julilili42/papers huggingface dataset:
Potentiation of neurotoxicity in double-mutant mice with Pink1 ablation and A53T-SNCA overexpression
2014-10-08

The common age-related neurodegeneration of Parkinson's disease can result from dominant causes like increased dosage of vesicle-associated alpha-synuclein (SNCA) or recessive causes like deficiency of mitophagy factor PINK1. Interactions between these triggers and their convergence onto shared pathways are crucial, but currently conflicting evidence exists. Here, we crossed previously characterized mice with A53T-SNCA overexpression and with Pink1 deletion to generate double mutants (DMs). We studied their lifespan and behavior, histological and molecular anomalies at late and early ages. DM animals showed potentiated phenotypes in comparison with both single mutants (SMs), with reduced survival and strongly reduced spontaneous movements from the age of 3 months onwards. In contrast to SMs, a quarter of DM animals manifested progressive paralysis at ages >1 year and exhibited protein aggregates immunopositive for pSer129-SNCA, p62 and ubiquitin in spinal cord and basal brain. Brain proteome quantifications of ubiquitination sites documented altered degradation of SNCA and the DNA-damage marker H2AX at the age of 18 months. Global brain transcriptome profiles and qPCR validation experiments identified many consistent transcriptional dysregulations already at the age of 6 weeks, which were absent from SMs. The observed downregulations for Dapk1, Dcaf17, Rab42 and the novel SNCA-marker Lect1 as well as the upregulations for Dctn5, Mrpl9, Tmem181a, Xaf1 and H2afx reflect changes in ubiquitination, mitochondrial/synaptic/microtubular/cell adhesion dynamics and DNA damage. Thus, our study confirmed that SNCA-triggered neurotoxicity is exacerbated by the absence of PINK1 and identified a novel molecular signature that is detectable early in the course of this double pathology.
Cerium tetrakis(diisopropylamide) – a useful precursor for cerium(iv) chemistry
2014-10-08

Homoleptic cerium(IV) diisopropylamide was synthesized via oxidation of ate complex Ce(NiPr2)4Li(thf) with trityl chloride or hexachloroethane. Due to its ready accessibility, and high pKa value of the proligand HNiPr2, Ce(NiPr2)4 features a promising candidate for protonolysis reactions, as shown for the synthesis of dimeric cerium(IV) tetrakis(1,1,3,3-N,N,N',N'-tetramethylguanidinate).
Cryopreservation of MHC multimers: Recommendations for quality assurance in detection of antigen specific T cells
2014-10-08

Abstract Fluorescence‐labeled peptide‐MHC class I multimers serve as ideal tools for the detection of antigen‐specific T cells by flow cytometry, enabling functional and phenotypical characterization of specific T cells at the single cell level. While this technique offers a number of unique advantages, MHC multimer reagents can be difficult to handle in terms of stability and quality assurance. The stability of a given fluorescence‐labeled MHC multimer complex depends on both the stability of the peptide‐MHC complex itself and the stability of the fluorochrome. Consequently, stability is difficult to predict and long‐term storage is generally not recommended. We investigated here the possibility of cryopreserving MHC multimers, both in‐house produced and commercially available, using a wide range of peptide‐MHC class I multimers comprising virus and cancer‐associated epitopes of different affinities presented by various HLA‐class I molecules. Cryopreservation of MHC multimers was feasible for at least 6 months, when they were dissolved in buffer containing 5–16% glycerol (v/v) and 0.5% serum albumin (w/v). The addition of cryoprotectants was tolerated across three different T‐cell staining protocols for all fluorescence labels tested (PE, APC, PE‐Cy7 and Quantum dots). We propose cryopreservation as an easily implementable method for stable storage of MHC multimers and recommend the use of cryopreservation in long‐term immunomonitoring projects, thereby eliminating the variability introduced by different batches and inconsistent stability. © 2014 2014 The Authors. Published by Wiley Periodicals, Inc.
Prolonged paradoxical reaction to antituberculous treatment after discontinuation of TNF-alpha- blocker therapy with adalimumab. Rare clinical documentation
2014-10-08

Abstract In the past decades, tumor necrosis factor alpha (TNF-a) antagonist has been a milestone in the treatment of many chronic inflammatory diseases. TNF antagonist can increase patients ́ susceptibility to many different kinds of infections especially those requiring granuloma formations despite regular performance of Screening for latent tuberculosis infection (LTBI). We report 2 cases of patients who developed tuberculosis under treatment with adalimumab, which was discontinued after the diagnosis of tuberculosis. During the tuberculosis therapy they unexpectedly developed a prolonged paradoxical reaction. In both cases we were only able to manage the progress of the paradoxical reaction through high steroid doses. Patients undergoing therapy with TNF- alphablocker are prone to develop tuberculosis infection, which could in turn lead to severe prolonged paradoxical reaction during anti-tuberculous treatment. An increased steroid dose may be required and is sometimes necessary
Sleep and memory in mammals, birds and invertebrates
2014-10-09

Sleep supports memory consolidation. Based on studies in mammals, sleep-dependent consolidation has been conceptualized as 'active system consolidation'. During waking, information is encoded into an initial store (hippocampus). During subsequent sleep, some of the newly encoded memories are selected to be reactivated and redistributed toward networks serving as long-term store (e.g., neocortex), whereby memories become transformed into more general, schema-like representations. Here we asked whether sleep in non-mammalian species might play a comparable role for memory. The literature review revealed that sleep produces enhancing effects on memory in all non-mammalian species studied. Furthermore, across species some of the hallmarking features of active system consolidation were identified: Studies of filial imprinting in chicks suggest that a redistribution of imprinting memory toward long-term storage sites occurs during sleep; song learning in birds appears to be driven by reactivations of song representations during sleep; studies of bees demonstrated the selectivity of sleep-dependent consolidation, benefiting extinction but not original classical conditioning. Although overall fragmentary, first evidence in non-mammalian species suggests active system consolidation might be an evolutionary conserved function of sleep.
Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession
2014-10-09

Summary Environmental selection and dispersal limitation are two of the primary processes structuring biotic communities in ecosystems, but little is known about these processes in shaping soil microbial communities during secondary forest succession. We examined the communities of ectomycorrhizal ( EM ) fungi in young, intermediate and old forests in a C hinese subtropical ecosystem, using 454 pyrosequencing. The EM fungal community consisted of 393 operational taxonomic units ( OTU s), belonging to 21 EM fungal lineages, in which three EM fungal lineages and 11 EM fungal OTU s showed significantly biased occurrence among the young, intermediate and old forests. The EM fungal community was structured by environmental selection and dispersal limitation in old forest, but only by environmental selection in young, intermediate, and whole forests. Furthermore, the EM fungal community was affected by different factors in the different forest successional stages, and the importance of these factors in structuring EM fungal community dramatically decreased along the secondary forest succession series. This study suggests that different assembly mechanisms operate on the EM fungal community at different stages in secondary subtropical forest succession.
Vertical shear instability in accretion disc models with radiation transport
2014-10-09

\\n Context. The origin of turbulence in accretion discs is still not fully understood. While the magneto-rotational instability is thought to operate in sufficiently ionised discs, its role in the poorly ionised protoplanetary disc is questionable. Recently, the vertical shear instability (VSI) has been suggested as a possible alternative. \\n Aims. Our goal is to study the characteristics of this instability and the efficiency of angular momentum transport, in extended discs, under the influence of radiative transport and irradiation from the central star. \\n Methods. We use multi-dimensional hydrodynamic simulations to model a larger section of an accretion disc. First we study inviscid and weakly viscous discs using a fixed radial temperature profile in two and three spatial dimensions. The simulations are then extended to include radiative transport and irradiation from the central star. \\n Results. In agreement with previous studies, for the isothermal disc we find a sustained unstable state with a weak positive angular momentum transport of the order of α ≈ 10-4. Under the inclusion of radiative transport the disc cools off and the turbulence terminates. For discs irradiated from the central star we again find a persistent instability with a similar α value as for the isothermal case. \\n Conclusions. We find that the VSI can indeed generate sustained turbulence in discs, albeit at a relatively low level with α about few times 10-4. \\n
Influence of Axial Length on Thickness Measurements Using Spectral-Domain Optical Coherence Tomography
2014-10-09

Axial length influences SD-OCT thickness measurements. Our findings demonstrate accuracy of the scaling in SD-OCT thickness measurements in emmetropic medium eyes. Caution is recommended when comparing the measured values of short and long eyes with the normative database of the instrument. There is a need for larger sample-size studies to confirm our results. (ClinicalTrials.gov number, NCT01024803.).
X-Ray Phase-Contrast Tomography of Renal Ischemia-Reperfusion Damage
2014-10-09

In conclusion GB-PCI with synchrotron radiation allows for non-destructive microstructural assessment of parenchymal kidney disease and vessel architecture. If translation to lab-based approaches generates sufficient density resolution, and with a time-optimized image analysis protocol, GB-PCI may ultimately serve as a non-invasive, non-enhanced alternative for imaging of pathological changes of the kidney.
A comprehensive test of evolutionarily increased competitive ability in a highly invasive plant species
2014-10-09

The use of both intra- and interspecific competition experiments in this study revealed opposing results. While the first experiment refutes the EICA hypothesis, the second shows strong support for it, suggesting evolutionarily increased competitive ability in invasive populations of L. salicaria. It is suggested that the use of naturally co-occurring heterospecifics, rather than conspecifics, may provide a better evaluation of the possible evolutionary shift towards greater competitive ability.
Fate of urine nitrogen through a volcanic vadose zone
2014-10-09

To investigate the fate of nitrogen (N) from urine, dairy cow urine was amended with bromide (Br) and chloride (Cl), and applied onto a loamy sand soil with an underlying vadose zone of gritty coarse sands and pumice fragments with groundwater at ~5.5 m depth. Textural changes and hydrophobicity resulted in heterogeneous flow and high variability in the Cl, Br and N masses captured. Three forms of N derived from the urine, organic-N (org-N), ammonium-N (NH4-N) and nitrate-N (NO3-N), were measured at 0.4 m depth. At 1.0 m depth, effectively all measured N was NO3-N. At 4.2 m, the mass of recovered N (average 33% of applied N, s.d. 21%), although solely speciated as NO3-N, was not significantly different from that at 0.4 m (average 24.5% of applied N, s.d. 0.1%), suggesting that no substantial assimilation of NO3-N had occurred in this vadose zone. Below the interface of the Taupo Ignimbrite and the Palaeosol at 4.2 m depth, recoveries of the Cl and Br tracers were negligible. In addition, the isotopic signatures (d18O and d15N) of the nitrate were different and the NO3-N concentrations were higher than in the upper vadose zone. These results all suggest that the Palaeosol was acting as a hydraulically limiting layer resulting in lateral unsaturated flow occurring at this interface. The fact that no nitrate assimilation was observed in this field study, despite previous laboratory studies showing substantial assimilative capacity, underlines that that the nitrate assimilative capacity in the vadose zone is a function of both hydrological and biogeochemical factors.
Type II diabetes and its therapy in clinical practice – results from the standardised non‐interventional registry SIRTA
2014-10-09

The registry confirms results from other epidemiologic studies on the therapy of T2DM in everyday practice. The treatment strategies applied effectively reduced blood glucose and avoided severe hypoglycaemias. An early therapy of insufficiently controlled patients with T2DM is important, as lower baseline values facilitated achieving HbA1c targets.
Truth Will Out
2014-10-10

Individual differences in morality and honesty are inherently connected such that individuals more likely to engage in immoral behavior will typically be less likely to admit to it. Indeed, this is a central prediction of the Honesty-Humility (HH) factor of personality, recently proposed as part of the HEXACO Model of Personality (Honesty-Humility [H], Emotionality [E], Extraversion [X], Agreeablenes [A], Conscientiousness [C], and Openness to Experience [O]). However, this very link between morality and honesty necessarily limits the conclusiveness of typical investigations—especially those relying on self-report data for both constructs. Herein, we apply an indirect questioning technique to overcome such limitations and provide evidence for individual differences in trait honesty and morality in line with the HH factor of personality. Specifically, results show that individuals low in (self-reported) HH are indeed more likely to engage in immoral behavior although less likely to be upfront about it when directly questioned.
Related but not the same: Ordinality, cardinality and 1-to-1 correspondence in finger-based numerical representations
2014-10-10

Finger-based numerical representations have gained increasing research interest. However, their description and assessment often refer to different numerical principles of ordinality, cardinality and 1-to-1 correspondence. Our aim was to investigate similarities and differences between these principles in finger-based numerical representations. Sixty-eight healthy adults performed ordinal finger counting, cardinal finger montring (showing the number of gestures) and finger-to-number mapping with twisted arms and fingers. We found that counting gestures and montring postures were identical for Number 10 but differed to varying degrees for other numbers. Interestingly, there was no systematic relation between finger-to-number mapping and ordinal finger counting habits. These data question the assumption of a unitary embodied finger-based numerical representation, but suggest that different finger-based representations co-exist and can be recruited flexibly depending on the numerical aspects to be conveyed.
Expanding evolutionary diversity in the Ustilaginomycotina: Fereydouniaceae fam. nov. and Fereydounia gen. nov., the first urocystidalean yeast lineage
2014-10-10

The systematic position of two strains of a yeast-like fungus isolated from plant remnants on the Kharg Island in the Persian Gulf of Iran is evaluated using morphological, physiological and phylogenetic analyses. In culture, this fungus produced cylindrical cells that reproduced by polar budding on short stalks. Production of ballistoconidia and blastospores was observed. The carbon source assimilation spectrum was broad, but fermentation ability was absent. Phylogenetic analyses of the nuclear SSU, LSU (D1/D2 domain), and ITS rDNA revealed that this fungus represents a new lineage in the Urocystidales of the subphylum Ustilaginomycotina. Based on the comparison of phenotypic characters, physiology, and DNA sequences, a new genus and species Fereydounia khargensis (IBRC-M 30116T = CBS 13305T) is described for this fungus and accommodated in the novel family Fereydouniaceae. This is the first report of anamorphic saprobic fungus residing in the Urocystidales, stressing the remarkable evolutionary diversity in the subphylum Ustilaginomycotina.
Y Pouch Neobladder—A Simplified Method of Intracorporeal Neobladder After Robotic Cystectomy
2014-10-10

In recent years, robot-assisted radical cystectomy (RARC) has shown similar oncologic outcomes compared with the gold standard open radical cystectomy with the added benefit of less blood loss and shorter hospital stay. Robot-assisted cystectomy with intracorporeal ileal neobladder is a complex surgical procedure and is usually performed in centers with experienced surgeons. We propose robot-assisted cystectomy with intracorporeal neobladder using the Y pouch previously described in open radical cystectomy. We think that the Y pouch is easier to perform than conventional spherical pouches without compromising functional outcomes. It may therefore be a good alternative for patients undergoing RARC with intracorporeal diversion.
Non-LTE spectral models for the gaseous debris-disk component of Ton 345
2014-10-10

For a fraction of single white dwarfs with debris disks, an additional\\ngaseous disk was discovered. Both dust and gas are thought to be created by the\\ndisruption of planetary bodies. The composition of the extrasolar planetary\\nmaterial can directly be analyzed in the gaseous disk component, and the disk\\ndynamics might be accessible by investigating the temporal behavior of the Ca\\nII infrared emission triplet, hallmark of the gas disk.\\n We obtained new optical spectra for the first helium-dominated white dwarf\\nfor which a gas disk was discovered (Ton 345) and modeled the non-LTE spectra\\nof viscous gas disks composed of carbon, oxygen, magnesium, silicon, sulfur,\\nand calcium with chemical abundances typical for solar system asteroids. Iron\\nand its possible line-blanketing effects on the model structure and spectral\\nenergy distribution was still neglected. A set of models with different radii,\\neffective temperatures, and surface densities as well as chondritic and\\nbulk-Earth abundances was computed and compared with the observed line profiles\\nof the Ca II infrared triplet.\\n Our models suggest that the Ca II emission stems from a rather narrow gas\\nring with a radial extent of R=0.44-0.94 Rsol, a uniform surface density\\nSigma=0.3 g/cm2, and an effective temperature of Teff=6000 K. The often assumed\\nchemical mixtures derived from photospheric abundances in polluted white dwarfs\\n- similar to a chondritic or bulk-Earth composition - produce unobserved\\nemission lines in the model and therefore have to be altered. We do not detect\\nany line-profile variability on timescales of hours, but we confirm the\\nlong-term trend over the past decade for the red-blue asymmetry of the\\ndouble-peaked lines.\\n
First‐trimester contingent screening for trisomies 21, 18 and 13 by fetal nuchal translucency and ductus venosus flow and maternal blood cell‐free DNA testing
2014-10-12

ABSTRACT Objective To examine performance of screening for major trisomies by a policy of first‐line assessment of risk according to maternal age, fetal nuchal translucency thickness ( NT ) and ductus venosus pulsatility index for veins ( DV‐PIV ) followed by cell‐free DNA ( cfDNA ) testing in pregnancies with an intermediate risk. Methods We estimated the distribution of risks based on maternal age, fetal NT and DV‐PIV in a dataset of 86 917 unaffected and 491 trisomic pregnancies undergoing prospective screening for trisomies. Performance of screening for trisomies by cfDNA testing was derived from a meta‐analysis of clinical validation studies. We estimated performance and cost of screening for trisomies using different combinations of ultrasound screening and cfDNA testing. Results Screening for trisomies 21, 18 and 13 according to a combination of maternal age, fetal NT and DV‐PIV in all pregnancies, followed by invasive testing in the high‐risk group (≥ 1:10) and cfDNA testing in the intermediate‐risk group (1:11–1:3000) can potentially detect about 96%, 95% and 91% of cases, respectively, with a false‐positive rate ( FPR ) of 0.8%. On the assumption that the costs for ultrasound screening, cfDNA testing and invasive testing are €150, €500 and €1000, respectively, the overall cost of such a policy would be about €250 per patient. The alternative policy, of universal screening by cfDNA testing, can potentially detect about 99%, 97% and 92% of cases of trisomies 21, 18 and 13, but at an overall cost of more than €500 per patient. Conclusion Incorporation of cfDNA testing into a contingent policy of early screening for the major trisomies, based on the risk derived from first‐line screening by a combination of maternal age, fetal NT and DV‐PIV, can detect a high proportion of affected cases with a low FPR. Copyright © 2014 ISUOG. Published by John Wiley &amp; Sons Ltd.
Context-sensitive timing simulation of binary embedded software
2014-10-12

We present an approach to accurately simulate the temporal behavior of binary embedded software based on timing data generated using static analysis. As the timing of an instruction sequence is significantly influenced by the microarchitecture state prior to its execution, which highly depends on the preceding control flow, a sequence must be separately considered for different control flow paths instead of estimating the influence of basic blocks or single instructions in isolation. We handle the thereby arising issue of an excessive or even infinite number of different paths by considering different execution contexts instead of control flow paths. Related approaches using context-sensitive cycle counts during simulation are limited to simulating the control flow that could be considered during analysis. We eliminate this limitation by selecting contexts dynamically, picking a suitable one when no predetermined choice is available, thereby enabling a context-sensitive simulation of unmodified binary code of concurrent programs, including asynchronous events such as interrupts. In contrast to other approximate binary simulation techniques, estimates are conservative, yet tight, making our approach reliable when evaluating performance goals. For a multi-threaded application the simulation deviates only by 0.24% from hardware measurements while the average overhead is only 50% compared to a purely functional simulation.