gebhart/patrepeval huggingface dataset:
Solid phase sequencing of double-stranded nucleic acids (2023)

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.
DualTrust: A Trust Management Model for Swarm-Based Autonomic Computing Systems (2010)

Trust management techniques must be adapted to the unique needs of the application architectures and problem domains to which they are applied. For autonomic computing systems that utilize mobile agents and ant colony algorithms for their sensor layer, certain characteristics of the mobile agent ant swarm -- their lightweight, ephemeral nature and indirect communication -- make this adaptation especially challenging. This thesis looks at the trust issues and opportunities in swarm-based autonomic computing systems and finds that by monitoring the trustworthiness of the autonomic managers rather than the swarming sensors, the trust management problem becomes much more scalable and still serves to protect the swarm. After analyzing the applicability of trust management research as it has been applied to architectures with similar characteristics, this thesis specifies the required characteristics for trust management mechanisms used to monitor the trustworthiness of entities in a swarm-based autonomic computing system and describes a trust model that meets these requirements.
Long-range phase-free propagation in a dielectric metasurface (2017)

We present a dielectric metasurface that supports in-plane guided waves with infinite wavelength, but suffers no material or radiation loss due to a bound-state in the continuum. This design can be extended to large areas.
Integrated technology platform for accelerated discovery of antiviral antibody therapeutics (2020)

Abstract The emergence and reemergence of highly virulent viral pathogens with pandemic potential has created an urgent need for accelerated discovery of antiviral therapeutics. Antiviral human monoclonal (mAbs) are promising drug candidates to prevent or treat severe viral diseases, but the long timelines needed for discovery limits their rapid deployment and use. Here, we report the development of an integrated sequence of technologies incorporating advances in single-cell mRNA sequence analysis, bioinformatics, synthetic biology, and high-throughput functional analysis that allowed us to discover highly potent antiviral human mAbs and validate their activity in vivo at an unprecedented scale, speed, and efficiency. In a 78-day study, modeling deployment of a rapid response platform to an outbreak, we isolated &gt;100 individual Zika virus (ZIKV) specific human mAbs, assessed their function, identified 29 broadly-neutralizing mAbs, and verified therapeutic potency of lead candidates with antibody-encoding mRNA formulation and/or IgG protein delivery in mice and nonhuman primates. Our work provides a roadmap for the rapid antibody discovery programs against viral pathogens of global concern.
Large Nonlinear Phase Modulation in Quasi-Phasematched KTP Waveguides Due to Cascaded Second-Order Processes (1993)

It has been known for many years that a nonlinear phase shift can be imparted on the fundamental in non-phasematched second-harmonic generation via down-conversion of the second-harmonic.1
Rapid reorganization of adult rat motor cortex somatic representation patterns after motor nerve injury. (1988)

The potential for peripheral nerve injury to reorganize motor cortical representations was investigated in adult rats. Maps reflecting functional connections between the motor cortex and somatic musculature were generated with intracortical electrical stimulation techniques. Comparison of cortical somatotopic maps obtained in normal rats with maps generated from rats with a facial nerve lesion indicated that the forelimb and eye/eyelid representations expanded into the normal vibrissa area. Repeated testing from an electrode placed chronically in the motor cortex showed a shift from vibrissa to forelimb within hours after facial nerve transection. These comparatively quick changes in motor cortex representation pattern suggest that synaptic relations between motor cortex and somatic musculature are continually reshaped in adult mammals.
Binding interactions of the peripheral stalk subunit isoforms from human V-ATPase (2016)

The mammalian peripheral stalk subunits of the vacuolar-type H(+)-ATPases (V-ATPases) possess several isoforms (C1, C2, E1, E2, G1, G2, G3, a1, a2, a3, and a4), which may play significant role in regulating ATPase assembly and disassembly in different tissues. To better understand the structure and function of V-ATPase, we expressed and purified several isoforms of the human V-ATPase peripheral stalk: E1G1, E1G2, E1G3, E2G1, E2G2, E2G3, C1, C2, H, a1NT, and a2NT. Here, we investigated and characterized the isoforms of the peripheral stalk region of human V-ATPase with respect to their affinity and kinetics in different combination. We found that different isoforms interacted in a similar manner with the isoforms of other subunits. The differences in binding affinities among isoforms were minor from our in vitro studies. However, such minor differences from the binding interaction among isoforms might provide valuable information for the future structural-functional studies of this holoenzyme.
Preparation of Indoles and Oxindoles fromN-(tert-Butoxycarbonyl)-2-alkylanilines (1991)

Treatment of dilithiated N-(tert-butoxycarbonyl)anilines 1 with dimethylformamide or carbon dioxide furnishes intermediates 3, 5, that are easily converted to N-(tert-butoxycarbonyl)indoles 4 and oxindoles (indol-2(3H)-ones, 7), respectively. Condensation of dilithiated 1 with N-methoxy-N-methylamides provides ketones 9 which are cyclized upon trifluoroacetic acid treatment to either 2-substituted 1-(tert-butoxycarbonyl)indoles 10 or 2-substituted indoles 11 depending on the reaction time. This general methodology has been applied to efficient synthesis of 1,2-alkyl-bridged indoles 12, 1,3,4,5-tetrahydrobenz[c,d]indole (16), 2a,3,4,5-tetrahydrobenz [c,d]indol-2(1H)-one (18), and 1-(tert-butoxycarbonyl) -1H-pyrrolo[2,3-b]pyridine (21).
ChemInform Abstract: Polymer Physics and Structure/Property Relationships of Thermally Stable Polyarylene Ethers for Second‐Order Nonlinear Optics. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Strong Magnetocrystalline Anisotropy Arising from Metal–Ligand Covalency in a Metal–Organic Candidate for 2D Magnetic Order (2021)

Layered metal–organic frameworks are promising candidates for new two-dimensional (2D) magnets, as the synthetic programmability of these materials can provide a route to diverse structural and electronic properties. However, such framework materials typically lack the heavy elements that engender magnetocrystalline anisotropy in the monolayer ferromagnets reported to date. Alternative sources of magnetic anisotropy are therefore needed in these materials. Here, we report the synthesis of single crystals of the framework material (NMe4)2[Fe2L3] (H2L = 3,6-dichloro-2,5-dihydroxybenzoquinone) and evaluate the angular dependence of its magnetic properties. Oriented-crystal magnetization measurements reveal strong uniaxial anisotropy, where the easy axis is aligned with the crystallographic c axis. While the spin carriers of this structure are isotropic S = 5/2 FeIII metal centers and S = 1/2 organic linkers, the anisotropy energy of the framework material is comparable to that of reported 2D ferromagnets. Density functional theory calculations indicate that the observed magnetocrystalline anisotropy arises from ligand-to-metal charge transfer that enhances the magnetic anisotropy of the otherwise-isotropic Fe centers, suggesting that metal–ligand covalency can be utilized as a general additive for the development of 2D magnets. These results show the possibility for (NMe4)2[Fe2L3] to retain magnetic order down to the 2D monolayer limit. In addition, the combination of large magnetic anisotropy and semiconducting character in (NMe4)2[Fe2L3] highlights its potential as a new 2D magnetic semiconductor.
Topical dual-stain difference imaging for rapid intra-operative tumor identification in fresh specimens (2013)

Assessing tumor margin status during surgery is critical to ensure complete resection of cancer tissue; however, current approaches are ineffective and often result in repeat surgery. We present an optical imaging approach for margin assessment using topical application of two fluorescent stains, one targeted to a tumor biomarker and the other a nontargeted reference, to freshly excised specimens. Computing a normalized difference image from fluorescence images of the targeted and untargeted stains suppresses the confounding effects of nonspecific uptake. Applying this approach in excised breast tumor models produced promising tumor-to-normal tissue contrasts that were significantly higher than single-targeted-stain imaging.
Novel Y 2− x Pr x Ru 2 O 7 ( x =0–2) Pyrochlore Oxides Prepared Using a Soft Chemistry Route and their Electrical Properties (2010)

Y 2− x Pr x Ru 2 O 7 (0≤ x ≤2) pyrochlore powders were prepared using a precipitation method, which allowed control of their composition and morphology. Materials structure and morphology were characterized by X‐ray diffraction analysis and field emission scanning electron microscopy, respectively. All the synthesized powders exhibited a single pyrochlore phase with particle size depending on the Pr content. Powders with Pr content smaller than 25 mol% were nanometric. X‐ray photoelectron spectroscopy analysis revealed a mixed oxidation state of both Pr and Ru, and a variation of the oxidation state of the elements in response to oxygen partial pressure changes. Electrical conductivity measurements were performed by dc 4‐probe method at several temperatures, showing that increasing the Pr content in the A site of the pyrochlore structure increased the oxide electrical conductivity.
Assessing the Mass Concentration of Microplastics and Nanoplastics in Wastewater Treatment Plants by Pyrolysis Gas Chromatography–Mass Spectrometry (2023)

The level of microplastics (MPs) in wastewater treatment plants (WWTPs) has been well evaluated by the particle number, while the mass concentration of MPs and especially nanoplastics (NPs) remains unclear. In this study, pyrolysis gas chromatography-mass spectrometry was used to determine the mass concentrations of MPs and NPs with different size ranges (0.01-1, 1-50, and 50-1000 μm) across the whole treatment schemes in two WWTPs. The mass concentrations of total MPs and NPs decreased from 26.23 and 11.28 μg/L in the influent to 1.75 and 0.71 μg/L in the effluent, with removal rates of 93.3 and 93.7% in plants A and B, respectively. The proportions of NPs (0.01-1 μm) were 12.0-17.9 and 5.6-19.5% in plants A and B, respectively, and the removal efficiency of NPs was lower than that of MPs (>1 μm). Based on annual wastewater effluent discharge, it is estimated that about 0.321 and 0.052 tons of MPs and NPs were released into the river each year. Overall, this study investigated the mass concentration of MPs and NPs with a wide size range of 0.01-1000 μm in wastewater, which provided valuable information regarding the pollution level and distribution characteristics of MPs, especially NPs, in WWTPs.
Loss or Somatic Mutations of hMSH2 Occur in Hereditary Nonpolyposis Colorectal Cancers with hMSH2 Germline Mutations (1996)

Hereditary nonpolyposis colorectal cancer (HNPCC) is a major cancer susceptibility syndrome known to be caused by the inheritance of mutations in DNA mismatch repair genes, such as hMSH2, hMLH1, hPMS1 and hPMS2. To investigate the role of genetic alterations of hMSH2 in HNPCC tumorigenesis, we analyzed 36 Japanese HNPCC kindreds as to hMSH2 germline mutations. Moreover, we also examined somatic mutations of hMSH2 or loss of heterozygosity at or near the hMSH2 locus in the tumors from the hMSH2-related kindreds. Germline mutations were detected in five HNPCC kindreds (5/36, 14%). Among them, three were nonsense mutations, one was a frameshift mutation and the other was a mutation in an intron where the mutation affected splicing. Loss of heterozygosity in four and somatic mutations in one were detected among the eight tumors with hMSH2 germline mutations. All these alterations were only detected in genomic instability(+) tumors, i.e., not in genomic instability(-) ones, indicating that mutations of hMSH2 were responsible for at least some of the tumors with genomic instability. These data establish a basis for the presymptomatic diagnosis of HNPCC patients, and constitute further evidence that both DNA mismatch repair genes and tumor suppressor genes may share the same requirement, i.e., two hits are necessary to inactivate the gene function.
Invited Review A Thermodynamic Frame for the Kinetics of Polymer Crystallization under Processing Conditions (2005)

Summary. A retrospective view is given on work, which has been carried out at the Johannes Kepler University during the last two decades on the structure formation in crystallizable polymers during their processing. Emphasis is laid on some useful principles lend from basic physical chemistry: use of the T,S-diagram and of the temperature dependent courses of (effective) surface tensions along coexistence lines of phases. These considerations should be helpful in creating an overview, where a deficiency of direct experimental crystallization kinetics data exists. For a series of industrially important, mostly fast crystallizing, polymers data are given in the present paper for the quiescent melt (temperature dependences of number densities of nuclei and of growth speeds). Critical minimum cooling speeds for bypassing crystallization are given on the basis of the given data. These critical cooling speeds vary by almost six decades from HDPE to i-PS. These results are also helpful in the formulation of a viable classification of materials in the light of their processing conditions. This classification includes metals and glass forming minerals as limiting cases for extremely fast and extremely slowly crystallizing materials.
Single-point reactive power control method on voltage rise mitigation in residential networks with high PV penetration (2018)

Voltage rise (VR) due to reverse power flow is an important obstacle for high integration of Photovoltaic (PV) into residential networks. This paper introduces and elaborates a novel methodology of an index-based single-point-reactive power-control (SPRPC) methodology to mitigate voltage rise by absorbing adequate reactive power from one selected point. The proposed index utilizes short circuit analysis to select the best point to apply this Volt/Var control method. SPRPC is supported technically and financially by distribution network operator that makes it cost effective, simple and efficient to eliminate VR in the affected network. With SPRPC none of the previous PV inverters need to upgrade and can retain their unity power factor to not to conflict with current grid codes. Comprehensive 24-h simulation studies are done on a modified IEEE 69-bus Network emulating a traditional residential power system with high r/x ratio. Efficacy, effectiveness and cost study of SPRPC is compared to droop control to evaluate its advantages.
Spiral modiolar vein: Its importance in inner ear inflammation (1990)

The inner ear responds immunologically to foreign proteins and pathogens introduced into the cochlea. The route of entry of the cells participating in the inner ear inflammatory process is the spiral modiolar vein with its collecting venules. Since this vein is located adjacent to the scala tympani, the end result of cellular infiltration is fibro-osseous obliteration of this scala preferentially. This observation has implications for the placement of cochlear implant electrodes of patients with labyrinthitis as the cause of hearing loss.
Effects of EDCF and endothelin on phosphatidylinositol hydrolysis and contraction in rat aorta (1990)

Endothelium-derived constricting factor (EDCF) and endothelin are peptidergic substances produced and released from endothelial cells that induce contraction of vascular smooth muscle. The purpose of the present study was to investigate possible mechanisms by which EDCF and endothelin elicit contraction. Exposure of rat aorta to EDCF or synthetic endothelin resulted in time- and concentration-dependent increases in tension and levels of inositol monophosphate, a breakdown product of the phosphatidylinositides. A 10-s exposure to endothelin elevated levels of inositol 1,4,5-trisphosphate. Trypsinization or heating of EDCF prevented the contraction and inositol monophosphate formation. To assess whether EDCF and endothelin may act as endogenous agonists of the dihydropyridine-sensitive Ca2+ channel, we evaluated the ability of the dihydropyridine Ca2+ channel agonist (+)-S202-791 to increase the formation of the inositol phosphates. (+)-S202-791 increased inositol monophosphate formation. However, in contrast to that elicited by EDCF and endothelin, the increase in inositol monophosphate because of (+)-S202-791 was abolished by pretreatment with the cyclooxygenase inhibitor indomethacin (10 microM). These results suggest that contractions induced by EDCFs may be mediated through activation of phospholipase C and subsequent production of second messengers.
The p110α and p110β isoforms of PI3K play divergent roles in mammary gland development and tumorigenesis (2012)

Class Ia phosphatidylinositol 3 kinase (PI3K) is required for oncogenic receptor-mediated transformation; however, the individual roles of the two commonly expressed class Ia PI3K isoforms in oncogenic receptor signaling have not been elucidated in vivo. Here, we show that genetic ablation of p110α blocks tumor formation in both polyoma middle T antigen (MT) and HER2/Neu transgenic models of breast cancer. Surprisingly, p110β ablation results in both increased ductal branching and tumorigenesis. Biochemical analyses suggest a competition model in which the less active p110β competes with the more active p110α for receptor binding sites, thereby modulating the level of PI3K activity associated with activated receptors. Our findings demonstrate a novel p110β-based regulatory role in receptor-mediated PI3K activity and identify p110α as an important target for treatment of HER2-positive disease.
METABOLIC CONVERSION OF FORMYCIN B TO FORMYCIN A AND TO OXOFORMYCIN B IN NOCARDIA INTERFORMA (1968)

A strain of Nocardia interforma having low productivity of formycin A was selected. Washed cells of this strain convert formycin B to oxoformycin B (reaction I), while those of the original strain collected during formycin A producing phase convert formycin B to formycin A (reaction II). Reaction I is inhibited by allopurinol, an inhibitor of xanthine oxidase. Reaction II is inhibited by hadacidin, an inhibitor of adenylosuccinate synthetase, but not by azaserine. As intermediates of reaction II, formycin B-monophosphate and formycin A-monophosphate were detected in the nucleotide pool of the cell. No other organisms than Nocardia interforma perform reaction II except Xanthomonas oryzae. Besides Nocardia interforma, Pseudomonas fluorescens and Streptomyces kasugaensis perform reaction I.
Multifidelity deep neural operators for efficient learning of partial differential equations with application to fast inverse design of nanoscale heat transport (2022)

Deep neural operators can learn operators mapping between infinite-dimensional function spaces via deep neural networks and have become an emerging paradigm of scientific machine learning. However, training neural operators usually requires a large amount of high-fidelity data, which is often difficult to obtain in real engineering problems. Here, we address this challenge by using multifidelity learning, i.e., learning from multifidelity datasets. We develop a multifidelity neural operator based on a deep operator network (DeepONet). A multifidelity DeepONet includes two standard DeepONets coupled by residual learning and input augmentation. Multifidelity DeepONet significantly reduces the required amount of high-fidelity data and achieves one order of magnitude smaller error when using the same amount of high-fidelity data. We apply a multifidelity DeepONet to learn the phonon Boltzmann transport equation (BTE), a framework to compute nanoscale heat transport. By combining a trained multifidelity DeepONet with genetic algorithm or topology optimization, we demonstrate a fast solver for the inverse design of BTE problems.
Cordycepin Attenuates Testosterone-Induced Benign Prostatic Hyperplasia in Rats via Modulation of AMPK and AKT Activation (2022)

Benign prostatic hyperplasia (BPH) is a disease that commonly affects elderly men. Cordycepin is an adenosine analog with a wide range of pharmacological activities including antiproliferative and prostatic smooth muscle relaxant effects. This study was designed to assess the actions of cordycepin in testosterone-induced BPH in rats. Animals were divided into six treatment groups: control, cordycepin-alone (10 mg/kg), testosterone-alone (3 mg/kg), cordycepin (5 mg/kg) + testosterone, cordycepin (10 mg/kg) + testosterone, and finasteride (0.5 mg/kg) + testosterone. Treatments were continued daily, 5 days a week, for 4 weeks. Cordycepin significantly prevented the increase in prostate weight and prostate index induced by testosterone. This was confirmed by histopathological examinations. Cordycepin antiproliferative activity was further defined by its ability to inhibit cyclin-D1 and proliferating cell nuclear antigen (PCNA) expression. In addition, cordycepin exhibited significant antioxidant properties as proven by the prevention of lipid peroxidation, reduced glutathione diminution, and superoxide dismutase exhaustion. This was paralleled by anti-inflammatory activity as shown by the inhibition of interleukin-6, tumor necrosis factor-α, and nuclear factor-κB expression in prostatic tissues. It also enhanced apoptosis as demonstrated by its ability to enhance and inhibit mRNA expression of Bax and Bcl2, respectively. Western blot analysis indicated that cordycepin augmented phospho-AMP-activated protein kinase (p-AMPK) and inhibited p-AKT expression. Collectively, cordycepin has the ability to prevent testosterone-induced BPH in rats. This is mediated, at least partially, by its antiproliferative, antioxidant, anti-inflammatory, and pro-apoptotic actions in addition to its modulation of AMPK and AKT activation.
Valuing and Engaging Stakeholders: The Effects of Engineering Students' Interactions During Capstone Design (2015)

Her research focuses on strategies for design innovations through divergent