Miracle-dz/UniFAR-FTUs huggingface dataset:
On Genetic Specificity in Symbiont-Mediated Host-Parasite Coevolution

Existing theory of host-parasite interactions has identified the genetic specificity of interaction as a key variable affecting the outcome of coevolution. The Matching Alleles (MA) and Gene For Gene (GFG) models have been extensively studied as the canonical examples of specific and non-specific interaction. The generality of these models has recently been challenged by uncovering real-world host-parasite systems exhibiting specificity patterns that fit neither MA nor GFG, and by the discovery of symbiotic bacteria protecting insect hosts against parasites. In the present paper we address both challenges, simulating a large number of non-canonical models of host-parasite interactions that explicitly incorporate symbiont-based host resistance. To assess the genetic specialisation in these hybrid models, we develop a quantitative index of specificity applicable to any coevolutionary model based on a fitness matrix. We find qualitative and quantitative effects of host-parasite and symbiont-parasite specificities on genotype frequency dynamics, allele survival, and mean host and parasite fitnesses.
Mass Models and Sunyaev-Zeldovich Effect Predictions for a Flux-Limited Sample of 22 Nearby X-Ray Clusters

We define a 90% complete, volume-limited sample of 31 z < 0.1 X-ray clusters and present a systematic analysis of public ROSAT PSPC data on 22 of these objects. Our efforts are undertaken in support of the Penn/OVRO Sunyaev-Zeldovich Effect (SZE) survey, and to this end we present predictions for the inverse Compton optical depth toward all 22 of these clusters. We have performed detailed Monte Carlo simulations in order to understand the effects of the cluster profile uncertainties on the SZE predictions given the OVRO 5.5 m telescope beam and switching patterns. We also present a similar analysis for the upcoming ACBAR experiment. For most of the clusters in the sample, we find less than a 5% uncertainty in the SZE predictions due to an imperfect knowledge of the profile. A comparison of different cooling-flow modeling strategies shows that our results are robust in this respect. The profile uncertainties are then one of the least significant components of our error budget for SZE-based distance measurements. The density models that result from this analysis also yield baryonic masses and, under the assumption of hydrostatic equilibrium, total masses and baryon mass fractions. Our Monte Carlo profile analysis indicates that the baryon masses within 1 h Mpc for these clusters are accurate to better than ~5% and unaffected by realistic PSPC systematics. In the sample as a whole, we find a mean gas mass fraction of (7.02 ± 0.28)h × 10-2 internal to R500 ~ 1 h Mpc. This is in agreement with previous X-ray cluster analyses, which indicate an overabundance of baryons relative to the prediction of big bang nucleosynthesis for an ΩM = 1 universe. Our analysis of the X-ray spectra confirms a previous claim of an excess absorbing column density toward A478, but we do not find evidence for anomalous column densities in the other 21 clusters. We also find some indications of an excess of soft counts in the ROSAT PSPC data. A measurement of H0 using these models and OVRO SZE determinations will be presented in a second paper.
Neural Expectation Maximization

Many real world tasks such as reasoning and physical interaction require identification and manipulation of conceptual entities. A first step towards solving these tasks is the automated discovery of distributed symbol-like representations. In this paper, we explicitly formalize this problem as inference in a spatial mixture model where each component is parametrized by a neural network. Based on the Expectation Maximization framework we then derive a differentiable clustering method that simultaneously learns how to group and represent individual entities. We evaluate our method on the (sequential) perceptual grouping task and find that it is able to accurately recover the constituent objects. We demonstrate that the learned representations are useful for next-step prediction.
Differential Evolution With Ranking-Based Mutation Operators

Differential evolution (DE) has been proven to be one of the most powerful global numerical optimization algorithms in the evolutionary algorithm family. The core operator of DE is the differential mutation operator. Generally, the parents in the mutation operator are randomly chosen from the current population. In nature, good species always contain good information, and hence, they have more chance to be utilized to guide other species. Inspired by this phenomenon, in this paper, we propose the ranking-based mutation operators for the DE algorithm, where some of the parents in the mutation operators are proportionally selected according to their rankings in the current population. The higher ranking a parent obtains, the more opportunity it will be selected. In order to evaluate the influence of our proposed ranking-based mutation operators on DE, our approach is compared with the jDE algorithm, which is a highly competitive DE variant with self-adaptive parameters, with different mutation operators. In addition, the proposed ranking-based mutation operators are also integrated into other advanced DE variants to verify the effect on them. Experimental results indicate that our proposed ranking-based mutation operators are able to enhance the performance of the original DE algorithm and the advanced DE algorithms.
Generalised Linear Pose Estimation

This paper investigates several aspects of 3D-2D camera pose estimation, aimed at robot navigation in poorly-textured scenes. The major contribution is a fast, linear algorithm for the general case with six or more points. We show how to specialise this to work with only four or five points, which is of utmost importance in a test and hypothesis framework. Our formulation allows for an easy inclusion of lines, as well as the handling of other camera geometries, such as stereo rigs. We also treat the special case of planar motion, a valid restriction for most indoor environments. We conclude the paper with extensive simulated tests and a real test case, which substantiate the algorithm’s usability for our application domain.
Role of nitric oxide in regulating the ductus arteriosus caliber in fetal rats.

The role of nitric oxide (NO) on the ductus arteriosus (DA) patency was examined in fetal rats at various stages of gestation. N(G)-nitro-L-arginine methyl ester (L-NAME, 50 mg/kg, i.p.), an NO synthase (NOS) inhibitor, or indomethacin (3 mg/kg, p.o.), a cyclooxygenase inhibitor, was administered at 3 hr before cesarean section to pregnant rats ranging from day 17 to day 21 of gestation. Dams were decapitated and the fetuses were obtained by cesarean section. The fetuses were rapidly frozen in an acetone-dry ice mixture. Using rapid-freezing and shaving methods, the calibers of the DA and pulmonary artery were measured. The constrictive effect of L-NAME on the fetal DA caliber was stronger than that of indomethacin in 19-day-old and immature fetuses. In near-term fetuses, the constrictive effects of L-NAME were reduced, while indomethacin caused marked DA constriction. We conclude that endogenous NO may play a major role in regulating the patency of the DA in earlier fetal stages, while dilator prostaglandins may play a greater role in regulating the ductal patency in the near-term fetus.
Hepatitis B surface antigen declines and clearance during long-term tenofovir therapy in patients coinfected with HBV and HIV.

BACKGROUND The kinetics of hepatitis B surface antigen (HBsAg) are predictive in HBV-infected patients treated with pegylated interferon. Knowledge about the value of HBsAg levels in patients coinfected with HBV and human immunodeficiency virus (HIV) is lacking. METHODS We quantified serum HBsAg in a Dutch multicenter cohort of 104 patients coinfected with HIV and HBV who were treated with tenofovir disoproxil fumarate (TDF) as part of highly active antiretroviral therapy. The median duration of therapy was 57 months (interquartile range, 34-72 months). RESULTS Hepatitis B e antigen (HBeAg)-positive patients achieved a decline of 2.2 log IU/mL in HBsAg, whereas HBeAg-negative patients only achieved a decline of 0.6 log IU/mL during 6 years of TDF therapy. Declines in HBsAg at months 6 and 12 correlated with CD4 cell count for HBeAg-positive patients. Five HBeAg-positive patients (8%) and 3 HBeAg-negative patients (8%) cleared HBsAg. HBeAg-negative patients who cleared HBsAg had lower baseline HBsAg as compared to patients who remained HBsAg positive. The majority of patients who cleared HBsAg achieved this end point within the first year. In HBeAg-positive patients, decline in HBsAg at month 6 was predictive of achieving HBsAg seroclearance. CONCLUSIONS Receipt of TDF therapy by HIV/HBV-coinfected patients for up to 6 years led to a significant decrease in HBsAg in the HBeAg-positive population. HBsAg kinetics early during treatment were predictive of HBsAg seroclearance and correlated with an increased CD4 cell count, underlining the importance of immune restoration in HBV clearance.
Growth hormone-releasing peptide-2 infusion synchronizes growth hormone, thyrotrophin and prolactin release in prolonged critical illness.

OBJECTIVE During prolonged critical illness, nocturnal pulsatile secretion of GH, TSH and prolactin (PRL) is uniformly reduced but remains responsive to the continuous infusion of GH secretagogues and TRH. Whether such (pertinent) secretagogues would synchronize pituitary secretion of GH, TSH and/or PRL is not known. DESIGN AND METHODS We explored temporal coupling among GH, TSH and PRL release by calculating cross-correlation among GH, TSH and PRL serum concentration profiles in 86 time series obtained from prolonged critically ill patients by nocturnal blood sampling every 20 min for 9 h during 21-h infusions of either placebo (n=22), GHRH (1 microg/kg/h; n=10), GH-releasing peptide-2 (GHRP-2; 1 microg/kg/h; n=28), TRH (1 microg/kg/h; n=8) or combinations of these agonists (n=8). RESULTS The normal synchrony among GH, TSH and PRL was absent during placebo delivery. Infusion of GHRP-2, but not GHRH or TRH, markedly synchronized serum profiles of GH, TSH and PRL (all P< or =0.007). After addition of GHRH and TRH to the infusion of GHRP-2, only the synchrony between GH and PRL was maintained (P=0.003 for GHRH + GHRP-2 and P=0.006 for TRH + GHRH + GHRP-2), and was more marked than with GHRP-2 infusion alone (P=0.0006 by ANOVA). CONCLUSIONS The nocturnal GH, TSH and PRL secretory patterns during prolonged critical illness are herewith further characterized to include loss of synchrony among GH, TSH and PRL release. The synchronizing effect of an exogenous GHRP-2 drive, but not of GHRH or TRH, suggests that the presumed endogenous GHRP-like ligand may participate in the orchestration of coordinated anterior pituitary hormone release.
Prevalence of obesity and metabolic syndrome in Indigenous Australian youths

We conducted a cross‐sectional study of Indigenous youths residing in the Torres Strait region of Australia to assess the prevalence of obesity and the metabolic syndrome. Data on body mass index (BMI), waist circumference, blood pressure, presence of acanthosis nigricans and blood glucose were collected. Fasting glucose, insulin, C‐Peptide, HbA1c and lipids were measured, and an oral glucose tolerance test was performed in those with a BMI greater than 25 (childhood‐equivalent cut‐points) or fasting glucometer reading >5.5 mmol/L. Of 158 youths, 31% were overweight and 15% were obese, 38% had enlarged waist circumference consistent with central obesity, 43% had acanthosis nigricans and 27% were hypertensive. More females than males had enlarged waist circumferences (59% vs. 13%, P < 0.001). Among overweight or obese youth, 56% had significantly elevated insulin (P = 0.021); they also had higher HOMA‐IR (P = 0.002). The metabolic syndrome was present in 17% of all youths (mostly females) and in 33% of the overweight or obese subgroup. Type 2 diabetes was diagnosed in two youths. These very high proportions of overweight or obese Torres Strait youth with metabolic risk factors have major public health implications.
Poly(ADP-ribose) Polymerase-1 Inhibition Prevents Eosinophil Recruitment by Modulating Th2 Cytokines in a Murine Model of Allergic Airway Inflammation: A Potential Specific Effect on IL-51

We recently used a murine model of allergic airway inflammation to show that poly(ADP-ribose) polymerase-1 (PARP-1) plays an important role in the pathogenesis of asthma-related lung inflammation. In this study, we show that PARP-1 inhibition, by a novel inhibitor (TIQ-A) or by gene deletion, prevented eosinophilic infiltration into the airways of OVA-challenged mice. Such impairment of eosinophil recruitment appeared to take place after IgE production. OVA challenge of wild-type mice resulted in a significant increase in IL-4, IL-5, IL-10, IL-13, and GM-CSF secretions. Although IL-4 production was moderately affected in OVA-challenged PARP-1−/− mice, the production of IL-5, IL-10, IL-13, and GM-CSF was completely inhibited in ex vivo OVA-challenged lung cells derived from these animals. A single TIQ-A injection before OVA challenge in wild-type mice mimicked the latter effects. The marked effect PARP-1 inhibition exerted on mucus production corroborated the effects observed on the Th2 response. Although PARP-1 inhibition by gene knockout increased the production of the Th1 cytokines IL-2 and IL-12, the inhibition by TIQ-A exerted no effect on these two cytokines. The failure of lung cells derived from OVA-challenged PARP-1−/− mice to synthesize GM-CSF, a key cytokine in eosinophil recruitment, was reestablished by replenishment of IL-5. Furthermore, intranasal administration of IL-5 restored the impairment of eosinophil recruitment and mucus production in OVA-challenged PARP-1−/− mice. The replenishment of either IL-4 or IgE, however, did not result in such phenotype reversals. Altogether, these results suggest that PARP-1 plays a critical role in eosinophil recruitment by specifically regulating the cascade leading to IL-5 production.
Evaluation of skin-core adhesion bond of out-of-autoclave honeycomb sandwich structures

Composite sandwich structures offer several advantages over conventional structural materials such as lightweight, high bending and torsional stiffness, superior thermal insulation and excellent acoustic damping. One failure mechanism in a composite sandwich structure is the debonding of the composite facesheets from the core structure. A well-formed adhesive fillet at the interface of the honeycomb core cell walls and the laminate is a significant factor in preventing bond failure. In the present work, honeycomb composite sandwich panels are manufactured using a low-cost vacuum-bag-pressure-only out-of-autoclave manufacturing process. CYCOM®5320 out-of autoclave prepreg is used for the facesheet laminates and FM® 300-2U film adhesive is used for the facesheet-to-core bond. The manufactured composite sandwich panels are of aerospace quality with a facesheet laminate void content of around 1%. In this study, adhesive fillet formation and adhesive mechanical strength are evaluated as a function of several different sandwich construction design variables. Both aluminum and aramid Nomex® honeycomb core materials are considered to study the effect of core cell size and core material. The effect of film adhesive thickness is studied. A process for reticulation of the adhesive is applied and studied. A quantitative investigation of the adhesive fillet geometry is carried out for all the panels. Manufactured panels are evaluated for flatwise tensile strength in accordance with test method ASTM C297. Optimized combinations of core material, core density, cell size and adhesive thickness are identified. Results show that the reticulation process improves fillet formation and increases flatwise tensile properties.
Interleukin-23 production in dendritic cells is negatively regulated by protein phosphatase 2A

IL-12 and IL-23 are produced by activated antigen-presenting cells but the two induce distinct immune responses by promoting Th1 and Th17 cell differentiation, respectively. IL-23 is a heterodimeric cytokine consisting of two subunits: p40 that is shared with IL-12 and p19 unique to IL-23. In this study, we showed that the production of IL-23 but not IL-12 was negatively regulated by protein phosphatase 2A (PP2A) in dendritic cells (DC). PP2A inhibits IL-23 production by suppressing the expression of the IL-23p19 gene. Treating DC with okadaic acid that inhibits the PP2A activity or knocking down the catalytic subunit of PP2A with siRNA enhanced IL-23 but not IL-12 production. Unlike PP2A, MAP kinase phosphatase-1 or CYLD did not show an effect on IL-23 production supporting the specificity of PP2A. PP2A-mediated inhibition requires a newly made protein that is likely responsible for bringing PP2A and IKKβ together upon LPS stimulation, which then results in the termination of IKK phosphorylation. Thus, our results uncovered an important role of the protein phosphatase in the regulation of IL-23 production and identified PP2A as a previously uncharacterized inhibitor of IL-23p19 expression in DC.
Determinants of Impaired Fasting Glucose Versus Glucose Intolerance in Polycystic Ovary Syndrome

OBJECTIVE To determine insulin resistance and response in patients with polycystic ovary syndrome (PCOS) and normal glucose tolerance (NGT), impaired fasting glucose (IFG), impaired glucose tolerance, and combined glucose intolerance (CGI). RESEARCH DESIGN AND METHODS In this cross-sectional study, 143 patients with PCOS (diagnosed on the basis of National Institutes of Health criteria) underwent oral glucose tolerance testing (OGTT), and 68 patients also had frequently sampled intravenous glucose tolerance tests. Changes in plasma glucose, insulin, cardiovascular risk factors, and androgens were measured. RESULTS Compared with patients with NGT, those with both IFG and CGI were significantly insulin resistant (homeostasis model assessment 3.3 ± 0.2 vs. 6.1 ± 0.9 and 6.4 ± 0.5, P < 0.0001) and hyperinsulinemic (insulin area under the curve for 120 min 973 ± 69 vs. 1,470 ± 197 and 1,461 ± 172 pmol/l, P < 0.0001). Insulin response was delayed in patients with CGI but not in those with IFG (2-h OGTT, insulin 1,001 ± 40 vs. 583 ± 45 pmol/l, P < 0.0001). Compared with the NGT group, the CGI group had a lower disposition index (1,615 ± 236 vs. 987 ± 296, P < 0.0234) and adiponectin level (11.1 ± 1.1 vs. 6.2 ± 0.8 ng/ml, P < 0.0096). Compared with the insulin-resistant tertile of the NGT group, those with IFG had a reduced insulinogenic index (421 ± 130 vs. 268 ± 68, P < 0.05). Compared with the insulin-sensitive tertile of the NGT group, the resistant tertile had higher triglyceride and high-sensitivity C-reactive protein (hs-CRP) and lower HDL cholesterol and sex hormone–binding globulin (SHBG). In the entire population, insulin resistance correlated directly with triglyceride, hs-CRP, and the free androgen index and inversely with SHBG. CONCLUSIONS Patients with PCOS develop IFG and CGI despite having significant hyperinsulinemia. Patients with IFG and CGI exhibit similar insulin resistance but very different insulin response patterns. Increases in cardiac risk factors and free androgen level precede overt glucose intolerance.
Angiotensin-Converting Enzyme Inhibitors and Calcium Channel Blockers for Coronary Heart Disease and Stroke Prevention

We investigated whether protection from coronary heart disease (CHD) and stroke conferred by angiotensin-converting enzyme inhibitors (ACEIs) and calcium channel blockers (CCBs) in hypertensive or high-risk patients may be explained by the specific drug regimen. We extracted summary statistics regarding CHD and stroke from 28 outcome trials that compared either ACEIs or CCBs with diuretics, β-blockers, or placebo for a total of 179 122 patients, 9509 incident cases of CHD, and 5971 cases of stroke. CHD included myocardial infarction and coronary death. In placebo-controlled trials, ACEIs decreased the risk of CHD (P<0.001), and CCBs reduced stroke incidence (P<0.001). There were no significant differences in CHD risk between regimens based on diuretics/β-blockers and regimens based on ACEIs (P=0.46) or CCBs (P=0.52). The risk of stroke was reduced by CCBs (P=0.041) but not by ACEIs (P=0.15) compared with diuretics/β-blockers. Because heterogeneity between trials was significant, we investigated potential sources of heterogeneity by metaregression. Examined covariates were the reduction in systolic blood pressure (BP), drug treatment (ACEIs versus CCBs), their interaction term, sex, age at randomization, year of publication, and duration of treatment. Prevention of CHD was explained by systolic BP reduction (P<0.001) and use of ACEIs (P=0.028), whereas prevention of stroke was explained by systolic BP reduction (P=0.001) and use of CCBs (P=0.042). These findings confirm that BP lowering is fundamental for prevention of CHD and stroke. However, over and beyond BP reduction, ACEIs appear superior to CCBs for prevention of CHD, whereas CCBs appear superior to ACEIs for prevention of stroke.
Further Wolf-Rayet stars in the starburst cluster Westerlund 1

We present new low and intermediate-resolution spectroscopic observations of the Wolf Rayet (WR) star population in the massive starburst cluster Westerlund 1. Finding charts are presented for five new WRs - four WNL and one WCL - raising the current total of known WRs in the cluster to 19. We also present new spectra and correct identifications for the majority of the 14 WR stars previously known, notably confirming the presence of two WNVL stars. Finally we briefly discuss the massive star population of Westerlund 1 in comparison to other massive young galactic clusters.
Causes and Predictors of Death in Cerebral Venous Thrombosis

Background and Purpose— The causes of death of patients with cerebral venous thrombosis (CVT) have not been systematically addressed in previous studies. We aimed to analyze the causes and predictors of death during the acute phase of CVT in the International Study on Cerebral Vein and Dural Sinus Thrombosis (ISCVT) to identify preventable or treatable causes. Methods— ISCVT is a multinational, prospective, observational study including 624 patients with CVT occurring between May 1998 and May 2001, in which 27 patients (4.3%) died during the acute phase, 21 (3.4%) within 30 days from symptom onset. Inclusion forms and a questionnaire assessing the causes of death were analyzed. A logistic regression analysis was performed to identify the predictors of death within 30 days from symptom onset of CVT. Results— Median time between onset of symptoms and death was 13 days and between diagnosis and death, 5 days. Causes of death were mainly transtentorial herniation due to a unilateral focal mass effect (10 patients) or to diffuse edema and multiple parenchymal lesions (10 patients). Independent predictors of death were coma (odds ratio [OR], 8.8; 95% confidence interval [CI], 2.8 to 27.7), mental disturbance (OR, 2.5; 95% CI 0.9 to 7.3), deep CVT thrombosis (OR, 8.5; 95% CI, 2.6 to 27.8), right intracerebral hemorrhage (OR, 3.4; 95% CI, 1.1 to 10.6), and posterior fossa lesion (OR, 6.5; 95% CI, 1.3 to 31.7). Worsening of previous focal or de novo focal deficits increased the risk of death. Conclusions— The main causes of acute death were neurologic, the most frequent mechanism being transtentorial herniation.