Miracle-dz/UniFAR-FTUs huggingface dataset:
Delivery of Iron-Sulfur Clusters to the Hydrogen-Oxidizing [NiFe]-Hydrogenases in Escherichia coli Requires the A-Type Carrier Proteins ErpA and IscA

During anaerobic growth Escherichia coli synthesizes two membrane-associated hydrogen-oxidizing [NiFe]-hydrogenases, termed hydrogenase 1 and hydrogenase 2. Each enzyme comprises a catalytic subunit containing the [NiFe] cofactor, an electron-transferring small subunit with a particular complement of [Fe-S] (iron-sulfur) clusters and a membrane-anchor subunit. How the [Fe-S] clusters are delivered to the small subunit of these enzymes is unclear. A-type carrier (ATC) proteins of the Isc (iron-sulfur-cluster) and Suf (sulfur mobilization) [Fe-S] cluster biogenesis pathways are proposed to traffic pre-formed [Fe-S] clusters to apoprotein targets. Mutants that could not synthesize SufA had active hydrogenase 1 and hydrogenase 2 enzymes, thus demonstrating that the Suf machinery is not required for hydrogenase maturation. In contrast, mutants devoid of the IscA, ErpA or IscU proteins of the Isc machinery had no detectable hydrogenase 1 or 2 activities. Lack of activity of both enzymes correlated with the absence of the respective [Fe-S]-cluster-containing small subunit, which was apparently rapidly degraded. During biosynthesis the hydrogenase large subunits receive their [NiFe] cofactor from the Hyp maturation machinery. Subsequent to cofactor insertion a specific C-terminal processing step occurs before association of the large subunit with the small subunit. This processing step is independent of small subunit maturation. Using western blotting experiments it could be shown that although the amount of each hydrogenase large subunit was strongly reduced in the iscA and erpA mutants, some maturation of the large subunit still occurred. Moreover, in contrast to the situation in Isc-proficient strains, these processed large subunits were not membrane-associated. Taken together, our findings demonstrate that both IscA and ErpA are required for [Fe-S] cluster delivery to the small subunits of the hydrogen-oxidizing hydrogenases; however, delivery of the Fe atom to the active site might have different requirements.
Smoke and flame detection in video sequences based on static and dynamic features

In this paper we propose efficient smoke and flame detection algorithms for intelligent video surveillance systems. Our algorithms consider dynamic and static features of smoke and flame: contrast, color, texture features and motion. For smoke detection the approach uses motion and contrast as the two key features of smoke. Motion is a primary sign and is used at the beginning for extraction from a current frame of candidate areas. In addition to consider a direction of smoke distribution the movement estimation based on the optical flow is applied. For flame detection we use color image segmentation, temporal and spatial wavelet analyses on the first step. After that color and texture features for candidate flame regions are extracted. Texture features are defined based on normalized gray level co-occurrence matrix after computation of local binary pattern. Experimental results are presented in the paper.
Genotyping Performance Assessment of Whole Genome Amplified DNA with Respect to Multiplexing Level of Assay and Its Period of Storage

Whole genome amplification can faithfully amplify genomic DNA (gDNA) with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA) has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at −70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy) of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex) of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy) due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy.
A critical role for ATF2 transcription factor in the regulation of E‐selectin expression in response to non‐endotoxin components of N eisseria meningitidis

Vascular injury is a serious complication of sepsis due to the gram‐negative bacterium Neisseria meningitidis. One of the critical early steps in initiating this injury is via the interaction of leucocytes, particularly neutrophils, with adhesion molecules expressed on inflamed endothelium. We have previously demonstrated that both lipopolysaccharide (LPS) and non‐LPS components of meningococci can induce very high levels of expression of the vascular endothelial cell adhesion molecule E‐selectin, which is critical for early tethering and capture of neutrophils onto endothelium under flow. Using an LPS‐deficient strain of meningococcus, we showed that very high levels of expression can be induced in primary endothelial cells, even in the context of weak activation of the major host signal transduction factor [nuclear factor‐κB (NF‐κB)]. In this study, we show that the particular propensity for N. meningitidis to induce high levels of expression is regulated at a transcriptional level, and demonstrate a significant role for phosphorylation of the ATF2 transcription factor, likely via mitogen‐activated protein (MAP) kinases, on the activity of the E‐selectin promoter. Furthermore, inhibition of E‐selectin expression in response to the lpxA− strain by a p38 inhibitor indicates a significant role of a p38‐dependent MAPK signalling pathway in ATF2 activation. Collectively, these data highlight the role that LPS and other bacterial components have in modulating endothelial function and their involvement in the pathogenesis of meningococcal sepsis. Better understanding of these multiple mechanisms induced by complex stimuli such as bacteria, and the specific inflammatory pathways they activate, may lead to improved, focused interventions in both meningococcal and potentially bacterial sepsis more generally.
Comparison of pixel-based and object-oriented knowledge-based classification methods using SPOT5 imagery

Land cover mapping is very important for evaluating natural recourses, understanding the societal and business activities. The remote sensing techniques provide effective and efficient methods to create such maps. To high spatial resolution imagery such as SPOT5 imagery, the land cover classification precision will be improved with the knowledge, Digital Elevation Model (DEM) data and the spatial information such as texture and. Both the pixel-based classification method based on the knowledge rule and the object-oriented fuzzy classification methods have been studied in this paper using SPOT5 high spatial resolution imagery. Some GIS dataset and the texture are integrated into the two knowledge-based classifications in this paper. And the result of accuracy assessment indicates that the two classifications can catch good classification precision, but the objected-oriented classification method does better. Besides, the shape and context information can be used fully to distinguish the roads from the buildings with the objected-oriented fuzzy classification method, which is hard to accomplish in pixel-based classification. Furthermore, the objected-oriented classification method is more suitable in land cover mapping due to its meaningful objects.
Adapting Standard Video Codecs for Depth Streaming

Cameras that can acquire a continuous stream of depth images are now commonly available, for instance the Microsoft Kinect. It may seem that one should be able to stream these depth videos using standard video codecs, such as VP8 or H.264. However, the quality degrades considerably as the compression algorithms are geared towards standard three-channel (8-bit) colour video, whereas depth videos are single-channel but have a higher bit depth.We present a novel encoding scheme that efficiently converts the single-channel depth images to standard 8-bit three-channel images, which can then be streamed using standard codecs. Our encoding scheme ensures that the compression affects the depth values as little as possible. We show results obtained using two common video encoders (VP8 and H.264) as well as the results obtained when using JPEG compression. The results indicate that our encoding scheme performs much better than simpler methods.
Recuperating and (re)learning the language of autogestión in Argentina’s empresas recuperadas worker cooperatives

ABSTRACT This article homes in on the recuperative and learning dimensions of Argentina’s empresas recuperadas por sus trabajadores worker cooperatives (ERTs, worker-recuperated enterprises). Drawing on the author’s sociological, ethnographic, and political economic work with Argentina’s ERTs since 2005, the article theorizes autogestión – the collective self-management of associated labour – from its take up by ERT movement protagonists. The article explores and theorizes how ERT workers come to practice autogestión, what they actually take back in the process of occupying and controlling the formerly capitalist workplaces that had employed them, and how their projects of cooperative production are ensconced in a ‘language of autogestión’ – recuperating and (re)learning other economic notions and practices against and beyond capitalocentric discourses. Grounded in a class-struggle Marxist perspective, the paper ultimately proposes that ERT workers collectively recuperate three overarching dimensions of productive life from capital: (1) the self-valorization of living labour, (2) cooperation in the labour process, and (3) the socialization of surpluses and wealth. These recuperations of autogestión, the article concludes, (their ‘language of autogestión’) offer evocative suggestions for envisioning less-exploitive forms of work, more socially just and democratic workplaces, and for challenging and beginning to move beyond neoliberal logics.
An intergenerational qualitative study of the good parenting ideal and active free play during middle childhood

ABSTRACT This study addressed the question: How and why has the good parenting ideal changed in relation to active free play (AFP) during middle childhood? Twenty-eight middle class and predominantly white adults (14 grandparent-parent dyads) completed individual semi-structured interviews. Data were subjected to a thematic analysis. Two themes (changing expectations for parental involvement in children's lives and increasing expectations to involve children in structured activities) depicted how the good parenting ideal has changed. A further two themes (news media influence on perceptions of safety and concerns about being judged on social media) explained some of the reasons why the good parenting ideal has changed. Perceived needs for parental involvement, supervision, and organized activities appear to contradict the notion of active free play. It may be useful to develop initiatives that are consistent with the good parenting ideal, and to examine parents’ use of traditional and social media in future AFP research.
The Efficacy of Four Sunburn Mitigation Strategies and Their Effects on Yield, Fruit Quality, and Economic Performance of Honeycrisp Cv. Apples under Eastern New York (USA) Climatic Conditions

ABSTRACT Sunburn is a serious economic problem in practically all apple-growing regions of the world. Losses of apple fruit due to sunburn can range from 10% as high as 50%. Several years ago, this problem started to be a concern in Eastern New York State, especially in the Hudson Valley region with the cultivar ‘Honeycrisp’. The study was conducted in three ‘Honeycrisp’ apple tree orchards in the Hudson Valley region (Southeast, New York State) during the 2015 and 2016 growing seasons. Four sunburn mitigation strategies were tested (evaporative cooling, 20% crystal net, the sunscreen Raynox Plus® and the particle film ScreenDuo®) at a variety of timings throughout each growing season. Yield, sunburn incidence/severity, quality, and economic returns were evaluated. Treatments did not affect horticulture performance and fruit quality, but they did reduce sunburn damage to varying degrees. The greatest sunburn mitigation was achieved with the use of netting, followed by spray applications of Raynox Plus® and ScreenDuo®. Apples with sunburn damage had higher flesh firmness, soluble solids content and titratable acidity. Treatment differences in sunburn mitigation did not result in higher net returns to the grower.
Remarks on bell-shaped lumps: Stability and fermionic modes

We consider nontopological, 'bell-shaped' localized and regular solutions available in some 1+1-dimensional scalar field theories. Several properties of such solutions are studied, namely, their stability and the occurrence of fermion bound states in the background of a kink and a kink-antikink solution of the sine-Gordon model.
Handling IDS' reliability in alert correlation: A Bayesian network-based model for handling IDS's reliability and controlling prediction/false alarm rate tradeoffs

Probabilistic graphical models are very efficient modeling and reasoning tools. In this paper, we propose an efficient and novel Bayesian network model for a major problem in alert correlation which plays a crucial role in nowadays computer security. Indeed, the use of multiple intrusion detection systems (IDSs) and complementary approaches is fundamental to improve the overall detection rates. This however inevitably rises huge amounts of alerts most of which are redundant and false alarms making the manual analysis of all the amounts of triggered alerts intractable. In this paper, we first propose a Bayesian network-based model allowing to handle the reliability of IDSs when predicting severe attacks by correlating the alerts reported by the IDSs monitoring the network. Then we propose a flexible and efficient approach especially designed to limit the false alarm rates by controlling the confidence of the prediction model. Finally, we provide experimental studies carried out on a real and representative alert corpus showing significant improvements regarding the tradeoffs between the prediction rates and the corresponding false alarm ones.
Fertility, class and gender in Britain, 1860–1940: Conceptions and refutations

Introduction Part I. Historiographical Introduction: A Genealogy of Approaches: 1. The construction and the study of the fertility decline in Britain: social science and history Part II. The Professional Model of Social Classes: An Intellectual History: 2. Social classification of occupations and the GRO in the nineteenth century 3. Social classification and nineteenth-century naturalistic social science 4. The emergence of a social explanation of class inequalities among environmentalists, 1901-1904 5. The emergence of the professional model as the official system of social classification, 1905-1928 Part III. A New Analysis of the 1911 Census Occupational Fertility Data: 6. A test of the coherence of the professional model of class-differential fertility decline 7. Multiple fertility declines in Britain: occupational variation in completed fertility and nuptiality 8. How was fertility controlled? The spacing versus stopping debate and the culture of abstinence Part IV. Conceptions and Refutations: 9. A general approach to fertility change and the history of falling fertilities in England and Wales 10. Social class, communities, gender and nationalism in the study of fertility change Appendices Bibliography Index.
The brain and fatigue: New opportunities for nutritional interventions?

Abstract It is clear that the cause of fatigue is complex, influenced by events occurring in both the periphery and the central nervous system. Work conducted over the last 20 years has focused on the role of brain serotonin and catecholamines in the development of fatigue, and the possibility that manipulation of neurotransmitter precursors may delay the onset of fatigue. While there is some evidence that branched-chain amino acid and tyrosine ingestion can influence perceived exertion and some measures of mental performance, the results of several apparently well-controlled laboratory studies have not demonstrated a positive effect on exercise capacity or performance under temperate conditions. As football is highly reliant upon the successful execution of motor skills and tactics, the possibility that amino acid ingestion may help to attenuate a loss in cognitive function during the later stages of a game would be desirable, even in the absence of no apparent benefit to physical performance. There are several reports of enhanced performance of high-intensity intermittent exercise with carbohydrate ingestion, but at present it is difficult to separate the peripheral effects from any potential impact on the central nervous system. The possibility that changes in central neurotransmission play a role in the aetiology of fatigue when exercise is performed in high ambient temperatures has recently been examined, although the significance of this in relation to the pattern of activity associated with football has yet to be determined.
Analysts ’ earnings forecasts and the recognition of nonrecurring charges

This paper examines how the recognition of nonrecurring charges affects analysts’ earnings per share forecasts. In a sample of 1,278 firms (22,579 firm-quarters), the dispersion of analyst EPS forecasts increases in fiscal quarters proximate to those that exhibit large nonrecurring charges. Further, for these same quarters, the accuracy of analyst EPS forecasts decreases and the optimistic bias inherent in analyst forecasts increases. This result does not hold simply for the fiscal quarters in which the nonrecurring charge is actually reported, but the majority of the effect is also demonstrated in surrounding fiscal quarters. This is evidence of the uncertainty faced by analysts in unwinding the implications of nonrecurring items for a series of earnings outcomes. In addition, the existence of nonrecurring accounting charges complicates the task of accurately measuring the characteristics of earnings per share (EPS) forecast errors. Analysts forecast earnings before the impact of nonrecurring charges. Comparing analyst forecasts to earnings realizations that include nonrecurring charges will systematically overstate analyst forecast errors. This overstatement is made increasingly important for empirical forecasting research because of the increasing frequency with which firms are reporting large nonrecurring charges. Mechanical time-series model predictions of EPS numbers are also affected by the presence of these nonrecurring accounting items. Studies measuring analyst forecast superiority (relative to time-series models), or studies relating observed analyst forecast errors to the historical variability of earnings are particularly sensitive to the existence of nonrecurring accounting charges. JEL classification: D84, E37, G20, M41
Automated Generation of Use Case Diagrams from Problem Frames Using Formal Concept Analysis

Problem-oriented approaches to software engineering are based on the principle that designing effective solutions requires a detailed understanding of the problem. These approaches could provide an effective support closing the gap between the solution and problem domains, and hence, reducing the risk of failure in software projects. Problem Frames (PF) is an effective problem-oriented approach for classifying, analyzing and structuring software development problems during the requirement phase. However, PF still lacks techniques and tools that support their use and integration in the mainstream software engineering lifecycles. Accordingly, in this paper, we present an approach to transform Problem Frames to the widely-used UML Use Case diagrams. The transformation exploits the notion of Formal Concept Analysis (FCA), a mathematical approach for clustering and categorization. FCA enables the formalization of the transformation process, and thus, allows for automation. The approach is demonstrated by the means of a case study.
Robust Non-Explicit Neural Discourse Parser in English and Chinese

Neural discourse models proposed so far are very sophisticated and tuned specifically to certain label sets. These are effective, but unwieldy to deploy or repurpose for different label sets or languages. Here, we propose a robust neural classifier for non-explicit discourse relations for both English and Chinese in CoNLL 2016 Shared Task datasets. Our model only requires word vectors and simple feed-forward training procedure, which we have previously shown to work better than some of the more sophisticated neural architecture such as long-short term memory model. Our Chinese model outperforms feature-based model and performs competitively against other teams. Our model obtains the state-of-the-art results on the English blind test set, which is used as the main criteria in this competition.
Influence of Methylenetetrahydrofolate Reductase C677T, A1298C, and G80A Polymorphisms on the Survival of Pediatric Patients with Acute Lymphoblastic Leukemia

The influence of genic polymorphisms involved in metabolism of chemotherapeutic agents as the methotrexate (MTX) has been studied mainly in acute lymphoblastic leukemia (ALL) of childhood. Advances in treatment may be attributed to identification of prognostic factors added to chemotherapy protocol. The aim of this study was to analyze the association of the C677T, A1298C, and G80A polymorphisms on MTHFR gene and on the overall survival of pediatric patients (n = 126) with lymphoblastic leukemia treated with MTX according to the Brazilian protocol in 187 months. The C677T and G80A polymorphisms were genotyped by PCR-RFLP and A1298C polymorphism by allele-specific PCR. We observed that ALL patients presented rate (dead/alive) of 0.36 for the 677CC genotype, corresponding also to lower overall survival (P = 0.0013); on the other hand, the 677TT genotype showed a better survival (98%). Thus, we believe that patients with 80AA genotype presented a small reduction in MTX plasma level, suggesting that ALL children, carrying the 80AA genotype, showed a high toxicity to MTX (P < 0.0001).