Miracle-dz/UniFAR-FTUs huggingface dataset:
The Divided Bacterial Genome: Structure, Function, and Evolution

SUMMARY Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure.
Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis)

Background Sexual segregation in vertebrate foraging niche is often associated with sexual size dimorphism (SSD), i.e., ecological sexual dimorphism. Although foraging behavior of male and female seabirds can vary markedly, differences in isotopic (carbon, δ13C and nitrogen, δ15N) foraging niche are generally more pronounced within sexually dimorphic species and during phases when competition for food is greater. We examined ecological sexual dimorphism among sympatric nesting Pygoscelis penguins asking whether environmental variability is associated with differences in male and female pre-breeding foraging niche. We predicted that all Pygoscelis species would forage sex-specifically, and that higher quality winter habitat, i.e., higher or lower sea ice coverage for a given species, would be associated with a more similar foraging niche among the sexes. Results P2/P8 primers reliably amplified DNA of all species. On average, male Pygoscelis penguins are structurally larger than female conspecifics. However, chinstrap penguins were more sexually dimorphic in culmen and flipper features than Adélie and gentoo penguins. Adélies and gentoos were more sexually dimorphic in body mass than chinstraps. Only male and female chinstraps and gentoos occupied separate δ15N foraging niches. Strong year effects in δ15N signatures were documented for all three species, however, only for Adélies, did yearly variation in δ15N signatures tightly correlate with winter sea ice conditions. There was no evidence that variation in sex-specific foraging niche interacted with yearly winter habitat quality. Conclusion Chinstraps were most sexually size dimorphic followed by gentoos and Adélies. Pre-breeding sex-specific foraging niche was associated with overall SSD indices across species; male chinstrap and gentoo penguins were enriched in δ15N relative to females. Our results highlight previously unknown trophic pathways that link Pygoscelis penguins with variation in Southern Ocean sea ice suggesting that each sex within a species should respond similarly in pre-breeding trophic foraging to changes in future winter habitat.
Cancer Immunotherapy in Older Patients

Abstract Advancing age remains one of the most significant risk factors for cancer development. Changes in the immune system occur with aging, and likely play a role in the increased incidence of malignancy in older patients. With the advent of immune checkpoint inhibitors, and their use in a variety of malignancies, there has been an explosion of clinical trials evaluating their use. Unfortunately, these trials have not shown consistent results in elderly patients, nor have age-specific outcomes been consistently reported. Further evaluation of the efficacy and toxicity of these agents in the elderly is needed, as they are now in frequent clinical use. By investigating how age-related changes in the immune system occur and intersect with use of immune checkpoint inhibitors, their use can be optimized in a clear and safe manner. Further study of age-related changes in the immune system can also lead to effective combination immunotherapeutic approaches, maximizing the efficacy of immune checkpoint inhibitors across tumor types and across the age spectrum of cancer patients.
Curve Shortening and its Application to Multi-Agent Systems

If a smooth, closed, and embedded curve is deformed along its normal vector field at a rate proportional to its curvature, it shrinks to a circular point. This curve evolution is called Euclidean curve shortening, and the result is known as the Gage-Hamilton-Grayson Theorem. Motivated by the rendezvous problem in multi-agent systems, we address the problem of creating a polygon shortening flow. A simple linear scheme is proposed that exhibits several properties similar to Euclidean curve shortening. The polygon shrinks to an elliptical point; convex polygons remain convex; and, the perimeter of the polygon is monotonically decreasing.
Deep Face Recognition

The goal of this paper is face recognition – from either a single photograph or from a set of faces tracked in a video. Recent progress in this area has been due to two factors: (i) end to end learning for the task using a convolutional neural network (CNN), and (ii) the availability of very large scale training datasets. We make two contributions: first, we show how a very large scale dataset (2.6M images, over 2.6K people) can be assembled by a combination of automation and human in the loop, and discuss the trade off between data purity and time; second, we traverse through the complexities of deep network training and face recognition to present methods and procedures to achieve comparable state of the art results on the standard LFW and YTF face benchmarks.
Scale-Free Fluctuations in Behavioral Performance: Delineating Changes in Spontaneous Behavior of Humans with Induced Sleep Deficiency

The timing and dynamics of many diverse behaviors of mammals, e.g., patterns of animal foraging or human communication in social networks exhibit complex self-similar properties reproducible over multiple time scales. In this paper, we analyze spontaneous locomotor activity of healthy individuals recorded in two different conditions: during a week of regular sleep and a week of chronic partial sleep deprivation. After separating activity from rest with a pre-defined activity threshold, we have detected distinct statistical features of duration times of these two states. The cumulative distributions of activity periods follow a stretched exponential shape, and remain similar for both control and sleep deprived individuals. In contrast, rest periods, which follow power-law statistics over two orders of magnitude, have significantly distinct distributions for these two groups and the difference emerges already after the first night of shortened sleep. We have found steeper distributions for sleep deprived individuals, which indicates fewer long rest periods and more turbulent behavior. This separation of power-law exponents is the main result of our investigations, and might constitute an objective measure demonstrating the severity of sleep deprivation and the effects of sleep disorders.
Stages of Cognitive Development in Uncertain-Logic-Based AI Systems

A novel theory of stages in cognitive development is presented, loosely corresponding to Piagetan theory but specifically oriented toward AI systems centered on uncertain inference components. Four stages are articulated (infantile, concrete, formal and reflexive), and are characterized both in terms of external cognitive achievements (a la Piaget) and in terms of internal inference control dynamics. The theory is illustrated via the analysis of specific problem solving tasks corresponding to the different stages. The Novamente AI Engine, with its Probabilistic Logic Networks uncertain inference component and its embodiment n the AGI-SIM simulation world, is used as an example throughout.
Gene Expression Profile of Patients with Mayer-Rokitansky-Küster-Hauser Syndrome: New Insights into the Potential Role of Developmental Pathways

Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is a rare disease characterized by congenital aplasia of uterus and vagina. Although many studies have investigated several candidate genes, up to now none of them seem to be responsible for the aetiology of the syndrome. In our study, we identified differences in gene expression profile of in vitro cultured vaginal tissue of MRHKS patients using whole-genome microarray analysis. A group of eight out of sixteen MRKHS patients that underwent reconstruction of neovagina with an autologous in vitro cultured vaginal tissue were subjected to microarray analysis and compared with five healthy controls. Results obtained by array were confirmed by qRT-PCR and further extended to other eight MRKHS patients. Gene profiling of MRKHS patients delineated 275 differentially expressed genes, of which 133 downregulated and 142 upregulated. We selected six deregulated genes (MUC1, HOXC8, HOXB2, HOXB5, JAG1 and DLL1) on the basis of their fold change, their differential expression in most patients and their relevant role in embryological development. All patients showed upregulation of MUC1, while HOXB2 and HOXB5 were downregulated, as well as Notch ligands JAG1 and DLL1 in the majority of them. Interestingly, HOXC8 was significantly upregulated in 47% of patients, with a differential expression only in MRKHS type I patients. Taken together, our results highlighted the dysregulation of developmental genes, thus suggesting a potential alteration of networks involved in the formation of the female reproductive tract and providing a useful clue for understanding the pathophysiology of MRKHS.
Mental disorder and victimisation in prison: Examining the role of mental health treatment

BACKGROUND There is evidence that people with mental disorders are at increased risk of victimisation in prison. It is unclear whether this risk of victimisation varies across types of disorders or symptoms and what role mental health treatment has on victimisation risk in this context. AIMS To examine the relationship between specific mental disorders, psychiatric symptoms, and victimisation in prison and the effect of treatment for the disorders on victimisation risk. METHODS Using a nationally-representative sample of prisoners, path analyses were conducted to examine the relationship between mental disorder and victimisation. The analyses also examined whether receiving mental health treatment in prison affected any such relationship. RESULTS Victimisation risk varied with the type of mental disorder or symptoms. Depression, personality disorder, hopelessness, paranoia, and hallucinations were associated with increased victimisation risk. Psychotic illnesses were otherwise negatively associated with victimisation. Receiving mental health treatment in prison was associated with greater risk of victimisation there. Receiving treatment appeared to mediate the relationship between mental disorders, symptoms, and victimisation. CONCLUSIONS The findings suggest that not all inmates with mental disorders are at an increased risk of victimisation. Further, mental health treatment in prison also appears to be a risk factor of victimisation. More research is needed to further elucidate the relationship between mental disorders, treatment, and victimisation. Copyright © 2017 John Wiley & Sons, Ltd.
A multi‐scenario genome‐wide medical population genetics simulation framework

Motivation: Recent technological advances in high‐throughput sequencing and genotyping have facilitated an improved understanding of genomic structure and disease‐associated genetic factors. In this context, simulation models can play a critical role in revealing various evolutionary and demographic effects on genomic variation, enabling researchers to assess existing and design novel analytical approaches. Although various simulation frameworks have been suggested, they do not account for natural selection in admixture processes. Most are tailored to a single chromosome or a genomic region, very few capture large‐scale genomic data, and most are not accessible for genomic communities. Results: Here we develop a multi‐scenario genome‐wide medical population genetics simulation framework called ‘FractalSIM’. FractalSIM has the capability to accurately mimic and generate genome‐wide data under various genetic models on genetic diversity, genomic variation affecting diseases and DNA sequence patterns of admixed and/or homogeneous populations. Moreover, the framework accounts for natural selection in both homogeneous and admixture processes. The outputs of FractalSIM have been assessed using popular tools, and the results demonstrated its capability to accurately mimic real scenarios. They can be used to evaluate the performance of a range of genomic tools from ancestry inference to genome‐wide association studies. Availability and implementation: The FractalSIM package is available at http://www.cbio. uct.ac. za/FractalSIM. Contact: emile.chimusa@uct.ac. za Supplementary information: Supplementary data are available at Bioinformatics online.
Dynamic Expression of Serotonin Receptor 5-HT3A in Developing Sensory Innervation of the Lower Urinary Tract

Sensory afferent signaling is required for normal function of the lower urinary tract (LUT). Despite the wide prevalence of bladder dysfunction and pelvic pain syndromes, few effective treatment options are available. Serotonin receptor 5-HT3A is a known mediator of visceral afferent signaling and has been implicated in bladder function. However, basic expression patterns for this gene and others among developing bladder sensory afferents that could be used to inform regenerative efforts aimed at treating deficiencies in pelvic innervation are lacking. To gain greater insight into the molecular characteristics of bladder sensory innervation, we conducted a thorough characterization of Htr3a expression in developing and adult bladder-projecting lumbosacral dorsal root ganglia (DRG) neurons. Using a transgenic Htr3a-EGFP reporter mouse line, we identified 5-HT3A expression at 10 days post coitus (dpc) in neural crest derivatives and in 12 dpc lumbosacral DRG. Using immunohistochemical co-localization we observed Htr3a-EGFP expression in developing lumbosacral DRG that partially coincides with neuropeptides CGRP and Substance P and capsaicin receptor TRPV1. A majority of Htr3a-EGFP+ DRG neurons also express a marker of myelinated Aδ neurons, NF200. There was no co-localization of 5-HT3A with the TRPV4 receptor. We employed retrograde tracing in adult Htr3a-EGFP mice to quantify the contribution of 5-HT3A+ DRG neurons to bladder afferent innervation. We found that 5-HT3A is expressed in a substantial proportion of retrograde traced DRG neurons in both rostral (L1, L2) and caudal (L6, S1) axial levels that supply bladder innervation. Most bladder-projecting Htr3a-EGFP+ neurons that co-express CGRP, Substance P, or TRPV1 are found in L1, L2 DRG, whereas Htr3a-EGFP+, NF200+ bladder-projecting neurons are from the L6, S1 axial levels. Our findings contribute much needed information regarding the development of LUT innervation and highlight the 5-HT3A serotonin receptor as a candidate for future studies of neurally mediated bladder control.
Income and Technology as Drivers of Australian Healthcare Expenditures

The roles of income and technology as the major determinants of aggregate healthcare expenditure (HEXP) continue to interest economists and health policy researchers. Concepts and measures of medical technologies remain complex; however, income (on the demand side) and technology (on the supply side) are important drivers of HEXP. This paper presents analysis of Australia's HEXP, using time-series econometrics modeling techniques applied to 1971-2011 annual aggregate data. Our work fills two important gaps in the literature. First, we model the determinants of Australia's HEXP using the latest and longest available data series. Second, this novel study investigates several alternative technology proxies (input and output measures), including economy-wide research and development expenditures, hospital research expenditures, mortality rate, and two technology indexes based on medical devices. We then apply the residual component method and the technology proxy approach to quantify the technology effects on HEXP. Our empirical results suggest that Australian aggregate healthcare is a normal good and a technical necessity with the income elasticity estimates ranging from 0.51 to 0.97, depending on the model. The estimated technology effects on HEXP falling in the 0.30-0.35 range and mimicking those in the literature using the US data, reinforce the global spread of healthcare technology. Copyright © 2016 John Wiley & Sons, Ltd.
Working Hours Mismatch, Macroeconomic Changes, and Mental Well-being in Europe

This study explores the association between involuntarily working less or more than the standard workweek and poor mental well-being, and whether this relationship is dependent upon (changing) national-level unemployment and gross domestic product growth rates. Data from the European Social Survey Round 2 (2004–2005) and Round 5 (2010) were analyzed. The sample included 16,224 male and 16,184 female employees. Mental well-being was assessed by the World Health Organization Well-being Index. Three-level linear multilevel modeling was used to account for clustering of employees within research years and countries. Working involuntary long hours was positively associated with poor mental well-being for men. For women, working voluntary long, involuntary long, and involuntary short hours were positively associated with poor mental well-being. The mental well-being of women working voluntary and involuntary long hours was negatively influenced by deteriorating economic conditions. This study suggests women are more vulnerable to the effects of long working hours and working hours mismatch on mental well-being, especially during difficult economic periods.
Low Medium pH Value Enhances Anthocyanin Accumulation in Malus Crabapple Leaves

Anthocyanin is a critical factor involved in coloration of plant tissues, but the mechanism how medium pH values affect anthocyanin accumulation in woody plants is unknown. We analyzed anthocyanin composition and the expression of elements encoding anthocyanin and flavonols biosynthesis underlying different medium pH values by using three different leave color type cultivars. HPLC analysis demonstrated that high medium pH values treatment induced a dramatic decrease in the concentration of cyaniding in crabapple leaves. Conversely, the high medium pH values induced up-regulation of the content of flavones and flavonols, suggesting that low pH treatment-induced anthocyanin accumulation. Quantitative real time PCR experiment showed the expression level of anthocyanidin synthase (McANS) and uridine diphosphate glucose flavonoid 3-O-glucosyltransferase (McUFGT) was up-regulated by low pH values treatment, and high medium pH value treatment up-regulate the transcription level of flavonol synthase (McFLS). Meanwhile, several MYB TFs have been suggested in the regulation of pH responses. These results strongly indicate that the low pH treatment-induced anthocyanin accumulation is mediated by the variation of mRNA transcription of the anthocyanin biosynthetic genes.
Relationship Satisfaction Reduces the Risk of Maternal Infectious Diseases in Pregnancy: The Norwegian Mother and Child Cohort Study

Objectives The aims of this study were to explore the degree to which relationship satisfaction predicts the risk of infectious diseases during pregnancy and to examine whether relationship satisfaction moderates the association between stressful life events and the risk of infections. Methods This was a prospective study based on data from the Norwegian Mother and Child Cohort Study (MoBa) conducted by the Norwegian Institute of Public Health. Pregnant women (n = 67,244) completed questionnaires concerning relationship satisfaction and nine different categories of infectious diseases as well as socioeconomic characteristics and stressful life events. Associations between the predictor variables and the infectious diseases were assessed by logistic regression analyses. A multiple regression analysis was performed to assess a possible interaction of relationship satisfaction with stressful life events on the risk for infectious diseases. Results After controlling for marital status, age, education, income, and stressful life events, high levels of relationship satisfaction at week 15 of gestation were found to predict a significantly lower risk for eight categories of infectious diseases at gestational weeks 17–30. No significant interaction effect was found between relationship satisfaction and stressful life events on the risk for infections.
Irreversible Investment in Oligopoly Jan-Henrik

We offer a new perspective on games of irreversible investment under uncertainty in continuous time. The basis is a particular approach to solve the involved stochastic optimal control problems which allows to establish existence and uniqueness of an oligopolistic open loop equilibrium in a very general framework without reliance on any Markovian property. It simultaneously induces quite natural economic interpretation and predictions by its characterization of optimal strategies through first order conditions. The construction of equilbrium policies is then enabled by a stochastic representation theorem. A stepwise specification of the general model leads to further economic conclusions. We obtain explicit solutions for Lévy processes. JEL subject classification: C73, D43, D92
Acoustic and Temporal Partitioning of Cicada Assemblages in City and Mountain Environments

Comparing adaptations to noisy city environments with those to natural mountain environments on the community level can provide significant insights that allow an understanding of the impact of anthropogenic noise on invertebrates that employ loud calling songs for mate attraction, especially when each species has its distinct song, as in the case of cicadas. In this study, we investigated the partitioning strategy of cicada assemblages in city and mountain environments by comparing the acoustic features and calling activity patterns of each species, recorded using automated digital recording systems. Our comparison of activity patterns of seasonal and diel calling revealed that there was no significant temporal partitioning of cicada assemblages in either environment. In addition, there was no correlation between the acoustic distance based on spectral features and temporal segregation. Heterospecific spectral overlap was low in both city and mountain environments, although city and mountain cicada assemblages were subject to significantly different levels of anthropogenic or interspecific noise. Furthermore, for the common species found in both environments, the calling activity patterns at both seasonal and diel time scales were significantly consistent across sites and across environments. We suggest that the temporal calling activity is constrained by endogenous factors for each species and is less flexible in response to external factors, such as anthropogenic noise. As a result, cicada assemblages in city environments with low species diversity do not demonstrate a more significant temporal partitioning than those in mountain environments with high species diversity.