Pollen and Phytoliths from Fired Ancient Potsherds as Potential Indicators for Deciphering Past Vegetation and Climate in Turpan, Xinjiang, NW China

It is demonstrated that palynomorphs can occur in fired ancient potsherds when the firing temperature was under 350°C. Pollen and phytoliths recovered from incompletely fired and fully fired potsherds (ca. 2700 yrs BP) from the Yanghai Tombs, Turpan, Xinjiang, NW China can be used as potential indicators for reconstructing past vegetation and corresponding climate in the area. The results show a higher rate of recovery of pollen and phytoliths from incompletely fired potsherds than from fully fired ones. Charred phytoliths recovered from both fully fired and incompletely fired potsherds prove that degree and condition of firing result in a permanent change in phytolith color. The palynological data, together with previous data of macrobotanical remains from the Yanghai Tombs, suggest that temperate vegetation and arid climatic conditions dominated in the area ca. 2700 yrs BP

Time Distribution of the Onset of Chest Pain in Subjects with Acute ST-Elevation Myocardial Infarction: An Eight-Year, Single-Center Study in China

Objective: The objective of this study was to explore the time distribution patterns of the onset of chest pain in subjects with acute ST-elevation myocardial infarction in a Chinese population. Methods: A total of 1467 patients with acute ST-elevation myocardial infarction were enrolled from 2003 to 2010. The hourly, daily, monthly, seasonal and day-of-week fluctuations in the prevalence of acute ST-elevation myocardial infarction were analyzed. Results: A peak was found between the morning hours of 07:31 and 08:30. A second peak was observed between 14:31 and 15:30, and a third peak was found between 23:31 and 00:30 (p,0.001). The monthly maximum was recorded in November and the minimum was in April (p,0.001). The number of daily cases was greatest in autumn and lowest in the spring (p = 0.001). Day-of-the-week variations of ST-elevation acute myocardial infarction were not found, except in patients more than 75-years-old. Conclusions: Periodic variations in the frequency of ST-elevation acute myocardial infarction in Chinese patients showed significant differences with regard to diurnal, monthly and seasonal patterns. The exact mechanisms underlying thes

Predicting Human Nucleosome Occupancy from Primary Sequence

Nucleosomes are the fundamental repeating unit of chromatin and comprise the structural building blocks of the living eukaryotic genome. Micrococcal nuclease (MNase) has long been used to delineate nucleosomal organization. Microarray-based nucleosome mapping experiments in yeast chromatin have revealed regularly-spaced translational phasing of nucleosomes. These data have been used to train computational models of sequence-directed nuclesosome positioning, which have identified ubiquitous strong intrinsic nucleosome positioning signals. Here, we successfully apply this approach to nucleosome positioning experiments from human chromatin. The predictions made by the human-trained and yeast-trained models are strongly correlated, suggesting a shared mechanism for sequence-based determination of nucleosome occupancy. In addition, we observed striking complementarity between classifiers trained on experimental data from weakly versus heavily digested MNase samples. In the former case, the resulting model accurately identifies nucleosome-forming sequences; in the latter, the classifier excels at identifying nucleosome-free regions. Using this model we are able to identify several characteristics of nucleosome-forming and nucleosome-disfavoring sequences. First, by combining results from each classifier applied de novo across the human ENCODE regions, the classifier reveals distinct sequence composition and periodicity features of nucleosome-forming and nucleosome-disfavoring sequences. Short runs of dinucleotide repeat appear as a hallmark of nucleosome-disfavoring sequences, while nucleosome-forming sequences contain short periodic runs of GC base pairs. Second, we show that nucleosome phasing is most frequently predicted flanking nucleosome-free regions. The results suggest that the major mechanism of nucleosome positioning in vivo is boundary-event-driven and affirm the classical statistical positioning theory of nucleosome organization

Topography as a modifier of breeding habitats and concurrent vulnerability to malaria risk in the western Kenya highlands

<p>Abstract</p> <p>Background</p> <p>Topographic parameters such as elevation, slope, aspect, and ruggedness play an important role in malaria transmission in the highland areas. They affect biological systems, such as larval habitats presence and productivity for malaria mosquitoes. This study investigated whether the distribution of local spatial malaria vectors and risk of infection with malaria parasites in the highlands is related to topography.</p> <p>Methods</p> <p>Four villages each measuring 9 Km²lying between 1400-1700 m above sea level in the western Kenya highlands were categorized into a pair of broad and narrow valley shaped terrain sites. Larval, indoor resting adult malaria vectors and infection surveys were collected originating from the valley bottom and ending at the hilltop on both sides of the valley during the rainy and dry seasons. Data collected at a distance of ≤500 m from the main river/stream were categorized as valley bottom and those above as uphill. Larval surveys were categorized by habitat location while vectors and infections by house location.</p> <p>Results</p> <p>Overall, broad flat bottomed valleys had a significantly higher number of anopheles larvae/dip in their habitats than in narrow valleys during both the dry (1.89 versus 0.89 larvae/dip) and the rainy season (1.66 versus 0.89 larvae/dip). Similarly, vector adult densities/house in broad valley villages were higher than those within narrow valley houses during both the dry (0.64 versus 0.40) and the rainy season (0.96 versus 0.09). Asymptomatic malaria prevalence was significantly higher in participants residing within broad than those in narrow valley villages during the dry (14.55% vs. 7.48%) and rainy (17.15% vs. 1.20%) season. Malaria infections were wide spread in broad valley villages during both the dry and rainy season, whereas over 65% of infections were clustered at the valley bottom in narrow valley villages during both seasons.</p> <p>Conclusion</p> <p>Despite being in the highlands, local areas within low gradient topography characterized by broad valley bottoms have stable and significantly high malaria risk unlike those with steep gradient topography, which exhibit seasonal variations. Topographic parameters could therefore be considered in identification of high-risk malaria foci to help enhance surveillance or targeted control activities in regions where they are most needed.</p

Presenting the Uncertainties of Odds Ratios Using Empirical-Bayes Prediction Intervals

Quantifying exposure-disease associations is a central issue in epidemiology. Researchers of a study often present an odds ratio (or a logarithm of odds ratio, logOR) estimate together with its confidence interval (CI), for each exposure they examined. Here the authors advocate using the empirical-Bayes-based ‘prediction intervals’ (PIs) to bound the uncertainty of logORs. The PI approach is applicable to a panel of factors believed to be exchangeable (no extra information, other than the data itself, is available to distinguish some logORs from the others). The authors demonstrate its use in a genetic epidemiological study on age-related macular degeneration (AMD). The proposed PIs can enjoy straightforward probabilistic interpretations—a 95% PI has a probability of 0.95 to encompass the true value, and the expected number of true values that are being encompassed is for a total of 95% PIs. The PI approach is theoretically more efficient (producing shorter intervals) than the traditional CI approach. In the AMD data, the average efficiency gain is 51.2%. The PI approach is advocated to present the uncertainties of many logORs in a study, for its straightforward probabilistic interpretations and higher efficiency while maintaining the nominal coverage probability

Contributions of Dopamine-Related Genes and Environmental Factors to Highly Sensitive Personality: A Multi-Step Neuronal System-Level Approach

Traditional behavioral genetic studies (e.g., twin, adoption studies) have shown that human personality has moderate to high heritability, but recent molecular behavioral genetic studies have failed to identify quantitative trait loci (QTL) with consistent effects. The current study adopted a multi-step approach (ANOVA followed by multiple regression and permutation) to assess the cumulative effects of multiple QTLs. Using a system-level (dopamine system) genetic approach, we investigated a personality trait deeply rooted in the nervous system (the Highly Sensitive Personality, HSP). 480 healthy Chinese college students were given the HSP scale and genotyped for 98 representative polymorphisms in all major dopamine neurotransmitter genes. In addition, two environment factors (stressful life events and parental warmth) that have been implicated for their contributions to personality development were included to investigate their relative contributions as compared to genetic factors. In Step 1, using ANOVA, we identified 10 polymorphisms that made statistically significant contributions to HSP. In Step 2, these polymorphism's main effects and interactions were assessed using multiple regression. This model accounted for 15% of the variance of HSP (p<0.001). Recent stressful life events accounted for an additional 2% of the variance. Finally, permutation analyses ascertained the probability of obtaining these findings by chance to be very low, p ranging from 0.001 to 0.006. Dividing these loci by the subsystems of dopamine synthesis, degradation/transport, receptor and modulation, we found that the modulation and receptor subsystems made the most significant contribution to HSP. The results of this study demonstrate the utility of a multi-step neuronal system-level approach in assessing genetic contributions to individual differences in human behavior. It can potentially bridge the gap between the high heritability estimates based on traditional behavioral genetics and the lack of reproducible genetic effects observed currently from molecular genetic studies

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Abstract Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free) and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase) and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site) and TTS (Transcription Termination Site) (at least in yeast) is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression

Graphene membranes for water desalination

Extensive environmental pollution caused by worldwide industrialization and population growth has led to a water shortage. This problem lowers the quality of human life and wastes a large amount of money worldwide each year due to the related consequences. One main solution for this challenge is water purification. State-of-the-art water purification necessitates the implementation of novel materials and technologies that are cost and energy efficient. In this regard, graphene nanomaterials, with their unique physicochemical properties, are an optimum choice. These materials offer extraordinarily high surface area, mechanical durability, atomic thickness, nanosized pores and reactivity toward polar and non-polar water pollutants. These characteristics impart high selectivity and water permeability, and thus provide excellent water purification efficiency. This review introduces the potential of graphene membranes for water desalination. Although literature reviews have mostly concerned graphene's capability for the adsorption and photocatalysis of water pollutants, updated knowledge related to its sieving properties is quite limited.Peer reviewe

Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV

The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal