Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetics and Molecular Biology of Industrial Organisms Horizontal Gene Transfer and Gene Conversion Drive Evolution of Modular Polyketide Synthases

Soil bacteria live in a very competitive environment and produce many secondary metabolites; there appears to be strong selective pressure for evolution of new compounds. Secondary metabolites are the most important source of chemical structures for the pharmaceutical industry and an understanding of the evolutionary process should help in finding novel chemical entities. Modular polyketide synthases are a particularly interesting case for evolutionary studies, because much of the chemical structure can be predicted from DNA sequence. Previous evolutionary studies have concentrated on individual modules or domains and were not able to study the evolution of orthologues. This study overcame this problem by considering complete clusters as ''organisms'', so that orthol-ogous modules and domains could be identified and used to characterise evolutionary pathways. Seventeen modular polyketide synthase clusters were identified that fell into six classes. Gene conversion within clusters was very common (affecting about 15 % of domains) and was detected by discordance in phylogenetic trees. An evolutionary model is proposed in which a single cross over between two different clusters (i.e. horizontal gene transfer) would generate a cluster of very different architecture with radically different chemical products; subsequent gene conversion and deletions would explore chemical variants. Two probable examples of such recombination were found. This model suggests strategies for detecting horizontal gene transfer in cluster evolution.
An Automatic Human Face Detection Method

This article contains a proposal for an automatic human face detection method, that tries to join several theories proposed by different authors. The method is based on detection of shape features (eye pairs) and skin color. The method assumes certain circumstances and constraints, respectively. Therefore it is not applicable universally. Given the constraints, it is effective enough for applications where fast execution is required. Test results are given and at the end some directives for future work are discussed.
Safe LTL Assumption-Based Planning

Planning for partially observable, nondeterministic domains is a very significant and computationally hard problem. Often, reasonable assumptions can be drawn over expected/nominal dynamics of the domain; using them to constrain the search may lead to dramatically improve the efficiency in plan generation. In turn, the execution of assumption-based plans must be monitored to prevent runtime failures that may happen if assumptions turn out to be untrue, and to replan in that case. In this paper, we use an expressive temporal logic, LTL, to describe assumptions, and we provide two main contributions. First, we describe an effective, symbolic forward-chaining mechanism to build (conditional) assumption-based plans for partially observable, nondeterministic domains. Second, we constrain the algorithm to generate safe plans, i.e. plans guaranteeing that, during their execution, the monitor will be able to univocally distinguish whether the domain behavior is one of those planned for or not. This is crucial to inhibit any chance of useless replanning episodes. We experimentally show that exploiting LTL assumptions highly improves the efficiency of plan generation, and that by enforcing safety we improve plan execution, inhibiting useless and expensive replanning episodes, without significantly affecting plan generation.
Searches for optimal G 2 wavelet bases for use in signal coding

We use the interpolating formulation of the lifting scheme to construct optimized second–generation wavelets for a given segment of data. We optimize with respect to an energy compaction cost function the Shannon entropy of the uniformly quantized transform coefficients. We determine the predict operator adaptively at each level (and thus there is no dilation relation between wavelets on different scales) and calculate an associated update operator to produce vanishing moments in the synthesis wavelet. Our initial adaptive algorithm is an inefficient search over the space of 4 tap linear predictor operators sampled at a finite resolution. This search provides a good estimate of the best we can hope to achieve using any efficient algorithm for the same task. We present results for three typical segments of PCM audio. A further 0 5.6% reduction in Shannon entropy (an improvement of 0 22%) is seen when compared to the standard polynomial interpolation predictors in our examples. Finally, we discuss possible techniques for determining an optimal, or near optimal linear predict operator efficiently for a given signal.
Lipoprotein abnormalities in human genetic CD36 deficiency associated with insulin resistance and abnormal fatty acid metabolism.

CD36 is an 88-kDa membranous protein with multiple relevant function that is widely expressed in human tissues (1). Because we and others (2) found human genetic deficiency of this molecule, we have elucidated the molecular bases and pathophysiology. We have reported that the human deficiency may be associated with insulin resistance (3) and abnormal dynamics of long-chain fatty acid (LCFA) (4). The aim of the present study was to further characterize lipid and lipoprotein metabolism in the human genetic CD36 deficiency, especially focusing on postprandial …
Epidemiology of constipation (EPOC) study in the United States: relation of clinical subtypes to sociodemographic features

OBJECTIVE:Constipation is a common heterogeneous condition, possibly encompassing different clinical subtypes. Little is known about the comparative epidemiology of constipation subtypes. This study was conducted to estimate the prevalence of constipation subtypes and determine whether subtypes differ by sociodemographic factors.METHODS:Between June and September 1997, a telephone interview was conducted with individuals about their bowel habits in the preceding 3 months. Survey data on 15 constipation-related symptoms were used to identify individuals who met prespecified symptom criteria for the following mutually exclusive subgroups: functional constipation, irritable bowel syndrome (IBS), outlet obstruction or delay (outlet), both IBS and outlet (IBS-outlet), and frequent laxative users (i.e., at least every other day). A total of 10,018 eligible individuals in the United States 18 yr of age or older completed the interview. Test–retest reliability of reporting symptoms was assessed in a separate national survey. The Spearman's correlation coefficient for reporting symptoms ranged from 0.54 to 0.83; all but three symptoms had correlations above 0.68. RESULTS:The overall prevalence of constipation was 14.7%. By subtype, prevalence was 4.6% for functional, 2.1% for IBS, 4.6% for outlet, and 3.4% for IBS-outlet. An additional 1.8% of respondents reported laxative use at least every other day. Outlet was the most common subtype among women, whereas functional constipation was the most common subtype among men. The gender ratio varied by subtype, with elevated ratios for outlet (F/M = 1.65) and IBS-outlet (F/M = 2.27) subtypes. The age pattern differed among each of the four subtypes. Prevalence of functional subtype decreased with increasing age. In contrast, outlet subtype did not seem to vary by age, and IBS (both men and women) and IBS-outlet (women only) subtypes increased to age 35 yr and declined thereafter. Prevalence of functional constipation increased with increasing education. Outlet type was more common in nonwhites compared to whites. Finally, 45% of individuals with constipation reported having the condition for 5 yr or more.CONCLUSIONS:Constipation is a heterogeneous condition. Differences in epidemiological profile by age, sex ratio, and relation to other sociodemographical factors support the distinction of two and possibly more symptom-based subtypes.
Predictive Modeling of Human Behavior: Supervised Learning from Telecom Metadata

Big data, specifically Telecom Metadata, opens new opportunities for human behavior understanding, applying machine learning and big data processing computational methods combined with interdisciplinary knowledge of human behavior. In this thesis new methods are developed for human behavior predictive modeling based on anonymized telecom metadata on individual level and on large scale group level, which were studied during research projects held in 2012-2016 in collaboration with Telecom Italia, Telefonica Research, MIT Media Lab and University of Trento. It is shown that human dynamics patterns could be reliably recognized based on human behavior metrics derived from the mobile phone and cellular network activity (call log, sms log, bluetooth interactions, internet consumption). On individual level the results are validated on use cases of detecting daily stress and estimating subjective happiness. An original approach is introduced for feature extraction, selection, recognition model training and validation. Experimental results based on ensemble stochastic classification and regression tree models are discussed. On large group level, following big data for social good challenges, the problem of crime hotspot prediction is formulated and solved. In the proposed approach we use demographic information along with human mobility characteristics as derived from anonymized and aggregated mobile network data. The models, built on and evaluated against real crime data from London, obtain accuracy of almost 70% when classifying whether a specific area in the city will be a crime hotspot or not in the following month. Electric energy consumption patterns are correlated with human behavior patterns in highly nonlinear way. Second large scale group behavior prediction result is formulated as predicting next week energy consumption based on human dynamics analysis derived out of the anonymized and aggregated telecom data, processed from GSM network call detail records (CDRs). The proposed solution could act on energy producers/distributors as an essential aid to smart meters data for making better decisions in reducing total primary energy consumption by limiting energy production when the demand is not predicted, reducing energy distribution costs by efficient buy-side planning in time and providing insights for peak load planning in geographic space. All the studied experimental results combine the introduced methodology, which is efficient to implement for most of multimedia and real-time applications due to highly reduced low-dimensional feature space and reduced machine learning pipelines. Also the indicators which have strong predictive power are discussed opening new horizons for computational social science studies.
The not so great divide? Psychologists and psychiatrists take stands on the medical and psychosocial models of mental illness.

Mental health practitioners' positions on the etiology and treatment of mental illness have traditionally been studied from a unidimensional perspective, assuming a bipolar attitudinal continuum ranging from psychosocial to medical ideology. This assumption is tested from the responses of 82 psychologists and 69 psychiatrists to the newly developed 63-item, 6-point Likert scale, Mental Health Questionnaire (MHQ). Factor analysis detected 6 distinctive factors: biogenetic psychopathology, psychosocial perspectives, medical ideology, diagnosis, drug treatment, and sociocultural values.
The murine CCR3 receptor regulates both the role of eosinophils and mast cells in allergen-induced airway inflammation and hyperresponsiveness

CCR3 is a chemokine receptor initially thought specific to eosinophils but subsequently identified on TH2 cell subsets, basophils, mast cells, neural tissue, and some epithelia. Because of the prominent role of these cells in allergic disease, including asthma, we generated mice deficient in CCR3 to determine its contribution in a model of allergic airway disease. Here we show that CCR3 is important for the basal trafficking of eosinophils to the intestinal mucosa but not the lung. In contrast, CCR3 disruption significantly curtails eosinophil recruitment to the lung after allergen challenge, with the majority of the eosinophils being arrested in the subendothelial space. Further, a role for CCR3 in mast cell homing has been identified; after sensitization and allergen challenge, we find increased numbers of intraepithelial mast cells in the trachea of knockout mice. Physiologically, we find that the net result of these complex cell fates after sensitization and allergen challenge is a paradoxical increase in airway responsiveness to cholinergic stimulation. These data underscore a more complex role for CCR3 in allergic disease than was anticipated.
Relationship Violence by Women: Issues and Implications

This article presents an analysis of the use of violence by women against their intimate partners. Although women may use violence as often as men do, both the motives for and the effects of women's violence are quite different. The political agenda of some observers caused them to ignore or downplay violence by women, fearing that attention would be diverted from the more serious problem of male violence. Such a strategy is likely to have negative consequences for women and science. Finally, implications for prevention, intervention, and research are discussed.
Autologous Minced Muscle Grafts Improve Muscle Strength in a Porcine Model of Volumetric Muscle Loss Injury

Objectives: The traumatic loss of muscle tissue, defined as volumetric muscle loss (VML) injury, has no definitive therapy. The purposes of this study were: (1) to develop a porcine model of VML and (2) to investigate autologous minced muscle grafts (1-mm3 pieces of muscle) as a potential therapeutic. Minced grafts were evaluated because they have promoted fiber regeneration and functional recovery in rat VML models and do not require US Food and Drug Administration approval for clinical use. Methods: In 5 female Yorkshire-cross pigs, ≈5 g (≈20%) of tissue was excised from the peroneous tertius muscle (≈3 × 3 × 1.5-cm defect) of each leg. The defect in one leg was treated with autologous minced grafts derived from the contralateral leg. Maximal isometric tetanic strength assessments of the dorsiflexor muscles (ie, the peroneous tertius muscle) were performed before and biweekly up to 12 weeks postinjury. Results: VML injury resulted in a −43.5% ± 7.2% strength deficit 12 weeks postinjury in nonrepaired legs. Autologous minced muscle graft repair significantly improved strength over 12 weeks (32% strength increase 12 weeks postinjury vs. nonrepaired muscles with a remaining −27.8% ± 7.0% strength deficit; P < 0.001). Nonrepaired muscles developed extensive fibrosis and presented no evidence of muscle fiber regeneration within the defect area. Minced graft-treated muscles presented areas of putative de novo muscle fiber regeneration within the defect area, although extensive fibrotic tissue deposition was also present. Conclusion: Autologous minced muscle grafts partially restored neuromuscular strength in a novel porcine model of VML.
The Structure of Organizational Incentives

0 The financial support of Peat Marwick Main & Co., Ernst & Young, David Hauck, and the Reginald H. Jones Center for Management Policy, Strategy, and Organization is gratefully acknowledged. We would like to thank Sherwin Rosen, Stanley Baiman, Marshall Meyer, three anonymous reviewers, and the workshop participants at the Wharton School, Harvard Business School, Washington University, Northwestern University, Odense University, Uppsala University, and the Shore Conference on Strategic Models for their helpful comments. To improve understanding and design of organizational incentives, we used confidential compensation data obtained for four distinct organizational levels (ranging from plant manager to corporate chief executive officer) to evaluate the ability of tournament, managerial power, and agency theories to explain these observed compensation data. Our results suggest that organizational incentives are most appropriately characterized by a combination of these models, rather than being completely described by a single theoretical description. '
A new approach to state observation of nonlinear systems with delayed output

The article presents a new approach for the construction of a state observer for nonlinear systems when the output measurements are available for computations after a nonnegligible time delay. The proposed observer consists of a chain of observation algorithms reconstructing the system state at different delayed time instants (chain observer). Conditions are given for ensuring global exponential convergence to zero of the observation error for any given delay in the measurements. The implementation of the observer is simple and computer simulations demonstrate its effectiveness.
Income, Public Works, and Mortality in Early Twentieth-Century American Cities

Mortality differentials for 122 cities in the United States in 1910 are examined with specific attention given to the influence of public works projects. Sewage systems are found to have significantly reduced mortality, while water filtration systems had no impact. This runs counter to the theories and beliefs of many public health officials and sanitary engineers of the era. Other factors, including the racial and immigrant composition of the population, urban density, number of physicians, and the standard of living, are also examined.
Relation of the Postnatal Attachment Questionnaire to the Attachment Q‐Set

We examined the relation of the relatively new parent‐to‐infant Postnatal Attachment Questionnaire (PAQ) and the Attachment Q‐Set (AQS) in mothers and fathers of 12‐month‐old infants. The PAQ represents the affective component and the AQS the behavioural component of caregiver–infant attachment. The PAQ has to do with the feelings of the parents towards the infant, whereas the AQS is concerned with the infant's and parents' behaviour vis‐à‐vis each other. Fifty‐nine mothers and 38 fathers of 59 infants (31 girls, 28 boys) completed the PAQ and the AQS when their infants were between the ages of 11 and 15 months. The results of multiple regression analyses indicate that the PAQ of both mothers and fathers, as a whole, is significantly related to the AQS. Also, interaction effects revealed that, for fathers of daughters, the relation between the PAQ and the AQS is positive, such that more pleasure in interacting was associated with more secure attachments; whereas for fathers of sons, the relation between the AQS and the absence of hostility PAQ subscale is significant and positive, with less hostility relating to more secure attachments. These findings lend support for the notion that parental feelings are one important correlate of infant secure‐base behaviour.
Registration of multi-resolution point clouds from terrestrial laser scanners

Registration of point clouds from terrestrial laser scanners plays the key role in feature extraction, 3D object modeling and 3D scene classification. An automated registration algorithm of pair-wise point clouds is presented, which is based on multi-resolution data created from raw point clouds, using geometric properties and point to point improved adjustment method, iteratively calculates six transformation parameters. RANSAC algorithm is also used to get reliable corresponding points. Convergence region and rate of proposed point clouds registration algorithm have been tested on a variety of data sets. Quality analysis of registration method is tested by using check points.
Comparison of Individual Criteria and Externally Imposed Criteria for Stage Allocation: Findings from an Internet Study Addressing Physical Activity

Stage-matched interventions can only be more effective than “one-size-fits-all” interventions if they target participants' specific needs. Therefore, individuals must be allocated to a stage that truly reflects their mindsets. Various criteria for stage allocation exist. This study's objective was to demonstrate the impact of different classification criteria on stage allocation, and which criterion yields the best reflection of individuals' mindsets. The sample consists of 569 internet users. Physical activity, intention to change, and four stages of change (Non-Intender, Intender, Maintaining Actor, and Changing Actor) were assessed. Staging was based on two criteria: individual criteria and externally imposed criteria (30 min of physical activity on at least 4 days of the week). Hypotheses were tested by multivariate analyses and validity tests. As predicted, the different criteria affected stage allocation, and staging based on the individual criterion seemed to reflect individuals' intention to change and behavior better than staging based on the external standard.
Genetic Interactions between DNA Demethylation and Methylation in Arabidopsis[OA]

DNA demethylation in Arabidopsis (Arabidopsis thaliana) is mediated by DNA glycosylases of the DEMETER family. Three DEMETER-LIKE (DML) proteins, REPRESSOR OF SILENCING1 (ROS1), DML2, and DML3, function to protect genes from potentially deleterious methylation. In Arabidopsis, much of the DNA methylation is directed by RNA interference (RNAi) pathways and used to defend the genome from transposable elements and their remnants, repetitive sequences. Here, we investigated the relationship between DML demethylation and RNAi-mediated DNA methylation. We found that genic regions demethylated by DML enzymes are enriched for small interfering RNAs and generally contain sequence repeats, transposons, or both. The most common class of small interfering RNAs was 24 nucleotides long, suggesting a role for an RNAi pathway that depends on RNA-DEPENDENT RNA POLYMERASE2 (RDR2). We show that ROS1 removes methylation that has multiple, independent origins, including de novo methylation directed by RDR2-dependent and -independent RNAi pathways. Interestingly, in rdr2 and drm2 mutant plants, we found that genes demethylated by ROS1 accumulate CG methylation, and we propose that this hypermethylation is due to the ROS1 down-regulation that occurs in these mutant backgrounds. Our observations support the hypothesis that DNA demethylation by DML enzymes is one mechanism by which Arabidopsis genes are protected from genome defense pathways.
A heuristic algorithm for video scene detection using shot cluster sequence analysis

In this paper, we present a novel scheme for segmenting video data into scenes. Based on visual similarity, the shots are first classified into clusters using modified k-means algorithm. Number of optimal clusters is decided using cluster validity analysis based on Davies-Bouldin index. Each shot is assigned a tag denoting the cluster it belongs to. Thus, the video data is represented by a sequence of cluster tags. The sequence is then analyzed by introducing the concept of stable and quasi-stable state. The elements of the sequence are merged into states and isolated elements are linked with the states to generate the scenes. The scheme is free from the dependency on critical parameters and capable of handling different types of scenes.