Miracle-dz/UniFAR-FTUs huggingface dataset:
Species dependent impact of helminth-derived antigens on human macrophages infected with Mycobacterium tuberculosis: Direct effect on the innate anti-mycobacterial response

Background In countries with a high prevalence of tuberculosis there is high coincident of helminth infections that might worsen disease outcome. While Mycobacterium tuberculosis (Mtb) gives rise to a pro-inflammatory Th1 response, a Th2 response is typical of helminth infections. A strong Th2 response has been associated with decreased protection against tuberculosis. Principal findings We investigated the direct effect of helminth-derived antigens on human macrophages, hypothesizing that helminths would render macrophages less capable of controlling Mtb. Measuring cytokine output, macrophage surface markers with flow cytometry, and assessing bacterial replication and phagosomal maturation revealed that antigens from different species of helminth directly affect macrophage responses to Mtb. Antigens from the tapeworm Hymenolepis diminuta and the nematode Trichuris muris caused an anti-inflammatory response with M2-type polarization, reduced macrophage phagosome maturation and ability to activate T cells, along with increased Mtb burden, especially in T. muris exposed cells which also induced the highest IL-10 production upon co-infection. However, antigens from the trematode Schistosoma mansoni had the opposite effect causing a decrease in IL-10 production, M1-type polarization and increased control of Mtb. Conclusion We conclude that, independent of any adaptive immune response, infection with helminth parasites, in a species-specific manner can influence the outcome of tuberculosis by either enhancing or diminishing the bactericidal function of macrophages.
ACE2 Receptor Expression and Severe Acute Respiratory Syndrome Coronavirus Infection Depend on Differentiation of Human Airway Epithelia

ABSTRACT Studies of patients with severe acute respiratory syndrome (SARS) demonstrate that the respiratory tract is a major site of SARS-coronavirus (CoV) infection and disease morbidity. We studied host-pathogen interactions using native lung tissue and a model of well-differentiated cultures of primary human airway epithelia. Angiotensin converting enzyme 2 (ACE2), the receptor for both the SARS-CoV and the related human respiratory coronavirus NL63, was expressed in human airway epithelia as well as lung parenchyma. As assessed by immunofluorescence staining and membrane biotinylation, ACE2 protein was more abundantly expressed on the apical than the basolateral surface of polarized airway epithelia. Interestingly, ACE2 expression positively correlated with the differentiation state of epithelia. Undifferentiated cells expressing little ACE2 were poorly infected with SARS-CoV, while well-differentiated cells expressing more ACE2 were readily infected. Expression of ACE2 in poorly differentiated epithelia facilitated SARS spike (S) protein-pseudotyped virus entry. Consistent with the expression pattern of ACE2, the entry of SARS-CoV or a lentivirus pseudotyped with SARS-CoV S protein in differentiated epithelia was more efficient when applied to the apical surface. Furthermore, SARS-CoV replicated in polarized epithelia and preferentially exited via the apical surface. The results indicate that infection of human airway epithelia by SARS coronavirus correlates with the state of cell differentiation and ACE2 expression and localization. These findings have implications for understanding disease pathogenesis associated with SARS-CoV and NL63 infections.
N250 effects for letter transpositions depend on lexicality: ‘casual’ or ‘causal’?

We examined the electrophysiological correlates of one of the most influential orthographic effects: the transposed-letter-masked priming effect. Transposed-letter nonword–word pairs (‘jugde–judge’), as well as transposed-letter word–word pairs (‘casual–causal’) were included to investigate the influence of prime's lexicality in the transposed-letter effect. The results showed that when compared with the substituted-letter control conditions (‘jugde–judge’ vs. ‘jupte–judge’), transposed-letter primes produced a lower negativity in the N250 component. In contrast, no differences were obtained between the two word–word priming conditions (‘casual–causal’ vs. ‘carnal–causal’). The influence of lexicality in the transposed-letter effect is discussed according to the models of visual word recognition and previous evidence from event-related potentials.
Cytokine production in whole blood cell cultures of patients with crohn's disease and ulcerative colitis

Levels of the cytokines interleukin‐1‐α, ‐1‐β, and ‐2 (IL‐1‐α, IL‐1‐β, IL‐2), tumor necrosis factor‐α (TNF‐α), and interferon‐γ (IFN‐γ) were measured in the mitogen‐stimulated whole blood cell cultures from 96 patients with Crohn's disease (48 untreated, 12 treated with sulfasalazine, 36 treated with corticosteroids), 74 patients with ulcerative colitis (21 untreated, 25 treated with sulfasalazine, 28 steroid treated), and 360 healthy controls. The cytokines were measured 4 days after induction by a sensitive immunoenzyme assay.
Free-form Lens Model and Mass Estimation of the High-redshift Galaxy Cluster ACT-CL J0102-4915, “El Gordo”

We examine the massive colliding cluster El Gordo, one of the most massive clusters at high redshift. We use a free-form lensing reconstruction method that avoids making assumptions about the mass distribution. We use data from the RELICS program and identify new multiply lensed system candidates. The new set of constraints and free-form method provide a new independent mass estimate of this intriguing colliding cluster. Our results are found to be consistent with earlier parametric models, indirectly confirming the assumptions made in earlier work. By fitting a double gNFW profile to the lens model and extrapolating to the virial radius, we infer a total mass for the cluster of M . We estimate the uncertainty in the mass due to errors in the photometric redshifts and discuss the uncertainty in the inferred virial mass due to the extrapolation from the lens model. We also find in our lens map a mass overdensity corresponding to the large cometary tail of hot gas, reinforcing its interpretation as a large tidal feature predicted by hydrodynamical simulations that mimic El Gordo. Finally, we discuss the observed relation between the plasma and the mass map, finding that the peak in the projected mass map may be associated with a large concentration of colder gas exhibiting possible star formation. El Gordo is one of the first clusters that will be observed with JWST, which is expected to unveil new high-redshift lensed galaxies around this interesting cluster and provide a more accurate estimation of its mass.
Women's Knowledge of and Support for Abortion Restrictions in Texas: Findings from a Statewide Representative Survey.

CONTEXT States have passed numerous laws restricting abortion, and Texas passed some of the most restrictive legislation between 2011 and 2013. Information about women's awareness of and support for the laws' provisions could inform future debates regarding abortion legislation. METHODS Between December 2014 and January 2015, some 779 women aged 18-49 participated in an online, statewide representative survey about recent abortion laws in Texas. Poisson regression analysis was used to assess correlates of support for a law that would make obtaining an abortion more difficult. Women's knowledge of specific abortion restrictions in Texas and reasons for supporting these laws were also assessed. RESULTS Overall, 31% of respondents would support a law making it more difficult to obtain an abortion. Foreign-born Latinas were more likely than whites to support such a law (prevalence ratio, 1.5), and conservative Republicans were more likely than moderates and Independents to do so (2.3). Thirty-six percent of respondents were not very aware of recent Texas laws, and 19% had never heard of them. Among women with any awareness of the laws, 19% supported the requirements; 42% of these individuals said this was because such laws would make abortion safer. CONCLUSIONS Many Texas women of reproductive age are unaware of statewide abortion restrictions, and some support these requirements because of misperceptions about the safety of abortion. Advocates and policymakers should address these knowledge gaps in efforts to protect access to legal abortion.
Detection of Sensory Events from Acute Spinal Cord Recordings

We used acute multi-channel extracellular recording techniques to extract neural activity associated with external sensory events from the spinal cords of rats. Five classes of sensory events were recorded - electrical stimulation of the nerves in each of four digits from one forepaw and periods during which no stimulation occurred (idle periods). A simple feature extraction and classification scheme was devised to classify external sensory events during single trials. The five classes of sensory events were correctly identified at a mean accuracy of over 93%. Thus, we have shown the feasibility to detect and classify peripheral sensory information from multichannel recordings of the spinal cord. This would be useful following spinal cord injury, for example, in a closed-loop neural prosthetic for partial restoration of motor function through functional electrical stimulation
The Frontier Fields lens modelling comparison project

Gravitational lensing by clusters of galaxies offers a powerful probe of their structure and mass distribution. Several research groups have developed techniques independently to achieve this goal. While these methods have all provided remarkably high-precision mass maps, particularly with exquisite imaging data from the Hubble Space Telescope (HST), the reconstructions themselves have never been directly compared. In this paper, we present for the first time a detailed comparison of methodologies for fidelity, accuracy and precision. For this collaborative exercise, the lens modelling community was provided simulated cluster images that mimic the depth and resolution of the ongoing HST Frontier Fields. The results of the submitted reconstructions with the un-blinded true mass profile of these two clusters are presented here. Parametric, free-form and hybrid techniques have been deployed by the participating groups and we detail the strengths and trade-offs in accuracy and systematics that arise for each methodology. We note in conclusion that several properties of the lensing clusters are recovered equally well by most of the lensing techniques compared in this study. For example, the reconstruction of azimuthally averaged density and mass profiles by both parametric and free-form methods matches the input models at the level of ∼10 per cent. Parametric techniques are generally better at recovering the 2D maps of the convergence and of the magnification. For the best-performing algorithms, the accuracy in the magnification estimate is ∼10 per cent at μ_(true) = 3 and it degrades to ∼30 per cent at μ_(true) ∼ 10.
The Pseudomonas aeruginosa Vfr Regulator Controls Global Virulence Factor Expression through Cyclic AMP-Dependent and -Independent Mechanisms

ABSTRACT Vfr is a global regulator of virulence factor expression in the human pathogen Pseudomonas aeruginosa. Although indirect evidence suggests that Vfr activity is controlled by cyclic AMP (cAMP), it has been hypothesized that the putative cAMP binding pocket of Vfr may accommodate additional cyclic nucleotides. In this study, we used two different approaches to generate apo-Vfr and examined its ability to bind a representative set of virulence gene promoters in the absence and presence of different allosteric effectors. Of the cyclic nucleotides tested, only cAMP was able to restore DNA binding activity to apo-Vfr. In contrast, cGMP was capable of inhibiting cAMP-Vfr DNA binding. Further, we demonstrate that vfr expression is autoregulated and cAMP dependent and involves Vfr binding to a previously unidentified site within the vfr promoter region. Using a combination of in vitro and in vivo approaches, we show that cAMP is required for Vfr-dependent regulation of a specific subset of virulence genes. In contrast, we discovered that Vfr controls expression of the lasR promoter in a cAMP-independent manner. In summary, our data support a model in which Vfr controls virulence gene expression by distinct (cAMP-dependent and -independent) mechanisms, which may allow P. aeruginosa to fine-tune its virulence program in response to specific host cues or environments.
Neural Systems Underlying the Recognition of Familiar and Newly Learned Faces

Memory for famous faces can be used to examine the neural systems underlying retrieval from long-term memory. To date, there have been a limited number of functional neuroimaging investigations examining famous face recognition. In this study, we compared recognition of famous faces to recognition of newly learned faces. Whole-brain, event-related functional magnetic resonance imaging was used to image regional changes in neural activity in 11 subjects during the encoding of unfamiliar faces and during familiarity judgments for: (1) newly learned faces, (2) unfamiliar face distractors, and (3) famous faces. Image analyses were restricted to correct recognition trials. Recognition accuracy and response time to famous and recently learned faces were equivalent. Recognition of famous faces was associated with a widespread network of bilateral brain activations involving the prefrontal, lateral temporal, and mesial temporal (hippocampal and parahippocampal regions) regions compared to recognition of recently encoded faces or unfamiliar faces seen for the first time. Findings are discussed in relation to current proposals concerning the neural regions thought to participate in long-term memory retrieval and, more specifically, in relation to retrieval of information from the person identity semantic system.
Naturally occurring polyphenolic antioxidants modulate IgE‐mediated mast cell activation

Reactive oxygen species (ROS) are known to modulate activities of a host of kinases, phosphatases and transcription factors. Rutin and chlorogenic acid (CGA) are the major polyphenolic antioxidants present in the small molecular fraction of smokeless tobacco leaf extracts, as ascertained by reverse‐phase high‐pressure liquid chromatography (HPLC) and mass spectrometry. Levels of intracellular ROS in resting versus antigen–immunoglobulin E (IgE)‐challenged murine mast cells were measured at 510 nm by fluorescence‐activated cell sorting (FACS) using carboxy‐dichlorofluorescein (DCFH‐DA). Enhanced ROS production was observed in IgE‐sensitized mast cells following antigenic challenge. Rutin and CGA reduced ROS levels in antigen–IgE‐activated mast cells. Concomitantly, they also profoundly inhibited histamine release by these activated mast cells. In contrast, rutin and CGA augmented the inducible cytokine messages, i.e. interleukin (IL)‐10, IL‐13, interferon‐γ (IFN‐γ), IL‐6 and tumour necrosis factor‐α (TNF‐α) in IgE‐sensitized mast cells following antigen challenge. This study indicates that tobacco polyphenolic antioxidants that quench intracellular ROS, differentially affect two effector functions of antigen–IgE‐activated mast cells. This model system may be employed to determine the molecular target of polyphenols. The potential role of these polyphenolic antioxidants on IgE‐mediated allergy in vivo depends on a balance of their differential effects on mast cell activation.
Imaging and Diagnostic Testing Peak VO 2 and VE / VCO 2 slope in patients with heart failure : A prognostic comparison

Background Exercise testing with ventilatory expired gas analysis has proven to be a valuable tool for assessing patients with heart failure (HF). Peak oxygen consumption (peak VO2) continues to be considered the gold standard for assessing prognosis in HF. The minute ventilation carbon dioxide production relationship (VE/VCO2 slope) has recently demonstrated prognostic significance in patients with HF, and in some studies, it has outperformed peak VO2. Methods Two hundred thirteen subjects, in whom HF was diagnosed, underwent exercise testing between April 1, 1993, and October 19, 2001. The ability of peak VO2 and VE/VCO2 slope to predict cardiac-related mortality and hospitalization was examined. Results Peak VO2 and VE/VCO2 slope were demonstrated with univariate Cox regression analysis both to be significant predictors of cardiac-related mortality and hospitalization (P .01). Multivariate analysis revealed that peak VO2 added additional value to the VE/VCO2 slope in predicting cardiac-related hospitalization, but not cardiac mortality. The VE/VCO2 slope was demonstrated with receiver operating characteristic curve analysis to be significantly better than peak VO2 in predicting cardiac-related mortality (P .05). Although area under the receiver operating characteristic curve for the VE/VCO2 slope was greater than peak VO2 in predicting cardiac-related hospitalization (0.77 vs 0.73), the difference was not statistically significant (P .14). Conclusions These results add to the present body of knowledge supporting the use of cardiopulmonary exercise testing in HF. Consideration should be given to revising clinical guidelines to reflect the prognostic importance of the VE/ VCO2 slope in addition to peak VO2. (Am Heart J 2004;147:354–60.)
Fast hashing with strong concentration bounds

Previous work on tabulation hashing by Pǎtraşcu and Thorup from STOC’11 on simple tabulation and from SODA’13 on twisted tabulation offered Chernoff-style concentration bounds on hash based sums, e.g., the number of balls/keys hashing to a given bin, but under some quite severe restrictions on the expected values of these sums. The basic idea in tabulation hashing is to view a key as consisting of c=O(1) characters, e.g., a 64-bit key as c=8 characters of 8-bits. The character domain Σ should be small enough that character tables of size |Σ| fit in fast cache. The schemes then use O(1) tables of this size, so the space of tabulation hashing is O(|Σ|). However, the concentration bounds by Pǎtraşcu and Thorup only apply if the expected sums are ≪ |Σ|. To see the problem, consider the very simple case where we use tabulation hashing to throw n balls into m bins and want to analyse the number of balls in a given bin. With their concentration bounds, we are fine if n=m, for then the expected value is 1. However, if m=2, as when tossing n unbiased coins, the expected value n/2 is ≫ |Σ| for large data sets, e.g., data sets that do not fit in fast cache. To handle expectations that go beyond the limits of our small space, we need a much more advanced analysis of simple tabulation, plus a new tabulation technique that we call tabulation-permutation hashing which is at most twice as slow as simple tabulation. No other hashing scheme of comparable speed offers similar Chernoff-style concentration bounds.
SUNLIGHT AND CUTANEOUS MALIGNANT MELANOMA: EVIDENCE FOR AND AGAINST CAUSATION

In recent decades, the reported incidence and mortality of cutaneous malignant melanoma has risen dramatically world-wide. Mounting evidence points to the possible role of sunlight as a cause of malignant melanoma. If such a causal link exists, ozone depletion and other environmental factors threaten to accelerate future melanoma incidence and subsequent mortality. Most of the emerging data comes from epidemiologic and case-control studies; relevant data from animal and in vitro experiments are sparse and can only examine small steps in the postulated etiology. A recent exhaustive monograph by the Environmental Protection Agency (Dr Janice Longstreth, Editor, 1987) has summarized many of the controversies involved in the proposed link between sunlight and melanoma. We review the current evidence studying sunlight as a cause for melanoma, place particular emphasis on the evolving "intermittent sun exposure" hypothesis, and offer projections for future challenges and trends.
AC resistance of planar power inductors and the quasidistributed gap technique

Low-AC-resistance planar or foil-wound inductors constructed using a quasidistributed gap comprising multiple small gaps that approximate a distributed gap are analyzed. Finite-element simulations are used systematically to develop a model broadly applicable to the design of such quasidistributed gap inductors. It is shown that a good approximation of a distributed gap is realized if the ratio of gap pitch to spacing between gap and conductor is less than four, or if the gap pitch is comparable to a skin depth or smaller. Large gaps can reduce AC resistance, but for most practical designs gap length has little effect. A closed-form expression, which closely approximates the AC resistance factor for a wide range of designs, is developed. The methods are illustrated with an inductor for a high-ripple-current fast-response voltage regulator module (VRM) for microprocessor power delivery.
Productivity Is a Poor Predictor of Plant Species Richness

Standardized sampling from many sites worldwide was used to address an important ecological problem. For more than 30 years, the relationship between net primary productivity and species richness has generated intense debate in ecology about the processes regulating local diversity. The original view, which is still widely accepted, holds that the relationship is hump-shaped, with richness first rising and then declining with increasing productivity. Although recent meta-analyses questioned the generality of hump-shaped patterns, these syntheses have been criticized for failing to account for methodological differences among studies. We addressed such concerns by conducting standardized sampling in 48 herbaceous-dominated plant communities on five continents. We found no clear relationship between productivity and fine-scale (meters−2) richness within sites, within regions, or across the globe. Ecologists should focus on fresh, mechanistic approaches to understanding the multivariate links between productivity and richness.
Nested variational autoencoder for topic modelling on microtexts with word vectors

Most of the information on the Internet is represented in the form of microtexts, which are short text snippets such as news headlines or tweets. These sources of information are abundant, and mining these data could uncover meaningful insights. Topic modelling is one of the popular methods to extract knowledge from a collection of documents; however, conventional topic models such as latent Dirichlet allocation (LDA) are unable to perform well on short documents, mostly due to the scarcity of word co‐occurrence statistics embedded in the data. The objective of our research is to create a topic model that can achieve great performances on microtexts while requiring a small runtime for scalability to large datasets. To solve the lack of information of microtexts, we allow our method to take advantage of word embeddings for additional knowledge of relationships between words. For speed and scalability, we apply autoencoding variational Bayes, an algorithm that can perform efficient black‐box inference in probabilistic models. The result of our work is a novel topic model called the nested variational autoencoder, which is a distribution that takes into account word vectors and is parameterized by a neural network architecture. For optimization, the model is trained to approximate the posterior distribution of the original LDA model. Experiments show the improvements of our model on microtexts as well as its runtime advantage.