Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipoteichoic Acid Induces Unique Inflammatory Responses when Compared to Other Toll-Like Receptor 2 Ligands

Toll-like receptors (TLRs) recognize evolutionarily-conserved molecular patterns originating from invading microbes. In this study, we were interested in determining if microbial ligands, which use distinct TLR2-containing receptor complexes, represent unique signals to the cell and can thereby stimulate unique cellular responses. Using the TLR2 ligands, R-FSL1, S-FSL1, Pam2CSK4, Pam3CSK4, and lipoteichoic acid (LTA), we demonstrate that these ligands activate NF-κB and MAP Kinase pathways with ligand-specific differential kinetics in murine macrophages. Most strikingly, LTA stimulation of these pathways was substantially delayed when compared with the other TLR2 ligands. These kinetics differences were associated with a delay in the LTA-induced expression of a subset of genes as compared with another TLR2 ligand, R-FSL1. However, this did not translate to overall differences in gene expression patterns four hours following stimulation with different TLR2 ligands. We extended this study to evaluate the in vivo responses to distinct TLR2 ligands using a murine model of acute inflammation, which employs intravital microscopy to monitor leukocyte recruitment into the cremaster muscle. We found that, although R-FSL1, S-FSL1, Pam2CSK4, and Pam3CSK4 were all able to stimulate robust leukocyte recruitment in vivo, LTA remained functionally inert in this in vivo model. Therefore distinct TLR2 ligands elicit unique cellular responses, as evidenced by differences in the kinetic profiles of signaling and gene expression responses in vitro, as well as the physiologically relevant differences in the in vivo responses to these ligands.
Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad

The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype.
Respiratory disability and impairment: what is new?

Purpose of review This review summarizes recent advances concerning respiratory impairment and disability. Recent findings The traditional impairment assessment approach, depending heavily on clinical pulmonary function testing to estimate the match between the patient's sustainable oxygen consumption and the workplace requirements, continues to be widely used. Recent work indicates the need to reassess underlying concepts for several reasons: The relationship between basic pulmonary function tests and sustainable oxygen consumption varies among patients and conditions. Studies of the respiratory demands of modern workplaces need to be updated. The concepts are less easily applied to asthma than other disorders. Research studies present differing definitions of ‘disability’, and therefore the methods of relating impairment (function loss) and disability require reassessment. Recent advances provide improved understanding of the large societal and personal impacts of respiratory impairment and disability. Summary Clinicians, policymakers, and researchers should carefully consider how well the current highly specified impairment rating systems can be improved for accuracy and relevance to current home and work activities. In addition to measuring ‘impairment’, clinicians should consider factors affecting how impairments lead to disability.
Game Theoretic Modelling of a Human Driver’s Steering Interaction with Vehicle Active Steering Collision Avoidance System

This is the accepted manuscript. The final version is available from IEEE at http://ieeexplore.ieee. org/xpl/articleDetails.jsp? arnumber=6951458&refinements%3D4262294079%26sortType%3Dasc_p_Sequence%26filter%3DAND%28p_IS_Number%3A7008592%29.
Characterization of Putative Iron Responsive Genes as Species-Specific Indicators of Iron Stress in Thalassiosiroid Diatoms

Iron (Fe) availability restricts diatom growth and primary production in large areas of the oceans. It is a challenge to assess the bulk Fe nutritional health of natural diatom populations, since species can differ in their physiological and molecular responses to Fe limitation. We assayed expression of selected genes in diatoms from the Thalassiosira genus to assess their potential utility as species-specific molecular markers to indicate Fe status in natural diatom assemblages. In this study, we compared the expression of the photosynthetic genes encoding ferredoxin (a Fe-requiring protein) and flavodoxin (a Fe-free protein) in culture experiments with Fe replete and Fe stressed Thalassiosira pseudonana (CCMP 1335) isolated from coastal waters and Thalassiosira weissflogii (CCMP 1010) isolated from the open ocean. In T. pseudonana, expression of flavodoxin and ferredoxin genes were not sensitive to Fe status but were found to display diel periodicities. In T. weissflogii, expression of flavodoxin was highly responsive to iron levels and was only detectable when cultures were Fe limited. Flavodoxin genes have been duplicated in most diatoms with available genome data and we show that T. pseudonana has lost its copy related to the Fe-responsive copy in T. weissflogii. We also examined the expression of genes for a putative high affinity, copper (Cu)-dependent Fe uptake system in T. pseudonana. Our results indicate that genes encoding putative Cu transporters, a multi-Cu oxidase, and a Fe reductase are not linked to Fe status. The expression of a second putative Fe reductase increased in Fe limited cultures, but this gene was also highly expressed in Fe replete cultures, indicating it may not be a useful marker in the field. Our findings highlight that Fe metabolism may differ among diatoms even within a genus and show a need to validate responses in different species as part of the development pipeline for genetic markers of Fe status in field populations.
Recognition of Nonmanual Markers in American Sign Language (ASL) Using Non-Parametric Adaptive 2D-3D Face Tracking

This paper addresses the problem of automatically recognizing linguistically significant nonmanual expressions in American Sign Language from video. We develop a fully automatic system that is able to track facial expressions and head movements, and detect and recognize facial events continuously from video. The main contributions of the proposed framework are the following: (1) We have built a stochastic and adaptive ensemble of face trackers to address factors resulting in lost face track; (2) We combine 2D and 3D deformable face models to warp input frames, thus correcting for any variation in facial appearance resulting from changes in 3D head pose; (3) We use a combination of geometric features and texture features extracted from a canonical frontal representation. The proposed new framework makes it possible to detect grammatically significant nonmanual expressions from continuous signing and to differentiate successfully among linguistically significant expressions that involve subtle differences in appearance. We present results that are based on the use of a dataset containing 330 sentences from videos that were collected and linguistically annotated at Boston University.
Microendemicity in the northern Hajar Mountains of Oman and the United Arab Emirates with the description of two new species of geckos of the genus Asaccus (Squamata: Phyllodactylidae)

Background The Hajar Mountains of Oman and the United Arab Emirates (UAE) is the highest mountain range in Eastern Arabia. As a result of their old geological origin, geographical isolation, complex topography and local climate, these mountains provide an important refuge for endemic and relict species of plants and animals with strong Indo-Iranian affinities. Among vertebrates, the rock climbing nocturnal geckos of the genus Asaccus represent the genus with the highest number of endemic species in the Hajar Mountains. Recent taxonomic studies on the Zagros populations of Asaccus have shown that this genus is much richer than it was previously thought and preliminary morphological and molecular data suggest that its diversity in Arabia may also be underestimated. Methods A total of 83 specimens originally classified as Asaccus caudivolvulus (including specimens of the two new species described herein), six other Asaccus species from the Hajar and the Zagros Mountains and two representatives of the genus Haemodracon were sequenced for up to 2,311 base pairs including the mitochondrial 12S and cytb and the nuclear c-mos, MC1R and ACM4 genes. Phylogenetic relationships were inferred using both Bayesian and maximum-likelihood approaches and the former method was also used to calibrate the phylogenetic tree. Haplotype networks and phylogenetic trees were inferred from the phased nuclear genes only. Sixty-one alcohol-preserved adult specimens originally classified as Asaccus caudivolvulus from the northern Hajar Mountains were examined for 13 morphometric and the five meristic variables using multivariate methods and were also used to diagnose and describe the two new species. Results The results of the molecular and morphological analyses indicate that the species originally classified as Asaccus caudivolvulus is, in fact, an assemblage of three different species that started diversifying during the Mid-Miocene. The molecular phylogenies consistently recovered the Hajar endemic A. montanus as sister taxon to all the other Asaccus species included in the analyses, rendering the Arabian species of Asaccus polyphyletic. Discussion Using this integrative approach we have uncovered a very old diversification event that has resulted in a case of microendemicity, where three morphologically and ecologically similar medium-sized lizard species coexist in a very short and narrow mountain stretch. Asaccus caudivolvulus is restricted to a small coastal area of the UAE and at risk from heavy development, while the two new species described herein are widely distributed across the northern tip of the Hajar Mountains and seem to segregate in altitude when found in close proximity in the Musandam Peninsula (Oman). Similarly to other integrative analyses of Hajar reptiles, this study highlights the high level of diversity and endemicity of this arid mountain range, underscoring its status as one of the top hotspots of reptile diversity in Arabia.
RHCG and TCAF1 promoter hypermethylation predicts biochemical recurrence in prostate cancer patients treated by radical prostatectomy

Purpose: The lack of biomarkers that can distinguish aggressive from indolent prostate cancer has caused substantial overtreatment of clinically insignificant disease. Here, by genome-wide DNA methylome profiling, we sought to identify new biomarkers to improve the accuracy of prostate cancer diagnosis and prognosis. Experimental design: Eight novel candidate markers, COL4A6, CYBA, TCAF1 (FAM115A), HLF, LINC01341 (LOC149134), LRRC4, PROM1, and RHCG, were selected from Illumina Infinium HumanMethylation450 BeadChip analysis of 21 tumor (T) and 21 non-malignant (NM) prostate specimens. Diagnostic potential was further investigated by methylation-specific qPCR analysis of 80 NM vs. 228 T tissue samples. Prognostic potential was assessed by Kaplan-Meier, uni- and multivariate Cox regression analysis in 203 Danish radical prostatectomy (RP) patients (cohort 1), and validated in an independent cohort of 286 RP patients from Switzerland and the U.S. (cohort 2). Results: Hypermethylation of the 8 candidates was highly cancer-specific (area under the curves: 0.79-1.00). Furthermore, high methylation of the 2-gene panel RHCG-TCAF1 was predictive of biochemical recurrence (BCR) in cohort 1, independent of the established clinicopathological parameters Gleason score, pathological tumor stage, and pre-operative PSA (HR (95% confidence interval (CI)): 2.09 (1.26 - 3.46); P = 0.004), and this was successfully validated in cohort 2 (HR (95% CI): 1.81 (1.05 - 3.12); P = 0.032). Conclusion: Methylation of the RHCG-TCAF1 panel adds significant independent prognostic value to established prognostic parameters for prostate cancer and thus may help to guide treatment decisions in the future. Further investigation in large independent cohorts is necessary before translation into clinical utility.
Local thermal sensation modeling—a review on the necessity and availability of local clothing properties and local metabolic heat production

Local thermal sensation modeling gained importance due to developments in personalized and locally applied heating and cooling systems in office environments. The accuracy of these models depends on skin temperature prediction by thermophysiological models, which in turn rely on accurate environmental and personal input data. Environmental parameters are measured or prescribed, but personal factors such as clothing properties and metabolic rates have to be estimated. Data for estimating the overall values of clothing properties and metabolic rates are available in several papers and standards. However, local values are more difficult to retrieve. For local clothing, this study revealed that full and consistent data sets are not available in the published literature for typical office clothing sets. Furthermore, the values for local heat production were not verified for characteristic office activities, but were adapted empirically. Further analyses showed that variations in input parameters can lead to local skin temperature differences (∆Tskin,loc = 0.4-4.4°C). These differences can affect the local sensation output, where ∆Tskin,loc = 1°C is approximately one step on a 9-point thermal sensation scale. In conclusion, future research should include a systematic study of local clothing properties and the development of feasible methods for measuring and validating local heat production.
Implementation and evaluation of rational communicative behavior in coordinated defense

This paper reports on results we obtained on communication among artificial and human agents interacting in a simulated air defense domain. In our research, we postulate that the artificial agents use a decision-theoretic method to select optimal communicative acts, given the characteristics of the particular situation. Thus, the agents we implemented compute the expected utilities of various alternative communicative acts, and execute the best one. We build on our earlier work that uses the Recursive Modeling Method @MM) for coordination, and apply RMM to rational communication in an anti-air defense domain. In this domain, distributed units coordinate and communicate to defend a specified territory from a number of attacking missiles. We meaSure the benefits of rational commutiication by showing the improvement in the quality of interactions the communication results in. We show how the benefit of rational communication measured after the interactions is related to the expected utilities of best messages computed before the interaction takes place. Further, we compare our results to improvement due to communication achieved by human subjects under the same circumstances.
DRAMA MANAGEMENT AND PLAYER MODELING FOR INTERACTIVE FICTION GAMES

A growing research community is working toward employing drama management components in story‐based games. These components gently guide the story toward a narrative arc that improves the player's gaming experience. In this article we evaluate a novel drama management approach deployed in an interactive fiction game called Anchorhead. This approach uses player's feedback as the basis for guiding the personalization of the interaction. The results indicate that adding our Case‐based Drama manaGer (C‐DraGer) to the game guides the players through the interaction and provides a better overall player experience. Unlike previous approaches to drama management, this article focuses on exhibiting the success of our approach by evaluating results using human players in a real game implementation. Based on this work, we report several insights on drama management which were possible only due to an evaluation with real players.
The Matthew Effect in Science

This account of the Matthew effect is another small exercise in the psychosociological analysis of the workings of science as a social institution. The initial problem is transformed by a shift in theoretical perspective. As originally identified, the Matthew effect was construed in terms of enhancement of the position of already eminent scientists who are given disproportionate credit in cases of collaboration or of independent multiple discoveries. Its significance was thus confined to its implications for the reward system of science. By shifting the angle of vision, we note other possible kinds of consequences, this time for the communication system of science. The Matthew effect may serve to heighten the visibility of contributions to science by scientists of acknowledged standing and to reduce the visibility of contributions by authors who are less well known. We examine the psychosocial conditions and mechanisms underlying this effect and find a correlation between the redundancy function of multiple discoveries and the focalizing function of eminent men of science—a function which is reinforced by the great value these men place upon finding basic problems and by their self-assurance. This self-assurance, which is partly inherent, partly the result of experiences and associations in creative scientific environments, and partly a result of later social validation of their position, encourages them to search out risky but important problems and to highlight the results of their inquiry. A macrosocial version of the Matthew principle is apparently involved in those processes of social selection that currently lead to the concentration of scientific resources and talent (50).
Multi-agent approach for task allocation and scheduling in cooperative heterogeneous multi-robot team: Simulation results

The paper presents a new approach for robots tasks allocation and scheduling in order to minimize the total execution time (makespan) of a mission while satisfying all the tasks constraints. This approach is implemented in a multi-agent architecture for remote control of heterogeneous multi-robot systems. The agents controlling the robots coordinate their actions and cooperate to achieve the assigned mission. The proposed approach is carried out in two phases. During the first phase, a negotiation process (based on the Contract-net protocol) is carried out between the agents of the system to allocate the tasks to the robot proposing the minimal execution time (cost). In the second phase, a local scheduling process based on priority rules is carried out by the corresponding agent for each allocated task in order to minimize its inoccupation (idle) time.
General Construction of Chameleon All-But-One Trapdoor Functions

Lossy trapdoor functions enable black-box construction of public key encryption (PKE) schemes secure against chosen-ciphertext attack [18]. Recently, a more efficient black-box construction of public key encryption was given in [12] with the help of chameleon all-but-one trapdoor functions (ABO-TDFs). In this paper, we propose a black-box construction for transforming any ABO-TDFs into chameleon ABO-TDFs with the help of chameleon hash functions. Instantiating the proposed general black-box construction of chameleon ABO-TDFs, we can obtain the first chameleon ABOTDFs based on the Decisional Diffie-Hellman (DDH) assumption.
Simultaneous determination of serum propafenone and its metabolites using high-performance liquid chromatography.

Propafenone, a class Ic antiarrhythmic agent, is metabolized to 5-hydroxypropafeone (5-OHP) and N-depropylpropafenone (NDPP). Simultaneous determination of serum propafenone and its metabolites was performed using HPLC equipped with a conventional octadecylsilyl silica column and ultraviolet detector. The wavelength was set at 250 nm. Propafenone and its metabolites in the serum were extracted using diethyl ether. The mobile phase solution, comprising 1-pentanesulfonic acid sodium salt (0.1 m), acetonitrile and acetic acid (280:185:2.5, v/v/v), was pumped at a flow rate of 1 mL/min. The recoveries of propafenone, 5-OHP and NDPP were greater than 85, 82 and 60%, respectively, with the coefficients of variation (CVs) less than 5.4, 1.9 and 2.9%, respectively. The calibration curves were linear for a concentration range of 12.5-1500 ng/mL for propafenone and 2-500 ng/mL for 5-OHP and NDPP (r > 0.999). CVs in the intraday assays were 1.0-3.8% for propafenone, 0.6-2.0% for 5-OHP and 0.6-1.7% for NDPP. CVs in interday assays were 1.3-7.7% for propafenone, 1.1-6.5% for 5-OHP and 5.4-8.0% for NDPP. The present HPLC method can be used to assess the disposition of propafenone and its metabolites for pharmacokinetic studies and therapeutic drug monitoring of propafenone.
Brain morphometry driven by DTI data in Moebius Syndrome and Hereditary Congenital Facial Paresis

Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA, Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA, Quantitative Medical Imaging Section, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA, National Institute of Mental Health, Bethesda, MD, USA, Radiology and Imaging Sciences, National Institutes of Health, Bethesda, MD, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, Departments of Neurology and Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, Howard Hughes Medical Institute, Chevy Chase, MD, United States