Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Perspective on Listeria monocytogenes Evolution

Listeria monocytogenes is a model organism for cellular microbiology and host–pathogen interaction studies and an important food-borne pathogen widespread in the environment, thus representing an attractive model to study the evolution of virulence. The phylogenetic structure of L. monocytogenes was determined by sequencing internal portions of seven housekeeping genes (3,288 nucleotides) in 360 representative isolates. Fifty-eight of the 126 disclosed sequence types were grouped into seven well-demarcated clonal complexes (clones) that comprised almost 75% of clinical isolates. Each clone had a unique or dominant serotype (4b for clones 1, 2 and 4, 1/2b for clones 3 and 5, 1/2a for clone 7, and 1/2c for clone 9), with no association of clones with clinical forms of human listeriosis. Homologous recombination was extremely limited (r/m<1 for nucleotides), implying long-term genetic stability of multilocus genotypes over time. Bayesian analysis based on 438 SNPs recovered the three previously defined lineages, plus one unclassified isolate of mixed ancestry. The phylogenetic distribution of serotypes indicated that serotype 4b evolved once from 1/2b, the likely ancestral serotype of lineage I. Serotype 1/2c derived once from 1/2a, with reference strain EGDe (1/2a) likely representing an intermediate evolutionary state. In contrast to housekeeping genes, the virulence factor internalin (InlA) evolved by localized recombination resulting in a mosaic pattern, with convergent evolution indicative of natural selection towards a truncation of InlA protein. This work provides a reference evolutionary framework for future studies on L. monocytogenes epidemiology, ecology, and virulence.
Flexibility quantification for thermal power generators using deterministic metric for high renewable energy penetration

Power system operation became a challenging with the integration of variable and uncertain Renewable Energy Sources (RES) generation. The operational flexibility describes the technical ability of the power system to respond to the net-load within a controllable power at a certain time to accommodate the RES power output. The main objective of this paper is to analyse and evaluate the impact of the variation of ramping and capacity weights on the flexibility quantification of the IEEE RTS-96 test system. This paper contributes to the up-rising field of flexibility by providing a precise analysis of a deterministic metric and weights variation to assets the available flexibility from the individual generator and as well as when aggregated within the power system. The analysis is executed using a deterministic metric with an iterative variation of both ramping and capacity weights simultaneously to quantify the technical flexibility of the overall system and each different technology of the test system. The results demonstrate that the increment of the capacity weight has more influence on the individual generators flexibility and the overall system flexibility as well. The incremental rate of flexibility is not linear for all the units at the test system. This metric is useful for the power system operators and planners who requires simple, fast and offline metric to quantify the technical flexibility of the power system.
Structural Estimates of Housing Supply Elasticity across Chinese Cities

We present a structural model of urban growth in a spatial equilibrium setting to aid the separation of the effects of demand shocks from those of the spatial variation in housing supply elasticity. The model is applied to an analysis of urban growth across Chines cities between 1998 and 2004, to evaluate the determinants of housing supply elasticity. The variation in supply, via urban expansion or price elasticity, is found to play a greater role in accounting for cross-city differences in population growth, but a lesser role for the differences in wage-rate and price growth, than do the demand shocks. The housing supply elasticity is lower in denser and more expensive cities but greater in cities of higher political status or with denser roads. Furthermore, our results show that local governments can raise the housing supply elasticity by lowering regulatory costs and improving land-use equity.
TREAT-AND-EXTEND REGIMEN WITH AFLIBERCEPT FOR RETINAL ANGIOMATOUS PROLIFERATION

Purpose: To evaluate the effects of aflibercept therapy using a treat-and-extend regimen on treatment-naïve retinal angiomatous proliferation (RAP) and development of retinal pigment epithelium (RPE) atrophy. Methods: We retrospectively studied 17 treated eyes with RAP and 13 untreated fellow eyes. We assessed best-corrected visual acuity (BCVA) in logarithm of the minimal angle of resolution (logMAR) units and recorded the total number of injections for 12 months. Central macular thickness (CMT) and central choroidal thickness (CCT) were assessed by optical coherence tomography (OCT), and RPE atrophy extent in the macular area was assessed by fundus autofluorescence. Results: Average BCVA in eyes with RAP was 0.57 logMAR units (Snellen 20/74 or approximately 56.5 ETDRS letters) before treatment and significantly improved to 0.38 (Snellen 20/48 or approximately 66 ETDRS letters, P < 0.01) after 3 months and 0.32 (Snellen 20/42 or approximately 69 ETDRS letters, P < 0.01) after 12 months. Average CMT was 340 &mgr;m before treatment and significantly reduced to 133 &mgr;m (P < 0.001) after 3 months and 130 &mgr;m (P < 0.001) after 12 months. Average CCT was 147 &mgr;m before treatment, 123 &mgr;m (P < 0.01) after 3 months, and 131 &mgr;m (P < 0.01) after 12 months. Average total number of injections was 7.2. Average area of RPE atrophy enlarged by 1.00 mm2 in treated eyes compared with 0.34 mm2 in fellow eyes (P < 0.01). The enlarged area of RPE atrophy was inversely correlated with central choroidal thickness after 12 months (rs = −0.49, P < 0.01) and positively correlated with the number of injections (rs = 0.58, P < 0.01). Conclusion: Treat-and-extend intravitreal therapy with aflibercept may be effective for improvement and stabilization of visual acuity and exudative change in eyes with RAP. However, choroidal thinning during the treatment regimen may accelerate enlargement of RPE atrophy.
Thrombotic thrombocytopenic purpura and deep vein thrombosis as the presenting manifestations of systemic lupus erythematosus: A case report and review of literature

Systemic lupus erythematosus (SLE), is sometimes complicated by the rare fatal syndrome, Thrombotic thrombocytopenic purpura (TTP), but the occurrence of TTP as the initial manifestation of SLE is very rare. Since they have similarities in some features, the differentiation of TTP from SLE may be missed. SLE patients are also more prone to thrombotic events. Here we report a case with TTP and deep vein thrombosis as the presenting symptoms of SLE.
Cigarette smoking predicts faster progression of type 2 established diabetic nephropathy despite ACE inhibition.

Blood pressure reduction and angiotensin-converting enzyme (ACE) inhibitors slow but do not stop progressive decline of renal function in established diabetic nephropathy (DN), but predictors of this decline in patients undergoing these interventions are unknown. We prospectively examined patients to determine whether age, sex, ethnicity, mean blood pressure, plasma creatinine, urine protein excretion, and cigarette smoking predict renal function decline in type 2 DN treated toward the recommended mean blood pressure goal of 92 mm Hg (about 125/75 mm Hg) with antihypertensives including ACE inhibitors. Thirty-three DN patients with initial plasma creatinine less than 1.4 mg/dL were followed 64.0 +/- 1.1 months. After correcting for differences in follow-up time, demographic variables, and other relevant variables, plasma creatinine increased, indicating renal function decline despite mean blood pressure reduction to 92 +/- 1 mm Hg and administration of ACE inhibitors. Regression analysis showed that smoking was the only examined parameter that significantly predicted renal function decline. Smokers (n = 13) and nonsmokers (n = 20) had similar follow-up (61.4 +/- 2.1 months versus 65.7 +/- 1.1 months), mean blood pressure (91 +/- 1 mm Hg versus 92 +/- 1 mm Hg), and initial plasma creatinine (1.05 +/- 0.08 mg/dL versus 1.08 +/- 0.03 mg/dL). Nevertheless, follow-up plasma creatinine was higher in smokers than nonsmokers (1.78 +/- 0.20 mg/dL versus 1.32 +/- 0.04 mg/dL). The data show that renal function declines faster in smokers than nonsmokers with type 2 DN undergoing treatment to improve blood pressure including ACE inhibitors. Cigarette smoking remains a risk factor for renal function decline in type 2 DN despite currently recommended therapy.
Column Bioleaching of a Saline, Calcareous Copper Sulfide Ore

“Deep in situ biomining”, widely considered to be a potentially environmentally-benign and cost effective biotechnology for extracting and recovering base metals from deep-buried base metal deposits, is being developed within the EU Horizon 2020 project “BioMOre”. Data are presented from non-aerated column experiments in which a saline, calcareous copper-rich ore (kupferschiefer) was subjected to a three-stage eaching protocol: (i) with water, to remove soluble salts; (ii) with sulfuric acid, to remove calcareous minerals and other acid-soluble salts; (iii) indirect bioleaching with a microbiologically-generated ferric iron lixiviant. Sequential leaching with water and acid removed ~85% of the chloride prior to bio-processing, while ~13% of the copper present in the ore was leached using sulfuric acid, and a further 39 - 59% by the lixiviant.
Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression

UNLABELLED We describe Sebida, a database of genes with sex-biased expression. The database integrates results from multiple, independent microarray studies comparing male and female gene expression in Drosophila melanogaster, Drosophila simulans and Anopheles gambiae. Sebida uses standard nomenclature, which allows individual genes to be compared across different microarray platforms and to be queried by gene name, symbol, or annotation number. In addition to ratios of male/female expression for each gene, Sebida also contains information useful for evolutionary studies, such as local recombination rate, degree of codon bias and interspecific divergence at synonymous and non-synonymous sites. AVAILABILITY Sebida can be accessed at http://www.sebida. de
Layout based document image retrieval by means of XY tree reduction

We analyze a system for the retrieval of document images on the basis of layout similarity. Layout objects are extracted and represented with the XY tree. Page similarity is computed with a tree-edit distance algorithm. The peculiarity of the approach is the use of tree grammars to model the variations in the tree, which are due to segmentation algorithms or to structural differences between documents with similar layout. A few class-independent grammatical rules are used to modify each tree and obtain a reduced tree that is supposed to preserve the most relevant features of the page.
Durable Freestanding Hierarchical Porous Electrode for Rechargeable Zinc–Air Batteries

The development of freestanding bifunctional air cathodes for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) is highly desirable for the next generation of flexible rechargeable metal–air batteries. It remains challenging to achieve efficient OER and ORR bifunctionality on a single lightweight and inexpensive electrode. In this article, a metal-free, and freestanding air cathode based on vertically aligned carbon nanotubes (VACNTs) functionalized with N, P heteroatoms doped carbon is first reported. In addition to the high catalytic activity caused by N, P heteroatoms doping, the importance of efficient gas diffusion and electron transfer provided by the VACNT-GF hierarchical structure is highlighted. The carbonization temperature has been identified to have pronounced effect on catalytic activity, and the samples with P–N bonds have smaller ORR and OER overpotentials, while the quantitative atomic ratio of either P or N has little effect on catalytic activity. The resulting air e.
Heat Release Experimental Analysis for RCCI Combustion Optimization

Over the past years, the increasingly stringent emission regulations for Internal Combustion Engines (ICE) spawned a great amount of research in the field of combustion control optimization. Nowadays, optimal combustion control has become crucial, especially to properly manage innovative Low Temperature Combustion (LTC) strategies, usually characterized by high instability, cycle-to-cycle variability and sensitivity to slight variations of injection parameters and thermal conditions. Many works demonstrate that stability and maximum efficiency of LTC strategies can be guaranteed using closed-loop control strategies that vary the standard injection parameters (mapped during the base calibration activity) to keep engine torque and center of combustion (CA50) approximately equal to their target values. However, the combination of standard base calibration and closed-loop control is usually not sufficient to accurately control Low Temperature Combustions in transient conditions. As a matter of fact, to properly manage LTC strategies in transient conditions it is usually necessary to investigate the combustion methodology of interest and implement specific functions that provide an accurate feed-forward contribution to the closed-loop controller. This work presents the experimental analysis performed running a light-duty compression ignited engine in dual-fuel RCCI mode, the goal being to highlight the way injection parameters and charge temperature affect combustion stability and ignition delay. Finally, the paper describes how the obtained results can be used to define the optimal injections strategy in the analyzed operating points, i.e. the combination of injection parameters to be used as a feed-forward for a closed-loop combustion control strategy.
Autonomic effects on estimates of time: evidence for a physiological correlate of temporal experience.

Abstract : Respiration rate and heart rate changes induced by administration of autonomically active drugs at usual clinical dosage levels tended to be significantly correlated with temporal judgments when using the method of pro uction. No correlation was found with blood pressure or skin temperature or when judging time with the reproduction method. Duration judgments with the method of production, in which time estimates are based upon internal events, are significantly correlated with rhythmic physiological activity when no external cues of time are present. (Author)
Evaluating Population Management Scenarios: Crunching the Numbers before Going to the Field

Effolts to mitigate wildlife-human conflicts tpically involve management of unacceptably abundant populations. Increasingly, however, reduction of dense or increasing populations of certain wild species evokes both support and contention kom the public. Management decisions involving population reduction, particularly those directed at highly visible species, should therefore be based on quantitative evaluation of potential outcomes prior to implementation. The purpose of th~s paper is to revisit a call for use of population modeling in management decisions by reviewing basic aspects of population analysis and the use of publicly available long-term data sets in environmental assessments and impact statements. Our objectives are to discuss I) the relationship of population parameters to population growth, 2) methods of population projection, 3) use of data for model calibration and validation, and 4) the evaluation of management scenarios. Justification and defense of lethal or reproductive conhol programs to solve vertebrate pest problems requires a sound understanding of population status and the dynamics of the problem species.
Impact of Study Design on Reported Incidences of Acute Mountain Sickness: A Systematic Review.

AIMS Published incidences of acute mountain sickness (AMS) vary widely. Reasons for this variation, and predictive factors of AMS, are not well understood. We aimed to identify predictive factors that are associated with the occurrence of AMS, and to test the hypothesis that study design is an independent predictive factor of AMS incidence. We did a systematic search (Medline, bibliographies) for relevant articles in English or French, up to April 28, 2013. Studies of any design reporting on AMS incidence in humans without prophylaxis were selected. Data on incidence and potential predictive factors were extracted by two reviewers and crosschecked by four reviewers. Associations between predictive factors and AMS incidence were sought through bivariate and multivariate analyses for different study designs separately. Association between AMS incidence and study design was assessed using multiple linear regression. RESULTS We extracted data from 53,603 subjects from 34 randomized controlled trials, 44 cohort studies, and 33 cross-sectional studies. In randomized trials, the median of AMS incidences without prophylaxis was 60% (range, 16%-100%); mode of ascent and population were significantly associated with AMS incidence. In cohort studies, the median of AMS incidences was 51% (0%-100%); geographical location was significantly associated with AMS incidence. In cross-sectional studies, the median of AMS incidences was 32% (0%-68%); mode of ascent and maximum altitude were significantly associated with AMS incidence. In a multivariate analysis, study design (p=0.012), mode of ascent (p=0.003), maximum altitude (p<0.001), population (p=0.002), and geographical location (p<0.001) were significantly associated with AMS incidence. Age, sex, speed of ascent, duration of exposure, or history of AMS were inconsistently reported and therefore not further analyzed. CONCLUSIONS Reported incidences and identifiable predictive factors of AMS depend on study design.
Formins as effector proteins of Rho GTPases

Formin proteins were recognized as effectors of Rho GTPases some 15 years ago. They contribute to different cellular actin cytoskeleton structures by their ability to polymerize straight actin filaments at the barbed end. While not all formins necessarily interact with Rho GTPases, a subgroup of mammalian formins, termed Diaphanous-related formins or DRFs, were shown to be activated by small GTPases of the Rho superfamily. DRFs are autoinhibited in the resting state by an N- to C-terminal interaction that renders the central actin polymerization domain inactive. Upon the interaction with a GTP-bound Rho, Rac, or Cdc42 GTPase, the C-terminal autoregulation domain is displaced from its N-terminal recognition site and the formin becomes active to polymerize actin filaments. In this review we discuss the current knowledge on the structure, activation, and function of formin-GTPase interactions for the mammalian formin families Dia, Daam, FMNL, and FHOD. We describe both direct and indirect interactions of formins with GTPases, which lead to formin activation and cytoskeletal rearrangements. The multifaceted function of formins as effector proteins of Rho GTPases thus reflects the diversity of the actin cytoskeleton in cells.
Improved approximation algorithm of RNA structure prediction with pseudoknots

Based on MFE principle and the relative stability of the n-stems in RNA molecules, Minimum free energy method is adopted widely to predict RNA secondary structure, an improved approximation algorithm is presented to predict RNA pseudoknotted structure, the algorithm can solve arbitrary nested or parallel pseudoknots the algorithm takes O(n3) time and O(n2) space. This algorithm not only reduces the time complexity to O(n3), but also widens the maximum length of the sequence. The preliminary experimental test on the RNA sub-sequences in PseudoBase confirm that the algorithm outperforms other known algorithms in predicting accuracy, sensitivity and specificity.
Abnormal Behavior Detection by Multi-SVM-Based Bayesian Network

Automatic recognition of human actions is an important but difficult problem in the area of computer vision. In this paper, an novel approach is introduced to handle the problem. Firstly, human body is detected through the use of contour information and the body is tracked by the hybrid method. The most prominent features are searched by using the mean-shift method based on the body structure and the history motion image information. Finally, a learning method based on the multiple support vector machines is used to learn action types dynamically. We propose a method which integrate the Bayesian framework with the SVM method, which largely improves the recognition rate using historic information. Experiments show that our system can run in realtime for the detection of abnormal behaviors with limited information and produces robust result by making full use of historic motion information.
Factors associated with attitude and hypothetical behaviour regarding brain death and organ transplantation: Comparison between medical and other university students

Abstract: The aim of this study was to investigate the factors, including knowledge, that determine an individual's attitudes and behaviours regarding brain death and organ transplantation using questionnaires among medical and other university students. A total of 522 students (388 medical and 134 other) answered a questionnaire. The survey included the individual's knowledge about brain death, attitudes towards brain death and organ transplantation, and hypothetical behaviours assuming their willingness to donate their own or their family's organs. Medical students were more likely to have knowledge about brain death and to accept brain death and organ transplantation compared with other students, while there was no difference in their willingness to donate their own or their family's organs. Logistic regression analysis was used to assess the effects of various factors on the attitudes and behaviours. In both medical and other students, confidence in brain‐death diagnosis by doctors was independently associated with their willingness to donate their own organs after the adjustment for other factors, including knowledge (odds ratio [OR], 1.85; 95% confidence interval [CI], 1.15 to 2.97 and OR, 4.97; 95% CI, 1.01 to 24.39, respectively). An increase in knowledge may cause positive attitudes towards brain death and organ transplant. Meanwhile, reducing uncertainty about the brain‐death diagnostic process might have a beneficial effect on the willingness to donate organs.
From environmental signals to regulators: Modulation of biofilm development in Gram‐positive bacteria

Bacterial lifestyle is influenced by environmental signals, and many differentiation processes in bacteria are governed by the threshold concentrations of molecules present in their niche. Biofilm is one such example where bacteria in their sessile state adapt to a lifestyle that causes several adaptive alterations in the population. Here, a brief overview is given on a variety of environmental signals that bias biofilm development in Gram‐positive bacteria, including nutrient conditions, self‐ and heterologously produced substances, like quorum sensing and host produced molecules. The Gram‐positive model organism, Bacillus subtilis is a superb example to illustrate how distinct signals activate sensor proteins that integrate the environmental signals towards global regulators related to biofilm formation. The role of reduced oxygen level, polyketides, antimicrobials, plant secreted carbohydrates, plant cell derived polymers, glycerol, and osmotic conditions are discussed during the transcriptional activation of biofilm related genes in B. subtilis.