Miracle-dz/UniFAR-FTUs huggingface dataset:
Species Interactions and the Evolution of Sex

The Red Queen hypothesis posits that sex has evolved in response to the shifting adaptive landscape generated by the evolution of interacting species. Previous studies supporting the Red Queen hypothesis have considered a narrow region of parameter space and only a subset of ecological and genetic interactions. Here, we develop a population genetics model that circumscribes a broad array of ecological and genetic interactions among species and derive the first general analytical conditions for the impact of species interactions on the evolution of sex. Our results show that species interactions typically select against sex. We conclude that, although the Red Queen favors sex under certain circumstances, it alone does not account for the ubiquity of sex.
In vitro cytotoxicity MTT assay in Vero, HepG2 and MCF -7 cell lines study of Marine Yeast

Abstract Marine yeasts isolated from coastal mangrove ecosystem namely Candida albicans, Kuraishia capsulate and Sacchromyces cerevisae were screened for the cytotoxicity against a non-transformed Vero (African green monkey kidney normal cell line) and two cancer cell lines human breast carcinoma cells (HepG2), human breast carcinoma cells (MCF -7) in different concentrations (1000 to 1.953 µg/ml). lower doses enhanced the viability of the cultured cells,MTT assay . higher doses decreased viability of the cells by 50% or more. MTT assay was used to measure the cell proliferation and survival. Of three yeast strains, Sacchromyces cerevisae showed more than 80% cell viability in Vero cell lines and were studied for further cytotoxicity against HepG2, MCF -7 cell lines respectively.
Activin and GDF11 collaborate in feedback control of neuroepithelial stem cell proliferation and fate

Studies of the olfactory epithelium model system have demonstrated that production of neurons is regulated by negative feedback. Previously, we showed that a locally produced signal, the TGFβ superfamily ligand GDF11, regulates the genesis of olfactory receptor neurons by inhibiting proliferation of the immediate neuronal precursors (INPs) that give rise to them. GDF11 is antagonized by follistatin (FST), which is also produced locally. Here, we show that Fst–/– mice exhibit dramatically decreased neurogenesis, a phenotype that can only be partially explained by increased GDF11 activity. Instead, a second FST-binding factor, activin βB (ACTβB), inhibits neurogenesis by a distinct mechanism: whereas GDF11 inhibits expansion of INPs, ACTβB inhibits expansion of stem and early progenitor cells. We present data supporting the concept that these latter cells, previously considered two distinct types, constitute a dynamic stem/progenitor population in which individual cells alternate expression of Sox2 and/or Ascl1. In addition, we demonstrate that interplay between ACTβB and GDF11 determines whether stem/progenitor cells adopt a glial versus neuronal fate. Altogether, the data indicate that the transition between stem cells and committed progenitors is neither sharp nor irreversible and that GDF11, ACTβB and FST are crucial components of a circuit that controls both total cell number and the ratio of neuronal versus glial cells in this system. Thus, our findings demonstrate a close connection between the signals involved in the control of tissue size and those that regulate the proportions of different cell types.
Increased mouse survival, tumor growth inhibition and decreased immunoreactive p53 after exposure to magnetic fields

The possibility that magnetic fields (MF) cause antitumor activity in vivo has been investigated. Two different experiments have been carried out on nude mice bearing a subcutaneous human colon adenocarcinoma (WiDr). In the first experiment, significant increase in survival time (31%) was obtained in mice exposed daily to 70 min modulated MF (static with a superimposition of 50 Hz) having a time average total intensity of 5.5 mT. In the second independent experiment, when mice bearing tumors were exposed to the same treatment for four consecutive weeks, significant inhibition of tumor growth (40%) was reported, together with a decrement in tumor cell mitotic index and proliferative activity. A significant increase in apoptosis was found in tumors of treated animals, together with a reduction in immunoreactive p53 expression. Gross pathology at necroscopy, hematoclinical/hematological and histological examination did not show any adverse or abnormal effects. Since pharmacological rescue of mutant p53 conformation has been recently demonstrated, the authors suggest that MF exposure may obtain a similar effect by acting on redox chemistry connected to metal ions which control p53 folding and its DNA‐binding activity. These findings support further investigation aimed at the potential use of magnetic fields as anti‐cancer agents. Bioelectromagnetics 23:230–238, 2002. © 2002 Wiley‐Liss, Inc.
Learning in human -dolphin interactions at zoological facilities

This research aimed to better understand learning in zoological settings, particularly learning about marine mammals, by investigating the research question, what do people learn through interacting with dolphins in zoological facilities? Sociocultural situated learning theory, specifically a Community of Practice (CoP) model of learning (Lave & Wenger, 1991), was the theoretical framework. The CoP model allowed for diversity of knowledge, interest, motivations, and goals that existed among the community of animal enthusiasts at three commercial zoological facilities, and also for peripheral to more central types of participation. I collected data through interviews of spectators, visitors, and trainers (n=51), observations (n=16), and an online questionnaire of past-visitors (n=933). Data were coded, categorized, and analyzed based on the National Science Foundation's (Friedman, 2008) and the National Research Council's (2009) frameworks for informal science education. Five principal findings answered the research question. First, all participants gained new knowledge within three broad categories: (a) dolphin physiology and natural history, (b) care and training of dolphins, and (c) conservation. Second, all participants constructed personal meanings by connecting the activity to experiences, beliefs, and practices outside the interaction context. Almost all participants made associations with conservation. Third, most participants shifted their attitudes and gained a sense of personal agency about beginning or increasing stewardship actions. Fourth, visitors learned interspecies etiquette skills; trainers learned skills in dolphin training and management, people management, and teaching. Fifth, visitors had long-lasting memories of the experience that occurred eight months to 18 years in the past. Popular cultural ideas about dolphins and the ways the dolphins were represented influenced visitors' expectations and the types of learning. Potential physical mediators of learning were close proximity to living dolphins and eye-to-eye immersion. Potential social mediators were membership in the CoP, and interacting with experts and co-participants. In the personal realm, potential mediators were the participants' strong affective responses to the experience, including interest, engagement, positive emotions, and feelings of affinity to the dolphins. The collective influences appeared to move participants towards stronger identities as environmentally-caring and responsible individuals who take stewardship action
XO-4b: An Extrasolar Planet Transiting an F5V Star

We report the discovery of the planet XO-4b, which transits the star XO-4 (GSC 03793-01994, V=10.7, F5V). Transits are 1.0% deep and 4.4 hours in duration. The star XO-4 has a mass of 1.32 M_sun. The planet XO-4b has a mass of 1.72 M_Jup. radius of 1.34 R_Jup. orbital period 4.125 days. We analyze scintillation-limited differential R-band photometry of XO-4b in transit made with a 1.8-m telescope under photometric conditions, yielding photometric precision of 0.6 to 2.0 millimag per one-minute interval. The declination of XO-4 places it within the continuous viewing zone of the Hubble Space Telescope (HST), which permits observation without interruption caused by occultation by the Earth. Because the stellar rotation periods of the three hottest stars orbited by transiting gas-giant planets are 2.0, 1.1, and 2.0 times the planetary orbital periods, we note the possibility of resonant interaction.
Two-Way Amplify-and-Forward Relaying with Gaussian Imperfect Channel Estimations

In this letter, we study the effect of channel estimation errors on the reception reliability of two-way relaying. For a network with two users that exchange information with each other through multiple amplify-and-forward relays, we investigate a single-relay selection scheme. Since the communication is two-way, the selection scheme aims at optimizing the worse performance of the two communication tasks between the pair of users. The signal-to-noise ratio (SNR) at the users' nodes of the relaying network is formulated and upper bounded. Then, the probability density function (PDF) of the upper bounded SNRs are determined. Subsequently, expressions for the error probabilities are obtained. Furthermore, an approximate PDF of the output instantaneous SNRs are derived, based on which simple and general asymptotic expressions for the error probabilities are presented and discussed. Numerical and simulation results are provided to verify the analysis and compare the performance of the two-way relaying network for different operating conditions and scenarios.
Association Between Early Lactate Levels and 30-Day Mortality in Clinically Suspected Sepsis in Children

Importance Improving emergency care of pediatric sepsis is a public health priority, but optimal early diagnostic approaches are unclear. Measurement of lactate levels is associated with improved outcomes in adult septic shock, but pediatric guidelines do not endorse its use, in part because the association between early lactate levels and mortality is unknown in pediatric sepsis. Objective To determine whether the initial serum lactate level is associated with 30-day mortality in children with suspected sepsis. Design, Setting, and Participants This observational cohort study of a clinical registry of pediatric patients with suspected sepsis in the emergency department of a tertiary children’s hospital from April 1, 2012, to December 31, 2015, tested the hypothesis that a serum lactate level of greater than 36 mg/dL is associated with increased mortality compared with a serum lactate level of 36 mg/dL or less. Consecutive patients with sepsis were identified and included in the registry following consensus guidelines for clinical recognition (infection and decreased mental status or perfusion). Among 2520 registry visits, 1221 were excluded for transfer from another medical center, no measurement of lactate levels, and patients younger than 61 days or 18 years or older, leaving 1299 visits available for analysis. Lactate testing is prepopulated in the institutional sepsis order set but may be canceled at clinical discretion. Exposures Venous lactate level of greater than 36 mg/dL on the first measurement within the first 8 hours after arrival. Main Outcomes and Measures Thirty-day in-hospital mortality was the primary outcome. Odds ratios were calculated using logistic regression to account for potential confounders. Results Of the 1299 patients included in the analysis (753 boys [58.0%] and 546 girls [42.0%]; mean [SD] age, 7.3 [5.3] years), 899 (69.2%) had chronic medical conditions and 367 (28.3%) had acute organ dysfunction. Thirty-day mortality occurred in 5 of 103 patients (4.8%) with lactate levels greater than 36 mg/dL and 20 of 1196 patients (1.7%) with lactate levels of 36 mg/dL or less. Initial lactate levels of greater than 36 mg/dL were significantly associated with 30-day mortality in unadjusted (odds ratio, 3.00; 95% CI, 1.10-8.17) and adjusted (odds ratio, 3.26; 95% CI, 1.16- 9.16) analyses. The sensitivity of lactate levels greater than 36 mg/dL for 30-day mortality was 20.0% (95% CI, 8.9%-39.1%), and specificity was 92.3% (90.7%-93.7%). Conclusions and Relevance In children treated for sepsis in the emergency department, lactate levels greater than 36 mg/dL were associated with mortality but had a low sensitivity. Measurement of lactate levels may have utility in early risk stratification of pediatric sepsis.
From In Vivo to In Vitro: Dynamic Analysis of Plasmodium falciparum var Gene Expression Patterns of Patient Isolates during Adaptation to Culture

Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), encoded by the var gene family, plays a crucial role in disease virulence through its involvement in binding to various host cellular receptors during infection. Growing evidence suggests that differential expression of the various var subgroups may be involved in parasite virulence. To further explore this issue, we have collected isolates from symptomatic patients in south China-Myanmar border, and characterized their sequence diversity and transcription profiles over time of var gene family, and cytoadherence properties from the time of their initial collection and extending through a two month period of adaptation to culture. Initially, we established a highly diverse, DBLα (4 cysteines) subtype-enriched, but unique local repertoire of var-DBL1α sequences by cDNA cloning and sequencing. Next we observed a rapid transcriptional decline of upsA- and upsB-subtype var genes at ring stage through qRT-PCR assays, and a switching event from initial ICAM-I binding to the CD36-binding activity during the first week of adaptive cultivation in vitro. Moreover, predominant transcription of upsA var genes was observed to be correlated with those isolates that showed a higher parasitemia at the time of collection and the ICAM-1-binding phenotype in culture. Taken together, these data indicate that the initial stage of adaptive process in vitro significantly influences the transcription of virulence-related var subtypes and expression of PfEMP1 variants. Further, the specific upregulation of the upsA var genes is likely linked to the rapid propagation of the parasite during natural infection due to the A-type PfEMP1 variant-mediated growth advantages.
Quantifying causal emergence shows that macro can beat micro

Significance Properly characterizing emergence requires a causal approach. Here, we construct causal models of simple systems at micro and macro spatiotemporal scales and measure their causal effectiveness using a general measure of causation [effective information (EI)]. EI is dependent on the size of the system’s state space and reflects key properties of causation (selectivity, determinism, and degeneracy). Although in the example systems the macro mechanisms are completely specified by their underlying micro mechanisms, EI can nevertheless peak at a macro spatiotemporal scale. This approach leads to a straightforward way of quantifying causal emergence as the supersedence of a macro causal model over a micro one. Causal interactions within complex systems can be analyzed at multiple spatial and temporal scales. For example, the brain can be analyzed at the level of neurons, neuronal groups, and areas, over tens, hundreds, or thousands of milliseconds. It is widely assumed that, once a micro level is fixed, macro levels are fixed too, a relation called supervenience. It is also assumed that, although macro descriptions may be convenient, only the micro level is causally complete, because it includes every detail, thus leaving no room for causation at the macro level. However, this assumption can only be evaluated under a proper measure of causation. Here, we use a measure [effective information (EI)] that depends on both the effectiveness of a system’s mechanisms and the size of its state space: EI is higher the more the mechanisms constrain the system’s possible past and future states. By measuring EI at micro and macro levels in simple systems whose micro mechanisms are fixed, we show that for certain causal architectures EI can peak at a macro level in space and/or time. This happens when coarse-grained macro mechanisms are more effective (more deterministic and/or less degenerate) than the underlying micro mechanisms, to an extent that overcomes the smaller state space. Thus, although the macro level supervenes upon the micro, it can supersede it causally, leading to genuine causal emergence—the gain in EI when moving from a micro to a macro level of analysis.
In-Vitro Antagonistic Characteristics of Crude Aqueous and Methanolic Extracts of Garcinia kola (Heckel) Seeds against Some Vibrio Bacteria

The methanolic and aqueous extracts of Garcinia kola seeds were screened for their anti-Vibrio activities against 50 Vibrio isolates obtained from wastewater final effluents in the Eastern Cape Province, South Africa. The crude extracts at 10 mg/mL exhibited appreciable inhibitory activities against most of the test Vibrio isolates, with zones of inhibition ranging from 10–19 mm for methanol extract and 8–15 mm for the aqueous extracts. The minimum inhibitory concentrations (MIC) of the methanol extract varied from 0.313 to 2.5 mg/mL while that for the aqueous extract was 10 mg/mL for all the susceptible Vibrio isolates. Rate of kill assay of the methanolic extracts against three selected Vibrio species showed bacteriostatic activities against all of them achieving 58% and 60% (Vibrio vulnificus AL042); 68% and 69% (Vibrio parahaemolyticus AL049);and 70% and 78% (Vibrio fluvialis AL040) killing of the test bacteria at 3× and 4 ×MIC values, respectively, after 2 h exposure time. We conclude that Garcinia kola seeds hold promise as a potential source of therapeutic compounds of relevance in Vibrio infections management.
Polymorphisms in the coagulation factor VII gene and the risk of myocardial infarction.

BACKGROUND High blood levels of coagulation factor VII are associated with a risk of ischemic vascular disease. Although factor VII levels may be genetically determined, the relation between genetic polymorphisms of factor VII, factor VII blood levels, and the risk of myocardial infarction has not been established. METHODS We performed a case-control study of 165 patients with familial myocardial infarction (mean [+/-SD] age, 55+/-9 years) and 225 controls without a personal or family history of cardiovascular disease (mean age, 56+/-8 years). The polymorphisms involving R353Q and hypervariable region 4 of the factor VII gene were studied. Factor VII clotting activity and antigen levels were also measured. RESULTS Patients with the QQ or H7H7 genotype had a decreased risk of myocardial infarction (odds ratios, 0.08 [95 percent confidence interval, 0.01 to 0.9] and 0.22 [95 percent confidence interval, 0.08 to 0.63], respectively). For the R353Q polymorphism, the RR genotype was associated with the highest risk, followed by the RQ genotype and then by the QQ genotype (P<0.001). For the polymorphism involving hypervariable region 4, the combined H7H5 and H6H5 genotypes were associated with the highest risk, followed in descending order by the H6H6, H6H7, and H7H7 genotypes (P<0.001). Patients with the QQ or H7H7 genotype had lower levels of both factor VII antigen and factor VII clotting activity than those with the RR or H6H6 genotype. Patients with the lowest level of factor VII clotting activity had a lower risk of myocardial infarction than those with the highest level (odds ratio, 0.13; 95 percent confidence interval, 0.05 to 0.34). CONCLUSIONS Our findings suggest that certain polymorphisms of the factor VII gene may influence the risk of myocardial infarction. It is possible that this effect may be mediated by alterations in factor VII levels.
Integrated Assessment and Prediction of Transcription Factor Binding

Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of chromatin binding does not necessarily imply regulation, and binding may be difficult to detect if it is condition or cofactor dependent. To address these challenges, we present an approach for reliably assigning transcription factors (TFs) to target genes that integrates many lines of direct and indirect evidence into a single probabilistic model. Using this approach, we analyze publicly available chIP-chip binding profiles measured for yeast TFs in standard conditions, showing that our model interprets these data with significantly higher accuracy than previous methods. Pooling the high-confidence interactions reveals a large network containing 363 significant sets of factors (TF modules) that cooperate to regulate common target genes. In addition, the method predicts 980 novel binding interactions with high confidence that are likely to occur in so-far untested conditions. Indeed, using new chIP-chip experiments we show that predicted interactions for the factors Rpn4p and Pdr1p are observed only after treatment of cells with methyl-methanesulfonate, a DNA-damaging agent. We outline the first approach for consistently integrating all available evidences for TF–target interactions and we comprehensively identify the resulting TF module hierarchy. Prioritizing experimental conditions for each factor will be especially important as increasing numbers of chIP-chip assays are performed in complex organisms such as humans, for which “standard conditions” are ill defined.
Technical Note: Optical properties of desert aerosol with non-spherical mineral particles: data incorporated to OPAC

Abstract. Mineral particles, in general, are not spheres and so the assumption of spherical particles, instead of more realistic shapes, has significant effects on modeled optical properties and therefore on remote-sensing procedures for desert aerosol and the derived radiative forcing. Thus, in a new version of the database OPAC (Optical Properties of Aerosols and Clouds; Hess et al., 1998), the optical properties of the mineral particles are modeled describing the particles as spheroids with size dependent aspect ratio distributions, but with the size distributions and the spectral refractive indices not changed against the previous version of OPAC. The spheroid assumption is known to substantially improve the scattering functions but pays regard to the limited knowledge on particle shapes in an actual case. The relative deviations of the optical properties of non-spherical mineral particles from those of spherical particles are for the phase function in the solar spectral range up to +60% at scattering angles of about 130° and up to −60% in the backscatter region, but less than 2% for the asymmetry parameter. The deviations are generally small in the thermal infrared and for optical properties that are independent of the scattering angle. The improved version of OPAC (4.0) is freely available at www.rascin. net .
Detecting Null-dereference Bugs via a Backward Analysis

Null dereference is a common occurring bug in programming languages such as C. In this paper, we propose a path-sensitive and context-sensitive approach that performs a backward dataflow analysis to identify null-dereference bugs. One novel feature of our approach is that with the help of aliasing predicates, it can perform strong updates in presence of aliasing, thus eliminating false positives. The aliasing predicates are introduced on the premise of a canonical representation for program being analyzed. Moreover, a context-sensitive algorithm for inter-procedural null-dereference analysis is also presented in this paper, which also contributes to improve accuracy. We have implemented this approach, and give an evaluation of it on a set of open source benchmarks. The experimental results verify the effectiveness of our approach, and show that it is suitable for exploring large real programs with reasonable accuracy.