Miracle-dz/UniFAR-FTUs huggingface dataset:
Varves, turbidites and cycles in upper Holocene sediments (Makran slope, northern Arabian Sea)

Abstract We have analysed two Late Holocene records, each about 5 ka long, consisting of varved sediments deposited in the oxygen minimum zone off Pakistan (upper continental slope off Ormara and west of Karachi). Varve counting was checked by accelerator mass spectrometry (AMS) 14C dating. Detailed lithofacies analysis, ultra-high-resolution X-ray fluorescence scanning, flux rates from sediment traps and the lamina-by-lamina-analysis of a 5 year record (1993–1998) support our interpretation of the annual character of the laminae. Although the pelagic material is deposited throughout the year, most of it is apparently laid down during the high-productivity period of the late summer monsoon. During the winter (mainly mid-December to February-March) mainly light-coloured detrital material (siliciclastic material and reworked carbonate flour) is deposited, probably by river flood events. Event deposits include turbid-plume or suspensate deposits (light grey homogeneous to graded silty clay layers), which are being laid down at decadal or shorter intervals; they are explained by episodically strong river floods after heavy rains transporting mud-charged waters to the narrow shelf and onto the steep continental slope. Medium grey or reddish grey, graded and laminated silt turbidites originated from less frequent, unchannelized, low-density turbidity currents. In general, periods with thin varves (generally correlated with rare turbidites) are correlated with minima of detrital element ratios (TiO2/Al2O3, Zr/Al2O3, K2O/Al2O3), especially in Period I (c. 5600-4700 a bp), suggesting a climate with reduced precipitation and river runoff (possibly winter monsoon dominated). Period II (4700-2600 a bp) is characterized by comparatively thick varves documenting a generally wet period (with possibly summer monsoon domination). During Period III (2600-1000 a bp) a gradual thinning of varves and a decrease of turbidite abundance (thickness) per century is interpreted as a gradual decline of precipitation and river runoff leading finally to dry conditions from 1600 to 1000 a bp. The sequence of cycles detected by autocorrelation and standard Fourier analysis seems to contain a large proportion of multiples of the lunar perigee cycle (4.425 a, 8.85 a) and the lunar (half) nodal cycle (9.3 a, 18.6 a). Our test for cyclicity in the series of varve thickness (varve cycles) and of abundance of turbidites (turbidite cycles) detected prominent high-frequency cycles. Some cycles of varve thickness match the cyclicity of turbidite frequency. We also detected the presence of a 1470 a cycle, previously reported from the glacial-age Greenland ice record.
Deposition of highly crystalline graphite from moderate-temperature fluids

Recognized large occurrences of fluid-deposited graphite displaying high crystallinity were previously restricted to high-temperature environments (mainly granulite facies terranes). However, in the extensively mined Borrowdale deposit (UK), the mineralogical assemblage, notably the graphite-epidote intergrowths, shows that fully ordered graphite precipitated during the propylitic hydrothermal alteration of the volcanic host rocks. Fluids responsible for graphite deposition had an average X CO2/(XCO2 + X CH4) ratio of 0.69, thus indicating temperatures of ~500 °C at the fayalite-magnetite-quartz buffered conditions. Therefore, this is the first reported evidence indicating that huge concentrations of highly crystalline graphite can precipitate from moderate-temperature fluids.
High-throughput analysis of epistasis in genome-wide association studies with BiForce

Motivation: Gene–gene interactions (epistasis) are thought to be important in shaping complex traits, but they have been under-explored in genome-wide association studies (GWAS) due to the computational challenge of enumerating billions of single nucleotide polymorphism (SNP) combinations. Fast screening tools are needed to make epistasis analysis routinely available in GWAS. Results: We present BiForce to support high-throughput analysis of epistasis in GWAS for either quantitative or binary disease (case–control) traits. BiForce achieves great computational efficiency by using memory efficient data structures, Boolean bitwise operations and multithreaded parallelization. It performs a full pair-wise genome scan to detect interactions involving SNPs with or without significant marginal effects using appropriate Bonferroni-corrected significance thresholds. We show that BiForce is more powerful and significantly faster than published tools for both binary and quantitative traits in a series of performance tests on simulated and real datasets. We demonstrate BiForce in analysing eight metabolic traits in a GWAS cohort (323 697 SNPs, >4500 individuals) and two disease traits in another (>340 000 SNPs, >1750 cases and 1500 controls) on a 32-node computing cluster. BiForce completed analyses of the eight metabolic traits within 1 day, identified nine epistatic pairs of SNPs in five metabolic traits and 18 SNP pairs in two disease traits. BiForce can make the analysis of epistasis a routine exercise in GWAS and thus improve our understanding of the role of epistasis in the genetic regulation of complex traits. Availability and implementation: The software is free and can be downloaded from http://bioinfo.utu. fi/BiForce/. Contact: wenhua.wei@igmm.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Temporal click model for sponsored search

Previous studies on search engine click modeling have identified two presentation factors that affect users' behavior: (1) position bias: the same result will get a different number of clicks when displayed in different positions and (2) externalities: the same result might get more clicks when displayed with results of relatively lower quality than when shown with higher quality results. In this paper we focus on analyzing the sequence of user actions to model users' click behavior on sponsored listings shown on the search results page. We first show that temporal click sequences are good indicators of externalities in the advertising domain. We then describe the positional rationality hypothesis to explain both the position bias and the externalities, and based on this hypothesis we further propose the temporal click model (TCM), a Bayesian framework that is scalable and computationally efficient. To the best of our knowledge, this is the first attempt in the literature to estimate positional bias, externalities and unbiased user-perceived ad quality from user click logs in a combined model. We finally evaluate the proposed model on two real datasets, each containing over 100 million ad impressions obtained from a commercial search engine. The experimental results show that TCM outperforms two other competitive methods at click prediction.
Effects of Dietary Garlic Extract on Growth, Feed Utilization and Whole Body Composition of Juvenile Sterlet Sturgeon (Acipenser ruthenus)

This study was carried out to investigate the supplemental effects of dietary garlic extract (GE) on growth performance of juvenile sterlet sturgeon (Acipenser ruthenus). The first experiment was designed to determine the optimum levels of garlic extract as growth promoter during 10 weeks. Three groups (two replicates/group) of 240 fish with mean body weight of 85 g were fed with diets containing 0 (control), 0.5 and 1.0% of GE. The highest weight gain (%) and feed efficiency (%) were found in fish groups fed with diet containing 0.5% GE. Subsequently, the supplemental effects of dietary GE was studied on growth of juvenile sterlet sturgeon (Acipenser ruthenus) with an average body weight of 59.6 g. Fish cultured in freshwater were randomly allotted to each of 10 tanks (two groups of five replicates, 20 fish/tank) and fed diets with 0.5% GE or without GE (control), respectively, at the level of 2.0% of fish body weight per day for 5 weeks. Weight gain (51.1%), feed efficiency (79.1%), specific growth rate (1.18%) and protein efficiency ratio (1.50) of fish fed 0.5% GE were significantly (p<0.05) higher than those fish fed the control diet. Significantly higher protein (PRE 20.4%) and lipid retention efficiencies (LRE, 74.5%) were also found in 0.5% GE group (p<0.05). The present results suggested that dietary GE could improve growth and feed utilization of juvenile sterlet sturgeons.
Interacting Vegetative and Thermal Contributions to Water Movement in Desert Soil

Thermally driven water‐vapor flow can be an important component of total water movement in bare soil and in deep unsaturated zones, but this process is often neglected when considering the effects of soil–plant–atmosphere interactions on shallow water movement. The objectives of this study were to evaluate the coupled and separate effects of vegetative and thermal‐gradient contributions to soil water movement in desert environments. The evaluation was done by comparing a series of simulations with and without vegetation and thermal forcing during a 4.7‐yr period (May 2001–December 2005). For vegetated soil, evapotranspiration alone reduced root‐zone (upper 1 m) moisture to a minimum value (25 mm) each year under both isothermal and nonisothermal conditions. Variations in the leaf area index altered the minimum storage values by up to 10 mm. For unvegetated isothermal and nonisothermal simulations, root‐zone water storage nearly doubled during the simulation period and created a persistent driving force for downward liquid fluxes below the root zone (total net flux ∼1 mm). Total soil water movement during the study period was dominated by thermally driven vapor fluxes. Thermally driven vapor flow and condensation supplemented moisture supplies to plant roots during the driest times of each year. The results show how nonisothermal flow is coupled with plant water uptake, potentially influencing ecohydrologic relations in desert environments.
Interface conditions for a singular reaction-diffusion system

For a chemical reaction/diffusion system, a very fast reaction $A+B\to C$ implies non-coexistence of $A,B$ with resulting interfaces. We try to understand how these interfaces evolve in time. In particular, we seek a characterizing system of equations and conditions for the sharp interface limit: when this fast reaction is taken as infinitely fast.
E-Government in Saudi Arabia: Between Promise and Reality

Saudi Arabia is in the process of transitioning to e-government. Many of the Saudi government agencies have their own web sites; however, most are ineffective. Based on the findings of this study, the Saudis should consider several reforms, chief among which include the following: Increasing the awareness of its e-government program among its employees and the public at-large; making Internet access more available across the full spectrum of society; equipping public facilities for Internet usage; developing a legal framework for secure e-transactions; adopting a flexible approach to technological change and the IT environment more generally; providing IT training to government employees; partnering with the private sector to establish electronic fund transfers; and, finally, fostering 2-way communication between government agencies and between the government and the public.
The Developmental Loss of the Ability of Purkinje Cells to Regenerate Their Axons Occurs in the Absence of Myelin: An In Vitro Model to Prevent Myelination

Axonal regeneration in the mammalian CNS is a property of immature neurons that is lost during development. Using organotypic culture of cerebellum, we have shown that in vitro Purkinje cells lose their regenerative capacity in parallel with the process of myelination. We have investigated whether myelination is involved in the age-dependent loss of regeneration of these neurons. By applying a high dose of bromodeoxyuridine in the culture medium of newborn cerebellar slices during the first 3 d in vitro, we have succeeded in obtaining cultures with oligodendrocyte depletion, together with a lack of ameboid microglia and enhancement of Purkinje cell survival. These cultures, after 14 d in vitro, are completely devoid of myelin. We have compared the ability of Purkinje cells to regenerate their axons in the presence or absence of myelin. Purkinje cells in cerebellar explants taken at birth, treated with bromodeoxyuridine and axotomized after 7 d in vitro, survive better than similar neurons in untreated cultures. However, despite the lack of myelin and the enhanced survival, Purkinje cells do not regenerate, whereas they do regenerate when the axotomy is done at postnatal day 0. Thus, the Purkinje cell developmental switch from axonal regeneration to lack of regeneration does not appear to be regulated by myelin.
Assessing trends in observed and modelled climate extremes over Australia in relation to future projections

Multiple simulations from nine globally coupled climate models were assessed for their ability to reproduce observed trends in a set of indices representing temperature and precipitation extremes over Australia. Observed trends over the period 1957–1999 were compared with individual and multi‐modelled trends calculated over the same period. When averaged across Australia, the magnitude of trends and interannual variability of temperature extremes were well simulated by most models, particularly for the index for warm nights. The majority of models also reproduced the correct sign of trend for precipitation extremes although there was much more variation between the individual model runs. A bootstrapping technique was used to calculate uncertainty estimates and also to verify that most model runs produce plausible trends when averaged over Australia. Although very few showed significant skill at reproducing the observed spatial pattern of trends, a pattern correlation measure showed that spatial noise could not be ruled out as dominating these patterns. Two of the models with output from different forcings showed that the observed trends over Australia for one of the temperature indices was consistent with an anthropogenic response, but was inconsistent with natural‐only forcings. Future projected changes in extremes using three emissions scenarios were also analysed. Australia shows a shift towards warming of temperature extremes, particularly a significant increase in the number of warm nights and heat waves with much longer dry spells interspersed with periods of increased extreme precipitation, irrespective of the scenario used. Copyright © 2008 Royal Meteorological Society
Organization of acetylcholine-containing structures in the cranial motor nuclei of the rhombencephalon of the pig

We explored the immunoreactivity of choline acetyltransferase (ChAT) in the cranial nerve motor nuclei of the porcine rhombencephalon to reveal the cholinergic nature of these regions. In our experiments we used an immunohistochemical method for the visualization of all acetylcholine-containing structures. All studied motor nuclei contained ChAT-positive cell bodies and fibres, but the intensity of staining differed between the nuclei. Furthermore, characteristic ChAT-immunoreactive bouton-like structures, which are known to be synaptic terminals of the cholinergic system, were observed in the borders of all studied regions. The localization of ChAT-positive "boutons" in the neuropil of the examined nuclei and their proximity to stained perikarya allowed us to d ifferentiate two groups of motor nuclei in the rhombencephalon of the pig: (a) Nuclei containing ChAT-positive bouton-like structures dispersed in the neuropil, often establishing contacts with the stained cell bodies - motor trigeminal, abducent, facial, ambiguous and hypoglossal nuclei. (b) Nuclei in which characteristic boutons were dispersed among the ChAT-positive cells, but were devoid of any contact with perikarya - dorsal motor nucleus of the vagus nerve. These results provide new data on the porcine central nervous system and could be useful in further experiments on amyotrophic lateral sclerosis (ALS) - the disease that results in the progressive degeneration of motoneurons in the brain and spinal cord.
Effects of High Versus Low Flux Membranes on O2 Saturation in Hemodialysis Patients

Background Several studies have been carried out to evaluate the effects of dialysis on O2 saturation. While the dialysis procedure may lead to hypoxia under different circumstances, there are few studies available on the effects of membrane type on O2 saturation in these patients. objectives This study was to appraise the effects of high and low flux membrane on pulse oxymetery in dialysis patients. Patients and Methods In a cross-sectional evaluation, 43 hemodialysis patients without pulmonary disease were enrolled. Of this group, dialysis was performed by low and high flux membranes, and pulse oxymetery was applied before and after the procedures. Results Mean age of the patients was 56.34 years. Of these patients, 23 (53.5%) and 20 (46.5%) were women and men, respectively. Type of membrane (high flux vs. low flux) did not show any significant effect on pulse oxymetery results (P > 0.05). Conclusions Due to the lack of a significant difference in pulse oxymetery and creation of hypoxia between two types of membranes in hemodialysis patients, as well as the high cost of high flux membrane as compared to the low flux membrane, we do not suggest the use of high flux membrane in dialysis.
Improved diagnosis of Trichuris trichiura by using a bead-beating procedure on ethanol preserved stool samples prior to DNA isolation and the performance of multiplex real-time PCR for intestinal parasites

SUMMARY For the majority of intestinal parasites, real-time PCR-based diagnosis outperforms microscopy. However, the data for Trichuris trichiura have been less convincing and most comparative studies have been performed in populations with low prevalence. This study aims to improve detection of T. trichuria DNA in human stool by evaluating four sample preparation methods. Faecal samples (n = 60) were collected at Flores island, Indonesia and examined by microscopy. Aliquots were taken and a bead-beating procedure was used both on directly frozen stool and on material preserved with 96% ethanol. PCR on frozen samples showed 40% to be positive for T. trichiura, compared with 45% positive by microscopy. The percentage positive increased when using ethanol preservation (45·0%), bead-beating (51·7%) and a combination (55·0%) and all three methods showed significantly higher DNA loads. The various procedures had a less pronounced effect on the PCR results of nine other parasite targets tested. Most prevalent were Ascaris lumbricoides (≈60%), Necator americanus (≈60%), Dientamoeba fragilis (≈50%) and Giardia lamblia (≈12%). To validate the practicality of the procedure, bead-beating was applied in a population-based survey testing 910 stool samples. Findings confirmed bead-beating before DNA extraction to be a highly efficient procedure for the detection of T. trichiura DNA in stool.
Indications for hematopoietic stem cell transplantation in patients with follicular lymphoma: a consensus project of the EBMT-Lymphoma Working Party

The aim of this project was to define indications for hematopoietic stem cell transplantation in follicular lymphoma in Europe. In the absence of evidence-based data, a RAND-modified Delphi procedure was used by an expert panel. After pre-defining statements, these were individually/anonymously scored by each participant using a 9-point scale. Consensus was reached that: 1) high-dose therapy with autologous stem cell rescue is not an appropriate option to consolidate first remission in patients responding to immuno-chemotherapy outside clinical trials; 2) in patients with first chemo-sensitive relapse, high-dose therapy with autologous stem cell rescue is an appropriate option to consolidate remission, especially in patients with a short response after immuno-chemotherapy or with high-risk FLIPI; 3) high-dose therapy with autologous stem cell rescue is also appropriate in second/subsequent chemo-sensitive relapses; 4) allotransplant (preferably a reduced intensity conditioning-allotransplant) should be considered at relapse after high-dose therapy with autologous stem cell rescue. No consensus was reached on the role of high-dose therapy with autologous stem cell rescue in low-risk first relapse, or on when an allotransplant should be preferred over high-dose therapy with autologous stem cell rescue. In the absence of evidence-based data, the consensus method used was a valuable tool to define indications for hematopoietic stem cell transplant in follicular lymphoma.
Deterministic modeling of landslide and rockfall risk

The article presents two deterministic methods for the elaboration of landslide and rock-fall source area maps and, considering human activity in the landscape, for the elaboration of landslide and rockfall risk maps. Risk maps are one of the fundamental bases for protection against natural disasters since they illustrate the risks to areas of human activity due to various natural processes. Using the weighting method and for the first time the matrix method, we established the extent of land-slide and rockfall source areas in the Upper Savinja Valley and the risk due to these processes relative to settlement, roads, land use, and rivers and streams. The methodology for elaborating maps using both approaches is described in detail as well as the differ-ences between them. The basic purpose of risk maps is to direct human encroachment in the landscape to safe areas.
Environmental effects on satellite galaxies: the link between concentration, size and colour profile

Using the Sloan Digital Sky Survey Data Release 4 group catalogue of Yang et al., we investigate sizes, concentrations, colour gradients and surface brightness profiles of central and satellite galaxies. We compare central and satellite galaxies at fixed stellar mass, in order to disentangle environmental from stellar mass dependencies. Early-and late-type galaxies are defined according to concentration. We find that at fixed stellar mass, late-type satellite galaxies have smaller radii and larger concentrations than late-type central galaxies. No such differences are found for early-type galaxies. We have also constructed surface brightness and colour profiles for the central and satellite galaxies in our sample. We find that late-type satellite galaxies have a lower surface brightness and redder colours than late-type central galaxies. We show that all observed differences between satellite and central galaxies can be explained by a simple fading model, in which the star formation in the disc decreases over time-scales of 2-3 Gyr after a galaxy becomes a satellite. Processes that induce strong morphological changes (e. g. harassment) and processes that strip the galaxy of its entire interstellar medium need not to be invoked in order to explain the environmental dependencies we find.
Impact of the Doppler spread parameterization on the simulation of the middle atmosphere circulation using the MA/ECHAM4 general circulation model

The zonal mean circulation of the middle atmosphere simulated by a general circulation model that includes the Doppler spread parameterization of gravity-wave momentum deposition is presented. To illustrate the impact of the parameterization, this simulation is compared to another obtained by using Rayleigh friction instead. It is found that the Doppler spread parameterization improves the extratropical zonal mean circulation in the mesosphere by reducing the strength of the zonal winds above the jet maximum. The parameterization also improves the simulation of the equatorial semiannual oscillation in the zonal mean zonal wind at the stratopause by enhancing the eastward phase and its downward propagation.