Miracle-dz/UniFAR-FTUs huggingface dataset:
Emerging Bordetella pertussis Strains Induce Enhanced Signaling of Human Pattern Recognition Receptors TLR2, NOD2 and Secretion of IL-10 by Dendritic Cells

Vaccines against pertussis have been available for more than 60 years. Nonetheless, this highly contagious disease is reemerging even in countries with high vaccination coverage. Genetic changes of Bordetella pertussis over time have been suggested to contribute to the resurgence of pertussis, as these changes may favor escape from vaccine-induced immunity. Nonetheless, studies on the effects of these bacterial changes on the immune response are limited. Here, we characterize innate immune recognition and activation by a collection of genetically diverse B. pertussis strains isolated from Dutch pertussis patients before and after the introduction of the pertussis vaccines. For this purpose, we used HEK-Blue cells transfected with human pattern recognition receptors TLR2, TLR4, NOD2 and NOD1 as a high throughput system for screening innate immune recognition of more than 90 bacterial strains. Physiologically relevant human monocyte derived dendritic cells (moDC), purified from peripheral blood of healthy donors were also used. Findings indicate that, in addition to inducing TLR2 and TLR4 signaling, all B. pertussis strains activate the NOD-like receptor NOD2 but not NOD1. Furthermore, we observed a significant increase in TLR2 and NOD2, but not TLR4, activation by strains circulating after the introduction of pertussis vaccines. When using moDC, we observed that the recently circulating strains induced increased activation of these cells with a dominant IL-10 production. In addition, we observed an increased expression of surface markers including the regulatory molecule PD-L1. Expression of PD-L1 was decreased upon blocking TLR2. These in vitro findings suggest that emerging B. pertussis strains have evolved to dampen the vaccine-induced inflammatory response, which would benefit survival and transmission of this pathogen. Understanding how this disease has resurged in a highly vaccinated population is crucial for the design of improved vaccines against pertussis.
Effect of nozzle orientation on the gas dynamics of inert-gas laser cutting of mild steel

This investigation applies sonic and supersonic coaxial and off‐axis nozzles to the cutting of mild steel sheet of 1–4 mm thickness. A 1.5 kW CW CO2 laser is used with nitrogen as the assist gas. Sonic coaxial cutting is compared to that of off‐axis nozzles, which vary in orientation from 20–60° behind the laser axis and in exit Mach number from 1 to 2.4. Results show a 50% increase in maximum cutting speed at approximately a 40° off‐axis nozzle angle. In comparison, variations in off‐axis nozzle exit Mach number have little effect. A scale‐model kerf was used to visualize the kerf gas dynamics, revealing that nozzle angles of 0–20° cause a shock wave/boundary layer interaction with flow separation inside the kerf. Angles of 20–45° alleviate this interaction, producing a uniform supersonic flow throughout the kerf, which yields high cutting speeds due to uniformly high shear forces. For nozzle angles greater than 45°, the assist gas is diverted away from the kerf, reducing cutting speed. Cut edge quality observations were also conducted to verify the results of the model tests.
What makes viewpoint-invariant properties perceptually salient?

It has been noted that many of the perceptually salient image properties identified by the Gestalt psychologists, such as collinearity, parallelism, and good continuation, age invariant to changes in viewpoint. However, I show that viewpoint invariance is not sufficient to distinguish these Gestalt properties; one can define an infinite number of viewpoint-invariant properties that are not perceptually salient. I then show that generally, the perceptually salient viewpoint-invariant properties are minimal, in the sense that they can be derived by using less image information than for nonsalient properties. This finding provides support for the hypothesis that the biological relevance of an image property is determined both by the extent to which it provides information about the world and by the ease with which this property can be computed. [An abbreviated version of this work, including technical details that are avoided in this paper, is contained in K. Boyer and S. Sarker, eds., Perceptual Organization for Artificial Vision Systems (Kluwer Academic, Dordrecht, The Netherlands, 2000), pp. 121-138. ]
Photoplethysmogram Measurement Without Direct Skin-to-Sensor Contact Using an Adaptive Light Source Intensity Control

We developed a chair-attached, nonintrusive photoplethysmogram (PPG) measuring system for everyday life, unconstrained monitoring using nonskin-contacting sensor-amplifier circuits capable of emitting suitable light intensity adaptable to clothing characteristics. Comparison between proposed and conventional systems showed reasonable correlation and root-mean-squared error levels, indicating its feasibility for unconstrained PPG monitoring.
Helicon Plasma Discharge in a Toroidal Magnetic Field of the Tokamak

A helicon wave plasma (HWP) discharge in an experimental advanced superconducting tokamak device with a toroidal magnetic field of 2 T is investigated. The HWP with an electron density of 1012 cm-3 was produced with two 4-turn flat spiral antennas in series that are perpendicular to the toroidal magnetic field and driven by a 13.56-MHz radio-frequency (RF) source at a power of 1500 W, a toroidal magnetic field of 2 T, and a pressure (helium) of 1 Pa. The increase of the toroidal magnetic field from 0.5 to 2 T, the increase of the RF power from 500 to 1500 W, and the decrease of the pressure (helium) from 1 to 0.01 Pa were found to improve the plasma uniformity from the CCD images.
Cancer Immunotherapy Out of the Gate: The 22nd Annual Cancer Research Institute International Immunotherapy Symposium

The 22nd annual Cancer Research Institute (CRI) International Immunotherapy Symposium was held from October 5–8, 2014, in New York City. Titled “Cancer Immunotherapy: Out of the Gate,” the symposium began with a Cancer Immunotherapy Consortium satellite meeting focused on issues in immunotherapy drug development, followed by five speaker sessions and a poster session devoted to basic and clinical cancer immunology research. The second annual William B. Coley lecture was delivered by Lieping Chen, one of the four recipients of the 2014 William B. Coley Award for Distinguished Research in Tumor Immunology; the other three recipients were Gordon Freeman, Tasuku Honjo, and Arlene Sharpe. Prominent themes of the conference were the use of genomic technologies to identify neoantigens and the emergence of new immune modulatory molecules, beyond CTLA-4 and PD-1/PD-L1, as new therapeutic targets for immunotherapy. Cancer Immunol Res; 3(5); 444–8. ©2015 AACR.
The Effect of Silver Nanoparticles on the Collagen Secondary Structure

Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR) spectroscopy is a label-free, non-destructive analytical technique that can be used extensively to study a wide variety of molecules in different conditions. Proteins have very complicated three dimensional structures with multi-level conformations, which are highly correlated with their biological activities. Recently, there is a significant increase of materials based on interaction between proteins and nanoparticles. The aim of this paper is to highlight the understanding of protein interaction with silver nanoparticles (AgNPs) surfaces. Information about the secondary structures of collagen with and without AgNPs was obtained from atomic force microscopy (AFM) measurements.ATR-FTIR spectroscopy was used for monitoring the changes in the secondary structures of collagen upon interaction with AgNPs. Amide I is the most sensitive band for detecting changes in the protein secondary structures. Its characteristic absorption band is located at 1600–1700 cm-1. Comparing the spectra of collagen with and without AgNPs in this region, information about the different types of secondary structures such as α-helix, β-sheets, turns and random coil can be obtained. The conjugation of AgNPs-collagen occurred mainly through electrostatic interactions. Based on these data, the effects of AgNPs stability and the conformational changes of collagen upon interaction with the AgNPs are discussed.
Bounds on locally recoverable codes with multiple recovering sets

A locally recoverable code (LRC code) is a code over a finite alphabet such that every symbol in the encoding is a function of a small number of other symbols that form a recovering set. Bounds on the rate and distance of such codes have been extensively studied in the literature. In this paper we derive upper bounds on the rate and distance of codes in which every symbol has t ≥ 1 disjoint recovering sets.
Timing variation-aware high level synthesis: Current results and research challenges

The timing closure problem is one of the most important problems to be addressed at all levels of the synthesis process. Currently, the timing problem is much complicated due to the presence of process variation. Recently in high-level synthesis (HLS), a shift in the timing analysis, from deterministic timing to statistical timing, to reflect the impact of the timing variation on the quality of results becomes an important research topic where the major considerations are the accurate statistical timing analysis of datapath and the tight and full integration of the SSTA into HLS framework. In this paper, we survey and discuss the state-of-art timing variation-aware HLS techniques, with the classification of (1) SSTAs for HLS, (2) HLS framework using SSTAs, and (3) limitations of the work, with suggestions on the future research directions.
Fast formal analysis of requirements via "topoi diagrams"

Early testing of requirements can decrease the cost of removing errors in software projects. However unless done carefully, that testing process can significantly add to the cost of requirements analysis. We show that requirements expressed as topoi diagrams can be built and tested cheaply /sup s/ing our SP2 algorithm, the formal temporal properties of a large class of topoi can be proven very quickly, in time nearly linear in the number of nodes and edges in the diagram. There are two limitations to our approach. Firstly, topoi diagrams cannot express certain complex concepts such as iteration and sub-routine calls. Hence, our approach is more useful for requirements engineering than for traditional model checking domains. Secondly, our approach is better for exploring the temporal occurrence of properties than the temporal ordering of properties. Within these restrictions, we can express a useful range of concepts currently seen in requirements engineering, and a wide range of interesting temporal properties.
Segmentation and Tracking of Multiple Humans in Crowded Environments

Segmentation and tracking of multiple humans in crowded situations is made difficult by interobject occlusion. We propose a model-based approach to interpret the image observations by multiple partially occluded human hypotheses in a Bayesian framework. We define a joint image likelihood for multiple humans based on the appearance of the humans, the visibility of the body obtained by occlusion reasoning, and foreground/background separation. The optimal solution is obtained by using an efficient sampling method, data-driven Markov chain Monte Carlo (DDMCMC), which uses image observations for proposal probabilities. Knowledge of various aspects, including human shape, camera model, and image cues, are integrated in one theoretically sound framework. We present experimental results and quantitative evaluation, demonstrating that the resulting approach is effective for very challenging data.
Immune-Stimulatory Effects of Althaea rosea Flower Extracts through the MAPK Signaling Pathway in RAW264.7 Cells

Althaea rosea (Linn.) is a medicinal plant from China and Korea that has been traditionally used to control inflammation, to stop bedwetting and as a mouthwash in cases of bleeding gums. Its flowers are employed medicinally for their emollient, demulcent and diuretic properties, which make them useful in chest complaints. Furthermore, a flower extract decoction is used to improve blood circulation, for the treatment of constipation, dysmenorrhoea, haemorrhages, etc. However, the possible mechanisms of the immune-stimulatory effect remains to be elucidated. Therefore, we investigated the role of Althaea rosea flower (ARF) extracts in the immune-stimulatory effect of macrophages and the underlying mechanisms of action. ARF water extract (ARFW) could dose-dependently increase NO production and cytokines (IL-6 and TNF-α). We also found that ARFW significantly increased the expression of iNOS and COX-2 proteins in RAW264.7 cells. Consistent with these results, MAPK protein (JNK, ERK, p38) expression levels were induced after treatment with ARFW. Additionally, ARFW showed a marked increase in the phosphorylation level of IκBα and subsequent IκBα degradation allowing NF-κB nuclear translocation. These results suggest that the immune-stimulatory effect of A. rosea flower extracts is mediated through the translocation of NF-κB p65 subunit into the nucleus from the cytoplasm and subsequent activation of pro-inflammatory cytokines (IL-6 and TNF-α) and other mediators (iNOS and COX-2), which occurs mainly through MAPK signalling pathway. Thus, we suggest that ARFW could be considered as a potential therapeutic agent useful in the development of immune-stimulatory compounds.
Optical fiber humidity sensor based on surface plasmon resonance in the infra-red region

Here, the fabrication and characterization of a novel optical fiber humidity sensor based on surface plasmon resonance (SPR) in the infra-red region is presented. Firstly, an indium tin oxide (ITO) coating is deposited onto a 200 μm core diameter optical fiber causing the shift of the SPR wavelength to the infra-red region. Then, the LbL method is used to deposit a polymeric coating onto the ITO layer. The variations in the external humidity originated changes in the thickness and refractive index of the polymeric coating and hence in the resonance.
Sickness absence and presence among employees in treatment for common mental disorders

Purpose: Common mental disorders are a major cause of long-term sickness absence and a reason for disability benefits, although many people with these disorders remain employed. Therefore, it is important to prevent them from taking sick leave or relying on disability benefits. Consequently, we wished to identify the factors associated with sickness presence among patients undergoing treatment. Method: Participants were recruited from patients who met for their first session at a Return to Work clinic. A total of 251 patients completed a questionnaire that included questions on background information, mental health and functioning, and psychosocial work factors. Of these, 49% were fully working, 21.9% were partially working, and 29.1% were on full sickness absence. Results: Fully working patients had fewer symptoms, functioned better, and experienced greater well-being than patients wholly on sick leave. They also experienced work as less demanding, were more appreciative, and had more employment security and autonomy. They reported symptoms, functioning, and well-being at the same level as the partially working group. However, their therapists reported that they functioned better and they themselves considered work demands somewhat less stressful. Conclusions: The results indicate that both symptoms and functional capacity, in addition to work environment, are perceived as more favorable among fully working patients, compared with those completely on sick leave. However, because of the cross-sectional design, we need more studies with prospective design to examine whether these relationships are causal, and to examine when sickness presence is beneficial for patients.
Model-Based Camera Calibration Using Analysis by Synthesis Techniques

A new technique for the determination of extrinsic and intrinsic camera parameters is presented. Instead of searching for a limited number of discrete feature points of the calibration test object, the entire image captured with the camera is exploited to robustly determine the unknown parameters. Shape and texture of the test object are described by a 3-D computer graphics model. With this 3-D representation, synthetic images are rendered and matched with the original frames in an analysis by synthesis loop. Therefore, arbitrary test objects with sophisticated patterns can be used to determine the camera settings. The scheme can easily be extended to deal with multiple frames for a higher intrinsic parameter accuracy.
Damage evaluation in metal structures subjected to high energy deposition due to particle beams

The unprecedented energy intensities of modern hadron accelerators yield special problems with the materials that are placed close to or into the high intensity beams. The energy stored in a single beam of LHC particle accelerator is equivalent to about 80 kg of TNT explosive, stored in a transverse beam area with a typical value of 0.2 mm×0.2 mm. The materials placed close to the beam are used at, or even beyond, their damage limits. However, it is very difficult to predict structural efficiency and robustness accurately: beam-induced damage for high energy and high intensity occurs in a regime where practical experience does not exist. The interaction between high energy particle beams and metals induces a sudden non uniform temperature increase. This provokes a dynamic response of the structure entailing thermal stress waves and thermally induced vibrations or even the failure of the component. This study is performed in order to estimate the damage on a copper component due to the impact with a 7 TeV proton beam generated by LHC. The case study represents an accidental case consequent to an abnormal release of the beam: the energy delivered on the component is calculated using the FLUKA code and then used as input in the numerical simulations, that are carried out via the FEM code LS-DYNA.
The Untapped Potential of IT Chargeback

The received wisdom on IT chargeback is that a chargeback system with certain key characteristics, such as usage-based charges, stable rates, understandable bills, and so forth, will help firms make effective decisions on IT investment and use. Eccles' model of transfer pricing provides a theoretical framework for this claim, and it also explains why chargeback systems can raise issues of fairness or create conflict between IT and its clients, as the IT literature has pointed out. Applying Eccles' model, this paper reports on a study of 10 organizations' IT chargeback systems and their impacts on business managers' economic decisions and on evaluations of IT and business unit performance. Respondents in just four of the 10 firms reported that chargeback had significantly influenced IT investment decisions. In addition, the business unit respondents at those same four firms offered more positive assessments of IT than their counterparts at other sites. These differences in chargeback-related outcomes could not be accounted for by looking at differences in the chargeback characteristics that are most commonly described in the IT literature. What was different in these four firms was that chargeback was being used to foster communication between IT and the business units. This communication was generating a rich shared understanding for both parties of the costs and benefits of alternative IT investments and service offerings. The literature on partnership argues that complex IT investment decisions demand a strong IT-business partnership. The analysis suggests that IT units in just four of the 10 firms were tapping into the potential of chargeback to facilitate the development of a partnership with their business unit counterparts.
Differential Effects of 7 and 16 Groups of Muscle Relaxation Training Following Repeated Submaximal Intensity Exercise in Young Football Players

This study compares two versions of progressive muscle relaxation (PMR) training (7 and 16 muscle groups) on oxygen consumption (VO2), heart rates, rating of perceived exertion and choice reaction time. Football (soccer) players (N = 26; M age = 13.4 yr., SD = 0.5) were randomly assigned to either 7 muscle groups PMR, 16 muscle groups PMR, or a control group. PMR training requires the participants to tense a muscle, hold the muscle contraction, and then relax it. Measurement was conducted prior to and after the completion of 12 sessions of PMR. The dependent variables were measured following four bouts of intermittent exercise consisting of 12 min. of running at 60% VO2max for 10 min. followed by running at 90% VO2max for 2 min. with a 3-min. rest for each bout. Lower VO2, heart rate, perceived exertion, and quicker reaction time were expected in both relaxation groups compared to the control group. The results revealed a significant reduction in heart rates and choice reaction time for both relaxation groups, but the longer version produced significantly quicker choice reaction time.
Loss of Cardiomyocyte Integrin-Linked Kinase Produces an Arrhythmogenic Cardiomyopathy in Mice

Background—Integrin-linked kinase (ILK), a serine/threonine protein kinase, has roles in cell signaling and molecular scaffolding. ILK mutation/deletion causes cardiomyopathic phenotypes, but the functional and electrophysiological features have not been characterized. This study investigated the structural, functional, ion channel, and electrophysiological changes associated with cardiomyocyte-directed ILK deletion in mice. Methods and Results—Adult mice with cardiomyocyte-directed ILK knockout were compared with littermate controls. Knockout mice showed markedly increased mortality, with sudden death beginning after 5 weeks and 100% mortality at 18 weeks. In 10-week-old knockout mice, spontaneous and inducible ventricular tachyarrhythmias were common, occurring in 60% and 86%, respectively, and absent in controls (P<0.001, P<0.05 versus knockout mice). Ventricular refractoriness was prolonged, along with both QRS and QT interval. Action potentials were prolonged and displayed triggered activity. A wide range of ion currents were downregulated, including total, fast and slow components of transient outward K+ current and inward rectifier K+ current, along with corresponding ion channel subunit genes, providing a plausible explanation of action potential prolongation. At 5 weeks, only voltage-dependent K+ currents were reduced, possibly related to direct ILK-Kv4.2 subunit interactions. Action potentials were prolonged, but no arrhythmias or cardiac dysfunction were noted. Structural remodeling was prominent at 10 weeks: connexin-43 was downregulated and redistributed to lateral cell margins, and left ventricular fibrosis occurred, with a strong regional distribution (predominating in the basal left ventricle). Conduction was slowed. High-throughput quantitative polymerase reaction gene-expression studies in 10-week-old ILK knockout showed upregulation of structural, remodeling and fibrosis-related genes, and downregulation of a wide range of ion channel and transporter subunits. Conclusions—Cardiomyocyte ILK deletion produces a lethal arrhythmogenic cardiomyopathy associated with important ion channel and structural remodeling.