Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys

ABSTRACT The current perception of evolutionary relationships and the natural diversity of ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA). However, only partial 16S rRNA sequences are available for many AOB species and most AOB have not yet been analyzed on the amoAlevel. In this study, the 16S rDNA sequence data of 10Nitrosomonas species and Nitrosococcus mobiliswere completed. Furthermore, previously unavailable 16S rRNA sequences were determined for three Nitrosomonas sp. isolates and for the gamma-subclass proteobacterium Nitrosococcus halophilus. These data were used to revaluate the specificities of published oligonucleotide primers and probes for AOB. In addition, partial amoA sequences of 17 AOB, including the above-mentioned 15 AOB, were obtained. Comparative phylogenetic analyses suggested similar but not identical evolutionary relationships of AOB by using 16S rRNA and AmoA as marker molecules, respectively. The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB. For 16S rRNA-independent evaluation of AOB species-level diversity in environmental samples, amoA and AmoA sequence similarity threshold values were determined which can be used to tentatively identify novel species based on cloned amoA sequences. Subsequently, 122 amoA sequences were obtained from 11 nitrifying wastewater treatment plants. Phylogenetic analyses of the molecular isolates showed that in all but two plants only nitrosomonads could be detected. Although several of the obtained amoAsequences were only relatively distantly related to known AOB, none of these sequences unequivocally suggested the existence of previously unrecognized species in the wastewater treatment environments examined.
The Minimal Phantom Sector of the Standard Model: Higgs Phenomenology and Dirac Leptogenesis

We propose the minimal, lepton-number conserving, SU(3)c × SU(2)L × U(1)Y gauge-singlet, or phantom, extension of the Standard Model. The extension is natural in the sense that all couplings are of (1) or forbidden due to a phantom sector global U(1)D symmetry, and basically imitates the standard Majorana see-saw mechanism. Spontaneous breaking of the U(1)D symmetry triggers consistent electroweak gauge symmetry breaking only if it occurs at a scale compatible with small Dirac neutrino masses and baryogenesis through Dirac leptogenesis. Dirac leptogenesis proceeds through the usual out-of-equilibrium decay scenario, leading to left and right-handed neutrino asymmetries that do not fully equilibrate after they are produced. The model contains two physical Higgs bosons and a massless Goldstone boson. The existence of the Goldstone boson suppresses the Higgs to bb branching ratio and instead the Higgs bosons will mainly decay to invisible Goldstone and/or to visible vector boson pairs. In a representative scenario, we estimate that with 30 fb−1 integrated luminosity, the LHC could discover this invisibly decaying Higgs, with mass ~ 120 GeV. At the same time a significantly heavier, partner Higgs boson with mass ~ 210 GeV could be found through its vector boson decays. Electroweak constraints as well as astrophysical and cosmological implications are analysed and discussed.
The Influence of Affect, Attitude and Usefulness in the Acceptance of Telemedicine Systems

Grounded in current theories of affect this study examines the role positive and negative moods play on the acceptance of a specialized telemedicine system for microbiology consultation and diagnostics, referred to as telepathology. From a laboratory experiment using microbiology laboratory assistants, the notion that healthcare users’ attitude is an important factor in the acceptance behavior of a healthcare information system is supported. A regression analysis of the data revealed the need to tailor the IS Technology Acceptance Model for the healthcare field. Specifically, our results show that ease of use which is thought to be a main antecedent of end-user acceptance of information technology may not be as important in the healthcare field. The results also indicated that affect is a significant antecedent of attitude and that positive affect is almost as effective in improving users’ attitude toward acceptance of a healthcare information system as the perception of usefulness of the system. In addition, negative affect, while not as powerful as positive affect and usefulness, can significantly and negatively influence a user’s attitude. Those interested in better understanding the adoption of IS within the healthcare industry would most benefit from our findings.
Dynamic networks: models and algorithms

The study of dynamic networks has come into popularity recently, and many models and algorithms for such networks have been suggested. In this column we survey some recent work on dynamic network algorithms, focusing on the effect that model parameters such as the type of adversary, the network diameter, and the graph expansion can have on the performance of algorithms. We focus here on high-level models that are not induced by some specific mobility pattern or geographic model (although much work has gone into geographic models of dynamic networks, and we touch upon them briefly in Section 2). Dynamic network behavior has long been studied in distributed computing literature, but initially it was modeled as a fault in the network; as such, it was typically bounded, either in duration or in the number of nodes affected (or both). For example, in the general omission-fault model, if two nodes that could once communicate can no longer send messages to each other, this is treated as a failure of one of the nodes, and the number of faulty nodes is assumed to be bounded. Another example is self-stabilizing algorithms, which are guaranteed to function correctly only when changes to the network have stopped [16]. These models are appropriate for modeling unreliable static networks, but they are not appropriate for mobile and ad hoc networks, where changes are unbounded in number and occur continually. In the sequel we survey several models for dynamic networks, both random and adversarial, and algorithms for these models. The literature on dynamic networks is vast, and this column is not intended as a comprehensive survey. We have chosen to focus on models and algorithms that exhibit the following properties.
Fetal hemoglobin rich cell therapy to combat adult anemia

Since the first hematopoietic stem cell transplantation in 1989 to treat Fanconi’s anemia, research in cord blood transplantation is currently and predominantly focused on exploiting only the 0.01% of the cord blood component rich in progenitor and stem cells [1]. The rest is often thrown away in the trash or incinerator as biological waste. Since, 1999 the paradigm changed and more and more research is now focused on utilizing the 99.9% of the cord blood and its cellular component. Bhattacharya et al., has reported the first successful HLA randomized, cord blood transfusion in more than 1000 patients suffering from severe anemia at the backdrop of different diseases.
Postpsychiatry and postmodern psychotherapy: Theoretical and ethical issues in mental health care in a Polish context

The article reconstructs postpsychiatry’s core propositions and briefly describes its theoretical background and assumptions. It also presents chosen aspects of postmodern psychotherapy, which seem to be in many ways similar to postpsychiatry’s ideas. Although they are drawn from different inspiration, postpsychiatry and postmodern psychotherapy seem to come to similar conclusions, especially regarding the role of the patient in the therapeutic process, the meaning of psychiatric diagnosis, and the importance of the institutional, cultural, and social contexts in mental health practice and research. The paper also aims to place postpsychiatry and postmodern psychotherapy in a Polish context, focusing on the ethical challenges faced by psychiatry and showing that some of postpsychiatry’s ideas and solutions to contemporary problems were already present in the Polish psychiatric literature of the 20th century. It also contains a brief description of the Polish social and historical context of psychiatry, as well as key aspects of the Polish legal system that relate to mental health and seem to reflect the nature of biomedical explanations of mental distress. It concludes that the model of psychiatric care postulated by “postmodern” approaches seems more ethical and scientifically and philosophically grounded and promises better treatment results than the “traditional” biomedical model.
Internalized Stigma and Psychological Well-Being in Gay Men and Lesbians in Italy and Belgium

Several studies have shown that internalized homophobia is a risk factor for mental health illness in homosexual individuals, whereas the perception of social support is a protective factor for their psychological well-being. In line with those studies, the present research has investigated the levels of internalized homophobia, anxiety, depression and social support, among two groups of gay men and lesbian individuals living in two European countries ( N = 194: 86 Italian and 108 Belgian), where legislations grant different civil rights to lesbian and gay individuals (LG). The main goal of this research has been to verify the possible differences between the two groups. Results showed some significant differences in terms of observed levels of internalized homophobia, which was higher in the Belgian gay men’s group compared to the Italian one. Furthermore, path analysis emphasized the role of social support as a potential factor of mediation between internalized homophobia and mental health.
Investment, Protection, Ownership, and the Cost of Capital

We investigate the cost of capital in a model with an agency conflict between inside managers and outside shareholders. Inside ownership reflects the classic tradeoff between incentives and risk diversification, and the severity of agency costs depends on a parameter representing investor protection. In equilibrium, the marginal cost of capital is a weighted average of terms reflecting both idiosyncratic and systematic risk, and weaker investor protection increases the weight on idiosyncratic risk. Using firm-level data from 38 countries, we estimate the predicted relationships among investor protection, inside ownership, and the marginal cost of capital. We discuss implications for the determinants of firm size, the relationship between Tobin's Q and ownership, and the effect of financial liberalizations.
Glycopeptide Resistance in Gram-Positive Cocci: A Review

Vancomycin-resistant enterococci (VRE) have emerged as important nosocomial pathogens in the past two decades all over the world and have seriously limited the choices available to clinicians for treating infections caused by these agents. Methicillin-resistant Staphylococcus aureus, perhaps the most notorious among the nosocomial pathogens, was till recently susceptible to vancomycin and the other glycopeptides. Emergence of vancomycin nonsusceptible strains of S. aureus has led to a worrisome scenario where the options available for treating serious infections due to these organisms are very limited and not well evaluated. Vancomycin resistance in clinically significant isolates of coagulase-negative staphylococci is also on the rise in many setups. This paper aims to highlight the genetic basis of vancomycin resistance in Enterococcus species and S. aureus. It also focuses on important considerations in detection of vancomycin resistance in these gram-positive bacteria. The problem of glycopeptide resistance in clinical isolates of coagulase-negative staphylococci and the phenomenon of vancomycin tolerance seen in some strains of Streptococcus pneumoniae has also been discussed. Finally, therapeutic options available and being developed against these pathogens have also found a mention.
Symplectic Homogenization

Let $H(q,p)$ be a Hamiltonian on $T^*T^n$. We show that the sequence $H_{k}(q,p)=H(kq,p)$ converges for the $\gamma$ topology defined by the author, to $\bar{H}(p)$. This is extended to the case where only some of the variables are homogenized, that is the sequence $H(kx,y,q,p)$ where the limit is of the type ${\bar H}(y,q,p)$ and thus yields an"effective Hamiltonian". We give here the proof of the convergence, and the first properties of the homogenization operator, and give some immediate consequences for solutions of Hamilton-Jacobi equations, construction of quasi-states, etc. We also prove that the function $\bar H$ coincides with Mather's $\alpha$ function which gives a new proof of its symplectic invariance proved by P. Bernard. A previous version of this paper relied on the former"On the capacity of Lagrangians in $T^*T^n$ which has been withdrawn. The present version of Symplectic Homogenization does not rely on it anymore.
Warlpiri Wh-Scope Marking

This article analyses the wh-scope-marking construction in Warlpiri. The literature on wh-scope-marking constructions in other languages debates the relative merits of two types of analyses—the direct-dependency account, which posits covert movement of an embedded wh-phrase to replace a matrix expletive, and the indirect-dependency account, which treats the embedded question as the restriction of a matrix wh-phrase. I argue that an explanation of the Warlpiri data can only be achieved through a variant of the indirect-dependency approach.
The Determinants of Corporate Leverage: A Panel Data Analysis

Widespread increases in corporate leverage occurred over the 1980s in Australia. There was also considerable variation in leverage across firms. This paper uses a sample of 209 firms, observed annually between 1973 and 1991, to explore both cross-sectional and time variation in financial structure. The paper begins with a survey of the literature on corporate financial structure. This leads to a model that incorporates the major determinants of leverage. The empirical model takes into account the influence of both firm-specific and time-specific effects. The dynamics of leverage are also tentatively explored. The results suggest that a number of firm-related factors influence the relative costs of debt, the level of demand for and the availability of funds. Most important among these are firm size, growth, collateral and cash flow. A number of macro-economic variables are also found to influence leverage. Most important among these are real asset prices which play a significant role in the post-financial deregulation period.
Geometry based mapping strategies for PDE computations

In this paper we formulate new mapping strategies for partial differential equations (PDE) computations into MIMD architectures. These mappings are based on decompositions of the geometric data (meshes) associated with the PDE domain, and distribute the solution of large linear systems across many parallel processors in such a way that the processor workload is balanced and the synchronization / communication cost among them is a minimal. For the allocation of computations associated with each subdomain to individual processors, we use an intermediate 2-D Euclidean space to represent the decomposition graph of the computation and the topology of the architecture. Then correlation between subdomains and processors is pursued according to a number of performance criteria and iterative improvement techniques. ated with the PDE domain, the discrete algebraic equations associated with some discretization of the PDE equations, and the data flow graph of the PDE solver. In this paper we study mapping techniques formulated at the geometric data structures of the PDE problem. Mapping approaches formulated on other levels have been studied in [Fox 86], [Sada 87], [Pomm 90], [Ayka 88] and [Hous 87, 90 b]. The mapping met hodology employed in this paper consists of two phases: the partitioning and allocation. In the partitioning phase we decompose the geometric data structures (meshes) to a prespecified number (usually equal to the number of processors) of sub domains or substructures such that the following criteria are approximately satisfied: (i) the subdomains have approximately the same number of elements (finite element meshes) or grid points (grids),
First-Generation Versus Second-Generation Drug-Eluting Stents in Coronary Chronic Total Occlusions: Two-Year Results of a Multicenter Registry

Background Limited data are available regarding the long-term clinical outcomes of second-generation drug-eluting stents (DES) versus first-generation DES in patients with coronary chronic total occlusion (CTO) who undergo percutaneous coronary intervention (PCI). The aim of this study was to compare the clinical outcomes of second-generation DES with those of first-generation DES for the treatment of CTO. Methods and Results Between March 2003 and February 2012, 1,006 consecutive patients with CTO who underwent successful PCI using either first-generation DES (n = 557) or second-generation DES (n = 449) were enrolled in a multicenter, observational registry. Propensity-score matching was also performed. The primary outcome was cardiac death over a 2-year follow-up period. No significant differences were observed between the two groups regarding the incidence of cardiac death (first-generation DES versus second-generation DES; 2.5% vs 2.0%; hazard ratio [HR]: 0.86; 95% confidence interval [CI]: 0.37 to 1.98; p = 0.72) or major adverse cardiac events (MACE, 11.8% vs 11.4%; HR: 1.00; 95% CI: 0.67 to 1.50; p = 0.99). After propensity score matching, the incidences of cardiac death (HR: 0.86; 95% CI: 0.35 to 2.06; p = 0.86) and MACE (HR: 0.93; 95% CI: 0.63 to 1.37; p = 0.71) were still similar in both groups. Furthermore, no significant differences were observed between sirolimus-eluting, paclitaxel-eluting, zotarolimus-eluting, and everolimus-eluting stents regarding the incidence of cardiac death or MACE. Conclusion This study shows that the efficacy of second-generation DES is comparable to that of first-generation DES for treatment of CTO over 2 years of follow-up.
Weighing the cusp at the Galactic Centre

As stars close to the galactic centre have short orbital periods it has been possible to trace large fractions of their orbits in the recent years. Previously the data of the orbit of the star S2 have been fitted with Keplerian orbits corresponding to a massive black hole (MBH) with a mass of MBH = 3–4 × 106M⊙ implying an insignificant cusp mass. However, it has also been shown that the central black hole resides in a ∼1″ diameter stellar cluster of a priori unknown mass. In a spherical potential which is neither Keplerian nor harmonic, orbits will precess resulting in inclined rosetta shaped trajectories on the sky. In this case, the assumption of non-Keplerian orbits is a more physical approach. It is also the only approach through which cusp mass information can be obtained via stellar dynamics of the cusp members. This paper presents the first exemplary modelling efforts in this direction. Using positional and radial data of star S2, we find that there could exist an unobserved extended mass component of several 105M⊙ forming a so-called ‘cusp’ centered on the black hole position. Considering only the fraction of the cusp mass M within the apo-center of the S2 orbit we find as an upper limit that M/(MBH + M) ≤ 0.05. A large extended cusp mass, if present, is unlikely to be composed of sub-solar mass constituents, but could be explained rather well by a cluster of high M/L stellar remnants, which we find to form a stable configuration. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
No Direct Association Between Asthma and the Microbiome Based on Currently Available Techniques

AbstractCurrent uses of culture-independent tools in previous studies have shown a significant relationship between microbiota and asthma. Although these studies are relatively new, there is also evidence of the possibility of new therapeutic strategies for the treatment or prevention of asthma.This article retrospectively examines the possible association between microorganisms and asthma.Data on all patients with different types of asthma were collected from hospital charts from the Department of Internal Medicine, Saarland University Medical Center, Germany, within the study period of 2011 to 2012.The tracheal secretions of asthmatics obtained by bronchoalveolar lavage, bronchial aspirates through flexible bronchoscopy, and directly in sputum were examined microbiologically for microorganisms. Thirty-one (10.47%, 95% CI, 6.98–13.96) of a total of 296 patients were found to have asthma microorganisms in their airways. We could not establish a causal relationship between microorganisms and asthma based on the results of our study (P = 0.893). Additionally, acute respiratory infections did not affect the microbiological colonization in asthmatics’ airways (P = 0.472). We were unable to find a direct association between asthma and the microbiome based on existing diagnostic techniques.
Cerebellar Cortical Molecular Layer Inhibition Is Organized in Parasagittal Zones

Molecular layer inhibitory interneurons generate on-beam and off-beam inhibition in the cerebellar cortex that is hypothesized to control the timing and/or spatial patterning of Purkinje cell discharge. On- and off-beam inhibition has been assumed to be spatially uniform and continuous within a folium. Using flavoprotein autofluorescence optical imaging in the mouse cerebellar cortex in vivo, this study demonstrates that the inhibition evoked by parallel fiber and peripheral stimulation results in parasagittal bands of decreases in fluorescence that correspond to zebrin II-positive bands. The parasagittal bands of decreased fluorescence are abolished by GABAA antagonists and reflect the activity of molecular layer interneurons on their targets. The same banding pattern was observed using Ca2+ imaging. The bands produce spatially specific decreases in the responses to peripheral input. Therefore, molecular layer inhibition is compartmentalized into zebrin II parasagittal domains that differentially modulate the spatial pattern of cerebellar cortical activity.