gebhart/patrepeval huggingface dataset:
A Molecularly Defined Duplication Set for the X Chromosome of <i>Drosophila melanogaster</i> (2010)

Abstract We describe a molecularly defined duplication kit for the X chromosome of Drosophila melanogaster. A set of 408 overlapping P[acman] BAC clones was used to create small duplications (average length 88 kb) covering the 22-Mb sequenced portion of the chromosome. The BAC clones were inserted into an attP docking site on chromosome 3L using ΦC31 integrase, allowing direct comparison of different transgenes. The insertions complement 92% of the essential and viable mutations and deletions tested, demonstrating that almost all Drosophila genes are compact and that the current annotations of the genome are reasonably accurate. Moreover, almost all genes are tolerated at twice the normal dosage. Finally, we more precisely mapped two regions at which duplications cause diplo-lethality in males. This collection comprises the first molecularly defined duplication set to cover a whole chromosome in a multicellular organism. The work presented removes a long-standing barrier to genetic analysis of the Drosophila X chromosome, will greatly facilitate functional assays of X-linked genes in vivo, and provides a model for functional analyses of entire chromosomes in other species.
Immobilization of trypsin in organic and aqueous media for enzymatic peptide synthesis and hydrolysis reactions (2015)

By immobilizing trypsin in dioxane, a beneficial effect on the synthetic trypsin activity resilience compared to aqueous immobilization medium was shown. The results indicate a substantial potential of the micro-aqueous organic protease immobilization method for preservation of enzymatic activity during enzyme coupling step. These results may be of substantial interest for enzymatic peptide synthesis reactions at mild conditions with high selectivity in industrial drug production.
Stable coronary artery disease - case report (2006)

Drug Prescribing for Patients with Chronic Kidney Disease in General Practice: a Cross-Sectional Study
Forecasting with trees (2021)

The prevalence of approaches based on gradient boosted trees among the top contestants in the M5 competition is potentially the most eye-catching result. Tree-based methods out-shone other solutions, in particular deep learning-based solutions. The winners in both tracks of the M5 competition heavily relied on them. This prevalence is even more remarkable given the dominance of other methods in the literature and the M4 competition. This article tries to explain why tree-based methods were so widely used in the M5 competition. We see possibilities for future improvements of tree-based models and then distill some learnings for other approaches, including but not limited to neural networks.
&lt;title&gt;The solid state silicon photomultiplier for a wide range of applications&lt;/title&gt; (2003)

The new type of photodetector - Silicon Photomultiplier (SiPM) is presented. The SiPM consists of the array (matrix) of p-n-junctions (~10<sup>3</sup> mm<sup>-2</sup>) joint together on a common silicon substrate. Each p-n-junction working in limited Geiger mode with a gain 10<sup>6</sup>, but SiPM in whole is analogue detector, because the SiPM output signal is a sum of the signals from p-n-junctions fired by photons. The main SiPM features are described and its performance is compared with other photodetectors.
Bit-interleaved coded differential space-time modulation (2002)

Bit-interleaved coded differential space-time modulation for transmission over spatially correlated Ricean flat fading channels is discussed. For improved noncoherent detection without channel state information at the receiver, iterative decoding employing hard-decision feedback and prediction-based metric computation is applied. The performance is assessed based on the associated cutoff rate, analytical expressions for the bit error rate and the outage probability, respectively and simulations. It is shown that the proposed scheme offers high power efficiency exploiting both space and time diversity, while the computational complexity is kept at a relatively low level.
Physics-based modeling of X-ray CT measurements with energy-integrating detectors (2014)

Computer simulation tools for X-ray CT are important for research efforts in developing reconstructionmethods, designing new CT architectures, and improving X-ray source and detector technologies. In this paper, we propose a physics-based modeling method for X-ray CT measurements with energy-integrating detectors. It accurately accounts for the dependence characteristics on energy, depth and spatial location of the X-ray detection process, which is either ignored or over simplified in most existing CT simulation methods. Compared with methods based on Monte Carlo simulations, it is computationally much more efficient due to the use of a look-up table for optical collection efficiency. To model the CT measurments, the proposed model considers five separate effects: energy- and location-dependent absorption of the incident X-rays, conversion of the absorbed X-rays into the optical photons emitted by the scintillator, location-dependent collection of the emitted optical photons, quantumefficiency of converting fromoptical photons to electrons, and electronic noise. We evaluated the proposed method by comparing the noise levels in the reconstructed images from measured data and simulations of a GE LightSpeed VCT system. Using the results of a 20 cm water phantom and a 35 cm polyethylene (PE) disk at various X-ray tube voltages (kVp) and currents (mA), we demonstrated that the proposed method produces realistic CT simulations. The difference in noise standard deviation between measurements and simulations is approximately 2% for the water phantom and 10% for the PE phantom.
A computational study of potential molecular switches that exploit Baird's rule on excited-state aromaticity and antiaromaticity (2014)

A series of tentative single-molecule conductance switches which could be triggered by light were examined by computational means using density functional theory (DFT) with non-equilibrium Green's functions (NEGF). The switches exploit the reversal in electron counting rules for aromaticity and antiaromaticity upon excitation from the electronic ground state (S0) to the lowest ππ* excited singlet and triplet states (S1 or T1), as described by Hückel's and Baird's rules, respectively. Four different switches and one antifuse were designed which rely on various photoreactions that either lead from the OFF to the ON states (switches 1, 2 and 4, and antifuse 5) or from the ON to the OFF state (switch 3). The highest and lowest ideal calculated switching ratios are 1175 and 5, respectively, observed for switches 1 and 4. Increased thermal stability of the 1-ON isomer is achieved by benzannulation (switch 1B-OFF/ON). The effects of constrained electrode-electrode distances on activation energies for thermal hydrogen back-transfer from 1-ON to 1-OFF and the relative energies of 1-ON and 1-OFF at constrained geometries were also studied. The switching ratio is strongly distance-dependent as revealed for 1B-ON/OFF where it equals 711 and 148 when the ON and OFF isomers are calculated in electrode gaps with distances confined to either that of the OFF isomer or to that of the ON isomer, respectively.
2DCOR-GC:  An Application of the Generalized Two-Dimensional Correlation Analysis as a Route To Optimization of Continuous Flow Supercritical Fluid Reactions (2004)

A new approach for optimization and monitoring of continuous reactions has been developed using 2D correlation methods for the analysis of GC data (2DCOR-GC). 2DCOR-GC maps are obtained following perturbation of the system that allow the effect of changing reaction parameters such as time, temperature, pressure, or concentration to be both monitored and sequenced with regard to changes in the raw GC data. In this paper, we describe the application of the 2DCOR-GC technique to monitoring the reverse water-gas shift reaction in scCO(2). 2DCOR-GC is combined with FT-IR data to validate the methodology. We also report the application of 2DCOR-GC to probe the mechanism of the alkylation of m-cresol with isopropyl alcohol in scCO(2) using Nafion SAC-13 as the catalyst. These results identify coeluting peaks that could easily be missed without exhaustive method development.
Comprehensive mass spectrometry lipidomics of human biofluids and ocular tissues (2023)

Evaluating lipid profiles in human tissues and biofluids is critical in identifying lipid metabolites in dysregulated metabolic pathways. Due to various chemical characteristics, single-run lipid analysis has not yet been documented. Such approach is essential for analyzing pathology-related lipid metabolites. Age-related macular degeneration, the leading cause of vision loss in western countries, is emblematic of this limitation. Several studies have identified alterations in individual lipids but the majority are based on targeted approaches. In this study, we analyzed and identified approximately 500 lipid species in human biofluids (plasma and erythrocytes) and ocular tissues (retina and retinal pigment epithelium) using the complementarity of hydrophilic interaction liquid chromatography (HILIC) and reversed-phase chromatography (RPC), coupled to high-resolution mass spectrometry. For that, lipids were extracted from human eye globes and blood from 10 subjects and lipidomic analysis was carried out through analysis in HILIC and RPC, alternately. Furthermore, we illustrate the advantages and disadvantages of both techniques for lipid characterization. RPC showed greater sensitivity in hydrophobicity-based lipid separation, detecting diglycerides, triglycerides, cholesterol, and cholesteryl esters, whereas no signal of these molecules was obtained in HILIC. However, due to coelution, RPC was less effective in separating polar lipids like phospholipids, which were separated effectively in HILIC in both ionization modes. The complementary nature of these analytical approaches was essential for the detection and identification of lipid classes/subclasses, which can then provide distinct insights into lipid metabolism, a determinant of the pathophysiology of several diseases involving lipids, notably age-related macular degeneration.
Chaotic Sensing (2018)

We propose a sparse imaging methodology called Chaotic Sensing (ChaoS) that enables the use of limited yet deterministic linear measurements through fractal sampling. A novel fractal in the discrete Fourier transform is introduced that always results in the artefacts being turbulent in nature. These chaotic artefacts have characteristics that are image independent, facilitating their removal through dampening (via image denoising) and obtaining the maximum likelihood solution. In contrast with existing methods, such as compressed sensing, the fractal sampling is based on digital periodic lines that form the basis of discrete projected views of the image without requiring additional transform domains. This allows the creation of finite iterative reconstruction schemes in recovering an image from its fractal sampling that is also new to discrete tomography. As a result, ChaoS supports linear measurement and optimisation strategies, while remaining capable of recovering a theoretically exact representation of the image. We apply the method to simulated and experimental limited magnetic resonance (MR) imaging data, where restrictions imposed by MR physics typically favour linear measurements for reducing acquisition time.
Abstract P135: Systemic targeting of a CNS tumor (medulloblastoma) using a novel cell-penetrating, nucleic acid binding, monoclonal antibody (2021)

Abstract Targeting tumors of the central nervous system remains challenging given the physiological barriers preventing the delivery of therapeutics across the blood brain barrier (BBB). This is particularly true for nucleic acids, which degrade rapidly in serum and often fail to penetrate cells even with proper formulation into AAVs or LNPs. To overcome these barriers, many current efforts rely on invasive methods of delivery, including intrathecal or intraparenchymal injection. Here we report studies evaluating the ability of a novel cell-penetrating antibody, GMAB, to penetrate the BBB and target a CNS model of medulloblastoma (DAOY) following intravenous administration. Studies with fluorescently labeled GMAB demonstrated that the antibody readily penetrated into the CNS following systemic administration, achieving tumor-specific delivery while sparing surrounding normal brain tissue. Subsequent studies with 3p-hpRNA, a known activator of RIG-I, a cytosolic pattern recognition receptor which detects viral RNA and elicits a type-I interferon response, demonstrated that GMAB could deliver RNA ligands to tumors, resulting in significantly reduced intracranial tumor burden 10 days after a single-dose administered systemically while also preventing the development of spinal metastases. These results highlight a novel approach for the systemic delivery of immunostimulatory RNAs in a targeted manner to multiple tumors including often difficult to treat CNS tumors, which may offer treatment advantages over current approaches. Citation Format: Elias Quijano, Minsoo Khang, Bruce C. Turner, Stephen Squinto, Ranjit Bindra, W. Mark Saltzman, Peter Glazer. Systemic targeting of a CNS tumor (medulloblastoma) using a novel cell-penetrating, nucleic acid binding, monoclonal antibody [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P135.
SpiDeR –Spill Detection and Recognition system for ROV operations (2021)

ABSTRACT The paper presents the outline of the Spill Detection and Recognition system – SpiDeR and its application to underwater oil and gas detection, classification and source characterization demonstrated in the remote-sensing survey of Mississippi Canyon area in the Gulf of Mexico founded by BSEE in 2017. The main objective of the operation was to deploy sensor package from a remotely-operated vehicle (ROV) to survey, detect, and map the location(s) of hydrocarbon emissions that are responsible for the surface oil spill and sheen footprint in the Mississippi Canyon Area. The objectives have been accomplished by conducting a multi-day, three-part survey mapping the area of interest, generation of georeferenced charts and 3D visualizations with detected oil active spills, all supported by a ROV intervention outfitted with oil spill detection and recognition system SpiDeR. SpiDeR is a modular sensor suite capable of detecting, recognizing the source and classifying the hydrocarbon underwater leaks. The sensor suit with selectable configuration can be installed on any type of ROV vehicle and interfaces to the ROV with a single cable conducting the power and data. The presented here and used during the mission complete sensor suite consist of two 3D, broad band, electronically scanning multibeam sonar systems NORBIT WBMS STX, one Forward Looking Sonar NORBIT WBMS FLS, fluorescent oil classifier LIF – Laser Induced Fluorescence detection unit and the video camera with lights. The most useful capability of the SpiDeR is the ability to generate 3D imagery (georeferenced bathymetry) even when the ROV is not moving. That combined with time gives 4D observable capabilities of the oil spill. The 4D capabilities have been proven useful during the u-bathymetry part in Phase 2 and forward-looking 3D in Phase 3 of this mission. The system has been deployed from the ROV in the area where it has been known for the last decade that the leak of hydrocarbons is coming from. The real task at hand was to recognize the leak source and that source contain hydrocarbons and accurately document the source location and provide measurable documentation of its character.
A hybrid numerical-composite UTD ray analysis of the radiation by large locally convex conformal arrays on large platforms (2013)

A new efficient hybrid numerical-composite UTD ray solution is presented to describe the radiation from an aperture formed by a large phased array antenna mounted conformally on a locally convex, but otherwise relatively arbitrary large platform. The aperture distribution is first obtained from a numerical solution for the array fields, which takes into account only the local array portion of the platform geometry, via the finite element-boundary integral (FE-BI) or the finite element method (FEM) based approaches. The electromagnetic (EM) equivalence theorem can be used to obtain the equivalent sources over the array aperture; the latter equivalent sources then radiate the array fields via a new composite uniform geometrical theory of diffraction (UTD) for arrays. This composite UTD describes the fields radiated by the entire array in terms of just a few rays arising from a point in the interior of the array aperture, and from specific points on the edges and corners of the array aperture boundary. These rays once launched from the array aperture then interact with the rest of the platform via the conventional UTD. Such an approach is far more efficient than solving the whole large complex array and its even larger platform simultaneously in some numerical fashion. Furthermore, it provides a physical insight into the array radiation mechanisms.
Novel /spl mu/trench phase-change memory cell for embedded and stand-alone non-volatile memory applications (2004)

A novel cell structure for chalcogenide-based non-volatile Phase-Change Memories is presented. The new /spl mu/trench approach is fully compatible with an advanced CMOS technology, is highly manufacturable and allows to optimize array density and cell performance. Programming currents of 600 /spl mu/A, endurance of 10/sup 11/ programming cycles and data retention capabilities for 10 years at 110/spl deg/C have been demonstrated. The manufacturability is proven by experimental results from multi-megabit arrays.
Self‐rated health scores predict mortality among people with type 2 diabetes differently across three different country groupings: findings from the ADVANCE and ADVANCE‐ON trials (2020)

Self-rated health appears to predict 10-year all-cause mortality for people with type 2 diabetes worldwide, but this relationship varies across groups of countries.
Millimeter-Wave SiGe Radiometer Front End With Transformer-Based Dicke Switch and On-Chip Calibration Noise Source (2021)

We present a co-designed Dicke switch and low-noise amplifier (LNA) in which the switch incorporates a transformer-based topology and serves as the input matching network of the LNA. This topology is configured to minimize the amplifier gain mismatch between the two switching states caused by process variations while providing a low noise figure (NF). The circuit is implemented in a 0.13- μm SiGe BiCMOS technology, and it achieves more than 20-dB gain and minimum NF values of 4.5 and 0.58 dB at 300 and 20 K, respectively. It consumes a dc power of 15 mW. The front-end switch presents a peak isolation of 17 dB, and the input return loss is better than 15 dB across 45-70 GHz. A noise source is also coupled to the front-end circuitry to enable on-chip calibration. The noise performance and reliability of several on-chip p-n junctions were characterized, and the one with the highest excess noise ratio was coupled to the front-end circuitry. To the best of our knowledge, the lowest NF of an integrated switch and LNA at V-band frequencies is achieved in the present work, along with the first reliability study of on-chip noise sources in a SiGe BiCMOS technology.
The effects of design details on cost and weight of fuselage structures (1993)

Crown panel design studies showing the relationship between panel size, cost, weight, and aircraft configuration are compared to aluminum design configurations. The effects of a stiffened sandwich design concept are also discussed. This paper summarizes the effect of a design cost model in assessing the cost and weight relationships for fuselage crown panel designs. Studies were performed using data from existing aircraft to assess the effects of different design variables on the cost and weight of transport fuselage crown panel design. Results show a strong influence of load levels, panel size, and material choices on the cost and weight of specific designs. A design tool being developed under the NASA ACT program is used in the study to assess these issues. The effects of panel configuration comparing postbuckled and buckle resistant stiffened laminated structure is compared to a stiffened sandwich concept. Results suggest some potential economy with stiffened sandwich designs for compression dominated structure with relatively high load levels.
Optimization of Bioprocess Extraction of Poria cocos Polysaccharide (PCP) with Aspergillus niger β-Glucanase and the Evaluation of PCP Antioxidant Property (2020)

<i>Poria cocos</i> mushroom is widely used as a food and an herb in East Asian and other countries due to its high nutritional value. Research has demonstrated that <i>Poria cocos</i> polysaccharides (PCP) are the major bioactives and possess antioxidation, anti-inflammation, immunoregulation, and other health promoting properties. However, the efficient preparation of PCP has been a challenge, particularly in large scale for industry. Herein, we investigated the biotransformation of PCP from <i>Poria cocos</i>, catalyzed by β-glucanase from <i>Aspergillus niger</i> and focused on optimizing the most four influencing parameters: Temperature, time, pH, and enzyme dosage in this study. After numerous optimizations with the assistance of response surface optimization methodology, we have established that the optimal conditions for the biotransformation PCP preparation were as following: Enzymolysis temperature 60 °C, time 120 min, pH 5.0 and enzyme dose 20 mL. Under these conditions, the extraction yield of PCP reached as high as 12.8%. In addition, the antioxidant activities of PCP were evaluated by reducing power assay and 1,1-diphenyl-2-picryl-hydrazyl, superoxide anion, and hydroxyl radicals scavenging assays. Resulting data showed that PCP presented outstanding antioxidant capacity. Thus, these findings indicate that PCP could be produced as a natural antioxidant for further development.
Tunable two-colour patterning of MEHPPV from a single precursor (2007)

We present here a new approach to the generation of two-colour patterned films of poly[2-methoxy-5-(2'-ethylhexyloxy)–p-phenylene vinylene] (MEHPPV) starting from a single precursor containing two different types of eliminable groups; one that is thermally labile only in the presence of an acid while the other is labile even in its absence. We demonstrate the potential use of these patterned structures for optoelectronic device applications.