSD) model, capable of capturing different reservoir properties through the whole scale spectrum without any data truncation. This new methodology introduces an extension of the VSD approach for reservoir simulation purposes. The results are showing that the Monteith A unit has better rock quality than the shallow marine sandstones of the Monteith C interval. This is most likey due to larger pore throat apertures ranging between 0.5 and 1 microns, relatively higher proportion of preserved intergranular pore space within these coarser-grained framework grains. Furthermore, the best production performance is found from wells that are actually producing from the uppermost interval. The resulting 3D reservoir model will allow to improve field development strategies for this and other similar unconventional gas reservoir in the Deep Basin of Alberta.
Stereotactic body radiotherapy (SBRT) and medical inoperability of early stage non-small cell lung cancer (2006)

17074 Background: Early stage NSCLC is commonly diagnosed in elderly patients who often have significant medical co-morbidity. SBRT is emerging as a treatment alternative that can provide 80–97% local control for peripheral tumors. We performed a literature review and a retrospective review of 24 patients referred to Princess Margaret Hospital for consideration of SBRT to assess what criteria were used to determine patient selection for this new treatment. Methods: Published papers reporting treating stage I NSCLC with SBRT were reviewed. Clinical and demographic characteristics of patients referred for consideration of SBRT over the last 15 months were analyzed. All patients were assessed by experienced thoracic surgeons to determine their operability status. Patients were retrospectively scored as average or high risk for surgery on the basis of accepted PFT guidelines (FEV 1 and DLCO &lt;40% predicted); Charlson Index of Comorbidity (CCI) was calculated (score &gt;2 associated with impaired survival). Results: Of 13 papers reporting Stage 1 SBRT results, 8 included details of medical inoperability. 2 papers had strict guidelines for PFTs, in addition to other criteria. In 6 studies reporting 276 pts, the most common reason for inoperability was non-specific medical comorbidity (60%). Our cohort (24 patients) referred for SBRT (median age 75, range 57–89) had a mean tumour size of 2.32cm (S.D. 1.11); 50% of patients had a good (0–1) Zubrod Performance status. Based upon PFT tests alone 10 patients (42%) were high risk and 5 (21%) average risk for surgery. The CCI score was ≥3 in 10 patients (42%). 3 patients who scored average risk and CCI ≤2 were deemed medically inoperable due a single severe medical comorbity. In 23/24 pts the surgeon recommended against surgery; one patient refused surgery. Conclusions: With an aging population and increased detection due to incidental finding or screening, it is important to know that there is effective alternative therapy for patients deemed too high risk for surgical resection. Comorbidity is an important factor influencing surgical mortality; defining explicit criteria for inoperability remains a clinical challenge. No significant financial relationships to disclose.
Expression and function of A<sub>2B</sub> adenosine receptors in the U87MG tumor cells (2003)

Abstract Adenosine is released in increased amounts during hypoxic conditions and is a potential mediator of angiogenesis. The aims of this study were to determine the effect of adenosine on the release of angiogenic factors from the glioblastoma cell line U87MG and the subtypes of adenosine receptors that mediate this effect of adenosine. The adenosine analog NECA increased the release of IL‐8 to 160±13% of control at 24 h. As a positive control, cobalt (100 µM), a metal ion capable of inducing hypoxia‐like effects, increased the release of IL‐8 to 362±99% of control at 24 h. Using real‐time RT‐PCR, it was found that U87MG cells expressed mRNA transcripts of the A 1 , A 2A , and A 2B adenosine receptors. The functional presence of A 2B adenosine receptors in this cell line was confirmed using pharmacological approaches. NECA stimulated cAMP accumulations with an EC 50 value of 2.93±0.91 µM and this effect of NECA was inhibited by the selective A 2B antagonist IPDX. In addition, NECA also caused an increase in the intracellular calcium concentration. Furthermore, cobalt increased the level of A 2B mRNA to 187±16% and 259±37% of the vehicle control at 5 h and 24 h, respectively. In conclusion, these results suggest that A 2B adenosine receptors are upregulated during hypoxia and may play an important role in mediating the effect of adenosine to increase the release of angiogenic factor IL‐8 by tumor cells. Drug Dev. Res. 58:405–411, 2003. © 2003 Wiley‐Liss, Inc.
Ultrafast Photoalignment: Recording a Lens in a Nanosecond (2017)

Liquid crystals can be photoaligned with a single nanosecond pulse acting on thin photoanisotropic coatings on the cell substrates. This phenomenon was demonstrated for pulses of 532 nm and 355 nm wavelengths (second and the third harmonics of a Nd:YAG laser). Direct printing of liquid crystal cycloidal diffractive waveplates and diffractive waveplate lenses characterized by high spatial frequencies required only a mJ energy. The liquid crystal alignment dynamics reveal a fast component related to photoalignment of molecules within the photoanisotropic layer and a slower component related to alignment of the liquid crystal within the cell.
Imaging Atomically Thin Transition Metal Dichalcogenides Using Deep Ultraviolet Photoelectron Emission Microscopy (2022)

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Factors Involved in the Pulmonary Targeting of Inhaled Glucocorticoids: The Use of Pharmacokinetic/ Dynamic Simulations (2001)

Despite the development of new antiasthmatic drugs, inhaled glucocorticoids remain important in the therapy of asthma. Beclomethasone dipropionate, the prototype of the ﬁrst generation of inhaled glucocorticoids, was successfully introduced without taking into consideration major targeting strategies. The second and third generations of inhaled glucocorticoids, with budesonide and ﬂuticasone propionate as the main representatives, incorporated a number of rationale design features into the drug development process that signiﬁcantly improved pulmonary selectivity (in the following, the term “pulmonary” is used synonymously for describing central and peripheral areas of the lung including the tracheobronchial region, unless stated otherwise). It is undisputed that further improvements in pulmonary selectivity of glucocorticoids will be difﬁcult and will not occur in quantum leaps but in discrete steps. Therefore, if further improvements in pulmonary selectivity are to be realized, it is necessary to fully comprehend the requirements for pulmonary targeting, while at the same time, suitable methods to monitor theGUNTHER HOCHHAUS, HARTMUT DERENDORF, and JAMES TALTON**Current afﬁliation: Nanosphere Inc., Alachua, Florida.