Miracle-dz/UniFAR-FTUs huggingface dataset:
Shewanella oneidensis MR-1-Induced Fe(III) Reduction Facilitates Roxarsone Transformation

Although microbial activity and associated iron (oxy)hydroxides are known in general to affect the environmental dynamics of 4-hydroxy-3-nitrobenzenearsonic acid (roxarsone), the mechanistic understanding of the underlying biophysico-chemical processes remains unclear due to limited experimental information. We studied how Shewanella oneidensis MR-1 –a widely distributed metal-reducing bacterium, in the presence of dissolved Fe(III), affects roxarsone transformations and biogeochemical cycling in a model aqueous system. The results showed that the MR-1 strain was able to anaerobically use roxarsone as a terminal electron acceptor and to convert it to a single product, 3-amino-4-hydroxybenzene arsonic acid (AHBAA). The presence of Fe(III) stimulated roxarsone transformation via MR-1-induced Fe(III) reduction, whereby the resulting Fe(II) acted as an efficient reductant for roxarsone transformation. In addition, the subsequent secondary Fe(III)/Fe(II) mineralization created conditions for adsorption of organoarsenic compounds to the yielded precipitates and thereby led to arsenic immobilization. The study provided direct evidence of Shewanella oneidensis MR-1-induced direct and Fe(II)-associated roxarsone transformation. Quantitative estimations revealed a candidate mechanism for the early-stage environmental dynamics of roxarsone in nature, which is essential for understanding the environmental dynamics of roxarsone and successful risk assessment.
The role of heritage attractions in sustainable tourism strategies: the experience in Ireland.

Abstract Ireland, located on the north‐west periphery of Europe, illustrates all the difficulties of a small, marginal, island economy. It is an ancient landscape rich in heritage and cultural features. Tourism is now a vital part of the Irish economy and recent research has demonstrated that ‘Irishness’. whilst difficult to define, is the major appeal to overseas visitors. In 1989 the Irish Government challenged Bord Failte (the Irish Tourist Board) to double revenue from overseas tourists and create 25,000 new jobs. Heritage attractions formed a fundamental feature of Bord Failte's Framework Plan for Tourism. The methodology adopted for the development and interpretation of heritage attractions is evaluated in this paper, together with an assessment of the outcomes of the strategy. This particular initiative is discussed in the context of sustainable tourism strategies.
Mutation and the experimental evolution of outcrossing in Caenorhabditis elegans

An understanding of the forces that contribute to the phylogenetically widespread phenomenon of sexual reproduction has posed a longstanding problem in evolutionary biology. Mutational theories contend that sex can be maintained when the deleterious mutation rate is sufficiently high, although empirical evidence is equivocal and experimental studies are rare. To test the influence of mutation on the evolution of obligate outcrossing, I introduced a genetic polymorphism for breeding system into populations of the nematode Caenorhabditis elegans with high‐ and low‐mutation rate genetic backgrounds and tracked the change in frequency of females, hermaphrodites, and males over approximately 21 generations. Hermaphrodites invaded all populations, regardless of mutational background. However, experimental populations with elevated mutation rates experienced more outcrossing and greater retention of females. This provides experimental evidence consistent with deleterious mutational explanations for the evolution of sex in principle, but the action of other processes is required to explain the evolution of sex in entirety.
The Role of Stress and Position in Determining First Words

The possibility that perceptual predispositions may assist young language learners in the initial identification of words in speech was investigated in a corpus of early words. The specific predispositions investigated included tendencies to attend to and extract stressed and final syllables. A total of 616 productions with multisyllabic adult targets were collected from three children at the one-word stage of language acquisition. These utterances were phonetically transcribed and coded, in relation to the adult target word, for omissions and accuracy of syllables. Results provided support for two predictions: Syllables that were stressed or final in the adult target word were (a) omitted much less frequently and (b) produced more accurately than were unstressed, nonfinal syllables. These results are consistent with the view that syllables that are stressed or final in adult speech are particularly salient to young children and, consequently, are particularly likely to be extracted and included in first .
Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids

The interactions of the human double-stranded RNA-binding zinc finger protein JAZ with RNA or DNA were investigated using electrophoretic mobility-shift assays, isothermal calorimetry, and nuclear magnetic resonance spectroscopy. Consistent with previous reports, JAZ has very low affinity for duplex DNA or single-stranded RNA, but it binds preferentially to double-stranded RNA (dsRNA) with no detectable sequence specificity. The affinity of JAZ for dsRNA is unaffected by local structural features such as loops, overhangs, and bulges, provided a sufficient length of reasonably well-structured A-form RNA (about 18 bp for a single zinc finger) is present. Full-length JAZ contains four Cys2His2 zinc fingers (ZF1–4) and has the highest apparent affinity for dsRNA; two-finger constructs ZF12 and ZF23 have lower affinity, and ZF34 binds even more weakly. The fourth zinc finger, ZF4, has no measurable RNA-binding affinity. Single zinc finger constructs ZF1, ZF2, and ZF3 show evidence for multiple-site binding on the minimal RNA. Fitting of quantitative NMR titration and isothermal calorimetry data to a two-site binding model gave Kd1 ∼ 10 μM and Kd2 ∼ 100 μM. Models of JAZ–RNA complexes were generated using the high-ambiguity-driven biomolecular docking (HADDOCK) program. Single zinc fingers bind to the RNA backbone without sequence specificity, forming complexes with contacts between the RNA minor groove and residues in the N-terminal β strands and between the major groove and residues in the helix–kink–helix motif. We propose that the non-sequence-specific interaction between the zinc fingers of JAZ with dsRNA is dependent only on the overall shape of the A-form RNA.
Transition to Adulthood for Vulnerable Youths: A Review of Research and Implications for Policy

Adolescents aging out of the child welfare system are particularly vulnerable to poor health, undereducation, unemployment, and homelessness; yet, they have not received sufficient research or policy attention. This article reviews what is known about these young people and the impact of independent living programming on youth outcomes. It also examines research on life transition, resilience, and social support. This research underscores the importance of continued family and community support to foster individual development, even after young people leave home. This article identifies from this research broader ideas for helping vulnerable youths transition successfully.
Inverse Problems with Invariant Multiscale Statistics

We propose a new approach to linear ill-posed inverse problems. Our algorithm alternates between enforcing two constraints: the measurements and the statistical correlation structure in some transformed space. We use a non-linear multiscale scattering transform which discards the phase and thus exposes strong spectral correlations otherwise hidden beneath the phase fluctuations. As a result, both constraints may be put into effect by linear projections in their respective spaces. We apply the algorithm to super-resolution and tomography and show that it outperforms ad hoc convex regularizers and stably recovers the missing spectrum.
Physical Self-Efficacy and Depressive Symptomatology in Older Women: A Group Treatment Approach

This article presents an outline of a practice model geared toward alleviating depressive symptomatology in older women. Based in Bandura's (1977) self-efficacy theory, and on empirical data reported in this article, the focus of the practice model is on physical self-efficacy as a cognitive mediator of depressive symptoms in older women. Through the use of a group treatment approach, an attempt is made to raise levels of physical self-efficacy, and to determine the concomitant changes in depressive symptoms. Finally, the importance of continued research, and the further refinement of practice methods based in theory is stressed.
The Effect of Mianserin on Alpha-2 Adrenergic Receptor Function in Depressed Patients

Summary Recent clinical investigations have shown that long term treatment with the tricyclic antidepressants desipramine and amitriptyline reduces the sensitivity of the alpha-2 adrenergic autoreceptor. In order to determine whether the tetracyclic antidepressant mianserin also has this action, the effect of clonidine, an alpha-2 adrenergic receptor agonist, on plasma levels of the norepinephrine metabolite 3-methoxy-4-hydroxyphenlethyleneglycol (MHPG), blood pressure, and patient-rated sedation were measured in fifteen depressed patients before and during mianserin treatment. Postsynaptic alpha-2 adrenergic receptor function was assessed by measuring the growth hormone response to clonidine before and during treatment. Mianserin had little or no effect on the ability of clonidine to lower plasma MHPG and blood pressure, and to increase sedation and growth hormone secretion. The findings of this investigation indicates that long term mianserin treatment does not produce significant subsensitivity of the alpha-2 adrenergic receptor and suggests that a reduction in alpha-2 adrenergic autoreceptor sensitivity is not a necessary action for all effective antidepressant treatments.
Production of Chitooligosaccharides and Their Potential Applications in Medicine

Chitooligosaccharides (CHOS) are homo- or heterooligomers of N-acetylglucosamine and D-glucosamine. CHOS can be produced using chitin or chitosan as a starting material, using enzymatic conversions, chemical methods or combinations thereof. Production of well-defined CHOS-mixtures, or even pure CHOS, is of great interest since these oligosaccharides are thought to have several interesting bioactivities. Understanding the mechanisms underlying these bioactivities is of major importance. However, so far in-depth knowledge on the mode-of-action of CHOS is scarce, one major reason being that most published studies are done with badly characterized heterogeneous mixtures of CHOS. Production of CHOS that are well-defined in terms of length, degree of N-acetylation, and sequence is not straightforward. Here we provide an overview of techniques that may be used to produce and characterize reasonably well-defined CHOS fractions. We also present possible medical applications of CHOS, including tumor growth inhibition and inhibition of TH2-induced inflammation in asthma, as well as use as a bone-strengthener in osteoporosis, a vector for gene delivery, an antibacterial agent, an antifungal agent, an anti-malaria agent, or a hemostatic agent in wound-dressings. By using well-defined CHOS-mixtures it will become possible to obtain a better understanding of the mechanisms underlying these bioactivities.
Soluble T Cell Receptor Vβ Domains Engineered for High-Affinity Binding to Staphylococcal or Streptococcal Superantigens

Staphylococcus aureus and group A Streptococcus secrete a collection of toxins called superantigens (SAgs), so-called because they stimulate a large fraction of an individual’s T cells. One consequence of this hyperactivity is massive cytokine release leading to severe tissue inflammation and, in some cases, systemic organ failure and death. The molecular basis of action involves the binding of the SAg to both a T cell receptor (TCR) on a T cell and a class II product of the major histocompatibility complex (MHC) on an antigen presenting cell. This cross-linking leads to aggregation of the TCR complex and signaling. A common feature of SAgs is that they bind with relatively low affinity to the variable region (V) of the beta chain of the TCR. Despite this low affinity binding, SAgs are very potent, as each T cell requires only a small fraction of their receptors to be bound in order to trigger cytokine release. To develop high-affinity agents that could neutralize the activity of SAgs, and facilitate the development of detection assays, soluble forms of the Vβ regions have been engineered to affinities that are up to 3 million-fold higher for the SAg. Over the past decade, six different Vβ regions against SAgs from S. aureus (SEA, SEB, SEC3, TSST-1) or S. pyogenes (SpeA and SpeC) have been engineered for high-affinity using yeast display and directed evolution. Here we review the engineering of these high-affinity Vβ proteins, structural features of the six different SAgs and the Vβ proteins, and the specific properties of the engineered Vβ regions that confer high-affinity and specificity for their SAg ligands.
A Model for Management of Virtual Networks in OpenFlow Environment

One of the main proposals for developing solutions for the future of the Internet is network virtualization, which has less impact on traffic. Within that paradigm, Software Defined Networks (SDN) stand out as networks that have two main innovations: separation of data and control planes. These innovations enable programming of the equipment and not just its configuration, as in the case of a traditional network. OpenFlow technology appears to be one of the most promising solutions with greater use of supported solutions within the SDN paradigm. Its architecture is characterized by the controller, responsible for defining how the package should be treated and providing central management of the entire network. The technology within the OpenFlow includes a special purpose controller called FlowVisor. It allows the division of the network device capacities by creating slices that enable multiple virtual networks to run on the same physical infrastructure, based on the deployment of rules for routing the packets together with the OpenFlow controllers and network devices. However, FlowVisor has a limitation in its architecture related to the lack of a specific model for managing the slices (virtual networks). This work presents a model of management of the slices. It focus the of data transmission by the application running on the network. It also uses automated interfaces with FlowVisor and Network Controllers for creating and adjusting the slices and policies (topology) in a network managed by FlowVisor.
Cis- and trans-platinum and palladium complexes: a comparative study review as antitumour agents.

A large body of novel platinum and palladium complexes, in both the cis- and trans-forms, with various donor ligands, e.g. beta-carboline alkaloids, pyrazoles, DMSO, ferrocenylphosphines,. have been tested for their antitumour activity against number of fluid suspension (P388, L1210, K562, and Raji) and solid tumour (KB, T47D, SW948, HeLa, A549, L929, Hep-2, RD,.) cell lines. Remarkable cytotoxic effects against these cell lines were observed by some of these complexes. The preliminary results indicated that most of the trans-palladium complexes showed a better activity than the cis-platinum isomers and superior activity than that of the cis-palladium isomers. More importantly they showed activities equal to (or superior than) those of cisplatin, carboplatin and oxaliplatin (the anti-cancer drugs) in vitro. Although these results are preliminary, however, encouraging since they are in a disagreement with the previous studies that cis-isomers are more active than trans-ones; the complexes which have not received the required attention from the vast number of researchers in this field.
Genetic Programming for Modelling Long-Term Hydrological Time Series

In recent years, artificial neural networks (ANN) have emerged as a novel identification technique for the forecasting of hydrological time series. However, they represent their knowledge in terms of a weight matrix that is not accessible to human understanding at present. The purpose of this study is to develop a flow prediction method, based on the genetic programming (GP), which is an evolutionary computing method that provides ‘transparent’ and structured system identification. In terms of statistical characteristic of reservoir inflow sequence data, the autocorrelation function is employed to make certain amount of lagged input variables and the root mean square error is adopted as fitness of evaluation. The GP model is examined using the long-term observations of monthly river flow discharges. Through the comparison of its performance with those of the ANN, it is demonstrated that the GP model is an effective algorithm to forecast the long-term discharges.
Level of Performance Accuracy for Core Halstead-Reitan Measures by Pooling Normal Controls from Published Studies: Comparison with Existing Norms in a Clinical Sample

The Halstead-Reitan Neuropsychological Test Battery offers a multifaceted, empirically supported interpretive framework for neuropsychological assessment founded upon raw scores referenced to a brain-damaged sample. Complementary approaches have used T scores from normal samples often composed of community volunteers or medical patients, augmented by regression. By pooling normal controls of all types from published studies, a sample large enough for stratification of core Halstead-Reitan measures by age and education was obtained (206 studies, N = 17,980). Comparisons based on T scores with two published normative systems in an outpatient sample produced a continuum: liberal norms for medical patients, intermediate pooled values from many types of subjects, and stringent norms for community volunteers. Features recommending clinical application of pooled norms include enhanced accuracy in clinical situations precluding a full battery, few empty cells or inversions for nonelderly subjects, and a screening application based upon a very large Trail Making Test sample (Trails B: n > 14,000).
GATMD: γ-Aminobutyric Acid Transporter Mutagenesis Database

It has been twenty years since the cloning of the first γ‐aminobutyric acid (GABA) transporter (GAT1; SLC6A1) in 1990. During this time, over fifty published studies have provided structure‐function information on investigator‐designed GAT1 mutants. To date, nearly 200 of 599 GAT1 residues have been replaced with different amino acids, and the resulting transporter functional properties have significantly advanced our understanding of this member of the neurotransmitter:sodium symporter family. Given this large body of mutagenesis data, there is merit in having a system which organizes this information and makes it publicly available through a searchable, internet‐based database portal. We first created a relational database which accommodates existing functional and pharmacological data reported on the GABA transporters. Using this database, we manually annotated published data on GAT1 mutants. Finally, we developed a web portal for accessing, searching, and managing the database. We have named this web portal GABA Transporter Mutagenesis Database (GATMD). GATMD is available on the internet at http://physiology.sci.csupomona.edu/GATMD. (Supported by NIH grant SC1GM086344)
Subcellular imaging of isotopically labeled carbon compounds in a biological sample by ion microprobe (NanoSIMS)

Here we demonstrate the technique of nanoscale secondary ion mass spectrometry, utilizing the Cameca NanoSIMS50® ion microprobe, to detect and image the metabolism of an isotopically labeled compound (NaH13CO3) in a biological sample. In particular, we have designed and verified protocols for imaging the subcellular distribution and determining the relative abundance of labeled 13C, within the coral Galaxea fascicularis. Analyses were conducted on 1‐μm thick sections of resin‐embedded material, using both scanned (mapping) and static (spot analysis) Cs+ primary ion beam of ∼100 nm diameter. Using these samples we establish that NanoSIMS has adequate mass resolution to reliably distinguish 13C from potential isobaric interference by 12C1H and that data extracted from ion maps are comparable to those acquired by spot analyses. Independent of the method of acquisition, ratioing of 13C to the naturally abundant 12C is essential if meaningful data, which can be statistically compared to standard and control samples, are to be obtained. These results highlight the potential of NanoSIMS for intracellular tracking of a variety of organic and inorganic compounds labeled with stable isotopes of C, N, O, S, P, and halogens. Microsc. Res. Tech., 2007. © 2007 Wiley‐Liss, Inc.
H-Walk: hierarchical distance computation for moving convex bodies

This paper presents the Hierarchical Walk, or H-Walk al-gorithm, which maintains the distance between two moving convex bodies by exploiting both motion coherence and hierarchical representations. For convex polygons, we prove that H-Walkimproves on the classic Lin-Canny and Dobkin-Kirkpatrick algorithms. We have implemented H-Walk for moving convex polyhedra in three dimensions. Experimental results indicate that, unlike previous incremental distance computation algorithms, H-Walk adapts well to variable coherence in the motion.
TESTING THE ROLE OF INTERSPECIFIC COMPETITION IN THE EVOLUTIONARY ORIGIN OF ELEVATIONAL ZONATION: AN EXAMPLE WITH BUARREMON BRUSH-FINCHES (AVES, EMBERIZIDAE) IN THE NEOTROPICAL MOUNTAINS

Abstract Interspecific competition might drive the evolution of ecological niches and result in pairs of formerly competing species segregating along ecological gradients following a process of character displacement. This mechanism has been proposed to account for replacement of related species along gradients of elevation in many areas of the world, but the fundamental issue of whether competition is responsible for the origin of elevational replacements has not been tested. To test hypotheses about the role of interspecific competition in the origin of complementary elevational ranges, I combined molecular phylogenetics, phylogeography, and population genetic analyses on Buarremon torquatus and B. brunneinucha (Aves, Emberizidae), whose patterns of elevational distribution suggest character displacement or ecological release. The hypothesis that elevational distributions in these species changed in opposite directions as a result of competition is untenable because: (1) a historical expansion of the range of B. brunneinucha into areas occupied by B. torquatus was not accompanied by a shift in the elevational range of the former species; (2) when B. brunneinucha colonized the range of B. torquatus, lineages of the latter distributions had already diverged; and (3) historical trends in effective population size do not suggest populations with elevational ranges abutting those of putative competitors have declined as would be expected if competition caused range contractions. However, owing to uncertainty in coalescent estimates of historical population sizes, the hypothesis that some populations of B. torquatus have declined cannot be confidently rejected, which suggests asymmetric character displacement might have occurred. I suggest that the main role of competition in elevational zonation may be to act as a sorting mechanism that allows the coexistence along mountain slopes only of ecologically similar species that differ in elevational distributions prior to attaining sympatry. The contrasting biogeographic histories of B. brunneinucha and B. torquatus illustrate how present-day ecological interactions can have recent origins, and highlights important challenges for testing the hypothesis of character displacement in the absence of data on population history and robust reconstructions of the evolution of traits and geographic ranges.