gebhart/patrepeval huggingface dataset:
Performing point-of-care molecular testing for SARS-CoV-2 with RNA extraction and isothermal amplification (2021)

To respond to the urgent need for COVID-19 testing, countries perform nucleic acid amplification tests (NAAT) for the detection of SARS-CoV-2 in centralized laboratories. Real-time RT-PCR (Reverse transcription-Polymerase Chain Reaction), used to amplify and detect the viral RNA., is considered, as the current gold standard for diagnostics. It is an efficient process, but the complex engineering required for automated RNA extraction and temperature cycling makes it incompatible for use in point of care settings [1]. In the present work, by harnessing progress made in the past two decades in isothermal amplification and paper microfluidics, we created a portable test, in which SARS-CoV-2 RNA is extracted, amplified isothermally by RT-LAMP (Loop-mediated Isothermal Amplification), and detected using intercalating dyes or fluorescent probes. Depending on the viral load in the tested samples, the detection takes between twenty minutes and one hour. Using a set of 16 pools of naso-pharyngal swab eluates, we estimated a limit of detection comparable to real-time RT-PCR (i.e. 1 genome copies per microliter of clinical sample) and no cross-reaction with eight major respiratory viruses currently circulating in Europe. We designed and fabricated an easy-to-use portable device called "COVIDISC" to carry out the test at the point of care. The low cost of the materials along with the absence of complex equipment will expedite the widespread dissemination of this device. What is proposed here is a new efficient tool to help managing the pandemics.
Ineluctable background checking on social networks: Linking job seeker's r&amp;#x00E9;sum&amp;#x00E9; and posts (2013)

A growing source of concern is that the privacy of individuals can be violated by linking information from multiple sources. For example, the linking of a person's anonymized information with other information about that person can lead to de-anonymization of the person. To investigate the social risks of such linking, we investigated the use of social networks for background checking, which is the process of evaluating the qualifications of job seekers, and evaluated the risk posed by the linking of information the employer already has with information on social networks. After clarifying the risk, we developed a system that links information from different sources: information extracted from a job seeker's résumé and anonymous posts on social networks. The system automatically calculates the similarity between information in the résumé and in the posts, and identifies the job seeker's social network accounts even though the profiles may have been anonymized. As a part of our system, we developed a novel method for quantifying the implications of terms in a résumé by using the posts on social networks. In an evaluation using the résumés of two job seekers and the tweets of 100 users, the system identified the accounts of both job seekers with reasonably good accuracy (true positive rate of 0.941 and true negative rate of 0.999). These findings reveal the real social threat of linking information from different sources. Our research should thus form the basis for further study of the relationship between privacy in social networks and the freedom to express opinions.
Continuous Monitoring of TATP Using Ultrasensitive, Low-Power Sensors (2020)

There is a growing need for a continuous monitoring system that can detect explosives such as triacetone triperoxide (TATP) in the vapor phase at trace levels. TATP is an energetic material commonly used by terrorists in improvised explosive devices both as the initiator and the energetic material itself. TATP is still going largely undetected in many densely populated venues such as train stations and airports. No electronic trace detection system currently exists that is capable of continuously monitoring TATP, or its precursors, in the vapor phase. Recently, we developed a thermodynamic sensor that can detect TATP and other nitrogen-based explosives in the vapor phase at the ppb level. These ultrathin sensors showed unparalleled sensitivity and could even be operated at low enough powers to enable them to be deployed on drones. The sensor relies on specific oxidation-reduction reactions between the energetic molecules and metal oxide catalysts. Here, catalyst coated microheaters measure the heat effects associated with redox reactions occurring on the surface of the metal oxide catalyst. Enhanced sensitivity and selectivity were achieved through implementation of ultrathin ($8~\mu \text{m}$ thick) yttria-stabilized-zirconia (YSZ) as the substrate for the sensor platform. This reduction in the thermal mass combined with the catalytic amplification associated with Pd microheaters and optimized catalyst porosity enabled us to detect TATP in the vapor phase at unprecedented levels.
Interferon regulatory factor‐1 gene deletion decreases glomerulonephritis in MRL/lpr mice (2006)

To investigate the role of interferon regulatory factor-1 (IRF-1) in the development of lupus nephritis, IRF-1(-/-) genotype mice were bred onto the MRL/lpJfas(lpr) (MRL/lpr) background. We examined kidney mesangial cell function and disease progression. Endpoints evaluated included inflammatory mediators, autoantibody production, immune complex deposition, renal pathology, T cell subset analysis, and duration of survival. Mesangial cells cultured from IRF-1(-/-) mice produced significantly lower levels of nitric oxide and IL-12 but not TNF-alpha when stimulated with LPS + IFN-gamma. IRF-1(-/-) mice showed less aggravated dermatitis compared to the wild-type mice. Anti-double-stranded DNA production and proteinuria were significantly decreased in IRF-1(-/-) mice compared to IRF-1(+/+) mice. IgG and C3 deposition as well as glomerulonephritis were decreased in IRF-1(-/-) mice at 26 wk of age compared to the IRF-1(+/+) mice. Splenic CD4- CD8- CD44+ T cells were decreased while CD4+ CD25+ T cells were increased in the IRF-1(-/-) mice when compared to IRF-1(+/+) mice. Survival rates (ED50) were 22 wk for IRF-1(+/+) mice and 45 wk for IRF-1(-/-) mice. These findings suggest an important role of IRF-1 in mediating renal disease in MRL/lpr mice.
DNA Strand Breaks: the DNA Template Alterations That Trigger p53-Dependent DNA Damage Response Pathways (1994)

The tumor suppressor protein p53 serves as a critical regulator of a G1 cell cycle checkpoint and of apoptosis following exposure of cells to DNA-damaging agents. The mechanism by which DNA-damaging agents elevate p53 protein levels to trigger G1/S arrest or cell death remains to be elucidated. In fact, whether damage to the DNA template itself participates in transducing the signal leading to p53 induction has not yet been demonstrated. We exposed human cell lines containing wild-type p53 alleles to several different DNA-damaging agents and found that agents which rapidly induce DNA strand breaks, such as ionizing radiation, bleomycin, and DNA topoisomerase-targeted drugs, rapidly triggered p53 protein elevations. In addition, we determined that camptothecin-stimulated trapping of topoisomerase I-DNA complexes was not sufficient to elevate p53 protein levels; rather, replication-associated DNA strand breaks were required. Furthermore, treatment of cells with the antimetabolite N(phosphonoacetyl)-L-aspartate (PALA) did not cause rapid p53 protein increases but resulted in delayed increases in p53 protein levels temporally correlated with the appearance of DNA strand breaks. Finally, we concluded that DNA strand breaks were sufficient for initiating p53-dependent signal transduction after finding that introduction of nucleases into cells by electroporation stimulated rapid p53 protein elevations. While DNA strand breaks appeared to be capable of triggering p53 induction, DNA lesions other than strand breaks did not. Exposure of normal cells and excision repair-deficient xeroderma pigmentosum cells to low doses of UV light, under conditions in which thymine dimers appear but DNA replication-associated strand breaks were prevented, resulted in p53 induction attributable to DNA strand breaks associated with excision repair. Our data indicate that DNA strand breaks are sufficient and probably necessary for p53 induction in cells with wild-type p53 alleles exposed to DNA-damaging agents.
Detection of Diabetic Foot Ulcers Using SVM Based Classification (2020)

Diabetic foot ulcers represent a significant health issue, for both patients’ quality of life and healthcare system costs. Currently, wound care is mainly based on visual assessment of wound size, which suffers from lack of accuracy and consistency. Hence, a more quantitative and computer-based method is needed. Supervised machine learning based object recognition is an attractive option, using training sample images with boundaries labeled by experienced clinicians. We use forty sample images collected from the UMASS Wound Clinic by tracking 8 subjects over 6 months with a smartphone camera. To maintain a consistent imaging environment and facilitate the capture process for patients with limited mobility, an image capture box was designed with two right angled front surface mirrors and LED lighting. We developed a novel foot ulcer recognition system using these sample images as our test data. Instead of operating at the pixel level, we use super-pixels, resulting from the quick shift algorithm, as the basic processing units. Then a support vector machine (SVM) based classifier is trained on the Bag-of-Words histogram representation of local Scale-Invariant Feature Transform (SIFT) features found in each super-pixel. As this classifier is very specific and the resulting histogram is very sparse, we merge the histograms from super-pixels in a size-specified neighborhood into one instance. Finally, to recover more precise boundaries of the foot ulcers, we apply conditional random field techniques to introduce new constraints that allow us to reduce misclassifications that occur near the edges of objects. Experimental results show that our method provides promising recognition results, outperforming the regular SVM-based classification as well as the sliding window based object recognition method when evaluated using the Matthew correlation coefficient (MCC). We are integrating these algorithms into the wound assessment module of our Android phone-based diabetic self-management app.
Modelling of fluid–structure interactions with the space–time finite elements: Arterial fluid mechanics (2007)

Abstract The stabilized space–time fluid–structure interaction (SSTFSI) techniques developed by the Team for Advanced Flow Simulation and Modeling (T★AFSM) are applied to FSI modelling in arterial fluid mechanics. Modelling of flow in arteries with aneurysm is emphasized. The SSTFSI techniques used are based on the deforming‐spatial‐domain/stabilized space–time (DSD/SST) formulation and include the enhancements introduced recently by the T★AFSM to increase the scope, accuracy, robustness and efficiency of these techniques. The arterial structures can be modelled with the membrane or continuum elements, both of which are geometrically nonlinear, and the continuum element can be made of linearly elastic or hyperelastic material. Test computations are presented for cerebral and abdominal aortic aneurysms and carotid‐artery bifurcation, where the arterial geometries used in the computations are close approximations to the patient‐specific image‐based data. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Thermodynamic Data for Mn3O4, Mn2O3 and MnO2 (2011)

Thermodynamic properties of Mn 3 O 4 , Mn 2 O 3 and MnO 2 are reassessed based on new measurements and selected data from the literature. Data for these oxides are available in most thermodynamics compilations based on older calorimetric measurements on heat capacity and enthalpy of formation, and high-temperature decomposition studies. The older heat capacity measurements did not extend below 50 K. Recent measurements have extended the low temperature limit to 5 K. A reassessment of thermodynamic data was therefore undertaken, supplemented by new measurements on high temperature heat capacity of Mn 3 O 4 and oxygen chemical potential for the oxidation of MnO 1 x , Mn 3 O 4 , and Mn 2 O 3 to their respective higher oxides using an advanced version of solid-state electrochemical cell incorporating a buffer electrode. Because of the high accuracy now achievable with solid-state electrochemical cells, phase-equilibrium calorimetry involving the "third-law" analysis has emerged as a competing tool to solution and combustion calorimetry for determining the standard enthalpy of formation at 298.15 K. The refined thermodynamic data for the oxides are presented in tabular form at regular intervals of temperature.
Severe Acute Respiratory Syndrome: Epidemiology, Pathogenesis, and Animal Models (2014)

Quantitative studies on viral load in the upper respiratory tract and the feces of patients infected with severe acute respiratory syndrome-coronavirus (SARS-CoV) revealed a progressive increase in viral load, peaking around day 10 after onset of disease symptoms. This explains the epidemiological observation that transmission mainly occurs after the fifth day of illness. Clinical and pathological studies of SARS cases indicate that cells in the lower respiratory tract, particularly type 1 pneumocytes, are the prime targets of SARS, with macrophages subsequently being infected. Although angiotensin-converting enzyme 2 (ACE2) is the primary receptor for SARS, other receptors such as L-SIGN and DC-SIGN may facilitate virus infection, even under circumstances when the virus has not fully adapted to a new host. Epithelial lung damage together with macrophage activation results in increased levels of proinflammatory cytokines. The initial phase of lung disease exists for 10 to 14 days, after which many of the changes present can be attributed to the sequelae of diffuse lung damage, including the effects of mechanical ventilation. As with many other newly emerging infections, SARS had zoonotic origins, highlighting the need for a better understanding of the virus ecology of both wild and domestic animals. As many of these zoonoses do not cause disease in their natural host, surveillance needs to encompass viruses causing unobvious infections as well as those causing overt disease and will require the cooperation of multiple agencies, including those dealing with public health, veterinary medicine, and wildlife or the environment.
Numerical Navier-Stokes solutions of high speed propeller flows (1986)

T HE search for improved fuel economy for subsonic aircraft has led to a renewed interest in propeller aerodynamics. There is a need for detailed aerodynamic analysis of the flow near and behind the propeller, including the effects of an engine nacelle to refine propeller and nacelle design and assess slipstream effects on the other components of the aircraft. The available data for flowfield details are quite limited. The flow near and behind the propeller is turbulent, and the downstream variation of the swirl, etc., is dominated by viscous effects. Previous detailed analysis for high-speed cases have been limited by an in viscid flow assumption. The goal of this work has been to extend detailed viscous analysis of propeller flows into the high-speed regime. The complete three-dimensional, periodic, unsteady, turbulent problem involved in the real case is too complex and large to be attacked at this time. Some simplifying assumptions were necessary. First, the flow was taken as axisymmetric. Second, and very important, the propeller has been represented by an actuator disk. The disk can be located arbitarily in space, so that the effects of propeller sweep can be included. Also, arbitrary radial variations of the thrust and torque are permitted. The calculations were made with a finite-difference solution of the compressible, axisymmetric (with swirl), Reynoldsaveraged, turbulent Navier-Stokes equations.
Dielectric relaxation in SrTiO3–SrMg1/3Nb2/3O3 and SrTiO3–SrSc1/2Ta1/2O3 solid solutions (2000)

Dielectric properties of ceramic samples of (1−x)SrTiO3–xSrMg1/3Nb2/3O3 and (1−x)SrTiO3–xSrSc1/2Ta1/2O3 solid solutions were studied at x⩽15% and x⩽10%, respectively. The real and imaginary parts of the dielectric constant were measured at frequencies between 10 Hz and 1 MHz and in a temperature range of 4.2–300 K. Remarkable relaxation was found between 80 and 300 K. The relaxation was suggested to be due to local charge compensation processes. The activation energy for these processes was determined to be (0.25±0.05) eV with τ0=(10−12…10−13) s.
Distinct HIV-1 Neutralization Potency Profiles of Ibalizumab-Based Bispecific Antibodies (2016)

Our data suggest that this panel of iMab-based biAbs could be used to probe the parameters for potent HIV-1 neutralization. Moreover, a few of these biAbs warrant further studies and possibly clinical development.
ChemInform Abstract: TETRABUTYLAMMONIUM HYDROXIDE: A REAGENT FOR THE BASE‐CATALYZED DEHYDRATION OF VICINAL DIHYDRODIOLS OF AROMATIC HYDROCARBONS. IMPLICATIONS TO ION‐PAIR CHROMATOGRAPHY (1982)

Abstract Die Dehydratisierung des trans‐7,8‐Dihydroxy‐7,8‐dihydro‐benz[a]‐ pyrens (II) mit methanolischem Tetrabutylammoniumhydroxid (I) liefert ein Phenolat (III), das erst bei erhöhter Temperatur zum Butyl‐phenolether (IV) führt.
Effects of Activation of Renal Adenosine A2 Receptor on Renal Function and Renin Release in Dogs (1999)

Direct effects of adenosine A2 receptor activation on renal function were examined in dogs. When renal perfusion pressure was maintained constant at 100 mmHg, renal administration of a selective A2 receptor agonist, CGS 21680C (sodium salt of CGS 21680, 2-[p-(2-carboxyethyl) phenethylamino]-5'-N-ethylcarboxamido adenosine) (1 microg x kg(-) x min (-1)), although it decreased blood pressure by 20 mmHg, increased renal blood flow and renin release, whereas glomerular filtration rate and urine flow were unaffected. These results suggest that stimulation of renal A2 receptor led to both afferent and efferent arteriolar dilatation, whereas renal A2 receptor plays a minor role in urine formation. CGS 21680C induced renin release and tachycardia that were blocked by propranolol, indicating these effects of A2 receptor stimulation appeared to be indirect.
Nanocomposite-seeded single-domain growth of single- domain LiNbO3 thin films for RF/Photonic applications. (2021)

Abstract not provided.
Radiation-Induced CXCL16 Release by Breast Cancer Cells Attracts Effector T Cells (2008)

Recruitment of effector T cells to inflamed peripheral tissues is regulated by chemokines and their receptors, but the factors regulating recruitment to tumors remain largely undefined. Ionizing radiation (IR) therapy is a common treatment modality for breast and other cancers. Used as a cytocidal agent for proliferating cancer cells, IR in combination with immunotherapy has been shown to promote immune-mediated tumor destruction in preclinical studies. In this study we demonstrate that IR markedly enhanced the secretion by mouse and human breast cancer cells of CXCL16, a chemokine that binds to CXCR6 on Th1 and activated CD8 effector T cells, and plays an important role in their recruitment to sites of inflammation. Using a poorly immunogenic mouse model of breast cancer, we found that irradiation increased the migration of CD8(+)CXCR6(+) activated T cells to tumors in vitro and in vivo. CXCR6-deficient mice showed reduced infiltration of tumors by activated CD8 T cells and impaired tumor regression following treatment with local IR to the tumor and Abs blocking the negative regulator of T cell activation, CTLA-4. These results provide the first evidence that IR can induce the secretion by cancer cells of proinflammatory chemotactic factors that recruit antitumor effector T cells. The ability of IR to convert tumors into "inflamed" peripheral tissues could be exploited to overcome obstacles at the effector phase of the antitumor immune response and improve the therapeutic efficacy of immunotherapy.
Manufacture and Assessment of High Loading Printing Paper using GCC-MFC Composite (I) : Particle Characteristics and Wire Abrasiveness of GCC-MFC Composite (2019)

In the advent of severe global warming and climate change, the demand for reduced energy consumption and carbon dioxide emissions pertaining to the paper industry is increasing. In order to solve this problem, an attempt was made to produce a GCC-MFC composite having the possibility of increasing the amount of filler used without causing a decrease in paper properties and productivity. In particular, this study focused on the change in wire abrasiveness and the possibility of particle size control, which are basic problems associated with increasing filler particle size. The average particle size and wire abrasiveness of GCC used in this study were about 1–2 ㎛ and 160–195 ㎎ respectively. However, the average particle size and wire abrasiveness of the prepared GCC-MFC composite were 10.26–18.32 ㎛ and 113–116 ㎎, respectively. In addition, it was confirmed that the average particle size of the GCC-MFC composite can be controlled by monitoring the amount of MFC and polymer flocculants. The study also observed that good formation paper can be obtained by dispersing the prepared GCC-MFC composite at 3,000 rpm. It is expected that the production of GCC-MFC composite may contribute in the improvement of productivity while reducing energy consumption by increasing the amount of filler use, thus solving the problem of decrease in paper strength.
ChemInform Abstract: Insertion of Reactive Rhodium Carbenes into Boron—Hydrogen Bonds of Stable N‐Heterocyclic Carbene Boranes. (2014)

Abstract This method also works with substituted imidazole‐borane adducts as well as 1,2,4‐triazole‐derived borane adducts.
Papillary Transitional Cell Carcinoma (1996)

Ribé, Adriana M.D.; Solé, Manel M.D.; Campo, Elías M.D.; Cardesa, Antonio M.D.; Ferrer, Carmen M.D.; Griño, Joan M.D.
Chromium–Carbyne Complexes: Intermediates for Organic Synthesis (2007)

Auf gleichem Wege: Chrom-Carbin-Komplexe sind durch Umsetzung von 1,1,1-Trichlormethylreagentien mit Chrom(II)-chlorid leicht zugänglich und dienen als Intermediate zur selektiven Bildung unterschiedlichster Produktarten. Hierzu gehören Alkine, Alkene, β-Hydroxyketone, Aldehyde, Allylalkohole und Allene (siehe Schema, E=Elektrophil).