Miracle-dz/UniFAR-FTUs huggingface dataset:
454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000–20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.
Overexpression of Arabidopsis FLOWERING LOCUS T (FT) gene improves floral development in cassava (Manihot esculenta, Crantz)

Cassava is a tropical storage-root crop that serves as a worldwide source of staple food for over 800 million people. Flowering is one of the most important breeding challenges in cassava because in most lines flowering is late and non-synchronized, and flower production is sparse. The FLOWERING LOCUS T (FT) gene is pivotal for floral induction in all examined angiosperms. The objective of the current work was to determine the potential roles of the FT signaling system in cassava. The Arabidopsis thaliana FT gene (atFT) was transformed into the cassava cultivar 60444 through Agrobacterium-mediated transformation and was found to be overexpressed constitutively. FT overexpression hastened flower initiation and associated fork-type branching, indicating that cassava has the necessary signaling factors to interact with and respond to the atFT gene product. In addition, overexpression stimulated lateral branching, increased the prolificacy of flower production and extended the longevity of flower development. While FT homologs in some plant species stimulate development of vegetative storage organs, atFT inhibited storage-root development and decreased root harvest index in cassava. These findings collectively contribute to our understanding of flower development in cassava and have the potential for applications in breeding.
Inflammation and Apoptosis: Dual Mediator Role for Toll-like Receptor 4 in the Development of Necrotizing Enterocolitis

Background: Necrotizing enterocolitis (NEC) is the leading cause of neonatal gastrointestinal mortality; effective interventions are lacking with limited understanding of the pathogenesis of NEC. The importance of Toll-like receptor 4 (TLR4) signaling in NEC is well documented; however, the potential mechanisms that regulate enterocyte inflammation and apoptosis remain unclear. The aim of this study was to characterize the role of TLR4-mediated inflammation and apoptosis in the development of NEC and to determine the major apoptotic pathways and regulators in the process. Methods: TLR4-deficient C57BL/10ScNJ mice and lentivirus-mediated stable TLR4-silent cell line (IEC-6) were used. NEC was induced by formula gavage, cold, hypoxia, combined with lipopolysaccharide in vivo or lipopolysaccharide stimulation in vitro. Enterocyte apoptosis was evaluated by TUNEL or Annexin analysis. The expression of TLR4, caspase3, caspase8, caspase9, Bip, Bax, Bcl-2, and RIP was detected by Western blot and immunofluorescence. Inflammatory factors such as tumor necrosis factor-&agr; and interleukin-2 were examined by Luminex. Results: Defect of TLR4 led to suppressed enterocytes apoptosis both in vitro and in vivo; the expression of caspase3, caspase8, Bip, and Bax was decreased; and caspase9 and Bcl-2 were increased. NEC severity was attenuated in TLR4-deficient mice compared with wild-type counterparts, and enterocytes apoptosis was correlated with NEC severity. RIP and cytokine level of tumor necrosis factor-&agr; and interleukin-2 were also decreased. Conclusions: TLR4-induced inflammation and apoptosis play a critical role in the pathogenesis of NEC. TLR4 inhibition, combined with extrinsic (caspase8) and/or endoplasmic reticulum stress (Bip) apoptosis signaling blockade could serve as a potential effective treating strategy for NEC.
Word Embeddings for the Construction Domain

We introduce word vectors for the construction domain. Our vectors were obtained by running word2vec on an 11M-word corpus that we created from scratch by leveraging freely-accessible online sources of construction-related text. We first explore the embedding space and show that our vectors capture meaningful construction-specific concepts. We then evaluate the performance of our vectors against that of ones trained on a 100B-word corpus (Google News) within the framework of an injury report classification task. Without any parameter tuning, our embeddings give competitive results, and outperform the Google News vectors in many cases. Using a keyword-based compression of the reports also leads to a significant speed-up with only a limited loss in performance. We release our corpus and the data set we created for the classification task as publicly available, in the hope that they will be used by future studies for benchmarking and building on our work.
When disgust leads to dysphoria: A three-wave longitudinal study assessing the temporal relationship between self-disgust and depressive symptoms

Research has shown that feelings of self-disgust may have a functional role in the genesis of depression by partially mediating the cross-sectional relationship between dysfunctional thoughts and depressive symptoms. However, there are many outstanding issues regarding these hypothesised associations. First, it is not yet clear whether self-disgust is a temporal antecedent, concomitant, or consequence of depressive experience. Second, it is not known whether the hypothesised mediation sequence is valid over time. Third, the relative contribution of disgust towards different aspects of the self has not yet been examined. In the present longitudinal study, participants completed measures of dysfunctional cognitions, self-disgust and depressive symptoms at baseline, and at six and 12-month follow-ups. Analysis showed that self-disgust is best considered as antecedent to depressive symptoms; the hypothesised mediation model was partially supported, but is too simplistic; and disgust towards physical aspects of the self, rather than behaviour, was more important as a temporal predictor of depressive symptoms. The current results help elucidate the role of self-disgust as an antecedent of depressive experience.
Improved speech discrimination after cochlear implantation in the Southern Cochlear Implant Adult Programme.

AIM To assess the rate and amount of improvement in speech discrimination scores following cochlear implant (CI) at the Southern Cochlear Implant Programme-Adult (SCIPA). METHODS A retrospective review of those implanted between 1999 and 2008 at SCIPA. We recorded type of implant, age of onset of deafness, age at implant, aetiology, and speech discrimination test (hearing in noise test, HINT) results pre-implant and over time post-implant. RESULTS The mean post-implant HINT score (auditory alone) for the 78 patients who had follow-up up to nine months was 74%, and at 18 months (52 patients) was 81%, compared with a mean pre-implant score of 15%. Performance plateaued at around 6 months post-implant. Age at operation was unrelated to outcome but earlier onset of deafness (and higher percentage of life deaf) gave a poorer outcome. Medium pre-implant scores were associated with lower post-implant scores than those with low or high pre-implant scores. CONCLUSIONS Our results compare favourably with world-wide standards. Benefit in speech discrimination appears to plateau 6 months post-implant. A shorter duration of deafness or percentage of life spent deaf gives better results, but patients with very poor pre-implant functioning may in fact perform better at long term follow-up than those with slightly better pre-implant functioning.
Simulated Sea Surface Salinity variability in the tropical Pacific

Sea Surface Salinity (SSS) variability from a hindcast run of an oceanic general circulation model (OGCM) forced by daily NCEP‐NCAR reanalysis from 1990 to 2001 is analyzed. The purpose is to test the capability of the model in terms of the salinity simulation and provide insights for the future SSS observation from space. With daily forcing, the model can reproduce SSS change of the tropical Pacific on different time scales by comparing with the Tropical Atmosphere Ocean (TAO) mooring observation. Our model results show that the western tropical Pacific is a large variability center on different time scales. On the interannual time scale, the standard deviation of SSS in the region could reach 0.5 practical salinity unit (psu). However, the eastern tropical Pacific shows relatively weak SSS variability (0.1 psu). On the intraannual time scale (60–360 days), the SSS variability in the western tropical Pacific is around 0.2 psu. The model SSS variability for the intraseasonal time scale (30–60 days) has a magnitude around 0.1 psu and tends to elongate along the latitudes of large meridional SSS gradient. On time scale shorter than 30 days, the model SSS variability center is near the equator and has a magnitude less than 0.1 psu. Relevance to the upcoming salinity satellite mission is discussed.
Contributions of Understory and/or Overstory Vegetations to Soil Microbial PLFA and Nematode Diversities in Eucalyptus Monocultures

Ecological interactions between aboveground and belowground biodiversity have received many attentions in the recent decades. Although soil biodiversity declined with the decrease of plant diversity, many previous studies found plant species identities were more important than plant diversity in controlling soil biodiversity. This study focused on the responses of soil biodiversity to the altering of plant functional groups, namely overstory and understory vegetations, rather than plant diversity gradient. We conducted an experiment by removing overstory and/or understory vegetation to compare their effects on soil microbial phospholipid fatty acid (PLFA) and nematode diversities in eucalyptus monocultures. Our results indicated that both overstory and understory vegetations could affect soil microbial PLFA and nematode diversities, which manifested as the decrease in Shannon–Wiener diversity index (H′) and Pielou evenness index (J) and the increase in Simpson dominance index (λ) after vegetation removal. Soil microclimate change explained part of variance of soil biodiversity indices. Both overstory and understory vegetations positively correlated with soil microbial PLFA and nematode diversities. In addition, the alteration of soil biodiversity might be due to a mixing effect of bottom-up control and soil microclimate change after vegetation removal in the studied plantations. Given the studied ecosystem is common in humid subtropical and tropical region of the world, our findings might have great potential to extrapolate to large scales and could be conducive to ecosystem management and service.
Nuclear matter symmetry energy and the neutron skin thickness of heavy nuclei

Correlations between the thickness of the neutron skin in finite nuclei and the nuclear matter symmetry energy are studied in the Skyrme Hartree-Fock model. From the most recent analysis of the isospin diffusion data in heavy-ion collisions based on an isospin- and momentum-dependent transport model with in-medium nucleon-nucleon cross sections, a value of $L=88\ifmmode\pm\else\textpm\fi{}25$ MeV for the slope of the nuclear symmetry energy at saturation density is extracted, and this imposes stringent constraints on both the parameters in the Skyrme effective interactions and the neutron skin thickness of heavy nuclei. Predicted thickness of the neutron skin is $0.22\ifmmode\pm\else\textpm\fi{}0.04$ fm for $^{208}\mathrm{Pb}$, $0.29\ifmmode\pm\else\textpm\fi{}0.04$ fm for $^{132}\mathrm{Sn}$, and $0.22\ifmmode\pm\else\textpm\fi{}0.04$ fm for $^{124}\mathrm{Sn}$.
The 'Good Enough' Approach to Language Comprehension

Ferreira and colleagues argued that the language comprehension system creates syntactic and semantic representations that are merely ‘good enough’ (GE) given the task that the comprehender needs to perform. GE representations contrast with ones that are detailed, complete, and accurate with respect to the input. In this article, we review the original argument for GE processing, and we present new evidence that supports the concept: first, local interpretations are computed, which can interfere with global ones; second, new findings based on the recording of event-related potentials show the use of simple heuristics rather than compositional algorithms for constructing sentence meaning; and recent studies show that the comprehension system has mechanisms for handling disfluencies, but they work imperfectly. We argue that the GE approach to language comprehension is similar to the use of fast and frugal heuristics for decision-making, and that future research should explore this connection more thoroughly.
A Finite Volume Scheme for Nonlinear Degenerate Parabolic Equations

We propose a second order finite volume scheme for nonlinear degenerate parabolic equations which admit an entropy functional. For some of these models (porous media equation, drift-diffusion system for semiconductors) it has been proved that the transient solution converges to a steady state when time goes to infinity. The present scheme preserves steady states and provides a satisfying long time behavior. Moreover, it remains valid and second order accurate in space even in the degenerate case. After describing the numerical scheme, we present several numerical results which confirm the high order accuracy in various regime degenerate and nondegenerate cases and underline the efficiency to preserve the large time asymptotic.
Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding

Protein disulfide isomerases comprise a large family of enzymes responsible for catalyzing the proper oxidation and folding of newly synthesized proteins in the endoplasmic reticulum (ER). Protein disulfide isomerase-related (PDIR) protein (also known as PDIA5) is a specialized member that participates in the folding of α1-antitrypsin and N-linked glycoproteins. Here, the crystal structure of the non-catalytic domain of PDIR was determined to 1.5 Å resolution. The structure adopts a thioredoxin-like fold stabilized by a structural disulfide bridge with a positively charged binding surface for interactions with the ER chaperones, calreticulin and ERp72. Crystal contacts between molecules potentially mimic the interactions of PDIR with misfolded substrate proteins. The results suggest that the non-catalytic domain of PDIR plays a key role in the recognition of protein partners and substrates.
A 1.8 V 3.2 /spl mu/W comparator for use in a CMOS imager column-level single-slope ADC

In this paper, a 1.8 V 3.2 /spl mu/W comparator is presented. It features a hybrid offset compensation scheme and achieves over 60 dB gain with an input offset below 150 /spl mu/V. The comparator is designed in a 0.18 /spl mu/m CMOS process and is specifically designed to be used as the key component of a column-level single-slope ADC of a CMOS imager. This ADC architecture is attractive because of its low noise, but so far this has come at the price of a relatively high power consumption. Using this comparator design, the power consumption of column-level single-slope ADC can be reduced significantly.
ICT and Productivity: A Review of the Literature

In this report we review the literature on the relationship between ICT and productivity. In Sect. 1 we discuss in broad terms the theoretical relationship between ICT and productivity, while in Sect. 2 we present the growth accounting methodology, which tries to measure the contributions to growth from difference sources (ICT and non ICT capital, human capital, total factor productivity). Within the growth-accounting methodology, in Sect. 3, we discuss the U.S. - E.U. productivity gap and the role of ICTs, and we show that the latter are responsible for the U.S. acceleration in productivity growth observed in the period 1996-2006 and for the widening of the U.S. – E.U. productivity gap in the same period. Then, in Sect. 4, we move to regression based studies, and we review the literature that uses macro, meso (sectoral) and firm/plant level data. While the overall message on the importance of ICT for growth coming from this literature is consistent with the findings of the studies based on growth accounting, the econometric approach allows researchers to investigate a wider set of questions. In particular, we focus on the role of ICT as a General Purpose Technology aspects and we review the literature studying the role of ICT and complementary assets in firms' productivity and the literature exploring the positive externalities related to ICT capital and the impact of ICT usage on the innovative capability of firms. Finally, we also review the literature on the relationship between ICT infrastructures and GDP growth.
Interrelationships between dairy product intake, microflora metabolism, faecal properties and plasmid dissemination in gnotobiotic mice

We previously described the effects of intake of dairy products on plasmid dissemination in the digestive tract of gnotobiotic mice associated with human faecal flora (HFF) and found that yoghurt, heat-treated yoghurt (HTY) and milk reduced population levels of transconjugants compared with findings in mice fed a standard mouse diet. In the case of lactose intake, transconjugants were not detected. The aim of the present study was to assess the possible interrelationships between these observations and other variables (bacterial ecology, pH, moisture, enzyme activities, short-chain fatty acid (SCFA) contents, lactic acid contents). Much of the interest of the present comparison lies in the fact that the animals were homogeneous in terms of age, gender, food and intestinal microflora, owing to the gnotobiotic mouse model maintained in sterile isolators. We observed no variation in SCFA and lactic acid contents or in the population levels of strictly anaerobic strains of Bacteroides and Bifidobacterium, and of the facultative anaerobic recipient Escherichia coli PG1 strain. The main modifications were the reduction of population levels of transconjugants in mice receiving yoghurt, HTY and milk, and concomitantly an increase of β-galactosidase and a decrease of β-glucosidase activities, compared with control mice fed a standard diet. Total inhibition of plasmid transfer was observed in HFF mice consuming lactose, and concomitantly the two enzyme activities (β-glucosidase and β-galactosidase) were increased, compared with the findings in control mice fed a standard diet. In axenic mice consuming lactose, plasmid transfer occurred, β-galactosidase was not detected and β-glucosidase was decreased. It is therefore proposed that these two enzyme activities influence plasmid transfer and persistence of transconjugants in the digestive tract of HFF associated mice. When both activities were increased there was a total inhibition of plasmid transfer (case of lactose intake). When β-galactosidase increased and β-glucosidase decreased (case of yoghurt, HTY and milk), plasmid transfer occurred at a lower efficiency than in the control group, resulting in lower population levels of transconjugants.
Risk Factors and Outcomes Associated with Isolation of Meropenem High-Level-Resistant Pseudomonas aeruginosa

Objective. To determine risk factors and outcomes for patients with meropenem high–level-resistant Pseudomonas aeruginosa (MRPA) (minimum inhibitory concentration [MIC] ≥ 32 μg/mL). Design. Case-control-control. Setting. An 867-bed urban, teaching hospital. Patients. Fifty-eight MRPA case patients identified from an earlier P. aeruginosa study; 125 randomly selected control patients with meropenem-susceptible P. aeruginosa (MSPA) (MIC ≤ 4 μg/mL), and 57 control patients without P. aeruginosa (sampled by case date/location). Methods. Patient data, outcomes, and costs were obtained via administrative database. Cases were compared to each control group while controlling for time at risk (days between admission and culture, or entire length of stay [LOS] for patients without P. aeruginosa). Results. A multivariable model predicted risks for MRPA versus MSPA (odds ratio [95% confidence interval]): more admissions (in the prior 12 months) (1.41 [1.15, 1.74]), congestive heart failure (2.19 [1.03, 4.68]), and Foley catheter (2.53 [1.18, 5.45]) (adj. R2 = 0.28). For MRPA versus no P. aeruginosa, risks were age (in 5-year increments) (1.17 [1.03, 1.33]), more prior admissions (1.40 [1.08, 1.81]), and more days in the intensive care unit (1.10 [1.03, 1.18]) (adj. R2 = 0.32). Other invasive devices (including mechanical ventilation) and previous antibiotic use (including carbapenems) were nonsignificant. MRPA mortality (31%) did not differ from that of MSPA (15%) when adjusted for time at risk (P = .15) but did from mortality without P. aeruginosa (9%) (P = .01 ). Median LOS and costs were greater for MRPA patients versus MSPA patients and patients without P. aeruginosa: 30 days versus 16 and 10 (P < .01 ) and $88,425 versus $28,620 and $22,605 (P <.01). Conclusions. Although antibiotic use has been shown to promote resistance, our data found that prior antibiotic use was not associated with MRPA acquisition. However, admission frequency and Foley catheters were, suggesting that infection control measures are essential to reducing MRPA transmission.