Miracle-dz/UniFAR-FTUs huggingface dataset:
Geographical Constraints Are Stronger than Invasion Patterns for European Urban Floras

Understanding the mechanisms that affect invasion success of alien species is an important prerequisite for the effective management of present and future aliens. To gain insight into this matter we asked the following questions: Are the geographical patterns of species distributions in urban floras different for native compared with alien plant species? Does the introduction of alien species contribute to the homogenization of urban floras? We used a Mantel test on Jaccard dissimilarity matrices of 30 urban floras across the British Isles, Italy and central Europe to compare the spatial distribution of native species with four classes of alien species: archaeophytes, all neophytes, non-invasive neophytes, and invasive neophytes. Archaeophytes and neophytes are species that were introduced into Europe before and after 1500 AD, respectively. To analyze the homogenizing effect of alien species on the native urban floras, we tested for differences in the average dissimilarity of individual cities from their group centroid in ordination space. Our results show that the compositional patterns of native and alien species seem to respond to the same environmental drivers, such that all four classes of alien species were significantly related to native species across urban floras. In this framework, alien species may have an impact on biogeographic patterns of urban floras in ways that reflect their history of introduction and expansion: archaeophytes and invasive neophytes tended to homogenize, while non-invasive neophytes tended to differentiate urban floras.
Hierarchical model reduction of nonlinear partial differential equations based on the adaptive empirical projection method and reduced basis techniques

In this paper we extend the hierarchical model reduction framework based on reduced basis techniques recently introduced in [M. Ohlberger and K. Smetana, SIAM J. Sci. Comput. 36 (2014) A714–A736] for the application to nonlinear partial differential equations. The major new ingredient to accomplish this goal is the introduction of the adaptive empirical projection method, which is an adaptive integration algorithm based on the (generalized) empirical interpolation method [M. Barrault, et al. , C. R. Math. Acad. Sci. Paris Series I 339 (2004) 667–672; Y. Maday and O. Mula, A generalized empirical interpolation method: Application of reduced basis techniques to data assimilation. In Analysis and Numerics of Partial Differential Equations . Vol. 4 of Springer INdAM Series . Springer Milan (2013) 221–235]. Different from other partitioning concepts for the empirical interpolation method we perform an adaptive decomposition of the spatial domain. We project both the variational formulation and the range of the nonlinear operator onto reduced spaces. Those reduced spaces combine the full dimensional (finite element) space in an identified dominant spatial direction and a reduction space or collateral basis space spanned by modal orthonormal basis functions in the transverse direction. Both the reduction and the collateral basis space are constructed in a highly nonlinear fashion by introducing a parametrized problem in the transverse direction and associated parametrized operator evaluations, and by applying reduced basis methods to select the bases from the corresponding snapshots. Rigorous a priori and a posteriori error estimators, which do not require additional regularity of the nonlinear operator are proven for the adaptive empirical projection method and then used to derive a rigorous a posteriori error estimator for the resulting hierarchical model reduction approach. Numerical experiments for an elliptic nonlinear diffusion equation demonstrate a fast convergence of the proposed dimensionally reduced approximation to the solution of the full-dimensional problem. Runtime experiments verify a close to linear scaling of the reduction method in the number of degrees of freedom used for the computations in the dominant direction.
Imatinib and hydroxyurea in pretreated progressive glioblastoma multiforme: a patient series.

BACKGROUND Grade IV malignancies of the brain, such as glioblastoma multiforme (GBM), are associated with a dismal prognosis. Autocrine and paracrine loops of platelet-derived growth factor (PDGF) signaling, as well as other signal transduction pathways, have been postulated to play a role in glioblastoma transformation, and molecules involved in these pathways can potentially serve as targets for therapeutic inhibitory agents. Imatinib, an inhibitor of PDGF receptors alpha and beta, as well as other selected tyrosine kinases, is indicated for treatment of chronic myelogenous leukemia (CML) and gastrointestinal stromal tumor (GIST). Unfortunately, imatinib, as with many conventional chemotherapeutic agents, has limited efficacy as monotherapy in GBM. In preclinical studies, the chemotherapeutic agent hydroxyurea is demonstrated to have cytotoxic effects additive with imatinib. PATIENTS AND METHODS We tested the combination of hydroxyurea and imatinib in 30 grade IV progressive GBM patients refractory to chemo- and radiotherapy. All 30 patients were evaluable after a median 19 weeks observation time. RESULTS Combination therapy with imatinib and hydroxyurea resulted in a 20% response rate, including complete and partial responses. Patients experiencing response or stable disease yielded a combined clinical benefit rate of 57%. Median time to progression was 10 weeks and median overall survival was 19 weeks. Three patients continue to survive on combination therapy, with the shortest duration being 106 weeks. Six-month and 2-year progression-free survival rates were 32% and 16%, respectively. CONCLUSION The efficacy results, combined with findings that imatinib and hydroxyurea were well tolerated, suggest that this combination shows promise as therapy for GBM.
Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of Caenorhabditis elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture. DOI: http://dx.doi. org/10.7554/eLife.09178. 001
The Flagellar Cytoskeleton of the Spirochetes

The recent discoveries of prokaryotic homologs of all three major eukaryotic cytoskeletal proteins (actin, tubulin, intermediate filaments) have spurred a resurgence of activity in the field of bacterial morphology. In spirochetes, however, it has long been known that the flagellar filaments act as a cytoskeletal protein structure, contributing to their shape and conferring motility on this unique phylum of bacteria. Therefore, revisiting the spirochete cytoskeleton may lead to new paradigms for exploring general features of prokaryotic morphology. This review discusses the role that the periplasmic flagella in spirochetes play in maintaining shape and producing motility. We focus on four species of spirochetes: Borrelia burgdorferi, Treponema denticola, Treponema phagedenis and Leptonema (formerly Leptospira) illini. In spirochetes, the flagella reside in the periplasmic space. Rotation of the flagella in the above species by a flagellar motor induces changes in the cell morphology that drives motility. Mutants that do not produce flagella have a markedly different shape than wild-type cells.
On the prospects for testing the Dvali–Gabadadze–Porrati gravity model with the outer planets of the Solar System

The multidimensional braneworld gravity model proposed by Dvali, Gabadadze and Porrati was primarily put forward to explain the observed acceleration of the expansion of the Universe without resorting to dark energy. One of the most intriguing features of such a model is that it also predicts small effects on the orbital motion of test particles, which could be tested in such a way that local measurements at Solar System scales would allow us to get information on the global properties of the Universe. Lue and Starkman derived a secular extra-perihelion ω precession of 5 × 10−4 arcsec per century, while Iorio showed that the mean longitude λ is affected by a secular precession of about 10−3 arcsec per century. Up to now, the observational efforts have focused on the dynamics of the inner planets of the Solar System whose orbits are the best known via radar ranging. Since the competing Newtonian and Einsteinian effects reduce with increasing distances, it would be possible to argue that an analysis of the orbital dynamics of the outer planets of the Solar System, with particular emphasis on Saturn because of the ongoing Cassini mission with its precision ranging instrumentation, could be helpful in evidencing the predicted new features of motion. In this paper we investigate this possibility by comparing both analytical and numerical calculations with the latest results in the planetary ephemeris field. Unfortunately, the current level of accuracy rules out this appealing possibility.
Trace: Tennessee Research and Creative Exchange

Escherichia coli O157:H7 is a potentially fatal foodborne pathogen with a putative reservoir for human infection in feedlot cattle. In order to more effectively identify targets for intervention strategies, we aimed to (1) assess the role of various feedlot habitats in E. coli O157:H7 propagation and (2) provide a framework for examining the relative contributions of animals and the surrounding environment to observed pathogen dynamics. To meet these goals we developed a mathematical model based on an ecological metapopulation framework to track bacterial population dynamics inside and outside the host. We used E. coli O157:H7 microbiological and epidemiological literature to characterize E. coli O157:H7 habitats at the pen level and account for E. coli O157:H7 population processes in water troughs, feedbunks, cattle hosts, and pen floors in the model. Simulations indicated that E. coli O157:H7 was capable of maintaining viable populations in the feedlot without net growth in the cattle gastro-intestinal tract, suggesting E. coli O157:H7 may not always act as an obligate parasite. Water troughs and contaminated pen floors appeared to be particularly influential sources driving E. coli O157:H7 population dynamics and thus would serve as prime environmental targets for interventions to effectively reduce the E. coli O157:H7 load at the pen level.
The University of the East-Ramon Magsaysay Memorial Medical Centre Inc. medical students' perception of the objective structured examination in pharmacology as an assessment tool

The teaching of pharmacology prepares the medical sophomore to prescribe drugs on a rational basis. In small group discussions (SGDs), the evaluation of individual competence poses a challenge. Hence, the Objective Structured Examination in Pharmacology (OSEP) was initiated, to provide an additional, objective means of assessing individual performance. The OSEP is an oral, time-bound, one-on-one examination given at the end of the course, designed with a rubric for scoring. The aim of this study was to determine the students’ perceptions of the OSEP as an assessment tool. A survey was conducted on all Pharmacology students of school year 2016-’17 as a post-activity evaluation for curricular improvement. After the approval of the institutional ethics review board was obtained, the data was collected retrospectively. The responses of participants who gave their informed consent were included in the study. The students' perceptions were based on the level of agreement to sixteen statements, using a Likert Scale. The median score for each statement and the proportion with positive perception were computed. The positive perception was operationally defined based on a pre-determined median score. A total of 414 students participated in the study. The mean response rate was 99% and the median score for all statements revealed that 88%, 93% and 94% have a positive perception of the effectiveness, content and conduct of the OSEP, respectively. In conclusion, the medical students perceived the OSEP as an effective assessment tool that can provide an additional, objective means of evaluating individual performance in the course.
Learning Rough Set Classifiers from Gene Expressions and Clinical Data

Biological research is currently undergoing a revolution. With the advent of microarray technology the behavior of thousands of genes can be measured simultaneously. This capability opens a wide range of research opportunities in biology, but the technology generates a vast amount of data that cannot be handled manually. Computational analysis is thus a prerequisite for the success of this technology, and research and development of computational tools for microarray analysis are of great importance. One application of microarray technology is cancer studies where supervised learning may be used for predicting tumor subtypes and clinical parameters. We present a general Rough Set approach for classification of tumor samples analyzed with microarrays. This approach is tested on a data set of gastric tumors, and we develop classifiers for six clinical parameters. One major obstacle in training classifiers from microarray data is that the number of objects is much smaller that the number of attributes. We therefore introduce a feature selection method based on bootstrapping for selecting genes that discriminate significantly between the classes, and study the performance of this method. Moreover, the efficacy of several learning and discretization methods implemented in the ROSETTA system [18] is examined. Their performance is compared to that of linear and quadratic discrimination analysis. The classifiers are also biologically validated. One of the best classifiers is selected for each clinical parameter, and the connection between the genes used in these classifiers and the parameters are compared to the establish knowledge in the biomedical literature.
Evidence for Consistent Intragenic and Intergenic Interactions between SNP Effects in the APOA1/C3/A4/A5 Gene Cluster

Objective: Evaluate the consistency of the contribution of interactions between single nucleotide polymorphism (SNP) genotype effects to variation in measures of lipid metabolism across ethnic strata within gender. Methods and Results: We considered 80 SNPs within the apolipoprotein (APO) A1/C3/A4/A5 gene cluster using an over-parameterized general linear model to identify SNPs whose genotype effects combine non-additively to influence plasma levels of high density lipoprotein cholesterol (HDL-C), total cholesterol (TC) and triglycerides (TG) in a consistent manner across ethnic strata. We analyzed population-based samples of unrelated 18 to 30 year old African-Americans (n = 1,858) and European-Americans (n = 1,973) ascertained without regard to health at four field centers (Birmingham, Ala.; Chicago, Ill.; Minneapolis, Minn. and Oakland, Calif., USA) by the Coronary Artery Risk Development in Young Adults (CARDIA) study. To identify which SNP genotype effects combine non-additively we used a two-tier analysis strategy. We first required that pairs of SNPs show statistically significant non-additivity in both ethnic strata within a gender, where experiment-wise significance was evaluated using a permutation test to determine the probability of observing the number of tests significant in both ethnic strata by chance alone. Second, we required no significant evidence of heterogeneity of the relationship between the phenotype and the two SNP genotypes across ethnic strata and across field centers within each ethnic group. From this strategy we identified ten pairs of SNPs, involving thirteen SNPs, that displayed statistically significant non-additivity of SNP genotype effects on TC. Only one of these thirteen SNPs had statistically significant genotype effects that were consistent across samples. Conclusion: Our analyses suggest that ignoring the contribution of interactions between SNP genotype effects when modeling multi-SNP genotype-phenotype relationships may result in an underestimate of the contribution of genetic variation to variation in quantitative cardiovascular disease (CVD) risk factor traits.
Infrastructuring European migration and border control: The logistics of registration and identification at Moria hotspot

This paper examines Moria hotspot in Greece as a logistical site which fulfills two different functions within the European migration and border regime. It locates, contains, and sorts individuals locally at the external borders of the EU and creates, inserts, and processes data for controlling people on the move. Based on ethnographic fieldwork in Greece, including interviews with local administrators from the Registration and Identification Service, Médecins du Monde, Frontex and Hellenic Police and a collection of internal and publicly available planning, policy, and management documents and handbooks, the paper scrutinizes how both the movement of migrants and data is organized at the site. By developing an analytic lens of logistics, it outlines a specific mode of infrastructuring which aligns staff from different organizations with databases, devices, and migrants all in one place and organizes mundane practices such as filling out forms, taking fingerprints, signing, and entering datasets along a chain. That way the hotspot is able to locate, sort, and detain those who arrive at the hardened EU border and to create a data infrastructure for controlling, monitoring, and governing further movement by processing data through the bureaucratic channels of the EU’s transnational control assemblages.
Postmenopausal hormone therapy and Alzheimer disease

Objective: To explore the association between postmenopausal hormone therapy (HT) and Alzheimer disease (AD). Methods: Twenty-year follow-up data from the Kuopio Osteoporosis Risk Factor and Prevention study cohort were used. Self-administered questionnaires were sent to all women aged 47–56 years, residing in Kuopio Province starting in 1989 until 2009, every 5th year. Register-based information on HT prescriptions was available since 1995. Probable AD cases, based on DSM-IV and National Institute of Neurological and Communicative Disorders and Stroke–Alzheimer's Disease and Related Disorders Association criteria, were identified from the special reimbursement register (1999–2009). The study population included 8,195 women (227 cases of incident AD). Results: Postmenopausal estrogen use was not associated with AD risk in register-based or self-reported data (hazard ratio/95% confidence interval 0.92/0.68–1.2, 0.99/0.75–1.3, respectively). Long-term self-reported postmenopausal HT was associated with reduced AD risk (0.53/0.31–0.91). Similar results were obtained with any dementia diagnosis in the hospital discharge register as an outcome. Conclusions: Our results do not provide strong evidence for a protective association between postmenopausal HT use and AD or dementia, although we observed a reduced AD risk among those with long-term self-reported HT use.
new Scala() instance of Java: a comparison of the memory behaviour of Java and Scala programs

While often designed with a single language in mind, managed runtimes like the Java virtual machine (JVM) have become the target of not one but many languages, all of which benefit from the runtime's services. One of these services is automatic memory management. In this paper, we compare and contrast the memory behaviour of programs written in Java and Scala, respectively, two languages which both target the same platform: the JVM. We both analyze core object demographics like object lifetimes as well as secondary properties of objects like their associated monitors and identity hash-codes. We find that objects in Scala programs have lower survival rates and higher rates of immutability, which is only partly explained by the memory behaviour of objects representing closures or boxed primitives. Other metrics vary more by benchmark than language.
Growth and structural change: trends, patterns and policy options

On of the most researched topics in recent growth theory if the issue of convergence of productivity levels (e.g., Bernard and Jones, 1996, Benhabib and Spiegel, 1994, to name only a few of the many recent contributions). Mainstream economic theory (under which I will group both the old Solowian tradition, and the new growth models) traditionally attributes convergence to 'transitional dynamics', Le. , the fact that countries have not yet reached the steady state growth path that is predicted by these theories. Investment in capital goods is the main vehicle for convergence in this case, because countries with low capital-labour ratios will have high marginal returns to investment, and hence grow rapidly. In a different set of theories that are known as 'technology gap' theories (Fagerberg, 1994), convergence is caused by the international diffusion of technological knowledge.
Cosmological simulations of galaxy clusters with feedback from active galactic nuclei : profiles and scaling relations.

We present results from a new set of 30 cosmological simulations of galaxy clusters, including the effects of radiative cooling, star formation, supernova feedback, black hole growth and AGN feedback. We first demonstrate that our AGN model is capable of reproducing the observed cluster pressure profile at redshift, z ≃ 0, once the AGN heating temperature of the targeted particles is made to scale with the final virial temperature of the halo. This allows the ejected gas to reach larger radii in higher mass clusters than would be possible had a fixed heating temperature been used. Such a model also successfully reduces the star formation rate in brightest cluster galaxies and broadly reproduces a number of other observational properties at low redshift, including baryon, gas and star fractions, entropy profiles outside the core and the X-ray luminosity–mass relation. Our results are consistent with the notion that the excess entropy is generated via selective removal of the densest material through radiative cooling; supernova and AGN feedback largely serve as regulation mechanisms, moving heated gas out of galaxies and away from cluster cores. However, our simulations fail to address a number of serious issues; for example, they are incapable of reproducing the shape and diversity of the observed entropy profiles within the core region. We also show that the stellar and black hole masses are sensitive to numerical resolution, particularly the gravitational softening length; a smaller value leads to more efficient black hole growth at early times and a smaller central galaxy.
Chemically Modulated Graphene Diodes

We report the manufacture of novel graphene diode sensors (GDS), which are composed of monolayer graphene on silicon substrates, allowing exposure to liquids and gases. Parameter changes in the diode can be correlated with charge transfer from various adsorbates. The GDS allows for investigation and tuning of extrinsic doping of graphene with great reliability. The demonstrated recovery and long-term stability qualifies the GDS as a new platform for gas, environmental, and biocompatible sensors.