gebhart/patrepeval huggingface dataset:
A deep learning-based automated closed-loop optogenetic system for neuromodulation during seizures (2022)

Abstract Closed-loop electrical brain stimulation is becoming a popular technique proposed for use as a treatment alternative to surgical resection of brain tissue for drug-resistant seizures in epilepsy patients. Closed-loop optogenetic stimulation is an experimental alternative to electrical stimulation since it can stimulate or inhibit neurons. The closed-loop part contains an online seizure detection algorithm, which, based on the design, can detect the onset of a seizure or evaluate a running window for seizure membership. Conventional configurations of closed-loop optogenetics have several limitations, ranging from the adaptability of hardware-based implementation to inadequate, customized feature selection of seizures, among others. Here we provide a detailed description of our closed-loop components. We used a sequential, fully convolutional neural network regressor for complex feature selection of seizures against the controls from local field potential recordings. Our modular design kept the local field potential-recording headset and optical probe separate. The seizure detection and execution of light delivery are fast and can be precisely timed. This automated system is robust to noise, modular in design, flexible in use, and simple execution. When applied in vivo, the proposed work shows efficacy over the state of the arts in terms of improved seizure detection and reduction in false positives.
Performance Analysis of an Adaptive Optics System with Scintillation-Resistant Phase-Contrast Wavefront Sensor (2019)

An adaptive optics system based on a novel high-resolution, scintillation resistant wavefront sensor that utilizes phase contrast (Zernike-filter arrangement) visualization technique for operation in deep turbulence conditions is introduced and analyzed using wave-optics numerical simulations.
Preliminary Findings on LignoDeco project: Optimized Pre-treatment of Fast Growing Woody and Nonwoody Brazilian Crops by Detailed Characterization of Chemical Changes Produced in the Lignin-carbohydrate Matrix (2012)

The emerging concepts regarding bioproducts from lignocellulosics are very suitable for existing pulp manufacturing facilities, to take advantage of infrastructure and process integration. The LignoDeco project is a partnership among 5 countries (Brazil, Finland, Denmark, Spain and France – Fig. 1), promoted by the EC FP7 programme. It focus on the development of pre-treatments for deconstruction of high productivity and fast-growing Brazilian eucalypt clones and elephant grass, aiming at production of special pulps and bioproducts, using modern analytical techniques for in-depth identification of the changes produced in the main plant polymers. The project is now on the 30th month and resulted 3 patents, 12 peer-reviewed papers, 28 oral/visual presentations, and many other dissemination activities.
Electric field probe using a differential amplifier circuit with high input impedance (2015)

Switching of power electronic equipment mounted in vehicles generates unwanted electromagnetic radiation and interferes with radios. In particular, it is difficult to secure performance in the AM radio band because its frequencies are near switching frequencies. In order to reduce extraneous electromagnetic radiation from power electronic equipment, identifying noise sources and propagation paths by measuring electric fields near equipment with probes is effective, but in AM radio and other low-frequency bands, the sensitivity of electric field probes dropped and measurement was difficult. We developed a high-sensitivity electric field probe using a differential input amplifier circuit with high input impedance. Also, as an example of measurement, the near electric field when a DC motor was driven with PWM was measured and the radiation source was identified.
A Comprehensive Analysis of Human Gene Expression Profiles Identifies Stromal Immunoglobulin κ C as a Compatible Prognostic Marker in Human Solid Tumors (2012)

Our findings provide IGKC as a novel diagnostic marker for risk stratification in human cancer and support concepts to exploit the humoral immune response for anticancer therapy. It could be validated in several independent cohorts and carried out similarly well in RNA from fresh frozen as well as from paraffin tissue and on protein level by immunostaining.
Challenges in Electronic Cooling: Opportunities for Enhanced Thermal Management Techniques — Microprocessor Liquid Cooled Minichannel Heat Sink (2003)

The volumetric heat dissipated by computer equipment at each level of the package from the chip to the chassis is having a tremendous impact on the thermal management of computer equipment. Because of the consumer’s insatiable desire for increased performance the competitive pressures are driving the computer manufacturer to pack as much processor/memory performance within the smallest volume possible. The consumer views high performance in a compact package as a benefit. These market pressures seem to be in direct conflict with the desire to continue to provide air cooling solutions for the foreseeable future. Because of these trends in power and package design other cooling technologies beside air are now becoming viable techniques but each must be weighed with many other factors that influence the cooling technology selected. These factors will discussed along with two specific IBM server packages and their associated cooling technology employed. Finally a microprocessor liquid cooled minichannel heat sink will be described and its performance presented as applied to a current microprocessor (IBM Power4) chip.
Controlling the Crystallization of Porous Organic Cages: Molecular Analogs of Isoreticular Frameworks Using Shape-Specific Directing Solvents (2014)

Small structural changes in organic molecules can have a large influence on solid-state crystal packing, and this often thwarts attempts to produce isostructural series of crystalline solids. For metal-organic frameworks and covalent organic frameworks, this has been addressed by using strong, directional intermolecular bonding to create families of isoreticular solids. Here, we show that an organic directing solvent, 1,4-dioxane, has a dominant effect on the lattice energy for a series of organic cage molecules. Inclusion of dioxane directs the crystal packing for these cages away from their lowest-energy polymorphs to form isostructural, 3-dimensional diamondoid pore channels. This is a unique function of the size, chemical function, and geometry of 1,4-dioxane, and hence, a noncovalent auxiliary interaction assumes the role of directional coordination bonding or covalent bonding in extended crystalline frameworks. For a new cage, CC13, a dual, interpenetrating pore structure is formed that doubles the gas uptake and the surface area in the resulting dioxane-directed crystals.
The two-stage standard in revision total hip replacement (2013)

Two-stage exchange remains the gold standard for treatment of peri-prosthetic joint infection after total hip replacement (THR). In the first stage, all components and associated cement if present are removed, an aggressive debridement is undertaken including a complete synovectomy, and an antibiotic-loaded cement spacer is put in place. Patients are then treated with six weeks of parenteral antibiotics, followed by an 'antibiotic free period' to help ensure the infection has been eradicated. If the clinical evaluation and serum inflammatory markers suggest the infection has resolved, then the second stage can be completed, which involves removal of the cement spacer, repeat debridement, and placement of a new THR.
Globally optimal segmentation of multi-region objects (2009)

Many objects contain spatially distinct regions, each with a unique colour/texture model. Mixture models ignore the spatial distribution of colours within an object, and thus cannot distinguish between coherent parts versus randomly distributed colours. We show how to encode geometric interactions between distinct region+boundary models, such as regions being interior/exterior to each other along with preferred distances between their boundaries. With a single graph cut, our method extracts only those multi-region objects that satisfy such a combined model. We show applications in medical segmentation and scene layout estimation. Unlike Li et al. we do not need “domain unwrapping” nor do we have topological limits on shapes.
Chloroplast-Derived Vaccine Antigens and Biopharmaceuticals: Protocols for Expression, Purification, or Oral Delivery and Functional Evaluation (2009)

Many vaccine antigens and biopharmaceutical proteins have been expressed at high levels via the chloroplast genome and their functionality has been evaluated using in vitro assays in cell cultures (i.e., macrophage lysis assay, inhibition of vesicular stomatitis virus-induced cytopathicity in baby hamster kidney cells, or inhibition of human HIV infection in TZM-BL cells) as well as protection after challenge with bacterial or viral pathogens or antitumor assays or delay the onset of insulitis in suitable animal models. Production of therapeutic proteins in chloroplasts eliminates the expensive fermentation technology. Moreover, oral delivery of chloroplast-derived therapeutic proteins eliminates expensive purification steps, cold storage, cold transportation, and delivery via sterile needles, thereby further decreasing their cost. In this chapter, we describe detailed protocols for chloroplast transformation including the construction of chloroplast transformation vectors, delivery of DNA into plant cells using particle bombardment, selection and regeneration of transformants by tissue culture, confirmation of transgene integration into the chloroplast genome and homoplasmy, evaluation of foreign gene expression, purification of foreign protein, or oral delivery via bioencapsulation, functional evaluation using in vitro and in vivo assays, and evaluation of immunity after challenge with pathogens in suitable animal models.
Analysis of line current wave diffraction from metal-backed dielectric strip by extended PO method (2002)

We present the modified physical optics (PO) analysis of line current wave scattering by planar metal-backed dielectric strips. The effects of dielectric coatings on the reflecting properties of planar strips are analyzed in the detail including the differences of pattern shape and null points' shift in the cases of E- and H-polarized scattering. It is shown that changing the dielectric permittivity and thickness of a coating may result in substantial pattern shape transformation for the same width of a reflector aperture. The robustness of proposed approach can also be used for studying the scattering properties of thin multilayered and varying thickness coatings by applying the corresponding expressions for the reflection coefficient.
Glycosylphosphatidylinositol (GPI) anchored protein deficiency serves as a reliable reporter of Pig‐a gene Mutation: Support from an in vitro assay based on L5178Y/Tk+/− cells and the CD90.2 antigen (2017)

Lack of cell surface glycosylphosphatidylinositol (GPI)-anchored protein(s) has been used as a reporter of Pig-a gene mutation in several model systems. As an extension of this work, our laboratory initiated development of an in vitro mutation assay based on the flow cytometric assessment of CD90.2 expression on the cell surface of the mouse lymphoma cell line L5178Y/Tk<sup>+/-</sup> . Cells were exposed to mutagenic and nonmutagenic compounds for 24 hr followed by washout and incubation for an additional 7 days. Following this mutant manifestation time, cells were labeled with fluorescent antibodies against CD90.2 and CD45 antigens. These reagents indicated the presence of GPI-anchored proteins and general cell surface membrane receptor integrity, respectively. Instrument set-up was aided by parallel processing of a GPI anchor-deficient subclone. Results show that the mutagens reproducibly caused increased frequencies of mutant phenotype cells, while the nonmutagens did not. Further modifications to the method, including application of a viability dye and an isotype control for instrument set-up, were investigated. As a means to verify that the GPI-anchored protein-negative phenotype reflects bona fide Pig-a gene mutation, sequencing was performed on 38 CD90.2-negative L5178Y/Tk<sup>+/-</sup> clones derived from cultures treated with ethyl methanesulfonate. All clones were found to have mutation(s) within the Pig-a gene. The continued investigation of L5178Y/Tk<sup>+/-</sup> cells, CD90.2 labeling, and flow cytometric analysis as the basis of an in vitro mutation assay is clearly supported by this work. These data also provide evidence of the reliability of using GPI anchor-deficiency as a valid reporter of Pig-a gene mutation. Environ. Mol. Mutagen. 59:18-29, 2018. © 2017 Wiley Periodicals, Inc.
Correction to Anti-inflammatory Efficacy of Combined Natural Alkaloid Berberine and S1PR Modulator Fingolimod at Low Doses in Ulcerative Colitis Preclinical Models (2021)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to Anti-inflammatory Efficacy of Combined Natural Alkaloid Berberine and S1PR Modulator Fingolimod at Low Doses in Ulcerative Colitis Preclinical ModelsQian HanQian HanMore by Qian Han, Hua-zheng TangHua-zheng TangMore by Hua-zheng Tang, Min ZouMin ZouMore by Min Zou, Jie ZhaoJie ZhaoMore by Jie Zhao, Ling WangLing WangMore by Ling Wanghttps://orcid.org/0000-0001-5116-7749, Zhao-xiang Bian*Zhao-xiang BianMore by Zhao-xiang Bian, and Yan-hong Li*Yan-hong LiMore by Yan-hong Lihttps://orcid.org/0000-0002-1410-2484Cite this: J. Nat. Prod. 2021, 84, 8, 2408–2409Publication Date (Web):August 18, 2021Publication History Published online18 August 2021Published inissue 27 August 2021https://pubs.acs.org/doi/10.1021/acs.jnatprod.1c00659https://doi.org/10.1021/acs.jnatprod.1c00659correctionACS PublicationsCopyright 2021 © 2020 American Chemical Society and American Society of Pharmacognosy. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views856Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (2 MB) Get e-Alertsclose Get e-Alerts
A Bioinspired Molybdenum-Copper Molecular Catalyst for CO2 Electroreduction (2020)

Non‐noble metal molecular catalysts mediating the electrocatalytic reduction of carbon dioxide are still scarce. This work reports the electrochemical reduction of CO2 to formate catalyzed by the bimetallic complex [(bdt)MoVI(O)S2CuICN]2‐ (bdt = benzenedithiolate), a mimic of the active site of the Mo‐Cu carbon monoxide dehydrogenase enzyme (CODH2). Infrared spectroelectrochemical (IR‐SEC) studies coupled with density functional theory (DFT) computations revealed that the complex is only a pre‐catalyst, the active catalyst being generated upon reduction in the presence of CO2. We found that the two‐electron reduction of [(bdt)MoVI(O)S2CuICN]2‐ triggers the transfer of the oxo moiety to CO2 forming CO3 2‐and the complex [(bdt)MoIVS2CuICN]2– and that a further oneelectron reduction is needed to generate the active catalyst. Its protonation yields a reactive MoVH hydride intermediate which reacts with CO2 to produce formate. These findings are particularly relevant to the design of catalysts from metal oxo precursors.&lt;br&gt;
Mutated EZH2 Collaborates with Myc in Inducing Lymphoma in a Mouse Model (2011)

Abstract Abstract 227 The histone methyl-transferase EZH2 is frequently mutated in germinal-center derived diffuse-large B cell lymphoma (DLBCL) and follicular lymphoma. We and others have demonstrated that these mutations in tyrosine 641 of EZH2 represent a dominant gain-of-function, enhancing the capability to trimethylate H3K27 in combination with wildtype activity (Yap et al, Blood 2011; Sneeringer et al, PNAS 2010). To further test if these EZH2 mutations can be driver mutations in lymphomagenesis we have now generated and characterized a mouse line transgenic for EZH2 Y641F (the most commonly observed mutant form). Transgenic mice were created on the C57/Bl6 background by pronuclear microinjection of a construct where EZH2 Y641F is expressed from a lymphoid specific Emu-lck promoter. Spleen cells isolated from the transgenic mice displayed a global increase in H3K27me3 when analyzed by Western Blot. However none of the mice showed signs of lymphoma even when observed for prolonged periods of time. As EZH2 mutations often coincide with other mutations in lymphoma, we also combined the expression of EZH2 Y641F with the over-expression of Myc by crossing one of the transgenic lines with Emu-myc transgenic mice. In this combination model, we observed a dramatic acceleration of lymphoma development with the combination of Myc and EZH2 Y641F as compared to Myc alone (Myc alone (n=26) 137.5 days, Myc+EZH2 Y641F (n=20) 51 days, p &lt; 0.0001 Log-Rank (Mantel-Cox) Test). The resulting lymphomas are characterized by a generalized massive lymphadenopathy, splenomegaly (spleen weight 0.416 +/− 0.133 g), bone marrow infiltration (72 +/− 8 %) and lymphocytosis (WBC 138.5 +/− 77.1 ×1000/μl). They show histological features of high-grade disease, and initiate disease in secondary recipients. In contrast to lymphomas observed with Emu-myc alone, all of the lymphomas observed in mice transgenic for both, Myc and EZH2 Y641F, presented with a mature B cell phenotype (B220+IgM+). This shift in differentiation can also be observed in the bone marrow even before development of overt lymphomas. While Myc transgenics mainly show an increase in the B220+IgM−compartment, this is shifted towards B220+IgM+ in double transgenics. Cell cycle analysis by in vivo Brdu incorporation before disease onset shows a drastic increase in the fraction of cells in cycle in the splenic B cells of double transgenic mice (43.3 and 44.9 % cells in S phase) as compared to mice transgenic for Myc alone (10.6 % and 14.2 % cells in S phase). Southern Blot analysis using a probe specific for JH4 showed more than one clonal rearrangement in a majority of the lymphomas in the double-transgenic mice. In summary, EZH2 Y641F can collaborate with Emu-myc in high efficiency lymphoma induction. This new murine lymphoma model now provides a powerful tool to study global changes in the epigenome caused by this frequent mutation and may be a useful system for testing novel treatments. Disclosures: No relevant conflicts of interest to declare.
Evaluation of wheat middlings as a supplement for beef cattle consuming dormant bluestem-range forage2 (1991)

Two experiments were conducted to evaluate wheat middlings as a supplement for cattle consuming dormant bluestem-range forage. Effects of supplement type and amount were evaluated in Exp. 1, which consisted of feeding supplements of soybean meal:grain sorghum (22:78) or two different amounts of wheat middlings. Sixteen ruminally fistulated steers were blocked by weight (BW = 374 +/- 8.3 kg) and assigned randomly to the following treatments: 1) control, no supplement (NS); 2) soybean meal:grain sorghum (SBM/GS) formulated to contain the same CP concentration (21%) and fed to provide a similar energy level (3.5 Mcal of ME/d); 3) a supplement of 100% wheat middlings fed at a low level (LWM); and 4) 100% wheat middlings fed at twice the amount of LWM (7 Mcal of ME/d; HWM). The influence of different supplemental CP concentrations in a wheat middlings-based supplement was evaluated in Exp. 2. Sixteen ruminally fistulated steers were blocked by weight (BW = 422 +/- 8.1 kg) and assigned randomly to the following treatments: 1) control, no supplement (NS); 2) 15% CP; 3) 20% CP; and 4) 25% CP supplements. These supplements consisted of 60% wheat middlings and various ratios of soybean meal and grain sorghum to achieve the desired CP concentration. In Exp. 1, SBM/GS and HWM supplements increased (P less than .10) and LWM tended to increase (P = .16) forage DMI compared with NS. All supplements in Exp. 1 increased (P less than .10) DM digestibility, ruminal DM fill, and ruminal indigestible ADF (IADF) passage rate compared with NS, although the greatest response in fill and passage was observed with HWM. In Exp. 2, forage DMI, DM digestibility, NDF digestibility, ruminal DM and IADF fill, IADF passage rate, and fluid dilution rate were increased (P less than .01) by supplementation. Forage DMI, ruminal IADF passage rate, and fluid dilution rate increased quadratically (P less than .10), and NDF digestibility, ruminal DM and IADF fill increased linearly (P less than .10) with increased supplemental CP concentration. These experiments indicate that wheat middlings performed similarly to a SBM/GS supplement of equal CP concentration, when both were fed to provide a similar amount of energy daily. Additionally, use of poor-quality range forage was enhanced when wheat middlings-based supplements were formulated to contain a CP concentration of 20% or greater.
Analysis of thermal stress in wafer bonding of dissimilar materials for the introduction of an InP-based light emitter into a GaAs-based three-dimensional photonic crystal (2003)

Thermal stresses generated by differences in the thermal expansion coefficients of InP and GaAs are analyzed in an attempt to introduce an InP-based light emitter into GaAs-based three-dimensional photonic crystal. Observations of the GaAs/InGaAsP bonding interface by scanning acoustic microscopy reveal that debonding occurs at approximately 300 °C due to thermal stress. Calculations of thermal stress by a two-dimensional finite element method suggested that thermal stress could be reduced by thinning the substrate, which was confirmed experimentally. Using these results, a three-dimensional photonic crystal with light emitter was successfully fabricated.
The DLR C-runner: Concept, design and experiments (2016)

Legged locomotion requires highly dynamic and efficient actuation as well as robust environment interaction. In the past years soft robots with elastic actuation have been investigated and their fitness for cyclic tasks and safe and robust environment interaction has been shown. To evaluate the benefits and drawbacks of series elastic actuation, variable impedance actuation as well as multi-articular elastic coupling in legged locomotion, we developed a two legged human size test-bed. These modular robotic legs give the possibility to evaluate and directly compare different elastic actuation concepts on a single system. Hopping and bipedal modal motion experiments where performed to proof the concept.