gebhart/patrepeval huggingface dataset:
Abstract IA7: Unraveling the complexities of p63 in cancer and stem cells (2012)

Abstract Aberrant expression of microRNAs (miRNAs) and the enzymes that control their processing have been reported in multiple biological processes including in cancer and the regulation of stem cells, but the mechanisms governing this are not clearly understood. We have generated conditional knockout mice that allow the functional separation of TAp63 and ΔNp63. Using the TAp63 conditional knock out mouse model, we found that TAp63 suppresses tumorigenesis and metastasis through coordinate transcriptional regulation of Dicer and miR-130b. Interestingly, we have recently found that ΔNp63 also plays an important role in miRNA processing by transcriptionally activating DGCR8. In turn, DGCR8 is required for processing of key miRNAs that repress genes required for stem cell pluripotency, Oct4, Sox2, and Nanog. Strikingly, epidermal cells derived from ΔNp63 deficient mice express markers of pluripotency at levels comparable to mouse embryonic stem cells. Moreover, these cells exhibit characteristics of stem cells that can self-renew and can differentiate into multiple cell fates in vitro and in vivo. Our data reveal a novel role for ΔNp63 in the commitment to epidermal differentiation through transcriptional regulation of DGCR8 and downstream modulation of key miRNAs required to maintain stem cell pluripotency. Taken together, our data show that p63 plays critical roles in regulating miRNAs in multiple biological processes. Citation Format: Elsa R. Flores. Unraveling the complexities of p63 in cancer and stem cells [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr IA7.
Viewpoint: Diagnosing antimicrobial resistance (2017)

Antimicrobial resistance constitutes a global burden and is one of the major threats
to public health. Although the emergence of resistant microorganisms is a natural
phenomenon, overuse or inappropriate use of antimicrobials has had a great impact
on resistance evolution. Rapid diagnostic tests that identify drug resistant bacteria,
determine antimicrobial susceptibility and distinguish viral from bacterial infection can
guide the effective treatment strategies. Moreover, rapid diagnostic tests could
facilitate epidemiological surveillance as emerging resistant infectious agents and
transmission can be monitored. In this Viewpoint article, several experts in the field
discuss the drawbacks of current diagnostic methods used to identify antimicrobial
resistance, novel diagnostic strategies and how such rapid tests can inform drug
development and the surveillance of resistance evolution.
Density and frequency dependence of resistance in early airway obstruction. (1987)

The forced oscillation technique is a noninvasive and effort-independent test used to characterize the mechanical impedance of the respiratory system. The aim of this study was to assess the sensitivity of this method in detecting early airway abnormalities caused by smoking or occupational hazards. Respiratory mechanical parameters by the forced oscillation technique and maximal expiratory flow volume (MEFV) curves were obtained in a group of 82 workers from a gas manufacturing plant. In addition, the variations in the frequency dependence of total respiratory resistance between air breathing and a mixture of helium-oxygen (He-O2) were measured. All parameters were normalized for age, height, and weight. In order to compare the 2 types of testing, multiple linear regressions were performed with smoking or exposure as independent variables on one hand and parameters of the 2 types of testing on the other hand. This statistical procedure showed that 2 parameters of the forced oscillation technique constantly reached higher levels of significance than those of the MEFV parameters in the regression equations describing smoking history and occupational exposure: these were the frequency dependence of resistance and the change in frequency dependence between air and He-O2 breathing. When nonsmokers, ex-smokers, and smokers were considered separately, the degree of frequency dependence of resistance and the change in frequency dependence between air and He-O2 breathing were the only parameters that were significantly different between these 3 groups (one-way analysis of variance).(ABSTRACT TRUNCATED AT 250 WORDS)
On deceiving malware classification with section injection (2022)

We investigate how to modify executable files to deceive malware classification systems. This work's main contribution is a methodology to inject bytes across a malware file randomly and use it both as an attack to decrease classification accuracy but also as a defensive method, augmenting the data available for training. It respects the operating system file format to make sure the malware will still execute after our injection and will not change its behavior. We reproduced five state-of-the-art malware classification approaches to evaluate our injection scheme: one based on GIST+KNN, three CNN variations and one Gated CNN. We performed our experiments on a public dataset with 9,339 malware samples from 25 different families. Our results show that a mere increase of 7% in the malware size causes an accuracy drop between 25% and 40% for malware family classification. They show that a automatic malware classification system may not be as trustworthy as initially reported in the literature. We also evaluate using modified malwares alongside the original ones to increase networks robustness against mentioned attacks. Results show that a combination of reordering malware sections and injecting random data can improve overall performance of the classification. Code available at https://github.com/adeilsonsilva/malware-injection.
Airborne Laser Infrared Absorption Spectrometer (ALIAS-II) for in situ Atmospheric Measurements of N(sub 2)0, CH(sub 4), CO, HCl, and NO(sub 2) from Balloon or RPA Platforms (1998)

The Airborne Laser Infrared Absorption Spectrometer II (ALIAS-II) is a lightweight, high-resolution (0.0003 cm-1), scanning, mid-infrared absorption spectrometer based on cooled (80 K) lead-salt tunable diode laser sources.
A Simple and Widely Applicable Method to 59Fe-Radiolabel Monodisperse Superparamagnetic Iron Oxide Nanoparticles for In Vivo Quantification Studies (2012)

A simple, fast, efficient, and widely applicable method to radiolabel the cores of monodisperse superparamagnetic iron oxide nanoparticles (SPIOs) with (59)Fe was developed. These cores can be used as precursors for a variety of functionalized nanodevices. A quality control using filtration techniques, size-exclusion chromatography, chemical degradation methods, transmission electron microscopy, and magnetic resonance imaging showed that the nanoparticles were stably labeled with (59)Fe. Furthermore, the particle structure and the magnetic properties of the SPIOs were unchanged. In a second approach, monodisperse SPIOs stabilized with (14)C-oleic acid were synthesized, and the stability of this shell labeling was studied. In proof of principle experiments, the (59)Fe-SPIOs coated with different shells to make them water-soluble were used to evaluate and compare in vivo pharmacokinetic parameters such as blood half-life. It could also be shown that our radiolabeled SPIOs embedded in recombinant lipoproteins can be used to quantify physiological processes in closer detail than hitherto possible. In vitro and in vivo experiments showed that the (59)Fe label is stable enough to be applied in vivo, whereas the (14)C label is rapidly removed from the iron core and is not adequate for in vivo studies. To obtain meaningful results in in vivo experiments, only (59)Fe-labeled SPIOs should be used.
Effect of Chronic Viral Infection on the Immune System (1973)

Abstract Immunoresponsiveness has been compared in mice chronically infected with lymphocytic choriomeningitis (LCM) virus and in noninfected mice. The antigens used were sheep red blood cells, keyhole limpet hemocyanin, human IgG (HuIgG), bovine IgG, chicken IgG, and turkey IgG. LCM-infected mice were found to have normal immune responses to sheep red blood cells and keyhole limpet hemocyanin over wide dose ranges, whereas against mammalian and avian IgG, LCM-infected mice showed depressed immune responsiveness. This depression in immune responses was not associated with differences in antibody avidity or antigen handling but with decreased numbers of antibody-forming cells. Unresponsiveness to HuIgG was difficult to induce with deaggregated antigen in mice chronically infected with LCM virus.
Paenibacillus algicola sp. nov., a novel alginate lyase-producing marine bacterium (2020)

A Gram-stain-variable, facultatively anaerobic, endospore-forming, rod-shaped bacterium, designated HB172198<sup>T</sup>, was isolated from brown alga collected at Qishui Bay, Hainan, PR China. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain HB172198<sup>T</sup> belonged to the genus <i>Paenibacillus</i>, and the closest phylogenetically related species was <i>Paenibacillus lemnae</i> NBRC 109972<sup>T</sup> (97.6% similarity). The other 16S rRNA gene sequence similarities were under 97.0%. The whole genome average nucleotide identity value between strain HB172198<sup>T</sup> and the closest type strain was 75.3% and the <i>in silico</i> DNA-DNA hybridization value was 20.2%. The predominant isoprenoid quinone was menaquinone 7 and the major fatty acids were anteiso-C<sub>15:0</sub>, C<sub>16:0</sub>, anteiso-C<sub>17:0</sub>, iso C<sub>16:0</sub> and C<sub>16:1</sub> ω11<i>c</i>. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB172198<sup>T</sup> represents a novel species of the genus <i>Paenibacillus</i>, for which the name <i>Paenibacillus algicola</i> sp. nov. is proposed. The type strain is HB172198<sup>T</sup> (=CGMCC 1.13583<sup>T</sup>=JCM 32683<sup>T</sup>).
Qualitatively Different Memory CD8+ T Cells Are Generated after Lymphocytic Choriomeningitis Virus and Influenza Virus Infections (2010)

Viral infections often induce robust T cell responses that are long-lived and protective. However, it is unclear to what degree systemic versus mucosal infection influences the generation of effector and memory T cells. In this study, we characterized memory CD8(+) T cells generated after respiratory influenza virus infection and compared the phenotypic and functional qualities of these cells with memory T cells generated after systemic infection with lymphocytic choriomeningitis virus (LCMV). Using a recombinant influenza virus expressing the LCMV gp(33-41) epitope and TCR transgenic CD8(+) T cells with a fixed TCR, we compared responses to the same Ag delivered by mucosal or systemic viral infection. Memory cells generated postinfection with either virus showed only a few phenotypic differences. Yet, influenza memory T cells produced lower amounts of effector cytokines upon restimulation and displayed reduced proliferation compared with LCMV-induced memory cells. Strikingly, we observed reduced expansion of spleen- and, in particular, lung-derived influenza memory cells after recall in vivo, which correlated with reduced early protection from secondary infection. These findings suggest that qualitatively different memory CD8(+) T cells are generated after respiratory or systemic virus infections.
C-STEM Girls Computing and Robotics Leadership Camp (2020)

Abstract Girl’s Leadership Camp for Computing and Robotics AbstractThe C-STEM Center hosted its first annual one-week C-STEM/NCWIT Girl's Leadership Campfor Computing and Robotics for middle school girls on July 22-26, 2013. The goal of this camp isto motivate girls in middle school to learn science, technology, engineering, and math (STEM)concepts through a fun and exciting robotics-based curriculum. We want them to be leadersamong their peers and inspire other young girls to gain interest in science and technology. Thecamp was led by three college female students as coaches and assisted by five high schoolfemale students as assistant coaches. The camp was attended by 15 middle school girls fromthe greater Sacramento region. Girls at the camp had learned the basics of robotics, theprinciples of engineering, and C/C++ programming. In addition, they had learned important lifeskills including teamwork, presentation skills, leadership skills, building confidence, andbreaking gender stereotypes The girls also had heard from and discussed with experts invarious science and technology fields to gain exposure to the variety of options they haveavailable to them. At the end of the camp, they had created multi-media video presentationswith robotics, similar to the RoboPlay Video Competition, and presented them to parents andpeers. The girls who participated in the camp were given modular robotics kits to take back totheir middle schools so they can start computing and robotics clubs of their own. Coaches andassistant coaches mentor girls over the academic school year to facilitate the development ofthese clubs and their participation in RoboPlay Competition. In this paper, the curriculum andlesions learned through this first camp will be presented. 1
Paediatric Code Stroke (2021)

Acute ischaemic stroke (AIS) is an important cause of disability and death in children.It affects 1.2-8 children per 100,000 per year, and almost 70% of survivors have significant ongoing disability, resulting in reduced quality of life, increased care requirements for families, and cost[1].Reperfusion therapies, which include intravenous thrombolysis and endovascular clot retrieval (ECR), are established as effective to improve long-term outcomes of adults with acute ischaemic stroke.Paediatric stroke consensus guidelines allow for reperfusion therapies in children, but access is currently limited due to diagnostic delays[2].
Introduction to Riemannian Geometry and Geometric Statistics: From Basic Theory to Implementation with Geomstats (2023)

As data is a predominant resource in applications, Riemannian geometry is a natural framework to model and unify complex nonlinear sources of data. However, the development of computational tools from the basic theory of Riemannian geometry is laborious. The work presented here forms one of the main contributions to the open-source project geomstats, that consists of a Python package providing efficient implementations of the concepts of Riemannian geometry and geometric statistics, both for mathematicians and for applied scientists for whom most of the difficulties are hidden under high-level functions. The goal of this monograph is two-fold. First, we aim at giving a self-contained exposition of the basic concepts of Riemannian geometry, providing illustrations and examples at each step and adopting a computational point of view. The second goal is to demonstrate how these concepts are implemented in Geomstats, explaining the choices that were made and the conventions chosen. The general concepts are exposed and specific examples are detailed along the text. The culmination of this implementation is to be able to perform statistics and machine learning on manifolds, with as few lines of codes as in the wide-spread machine learning tool scikit-learn. We exemplify this with an introduction to geometric statistics.
A Convex Semi-Definite Positive Framework for DTI Estimation and Regularization (2007)

International audience
Facile manipulation of individual carbon nanotubes assisted by inorganic nanoparticles (2013)

Carbon nanotubes (CNTs) are promising building blocks for nanodevices owing to their superior electrical, thermal and mechanical properties. One of the key issues for their study and application is the efficient location, transfer and manipulation of individual CNTs. In this contribution, we show that the manipulation of individual suspended CNTs has been carried out on the macroscale under low magnification, using inorganic nanoparticles (NPs) as indicators. Individual ultralong CNTs can be stretched, cut, and transferred to other substrates for further characterization. Complicated CNT structures were fabricated under optical microscopes. The inorganic NPs also facilitate the manipulation and characterization of individual CNTs under a scanning electron microscope with low magnification. Additionally, the irregular NPs deposited on suspended CNTs can also make the outer shell of the suspended CNTs display torsion or rotation around the inner shells when placed in a flow of gas, making the fabrication of CNT-NP-hybrid-based nanodevices feasible. Our results demonstrate the extraordinary capability of this manipulation technique for individual CNTs, enabled by decoration with inorganic NPs.
Transcranial Neuromodulation Array With Imaging Aperture for Simultaneous Multifocus Stimulation in Nonhuman Primates (2021)

Even simple behaviors arise from the simultaneous activation of multiple regions in the brain. Thus, the ability to simultaneously stimulate multiple regions within a brain circuit should allow for better modulation of function. However, performing simultaneous multifocus ultrasound neuromodulation introduces challenges to transducer design. Using 3-D Fullwave simulations, we have designed an ultrasound neuromodulation array for nonhuman primates that: 1) can simultaneously focus on multiple targets and 2) include an imaging aperture for additional functional imaging. This design is based on a spherical array, with 128 15-mm elements distributed in a spherical helix pattern. It is shown that clustering the elements tightly around the 65-mm imaging aperture located at the top of the array improves targeting at shallow depths, near the skull surface. Spherical arrays have good focusing capabilities through the skull at the center of the array, but focusing on off-center locations is more challenging due to the natural geometric configuration and the angle of incidence with the skull. In order to mitigate this, the 64 elements closest to the aperture were rotated toward and focusing on a shallow target, and the 64 elements farthest from the aperture were rotated toward and focusing on a deeper target. Data illustrated that this array produced focusing on the somatosensory cortex with a gain of 4.38 and to the thalamus with a gain of 3.82. To improve upon this, the array placement was optimized based on phase aberration simulations, allowing for the elements with the largest impact on the gain at each focal point to be found. This optimization resulted in an array design that can focus on the somatosensory cortex with a gain of 5.19 and the thalamus with a gain of 4.45. Simulations were also performed to evaluate the ability of the array to focus on 28 additional brain regions, showing that off-center target regions can be stimulated, but those closer to the skull will require corrective steps to deliver the same amount of energy to those locations. This simulation and design process can be adapted to an individual monkey or human skull morphologies and specific target locations within individuals by using orientable 3-D printing of the transducer case and by electronic phase aberration correction.
Modelling of human motor control in an unstable task through operational space formulation (2010)

Human motor control computational model is an important component in the study and the successful realisation of human-robot interaction. In this paper, the Operational Space Formulation is presented as a suitable framework of human motor control computational model based on the Equilibrium Point Hypothesis (EPH) approach. The iterative adaptive control strategy was incorporated to simulate human motor adaptation to different tasks. The strategy involves the use of an Equilibrium Model which represents the ideal human motor response to a given task. The combined strategy was simulated to match a set of data gathered experimentally from several human subjects. The results were observed to explain many of the features found in the recorded behaviours in the EPH-based approach of human motor modelling.
Non-adherence among women enrolled in a contraceptive vaginal ring use study in Kisumu, Kenya, 2014-2015 (2018)

Given future potential use of vaginal rings to prevent HIV infection, we examined the association of contraceptive vaginal ring (CVR) non-adherence with user dissatisfaction, tolerability, demographic, and behavioral factors.
HyperSPECT: a new system for pre-clinical imaging in vivo (2009)

Imaging in general is becoming increasingly important in the medical science. At the cell level it is possible to label and trace almost individual molecules in vivo to study biochemical reactions using microscopy. In vivo imaging of living organisms is today mainly accomplished by PET, SPECT and fMRI. The problem is that the spatial resolution for realistic image acquisition times is of the order 1-3 mm, which is a serious limitation. We propose a new imaging modality, based on the same principles as SPECT but with drastically improved efficiency and spatial resolution. This is achieved by incorporating a large number of x-ray lenses between the detectors and the object. In current SPECT a pin-hole geometry is standard, involving an unfortunate trade-off between efficiency and spatial resolution, our solution would change this. The agent for radiolabelling is assumed to be <sup>125</sup>I, with an emission peak at 27 keV, since it is widely used and easy to handle. The large area, photon counting detectors will consist of a columnar CsI scintillator coupled to a CMOS integrated circuit for electronic read-out. Our simulations of the entire system and of the detector indicate that a resolution of 50 &mu;m for the system is possible.
ChemInform Abstract: 3‐Bromomethyl‐6,7‐methylenedioxy‐1‐methyl‐2(1H)‐quinoxalinone as a Highly Sensitive Fluorescence Derivatization Reagent for Carboxylic Acids in High‐Performance Liquid Chromatography. (1989)

ChemInformVolume 20, Issue 3 Other Subjects ChemInform Abstract: 3-Bromomethyl-6,7-methylenedioxy-1-methyl-2(1H)-quinoxalinone as a Highly Sensitive Fluorescence Derivatization Reagent for Carboxylic Acids in High-Performance Liquid Chromatography. M. YAMAGUCHI, M. YAMAGUCHI Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorO. TAKEHIRO, O. TAKEHIRO Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorS. HARA, S. HARA Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorM. NAKAMURA, M. NAKAMURA Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorY. OHKURA, Y. OHKURA Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this author M. YAMAGUCHI, M. YAMAGUCHI Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorO. TAKEHIRO, O. TAKEHIRO Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorS. HARA, S. HARA Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorM. NAKAMURA, M. NAKAMURA Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this authorY. OHKURA, Y. OHKURA Fac. Pharm. Sci., Fukuoka Univ., Jonan, Fukuoka 814-01, JapanSearch for more papers by this author First published: January 17, 1989 https://doi.org/10.1002/chin.198903316AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume20, Issue3January 17, 1989 RelatedInformation