gebhart/patrepeval huggingface dataset:
Contrasting ABCB1 Pharmacogenetics and Psychotropic Responses in Child and Adolescent Psychiatry: A case comparison (2023)

This case comparison illustrates pharmacogenetic testing in psychotropic and clinical management in relation to the <i>ABCB1</i> gene, which encodes the P-glycoprotein transporter affecting blood-brain barrier (BBB) permeability. Two pediatric patients (9 and 11 years old) were selected for similar clinical presentations with opposing <i>ABCB1</i> genotype, while they were identically matched for key CYP450, dopaminergic and serotonergic genes (<i>CYP2C9</i>, <i>CYP2C19</i>, <i>DRD2</i>, <i>SLC6A4</i>, <i>5HTR2A</i>). Case A was functional for the <i>ABCB1</i> gene (<i>G/G</i> rs1045642), suggesting that the BBB had a functional P-glycoprotein transporter. Case B was subfunctional for the <i>ABCB1</i> gene (<i>A/A</i> rs1045642), suggesting that the patient's BBB may be permeable to psychotropic drugs. Case A had more medication trials and dose adjustments than Case B. Case A had two inpatient admissions and interspersed emergency room visits, while case B had none.
Negatively charged silver nanoparticles cause retinal vascular permeability by activating plasma contact system and disrupting adherens junction (2015)

Silver nanoparticles (AgNPs) have been extensively used as antibacterial component in numerous healthcare, biomedical and consumer products. Therefore, their adverse effects to biological systems have become a major concern. AgNPs have been shown to be absorbed into circulation and redistributed into various organs. It is thus of great importance to understand how these nanoparticles affect vascular permeability and uncover the underlying molecular mechanisms. A negatively charged mecaptoundeonic acid-capped silver nanoparticle (MUA@AgNP) was investigated in this work. Ex vivo experiments in mouse plasma revealed that MUA@AgNPs caused plasma prekallikrein cleavage, while positively charged or neutral AgNPs, as well as Ag ions had no effect. In vitro tests revealed that MUA@AgNPs activated the plasma kallikrein-kinin system (KKS) by triggering Hageman factor autoactivation. By using specific inhibitors aprotinin and HOE 140, we demonstrated that KKS activation caused the release of bradykinin, which activated B2 receptors and induced the shedding of adherens junction protein, VE-cadherin. These biological perturbations eventually resulted in endothelial paracellular permeability in mouse retina after intravitreal injection of MUA@AgNPs. The findings from this work provided key insights for toxicity modulation and biomedical applications of AgNPs.
Mathematical modeling and EDA-based network planning for broadband power line communication access systems (2014)

In this paper, we present a mathematical model of power line communication access systems and a technique for an efficient network deployment. We focus on the problem of designing an infrastructure network model which fits the power line communication needs and installing an apt number of base stations and repeaters at adequate locations suited to serve all the subscribers to the required level at a low cost to the utility company. The computational complexity of determining an optimal deployment by using exhaustive search grows exponentially with the number of base stations, repeaters and the users. We propose a heuristic method combined with an Estimation-of-Distribution Algorithm (EDA) for this assignment problem. EDA is a probabilistic evolutionary algorithm which updates its population at each iteration on the basis of the probability densities obtained from the population of superior candidates evaluated and chosen at the previous iteration.
Purification and crystallization of the polypeptide hormone human chorionic somatomammotropin. (1981)

We have purified the large polypeptide hormone human chorionic somatomammotropin to near electrophoretic homogeneity by a new purification scheme. The hormone crystallized from polyethylene glycol in a form suitable for high resolution x-ray analysis; the crystals are monoclinic, space group C2, a = 123.9, b = 30.3, c = 53.8 A, beta = 119 degrees 30 min, with 1 molecule/asymmetric unit. The growth-promoting activity of homogeneous hormone and of dissolved crystals was measured through their effect on committed erythroid precursor cells in tissue culture assays. Both homogeneous and redissolved crystalline hormone had activities comparable to that of hormone purified by standard procedures. The latter preparations yielded either no crystals, or disordered crystals unsuitable for x-ray analysis.
Recent Progress in Molecular Dynamics Simulations of Dihydrofolate Reductase (2012)

This brief review will cover recent advances and applications of molecular dynamics simulations of dihydrofolate reductase over the course of the past few years. The application of the technique to the study of kinetic isotope effects, binding free energy of drugs, impact of ligand binding on protein conformation and study of coupled motions in hydrogen tunneling reactions will be discussed.
Three‐year clinical effectiveness of a two‐step self‐etch adhesive in cervical lesions (2005)

A 3-yr randomized, controlled prospective study evaluated the clinical effectiveness of a mild two-step self-etch adhesive, Clearfil SE, in Class-V non-carious lesions. The hypothesis tested was that prior selective etching of enamel with phosphoric acid does not affect the 3-yr clinical performance of this adhesive. A total of 100 lesions in 29 patients were randomly restored in one or two pairs, according to two experimental protocols: (i) application of Clearfil SE according to the instructions of the manufacturer (C-SE non-etch); and (ii) similar application of Clearfil SE with prior etching of enamel cavity margins with phosphoric acid (C-SE etch). Clearfil AP-X was used as a restorative material. At 3 yr, 90% of the restorations were examined for retention, marginal integrity, marginal discoloration, caries recurrence, postoperative sensitivity, and preservation of tooth vitality. An excellent retention rate (100%) was noted after 3 yr of clinical functioning. Only one restoration of the C-SE etch group was clinically unacceptable owing to the presence of a severe cervical marginal defect. A pairwise comparison between both groups showed a significant difference only in the number of small marginal defects at the enamel side, which was higher in the C-SE non-etch group. These incisal defects were small and clinically irrelevant. Superficial marginal discoloration increased slightly in the C-SE non-etch group and was related to the higher frequency of small incisal marginal defects. In this latter group, localized marginal discoloration was observed significantly more in smokers. In conclusion, the clinical performance of the mild two-step self-etch adhesive, Clearfil SE, remained excellent after 3 yr of clinical functioning. Additional etching of the enamel cavity margins was not critical for its clinical performance.
Resistance to TNF-alpha and adriamycin in the human breast cancer MCF-7 cell line: relationship to MDR1, MnSOD, and TNF gene expression. (1994)

The molecular basis of cross-resistance to tumor necrosis factor (TNF) and Adriamycin has been investigated using the breast adenocarcinoma cell line MCF7/p, its Adriamycin-resistant counterpart MCF7AdrR, and the MDR1 gene-transduced MCF-7 cells (MCF7/MDR1). While the parental cell line MCF7/p was TNF-sensitive, MCF7AdrR was TNF-resistant. The TNF resistance exhibited by MCF7AdrR cells was not due to a lack of TNF receptor expression because both cell lines express comparable levels of p75 and p55 receptors as revealed by immunofluorescence analysis. NF-kappa B translocation, which is an essential transducing signal of the TNF-induced lysis pathway, does not appear to be involved in this resistance as assessed by gel shift experiments. In order to determine the role of MDR1 gene expression in the development of this cross-resistance, MCF7/p cells transfected by the MDR1 gene were examined. Our data showed that the expression of the MDR1 gene in these cells resulted in a relative resistance of these cells to Adriamycin without affecting their susceptibility to TNF killing. The implication of the manganese superoxide dismutase and endogenous TNF expression in the cross-resistance by MCF7AdrR cells to Adriamycin and TNF has also been investigated. Northern blot analysis indicated that following TNF stimulation, the expression of 4-kilobase and 1-kilobase manganese superoxide dismutase mRNAs were 9- to 10-fold induced in MCF7AdrR cells as compared to MCF7/p and MCF7/MDR1 cells. This suggests a possible involvement of this enzyme in the Adriamycin-induced resistance to TNF. Although TNF-treatment of MCF7/p and MDR-cells induced endogenous TNF expression in these cells, the level of mRNA induction was selectively enhanced in MCF7AdrR cells (7- to 8-fold greater in MCF7AdrR cells as compared to MCF7/p and MCF7/MDR1 cells). Collectively, these data indicate that the expression of the MDR1 gene in MCF7/p cells following gene transfection is not sufficient for the acquisition of TNF resistance by MCF7/MDR1 cells. Furthermore, our data provide the first evidence that Adriamycin-induced resistance to TNF in MCF7AdrR cells may, in part, involve an overexpression of endogenous TNF and manganese superoxide dismutase genes.
Nano-Dispersed Liquid Crystal Tunable Negative-Zero-Positive Index Metamaterials (2007)

Nematic LC's offer an excellent path toward achieving tunability in a variety of different terahertz and optical devices. We have presented technology that can take advantage of the properties of LC to realize the index of refraction tuning. Metamaterials consisting of LC-dispersed coated spheres were designed to have an index of refraction that tuned from negative to zero to positive at the frequency of operation.
Residential Load Control: Distributed Scheduling and Convergence With Lost AMI Messages (2012)

This paper deals with load control in a multiple-residence setup. The utility company adopts a cost function representing the cost of providing energy to end-users. Each residential end-user has a base load, two types of adjustable loads, and possibly a storage device. The first load type must consume a specified amount of energy over the scheduling horizon, but the consumption can be adjusted across different slots. The second type does not entail a total energy requirement, but operation away from a user-specified level results in user dissatisfaction. The research issue amounts to minimizing the electricity provider cost plus the total user dissatisfaction, subject to the individual constraints of the loads. The problem can be solved by a distributed subgradient method. The utility company and the end-users exchange information through the Advanced Metering Infrastructure (AMI)-a two-way communication network-in order to converge to the optimal amount of electricity production and the optimal power consumption schedule. The algorithm finds near-optimal schedules even when AMI messages are lost, which can happen in the presence of malfunctions or noise in the communications network. The algorithm amounts to a subgradient iteration with outdated Lagrange multipliers, for which convergence results of wide scope are established.
A Boltzmann-weighted hopping model of charge transport in organic semicrystalline films (2011)

We present a model of charge transport in polycrystalline electronic films, which considers details of the microscopic scale while simultaneously allowing realistically sized films to be simulated. We discuss the approximations and assumptions made by the model, and rationalize its application to thin films of directionally crystallized poly(3-hexylthiophene). In conjunction with experimental data, we use the model to characterize the effects of defects in these films. Our findings support the hypothesis that it is the directional crystallization of these films, rather than their defects, which causes anisotropic mobilities.
Structure of 1,3,5-trichloro-2,4,6-trimethylbenzene at 150 and 297 K, molecular motion and reorientation (1995)

C 9 H 9 Cl 3 , triclinic P1 with Z=2, M r =223.53, crystal data at 150K [297]: a=7.646(3) [7.738(6)], b = 8.789 (6) [8.842 (4)], c = 8.827 (3) A [8.880 (3)], α = 59.78 (4) [59.74 (3)], β=66.03(3) [66.51(5)], γ = 72.69 (4)° [73.06 (4)], V = 465.1 A 3 [478.1], D x = 1.593 g cm 3 [1.553], Mo Kα, λ = 0.71073 A, μ = 9.278 cm -1 [9.025], F(000) = 228, R = 0.0349 [0.0378], wR=0.0472 [0.0506] for 1222 [1074] reflections with I≥3σ(I). The thermal motion of 1,3,5-trichloro-2,4,6-trimethylbenzene (or TCM) is rather high; no disorder can be detected in the range 150-297 K and X-rays provide information on H atoms. The quantum chemistry program AM1 gives a molecular conformation in reasonable accordance with the experimental results. Using atom-atom interactions of Buckingham-type, we were able to calculate phonon frequencies in accordance with spectroscopic results. From the calculus of the variations of the crystalline potential energy when one molecule is rotated in its plane and from protonic magnetic resonance results, we can understand why, above 150K, TCM molecules undergo fast 2π/3 reorientations while keeping an ordered structure. Furthermore, we were able to explain why each of the three methyls in one molecule has a specific tunneling splitting.
MN Solar Pathways: Opportunities for Widespread Solar Development in Minnesota (2022)

Finding of the Solar Potential Analysis- a study to determine best practices and most cost effective strategies to achieve 10% of Minnesota's electric load is serviced by solar by 2030
Genome im Fokus: Entwicklung und Anwendungen von CRISPR‐Cas9‐Bildgebungstechnologien (2017)

Abstract Die Entdeckung der CRISPR‐Cas9‐Endonuklease ermöglicht die einfache Genom‐Editierung von lebenden Zellen und Organismen. Katalytisch deaktivierte Cas9 (dCas9) behält die Fähigkeit, DNA in einer RNA‐abhängigen Weise zu binden, und wurde zusätzlich als ein Werkzeug für die Transkriptionsmodulation, die Epigenom‐Editierung und die genomische Bildgebung entwickelt. Dieser Aufsatz zeigt die jüngsten Fortschritte und Herausforderungen bei der Entwicklung von dCas9 für die Bildgebung genomischer Loci auf. Die Entstehung und Weiterentwicklung dieser Technologie bietet das Potenzial, neue mechanistische Fragen über die Chromosomendynamik und die dreidimensionale Genomorganisation in vivo zu beantworten.
F-18 FDG PET/CT Imaging of Extramammary Paget Disease of the Perianal Region (2006)

Extramammary Paget disease (EMPD) is rare, typically afflicting older Caucasians in the anogenital or axillary regions. It can arise either as a primary intraepithelial adenocarcinoma with potential for invasiveness or as the secondary spread of an underlying internal malignancy to the skin surface. EMPD in the perianal region is strongly associated with colorectal and anal adenocarcinoma. Biopsy is required for accurate diagnosis. Wide local excision is the standard treatment, but abdominoperineal resection is considered in cases of invasive perianal EMPD. We report a case of abnormal perianal FDG uptake in biopsy-proven EMPD in a patient with coexisting perianal adenocarcinoma.
Analytical design of permanent-magnet traction-drive motors (2006)

This paper presents an analytical method for the design of permanent-magnet (PM) traction-drive motors with emphasis on calculation of the magnet's volume and size. The method uses a set of formulas to properly size the magnets without the high effort of finite-element analysis (FEA). The formulas not only give optimized magnet sizes, but also provide quick solutions for the preliminary designs. The method can be used in the initial design stage to set up the base for FEA and optimization, as well as throughout the entire design and optimization process to validate a PM motor design. Numerical methods and experiments confirm the accuracy of the proposed method.
Fully epitaxial magnetic tunnel junction on a silicon wafer (2019)

We developed a fully epitaxial magnetic tunnel junction on an 8″ silicon wafer by using a mass-production sputtering apparatus and achieved a high magnetoresistance ratio exceeding 240% at room temperature. One of the key factors in this achievement is the use of a B2-type Ni-Al seed layer on the wafer as a (001)-oriented and an atomically smooth template. Another is the insertion of a thin Al layer prior to MgO sputtering as protection from plasma damage, resulting in the formation of a spinel-type single-crystal Mg-Al-O tunnel barrier after in situ annealing. This epitaxial technology for transition metals on large wafers will lead to advanced practical spintronics devices incorporating high-performance single-crystalline materials such as chemical-ordered alloys and tunnel barriers.
Does the combination of hyperthermia with low LET (linear energy transfer) radiation induce anti-tumor effects equivalent to those seen with high LET radiation alone? (2021)

Combining hyperthermia with low LET radiation can be as effective as high LET at inducing tumor control, but the temperature needed depended on the time interval between the two modalities.
Visible‐Light‐Driven Hydrogen Evolution Using Planarized Conjugated Polymer Photocatalysts (2015)

Linear poly(p-phenylene)s are modestly active UV photocatalysts for hydrogen production in the presence of a sacrificial electron donor. Introduction of planarized fluorene, carbazole, dibenzo[b,d]thiophene or dibenzo[b,d]thiophene sulfone units greatly enhances the H2 evolution rate. The most active dibenzo[b,d]thiophene sulfone co-polymer has a UV photocatalytic activity that rivals TiO2, but is much more active under visible light. The dibenzo[b,d]thiophene sulfone co-polymer has an apparent quantum yield of 2.3 % at 420 nm, as compared to 0.1 % for platinized commercial pristine carbon nitride.
AI-aided Geometric Design of Anti-infection Catheters (2023)

Bacteria can swim upstream due to hydrodynamic interactions with the fluid flow in a narrow tube, and pose a clinical threat of urinary tract infection to patients implanted with catheters. Coatings and structured surfaces have been proposed as a way to suppress bacterial contamination in catheters. However, there is no surface structuring or coating approach to date that thoroughly addresses the contamination problem. Here, based on the physical mechanism of upstream swimming, we propose a novel geometric design, optimized by an AI model predicting in-flow bacterial dynamics. The AI method, based on Fourier neural operator, offers significant speedups over traditional simulation methods. Using Escherichia coli, we demonstrate the anti-infection mechanism in quasi-2D micro-fluidic experiments and evaluate the effectiveness of the design in 3Dprinted prototype catheters under clinical flow rates. Our catheter design shows 1-2 orders of magnitude improved suppression of bacterial contamination at the upstream end of the catheter, potentially prolonging the in-dwelling time for catheter use and reducing the overall risk of catheter-associated urinary tract infections.
3D-printed polymer composite devices based on a ferroelectric chiral ammonium salt for high-performance piezoelectric energy harvesting (2023)

Three-dimensional printing (3DP) is an emerging technology to fabricate complex architectures, necessary to realize state-of-the-art flexible and wearable electronic devices. In this regard, top-performing devices containing organic ferro- and piezoelectric compounds are desired to circumvent significant shortcomings of conventional piezoceramics, <i>e.g.</i> toxicity and high-temperature device processibility. Herein, we report on a 3D-printed composite of a chiral ferroelectric organic salt {[Me<sub>3</sub>CCH(Me)NH<sub>3</sub>][BF<sub>4</sub>]} (1) with a biodegradable polycaprolactone (PCL) polymer that serves as a highly efficient piezoelectric nanogenerator (PENG). The ferroelectric property of 1 originates from its polar tetragonal space group <i>P</i>4<sub>2</sub>, verified by <i>P</i>-<i>E</i> loop measurements. The ferroelectric domain characteristics of 1 were further probed by piezoresponse force microscopy (PFM), which gave characteristic 'butterfly' and hysteresis loops. The PFM amplitude <i>vs.</i> drive voltage measurements gave a relatively high magnitude of the converse piezoelectric coefficient for 1. PCL polymer composites with various weight percentages (wt%) of 1 were prepared and subjected to piezoelectric energy harvesting tests, which gave a maximum open-circuit voltage of 36.2 V and a power density of 48.1 μW cm<sup>-2</sup> for the 10 wt% 1-PCL champion device. Furthermore, a gyroid-shaped 3D-printed 10 wt% 1-PCL composite was fabricated to test its practical utility, which gave an excellent output voltage of 41 V and a power density of 56.8 μW cm<sup>-2</sup>. These studies promise the potential of simple organic compounds for building PENG devices using advanced manufacturing technologies.
Defective transport and other phenotypes of a periplasmic "leaky" mutant of Escherichia coli K-12 (1979)

A mutant of Escherichia coli K-12 deficient in high-affinity leucine transport and related binding proteins was obtained by selecting for azaleucine resistance after bacteriophage Mu mutagenesis. We determined that the cause was a generalized loss of periplasmic binding proteins and a sharp decrease in the activity of transport systems requiring them. Other transport systems resistant to osmotic shock and present in membrane vesicles, were affected to a lesser degree or not at all. The mutation, designated lky::Mucts, was shown to be a pleiotropic envelope mutation, rendering the mutant sensitive to ionic and nonionic detergents, antibiotics, and ethylenediaminetetraacetic acid: the strain had also acquired tolerance to colicins E1, E2, and E3, while remaining normally sensitive to a variety of bacteriophages. An analysis of the lipopolysaccharide of parent and mutant strains revealed a twofold reduction in the neutral sugar content of the core oligosaccharide of the lky strain, but no change in sensitivities to phages which utilize lipopolysaccharide or outer membrane proteins for absorption. The lky::Mucts locus was mapped by transduction and found to be located near, or in, the tolPAB gene cluster linked to gal. Secondary mutations suppressing the detergent sensitivity of lky arose at a frequency of 10(-7), yielding a variety of new phenotypes. The lky::Mucts mutation did not give rise to obvious alterations in the gross morphology of the cell or in cell division.
Universal Design Curves for Elastomeric Direct Ink-Writing Architectures (2016)

Direct ink writing of silicone elastomers enables printing with precise control of porosity and mechan- ical properties of ordered cellular solids, suitable for shock absorption and stress mitigation applications. With the ability to manipulate structure and feedstock stiffness, the design space becomes challenging to parse to obtain a solution producing a desired mechanical response. Here we derive an analytical design approach for a specific architecture. Results from finite element simulations and quasi-static mechanical tests of two different parallel strand architectures were analyzed to understand the structure-property relationships under compressive strain. Combining effective stiffness-density scaling with least squares optimization of the stress responses yielded general response curves parameterized by resin modulus and strand spacing. An analytical expression of these curves serves as a reduced order model, which, when optimized, provides a rapid design capability for filament-based 3D printed structures. As a demonstration, the optimal design of a face-centered tetragonal architecture is computed that satisfies prescribed minimum and maximum load constraints.