julilili42/papers huggingface dataset:
Probing the acetylation code of histone H4
2013-08-23

Histone modifications play crucial roles in genome regulation with lysine acetylation being implicated in transcriptional control. Here we report a proteome‐wide investigation of the acetylation‐dependent protein–protein interactions of the N ‐terminal tail of histone H 4. Quantitative peptide‐based affinity MS experiments using the SILAC approach determined the interactomes of H 4 tails monoacetylated at the four known acetylation sites K 5, K 8, K 12, and K 16, bis‐acetylated at K 5/ K 12, triple‐acetylated at K 8/12/16 and fully tetra‐acetylated. A set of 29 proteins was found enriched on the fully acetylated H 4 tail while specific binders of the mono and bis‐acetylated tails were barely detectable. These observations are in good agreement with earlier reports indicating that the H 4 acetylation state establishes its regulatory effects in a cumulative manner rather than via site‐specific recruitment of regulatory proteins.
Secondary Descemet Membrane Endothelial Keratoplasty After Failed Primary Descemet Membrane Endothelial Keratoplasty
2013-08-23

To manage DMEK cases with graft failure, secondary DMEK may be a feasible procedure potentially resulting in full visual rehabilitation, as in primary DMEK. In the event of a DMEK graft failure, a secondary DMEK may be an effective back-up procedure because it may give a clinical outcome similar to that given after a primary DMEK.
BI-RADS® 3 lesions at contrast-enhanced breast MRI: is an initial short-interval follow-up necessary?
2013-08-23

Background Magnetic resonance imaging (MRI) BI-RADS® 3 lesions should have a very high probability of being benign. To prove benignity most institutions do follow-up MRI. Purpose To evaluate the necessity of initial short-interval follow-up after 6 months as it is suggested for mammographic BI-RADS®3 lesions. Material and Methods We analyzed 163 consecutive MRI-BI-RADS® 3 lesions on follow-up MRI: 75 masses (46%), 67 foci (41.1%), and 21 (12.9%) non-mass-like enhancing lesions (NMLE). Results During MRI follow-up (mean time, 563 days) 20% of the lesions disappeared, 23% decreased, 52% did not change, and 4.9% showed increase. All increasing lesions were biopsied (5 benign, 2 ductal carcinoma in situ, 1 invasive carcinoma). The rate of malignancy was 1.8%. All malignant lesions (1 mass, 1 focus, 1 NMLE) showed increase at initial follow-up after a mean interval of 190 days. Conclusion In this study the malignancy rate of MRI-BI-RADS® 3 lesions corresponded to mammographic BI-RADS® 3 lesions. Initial short-interval MRI should be suggested to identify malignant MRI-BI-RADS® 3 lesions.
Mapping of Heavy Metal Ion Sorption to Cell-Extracellular Polymeric Substance-Mineral Aggregates by Using Metal-Selective Fluorescent Probes and Confocal Laser Scanning Microscopy
2013-08-24

ABSTRACT Biofilms, organic matter, iron/aluminum oxides, and clay minerals bind toxic heavy metal ions and control their fate and bioavailability in the environment. The spatial relationship of metal ions to biomacromolecules such as extracellular polymeric substances (EPS) in biofilms with microbial cells and biogenic minerals is complex and occurs at the micro- and submicrometer scale. Here, we review the application of highly selective and sensitive metal fluorescent probes for confocal laser scanning microscopy (CLSM) that were originally developed for use in life sciences and propose their suitability as a powerful tool for mapping heavy metals in environmental biofilms and cell-EPS-mineral aggregates (CEMAs). The benefit of using metal fluorescent dyes in combination with CLSM imaging over other techniques such as electron microscopy is that environmental samples can be analyzed in their natural hydrated state, avoiding artifacts such as aggregation from drying that is necessary for analytical electron microscopy. In this minireview, we present data for a group of sensitive fluorescent probes highly specific for Fe 3+ , Cu 2+ , Zn 2+ , and Hg 2+ , illustrating the potential of their application in environmental science. We evaluate their application in combination with other fluorescent probes that label constituents of CEMAs such as DNA or polysaccharides and provide selection guidelines for potential combinations of fluorescent probes. Correlation analysis of spatially resolved heavy metal distributions with EPS and biogenic minerals in their natural, hydrated state will further our understanding of the behavior of metals in environmental systems since it allows for identifying bonding sites in complex, heterogeneous systems.
High apolipoprotein E in cerebrospinal fluid of patients with Lewy body disorders is associated with dementia
2013-08-24

Abstract Apolipoprotein E ε4 allele ( APOE ε4) increases the apolipoprotein E (apoE) protein levels in Alzheimer's disease (AD) cerebrospinal fluid (CSF). Thus, we hypothesized that apoE levels were also associated with the APOE genotype, and amyloid‐β (Aβ)‐associated clinical, functional, and imaging parameters in patients with Lewy body‐associated disorders (LBD). Indeed, similar to AD, patients with LBD displayed high CSF apoE levels (greatest in patients with dementia with LBD), and this was linked to APOE ε4. High CSF apoE protein correlated positively with CSF soluble amyloid precursor protein, total tau, and cortical and striatal Pittsburgh compound B retention; and correlated negatively with CSF Aβ 42 , cognitive tests scores, and glucose uptake ratio in the temporal and parietal cortices. APOE ε4‐triggered accumulation of apoE in CSF is related to Aβ‐associated clinical and functional imaging parameters in LBD. Accordingly, therapeutic strategies aimed at reducing apoE levels in the brain should be explored not only in AD but also in LBD, particularly when accompanied with dementia.
Evidence for Less Marked Potential Signs of T-Cell Immunosenescence in Centenarian Offspring Than in the General Age-Matched Population
2013-08-24

People may reach the upper limits of the human life span at least partly because they have maintained more appropriate immune function, avoiding changes to immunity termed "immunosenescence." Exceptionally long-lived people may be enriched for genes that contribute to their longevity, some of which may bear on immune function. Centenarian offspring would be expected to inherit some of these, which might be reflected in their resistance to immunosenescence, and contribute to their potential longevity. We have tested this hypothesis by comparing centenarian offspring with age-matched controls. We report differences in the numbers and proportions of both CD4(+) and CD8(+) early- and late-differentiated T cells, as well as potentially senescent CD8(+) T cells, suggesting that the adaptive T-cell arm of the immune system is more "youthful" in centenarian offspring than controls. This might reflect a superior ability to mount effective responses against newly encountered antigens and thus contribute to better protection against infection and to greater longevity.
Unrestrained beta reduction
2013-08-24

A major argument for syntactic reconstruction is based on the well-known fact that semantic reconstruction by beta-reduction is possible only if the term to be substituted for a variable does not contain any variable that would become bound as a result of substitution. This way, we derive a theoretical argument for syntactic reconstruction. However, syntactic reconstruction is not without its problems, simply because the surface form and the reconstructed form may still differ with respect to other syntactic, semantic, and information theoretic properties. This is particularly troublesome for minimalist theories which do not allow for multiple levels of representation. In this paper we propose a technique that might help to overcome these difficulties (ie. the limitation imposed by beta-reduction on semantic reconstruction) by defining a translation function T for expressions of a predicate logic L0 with lambda-abstraction into expressions of a higher-order language L1, with the desirable property that the translation of a formula in L0 is equivalent with the translation of its unrestricted reduction. In linguistic applications this will facilitate the binding of a pronoun without presupposing c-command. We will sketch a formal proof showing that unrestricted beta-reduction is a property of the target expressions in L1, the translations of L0 under T.
Magnetostratigraphic and radiometric constraints on salt formation in the Qaidam Basin, NE Tibetan Plateau
2013-08-25

The Qaidam Basin is the largest Cenozoic intermontane basin within the northeast (NE) Tibetan Plateau. It contains large amounts of nonmarine evaporite deposits formed during the Pliocene-Quaternary. Even at present, extensive salt deposits dominated by halite and potash are formed by solar-driven concentration of brine water in the basin interior, making it the most important industrial base for potash exploitation in China. The formation of salt required an arid climatic, appropriate hydrological and tectonic setting through geologic times and will do so in the future. Studying the salt formation in the Qaidam Basin will enhance our understanding of processes driven by saline lake evolution, regional climate change, and tectonic movements, not only for the setting of the Tibetan Plateau. Reliable dating is crucial for assessing the time of salt formation in Qaidam Basin and the accumulation process, yet no comprehensive scientific studies have been reported on this important issue until now. In this paper, we critically review and compile magnetostratigraphic and radiometric studies of the salt-bearing strata within seven depressions of the basin. We find that the ages of salt formation are very different in these depressions: for the Dalangtan, Yiliping, Chahansilatu, and Kunteyi depressions, first salt deposits occurred at &gt;3.90 +/- 0.02 Ma, 2.88 +/- 0.04 Ma, 2.24 +/- 0.01 Ma and 1.18 +/- 0.02 Ma, respectively. For the Mahai, Gasikule, and Qarhan, the ages of earliest salt formation are much younger i.e., 302 +/- 56 ka, 608 +/- 38 ka, and 54-24 ka, respectively. However, the result from Mahai has to be considered with caution. The variability of ages suggests an older salt-forming stage in the center of the western basin and a younger salt accumulation period along the basin margin. In a regional view, previous results from stratigraphy, sedimentology, geomorphology, and tectonic history allow us to conclude that the salt formation in the Qaidam Basin was probably controlled by pulsed intrabasinal tectonic movements and the distribution and migration of paleo-rivers during the Pliocene-Quaternary. However, the climatic shift towards drier and colder conditions in the Asian interior during this time also promoted salt formation. (C) 2013 Elsevier Ltd. All rights reserved.
Using generalized additive models and random forests to model prosodic prominence in German
2013-08-25

The perception of prosodic prominence is influenced by different sources like different acoustic cues, linguistic expectations and context. We use a generalized additive model and a random forest to model the perceived prominence on a corpus of spoken German. Both models are able to explain over 80% of the variance. While the random forests give us some insights on the relative importance of the cues, the general additive model gives us insights on the interaction between different cues to prominence.
Word frequency, vowel length and vowel quality in speech production: an EMA study of the importance of experience
2013-08-25

A frequently replicated finding is that higher frequency words tend to be shorter and contain more strongly reduced vowels. However, little is known about potential differences in the articulatory gestures for high vs. low frequency words. The present study made use of electromagnetic articulography to investigate the production of two German vowels, [i] and [a], embedded in high and low frequency words. We found that word frequency differently affected the production of [i] and [a] at the temporal as well as the gestural level. Higher frequency of use predicted greater acoustic durations for long vowels; reduced durations for short vowels; articulatory trajectories with greater tongue height for [i] and more pronounced downward articulatory trajectories for [a]. These results show that the phonological contrast between short and long vowels is learned better with experience, and challenge both the Smooth Signal Redundancy Hypothesis and current theories of German phonology.
Association of Cerebrospinal Fluid β-Amyloid 1-42, T-tau, P-tau181, and α-Synuclein Levels With Clinical Features of Drug-Naive Patients With Early Parkinson Disease
2013-08-26

In this first report of CSF biomarkers in PPMI study subjects,we found that measures of CSF Aβ1-42, T-tau, P-tau181, and α-synuclein have prognostic and diagnostic potential in early-stage PD. Further investigations using the entire PPMI cohort will test the predictive performance of CSF biomarkers for PD progression
Effective potential of the confinement order parameter in the Hamiltonian approach
2013-08-26

The effective potential of the order parameter for confinement is calculated\\nfor SU(N) Yang--Mills theory in the Hamiltonian approach. Compactifying one\\nspatial dimension and using a background gauge fixing, this potential is\\nobtained within a variational approach by minimizing the energy density for\\ngiven background field. In this formulation the inverse length of the\\ncompactified dimension represents the temperature. Using Gaussian trial wave\\nfunctionals we establish an analytic relation between the propagators in the\\nbackground gauge at finite temperature and the corresponding zero-temperature\\npropagators in Coulomb gauge. In the simplest truncation, neglecting the ghost\\nand using the ultraviolet form of the gluon energy, we recover the Weiss\\npotential. We explicitly show that the omission of the ghost drastically\\nincreases the transition temperature. From the full non-perturbative potential\\n(with the ghost included) we extract a critical temperature of the\\ndeconfinement phase transition of 269 MeV for the gauge group SU(2) and 283 MeV\\nfor SU(3).\\n
PIK3R1 mutations in SHORT syndrome
2013-08-26

SHORT syndrome ( OMIM 269880) is a rare autosomal‐dominant disorder characterized by short stature, hyperextensibility of joints, hernias, ocular depression, ophthalmic anomalies (Rieger anomaly, posterior embryotoxon, glaucoma), teething delay, partial lipodystrophy, insulin resistance and facial dysmorphic signs. Heterozygous mutations in PIK3R1 were recently identified in 14 families with SHORT syndrome. Eight of these families had a recurrent missense mutation (c. 1945C &gt;T; p. Arg649Trp ). We report on two unrelated patients with typical clinical features of SHORT syndrome and additional problems such as pulmonary stenosis and ectopic kidney. Analysis of PIK3R1 revealed the mutation c. 1945C &gt;T; p. Arg649Trp de novo in both patients. These two patients not only provide additional evidence that PIK3R1 mutations cause SHORT syndrome, but also broaden the clinical spectrum of this syndrome and further confirm that the amino acid exchange c. 1945C &gt;T; p. Arg649Trp is a hotspot mutation in this gene.
Personality traits and living arrangements in young adulthood: Selection and socialization.
2013-08-26

Based on the social investment principle and theories of social relationship differentiation, the present study was conducted to investigate whether personality differences in high school predict young adults' living arrangements (with roommates or a romantic partner, alone, or staying with parents) 2 years later (selection) and whether these different social contexts provoke long-term personality changes (socialization). Using data from a 3-wave longitudinal study of 8,052 high school graduates in Germany, multinomial logistic regression analyses revealed substantial selection effects of the Big Five traits on living arrangements. Propensity score matching was applied to provide a strong test of the socialization effects of these living arrangements. Young adults who lived with roommates showed increases in Openness but the smallest increases in Conscientiousness. Living with a romantic partner was the most beneficial arrangement for the development of Conscientiousness. These results highlight the importance of social contexts for personality development in young adulthood.
Linear State Space Modeling of Gamma-Ray Burst Lightcurves
2013-08-26

Abstract. Linear State Space Modeling determines the hidden autoregressive (AR) process in a noisy time series; for an AR process the time series ’ current value is the sum of current stochastic “noise ” and a linear combination of previous values. We present preliminary results from modeling a sample of 4 channel BATSE LAD lightcurves. We determine the order of the AR process necessary to model the bursts. The comparison of decay constants for different energy bands shows that structure decays more rapidly at high energy. The resulting models can be interpreted physically; for example, they may reveal the response of the burst emission region to the injection of energy.
What Drives Contagion in Financial Markets? Liquidity Effects versus Information Spill‐Over
2013-08-27

Abstract The objective of this paper is to study how contagion works in financial markets by identifying the mechanisms which drive the spill‐over of shocks from one market to other markets. To address this question we use open‐ended property funds (OPFs) as they offer a unique institutional setting which allows separating between liquidity and information spill‐over. We find that that liquidity risk captures the observed discounts very well when the danger of potential future impairments is low. Once the impending NAV impairments become very likely, also this component matters and attributes for a fraction of the total discount.
Two-neutrino double-βdecay Fermi transition and two-nucleon interaction
2013-08-27

An exactly solvable model for a description of the two-neutrino double beta\\ndecay transition of the Fermi type is considered. By using perturbation theory\\nan explicit dependence of the two-neutrino double beta decay matrix element on\\nthe like-nucleon pairing, particle-particle and particle-hole proton-neutron\\ninteractions by assuming a weak violation of isospin symmetry of Hamiltonian\\nexpressed with generators of the SO(5) group. It is found that there is a\\ndominance of double beta decay transition through a single state of the\\nintermediate nucleus. Then, an energy weighted sum rule connecting Delta Z=2\\nnuclei is presented and discussed. It is suggested that this sum rule can be\\nexploited to study the residual interactions of the nuclear Hamiltonian.\\n
Gravitational wave asteroseismology of fast rotating neutron stars with realistic equations of state
2013-08-28

In the present paper we study the oscillations of fast rotating neutron stars\\nwith realistic equations of state (EoS) within the Cowling approximation. We\\nderive improved empirical relations for gravitational wave asteroseismology\\nwith f-modes and for the first time we consider not only quadrupolar\\noscillations but also modes with higher spherical order (l=|m|=3,4). After\\nperforming a systematic comparison with polytropic EoS, it is shown that the\\nempirical relations found in this case approximately also hold for realistic\\nEoS. Even more, we show that these relations will not change significantly even\\nif the Cowling approximation is dropped and the full general relativistic case\\nis considered, although the normalization used here(frequencies and damping\\ntimes in the nonrotating limit) could differ considerably. We also address the\\ninverse problem, i.e. we investigate in detail what kind of observational data\\nis required in order to determine characteristical neutron star parameters. It\\nis shown that masses, radii and rotation rates can be estimated quite\\naccurately using the derived asteroseismology relations. We also compute the\\ninstability window for certain models, i.e. the limiting curve in a\\nT-\\\\Omega-plane where the secular Chandrasekhar-Friedman-Schutz(CFS) instability\\novercomes dissipative effects, and show that some of the modern realistic EoS\\nwill lead to a larger instability window compared to all of the polytropic ones\\npresented so far in the literature. Additionally, we calculate the r-mode\\ninstability window and compare it with the f-mode-case. The overall results for\\nthe instability window suggest that it is vital to take into account\\noscillations with l=3,4 when considering gravitational wave asteroseismology\\nusing the f-mode in rapidly rotating neutron stars, as these modes can become\\nCFS unstable for a much larger range of parameters than pure quadrupolar\\noscillations.\\n
Hydroa vacciniforme-like lymphoma: a chronic EBV+ lymphoproliferative disorder with risk to develop a systemic lymphoma
2013-08-28

Key Points HVLL is a chronic EBV+ lymphoproliferative disorder of childhood with risk to develop systemic lymphoma. The disease shows favorable response to conservative therapy despite the presence of a T- or NK-cell monoclonal proliferation.
LRRK2 and RIPK2 Variants in the NOD 2-Mediated Signaling Pathway Are Associated with Susceptibility to Mycobacterium leprae in Indian Populations
2013-08-28

In recent years, genome wide association studies have discovered a large number of gene loci that play a functional role in innate and adaptive immune pathways associated with leprosy susceptibility. The immunological control of intracellular bacteria M. leprae is modulated by NOD2-mediated signaling of Th1 responses. In this study, we investigated 211 clinically classified leprosy patients and 230 ethnically matched controls in Indian population by genotyping four variants in NOD2 (rs9302752A/G), LRRK2 (rs1873613A/G), RIPK2 (rs40457A/G and rs42490G/A). The LRRK2 locus is associated with leprosy outcome. The LRRK2 rs1873613A minor allele and respective rs1873613AA genotypes were significantly associated with an increased risk whereas the LRRK2 rs1873613G major allele and rs1873613GG genotypes confer protection in paucibacillary and leprosy patients. The reconstructed GA haplotypes from RIPK2 rs40457A/G and rs42490G/A variants was observed to contribute towards increased risk whereas haplotypes AA was observed to confer protective role. Our results indicate that a possible shared mechanisms underlying the development of these two clinical forms of the disease as hypothesized. Our findings confirm and validates the role of gene variants involved in NOD2-mediated signalling pathways that play a role in immunological control of intracellular bacteria M. leprae.