gebhart/patrepeval huggingface dataset:
A Nanoplotter with Both Parallel and Serial Writing Capabilities (2000)

The development of an eight-pen nanoplotter capable of doing parallel dip-pen nanolithography (DPN) is reported. Because line width and patterning speed in DPN are independent of contact force, only one of the tips in the parallel writing mode (the "imaging" tip) has a feedback system to monitor tip position and to write the pattern; all other tips reproduce what occurs at the imaging tip in a passive fashion. Proof-of-concept experiments that demonstrate eight-pen parallel writing, ink and rinsing wells, and "molecular corralling" via a nanoplotter-generated structure are reported.
Augmenting a pH Medical Study with Wearable Video for Treatment of GERD (2004)

In this paper we present an augmentation to the wearable computers typically used to determine if a patient is a candidate for surgery to correct problems associated with Gastroesophageal Reflux disease (GERD). A wearable camera was used by the first author while participating in a 24-hour stomach acid pH study. After the study's conclusion, an examination of the captured video and pH record revealed some results that allowed the first author to avoid many of the activities that result in symptoms related to GERD.
A 10-year follow-up of a patient affected by myotonic dystrophy type 1 with implantable cardioverter–defibrillator implanted for secondary prevention (2019)

De Ambroggi, Guidoa; Ali, Hussama; Cappato, Riccardoa; Sansone, Valeria A.b; De Ambroggi, Luigib Author Information
Identification and reconstitution of genetic regulatory networks for improved microbial tolerance to isooctane (2012)

Microbial tolerance to hydrocarbons has been studied in an effort to improve the productivity of biochemical processes and to enhance the efficiency of hydrocarbon bioremediation. Despite these studies, few attempts have been made to design rational strategies to improve microbial tolerance to hydrocarbons. Herein, we present an engineering framework that enables us to harness our understanding of genetic regulatory networks to improve hydrocarbon tolerance. In this study, isooctane was used as a representative hydrocarbon due to its use in petroleum refining and in biochemical processes. To increase isooctane tolerance, we first identified essential transcriptional determinants and genetic regulatory networks underlying cellular responses to isooctane in Escherichia coli using genome-wide microarray analysis. Based on functional transcriptome and bioinformatics analysis, a range of combinations of transcription factors whose activity was predictably perturbed by isooctane were knocked out and overexpressed to reconstitute the regulatory networks. We demonstrated that the reconstitution of the regulatory networks led to a significant improvement in isooctane tolerance, and especially, engineered E. coli strains lacking and overexpressing some of the perturbed transcription factors showed 3- to 5-fold improvement. This microbe with high tolerance to isooctane can be harnessed for biochemical processes, fuel oil bioremediation and metabolic engineering for biofuel production. Furthermore, we envision that the engineering framework employed to improve the tolerance in this study can be exploited for developing other microbes with desired phenotypes.
Transgenic quail as a model for research in the avian nervous system: A comparative study of the auditory brainstem (2012)

Abstract Research performed on transgenic animals has led to numerous advances in biological research. However, using traditional retroviral methods to generate transgenic avian research models has proved problematic. As a result, experiments aimed at genetic manipulations on birds have remained difficult for this popular research tool. Recently, lentiviral methods have allowed the production of transgenic birds, including a transgenic Japanese quail ( Coturnix coturnix japonica ) line showing neuronal specificity and stable expression of enhanced green fluorescent protein (eGFP) across generations (termed here GFP quail ). To test whether the GFP quail may serve as a viable alternative to the popular chicken model system, with the additional benefit of genetic manipulation, we compared the development, organization, structure, and function of a specific neuronal circuit in chicken ( Gallus gallus domesticus ) with that of the GFP quail. This study focuses on a well‐defined avian brain region, the principal nuclei of the sound localization circuit in the auditory brainstem, nucleus magnocellularis (NM), and nucleus laminaris (NL). Our results demonstrate that structural and functional properties of NM and NL neurons in the GFP quail, as well as their dynamic properties in response to changes in the environment, are nearly identical to those in chickens. These similarities demonstrate that the GFP quail, as well as other transgenic quail lines, can serve as an attractive avian model system, with the advantage of being able to build on the wealth of information already available from the chicken. J. Comp. Neurol.5–23, 2013. © 2012 Wiley Periodicals, Inc.
DNA-protein interactions in the Drosophila melanogaster mitochondrial genome as deduced from trimethylpsoralen crosslinking patterns. (1980)

The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila melanogaster was investigated by trimethylpsoralen photoreaction of embryos disrupted by gentle homogenization. After photoreaction, the mtDNA was isolated and the pattern of DNA crosslinking was determined by electron microscopy of the DNA under totally denaturing conditions. In contrast to nuclear DNA, which showed periodic crosslinks indicative of a nucleosome structure, most of each mtDNA molecule exhibited uniformly heavy crosslinking. A 10% region of the mtDNA was, however, protected from psoralen crosslinking in a distinctive manner: five uncrosslinked segments were closely clustered in the mtDNA. Four were 394 +/- 13 (SD) base pairs in size, while the fifth measured about 200 base pairs. These protected segments mapped within the A+T-rich region of the mtDNA, extending from the end of the A+T-rich region near the Bg1 II cleavage site to the center of the A+T-rich region. Protection of this part of the mtDNA from crosslinking was interpreted to be the result of association with proteins in the mitochondrion because mtDNA that was deproteinized before the photoreaction was uniformly crosslinked over its entire length. The origin of replication of the mtDNA is also located at the center of the A+T-rich region, which suggests that the protection from the psoralen photoreaction may be due to proteins involved in membrane attachment or replication.
Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design (2016)

An optimal HIV vaccine should induce broadly neutralizing antibodies (bnAbs) that neutralize diverse viral strains and subtypes. However, potent bnAbs develop in only a small fraction of HIV-infected individuals, all contain rare features such as extensive mutation, insertions, deletions, and/or long complementarity-determining regions, and some are polyreactive, casting doubt on whether bnAbs to HIV can be reliably induced by vaccination. We engineered two potent VRC01-class bnAbs that minimized rare features. According to a quantitative features frequency analysis, the set of features for one of these minimally mutated bnAbs compared favorably with all 68 HIV bnAbs analyzed and was similar to antibodies elicited by common vaccines. This same minimally mutated bnAb lacked polyreactivity in four different assays. We then divided the minimal mutations into spatial clusters and dissected the epitope components interacting with those clusters, by mutational and crystallographic analyses coupled with neutralization assays. Finally, by synthesizing available data, we developed a working-concept boosting strategy to select the mutation clusters in a logical order following a germline-targeting prime. We have thus developed potent HIV bnAbs that may be more tractable vaccine goals compared to existing bnAbs, and we have proposed a strategy to elicit them. This reductionist approach to vaccine design, guided by antibody and antigen structure, could be applied to design candidate vaccines for other HIV bnAbs or protective Abs against other pathogens.
<title>Optical calibration of the FUV spectrographic imager for the IMAGE mission</title> (1999)

The FUV Spectrographic Imager for IMAGE is simultaneously imaging auroras at 1218 and 1358 angstrom. It is designed to efficiently reject the Lyman-(alpha) emission line at 1215.7 angstrom. This paper describes the optical calibration. The content is: 1) field of view calibration: detector pixels location with respect to the reference optical cube; distortion matrix used to computer the TDI. b) Radiometric calibration: detector response and linearity; instrument throughput according to its clear aperture and mirror reflection lost; response vs. wavelength and band-rejection certification.
Autocorrection of Three-Dimensional Time-of-Flight MR Angiography of the Circle of Willis (2001)

Autocorrection can reduce artifacts in motion-corrupted MR angiography of the circle of Willis without distorting motion-free examinations.
Quantization of Hall Conductance For Interacting Electrons Without Averaging Assumptions (2009)

We consider two-dimensional Hamiltonians on a torus with finite range, finite strength interactions and a unique ground state with a non-vanishing spectral gap, and a conserved local charge, as defined precisely in the text. Using the local charge operators, we introduce a boundary magnetic flux in the horizontal and vertical direction and evolve the ground state quasi-adiabatically around a square of size one magnetic flux, in flux space. At the end of the evolution we obtain a trivial Berry phase, which we compare, via a method reminiscent of Stokes' Theorem, to the Berry phase obtained from an evolution around a small loop near the origin. As a result, we prove, without any averaging assumption, that the Hall conductance for interacting electron systems is quantized in integer multiples of e^2/h up to small corrections bounded by a function that decays as a stretched exponential in the linear size L. Finally, we discuss extensions to the fractional case under an additional topological order assumption to describe the multiple degenerate ground states.
Strategien beim Datenmanagement von Inventur- und Versuchsdaten (2002)

Die Datenverwaltung muss in viele Einzelaufgaben zerlegt werden. Auf die grosen Aufgabenkomplexe Datenbanken, Datenerfassung, Datenselektion sowie Datenauswertung, -analyse und -prasentation wurde zuvor hingewiesen. Fur alle Teilaufgaben sind separate Komponenten zu entwickeln, die wie ein Baukastensystem kombiniert werden konnen. Prioritat muss auf die Entwicklung der Datenbanken sowie Erfassungs- und Selektionssoftware gelegt werden, weil diesbezuglich die Standardsoftware nicht ausreichend an die Bedurfnisse der Menschen angepasst ist. - Die Datenverwaltung ist vielfach unzureichend organisiert. Deshalb sind beim Datenmanagement Veranderungen erforderlich. Wie die BFH- Institute 7 (Institut fur Forstokologie und Walderfassung in Eberswalde) und 2 (Institut fur Forstgenetik und Forstpflanzenzuchtung in Waldsieversdorf) diese Veranderungen im Rahmen ihrer Moglichkeiten herbeifuhren wollen und wo sie Schwerpunkte der Arbeit sehen, ist Inhalt dieses Artikels.
Custom-Made Synthetic Scaffolds for Bone Reconstruction: A Retrospective, Multicenter Clinical Study on 15 Patients (2016)

<i>Purpose</i>. To present a computer-assisted-design/computer-assisted-manufacturing (CAD/CAM) technique for the design, fabrication, and clinical application of custom-made synthetic scaffolds, for alveolar ridge augmentation. <i>Methods</i>. The CAD/CAM procedure consisted of (1) virtual planning/design of the custom-made scaffold; (2) milling of the scaffold into the exact size/shape from a preformed synthetic bone block; (3) reconstructive surgery. The main clinical/radiographic outcomes were vertical/horizontal bone gain, any biological complication, and implant survival. <i>Results</i>. Fifteen patients were selected who had been treated with a custom-made synthetic scaffold for ridge augmentation. The scaffolds closely matched the shape of the defects: this reduced the operation time and contributed to good healing. A few patients experienced biological complications, such as pain/swelling (2/15: 13.3%) and exposure of the scaffold (3/15: 20.0%); one of these had infection and complete graft loss. In all other patients, 8 months after reconstruction, a well-integrated newly formed bone was clinically available, and the radiographic evaluation revealed a mean vertical and horizontal bone gain of 2.1 ± 0.9 mm and 3.0 ± 1.0 mm, respectively. Fourteen implants were placed and restored with single crowns. The implant survival rate was 100%. <i>Conclusions</i>. Although positive outcomes have been found with custom-made synthetic scaffolds in alveolar ridge augmentation, further studies are needed to validate this technique.
A 65nm ultra low power logic platform technology using uni-axial strained silicon transistors (2006)

A leading edge 65nm logic process technology employing uni-axial strained silicon transistors has been optimized for ultra low power products. Record PMOS/NMOS drive currents of 0.38/0.66 mA/mum, respectively, have been achieved at 1.2V and off-state leakage of 100 pA/mum. Greater than 1000times reduction of SRAM cell standby leakage through implementation of sleep transistors and other leakage suppression schemes are also discussed
On-chip integration and high-speed switching of multi-wavelength narrowband thermal emitters (2016)

We experimentally demonstrate the high-speed, on-chip wavelength switching of thermal emission in the mid-infrared region. Our device consists of multiple integrated thermal emitters of different colors, each of which is composed of quantum wells and a photonic crystal. On current injection, the device exhibits narrowband (Q &amp;gt; 70) thermal emission with low electric power consumption. By applying a reverse bias to each section of the device, we achieve high-speed (&amp;gt;kHz) switching of multiple thermal emission wavelengths, opening a route towards compact, highly efficient mid-infrared light sources for various sensing applications.
Abstract TMP98: A New Class of Precision Oral Anticoagulants (proacs) That Mostly Preserves Platelet Activity in vitro and in vivo (2019)

Introduction: Anticoagulants, while an effective prophylactic for ischemic stroke increase a patient’s risk of major bleeding. There is currently an unmet need for new anticoagulants with the ideal combination of efficacy and low bleeding risk. Here we describe the in vitro and in vivo pharmacology of two development candidates VE-01902 and VE-02851, expected to enter phase I clinical trials in 2018 and 2019 respectively. These compounds belong to a new class of anti-coagulants, the PRecision Oral AntiCoagulants (PROACs), which inhibit fibrinogen cleavage at potencies comparable to the known Direct Thrombin Inhibitors (DTIs) while only weakly inhibiting thrombin induced platelet activation in plasma and whole blood. Methods: Enzyme activity assays by optical methods. Platelet status by expression of CD62P by flow cytometry. In vitro coagulation by Thrombin Generation Assay (TGA). In vivo efficacy and bleeding risk evaluated by rodent models of thrombosis and bleeding time tests. Results and Conclusions: The PROACs are a class of compounds that share a unique mechanism of action: reversible covalent inhibitors of thrombin with slow enzyme kinetics. We examined Thrombin Generation in platelet Poor Plasma (PPP) and Platelet Rich Plasma (PRP) of VE-01902 and VE-02851 and compared it to the known DTIs argatroban and dabigatran. In both plasma samples the PROACs potently inhibit the propagation phase (Endogenous Thrombin Potential (ETP)) while, unlike the known DTIs, only weakly affect the initiation phase of thrombin generation (10 to 20-fold weaker). In the PRP samples the PROACs do not significantly affect platelet activation even while suppressing ETP. To better understand the unique in vitro properties of the PROACs we studied the activity of multiple key factors of the coagulation cascade. Like argatroban and dabigatran, the PROACs protect mice from the effects of thrombin-induced pulmonary embolism and inhibit clot formation in the arteriovenous shunt rat model. However unlike these DTIs, they do not significantly inhibit platelet activation in either of these rodent models. Despite its strong anticoagulant properties, the PROACs show significantly lower bleeding than comparators.
Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes (2021)

Pin nematodes of the genus <i>Paratylenchus</i> are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen <i>Paratylenchus</i> species, including <i>P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni</i> and <i>P. veruculatus</i>, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and <i>COI</i> gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 <i>COI</i> new gene sequences are presented. <i>Paratylenchus elachistus</i>, <i>P. holdemani</i> and <i>P. neoamblycephalus</i> are recorded for the first time in Belgium and <i>P. idalimus</i> for the first time in Europe. <i>Paratylenchus</i> is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated <i>Paratylenchus</i> phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 <i>COI</i> gene sequences that were previously unidentified or incorrectly classified.
Influences of reopening businesses and social venues: COVID-19 incidence rate in East Texas county (2021)

As the on-going severe acute respiratory syndrome coronavirus 2 pandemic, we aimed to understand whether economic reopening (EROP) significantly influenced coronavirus disease 2019 (COVID-19) incidence. COVID-19 data from Texas Health and Human Services between March and August 2020 were analysed. COVID-19 incidence rate (cases per 100 000 population) was compared to statewide for selected urban and rural counties. We used joinpoint regression analysis to identify changes in trends of COVID-19 incidence and interrupted time-series analyses for potential impact of state EROP orders on COVID-19 incidence. We found that the incidence rate increased to 145.1% (95% CI 8.4-454.5%) through 4th April, decreased by 15.5% (95% CI -24.4 -5.9%) between 5th April and 30th May, increased by 93.1% (95% CI 60.9-131.8%) between 31st May and 11th July and decreased by 13.2% (95% CI -22.2 -3.2%) after 12 July 2020. The study demonstrates the EROP policies significantly impacted trends in COVID-19 incidence rates and accounted for increases of 129.9 and 164.6 cases per 100 000 populations for the 24- or 17-week model, respectively, along with other county and state reopening ordinances. The incidence rate decreased sharply after 12th July considering the emphasis on a facemask or covering requirement in business and social settings.
Adversarial attack vulnerability of medical image analysis systems: Unexplored factors (2021)

Adversarial attacks are considered a potentially serious security threat for machine learning systems. Medical image analysis (MedIA) systems have recently been argued to be vulnerable to adversarial attacks due to strong financial incentives and the associated technological infrastructure. In this paper, we study previously unexplored factors affecting adversarial attack vulnerability of deep learning MedIA systems in three medical domains: ophthalmology, radiology, and pathology. We focus on adversarial black-box settings, in which the attacker does not have full access to the target model and usually uses another model, commonly referred to as surrogate model, to craft adversarial examples that are then transferred to the target model. We consider this to be the most realistic scenario for MedIA systems. Firstly, we study the effect of weight initialization (pre-training on ImageNet or random initialization) on the transferability of adversarial attacks from the surrogate model to the target model, i.e., how effective attacks crafted using the surrogate model are on the target model. Secondly, we study the influence of differences in development (training and validation) data between target and surrogate models. We further study the interaction of weight initialization and data differences with differences in model architecture. All experiments were done with a perturbation degree tuned to ensure maximal transferability at minimal visual perceptibility of the attacks. Our experiments show that pre-training may dramatically increase the transferability of adversarial examples, even when the target and surrogate's architectures are different: the larger the performance gain using pre-training, the larger the transferability. Differences in the development data between target and surrogate models considerably decrease the performance of the attack; this decrease is further amplified by difference in the model architecture. We believe these factors should be considered when developing security-critical MedIA systems planned to be deployed in clinical practice. We recommend avoiding using only standard components, such as pre-trained architectures and publicly available datasets, as well as disclosure of design specifications, in addition to using adversarial defense methods. When evaluating the vulnerability of MedIA systems to adversarial attacks, various attack scenarios and target-surrogate differences should be simulated to achieve realistic robustness estimates. The code and all trained models used in our experiments are publicly available.<sup>3</sup>.
Features of defining three-phase transformer no-load parameters by 3D modeling methods (2017)

Theoretical researches and modeling data are represented on the numerical realization basis by finite elements method of a 3-D mathematical model of a three-phase power transformer, which displays electromagnetic processes transformation features in no-load mode. The article has identified the regularities of magnetic flux density and magnetic field energy distribution for transformer active part in no-load mode. Also their quantitative correlations for core of various phases were established, which define ratios between transformer currents and resistances of direct and reverse sequence. In the research it has been determined that no-load currents are nonsinusoidal and asymmetrical. In harmonic spetrum no-load currents prevail 1-st, 5-th and 7-th harmonic components. But at the same time the first harmonic component dominates. The direct and reverse phase sequence parameters are determined on the basis of the symmetrical components method. This made it possible to propose a correcting technique. It is specifying traditional engineering approach and significantly reducing the error of calculation parameters for the steady-state no-load mode by 7-10 % in comparison to well-known engineering designing techniques of three-phase power transformers.