Miracle-dz/UniFAR-FTUs huggingface dataset:
Associations with early-life socio-economic position in adult DNA methylation.

BACKGROUND Disadvantaged socio-economic position (SEP) in childhood is associated with increased adult mortality and morbidity. We aimed to establish whether childhood SEP was associated with differential methylation of adult DNA. METHODS Forty adult males from the 1958 British Birth Cohort Study were selected from SEP extremes in both early childhood and mid-adulthood. We performed genome-wide methylation analysis on blood DNA taken at 45 years using MeDIP (methylated DNA immunoprecipitation). We mapped in triplicate the methylation state of promoters of approximately 20,000 genes and 400 microRNAs. Probe methylation scores were averaged across triplicates and differential methylation between groups of individuals was determined. Differentially methylated promoter sites of selected genes were validated using pyrosequencing of bisulfite-converted DNA. RESULTS Variably methylated probes (9112 from n = 223,359 on the microarray) corresponded to 6176 gene promoters with at least one variable probe. Unsupervised hierarchical clustering of probes obtained from the 500 most variable promoters revealed a cluster enriched with high SEP individuals confirming that SEP differences contribute to overall epigenetic variation. Methylation levels for 1252 gene promoters were associated with childhood SEP vs 545 promoters for adulthood SEP. Functionally, associations with childhood SEP appear in promoters of genes enriched in key cell signalling pathways. The differentially methylated promoters associated with SEP cluster in megabase-sized regions of the genome. CONCLUSIONS Adult blood DNA methylation profiles show more associations with childhood SEP than adult SEP. Organization of these associations across the genome suggests a well-defined epigenetic pattern linked to early socio-economic environment.
A Universal Rank-Size Law

A mere hyperbolic law, like the Zipf’s law power function, is often inadequate to describe rank-size relationships. An alternative theoretical distribution is proposed based on theoretical physics arguments starting from the Yule-Simon distribution. A modeling is proposed leading to a universal form. A theoretical suggestion for the “best (or optimal) distribution”, is provided through an entropy argument. The ranking of areas through the number of cities in various countries and some sport competition ranking serves for the present illustrations.
eggNOG: automated construction and annotation of orthologous groups of genes

The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database (‘evolutionary genealogy of genes: Non-supervised Orthologous Groups’), which contains orthologous groups constructed from Smith–Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl. de.
On the Functional Unity of Phonological Rules

V~. p/VC[_ _]CV-long V_. pI{VC [_V]cv}-long The structural sameness in this example is limited entirely to the fact that in both rules vowels are deleted; this deletion does not occur in similar environments, and, furthermore, only short vowels are deleted in (5), but both long and short vowels are deleted in (4). It is not, of course, sufficient that rules be structurally similar for collapsing to be In the standard theory of generative phonology (as represented, for example, by Chomsky and Halle, 1968), the principal requirement which determines whether or not two or more phonological rules may be partially collapsed is that the rules share overt structural propertiea. For example, rule (I) and (2) below may be collapsed by means of the brace notation into (3) by virtue of the fact that the rules contain a largely identical environment and the same class of segments undergoes the same structural change in both cases: (1) . p~V IC-O#-(2) . p~V IO-CC (3) . p~V/O-C{~ The above example is one where the structural similarity of the rules is striking. But the brace notational convention will also collapse rules such as (4) and (5) as well: 1 I would like to thank Morris Halle both for suggesting that I undertake the detailed examination of Yawelmani which led to thiJ paper, and for suggesting to me certain elements of the analysis of Yawelmani . which I have edcpted. I wo~ld abo like.to thank a number of people for reading this paper and/or discuaing
Prediction of Conserved Motif Networks based on Comparative Genomics

Discovery of regulatory motifs in unaligned DNA sequences remains a fundamental problem in computational biology. Most motif finding algorithms perform well in finding over-represented substrings in a small collection of sequences. This requires some prior knowledge about the functional relations among genes in a study in order to select a good collection of promoters. Microarray gene profiling and Chromotin-IP are often used to provide a list of sequences that may be enriched for binding sites of some transcription factors (TFs). However, any limitation in such experiments will propagate to the motif finding step, preventing us from finding motifs for many TFs, as well as from getting a global view of motif network in the whole genome. To date, over 200 yeast TFs have been assayed, but less than 100 have confident motif predictions.
Augmenting the scope of interactions with implicit and explicit graphical structures

When using interactive graphical tools, users often have to manage a structure, i.e. the arrangement of and relations between the parts or elements of the content. However, interaction with structures may be complex and not well integrated with interaction with the content. Based on contextual inquiries and past work, we have identified a number of requirements for the interaction with graphical structures. We have designed and explored two interactive tools that rely on implicit and explicit structures: ManySpector, an inspector for multiple objects that help visualize and interact with used values; and links that users can draw between object properties to provide a dependency. The interactions with the tools augment the scope of interactions to multiple objects. A study showed that users understood the interactions and could use them to perform complex graphical tasks.
International Journal of Production Research an Efficient Local Search Heuristic for the Double Row Layout Problem with Asymmetric Material Flow an Efficient Local Search Heuristic for the Double Row Layout Problem with Asymmetric Material Flow

Taylor & Francis makes every effort to ensure the accuracy of all the information (the " Content ") contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. The double row layout problem (DRLP) consists of arranging a number of rectangular machines of varying widths on either side of a corridor to minimize the total cost of material handling for products that move between these machines. This problem arises in the context of many production environments, most notably semiconductor manufacturing. Because the DRLP contains both combinatorial and continuous aspects, traditional solution approaches are not well suited to obtain solutions within a reasonable time. Moreover, previous approaches to this problem did not consider asymmetric flows. In this paper, an effective local search procedure featuring linear programming is proposed for solving the DRLP with asymmetric flows (symmetric flows being a special case). This approach is compared against several constructive heuristics and solutions obtained by a commercial mixed integer linear programming solver to evaluate its performance. Computational results show that the proposed heuristic is an effective approach, both in terms of solution quality and computational effort. 1. Introduction The double row layout problem (DRLP) consists of arranging a number of rectangular machines of varying widths on either side of a corridor to minimise the total cost of material handling. An automated guided vehicle (AGV) system operates along the aisle to move material from one machine to another. Feasible layouts must observe a predefined minimum clearance between adjacent machines, such that each pair of machines may require a unique amount of separation. The clearance takes into account machine access, heat dissipation and work in progress (WIP) storage. This problem, as illustrated in Figure 1, was first discussed in …
Joint Media Streaming Optimization of Energy and Rebuffering Time in Cellular Networks

Streaming services are gaining popularity and have contributed a tremendous fraction of today's cellular network traffic. Both playback fluency and battery endurance are significant performance metrics for mobile streaming services. However, because of the unpredictable network condition and the loose coupling between upper layer streaming protocols and underlying network configurations, jointly optimizing rebuffering time and energy consumption for mobile streaming services remains a significant challenge. In this paper, we propose a novel framework that effectively addresses the above limitations and optimizes video transmission in cellular networks. We design two complementary algorithms, Rebuffering Time Minimization Algorithm (RTMA) and Energy Minimization Algorithm (EMA) in this framework, to achieve smoothed playback and energy-efficiency on demand over multi-user scenarios. Our algorithms integrate cross-layer parameters to schedule video delivery. Specifically, RTMA aims at achieving the minimum rebuffering time with limited energy and EMA tries to obtain the minimum energy consumption while meeting the rebuffering time constraint. Extensive simulation demonstrates that RTMA is able to reduce at least 68% rebuffering time and EMA can achieve more than 27% energy reduction compared with other state-of-the-art solutions.
Analyzing operational flexibility of electric power systems

Operational flexibility is an important property of electric power systems and plays a crucial role for the transition of today's power systems, many of them based on fossil fuels, towards power systems that can efficiently accommodate high shares of variable Renewable Energy Sources (RES). The availability of sufficient operational flexibility in a given power system is a necessary prerequisite for the effective grid integration of large shares of fluctuating power in-feed from variable RES, especially wind power and Photovoltaics (PV). This paper establishes the necessary framework for quantifying and visualizing the technically available operational flexibility of individual power system units and ensembles thereof. Necessary metrics for defining power system operational flexibility, namely the power ramp-rate, power and energy capability of generators, loads and storage devices, are presented. The flexibility properties of different power system unit types, e.g. load, generation and storage units that are non-controllable, curtailable or fully controllable are qualitatively analyzed and compared to each other. Quantitative results and flexibility visualizations are presented for intuitive power system examples.
Local Grading of Learners

We propose a technique of localized grading of weak classifiers. This technique identifies local regions having similar characteristics and then uses grading of weak classifiers to describe the relationship between the data characteristics and the target class. Our experiment for several UCI datasets shows that the proposed combining method outperforms other combining methods we tried as well as any base classifier.
New Edge Detection Technique based on the Shannon Entropy in Gray Level Images

Abstract: Edge detection is an important field in image processing. Edges characterize object boundaries and are therefore useful for segmentation, registration, feature extraction, and identification of objects in a scene. In this paper, an approach utilizing an improvement of Baljit and Amar method which uses Shannon entropy other than the evaluation of derivates of the image in detecting edges in gray level images has been proposed. The proposed method can reduce the CPU time required for the edge detection process and the quality of the edge detector of the output images is robust. A standard test images, the real-world and synthetic images are used to compare the results of the proposed edge detector with the Baljit and Amar edge detector method. In order to validate the results, the run time of the proposed method and the pervious method are presented. It has been observed that the proposed edge detector works effectively for different gray scale digital images. The performance evaluation of the proposed technique in term s of the measured CPU time and the quality of edge detector method are presented. Experimental results demonstrate that the proposed method achieve better result than the relevant classic method.
Nature Genetics Advance Online Publication Resequencing of 31 Wild and Cultivated Soybean Genomes Identifies Patterns of Genetic Diversity and Selection

Cultivated soybean (Glycine max) was domesticated in China ~3,000– 5,000 years ago 1 and introduced to the United States in 1765 (ref. 2). Since then it has become an important cash crop, providing 69% and 30% of dietary protein and oil, respectively (see URLs). Given its economic importance, soybean productivity has garnered a great deal of attention in the scientific arena 3,4 , and this has resulted in the recent sequencing of a cultivated soybean genome 5. As a member of the Fabaceae family, soybean exhibits stringent cleistogamy (closed flower pollination). This characteristic may have a strong impact on maintaining genome homogeneity and reducing genomic variation, which may have been further exacerbated by the domestication process. Wild soybean (Glycine soja) may have retained genetic information before domestication and artificial selection, making it a unique resource for studying the impact of human selection on genetic variation in the soybean genome. To obtain a comprehensive overview of the sequence variation of soybean at the population level, we resequenced the genomes of a diverse group of 17 wild and 14 cultivated soybean accessions. Using these data, we identified two unique features of the soybean genome that are distinct from other crop plants: they have exceptionally high linkage disequilibrium (LD) and a high ratio of average nonsynony-mous versus synonymous nucleotide differences (Nonsyn/Syn). We also found that wild soybeans have retained allelic diversity that seems to have been lost in cultivated soybeans. These data and analyses should provide a valuable resource for recovering useful alleles and genes from wild soybeans. RESULTS Sequencing and variation calling Samples for resequencing were taken from soybean accessions that originated or were popularized in different Asian and international regions (Supplementary Fig. 1 and Supplementary Table 1). The advanced lines have been bred independently and have no known history of common ancestral lines. Additionally, some of these accessions have been used extensively as parental lines in breeding programs. Resequencing of the 17 wild and 14 cultivated soybean accessions generated a total of 901.75 million (M) paired-end reads of 45-bp or 76-bp read length (180 Gb of sequence), with most to an approximately ×5 depth and >90% coverage (Supplementary Table 1). All sequence reads were aligned against the reference genome Williams 82 (ref. 5) using SOAP2 (ref. 6) with parameters that included sequence similarity, pair-end relationships and sequence quality. We called SNPs using SOAPsnp, filtered them 7 and identified present and absent …
A review of telecollaboration technologies with respect to closely coupled collaboration

Many existing Computer-Supported Cooperative Work (CSCW) systems have two major deficiencies. Firstly, they support the situation of face-to-face meetings poorly. Secondly, many systems deal badly with data sets and workspaces. This paper outlines the requirements for a class of CSCW tools that would focus on supporting closely coupled collaborative activity around shared objects. These requirements include the ability to refer to a common model of the shared space through speech and gesture and for each person to be able to manipulate objects within that space. Based on that, this paper describes the current state-of-the-art in collaborative technologies with a critique of how well they support the required collaborative activities. Essentially, this paper suggests that, as of now, only through immersive Collaborative Virtual Environments (CVE) we are close to being able to achieve the seamless collaboration that exists in a face to face meeting.
Helminths and their implication in sepsis – a new branch of their immunomodulatory behaviour?

The prevalence of autoimmune and allergic disorders has dramatically increased in developed countries, and it is believed that our ‘cleaner living’ reduces exposure to certain microorganisms and leads to deviated and/or reduced regulation of the immune system. In substantiation of this health hygiene hypothesis, multiple epidemiological studies and animal models have characterized the protective immune responses induced by helminths during auto-inflammatory disorders. The beneficial effects of such helminths, like schistosomes and filariae, are thought to lie in their immunomodulatory capacity, which can be induced by different life-cycle stages or components thereof. In addition to suppressing autoimmunity recent evidence indicates that concurrent helminth infections also counterbalance exacerbated pro-inflammatory immune responses that occur during sepsis, improving survival. As with allergy, epidemiological studies have observed a steady rise in severe sepsis cases and although this may have resulted from several factors (immunosuppressive drugs, chemotherapy, transplantation, increased awareness and increased surgical procedures), it is tempting to hypothesize that the lack of helminth infections in Western countries may have contributed to this phenomenon. This review summarizes how helminths modulate host immunity during sepsis, such as manipulating macrophage activation and provides an overview about the possible implications that may arise during overwhelming bacterial co-infections. This well written review gives a comprehensive overview on the immunopathology of sepsis and the modulation of immune responses by helminths. It provides evidence that helminths or components thereof may improve the outcome of severe infections. This will allow the development of therapeutic strategies to fight infections and sepsis.
Association between persistent tachycardia and tachypnea and in-hospital mortality among non-hypotensive emergency department patients admitted to the hospital

Objective Vital sign trends are used in clinical practice to assess treatment response and aid in disposition, yet quantitative data to support this practice are lacking. This study aimed to determine the prognostic value of vital sign normalization. Methods Secondary analysis of a prospective cohort of adult emergency department (ED) patients admitted a single urban tertiary care hospital. A random sample of 182 days was chosen, and a manual review of all admissions was undertaken. Persistent tachycardia or tachypnea was defined as failure to decrease to a normal value in the ED. Elevated upon admission was defined as an abnormal value at the last set of vital signs documented. The primary outcome was in-hospital mortality. Results 4,878 patients were enrolled and 4.5 (±3.8) sets of vital signs were checked per patient. 1,770 patients were tachycardic and 1,499 were tachypneic. Among tachycardic patients, 941 (53%) were persistently tachycardic and 1,074 (61%) were tachycardic upon admission. Among tachypneic patients 639 (42%) were persistently tachypneic and 768 (51%) were tachypneic upon admission. Mortality was higher in patients persistently tachycardic (5.7% vs. 3.1%, P=0.008) or tachycardic upon admission (5.5% vs. 3.0%, P=0.014). Similar results were found in tachypneic patients (8.3% vs. 4.5%, P=0.003; 7.8% vs. 4.4%, P=0.006). Conclusion Persistent tachycardia and tachypnea are associated with an increased risk of mortality in ED patients admitted to the hospital. Further study is necessary to determine if improved recognition or earlier interventions can affect outcomes.
Wave-of-Advance Models of the Diffusion of the Y Chromosome Haplogroup R1b1b2 in Europe

Whether or not the spread of agriculture in Europe was accompanied by movements of people is a long-standing question in archeology and anthropology, which has been frequently addressed with the help of population genetic data. Estimates on dates of expansion and geographic origins obtained from genetic data are however sensitive to the calibration of mutation rates and to the mathematical models used to perform inference. For instance, recent data on the Y chromosome haplogroup R1b1b2 (M269) have either suggested a Neolithic origin for European paternal lineages or a more ancient Paleolithic origin depending on the calibration of Y-STR mutation rates. Here we examine the date of expansion and the geographic origin of hgR1b1b2 considering two current estimates of mutation rates in a total of fourteen realistic wave-of-advance models. We report that a range expansion dating to the Paleolithic is unlikely to explain the observed geographical distribution of microsatellite diversity, and that whether the data is informative with respect to the spread of agriculture in Europe depends on the mutation rate assumption in a critical way.