gebhart/patrepeval huggingface dataset:
A novel peptide targeting Clec9a on dendritic cell for cancer immunotherapy (2016)

Dendritic cells (DCs) are professional antigen-presenting cells with antigen recognition molecules on the surface. Clec9a is selectively expressed on mouse CD8a+ DCs and CD103+ DCs subsets, which are functionally similar to human BDCA3+ DCs. It is reported that Clec9a is responsible for the antigen cross-presentation of these DC subsets. In the present study, by using phage display technique, we discovered a novel peptide WH, which can selectively bind to mouse Flt3L induced Clec9a+ DCs or Clec9a over-expressed HEK-293T cells. Furthermore, by using computer-aided docking model and mutation assay, we observed that Asp248 and Trp250 are two key residues for Clec9a to bind with peptide WH. When coupled with OVA257-264 epitope, peptide WH can significantly enhance the ability of Clec9a+ DCs to activate OVA-specific CD8+ T cells, which elicit strong ability to secret IFN-γ, express perforin and granzyme B mRNA. In B16-OVA lung metastasis mouse model, WH-OVA257-264 fusion peptide can also enhance the activation of CD8+ T cells and decrease the lung metastasis loci. All these results suggested that peptide WH could be considered as an antigen delivery carrier targeting Clec9a+ DCs for cancer immunotherapy.
Challenge 2006: QT interval measurement (2006)

This years challenge addresses the question if it is possible to measure the QT interval by fully automated methods. For this task we implemented an algorithm which (1) performs beat detection, measures wave boundaries on a beat-to-beat basis and (2) selects a representative beat whose QT interval is used. To get the positions of the wave boundaries, the algorithm searches for peaks in the 1st derivative of bandpass filtered ECG signals using thresholds which are adapted to the amplitudes in the segments of interest. When the peaks associated with the QRS complex and the T wave are found, the beginning of the QRS complex and the end of the T wave are assessed using the ”Philips Diagnostic ECG Interval Measurement ” method [1]. For the selection of the representative beat, a noise level for each single beat was calculated by determining the standard deviation of the ECG 30ms before the onset of the QRS complex and 30ms after the end to the T wave. The beat with the lowest noise level was selected as the representative beat and from this the QT interval was used. This approach results in a score of 70.94ms. 1.
Coherent Mitigation of Radio Frequency Interference in 10{100 MHz (2008)

This dissertation describes methods of mitigating radio frequency interference (RFI) in the frequency range 10-100 MHz, developing and evaluating coherent methods with which RFI is subtracted from the afflicted data, nominally resulting in no distortion of the underlying signals. This approach is of interest in weak signal applications such as radio astronomy, where the signal of interest may have interference-to-noise ratio much less than one, and so can be easily distorted by other methods. Environmental noise in this band is strong and non-white, so a realistic noise model is developed, with which we characterize the performance of signal parameter estimation, a key component of the proposed algorithms. Two classes of methods are considered: "generic" parameter estimation/subtraction (PE/S) and a modulation-specific form known as demodulation-remodulation ("demod--remod") PE/S. It is demonstrated for RFI in the form of narrowband FM and Broadcast FM that generic PE/S has the problem of severely distorting underlying signals of interest and demod-remod PE/S is less prone to this problem. Demod-remod PE/S is also applied and evaluated for RFI in the form of Digital TV signals. In both cases, we compare the performance of the demod-remod PE/S with that of a traditional adaptive canceling method employing a reference antenna, and propose a hybrid method to further improve performance. A new metric for "toxicity" is defined and employed to determine the degree to which RFI mitigation damages the underlying signal of interest.
Development of a Physics-based Approach For the Prediction of Strain Capacity of Welded Pipelines (2009)

Various industry efforts are underway to develop or improve methods to address design of pipelines for harsh arctic or seismically active regions. The design challenges associated with these regions involve multiple limit states that require characterization of load from large ground deformations, as well as material capacity. The focus of this paper is the development of a physics-based approach to characterize the strain capacity of a welded pipeline for the tensile limit state. Fullscale pressurized pipe tests and three dimensional (3D) finite element analyses (FEA) were conducted to develop the limit states. An experimental program was conducted to measure the strain capacity of full-scale pressurized pipes and provide validation to the physics-based approach. In addition to full-scale tests, round bar tensile and single edge notched tension (SENT) specimens were employed in the experimental program to characterize the weld properties. Multiple measures were taken to account for the influence of natural material variability on the full-scale test results to facilitate validation of the physics based approach. The measures included the use of gas metal arc welding (GMAW) mechanized welding procedure and the production of additional welds to characterize material variability around the circumference of the welded pipes and across multiple welds. Finite element analysis (FEA) based parametric study was conducted to model both fracture and plastic collapse failure mechanisms observed in full-scale tests. The parametric study shows that in addition to fracture toughness and overmatch, misalignment may also significantly affect strain capacity due to transition in failure mode from plastic collapse to ductile tearing. The study illustrates a need to incorporate the observed effect of these parameters in experimental programs designed to characterize strain capacity for development of next generation fracture assessment procedures.
Offshore gas liquefaction without offshore LNG plants (1980)

Constructors John Brown Ltd.'s Cold Box Shuttle liquefaction system offers an economical means of recovering offshore gas by eliminating the need for platform liquefaction facilities and by producing onshore the bulk of the cold for LNG refrigeration. Under the C.B.S. concept, a ship provided with heat-exchange equipment conveys liquid nitrogen from a shore terminal out to the platform, where the ship is attached to a single-point mooring (SPM). Heat exchange between the liquid nitrogen and the gas from the platform produces LNG for transport back to port in the same ship. At the port terminal, the cold in LNG can help generate the power needed in the liquid-nitrogen plant. The production efficiency of the C.B.S. system depends upon the gas production rate, the number and size of LNG vessels served by the shore terminal, the limiting wave heights for mooring and loading, the journey time, the mooring time, the planned maintenance of SPM, and the unplanned downtime of the SPM.
THE EFFECTS OF RANITIDINE and CYSTEAMINE ON INTESTINAL METAPLASIA INDUCED BY X‐IRRADIATION IN RATS (1988)

The influence of ranitidine and cysteamine on intestinal metaplasia was examined in 7-month-old male Crj: CD (SD) rats. At the age of 5 weeks, the animals were treated with 10 Gy doses of X-rays at 3-day intervals up to a total of 20 Gy in the gastric region, and 6 months after irradiation, the rats received either ranitidine (0.02% in diet) or cysteamine (0.1% in drinking water) for 2 months. The incidence and number of intestinal metaplasia with alkaline phosphatase-positive foci in rats given X-rays and cysteamine (group 4) were significantly low compared with those in rats given X-rays and ranitidine (group 3) (p less than 0.01). In both the pyloric and the fundic gland mucosae, the average numbers of type C metaplasia (intestinal crypts with Paneth cells) and total numbers of metaplastic foci in rats of group 3 were much higher than those in group 4 (P less than 0.05). The present results showed that the occurrence of intestinal metaplasia was significantly increased after administration of ranitidine and decreased by cysteamine.
Fast 3-D temporal focusing microscopy using an electrically tunable lens (2015)

In this paper, we present a 3-D temporal focusing microscope based on an electrically tunable lens (ETL) and a femtosecond regenerative laser amplifier. The focus-tunable lens provides a fast and compact way to perform non-mechanical z-scanning and resolves the blurry image issue compared with GVD-based z-scanning methods. The optical performance of the temporal focusing system, including z-scanning characteristics, the associated the magnification variation, and the lateral and axial resolution, has been studied and characterized using calibrated Rhodamine-6G thin film sample, fluorescent beads, and pollen samples. Lastly, we demonstrate the optical cross-sectioning and z-scanning capability with an in vivo experiment, where Ca(2+) imaging of neurons in GaCamp6 labeled zebrafish was performed.
Role of the nervous system in sarcopenia and muscle atrophy with aging: strength training as a countermeasure (2010)

Aging is characterized by loss of spinal motor neurons (MNs) due to apoptosis, reduced insulin-like growth factor I signaling, elevated amounts of circulating cytokines, and increased cell oxidative stress. The age-related loss of spinal MNs is paralleled by a reduction in muscle fiber number and size (sarcopenia), resulting in impaired mechanical muscle performance that in turn leads to a reduced functional capacity during everyday tasks. Concurrently, maximum muscle strength, power, and rate of force development are decreased with aging, even in highly trained master athletes. The impairment in muscle mechanical function is accompanied and partly caused by an age-related loss in neuromuscular function that comprise changes in maximal MN firing frequency, agonist muscle activation, antagonist muscle coactivation, force steadiness, and spinal inhibitory circuitry. Strength training appears to elicit effective countermeasures in elderly individuals even at a very old age (>80 years) by evoking muscle hypertrophy along with substantial changes in neuromuscular function, respectively. Notably, the training-induced changes in muscle mass and nervous system function leads to an improved functional capacity during activities of daily living.
Probiotics in the critically ill (2012)

Probiotics appear to reduce infectious complications including ventilator-associated pneumonia and may influence intensive care unit mortality. However, clinical and statistical heterogeneity and imprecise estimates preclude strong clinical recommendations. Further research on probiotics in the critically ill is warranted.
Leveraging the Wisdom of the Crowd for Fine-Grained Recognition (2015)

Fine-grained recognition concerns categorization at sub-ordinate levels, where the distinction between object classes is highly local. Compared to basic level recognition, fine-grained categorization can be more challenging as there are in general less data and fewer discriminative features. This necessitates the use of a stronger prior for feature selection. In this work, we include humans in the loop to help computers select discriminative features. We introduce a novel online game called "Bubbles" that reveals discriminative features humans use. The player's goal is to identify the category of a heavily blurred image. During the game, the player can choose to reveal full details of circular regions ("bubbles"), with a certain penalty. With proper setup the game generates discriminative bubbles with assured quality. We next propose the "BubbleBank" representation that uses the human selected bubbles to improve machine recognition performance. Finally, we demonstrate how to extend BubbleBank to a view-invariant 3D representation. Experiments demonstrate that our approach yields large improvements over the previous state of the art on challenging benchmarks.
A Busbar Like Power Module Based On 3D Chip On Chip Hybrid Integration (2009)

The paper focuses on a new generation of power modules, trying to optimize the tradeoff between thermal and EMI managements. At the same time, the packaging approach is considered in order to simplify the implementation of the power dies while improving the reliability of the structure. The approach considers the hybrid integration of the power dies, one on top of the other into a 3D chip on chip configuration. Thanks to this structure, the power dies can be directly inserted within electrical plates, the whole structure emulating a busbar like power module. The paper presents the characteristics and the benefits of the approach. Then, it focuses on the practical characterization of two prototypes: a buck converter structure and a full bridge, single phase diode rectifier. Both of them are based on double sided thermal cooling and electro-thermal contacts are obtained by pressure. The prototypes exhibit great performances while offering really reduced parasitic and EMI coupling.
Microrelays With Bidirectional Electrothermal Electromagnetic Actuators and Liquid Metal Wetted Contacts (2007)

Microrelays with liquid metal wetted contacts have been demonstrated using bidirectional electrothermal electromagnetic actuators. These relays were fabricated with the Metal MUMPs foundry process, which has a 20-mum-thick nickel structural layer. The operating voltage is under 0.5 V. The measured breakdown voltage and off-state resistance are greater than 200 V and 100 MOmega, respectively, and the gold-to-gold contact resistance is around 0.3 Omega. When the contacts are wetted with liquid gallium alloy (melting point at -20degC), the measured contact resistance can be as low as 0.015 Omega. As such, these bidirectional relays could have potential applications in high-power switching systems with low contact resistance using liquid metal wetted contacts.
Sitting Phase Monolayers of Polymerizable Phospholipids Create Dimensional, Molecular-Scale Wetting Control for Scalable Solution-Based Patterning of Layered Materials (2017)

The use of dimensionally ordered ligands on layered materials to direct local electronic structure and interactions with the environment promises to streamline integration into nanostructured electronic, optoelectronic, sensing, and nanofluidic interfaces. Substantial progress has been made in using ligands to control substrate electronic structure. Conversely, using the exposed face of the ligand layer to structure wetting and binding interactions, particularly with scalable solution- or spray-processed materials, remains a significant challenge. However, nature routinely utilizes wetting control at scales from nanometer to micrometer to build interfaces of striking geometric precision and functional complexity, suggesting the possibility of leveraging similar control in synthetic materials. Here, we assemble striped "sitting" phases of polymerizable phospholipids on highly oriented pyrolytic graphite, producing a surface consisting of 1 nm wide hydrophilic stripes alternating with 5 nm wide hydrophobic stripes. Protruding, strongly wetting headgroup chemistries in these monolayers enable formation of rodlike wetted patterns with widths as little as ∼6 nm and lengths up to 100 nm from high-surface-tension liquids (aqueous solutions of glycerol) commonly utilized to assess interfacial wetting properties at larger length scales. In contrast, commonly used lying-down phases of diynoic acids with in-plane headgroups do not promote droplet sticking or directional spreading. These results point to a broadly applicable strategy for achieving high-resolution solution-based patterning on layered materials, utilizing nanometer-wide patterns of protruding, charged functional groups in a noncovalent monolayer to define pattern edges.
Vitamin C and E supplementation hampers cellular adaptation to endurance training in humans: a double‐blind, randomised, controlled trial (2014)

In this double-blind, randomised, controlled trial, we investigated the effects of vitamin C and E supplementation on endurance training adaptations in humans. Fifty-four young men and women were randomly allocated to receive either 1000 mg of vitamin C and 235 mg of vitamin E or a placebo daily for 11 weeks. During supplementation, the participants completed an endurance training programme consisting of three to four sessions per week (primarily of running), divided into high-intensity interval sessions [4-6 × 4-6 min; >90% of maximal heart rate (HRmax)] and steady state continuous sessions (30-60 min; 70-90% of HRmax). Maximal oxygen uptake (VO2 max ), submaximal running and a 20 m shuttle run test were assessed and blood samples and muscle biopsies were collected, before and after the intervention. Participants in the vitamin C and E group increased their VO2 max (mean ± s.d.: 8 ± 5%) and performance in the 20 m shuttle test (10 ± 11%) to the same degree as those in the placebo group (mean ± s.d.: 8 ± 5% and 14 ± 17%, respectively). However, the mitochondrial marker cytochrome c oxidase subunit IV (COX4) and cytosolic peroxisome proliferator-activated receptor-γ coactivator 1 α (PGC-1α) increased in the m. vastus lateralis in the placebo group by 59 ± 97% and 19 ± 51%, respectively, but not in the vitamin C and E group (COX4: -13 ± 54%; PGC-1α: -13 ± 29%; P ≤ 0.03, between groups). Furthermore, mRNA levels of CDC42 and mitogen-activated protein kinase 1 (MAPK1) in the trained muscle were lower in the vitamin C and E group than in the placebo group (P ≤ 0.05). Daily vitamin C and E supplementation attenuated increases in markers of mitochondrial biogenesis following endurance training. However, no clear interactions were detected for improvements in VO2 max and running performance. Consequently, vitamin C and E supplementation hampered cellular adaptations in the exercised muscles, and although this did not translate to the performance tests applied in this study, we advocate caution when considering antioxidant supplementation combined with endurance exercise.
Effect of Microstructure of Nitrogen-Doped Graphene on Oxygen Reduction Activity in Fuel Cells (2012)

The development of fuel cells as clean-energy technologies is largely limited by the prohibitive cost of the noble-metal catalysts needed for catalyzing the oxygen reduction reaction (ORR) in fuel cells. A fundamental understanding of catalyst design principle that links material structures to the catalytic activity can accelerate the search for highly active and abundant nonmetal catalysts to replace platinum. Here, we present a first-principles study of ORR on nitrogen-doped graphene in acidic environment. We demonstrate that the ORR activity primarily correlates to charge and spin densities of the graphene. The nitrogen doping and defects introduce high positive spin and/or charge densities that facilitate the ORR on graphene surface. The identified active sites are closely related to doping cluster size and dopant-defect interactions. Generally speaking, a large doping cluster size (number of N atoms >2) reduces the number of catalytic active sites per N atom. In combination with N clustering, Stone-Wales defects can strongly promote ORR. For four-electron transfer, the effective reversible potential ranges from 1.04 to 1.15 V/SHE, depending on the defects and cluster size. The catalytic properties of graphene could be optimized by introducing small N clusters in combination with material defects.
On the Number of Linear Regions of Deep Neural Networks (2014)

We study the complexity of functions computable by deep feedforward neural networks with piecewise linear activations in terms of the symmetries and the number of linear regions that they have. Deep networks are able to sequentially map portions of each layer's input-space to the same output. In this way, deep models compute functions that react equally to complicated patterns of different inputs. The compositional structure of these functions enables them to re-use pieces of computation exponentially often in terms of the network's depth. This paper investigates the complexity of such compositional maps and contributes new theoretical results regarding the advantage of depth for neural networks with piecewise linear activation functions. In particular, our analysis is not specific to a single family of models, and as an example, we employ it for rectifier and maxout networks. We improve complexity bounds from pre-existing work and investigate the behavior of units in higher layers.
The pannexins: past and present (2014)

The pannexins (Panxs) are a family of chordate proteins homologous to the invertebrate gap junction forming proteins named innexins. Three distinct Panx paralogs (Panx1, Panx2, and Panx3) are shared among the major vertebrate phyla, but they appear to have suppressed (or even lost) their ability to directly couple adjacent cells. Connecting the intracellular and extracellular compartments is now widely accepted as Panx's primary function, facilitating the passive movement of ions and small molecules along electrochemical gradients. The tissue distribution of the Panxs ranges from pervasive to very restricted, depending on the paralog, and are often cell type-specific and/or developmentally regulated within any given tissue. In recent years, Panxs have been implicated in an assortment of physiological and pathophysiological processes, particularly with respect to ATP signaling and inflammation, and they are now considered to be a major player in extracellular purinergic communication. The following is a comprehensive review of the Panx literature, exploring the historical events leading up to their discovery, outlining our current understanding of their biochemistry, and describing the importance of these proteins in health and disease.
A <i>Bacillus subtilis</i> dipeptide transport system expressed early during sporulation (1991)

Two previously identified Bacillus subtilis DNA segments, dciA and dciB, whose transcripts accumulate very rapidly after induction of sporulation, were found in the same 6.2 kb transcription unit, now known as the dciA operon. Analysis of the sequence of the dciA operon showed that its putative products are homologous to bacterial peptide transport systems. The product of the fifth gene, DciAE, is similar to peptide-binding proteins from Escherichia coli and Salmonella typhimurium (DppA and OppA) and B. subtilis (OppA). A null mutation in dciAE abolished the ability of a proline auxotroph to grow in a medium containing the dipeptide Pro-Gly as sole proline source, suggesting that the dciA operon encodes a dipeptide transport system.
Post-treatment changes in hematological parameters predict response to nivolumab monotherapy in non-small cell lung cancer patients (2018)

Post-treatment ANC, ALC and NLR are independent prognostic factors in NSCLC patients treated with nivolumab. Changes in NLR can be an early biomarker for response in NSCLC patients treated with nivolumab.