Miracle-dz/UniFAR-FTUs huggingface dataset:
Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

Summary The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense – an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems.
Multiscale Vessel-guided Airway Tree Segmentation

This paper presents a method for airway tree segmentation that uses a combination of a trained airway appearance model, vessel and airway orientation information, and region growing. The method uses a voxel classification based appearance model, which involves the use of a classifier that is trained to differentiate between airway and non-airway voxels. Vessel and airway orientation information are used in the form of a vessel orientation similarity measure, which indicates how similar the orientation of the an airway candidate is to the orientation of the neighboring vessel. The method is evaluated within EXACT’09 on a diverse set of CT scans. Results show a favorable combination of a relatively large portion of the tree detected correctly with very few false positives.
Global alterations of DNA methylation in cholangiocarcinoma target the Wnt signaling pathway

The molecular mechanisms underlying the genesis of cholangiocarcinomas (CCs) are poorly understood. Epigenetic changes such as aberrant hypermethylation and subsequent atypical gene expression are characteristic features of most human cancers. In CC, data regarding global methylation changes are lacking so far. We performed a genome‐wide analysis for aberrant promoter methylation in human CCs. We profiled 10 intrahepatic and 8 extrahepatic CCs in comparison to non‐neoplastic biliary tissue specimens, using methyl‐CpG immunoprecipitation (MCIp) combined with whole‐genome CpG island arrays. DNA methylation was confirmed by quantitative mass spectrometric analysis and functional relevance of promoter hypermethylation was shown in demethylation experiments of two CC cell lines using 5‐aza‐2′deoxycytidine (DAC) treatment. Immunohistochemical staining of tissue microarrays (TMAs) from 223 biliary tract cancers (BTCs) was used to analyze candidate gene expression at the protein level. Differentially methylated, promoter‐associated regions were nonrandomly distributed and enriched for genes involved in cancer‐related pathways including Wnt, transforming growth factor beta (TGF‐β), and PI3K signaling pathways. In CC cell lines, silencing of genes involved in Wnt signaling, such as SOX17, WNT3A, DKK2, SFRP1, SFRP2, and SFRP4 was reversed after DAC administration. Candidate protein SFRP2 was substantially down‐regulated in neoplastic tissues of all BTC subtypes as compared to normal tissues. A significant inverse correlation of SFRP2 protein expression and pT status was found in BTC patients. Conclusion: We provide a comprehensive analysis to define the genome‐wide methylation landscape of human CC. Several candidate genes of cancer‐relevant signaling pathways were identified, and closer analysis of selected Wnt pathway genes confirmed the relevance of this pathway in CC. The presented global methylation data are the basis for future studies on epigenetic changes in cholangiocarcinogenesis. (Hepatology 2014;59:544–554)
Highly Oriented Atomically Thin Ambipolar MoSe2 Grown by Molecular Beam Epitaxy

Transition metal dichalcogenides (TMDCs), together with other two-dimensional (2D) materials, have attracted great interest due to the unique optical and electrical properties of atomically thin layers. In order to fulfill their potential, developing large-area growth and understanding the properties of TMDCs have become crucial. Here, we have used molecular beam epitaxy (MBE) to grow atomically thin MoSe2 on GaAs(111)B. No intermediate compounds were detected at the interface of as-grown films. Careful optimization of the growth temperature can result in the growth of highly aligned films with only two possible crystalline orientations due to broken inversion symmetry. As-grown films can be transferred onto insulating substrates, allowing their optical and electrical properties to be probed. By using polymer electrolyte gating, we have achieved ambipolar transport in MBE-grown MoSe2. The temperature-dependent transport characteristics can be explained by the 2D variable-range hopping (2D-VRH) model, indicating that the transport is strongly limited by the disorder in the film.
Rapid combined T1 and T2 mapping using gradient recalled acquisition in the steady state

A novel, fully 3D, high‐resolution T1 and T2 relaxation time mapping method is presented. The method is based on steady‐state imaging with T1 and T2 information derived from either spoiling or fully refocusing the transverse magnetization following each excitation pulse. T1 is extracted from a pair of spoiled gradient recalled echo (SPGR) images acquired at optimized flip angles. This T1 information is combined with two refocused steady‐state free precession (SSFP) images to determine T2. T1 and T2 accuracy was evaluated against inversion recovery (IR) and spin‐echo (SE) results, respectively. Error within the T1 and T2 maps, determined from both phantom and in vivo measurements, is approximately 7% for T1 between 300 and 2000 ms and 7% for T2 between 30 and 150 ms. The efficiency of the method, defined as the signal‐to‐noise ratio (SNR) of the final map per voxel volume per square root scan time, was evaluated against alternative mapping methods. With an efficiency of three times that of multipoint IR and three times that of multiecho SE, our combined approach represents the most efficient of those examined. Acquisition time for a whole brain T1 map (25 × 25 × 10 cm) is less than 8 min with 1 mm3 isotropic voxels. An additional 7 min is required for an identically sized T2 map and postprocessing time is less than 1 min on a 1 GHz PIII PC. The method therefore permits real‐time clinical acquisition and display of whole brain T1 and T2 maps for the first time. Magn Reson Med 49:515–526, 2003. © 2003 Wiley‐Liss, Inc.
Rapid Emergence of Highly Pathogenic Avian Influenza Subtypes from a Subtype H5N1 Hemagglutinin Variant

In 2014, novel highly pathogenic avian influenza A H5N2, H5N5, H5N6, and H5N8 viruses caused outbreaks in Asia, Europe, and North America. The H5 genes of these viruses form a monophyletic group that evolved from a clade 2.3. 4 H5N1 variant. This rapid emergence of new H5Nx combinations is unprecedented in the H5N1 evolutionary history.
Benchmarking of Monte Carlo simulation of bremsstrahlung from thick targets at radiotherapy energies.

Several Monte Carlo systems were benchmarked against published measurements of bremsstrahlung yield from thick targets for 10-30 MV beams. The quantity measured was photon fluence at 1 m per unit energy per incident electron (spectra), and total photon fluence, integrated over energy, per incident electron (photon yield). Results were reported at 10-30 MV on the beam axis for Al and Pb targets and at 15 MV at angles out to 90 degrees for Be, Al, and Pb targets. Beam energy was revised with improved accuracy of 0.5% using an improved energy calibration of the accelerator. Recently released versions of the Monte Carlo systems EGSNRC, GEANT4, and PENELOPE were benchmarked against the published measurements using the revised beam energies. Monte Carlo simulation was capable of calculation of photon yield in the experimental geometry to 5% out to 30 degrees, 10% at wider angles, and photon spectra to 10% at intermediate photon energies, 15% at lower energies. Accuracy of measured photon yield from 0 to 30 degrees was 5%, 1 s.d. , increasing to 7% for the larger angles. EGSNRC and PENELOPE results were within 2 s.d. of the measured photon yield at all beam energies and angles, GEANT4 within 3 s.d. Photon yield at nonzero angles for angles covering conventional field sizes used in radiotherapy (out to 10 degrees), measured with an accuracy of 3%, was calculated within 1 s.d. of measurement for EGSNRC, 2 s.d. for PENELOPE and GEANT4. Calculated spectra closely matched measurement at photon energies over 5 MeV. Photon spectra near 5 MeV were underestimated by as much as 10% by all three codes. The photon spectra below 2-3 MeV for the Be and Al targets and small angles were overestimated by up to 15% when using EGSNRC and PENELOPE, 20% with GEANT4. EGSNRC results with the NIST option for the bremsstrahlung cross section were preferred over the alternative cross section available in EGSNRC and over EGS4. GEANT4 results calculated with the "low energy" physics list were more accurate than those calculated with the "standard" physics list.
Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito-Associated Spiroplasma

Abstract Genetic differentiation among symbiotic bacteria is important in shaping biodiversity. The genus Spiroplasma contains species occupying diverse niches and is a model system for symbiont evolution. Previous studies have established that two mosquito-associated species have diverged extensively in their carbohydrate metabolism genes despite having a close phylogenetic relationship. Notably, although the commensal Spiroplasma diminutum lacks identifiable pathogenicity factors, the pathogenic Spiroplasma taiwanense was found to have acquired a virulence factor glpO and its associated genes through horizontal transfer. However, it is unclear if these acquired genes have been integrated into the regulatory network. In this study, we inferred the gene content evolution in these bacteria, as well as examined their transcriptomes in response to glucose availability. The results indicated that both species have many more gene acquisitions from the Mycoides-Entomoplasmataceae clade, which contains several important pathogens of ruminants, than previously thought. Moreover, several acquired genes have higher expression levels than the vertically inherited homologs, indicating possible functional replacement. Finally, the virulence factor and its functionally linked genes in S. taiwanense were up-regulated in response to glucose starvation, suggesting that these acquired genes are under expression regulation and the pathogenicity may be a stress response. In summary, although differential gene losses are a major process for symbiont divergence, gene gains are critical in counteracting genome degradation and driving diversification among facultative symbionts.
Mood Influence on the Valuation of Multiple Gains and Losses

An experiment tests predictions on the influence of mood and information processing on the valuation of segregated versus integrated gains and losses. The results confirm that mood-management goals determine information processing and preferences only if the valence of mood (i.e. positive mood) is incongruent with the valence of a stimulus (i.e. a negative event such as a loss). Incongruence elicits heuristic information processing, triggering a preference for segregated gains and integrated losses, respectively. If the valence of mood and stimuli are congruent, subjects show a lower preference for an integration of losses or a segregation of gains.
Two models for Bayesian supervised dimension reduction

We study and develop two Bayesian frameworks for supervised dimension reduction that apply to nonlinear manifolds: Bayesian mixtures of inverse regression s and gradient based methods. Formal probabilistic models with likelihoods and priors are given for both method s and efficient posterior estimates of the effective dimension reduction space and predictive factors can b e obtained by a Gibbs sampling procedure. In the case of the gradient based methods estimates of conditio nal dependence between covariates predictive of the response can also be inferred. Relations to manifold l earning and Bayesian factor models are made explicit. The utility of the approach is illustrated on simu lated and real examples. Some
Unusual event detection in low resolution video for enhancing ATM security

In real world applications, tracking target in low resolution video is a challenging task because there is loss of discriminative detail in the visual appearance of moving object. The existing methods are mostly based on the enhancement of LR (low resolution) video by super resolution techniques. But these methods require high computational cost. This cost further increases if we are dealing with events detection. In this paper we present an algorithm which is able to detect unusual events without such type of conversion and well suited for enhancement of security of ATMs where conventional low resolution cameras are generally used due to their low cost. Proposed algorithm only uses close morphological operation with disk like structuring element in the preprocessing steps to cope up with low resolution video. It further uses rolling average background subtraction technique to detect foreground object from dynamic background in a scene. Our proposed algorithm is able to recognize the occurrence of uncommon events such as overcrowding or fight in the low resolution video simply by using statistical property, standard deviation of moving objects. It is fast enough because it process low resolution frames and could be helpful in surveillance system for enhancing the security of ATMs where conventional camera of low resolution are still used. It does not use any classifier and avoids the requirement of training the system initially.
Data acquisition system for multi channel silicon drift diode-based detector

We have developed front-end electronics and data acquisition unit for a silicon drift diode (SDD) based prototype detector. The prototype detector consists of an array of 67 SDDs. The array is bump-bonded on a mother board which is cooled by Peltier-water based cooling system. In this study, we describe the function of front-end electronics (including preamplifier, shaper and peak stretcher units) and a data acquisition (DAQ) unit. The hardware consists of three major blocks: 1) a preamplifier board that amplifies the SDD signal, 2) a shaping and stretcher board that shapes event signal and stretches it, and 3) DAQ board that converts analog signal to digital and acquires digitized data. The preamp board amplifies 67 channel SDD signals with OP-amps and controls the jFET of each SDD to optimize reset interval and gain. The shaping board consists of 5 sub-blocks that are shaper, peak stretcher, MUX, discriminator and SHP_ctrl. It shapes the preamplifier signal and generates event signals. The DAQ consists of an array of A/D converters and FPGAs. In our FPGA simulation, the system uses 62% of memory, 21% of LOGIC slice. We evaluated and verified 3 boards with including FPGA program. In the result we found and settled some problems which cross talk and noise. However, we meet two problems that are SDD sensor board and synchronous reset circuit. We will fix some problems and evaluate the detector performance such as spatial resolution and energy spectrum, etc. We will also include the results of phantom study later.
Constraint Projections for Ensemble Learning

It is well-known that diversity among base classifiers is crucial for constructing a strong ensemble. Most existing ensemble methods obtain diverse individual learners through resampling the instances or features. In this paper, we propose an alternative way for ensemble construction by resampling pairwise constraints that specify whether a pair of instances belongs to the same class or not. Using pairwise constraints for ensemble construction is challenging because it remains unknown how to influence the base classifiers with the sampled pairwise constraints. We solve this problem with a two-step process. First, we transform the original instances into a new data representation using projections learnt from pairwise constraints. Then, we build the base classifiers with the new data representation. We propose two methods for resampling pairwise constraints following the standard Bagging and Boosting algorithms, respectively. Extensive experiments validate the effectiveness of our method.
A high-accuracy and high-efficiency on-chip current sensing for current-mode control CMOS DC-DC buck converter

In this paper, a high accuracy, high efficiency, and wide current sensing range on chip current sensing technique is presented. The proposed current sensing circuit uses simple switch technique to achieve high accuracy. The current sensing circuit has no OP amplifier so that it would not reduce the power efficiency. The test chip is fabricated in TSMC 0.18 mum 1P6M 3.3 V CMOS process. The measurement results show that the buck converter with on-chip current sensing circuit can operate from 700 KHz to 1.4 MHz with supply voltage from 2.5 to 5 V for lithium ion battery application. The accuracy of proposed current sensing circuit is higher than 89.8% for load current from 50 to 500 mA and for temperature from 0 to 100degC. The power efficiency of the buck converter is up to 91.2%.
On the complementarity of workflow management and business process modeling

The way business processes are implemented currently is out-of-date. It cannot keep pace with the rapid changes of today's business behavior. Thus, new ways to structure business processes have to be investigated. Business process reengineering is the upcoming discipline that is able to cope with the requirements posted by today's way of conducting business. However, models of business processes defined through business process reengineering still lack a suitable execution environment. Conventional infrastructures are too static and inflexible to adequately reflect rapid changes in business processes. Workflow management promises to cope with this requirement by providing a highly dynamic execution platform for multi-faceted business processes. In this research paper we discuss the interrelationship between business process modeling and workflow management and show how they can mutually benefit from each other.
Genetic Variation in Plant CYP51s Confers Resistance against Voriconazole, a Novel Inhibitor of Brassinosteroid-Dependent Sterol Biosynthesis

Brassinosteroids (BRs) are plant steroid hormones with structural similarity to mammalian sex steroids and ecdysteroids from insects. The BRs are synthesized from sterols and are essential regulators of cell division, cell elongation and cell differentiation. In this work we show that voriconazole, an antifungal therapeutic drug used in human and veterinary medicine, severely impairs plant growth by inhibiting sterol-14α-demethylation and thereby interfering with BR production. The plant growth regulatory properties of voriconazole and related triazoles were identified in a screen for compounds with the ability to alter BR homeostasis. Voriconazole suppressed growth of the model plant Arabidopsis thaliana and of a wide range of both monocotyledonous and dicotyledonous plants. We uncover that voriconazole toxicity in plants is a result of a deficiency in BRs that stems from an inhibition of the cytochrome P450 CYP51, which catalyzes a step of BR-dependent sterol biosynthesis. Interestingly, we found that the woodland strawberry Fragaria vesca, a member of the Rosaceae, is naturally voriconazole resistant and that this resistance is conferred by the specific CYP51 variant of F. vesca. The potential of voriconazole as a novel tool for plant research is discussed.
Science of the World Wide Web

Web science must remain an interdisciplinary pursuit Ten years ago, Wikipedia was still in its infancy (and totally dismissed by the establishment), Facebook was still restricted to university users, Twitter was in beta testing, and improving search capabilities was the topic that dominated Web conference research agendas. There were virtually no smartphones, online surveillance of activity and data storage was largely unknown beyond security services, and no one knew that being a data scientist was one day going to be “the sexiest job in the world” (1).
Stressors and coping mechanisms associated with perceived stress in Latinos.

OBJECTIVE To evaluate the relationship between causes of perceived stress and the coping mechanisms used by Latino adults with perceived stress. DESIGN, SETTING, PARTICIPANTS This cross-sectional survey was conducted on a convenience sample of 200 Latino adults (aged ≥18 years). They were recruited from clinics, migrant camps, community events, and churches located in Charleston, S.C. This survey included questions regarding causes of perceived stress, perceived stress (Perceived Stress Scale 10), coping mechanisms (Brief COPE), and depression (Perceived Health Questionnaire 9). MEASURES High perceived stress (PSS ≥15) was the primary outcome measure. Coping mechanisms and stressors were secondary outcomes. RESULTS Most (92%) of the sample was born outside the United States, and 66% reported high perceived stress. Stressors associated with high perceived stress included discrimination (P=.0010), lack of insurance (P=.0193), health problems (P=.0058), and lack of money (P=.0015). The most frequently utilized coping mechanisms were self-distraction (54.77%), active coping (69.85%), positive reframing (56.78%), planning (63.82%), acceptance (57.87%), and religion (57.79%). Latinos with higher perceived stress were more likely to report discrimination (OR: 3.401; 95%CI 1.285-9.004) and health problems (OR: 2.782; 95%CI 1.088-7.111) as stressors, and to use denial as a coping mechanism (OR: 2.904; 95%CI 1.280-6.589). CONCLUSION An increased prevalence of perceived stress among the Latinos evaluated in this study was associated with using denial as a coping mechanism, and encountering discrimination and health problems as sources of perceived stress. Most individuals responded to stressors by utilizing a variety of both adaptive and maladaptive coping mechanisms.