Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock

When Escherichia coli K-12 was shifted from a medium lacking salt to one containing 0.5 M NaCl, both the [ATP]/[ADP] ratio and negative supercoiling of plasmid DNA increased within a few minutes. After about 10 min both declined, eventually reaching a level slightly above that observed with cells growing exponentially in the absence of salt. Since in vitro the [ATP]/[ADP] ratio influences the level of supercoiling generated by gyrase (H. Westerhoff, M. O'Dea, A. Maxwell, and M. Gellert, Cell Biophys. 12:157-181, 1988), the physiological response of supercoiling to salt shock is most easily explained by the sensitivity of gyrase to changes in the intracellular [ATP]/[ADP] ratio. This raises the possibility that the [ATP]/[ADP] ratio is an important factor in the control of supercoiling.
Genetic Manipulation of Nocardia Species

Nocardia spp. are aerobic, Gram‐positive, catalase positive, and non‐motile actinomycetes. They are associated with human infections. However, some species produce important natural products, degrade toxic chemicals, and are involved in biotransformation of valuable products. The lack of robust genetic tools has hindered detailed studies and advanced research. This unit describes the major genetic engineering approaches using Nocardia sp. CS682 as a prototype. These methods will certainly help in understanding the basis of their pathogenicity as well as biosynthetic and biotransforming abilities. It can be expected that knowledge of the biochemistry behind their pathogenicity will be crucial in developing effective treatment strategies. These genetic tools can be utilized to develop rational metabolic engineering approaches for crafting host strains with higher production or biotransformation ability. © 2016 by John Wiley & Sons, Inc.
Locating Knowledge through Automated Organizational Cartography [Autocart]

The Post-Globalization aeon has placed businesses everywhere in new and different competitive situations where knowledgeable, effective and efficient behaviour has come to provide the competitive and comparative edge. Enterprises have turned to explicitand even conceptualising on tacitKnowledge Management to elaborate a systematic approach to develop and sustain the Intellectual Capital needed to succeed. To be able to do that, you have to be able to visualize your organization as consisting of nothing but knowledge and knowledge flows, whilst being presented in a graphical and visual framework, referred to as automated organizational cartography. Hence, creating the ability of further actively classifying existing organizational content evolving from and within data feeds, in an algorithmic manner, hence potentially giving insightful schemes and dynamics by which organizational know-how is visualised. It is discussed and elaborated on most recent and applicable definitions and classifications of knowledge management, representing a wide range of views from mechanistic (systematic, data driven) to a more socially (psychologically, cognitive/metadata driven) orientated. More elaborate continuum models, for knowledge acquisition and reasoning purposes, are being used for effectively representing the domain of information that an end user may contain in their decision making process for utilization of available organizational intellectual resources.
Gradually morphing a thematic map series based on cellular automata

ABSTRACT Maps are often animated to help users make comparisons and comprehend trends. However, large and complex differences between sequential maps can inhibit users from doing so. This paper proposes a morphing technique to highlight trends without manual intervention. Changes between sequential maps are considered as the diffusion processes of expanding classes, with these processes simulated by cellular automata. A skeleton extraction technique is introduced to handle special cases. Experimental results demonstrate that the proposed morphing technique can reveal obvious trends between dramatically changed maps. The potential application of the proposed morphing technique in sequential spatial data (e.g. remote-sensing images) is discussed.
EVOLUTION IN STRESSFUL ENVIRONMENTS. I. PHENOTYPIC VARIABILITY, PHENOTYPIC SELECTION, AND RESPONSE TO SELECTION IN FIVE DISTINCT ENVIRONMENTAL STRESSES

Abstract Considerable debate has accompanied efforts to integrate the selective impacts of environmental stresses into models of life-history evolution. This study was designed to determine if different environmental stresses have consistent phenotypic effects on life-history characters and whether selection under different stresses leads to consistent evolutionary responses. We created lineages of a wild mustard (Sinapis arvensis) that were selected for three generations under five stress regimes (high boron, high salt, low light, low water, or low nutrients) or under near-optimal conditions (control). Full-sibling families from the six selection histories were divided among the same six experimental treatments. In that test generation, lifetime plant fecundity and six phenotypic traits were measured for each plant. Throughout this greenhouse study, plants were grown individually and stresses were applied from the early seedling stage through senescence. Although all stresses consistently reduced lifetime fecundity and most size- and growth-related traits, different stresses had contrasting effects on flowering time. On average, stress delayed flowering compared to favorable conditions, although plants experiencing low nutrient stress flowered earliest and those experiencing low light flowered latest. Contrary to expectations of Grime's triangle model of life-history evolution, this ruderal species does not respond phenotypically to poor environments by flowering earlier. Most stresses enhanced the evolutionary potential of the study population. Compared with near-optimal conditions, stresses tended to increase the opportunity for selection as well as phenotypic variance, although both of these quantities were reduced in some stresses. Rather than favoring traits characteristic of stress tolerance, such as slow growth and delayed reproduction, phenotypic selection favored stress- avoidance traits: earlier flowering in all five stress regimes and faster seedling height growth in three stresses. Phenotypic correlations reinforced direct selection on these traits under stress, leading to predicted phenotypic change under stress, but no significant selection in the control environment. As a result of these factors, selection under stress resulted in an evolutionary shift toward earlier flowering. Environmental stresses may drive populations of ruderal plant species like S. arvensis toward a stress-avoidance strategy, rather than toward stress tolerance. Further studies will be needed to determine when selection in stressful environments leads to these alternative life-history strategies. Corresponding Editor: T. Markow
A Semiparametric Regression Cure Model for Interval-Censored Data

Motivated by medical studies in which patients could be cured of disease but the disease event time may be subject to interval censoring, we present a semiparametric nonmixture cure model for the regression analysis of interval-censored time-to-event data. We develop semiparametric maximum likelihood estimation for the model using the expectation-maximization method for interval-censored data. The maximization step for the baseline function is nonparametric and numerically challenging. We develop an efficient and numerically stable algorithm via modern convex optimization techniques, yielding a self-consistency algorithm for the maximization step. We prove the strong consistency of the maximum likelihood estimators under the Hellinger distance, which is an appropriate metric for the asymptotic property of the estimators for interval-censored data. We assess the performance of the estimators in a simulation study with small to moderate sample sizes. To illustrate the method, we also analyze a real dataset from a medical study for the biochemical recurrence of prostate cancer among patients who have undergone radical prostatectomy. Supplemental materials for the computational algorithm are available online.
EFFECTS OF THE VERTICAL CoM MOTION ON ENERGY CONSUMPTION FOR WALKING HUMANOIDS

This paper proposes an analysis of the effect of vertical motion of the CoM during humanoid walking. The linear inverted pendulum (LIP) model is classically used to deal with humanoid balance during walking. The effects on energy consumption of the CoM height remaining constant for humanoid robots, or varying like human beings, are badly known and are studied here. Two approaches are introduced for the comparison: the LIP which offers the great advantage of analytical solving (i.e. fast and easy calculations), and a numerical solving of the IP dynamics, which allows varying the height of the center of mass during walking. The results are compared in a dynamics simulation of the humanoid robot ROMEO (Aldebaran Robotics).
Community empowerment in changing environments: creating value through food security

ABSTRACT Methodologies that are locally relevant, empowering and replicable offer a way forward for improved policymaking and efficient resource governance in a globalised landscape of rapid change and scarce resources. Using the principles of equal participation and distribution, this article shows how the use of participatory methods can lead to greater community ownership and cohesion around shared concerns over access to healthy food and sustainable resource use in challenging urban environments. Drawing on contextualised examples from small-scale projects carried out by Charushila, an international environmental design charity, in Venezuela and Palestine, the article presents a co-design approach that puts people in touch with food growing and the reuse of resources to transform open spaces. An analysis of community-led co-production projects in these two contrasting urban environments shows how such processes can contribute to policymaking for longer-term sustainable development in the field of disaster relief and amid political upheaval in low- and middle-income countries.
Lower urinary tract symptoms and male sexual dysfunction: the multinational survey of the aging male (MSAM-7).

OBJECTIVES Lower urinary tract symptoms (LUTS), which are often caused by benign prostatic hypertrophy (BPH), and sexual dysfunction are common in older men, with an overall prevalence of >50% in men aged > or =50 years. Men with LUTS have been reported to experience sexual dysfunction, including ejaculatory loss, painful ejaculation, and erectile dysfunction. This study was conducted to investigate the relationship between LUTS and sexual problems in aging men. METHODS A large-scale, multinational survey was conducted in the US and six European countries to systematically investigate the relationship between LUTS and sexual dysfunction in older men. Detailed questionnaires were mailed to a national representative sample of men aged 50 to 80 years in each country. Selection was made on the basis of age, occupation, geographic region, and population density. LUTS and sexual function were assessed by validated symptom scales, including the International Prostate Symptom Score, the Danish Prostatic Symptom Score, and the International Index of Erectile Function. Subjects also completed a health and demographics questionnaire. RESULTS A total of 34,800 surveys were mailed out, 14,254 were completed and returned, and 12,815 were deemed evaluable and included in the analysis. Results were consistent from one country to another. Although 90% of the men had LUTS, only 19% had sought medical help for urinary problems and only 11% were medically treated. Sexual activity was reported by 83% of the sample, with 71% reporting at least one episode of sexual activity during the previous 4 weeks. Sexual disorders and their bothersomeness were strongly related to both age and severity of LUTS. The relationship between sexual problems and LUTS is independent of comorbidities such as diabetes, hypertension, cardiac disease, and hypercholesterolemia. CONCLUSIONS Sexual activity is common in a majority of men over age 50 and is an important component of overall quality of life. The presence and severity of LUTS are independent risk factors for sexual dysfunction in older men. These results highlight the clinical importance of evaluating LUTS in patients with sexual dysfunction, and the need to consider sexual issues in the management of patients with benign prostatic hypertrophy.
The return of the anomalous cosmic rays to 1 AU in 1992

New observations of low energy (approximately 1 to 200 MeV/nuc) cosmic rays measured by three newly launched experiments on Solar, Anomalous, and Magnetospheric Particle Explorer (SAMPEX) during 1992 and 1993 show the strong presence of anomalous cosmic ray (ACR) nitrogen and oxygen, well before the approaching solar minimum. When compared with ACR temporal variations over the past two solar cycles we find that the 1992-1993 fluxes are approximately 5 to 10 times their level at corresponding neutron monitor counting rates in 1969-1970 and 1985
Affective matching moderates S–R binding

We investigated the moderating influence of affective matching on S–R binding processes in a sequential priming study in which positive and negative nouns had to be categorised as referring to a person or to an object. Irrelevant positive and negative distractor words (adjectives) were integrated with responses into S–R episodes if they had the same valence as the target (affective match condition). In this case, repeating the prime distractor in the probe led to a retrieval of the prime response, which facilitated performance for response repetition sequences but had no effect on performance when responses changed between prime and probe. However, if target and distractor had different valences (affective mismatch condition), no interaction of distractor relation and response relation occurred, indicating that distractors were less likely to be associated with responses into event files during the prime trial episode. Findings reveal that affective mismatches are detected automatically and modulate a binding of irrelevant information with responses.
Price Search Across Stores and Across Time

In response to price dispersion across stores and price promotions over time, consumers search across both stores (spatial) and time (temporal), in many retail settings. Yet there is no search model in extant research that jointly endogenizes search in both dimensions. We develop a model of spatiotemporal search that nests a finite horizon model of spatial search across stores within an infinite horizon model of inter-temporal search. The model is estimated using an iterative procedure that formulates it as a mathematical program with equilibrium constraints (MPEC) embedded within an E-M algorithm to allow estimation of latent class heterogeneity. The empirical analysis uses data on household store visits and purchases in the milk category. In contrast to extant research, we find that omitting the temporal dimension underestimates price elasticity. We attribute this difference to the relative frequency of household stock outs and purchase frequency in the milk category. Further, contrary to the conventional wisdom that promotions increase store switching and reduces store loyalty, we find that in the presence of search frictions, price promotions can be a store loyalty-enhancing tool.
Feeding amount, feeding type and pathogenesis of retinopathy of prematurity

Stoltz Sjostrom et al 1 have demonstrated that higher intakes of energy, fat and carbohydrates, but not protein, were significantly associated with a lower risk of severe retinopathy of prematurity (ROP). Based on their current results and previous published studies, they propose a mechanism for the first phase of ROP pathogenesis. In this model, they suggest that a low-energy intake during the first 4 weeks of life can lead to arrested vascularisation. We commend the authors for this observation as well as for their comprehensive review of ROP pathogenesis. However, although …
Function of constitutive IκB Kinase 2 activation in the intestinal epithelium of mice

Die NF-κB Signalkaskade stellt eine Verbindung zwischen Entzundungsprozessen und Krebs dar. Der NF-κB Signalweg wird durch Stress-assoziierte Reize wie Pathogen-assoziierte Molekulare Muster (PAMPs), inflammatorische Zytokine und UV-Licht initiiert. Da die Aktivierung dieses Signalweges zur Expression von antiapoptotischen Molekulen, inflammatorischen Signalkomponenten, sowie antibakteriellen Peptiden fuhrt, stellt NF-κB einen zentralen Regulator von entzundlichen Prozessen dar. Daruber hinaus weisen verschiedene Krebsarten eine erhohte NF-κB Aktivitat auf, die sich nicht nur auf Tumor-infiltrierende Immunzellen beschrankt,sondern auch in den Krebszellen selber aufzufinden ist. Es wird vermutet, dass die Wirkung von NF-κB in Tumorzellen den Zelltod verhindert und die Zellproliferation fordert. Dahingegen induziert NF-κB in Zellen des Immunsystems die Sekretion von Zytokinen und Wachstumsfaktoren, wodurch Tumorwachstum und Angiogenese gefordert werden. Allerdings ist bisher nicht geklart worden, ob die Aktivierung von NF-κB die Entstehung von Tumoren durch zellinterne Tumor-fordernde Wirkungen in nicht transformierten Zellen zu initiieren vermag. In dieser Arbeit wird gezeigt, dass die Expression einer konstitutiv aktiven Form der zur Aktivierung des kanonischen NF-κB Signalwegs notwendigen zentralen Kinase IKK2 (IKK2ca) in intestinalen Epithelzellen von Mausen zu einer spontanen Entzundung sowohl des Dick- als auch des Dunndarms fuhrte. Die konstitutive Aktivierung von IKK2/NF-κB im Darmepithel resultierte in einer Rekrutierung und Aktivierung von Immunzellen und Fibroblasten. Daruber hinaus erhohte die Expression von IKK2ca im Darmepithel die Sensitivitat gegenuber DSS-induzierter Colitis und steigerte die Tumorrate in chemisch- sowie Apc-Mutation-initiiertem Darmkrebs. Intestinale Epithelzellen, die konstitutiv aktive IKK2 exprimierten, zeigten eine erhohte Proliferationsrate, eine Stabilisierung von β-catenin und eine verstarkte Transkription von Stammzell-assoziierten Faktoren. Hierbei ist zu betonen, dass die Expression von IKK2ca im Darmepithel von Mausen zur spontanen Entwicklung von Colon- und Dunndarmtumoren fuhrte. Die in dieser Dissertation vorgelegten Daten implizieren, dass die konstitutive Aktivierung von IKK2/NF-κB im Darmepithel ausreichend ist um sowohl durch zellinterne Faktoren, als auch durch die Erzeugung eines Tumor-forderlichen, entzundlichen Milieus, eine Tumorgenese nicht nur zu unterstutzten, sondern auch zu induzieren.
Construction et analyse de modèles d'endommagement à gradient

L'objectif de cette these est d'etudier les materiaux adoucissants a l'aide de modeles d'endommagement a gradient. On construit dans un premier temps le modele local sous-jacent en montrant sa forme necessairement standard, ce qui fournit automatiquement un cadre variationnel a l'ecriture du probleme d'evolution quasi-statique. Celui-ci est constitue des trois principes physiques d'irreversibilite, de stabilite et de bilan d'energie. Cependant, la modelisation des materiaux adoucissants requiert un enrichissement du modele local. La regularisation se fait par l'introduction de termes `a gradient d'endommagement dans le travail de deformation. Les merites de l'approche variationnelles ainsi que les apports de la regularisation sont mis en evidence via l'etude des etats homogenes. Dans une deuxieme partie, on mene une etude de bifurcations et de stabilite d'une barre adoucissante en traction simple. On construit explicitement des etats localises bifurquant depuis la branche fondamentale homogene. On peut alors mettre en lumiere differents phenomenes tels que la localisation conduisant `a la ruine de la structure ou les snap-back dans la reponse globale. Cette etude permet aussi mieux de comprendre le phenomene de localisation en termes de criteres de selection tels que ceux de non-bifurcation ou de stabilite. Par ailleurs, on illustre sur cet exemple l'utilisation du principe de conservation d'energie pour gerer dans le cadre quasi-statique les evolutions non-regulieres en temps. Finalement on propose dans une derniere partie des methodes pour l'identification des parametres du modele dans le cas du beton. Par une analogie avec la mecanique de la rupture, on identifie tout d'abord la longueur interne au modele `a l'aide de la densite d'energie de surface du materiau. Les lois de rigidite et de dissipation sont quant a elles identifiees par le biais des etats homogenes en se servant des diagrammes contrainte-deformation et de stabilite de la reponse homogene. On reprend alors l'essai PIED qui vise a stabiliser ces etats dans un essai de traction simple en l'analysant dans le detail et en soulignant par une etude theorique et numerique l'utilite et le potentiel de cet essai.
Economic Turbulence in the Iron Kitchenware Industry in Italy

Companies in turbulent economies are required to face several difficulties, mainly related to the specific features of an extremely volatile environment. Although a similar, hypercompetitive context can be considered a global condition today, it is not perceived in the same way worldwide. Thus, international development could be the best method for exporting to different locations and getting the best opportunities to survive in this unstable environment. Italy is one of the European Union countries affected the most by turbulence and the financial crisis with a loss of competitiveness compared to other countries in the Union. The economic system has changed considerably, rising the bankruptcy cases and lowering reported earnings. This paper claims to give an overview of the Italian situation inside the European Community as Italy is recognized as one of the most industrialized areas of northern Italy; the province of Brescia is home of one of the two Italian districts devoted to the iron kitchenware industry—an industry in which Italy held a leading position worldwide for a long time. Ten years after the financial crisis, and supported by exports flows analysis, we evaluate the Italian competitive position in this industry compared to that of the country’s European competitors. Export data (inside and outside the European Union) in three years (2007, 2010, and 2014) show Italy’s leading global role in this industry but also the negative effect of the crisis on the country, witnessed by the strong rise of other competitors.