julilili42/papers huggingface dataset:
Abundance, Distribution, and Activity of Fe(II)-Oxidizing and Fe(III)-Reducing Microorganisms in Hypersaline Sediments of Lake Kasin, Southern Russia
2012-04-14

ABSTRACT The extreme osmotic conditions prevailing in hypersaline environments result in decreasing metabolic diversity with increasing salinity. Various microbial metabolisms have been shown to occur even at high salinity, including photosynthesis as well as sulfate and nitrate reduction. However, information about anaerobic microbial iron metabolism in hypersaline environments is scarce. We studied the phylogenetic diversity, distribution, and metabolic activity of iron(II)-oxidizing and iron(III)-reducing Bacteria and Archaea in pH-neutral, iron-rich salt lake sediments (Lake Kasin, southern Russia; salinity, 348.6 g liter −1 ) using a combination of culture-dependent and -independent techniques. 16S rRNA gene clone libraries for Bacteria and Archaea revealed a microbial community composition typical for hypersaline sediments. Most-probable-number counts confirmed the presence of 4.26 × 10 2 to 8.32 × 10 3 iron(II)-oxidizing Bacteria and 4.16 × 10 2 to 2.13 × 10 3 iron(III)-reducing microorganisms per gram dry sediment. Microbial iron(III) reduction was detected in the presence of 5 M NaCl, extending the natural habitat boundaries for this important microbial process. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of total Bacteria , total Archaea , and species dominating the iron(III)-reducing enrichment cultures (relatives of Halobaculum gomorrense , Desulfosporosinus lacus , and members of the Bacilli ) were highest in an iron oxide-rich sediment layer. Combined with the presented geochemical and mineralogical data, our findings suggest the presence of an active microbial iron cycle at salt concentrations close to the solubility limit of NaCl.
The Iranian Plateau
2012-04-14

This chapter contains sections titled: Introduction Archaeological Sources, Sequences, and Biases Becoming Neolithic The Fully Established Pottery Neolithic Technical and Social Innovations in the Chalcolithic Period Craft Specialization and Trade Contacts Proto-urban Centers in the Highlands: The Proto-Elamite Period Guide to Further Reading
Levantine Kingdoms of the Late Bronze Age
2012-04-14

This chapter contains sections titled: Introduction Historical Outline Written Sources Historical and Archaeological Topography of the Northern Levantine Kingdoms Courts and Palaces Dying in the LBA Kingdoms The Topography of Cult in LBA Levantine Kingdoms Exchange and Interregional Contacts in the LBA Levant Guide to Further Reading
Defining at‐risk populations for Parkinson's disease: Lessons from ongoing studies
2012-04-15

Abstract It is currently widely acknowledged that the natural history of PD includes a preclinical phase, and there are increasing efforts to identify markers that would allow the identification of individuals at risk for PD. Here, we discuss the issues related to defining at‐risk populations for PD and review findings of current population‐based cohorts that have reported potential biomarkers for PD, such as the Honolulu‐Asia Aging Study (HAAS) and the PRIPS (Prospective Validation of Risk factors for the development of Parkinson Syndromes) study. We also discuss enriched risk cohorts designed to evaluate specificity and predictive value of markers exemplified by the PARS (Parkinson Associated Risk Study) and the TREND (Tübinger evaluation of Risk factors for the Early detection of NeuroDegeneration) study. Although there is still a long way to go, studies designed according to these concepts might eventually provide sufficient data to form the basis for future screening programs for PD risk to be applied at a population level. © 2012 Movement Disorder Society
Neuroimaging: Current role in detecting pre‐motor Parkinson's disease
2012-04-15

Abstract Convergent evidence suggests a pre‐motor period in Parkinson's disease (PD) during which typical motor symptoms have not yet developed although dopaminergic neurons in the substantia nigra have started to degenerate. Advances in different neuroimaging techniques have allowed the detection of functional and structural changes in early PD. This review summarizes the state of the art knowledge concerning structural neuroimaging techniques including magnetic resonance imaging (MRI) and transcranial B‐mode‐Doppler‐sonography (TCS) as well as functional neuroimaging techniques using radiotracer imaging (RTI) with different radioligands in detecting pre‐motor PD. © 2012 Movement Disorder Society
Impairment of the Bacterial Biofilm Stability by Triclosan
2012-04-16

The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition--isolated from sediments of the Eden Estuary (Scotland, UK)--on non-cohesive glass beads (<63 μm) and exposed to a range of triclosan concentrations (control, 2-100 μg L(-1)) was monitored over time by Magnetic Particle Induction (MagPI). In parallel, bacterial cell numbers, division rate, community composition (DGGE) and EPS (extracellular polymeric substances: carbohydrates and proteins) secretion were determined. While the triclosan exposure did not prevent bacterial settlement, biofilm development was increasingly inhibited by increasing TCS levels. The surface binding capacity (MagPI) of the assemblages was positively correlated to the microbial secreted EPS matrix. The EPS concentrations and composition (quantity and quality) were closely linked to bacterial growth, which was affected by enhanced TCS exposure. Furthermore, TCS induced significant changes in bacterial community composition as well as a significant decrease in bacterial diversity. The impairment of the stabilization potential of bacterial biofilm under even low, environmentally relevant TCS levels is of concern since the resistance of sediments to erosive forces has large implications for the dynamics of sediments and associated pollutant dispersal. In addition, the surface adhesive capacity of the biofilm acts as a sensitive measure of ecosystem effects.
Performance of Survivin mRNA as a Biomarker for Bladder Cancer in the Prospective Study UroScreen
2012-04-16

In this prospective and so far largest study on survivin, the marker showed a good NPV and specificity but a low PPV and sensitivity. This was partly due to the low number of cases, which limits the validity of the results. Compliance, urine quality, problems with the assay, and mRNA stability influenced the performance of survivin. However, most issues could be addressed with a more reliable assay in the future. One important finding is that survivin was not influenced by confounders like inflammation and exhibited a relatively low number of false-positives. Therefore, despite the low sensitivity, survivin may still be considered as a component of a multimarker panel.
Quantitative phase contrast optimised cancerous cell differentiation via ptychography
2012-04-16

This paper shows that visible-light ptychography can be used to distinguish quantitatively between healthy and tumorous unstained cells. Advantages of ptychography in comparison to conventional phase-sensitive imaging techniques are highlighted. A novel procedure to automatically refocus ptychographic reconstructions is also presented, which improves quantitative analysis.
Glucocorticoid receptor gene polymorphisms are associated with reduced first‐phase glucose‐stimulated insulin secretion and disposition index in women, but not in men
2012-04-16

Diabet. Med. 29, e211–e216 (2012) Abstract Aim Glucocorticoids are efficacious anti‐inflammatory agents, but, in susceptible individuals, these drugs may induce glucose intolerance and diabetes by affecting β‐cell function and insulin sensitivity. We assessed whether polymorphisms in the glucocorticoid receptor gene NR3C1 associate with measures of β‐cell function and insulin sensitivity derived from hyperglycaemic clamps in subjects with normal or impaired glucose tolerance. Methods A cross‐sectional cohort study was conducted in four academic medical centres in the Netherlands and Germany. Four hundred and forty‐nine volunteers (188 men; 261 women) were recruited with normal glucose tolerance ( n = 261) and impaired glucose tolerance ( n = 188). From 2‐h hyperglycaemic clamps, first‐ and second‐phase glucose‐stimulated insulin secretion, as well as insulin sensitivity index and disposition index, were calculated. All participants were genotyped for the functional NR3C1 polymorphisms N363S (rs6195), Bcl I (rs41423247), ER22/23EK (rs6189/6190), 9β A/G (rs6198) and ThtIII I (rs10052957). Associations between these polymorphisms and β‐cell function parameters were assessed. Results In women, but not in men, the N363S polymorphism was associated with reduced disposition index ( P = 1.06 10 −4 ). Also only in women, the ER22/23EK polymorphism was associated with reduced first‐phase glucose‐stimulated insulin secretion ( P = 0.011) and disposition index ( P = 0.003). The other single‐nucleotide polymorphisms were not associated with β‐cell function. Finally, none of the polymorphisms was related to insulin sensitivity. Conclusion The N363S and ER22/23EK polymorphisms of the NR3C1 gene are negatively associated with parameters of β‐cell function in women, but not in men.
Using Statistics for Cross-linguistic Semantics: A Quantitative Investigation of the Typology of Colour Naming Systems
2012-04-16

The paper presents a statistical evaluation of the typological data about colour naming systems across the languages of the world that have been obtained by the World Color Survey. In a first step, we discuss a principal component analysis of the categorization data. This leads to a small set of easily interpretable features that are dominant in colour categorization. These features were used for a dimensionality reduction of the categorization data. Based on the thus preprocessed data, it is investigated how the participants of the World Color Survey partition the six primary colours black, white, red, green, yellow and blue into semantic categories. We find a substantial number of counter-examples to the implicative semantic universals that have been suggested in the literature. Finally, an alternative system of semantic universals pertaining to colour naming systems is proposed that provides a better fit of the data.
Lack of sequence variations in THAP1 gene and THAP1‐binding sites in TOR1A promoter of DYT1 patients
2012-04-16

Pilar Gómez-Garre, F ́tima Carrillo, and Pablo Mir were supported by grants from the Ministerio de Ciencia e Innovación de España (SAF2007-60700), the Instituto de Salud Carlos III (PI10/01674), the Consejería de Innovación, Ciencia y Empresa de la Junta de Andalucía (CVI-02526), the Consejería de Salud de la Junta de Andalucía (PI-0377/2007, PI-0741/2010), the Sociedad Andaluza de Neurología, and the Jaques and Gloria Gossweiler Foundation. Pilar Gómez-Garre was supported by the “Miguel Servet” program from the Instituto de Salud Carlos III.
Gender differences in the development of numerical Skills in four European countries
2012-04-16

Gender differences have been reported frequently for mathematical performance of boys and girls but usually not before adolescence. Therefore, developmental origins of a possible male advantage in numerical skills are understudied. In a large sample of second graders from four European countries, we found significant gender differences in favour of boys in writing multi-digit Arabic numerals from dictation, and in subtraction and multiplication. We discuss the latter findings with reference to a possible male advantage in visual-spatial cognition ability.
Cks1 Promotion of S Phase Entry and Proliferation Is Independent of p27Kip1 Suppression
2012-04-17

Cks1 is an activator of the SCF(Skp2) ubiquitin ligase complex that targets the cell cycle inhibitor p27(Kip1) for degradation. The loss of Cks1 results in p27(Kip1) accumulation and decreased proliferation and inhibits tumorigenesis. We identify here a function of Cks1 in mammalian cell cycle regulation that is independent of p27(Kip1). Specifically, Cks1(-/-); p27(Kip1-/-) mouse embryonic fibroblasts retain defects in the G(1)-S phase transition that are coupled with decreased Cdk2-associated kinase activity and defects in proliferation that are associated with Cks1 loss. Furthermore, concomitant loss of Cks1 does not rescue the tumor suppressor function of p27(Kip1) that is manifest in various organs of p27(Kip1-/-) mice. In contrast, defects in mitotic entry and premature senescence manifest in Cks1(-/-) cells are p27(Kip1) dependent. Collectively, these findings establish p27(Kip1)-independent functions of Cks1 in regulating the G(1)-S transition.
An Iterative Jackknife Approach for Assessing Reliability and Power of fMRI Group Analyses
2012-04-17

For functional magnetic resonance imaging (fMRI) group activation maps, so-called second-level random effect approaches are commonly used, which are intended to be generalizable to the population as a whole. However, reliability of a certain activation focus as a function of group composition or group size cannot directly be deduced from such maps. This question is of particular relevance when examining smaller groups (<20-27 subjects). The approach presented here tries to address this issue by iteratively excluding each subject from a group study and presenting the overlap of the resulting (reduced) second-level maps in a group percent overlap map. This allows to judge where activation is reliable even upon excluding one, two, or three (or more) subjects, thereby also demonstrating the inherent variability that is still present in second-level analyses. Moreover, when progressively decreasing group size, foci of activation will become smaller and/or disappear; hence, the group size at which a given activation disappears can be considered to reflect the power necessary to detect this particular activation. Systematically exploiting this effect allows to rank clusters according to their observable effect size. The approach is tested using different scenarios from a recent fMRI study (children performing a "dual-use" fMRI task, n = 39), and the implications of this approach are discussed.
Urinary Neutrophil Gelatinase-Associated Lipocalin Accurately Detects Acute Allograft Rejection Among Other Causes of Acute Kidney Injury in Renal Allograft Recipients
2012-04-18

Urinary NGAL, at respective cut-off, accurately discriminates acute allograft rejection from other causes of AKI in follow-up after kidney transplantation. As a readily available parameter, urinary NGAL may guide differential diagnosis and initial therapy in allograft recipients with AKI.
Discovery of VHE emission towards the Carina arm region with the HESS telescope array: HESSJ1018-589
2012-04-18

The Carina arm region, containing the supernova remnant SNR G284.3–1.8, the high-energy (HE; E &gt; 100 MeV) binary 1FGL J1018.6–5856 and the energetic pulsar PSR J1016–5857 and its nebula, has been observed with the H.E.S.S. telescope array. The observational coverage of the region in very-high-energy (VHE; E &gt; 0.1 TeV) γ-rays benefits from deep exposure (40 h) of the neighboring open cluster Westerlund 2. The observations have revealed a new extended region of VHE γ-ray emission. The new VHE source HESS J1018–589 shows a bright, point-like emission region positionally coincident with SNR G284.3–1.8 and 1FGL J1018.6–5856 and a diffuse extension towards the direction of PSR J1016–5857. A soft (Γ = 2.7 ± 0.5stat) photon index, with a differential flux at 1 TeV of N0 = (4.2 ± 1.1) × 10-13 TeV-1 cm-2 s-1 is found for the point-like source, whereas the total emission region including the diffuse emission region is well fit by a power-law function with spectral index Γ = 2.9 ± 0.4stat and differential flux at 1 TeV of N0 = (6.8 ± 1.6) × 10-13 TeV-1 cm-2 s-1. This H.E.S.S. detection motivated follow-up X-ray observations with the XMM-Newton satellite to investigate the origin of the VHE emission. The analysis of the XMM-Newton data resulted in the discovery of a bright, non-thermal point-like source (XMMU J101855.4–58564) with a photon index of Γ = 1.65 ± 0.08 in the center of SNR G284.3–1.8, and a thermal, extended emission region coincident with its bright northern filament. The characteristics of this thermal emission are used to estimate the plasma density in the region as n ≈ 0.5 cm-3 (2.9 kpc/d)2. The position of XMMU J101855.4–58564 is compatible with the position reported by the Fermi-LAT collaboration for the binary system 1FGL J1018.6–5856 and the variable Swift XRT source identified with it. The new X-ray data are used alongside archival multi-wavelength data to investigate the relationship between the VHE γ-ray emission from HESS J1018–589 and the various potential counterparts in the Carina arm region.
Metastable Energy Strata in Weakly Nonlinear Wave Equations
2012-04-18

We consider the problem of the long-time stability of plane waves under nonlinear perturbations of linear Klein-Gordon equations. This problem reduces to studying the distribution of the mode energies along solutions of one-dimensional semilinear Klein–Gordon equations with periodic boundary conditions when the initial data are small and concentrated in one Fourier mode. It is shown that for all except finitely many values of the mass parameter, the energy remains essentially localized in the initial Fourier mode over time scales that are much longer than predicted by standard perturbation theory. The mode energies decay geometrically with the mode number with a rate that is proportional to the total energy. The result is proved using modulated Fourier expansions in time.
Determination of the subcooled liquid solubilities of PAHs in partitioning batch experiments
2012-04-18

Subcooled liquid solubility is the water solubility for a hypothetical state of liquid. It is an important parameter for multicomponent nonaqueous phase liquids (NAPLs) containing polycyclic aromatic hydrocarbons (PAHs), which can exist as liquids even though most of the solutes are solid in their pure form at ambient temperature. So far, subcooled liquid solubilities were estimated from the solid water solubility and fugacity ratio of the solid and (subcooled) liquid phase, but rarely derived from experimental data. In our study, partitioning batch experiments were performed to determine the subcooled liquid solubility of PAHs in NAPL-water system. For selected PAH, a series of batch experiments were carried out at increased mole fractions of the target component in the NAPL and at a constant NAPL/water volume ratio. The equilibrium aqueous PAH concentrations were measured with HPLC and/or GC-MS. The subcooled liquid solubility was derived by extrapolation of the experimental equilibrium aqueous concentration to a mole fraction of unity. With the derived subcooled liquid solubility, the fugacity ratio and enthalpy of fusion of the solute were also estimated. Our results show a good agreement between the experimentally determined and published data.
Non-linear viscous damping and gravitational wave detectability of the f-mode instability in neutron stars
2012-04-18

We study the damping of the gravitational radiation-driven f-mode instability\\nin rotating neutron stars by nonlinear bulk viscosity in the so-called\\nsupra-thermal regime. In this regime the dissipative action of bulk viscosity\\nis known to be enhanced as a result of nonlinear contributions with respect to\\nthe oscillation amplitude. Our analysis of the f-mode instability is based on a\\ntime-domain code that evolves linear perturbations of rapidly rotating\\npolytropic neutron star models. The extracted mode frequency and eigenfunctions\\nare subsequently used in standard energy integrals for the gravitational wave\\ngrowth and viscous damping. We find that nonlinear bulk viscosity has a\\nmoderate impact on the size of the f-mode instability window, becoming an\\nimportant factor and saturating the mode's growth at a relatively large\\noscillation amplitude. We show similarly that nonlinear bulk viscosity leads to\\na rather high saturation amplitude even for the r-mode instability. In\\naddition, we show that the action of bulk viscosity can be significantly\\nmitigated by the presence of superfluidity in neutron star matter. Apart from\\nrevising the f-mode's instability window we provide results on the mode's\\ngravitational wave detectability. Considering an f-mode-unstable neutron star\\nlocated in the Virgo cluster and assuming a mode amplitude at the level allowed\\nby bulk viscosity, we find that the emitted gravitational wave signal could be\\ndetectable by advanced ground-based detectors such as Advanced LIGO/Virgo and\\nthe Einstein Telescope.\\n
Profit Shifting Despite Symmetric Tax Rates? A Note on the Role of Tax Enforcement
2012-04-18

This paper analyzes a multinational corporation that may use tax evasion and profit shifting as a means to minimize tax liabilities. Our main finding is that profit shifting may occur even when tax rates are the same across countries. This will be the case whenever there is a tax differential in effective tax rates resulting from differences in tax enforcement. In this context, profit shifting occurs to enable tax evasion in a country where tax enforcement is less harsh. Moreover, for a given differential in tax rates, differences in tax enforcement may either accentuate or dampen profit shifting. Importantly, the predictions regarding the direction of profit shifting that would result in our set-up may contrast sharply with those of the preceding literature.
Anticancer Drugs
2012-04-18

This chapter contains sections titled: Introduction Alkylating Drugs Platinum-Containing Agents Antimetabolites Natural Products Endocrine Therapy Histone Deacetylase Inhibitor (Vorinostat) Tyrosine Kinase Inhibitors Proteasome Inhibitor (Bortezomib) References
Model Systems for Spinocerebellar Ataxias: Lessons Learned About the Pathogenesis
2012-04-18

Ataxia 2 made important contributions to the understanding of disease progression and will be important tools for the first line tests of potential treatment strategies.This review aims to sum up the model systems used for the investigation of SCA and especially focuses on the lessons learned from these models about the pathogenesis of SCA.We also compare commons and differences in the results obtained using these animal models and highlight the species-specific advantages and possible problems associated with the use of this species as a model organism. Lessons learned from non-mammalian models of SCA Lessons learned from worm modelsThe nematode Caenorhabditis elegans is frequently used as a model organism, primarily because of its anatomic and biochemical simplicity as well as its genetic tractability.The worm genome encodes orthologues for about 65% of all known human disease genes.Moreover, it allows for easy and rapid establishment of transgenic lines, thus facilitating screening and characterization of human disease-causing mutations in vivo.Overall it is an often used model organism to analyze pathological features of neurodegenerative diseases (Huntington's disease, Parkinson's disease or Alzheimer's disease) (reviewed in Driscoll andGerstbrein, 2003 and Brignull et al., 2006b).Except for ataxin-7, the worm contains orthologues for all SCA caused by polyQ expansion.Interestingly, for SCA C. elegans strains have only been generated and characterized for SCA2 and SCA3 (Ciosk et al.,