gebhart/patrepeval huggingface dataset:
Genome rearrangements induce biofilm formation in Escherichia coli C – an old model organism with a new application in biofilm research (2019)

Biofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.
Determination of cathepsin V activity and intracellular trafficking by N‐glycosylation (2012)

Cathepsin V (L2), a lysosomal cysteine protease, is a member of cathepsin family, relating to cancer invasion and metastasis. Cathepsin V contains two predicted N-glycosylation sites, but it has not been reported whether cathepsin V is glycosylated or not. In this study, we clarified the role of N-glycosylation of cathepsin V for its functions. We demonstrated that cathepsin V is N-glycosylated at both Asn(221) and Asn(292) using mass spectrometry and site-directed mutagenesis. N-glycosylation of cathepsin V was important for transportation to lysosome, secretion, and activity in HT1080 cells. These data demonstrated that functions of cathepsin V are controlled by N-glycosylation.
Synergistic Impact of Systolic Blood Pressure and Perfusion Status on Mortality in Acute Heart Failure (2021)

Hypoperfusion confers an incremental risk of 30-day all-cause mortality not only in patients with low SBP but also in normotensive patients. On admission, physical examination plays a major role in determining prognosis in patients with acute heart failure.
Author response for "Suppression of active phase voluntary wheel running in male rats by unilateral chronic constriction injury: Enduring therapeutic effects of a brief treatment of morphine combined with TLR4 or P2X7 antagonists" (2020)

Suppression of active phase voluntary wheel running in male rats by unilateral chronic constriction injury: Enduring therapeutic effects of a brief treatment of morphine combined with TLR4 or P2X7 antagonists
Default mode network connectivity in patients with idiopathic normal pressure hydrocephalus (2015)

This is the first study to establish alterations in the DMN of patients with iNPH. DMN connectivity may be a useful indicator of the severity of clinical symptoms in patients with iNPH.
Fabrication of CoTiO<sub>3</sub>–TiO<sub>2</sub>composite films from a heterobimetallic single source precursor for electrochemical sensing of dopamine (2016)

Cobalt titanate-titania composite oxide films have been grown on FTO-coated glass substrates using a single-source heterometallic complex [Co2Ti4(μ-O)6(TFA)8(THF)6]·THF () which was obtained in quantitative yield from the reaction of diacetatocobalt(ii) tetrahydrate, tetraisopropoxytitanium(iv), and trifluoroacetic acid from a tetrahydrofuran solution. Physicochemical investigations of complex have been carried out by melting point, FT-IR, thermogravimetric and single-crystal X-ray diffraction analyses. CoTiO3-TiO2 films composed of spherical objects of various sizes have been grown from by aerosol-assisted chemical vapor deposition at different temperatures of 500, 550 and 600 °C. Thin films characterized by XRD, Raman and X-ray photoelectron spectroscopy, scanning electron microscopy, energy-dispersive X-ray analysis have been explored for electrochemical detection of dopamine (DA). The cyclic voltammetry with the CoTiO3-TiO2 electrode showed a DA oxidation peak at +0.215 V while linear sweep voltammetry displayed a detection limit (LoD) of 0.083 μM and a linear concentration range of 20-300 μM for DA. Thus, the CoTiO3-TiO2 electrode is a potential candidate for the sensitive and selective detection of DA.
Adenosine stress native T1 mapping in severe aortic stenosis: evidence for a role of the intravascular compartment on myocardial T1 values (2014)

Our study suggests that native myocardial T1 values are not only influenced by interstitial and intracellular water changes, but also by changes in the intravascular compartment. Performing T1 mapping during or soon after vasodilator stress may affect ECV measurements given that hyperemia alone appears to substantially alter T1 values.
User-Centered Design and Development of the Modular TWIN Lower Limb Exoskeleton (2021)

For decades, powered exoskeletons have been considered for possible employment in rehabilitation and personal use. Yet, these devices are still far from addressing the needs of users. Here, we introduce TWIN, a novel modular lower limb exoskeleton for personal use of spinal-cord injury (SCI) subjects. This system was designed according to a set of user requirements (lightweight and autonomous portability, quick and autonomous donning and setup, stability when standing/walking, cost effectiveness, long battery life, comfort, safety) which emerged during participatory investigations that organically involved patients, engineers, designers, physiatrists, and physical therapists from two major rehabilitation centers in Italy. As a result of this user-centered process, TWIN's design is based on a variety of small mechatronic modules which are meant to be easily assembled and donned on or off by the user in full autonomy. This paper presents the development of TWIN, an exoskeleton for personal use of SCI users, and the application of user-centered design methods that are typically adopted in medical device industry, for its development. We can state that this approach revealed to be extremely effective and insightful to direct and continuously adapt design goals and activities toward the addressment of user needs, which led to the development of an exoskeleton with modular mechatronics and novel lateral quick release systems. Additionally, this work includes the preliminary assessment of this exoskeleton, which involved healthy volunteers and a complete SCI patient. Tests validated the mechatronics of TWIN and emphasized its high potential in terms of system usability for its intended use. These tests followed procedures defined in existing standards in usability engineering and were part of the formative evaluation of TWIN as a premise to the summative evaluation of its usability as medical device.
Monitoring Health Parameters of Elders to Support Independent Living and Improve Their Quality of Life (2021)

Improving the well-being and quality of life of the elderly population is closely related to assisting them to effectively manage age-related conditions such as chronic illnesses and anxiety, and to maintain their independence and self-sufficiency as much as possible. This paper presents the design, architecture and implementation structure of an adaptive system for monitoring the health and well-being of the elderly. The system was designed following best practices of the Human-Centred Design approach involving representative end-users from the early stages.
Transcription Factors Responsible for Megakaryocyte-specific Gene Expression (2005)

Megakaryocytes are the hematopoietic precursors of platelets, which play an essential role in thrombosis and hemostasis. Platelet factor 4 (PF4) is expressed exclusively in megakaryocytes and platelets and serves as a lineage-specific marker of megakaryocytic differentiation. We previously characterized a number of upstream enhancer and repressor elements and demonstrated that GATA-1 and ETS-1 are important for PF4 gene expression. Recently, we have determined the novel regulatory element termed "TME" in the PF4 promoter and identified a group of binding proteins from megakaryocytic HEL cells. Here we review the function of these proteins in PF4 gene expression and discuss megakaryocyte-specific gene expression and megakaryocytepoiesis.
A new type of thin and compact SIW horn antenna with radiation improvements (2013)

International audience
Proposal of a Design Principle of Multilayer Media (2011)

We propose a design principle of stacking-type super-multilayer media in this paper. By the use of an original high-transmittance and high-recording-sensitivity recording material, bismuth–germanium–oxide, the recording layers of a 10-layer super-multilayer disc can be designed using only two types of recording layer. This leads the conventional super-multilayer media structure to a much simpler structure with only two thicknesses of spacer layers while maintaining a satisfactory signal quality on the farthest layer from the incident laser beam, where signal fluctuation due to coherent crosstalk is the strongest. The above design principle will greatly contribute to the reduction of the cost of super-multilayer media.
Understanding Structural and Chemical Modifications of ZIF MOF Under Electron-Beam Irradiation using STEM-EELS (2022)

An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
Infrared light sources with semimetal electron injection (1999)

An infrared light source is disclosed that comprises a layered semiconductor active region having a semimetal region and at least one quantum-well layer. The semimetal region, formed at an interface between a GaAsSb or GalnSb layer and an InAsSb layer, provides electrons and holes to the quantum-well layer to generate infrared light at a predetermined wavelength in the range of 2-6 mu m. Embodiments of the invention can be formed as electrically-activated light-emitting diodes (LEDs) or lasers, and as optically-pumped lasers. Since the active region is unipolar, multiple active regions can be stacked to form a broadband or multiple-wavelength infrared light source.
Introduction to the DArTseq genotyping method and its data outputs (2019)

This guide describes the DArTseq genotyping method, marker naming conventions, data output formats, data file column headers, and BLAST parameters used for aligning markers to a genome sequence.
Hepatitis A virus infections associated with clotting factor concentrate in the United States (1998)

These data document the transmission of HAV by a factor VIII concentrate and implicate factor IX products manufactured from a common source-plasma pool.
Active pixel sensors for imaging X-ray spectrometers (2003)

Active Pixel Sensors (APS) offer high-resolution imaging in combination with a fast and flexible readout. The MPI Halbleiterlabor develops and produces DEPFET (Depleted Field Effect Transistor) based APS devices. They are additionally characterized by enhanced sensitivity for X-ray photons in the range from 0.1 keV to 25 keV, spectroscopic energy resolution (below 1 electron r.m.s.) and radiation hardness. Moreover, the production process on high-ohmic silicon allows incorporating additional high-speed spectrometers based on silicon drift detectors. Such a detector system is proposed as a wide field imager for the XEUS (X-ray Evolving Universe Spectroscopy) mission. XEUS is a planned project within the European Space Agency's Horizon 2000+ program. We will present a focal plane concept for XEUS and measurement results from DEPFET-APS prototypes and high speed drift detectors.
Model for degradation of band-gap photoluminescence in GaAs (1988)

A recombination-enhanced defect reaction model is described. It is based on nonradiative recombination of photoexcited carriers at particular crystal defect sites near a semiconductor surface. The model is general and correctly predicts, with only one adjustable parameter, the photoluminescence degradation rate in GaAs, its power dependence, and its independence on lattice temperature.
Retinoblastoma from human stem cell-derived retinal organoids (2021)

Retinoblastoma is a childhood cancer of the developing retina that initiates with biallelic inactivation of the RB1 gene. Children with germline mutations in RB1 have a high likelihood of developing retinoblastoma and other malignancies later in life. Genetically engineered mouse models of retinoblastoma share some similarities with human retinoblastoma but there are differences in their cellular differentiation. To develop a laboratory model of human retinoblastoma formation, we make induced pluripotent stem cells (iPSCs) from 15 participants with germline RB1 mutations. Each of the stem cell lines is validated, characterized and then differentiated into retina using a 3-dimensional organoid culture system. After 45 days in culture, the retinal organoids are dissociated and injected into the vitreous of eyes of immunocompromised mice to support retinoblastoma tumor growth. Retinoblastomas formed from retinal organoids made from patient-derived iPSCs have molecular, cellular and genomic features indistinguishable from human retinoblastomas. This model of human cancer based on patient-derived iPSCs with germline cancer predisposing mutations provides valuable insights into the cellular origins of this debilitating childhood disease as well as the mechanism of tumorigenesis following RB1 gene inactivation.
Characterization of recombinant yellow fever-dengue vaccine viruses with human monoclonal antibodies targeting key conformational epitopes (2018)

The recombinant yellow fever-17D-dengue virus, live, attenuated, tetravalent dengue vaccine (CYD-TDV) is licensed in several dengue-endemic countries. Although the vaccine provides protection against dengue, the level of protection differs by serotype and warrants further investigation. We characterized the antigenic properties of each vaccine virus serotype using highly neutralizing human monoclonal antibodies (hmAbs) that bind quaternary structure-dependent epitopes. Specifically, we monitored the binding of dengue virus-1 (DENV-1; 1F4), DENV-2 (2D22) or DENV-3 (5J7) serotype-specific or DENV-1-4 cross-reactive (1C19) hmAbs to the four chimeric yellow fever-dengue vaccine viruses (CYD-1-4) included in phase III vaccine formulations using a range of biochemical and functional assays (dot blot, ELISA, surface plasmon resonance and plaque reduction neutralization assays). In addition, we used the "classic" live, attenuated DENV-2 vaccine serotype, immature CYD-2 viruses and DENV-2 virus-like particles as control antigens for anti-serotype-2 reactivity. The CYD vaccine serotypes were recognized by each hmAbs with the expected specificity, moreover, surface plasmon resonance indicated a high functional affinity interaction with the CYD serotypes. In addition, the hmAbs provided similar protection against CYD and wild-type dengue viruses in the in vitro neutralization assay. Overall, these findings demonstrate that the four CYD viruses used in clinical trials display key conformational and functional epitopes targeted by serotype-specific and/or cross-reactive neutralizing human antibodies. More specifically, we showed that CYD-2 displays serotype- specific epitopes present only on the mature virus. This indicates that the CYD-TDV has the ability to elicit antibody specificities which are similar to those induced by the wild type DENV. Future investigations will be needed to address the nature of CYD-TDV-induced responses after vaccine administration, and how these laboratory markers relate to vaccine efficacy and safety.
Locations, metadata, and species cover from field sampling survey associated with NEON AOP survey, East River, CO 2018 (2020)

Locations and descriptions of the sites where field sampling was conducted during the 2018 National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) imaging spectroscopy and lidar surveys in Gunnison County, Colorado. The sampling sites were located across East River, Washington Gulch, Slate River, and Coal Creek watersheds and contained a mixture of meadow, shrub, and tree sampling sites. This data package contains the location, metadata, species composition, and vector files for the sampling sites in this project. Species vouchers that have been preserved in the Rocky Mountain Biological Laboratory herbarium can be found on the Consortia of Southern Rocky Mountain Herbaria website: http://soroherbaria.org/portal/collections/index.php. Vector files provided here are for areas delineated based on the AOP reflectance data and mosaic developed by Brodrick et al. (doi: 10.15485/1618131), and use with other datasets should be closely evaluated. Subsequent data packages will contain additional biogeochemical, microbial, and geophysical data as they become available for these sampling sites. For full documentation, please see associated reference and additional references will be added here as they become available.
Prognostic value of low-level MRD in adult acute lymphoblastic leukemia detected by low- and high-throughput methods (2022)

Persistence of minimal residual disease (MRD) after induction/consolidation therapy in acute lymphoblastic leukemia is the leading cause of relapse. The GMALL 07/2003 study used MRD detection by real-time quantitative polymerase chain reaction of clonal immune gene rearrangements with 1 × 10-4 as discriminating cutoff: levels ≥1 × 10-4 define molecular failure and MRD-negativity with an assay sensitivity of at least 1 × 10-4 defining complete molecular response. The clinical relevance of MRD results not fitting into these categories is unclear and termed "molecular not evaluable" (MolNE) toward MRD-based treatment decisions. Within the GMALL 07/03 study, 1019 consecutive bone marrow samples after first consolidation were evaluated for MRD. Patients with complete molecular response had significantly better outcome (5-year overall survival [OS] = 85% ± 2%, n = 603; 5-year disease-free survival [DFS] = 73% ± 2%, n = 599) compared with patients with molecular failure (5-year OS = 40% ± 3%, n = 238; 5-year DFS = 29% ± 3%, n = 208), with patients with MolNE in between (5-year OS = 66% ± 4%; 5-year DFS = 52% ± 4%, n = 178). Of MolNE samples reanalyzed using next-generation sequencing (NGS), patients with undetectable NGS-MRD (n = 44; 5-year OS = 88% ± 5%, 5-year DFS = 70% ± 7%) had significantly better outcome than those with positive NGS-MRD (n = 42; 5-year OS = 37% ± 8%; 5-year DFS = 33% ± 8%). MolNE MRD results not just are borderline values with questionable relevance but also form an intermediate-risk group, assignment of which can be further improved by NGS.
Effect of Process Parameters on Burrs Produced in Micromilling of a Thin Nitinol Foil (2013)

This paper examines the formation of burrs in micromilling of a thin nickel–titanium alloy (nitinol) foil used in implantable biomedical device applications. The paper analyzes the effects of key micromilling process parameters such as spindle speed, feed, tool wear, backing material, and adhesive used to attach the foil to the backing material on the burr height. It is found that burr height is larger on the downmilling side for grooves cut with a worn tool at high feeds, low spindle speeds with a softer backing material, and a weaker adhesive bond. Some important interaction effects of these factors are also studied. The study also shows that the mechanics of burr formation in such thin materials depends on whether the mode of cutting is dominated by tearing or chip formation, which is a function of the feed rate. A kinematic model to predict burr widths is developed and verified through experiments.
Nationwide Temporal Trends in Clinical Characteristics and Treatment of Dilated Cardiomyopathy From 2003 to 2013 in Japan　― A Report From Clinical Personal Records ― (2023)

Although the clinical characteristics of DCM changed, the implementation of optimal medical therapy for DCM increased from 2003 to 2013 in Japan.
Osteopontin Expression in Small Airway Epithelium in Copd is Dependent on Differentiation and Confined to Subsets of Cells (2019)

Osteopontin (OPN) plays a role in inflammation via recruitment of neutrophils and tissue remodeling. In this study, we investigated the distribution of OPN-expressing cells in the airway epithelium of normal lung tissue and that from patients with chronic obstructive pulmonary disease (COPD). OPN was detected on the epithelial cell surface of small airways and in scattered cells within the epithelial cell layer. Staining revealed higher OPN concentrations in tissue showing moderate to severe COPD compared to that in controls. In addition, OPN expression was confined to goblet and club cells, and was absent from ciliated and basal cells as detected via immunohistochemistry. However, OPN expression was up-regulated in submerged basal cells cultures exposed to cigarette smoke (CS) extract. Cell fractioning of air-liquid interface cultures revealed increased OPN production from basal compartment cells compared to that in luminal fraction cells. Furthermore, both constitutive and CS-induced expression of OPN decreased during differentiation. In contrast, cultures stimulated with interleukin (IL)-13 to promote goblet cell hyperplasia showed increased OPN production in response to CS exposure. These results indicate that the cellular composition of the airway epithelium plays an important role in OPN expression and that these levels may reflect disease endotypes in COPD.
Partial Distinguishability in Femtosecond Optical Spontaneous Parametric Down-Conversion (1999)

Quantum interference is observed using femtosecond parametric down-conversion in the absence of spectral filtering of the down-converted light. The well-known symmetric dip observed in cw polarization-interferometry experiments becomes less pronounced and substantially asymmetric under such pulsed excitation. We show that this asymmetry arises from the partial distinguishability of contributions from space-time segments within the down-conversion crystal. We develop a theory that achieves agreement with experiment by coherently adding intrasegment contributions while incoherently adding intersegment contributions.
SINGLE-CRYSTAL DIAMOND NEMS DEVICES FOR THE STUDY OF COLOR CENTERS (2016)

We demonstrate fabrication methods for micro-/nanoelectromechanical systems (MEMS/NEMS) in single-crystal diamond chip. Such devices can be used to study embedded color centers, such as the nitrogen vacancy (NV) or the silicon vacancy (SiV). Color centers have discrete electronic and spin energy levels, which can be controlled by engineering the amount of strain in the diamond lattice. These strain fields can be effectively controlled using conventional MEMS/NEMS devices. As a specific demonstration, we show the tuning of SiV electronic energy levels via static actuation. The device design process accounting for various fundamental and experimental constraints is discussed.
Multiplexed lighting system using time-division multiplexing (2022)

Improvements in lighting and other indoor environmental conditions have gained considerable attention in different areas, including health and economics. Controlling the lighting environment is essential because, among the indoor factors, visual stimulation affects numerous human characteristics. Further, visual stimulation, including peripheral vision, affects people differently. Therefore, to improve the indoor environment with multiple occupants, each occupant must have an independent lighting environment. However, this cannot be achieved through conventional approaches. In this study, we propose a multiplexed lighting environment that can simultaneously realize multiple mutually independent lighting environments within a single space. We developed the proposed system using time-division multiplexing and conducted an experiment to clarify the influence of light multiplexing on human behavior and impression of the indoor environment. The experimental results showed that the proposed method changed the lighting operations of the users and improved their impression of the lighting environment. Furthermore, the proposed method provides a desirable lighting environment for all people within a single space, even when people in the same space desire different lighting environments.