gebhart/patrepeval huggingface dataset:
The ability to form biofilm influences Mycobacterium avium invasion and translocation of bronchial epithelial cells (2005)

Organisms of the Mycobacterium avium complex (MAC) are widely distributed in the environment, form biofilms in water pipes and potable water tanks, and cause chronic lung infections in patients with chronic obstructive pulmonary disease and cystic fibrosis. Pathological studies in patients with pulmonary MAC infection revealed granulomatous inflammation around bronchi and bronchioles. BEAS-2B human bronchial epithelial cell line was used to study MAC invasion. MAC strain A5 entered polarized BEAS-2B cells with an efficiency of 0.1 +/- 0.03% in 2 h and 11.3 +/- 4.0% in 24 h. In contrast, biofilm-deficient transposon mutants 5G4, 6H9 and 9B5 showed impaired invasion. Bacteria exposed to BEAS-2B cells for 24 h had greater ability to invade BEAS-2B cells compared with bacteria incubated in broth. M. avium had no impact on the monolayer transmembrane resistance. Scanning electron microscopy showed that MAC A5 forms aggregates on the surface of BEAS-2B cell monolayers, and transmission electron microscopy evidenced MAC within vacuoles in BEAS-2B cells. Cells infected with the 5G4 mutant, however, showed significantly fewer bacteria and no aggregates on the cell surface. Mutants had impaired ability to cause infection in mice, as well. The ability to form biofilm appeared to be associated with the invasiveness of MAC A5.
160 W 800 fs Yb:YAG single crystal fiber amplifier without CPA (2015)

We demonstrate a compact and simple two-stage Yb:YAG single crystal fiber amplifier which delivers 160 W average power, 800 fs pulses without chirped pulse amplification. This is the highest average power of femtosecond laser based on SCF. Additionally, we demonstrate the highest small signal gain of 32.5 dB from the SCF in the first stage and the highest extraction efficiency of 42% in the second stage. The excellent performance of the second stage was obtained using the bidirectional pumping scheme, which is applied to SCF for the first time.
Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius) (2021)

The results provided structural genomic evidence for the ZZ/ZW sex determination system in P. hyalocranius discovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species.
Data from CD137 Stimulation Enhances Cetuximab-Induced Natural Killer: Dendritic Cell Priming of Antitumor T-Cell Immunity in Patients with Head and Neck Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Cetuximab, an EGFR-specific antibody (mAb), modestly improves clinical outcome in patients with head and neck cancer (HNC). Cetuximab mediates natural killer (NK) cell:dendritic cell (DC) cross-talk by cross-linking FcγRIIIa, which is important for inducing antitumor cellular immunity. Cetuximab-activated NK cells upregulate the costimulatory receptor CD137 (4-1BB), which, when triggered by agonistic mAb urelumab, might enhance NK-cell functions, to promote T-cell–based immunity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental design:&lt;/b&gt; CD137 expression on tumor-infiltrating lymphocytes was evaluated in a prospective cetuximab neoadjuvant trial, and CD137 stimulation was evaluated in a phase Ib trial, in combining agonistic urelumab with cetuximab. Flow cytometry and cytokine release assays using NK cells and DC were used &lt;i&gt;in vitro&lt;/i&gt;, testing the addition of urelumab to cetuximab-activated NK, DC, and cross presentation to T cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; CD137 agonist mAb urelumab enhanced cetuximab-activated NK-cell survival, DC maturation, and tumor antigen cross-presentation. Urelumab boosted DC maturation markers, CD86 and HLA DR, and antigen-processing machinery (APM) components TAP1/2, leading to increased tumor antigen cross-presentation. In neoadjuvant cetuximab-treated patients with HNC, upregulation of CD137 by intratumoral, cetuximab-activated NK cells correlated with FcγRIIIa V/F polymorphism and predicted clinical response. Moreover, immune biomarker modulation was observed in an open label, phase Ib clinical trial, of patients with HNC treated with cetuximab plus urelumab.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These results suggest a beneficial effect of combination immunotherapy using cetuximab and CD137 agonist in HNC. &lt;i&gt;Clin Cancer Res; 23(3); 707–16. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Correction: An oxygen-blocking oriented multifunctional solid–electrolyte interphase as a protective layer for a lithium metal anode in lithium–oxygen batteries (2021)

Correction for ‘An oxygen-blocking oriented multifunctional solid–electrolyte interphase as a protective layer for a lithium metal anode in lithium–oxygen batteries’ by Xiao-Dong Lin <italic>et al.</italic>, <italic>Energy Environ. Sci.</italic>, 2021, <bold>14</bold>, 1439–1448, DOI: 10.1039/D0EE02931A.
Hard Play (1999)

Gary sits in the cab of an idling semi and waits.The engine mutters, the flap on the semi's exhaust stack punctuating the wait: cling, cling, cling.The town square in Auburn is a chaos of equipment, of trucks, game joints, par tially assembled rides, half-open concession stands; the streets are criscrossed with heavy duty electric wires, water hoses; people on foot, on bikes and in golf carts dodge in and out between pickups and semis.Gary sits behind the wheel of the semi that carries the Merry-Go-Round.He needs to move the semi from his corner of the square to the other corner a few blocks distant, but a pickup truck pulling a fried onion concession stand is in the way.The driver moves forward, stops, jerks his steering wheel right, backs up, hits the brakes.He can't figure out how to maneuver his booth into its spot.Gary's brother Tim zooms by on his mountain bike.He sees what needs to be done, jumps off his bike, stands behind the pickup and guides the man into his spot, gesturing to him, coaxing him: C'mon back, Cymon back.The onion booth slowly edges into place, until finally there is enough room for Gary to pull through.The huge semi rolls forward, inching down the crowded street.Tim guides him into a straight course.Then he jumps back on his bike and zooms off to solve another problem in another place.As it has been all summer, there are a thousand unremarkable details here that need to be looked after before the carnival can open.There are rides to be spotted and assembled, wiring to be laid out, hoses to be uncoiled and hooked up, windows to be washed and steam tables cleaned, stock unpacked and hung up, help to be hired and trained and watched.But this is the last time, the last fair of the season.James says aloud what everyone has been thinking, and his words echo in our minds: One more time . . .one more time . . .
Exosomes from Bone Marrow Dendritic Cells Pulsed with Diphtheria Toxoid Preferentially Induce Type 1 Antigen-Specific IgG Responses in Naive Recipients in the Absence of Free Antigen (2006)

Exosomes derived from dendritic cells (DC) activate T cells in vivo, but whether exosomes are able to induce and/or modulate humoral immune responses is still unknown. We show that murine bone marrow DC pulsed in vitro with an intact protein (diphtheria toxoid (DT)) produce exosomes that induce, in the absence of free protein, in vivo Ig responses specific for DT in naive recipients. Furthermore, these exosomes stimulate secondary IgG anti-DT responses in mice primed with intact DT. Exosomes from mature, relative to immature, DC were more effective at inducing primary, although not secondary, IgG anti-DT responses. Whereas intact DT preferentially induced a type 2 (IgG1) anti-DT response, exosomes from DT-pulsed bone marrow DC favored induction of type 1 (IgG2b and IgG2a) DT-specific IgG. These results are the first to demonstrate the ability of exosomes derived from Ag-pulsed DC to induce and modulate Ag-specific humoral immunity in vivo.
Use of Hyphenated Liquid-Phase Analyses—Mass Spectrometric Approaches for the Characterization of Glycoproteins Derived from Recombinant DNA (1996)

The analysis of recombinant Desmodus Salivary Plasminogen Activator (DSPAα1), a heterogeneous glycoprotein, is demonstrated through the use of High Performance Liquid Chromatography (HPLC), High Performance Capillary Electrophoresis (HPCE), Electrospray Liquid Chromatography Mass Spectrometry. (ES-LC/MS) and Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS). The protein is analyzed at three specific levels of detail: the intact protein, proteolytic digests of the protein and fractions from the proteolytic digest. A method for "on-column" collection of HPLC fractions for subsequent transfer and analysis by HPCE and MALDI-TOF is shown.
Costs of Different Methods for Ships Ballast Water Treatment (2003)

A review of costs of different methods for ships ballast water treatment is given in this paper.
Synthesis of titanium phosphate by the sol-gel method and reproducibility of the composition and properties of the sorbent (1988)

Titanium phosphate is a promising ion-exchanger for extracting rare, scattered, and radioactive elements from solutions of complex composition, and for purification of wastewaters. The purpose of this work was to study the dependence of the chemical composition and properties of titanium phosphate on the conditions of gel formation and on the concentration of orthophosphoric acid during conversion of titanium hydroxide into the phosphate. Based on the sol-gel technique, a reproducible method was devised for synthesis of titanium phosphate in the form of spherical granules 1.3-2.1 mm in size, having an extensive specific surface (160-190 m/sup 2//g) and high strength (18-30 MPa). The average values of the reproducibility of composition, capacity, distribution coefficient, strength, and specific surface are 12, 10, 33, 48, and 11%, respectively. The sorbent is not inferior in its sorption-selective properties with respect to cesium to titanium phosphate samples obtained by traditional precipitation or hydrolysis methods.
An Efficient ERP-Based Brain-Computer Interface Using Random Set Presentation and Face Familiarity (2014)

Event-related potential (ERP)-based P300 spellers are commonly used in the field of brain-computer interfaces as an alternative channel of communication for people with severe neuro-muscular diseases. This study introduces a novel P300 based brain-computer interface (BCI) stimulus paradigm using a random set presentation pattern and exploiting the effects of face familiarity. The effect of face familiarity is widely studied in the cognitive neurosciences and has recently been addressed for the purpose of BCI. In this study we compare P300-based BCI performances of a conventional row-column (RC)-based paradigm with our approach that combines a random set presentation paradigm with (non-) self-face stimuli. Our experimental results indicate stronger deflections of the ERPs in response to face stimuli, which are further enhanced when using the self-face images, and thereby improving P300-based spelling performance. This lead to a significant reduction of stimulus sequences required for correct character classification. These findings demonstrate a promising new approach for improving the speed and thus fluency of BCI-enhanced communication with the widely used P300-based BCI setup.
Ten-year survival trends of neovascular age-related macular degeneration at first presentation (2020)

The chronicity of nAMD disease and its management highlights the importance of long-term visual prognosis. Our analyses suggest that one in five patients will retain good vision (BCVA ≥70 ETDRS letters) in the first-affected eye at 10 years after starting anti-VEGF treatment; yet, one in two patients will have good vision in their better-seeing eye. Moreover, our data suggest that early treatment of nAMD is associated with better visual outcomes.
Comparison of UHF-ECG with Other Noninvasive Electrophysiological Mapping Tools for Assessing Ventricular Dyssynchrony (2021)

This paper compares Ultra High Frequency ECG (UHF-ECG) with other techniques in the capacity to assess ventricular dyssynchrony. Ventricular dyssynchrony is important to identify patients that qualify for Cardiac Resynchronization Therapy (CRT) and to measure effects of CRT and other pacing therapies. Currently used tools are: duration of the QRS complex in the 12-lead ECG, vectorcardiographically determined QRSarea, ECG belt and ECG imaging. QRS duration is crude, QRSarea has been shown to predict CRT response in three large single center studies, ECG belt is a novel approach using 50&#x2013;60 body surface electrodes and yields (variation in) activation times. ECG imaging requires cardiothoracic imaging and recordings using 150&#x2013;250 electrodes and results in images of activation, which are converted into inter and intraventricular AT differences. UHF-ECG requires 12&#x2013;14 lead ECG but provides two measures: (also) a measure of interventricular dyssynchrony (e-DYS) and a marker of width of the activation wavefront that reflects the contribution of rapid conduction. The latter is a unique feature that appears particularly useful in studies on different modes of physiological pacing.
The Alterations of Mitochondrial Function during NAFLD Progression—An Independent Effect of Mitochondrial ROS Production (2021)

The progression of non-alcoholic fatty liver (NAFL) into non-alcoholic steatohepatitis implicates multiple mechanisms, chief of which is mitochondrial dysfunction. However, the sequence of events underlying mitochondrial failure are still poorly clarified. In this work, male C57BL/6J mice were fed with a high-fat plus high-sucrose diet for 16, 20, 22, and 24 weeks to induce NAFL. Up to the 20th week, an early mitochondrial remodeling with increased OXPHOS subunits levels and higher mitochondrial respiration occurred. Interestingly, a progressive loss of mitochondrial respiration along "Western diet" feeding was identified, accompanied by higher susceptibility to mitochondrial permeability transition pore opening. Importantly, our findings prove that mitochondrial alterations and subsequent impairment are independent of an excessive mitochondrial reactive oxygen species (ROS) generation, which was found to be progressively diminished along with disease progression. Instead, increased peroxisomal abundance and peroxisomal fatty acid oxidation-related pathway suggest that peroxisomes may contribute to hepatic ROS generation and oxidative damage, which may accelerate hepatic injury and disease progression. We show here for the first time the sequential events of mitochondrial alterations involved in non-alcoholic fatty liver disease (NAFLD) progression and demonstrate that mitochondrial ROS are not one of the first hits that cause NAFLD progression.
3D ResNet with Ranking Loss Function for Abnormal Activity Detection in\n Videos (2020)

Abnormal activity detection is one of the most challenging tasks in the field\nof computer vision. This study is motivated by the recent state-of-art work of\nabnormal activity detection, which utilizes both abnormal and normal videos in\nlearning abnormalities with the help of multiple instance learning by providing\nthe data with video-level information. In the absence of temporal-annotations,\nsuch a model is prone to give a false alarm while detecting the abnormalities.\nFor this reason, in this paper, we focus on the task of minimizing the false\nalarm rate while performing an abnormal activity detection task. The mitigation\nof these false alarms and recent advancement of 3D deep neural network in video\naction recognition task collectively give us motivation to exploit the 3D\nResNet in our proposed method, which helps to extract spatial-temporal features\nfrom the videos. Afterwards, using these features and deep multiple instance\nlearning along with the proposed ranking loss, our model learns to predict the\nabnormality score at the video segment level. Therefore, our proposed method 3D\ndeep Multiple Instance Learning with ResNet (MILR) along with the new proposed\nranking loss function achieves the best performance on the UCF-Crime benchmark\ndataset, as compared to other state-of-art methods. The effectiveness of our\nproposed method is demonstrated on the UCF-Crime dataset.\n
Antigen presentation and T cell activation by Coccidioides -Ag2/PRA-cDNA-transfected primary murine dendritic cells (78.21) (2009)

Abstract The dendritic cells (DCs) have an important role in antigen presentation and regulation of host defense. Immunization with in vitro modified DCs has been shown to activate protective immune responses. Among various approaches used for modifying DCs, the nonviral genetic transfection of DCs is easy and safe as compared to viral-mediated transfection methods. In this study, we investigated antigen presentation and T cell stimulatory ability of nonvirally, gene-transfected primary murine DCs. We isolated primary murine bone marrow derived DCs and transfected isolated DCs with Ag2/PRA-cDNA (protective epitope of Coccidioides, a fungal pathogen) using TransIT-TKO (Mirus Bio, WI)- a nonviral transfection reagent. We found that upto 30-40% of primary murine DCs were transfected with the plasmid DNA carrying Ag2/PRA-cDNA. The transfected DCs remained viable and expressed the transgene (Ag2/PRA-cDNA)-encoded protein. Only moderate changes were observed in the immunophenotype of genetically-transfected DCs. The activation of T cells was studied by flow-cytometry after co-culture of naive splenic T cells with DCs. The T cells co-incubated with Ag2/PRA-cDNA transfected DCs showed upregulation of cell-surface CD25 and CD69 (activation markers). These results suggest that the primary DCs can be efficiently transfected in vitro using a non viral method; the transfected primary DCs can process and present the antigens and stimulate T cells.
ChemInform Abstract: Substituted Quinazolines. Part 1. Synthesis and Antitumor Activity of Certain Substituted 2‐Mercapto‐4(3H)‐quinazolinone Analogues. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Study of electronic lab notebook design and practices that emerged in a collaborative scientific environment (2014)

Prolific adoption of digital media across scientific fields has led to inevitable transformation of a traditional lab book into an electronic lab notebook (ELN). Research so far has focussed on designing ELN prototypes and learning from their limited deployments. At the same time, a variety of commercially available ELNs have been adopted by industrial and academic laboratories. That provides opportunities for situated research and a deeper understanding of the role that ELNs assumes as an integral part of a scientific environment. In this paper we present a study of ELN design that has emerged as scientists appropriated commercial off-the-shelf note-taking software and adapted it to their work. Through in-situ observations we analysed the interplay between the technology and emerging practices. Our study reveals a tension that is intrinsic to the digital nature of ELNs: a conflict between the flexibility, fluidity, and low threshold for modifying digital records and the requirement for persistence and consistency. This led to refined requirements and design considerations for ELNs.
Performance evaluation of H.264/AVC decoding and visualization using the GPU (2007)

The coding efficiency of the H.264/AVC standard makes the decoding process computationally demanding. This has limited the availability of cost-effective, high-performance solutions. Modern computers are typically equipped with powerful yet cost-effective Graphics Processing Units (GPUs) to accelerate graphics operations. These GPUs can be addressed by means of a 3-D graphics API such as Microsoft Direct3D or OpenGL, using programmable shaders as generic processing units for vector data. The new CUDA (Compute Unified Device Architecture) platform of NVIDIA provides a straightforward way to address the GPU directly, without the need for a 3-D graphics API in the middle. In CUDA, a compiler generates executable code from C code with specific modifiers that determine the execution model. This paper first presents an own-developed H.264/AVC renderer, which is capable of executing motion compensation (MC), reconstruction, and Color Space Conversion (CSC) entirely on the GPU. To steer the GPU, Direct3D combined with programmable pixel and vertex shaders is used. Next, we also present a GPU-enabled decoder utilizing the new CUDA architecture from NVIDIA. This decoder performs MC, reconstruction, and CSC on the GPU as well. Our results compare both GPU-enabled decoders, as well as a CPU-only decoder in terms of speed, complexity, and CPU requirements. Our measurements show that a significant speedup is possible, relative to a CPU-only solution. As an example, real-time playback of high-definition video (1080p) was achieved with our Direct3D and CUDA-based H.264/AVC renderers.
9 i. Introduction (1999)

Terrestrial life evolved with a sidereal period of Earth’s revolution about the sun close to 365 days and an axial rotation near 24 hr. It is thus not surprising that nearly all organisms studied, including prokaryotes and eukaryotes, possess a(n) internal biological clock(s) with a near-24-hr periodicity. These internal clock mechanisms or endogenous pacemakers determine the appropriate environmental timing for species specific biological and behavioral events (e.g., sleep, endocrine function, temperature regulation). It is generally accepted that the periodic lightdark cycle, associated with the earth’s daily axial rotation, is the dominant envi­ ronmental synchronizer used by nearly all organisms to entrain to the 24-hr geo­ physical day. Entrainment is a fundamental property of endogenous oscillators by which the period of the pacemaker is synchronized to the period of the entraining stimuli. In the absence of periodic synchronizing agents, endogenous pacemakers oscillate at their own intrinsic period. Controlled experimental studies have shown the endogenous pacemaker in humans to cycle with an average period that is somewhat longer than 24 hr (1-4). Stable entrainment of the endogenous pace­ maker to the light-dark cycle is achieved when the resetting response to lightexposure offsets the drift due to the longer-than-24-hr intrinsic period of the human circadian pacemaker.