Miracle-dz/UniFAR-FTUs huggingface dataset:
A low-frequency variational model for energetic particle effects in the pressure-coupling scheme

Energetic particle effects in magnetic confinement fusion devices are commonly studied by hybrid kinetic-fluid simulation codes whose underlying continuum evolution equations often lack the correct energy balance. While two different kinetic-fluid coupling options are available (current coupling and pressure coupling), this paper applies the Euler–Poincaré variational approach to formulate a new conservative hybrid model in the pressure-coupling scheme. In our case the kinetics of the energetic particles are described by guiding center theory. The interplay between the Lagrangian fluid paths and phase space particle trajectories reflects an intricate variational structure which can be approached by letting the four-dimensional guiding center trajectories evolve in the full six-dimensional phase space. Then, the redundant perpendicular velocity is integrated out to recover a four-dimensional description. A second equivalent variational approach is also reported, which involves the use of phase space Lagrangians. Not only do these variational structures confer on the new model a correct energy balance, but also they produce a cross-helicity invariant which is lost in the other pressure-coupling schemes reported in the literature.
Historical perspective: phosphatidylserine and phosphatidylethanolamine from the 1800s to the present

This article provides a historical account of the discovery, chemistry, and biochemistry of two ubiquitous phosphoglycerolipids, phosphatidylserine (PS) and phosphatidylethanolamine (PE), including the ether lipids. In addition, the article describes the biosynthetic pathways for these phospholipids and how these pathways were elucidated. Several unique functions of PS and PE in mammalian cells in addition to their ability to define physical properties of membranes are discussed. For example, the translocation of PS from the inner to the outer leaflet of the plasma membrane of cells occurs during apoptosis and during some other specific physiological processes, and this translocation is responsible for profound life-or-death events. Moreover, mitochondrial function is severely impaired when the PE content of mitochondria is reduced below a threshold level. The discovery and implications of the existence of membrane contact sites between the endoplasmic reticulum and mitochondria and their relevance for PS and PE metabolism, as well as for mitochondrial function, are also discussed. Many of the recent advances in these fields are due to the use of isotope labeling for tracing biochemical pathways. In addition, techniques for disruption of specific genes in mice are now widely used and have provided major breakthroughs in understanding the roles and metabolism of PS and PE in vivo.
Force and time-dependent self-assembly, disruption and recovery of supramolecular peptide amphiphile nanofibers

Biological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix, and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent biomaterials systems. Here, we investigated real-time self-assembly, deformation, and recovery of PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning atomic force microscopy imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We demonstrate that nanofiber damage occurs at tip-sample interaction forces exceeding 1 nN, and the damaged fibers subsequently recover when the tip pressure is reduced. Nanofiber ends occasionally fail to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) support our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. Consequently, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.
ESL Black Box Power Estimation: Automatic Calibration for IEEE UPF 3.0 Power Models

Power-aware design space exploration at early electronic system level (ESL) is highly facilitated by virtual platforms. In order to define and exchange power models, the IEEE standard 1801-2015 -- UPF has been defined to allow developers, vendors and customers seamless usage of the same power models. However, one obstacle is still not covered by the standard: it is not specified and solved how to construct the model in the first place. This paper offers a solution to close this gap. A well proven semi-automatic black box ESL power estimation methodology [17], which allows to have power estimates with approximately 5% error, is combined with UPF. Although the standard is based on power state machines and requires another tracing method, a procedure is presented to overcome these differences. Representative case studies show that similar estimation accuracy can be achieved.
JWA suppresses the invasion of human breast carcinoma cells by downregulating the expression of CXCR4

Breast cancer is the second leading cause of cancer-associated mortality, and metastatic breast cancer is responsible for 90% of patient mortalities. Given that JWA represses the proliferation, invasion and metastasis of a number of other human tumor cells, including melanoma, esophageal, hepatocellular and gastric carcinomas, via mitogen-activated protein kinase or integrin signaling, the present study investigated the expression and function of JWA in human breast cancers. The results showed that the expression level of JWA was significantly reduced in human primary breast cancers when compared with the paired adjacent tissues. Downregulating JWA enhanced, while overexpressing JWA suppressed, the migration and invasion abilities of the two breast cancer cell lines, MDA-MB-468 and MDA-MB-231, without affecting their proliferations in vitro. In addition, JWA negatively regulated the surface expression of CXCR4 in the two cell lines via proteasome degradation, though not via transcriptional inhibition. Functionally, normalizing the disturbed expressions of CXCR4 largely reversed the inhibitory effect of JWA on cell invasion. These data demonstrated that JWA suppressed the migration/invasion of breast carcinoma cells by downregulating the expression of CXCR4, and suggested that JWA may harbor prognostic and therapeutic potential in patients with breast cancer.
The Homeopathic Preparation Neurexan® vs. Valerian for the Treatment of Insomnia: An Observational Study

Insomnia is prevalent and complementary therapies are common, but data are lacking on the effectiveness and tolerability of preparations beyond valerian. Here we report on an open-label, prospective cohort study in 89 German centers offering both conventional and complementary therapies. Subjects received the homeopathic preparation Neurexan® or valerian for 28 days. Doses were at physicians' judgments. Sleep duration and latency were evaluated based on patients' sleep diaries over 14 days; sleep quality was evaluated at 28 ± 1 days. A total of 409 subjects were enrolled. The groups were balanced at baseline for age, sex, weight, and sleep disturbances. At day 14, both groups reported improved sleep latency and duration; latency was reduced from baseline by 37.3 ± 36.3 min with Neurexan and by 38.2 ± 38.5 min with valerian. The duration of sleep increased by 2.2 (±1.6) h in the Neurexan group and by 2.0 (±1.5) h in the valerian group. Differences between the groups in improvement on sleep duration were significantly in favor of Neurexan therapy at days 8, 12, and 14. At day 28, quality of sleep was improved in both groups with no significant differences between the treatments. Significantly more patients reported lack of daytime fatigue with Neurexan than with valerian therapies (49% vs. 32%; p < 0.05 for the comparison). For patients favorable towards a CAM-based therapy, Neurexan might be an effective and well-tolerated alternative to conventional valerian-based therapies for the treatment of mild to moderate insomnia.
Predicting Cyber Events by Leveraging Hacker Sentiment

Recent high-profile cyber-attacks exemplify why organizations need better cyber-defenses. Cyber-threats are hard to accurately predict because attackers usually try to mask their traces. However, they often discuss exploits and techniques on hacking forums. The community behavior of the hackers may provide insights into the groups’ collective malicious activity. We propose a novel approach to predict cyber-events using sentiment analysis. We test our approach using cyber-attack data from two major business organizations. We consider three types of events: malicious software installation, malicious-destination visits, and malicious emails that surmounted the target organizations’ defenses. We construct predictive signals by applying sentiment analysis to hacker forum posts to better understand hacker behavior. We analyze over 400 K posts written between January 2016 and January 2018 on over 100 hacking forums both on the surface and dark web. We find that some forums have significantly more predictive power than others. Sentiment-based models that leverage specific forums can complement state-of-the-art time-series models on forecasting cyber-attacks weeks ahead of the events.
Characterization of Chicken Tumor Necrosis Factor-α, a Long Missed Cytokine in Birds

Tumor necrosis factor-α (TNF-α) is a pleiotropic cytokine playing critical roles in host defense and acute and chronic inflammation. It has been described in fish, amphibians, and mammals but was considered to be absent in the avian genomes. Here, we report on the identification and functional characterization of the avian ortholog. The chicken TNF-α (chTNF-α) is encoded by a highly GC-rich gene, whose product shares with its mammalian counterpart 45% homology in the extracellular part displaying the characteristic TNF homology domain. Orthologs of chTNF-α were identified in the genomes of 12 additional avian species including Palaeognathae and Neognathae, and the synteny of the closely adjacent loci with mammalian TNF-α orthologs was demonstrated in the crow (Corvus cornix) genome. In addition to chTNF-α, we obtained full sequences for homologs of TNF-α receptors 1 and 2 (TNFR1, TNFR2). chTNF-α mRNA is strongly induced by lipopolysaccharide (LPS) stimulation of monocyte derived, splenic and bone marrow macrophages, and significantly upregulated in splenic tissue in response to i.v. LPS treatment. Activation of T-lymphocytes by TCR crosslinking induces chTNF-α expression in CD4+ but not in CD8+ cells. To gain insights into its biological activity, we generated recombinant chTNF-α in eukaryotic and prokaryotic expression systems. Both, the full-length cytokine and the extracellular domain rapidly induced an NFκB-luciferase reporter in stably transfected CEC-32 reporter cells. Collectively, these data provide strong evidence for the existence of a fully functional TNF-α/TNF-α receptor system in birds thus filling a gap in our understanding of the evolution of cytokine systems.
In Vivo Pharmacokinetic/Pharmacodynamic Profiles of Danofloxacin in Rabbits Infected With Salmonella typhimurium After Oral Administration

Salmonella typhimurium is a highly transmissible pathogen in rabbits that causes significant losses. Danofloxacin shows excellent efficacy against S. typhimurium infections. However, there are few reports of the pharmacokinetic/pharmacodynamic (PK/PD) modeling of danofloxacin against this pathogen. The aim of this study was to evaluate the in vivo PK/PD relationship of danofloxacin in rabbits infected with S. typhimurium. We used the reduction of bacterial burden in the blood, liver, spleen, and lung as the target PD endpoints, and determined the PK/PD indexes that best correlated with the efficacy and its corresponding magnitude. Danofloxacin was administrated orally to experimentally S. typhimurium-infected rabbits once daily for three successive days. The concentrations of danofloxacin in the serum and the bacterial burden in the blood, liver, spleen, and lung were determined. The PK/PD relationships of danofloxacin against S. typhimurium were evaluated using a Sigmoid Emax model. The results showed that the area under the concentration-time curve from 0 to 24 h/minimum inhibitory concentration (AUC24 h/MIC) ratio correlated well with the in vivo antibacterial effectiveness in different organs, with an r2 of 0.8971, 0.9186, 0.9581, and 0.8708 in the blood, liver, spleen, and lung, respectively. The AUC24 h/MIC ratios for the bactericidal effect (3 × Log10 colony forming units/mL reductions) were 121.30, 354.28, 216.64, and 228.66 in the blood, liver, spleen, and lung, respectively, indicating that the in vivo effectiveness of danofloxacin against S. typhimurium using bacterial reduction in different organs as PD endpoints was not identical. This study illustrated that the selection of the target organ for bacterial reduction determination had little effect on best PK/PD parameter determination, but is critical for parameter magnitude calculation in antimicrobial PK/PD modeling, and furthermore, has an impact on the rational dosage optimization process.
On the realization of OTA-C filters

A synthesis procedure based on the signal flow graph is given for generating second-order active filters using a minimum number of operational transconductance amplifiers and grounded capacitors. the pole quality factor and pole frequency sensitivities are studied for the proposed filters. Furthermore, the limitations on input signal amplitude are studied and a simple formula is derived for the input signal amplitude not causing clipping and slew-rate-limiting problems.
A Hybrid Approach for Accurate Application Traffic Identification

The traffic dynamics of the Internet's dominant applications, such as peer-to-peer and multimedia, worsen the accuracy of the existing application traffic identification. There is a strong need for both practical and reliable identification methods with proof of accuracy. This paper proposes a hybrid approach of signature matching and session behavior mapping methods for accurate application traffic identification. In particular, the paper explores a priority-based signature matching scheme on early packet samples to replace conventional signature matching. It then uses session relationships to identify application traffic from the remaining, unidentified traffic. In validation, we present the accuracy analysis of applications using the Port Dependency Ratio (PDR) method for simulated traffic as well as real traffic.
Subgroups of Dutch homeless young adults based on risk‐ and protective factors for quality of life: Results of a latent class analysis

It is important to gain more insight into specific subgroups of homeless young adults (HYA) to enable the development of tailored interventions that adequately meet their diverse needs and to improve their quality of life. Within a heterogeneous sample of HYA, we investigated whether subgroups are distinguishable based on risk- and protective factors for quality of life. In addition, differences between subgroups were examined regarding the socio-demographic characteristics, the use of cognitive coping strategies and quality of life. A total of 393 HYA using shelter facilities in the Netherlands were approached to participate, between December 2011 and March 2013. Structured face-to-face interviews were administered approximately 2 weeks after shelter admission by trained research assistants. A latent class analysis was conducted to empirically distinguish 251 HYA in subgroups based on common risk factors (former abuse, victimisation, psychological symptoms and substance use) and protective factors (resilience, family and social support and perceived health status). Additional analysis of variance and chi-square tests were used to compare subgroups on socio-demographic characteristics, the use of cognitive coping strategies and quality of life. The latent class analysis yielded four highly interpretable subgroups: the at-risk subgroup, the high-risk and least protected subgroup, the low-risk subgroup and the higher functioning and protected subgroup. Subgroups of HYA with lower scores in risk factors showed higher scores in protective factors, the adaptive cognitive coping strategies and quality of life. Our findings confirm the need for targeted and tailored interventions for specific subgroups of HYA. Social workers need to be attentive to the pattern of risk- and protective factors in each individual to determine which risk factors are prominent and need to be targeted and which protective factors need to be enhanced to improve the quality of life of HYA.
Neural Activity in Ventral Medial Prefrontal Cortex Is Modulated More Before Approach Than Avoidance During Reinforced and Extinction Trial Blocks

Ventromedial prefrontal cortex (vmPFC) is thought to provide regulatory control over Pavlovian fear responses and has recently been implicated in appetitive approach behavior, but much less is known about its role in contexts in which appetitive and aversive outcomes can be obtained and avoided, respectively. To address this issue, we recorded from single neurons in vmPFC while male rats performed our combined approach and avoidance task under reinforced and non-reinforced (extinction) conditions. Surprisingly, we found that cues predicting reward modulated cell firing in vmPFC more often and more robustly than cues preceding avoidable shock; in addition, firing of vmPFC neurons was both response (press or no-press) and outcome (reinforced or extinction) selective. These results suggest a complex role for vmPFC in regulating behavior and support its role in appetitive contexts during both reinforced and non-reinforced conditions. SIGNIFICANCE STATEMENT Selecting context-appropriate behaviors to gain reward or avoid punishment is critical for survival. Although the role of ventromedial prefrontal cortex (vmPFC) in mediating fear responses is well established, vmPFC has also been implicated in the regulation of reward-guided approach and extinction. Many studies have used indirect methods and simple behavioral procedures to study vmPFC, which leaves the literature incomplete. We recorded vmFPC neural activity during a complex cue-driven combined approach and avoidance task and during extinction. Surprisingly, we found very little vmPFC modulation to cues predicting avoidable shock, whereas cues predicting reward approach robustly modulated vmPFC firing in a response- and outcome-selective manner. This suggests a more complex role for vmPFC than current theories suggest, specifically regarding context-specific behavioral optimization.
Water-use responses of 'living fossil' conifers to CO2 enrichment in a simulated Cretaceous polar environment.

BACKGROUND AND AIMS During the Mesozoic, the polar regions supported coniferous forests that experienced warm climates, a CO(2)-rich atmosphere and extreme seasonal variations in daylight. How the interaction between the last two factors might have influenced water use of these conifers was investigated. An experimental approach was used to test the following hypotheses: (1) the expected beneficial effects of elevated [CO(2)] on water-use efficiency (WUE) are reduced or lost during the 24-h light of the high-latitude summer; and (2) elevated [CO(2)] reduces plant water use over the growing season. METHODS Measurements of leaf and whole-plant gas exchange, and leaf-stable carbon isotope composition were made on one evergreen (Sequoia sempervirens) and two deciduous (Metasequoia glyptostroboides and Taxodium distichum) 'living fossil' coniferous species after 3 years' growth in controlled-environment simulated Cretaceous Arctic (69 degrees N) conditions at either ambient (400 micromol mol(-1)) or elevated (800 micromol mol(-1)) [CO(2)]. KEY RESULTS Stimulation of whole-plant WUE (WUE(P)) by CO(2) enrichment was maintained over the growing season for the three studied species but this pattern was not reflected in patterns of WUE inferred from leaf-scale gas exchange measurements (iWUE(L)) and delta(13)C of foliage (tWUE(L)). This response was driven largely by increased rates of carbon uptake, because there was no overall CO(2) effect on daily whole-plant transpiration or whole-plant water loss integrated over the study period. Seasonal patterns of tWUE(L) differed from those measured for iWUE(L). The results suggest caution against over simplistic interpretations of WUE(P) based on leaf isotopic composition. CONCLUSIONS The data suggest that the efficiency of whole-tree water use may be improved by CO(2) enrichment in a simulated high-latitude environment, but that transpiration is relatively insensitive to atmospheric CO(2) in the living fossil species investigated.
Implementation of smoke-free legislation in Malaysia: are adolescents protected from respiratory health effects?

BACKGROUND This study aimed to examine the relationship between respiratory health of Malaysian adolescents with secondhand smoke (SHS) exposure and smoke-free legislation (SFL) implementation. MATERIALS AND METHODS A total of 898 students from 21 schools across comprehensive- and partial-SFL states were recruited. SHS exposures and respiratory symptoms were assessed via questionnaire. Prenatal and postnatal SHS exposure information was obtained from parental-completed questionnaire. RESULTS The prevalence of respiratory symptoms was: 11.9% ever wheeze, 5.6% current wheeze, 22.3% exercise-induced wheeze, 12.4% nocturnal cough, and 13.1% self-reported asthma. SHS exposure was most frequently reported in restaurants. Hierarchical logistic regression indicates living in a comprehensive-SFL state was not associated with a lower risk of reporting asthma symptoms. SHS exposure in public transport was linked to increased risk for wheeze (Adjusted Odds Ratio (AOR) 16.6; 95%confidence interval (CI), 2.69-101.7) and current wheezing (AOR 24.6; 95%CI, 3.53-171.8). CONCLUSIONS Adolescents continue to be exposed to SHS in a range of public venues in both comprehensive- and partial-SFL states. Respiratory symptoms are common among those reporting SHS exposure on public transportation. Non-compliance with SFL appears to be frequent in many venues across Malaysia and enforcement should be given priority in order to reduce exposure.
Engineering Infra-red Photon Absorbing Materials for Organic Solar Cells

This thesis aims to investigate different infrared absorbing molecules and how their properties are affected by their incorporation into polymer nanoparticles. Metal-free phthalocyanine-H2Pc, uranyl super phthalocyanine-USPc, and europium bisphthalocyanine were studied-EuPc2; the latter two capable of IR absorption. Due to the discovery of USPc’s moisture sensitivity, only H2Pc and EuPc2 were derivatized to facilitate encapsulation in polystyrene nanoparticles through a miniemulsion polymerization. These novel phthalocyanines attained loadings of up to 41wt% and exhibit substantial broadening of absorption peaks. Furthermore, the EuPc2 loaded particles also reveal an unprecedented gain in extinction coefficient of the NIR and radical absorption peaks. The leaching behavior of the dye was also studied, as this had not been undertaken in the literature, and revealed the need for a method of polymerizing/chemically binding phthalocyanines into nanoparticles; with preliminary steps taken to realize this goal.