Miracle-dz/UniFAR-FTUs huggingface dataset:
Poly(ADP-ribose) polymers regulate DNA topoisomerase I (Top1) nuclear dynamics and camptothecin sensitivity in living cells

Topoisomerase 1 (Top1) is essential for removing the DNA supercoiling generated during replication and transcription. Anticancer drugs like camptothecin (CPT) and its clinical derivatives exert their cytotoxicity by reversibly trapping Top1 in covalent complexes on the DNA (Top1cc). Poly(ADP-ribose) polymerase (PARP) catalyses the addition of ADP-ribose polymers (PAR) onto itself and Top1. PARP inhibitors enhance the cytotoxicity of CPT in the clinical trials. However, the molecular mechanism by which PARylation regulates Top1 nuclear dynamics is not fully understood. Using live-cell imaging of enhanced green fluorescence tagged-human Top1, we show that PARP inhibitors (Veliparib, ABT-888) delocalize Top1 from the nucleolus to the nucleoplasm, which is independent of Top1–PARP1 interaction. Using fluorescence recovery after photobleaching and subsequent fitting of the data employing kinetic modelling we demonstrate that ABT-888 markedly increase CPT-induced bound/immobile fraction of Top1 (Top1cc) across the nuclear genome, suggesting Top1-PARylation counteracts CPT-induced stabilization of Top1cc. We further show Trp205 and Asn722 of Top1 are critical for subnuclear dynamics. Top1 mutant (N722S) was restricted to the nucleolus in the presence of CPT due to its deficiency in the accumulation of CPT-induced Top1-PARylation and Top1cc formation. This work identifies ADP-ribose polymers as key determinant for regulating Top1 subnuclear dynamics.
Micro- and macroevolutionary trade-offs in plant-feeding insects

A long-standing hypothesis asserts that plant-feeding insects specialize on particular host plants because of negative interactions (trade-offs) between adaptations to alternative hosts, yet empirical evidence for such trade-offs is scarce. Most studies have looked for microevolutionary performance trade-offs within insect species, but host-use could also be constrained by macroevolutionary trade-offs caused by epistasis and historical contingency. On the other hand, evolutionary interactions between adaptations to diverse hosts could be neutral or positive rather than negative. Here we used a phylogenetic approach to estimate the micro-and macroevolutionary correlations between use of alternative host plants within two major orders of plant-feeding insects: Lepidoptera (caterpillars) and Hemiptera (true bugs). Across 1604 caterpillar species, we found both positive and negative pairwise correlations between use of diverse host taxa, with overall network patterns suggesting that different host-use constraints act over micro-and macroevolutionary timescales. In contrast, host-use patterns of 955 true bug species revealed uniformly positive correlations between presence on the same host taxa over both timescales. The lack of consistent patterns across timescales and insect orders indicates that host-use trade-offs are historically contingent rather than universal constraints. Moreover, we observed few negative correlations overall despite the wide taxonomic and ecological diversity of the focal host taxa, suggesting that positive interactions between host-use adaptations, not trade-offs, dominate the long-term evolution of host use in plant-feeding insects.
A Novel Physical Layer Secure Key Generation and Refreshment Scheme for Wireless Sensor Networks

Physical layer secure key generation (PL-SKG) schemes have received a lot of attention from the wireless security community in recent years because of the potential benefits that they could bring to the security landscape. These schemes aim to strengthen current security protocols by reducing the amount of key material that devices need for deployment. They do this by harnessing the common source of randomness provided by the wireless channel that the physical layer is communicating over. This is of particular importance in wireless sensor networks (WSNs) where resources are particularly scarce and where issues, such as key revocation and recovery make the design of efficient key management schemes extremely difficult. This paper discusses the issues and challenges encountered in the design and implementation of PL-SKG schemes on off-the-shelf WSNs. It then proposes a novel key generation scheme that takes advantage of both the power and simplicity of classic error correcting codes and also the diversity of frequency channels available on 802.15. 4 compliant nodes to generate keys from received signal strength readings. This paper shows that our key generation and refreshment scheme can achieve a near 100% key reconciliation rate whilst also providing perfect forward and backward security.
Popdc1/Bves Functions in the Preservation of Cardiomyocyte Viability While Affecting Rac1 Activity and Bnip3 Expression

The Popeye domain containing1, also called Bves (Popdc1/Bves), is a transmembrane protein that functions in muscle regeneration, heart rate regulation, hypoxia tolerance, and ischemia preconditioning. The expression of Popdc1/Bves is elevated in cardiomyocytes maintained in serum free defined medium. We hypothesized that Popdc1/Bves is important for cardiomyocyte survival under the stress of serum deprivation and investigated the mechanisms involved. A deficit in Popdc1/Bves, achieved by siRNA‐mediated gene silencing, results in cardiomyocyte injury and death, upregulation of the pro‐apoptotic protein Bcl‐2/adenovirus E1B 19‐kDa interacting protein3 (Bnip3), as well as reduction in Rac1‐GTPase activity and in Akt phosphorylation. Combined Popdc1/Bves and Bnip3 silencing attenuated cell injury and prevented Bnip3 upregulation induced by the silencing of Popdc1/Bves alone. Chromatin immunoprecipitation indicated an increased binding of the transcription factor FoxO3 to the Bnip3 promoter although augmentation of FoxO3 in the nuclei was not detected. By contrast, the transcription factor NFκB was excluded from the nuclei of Popdc1/Bves deficient cardiomyocytes and exhibited decreased binding to the Bnip3 promoter. The data indicates that Popdc1/Bves plays a role in the preservation of cardiomyocyte viability under serum deficiency through the alteration of Rac1 activity and the regulation of Bnip3 expression by FoxO3 and NFκB transcription factors pointing to Popdc1/Bves as a potential target to enhance heart protection. J. Cell. Biochem. 118: 1505–1517, 2017. © 2016 Wiley Periodicals, Inc.
Macroecology of Sexual Selection: A Predictive Conceptual Framework for Large-Scale Variation in Reproductive Traits*

Abiotic factors exert direct and indirect influences on behavioral, morphological, and life-history traits. Because some of these traits are related to reproduction, there is a causal link between climatic conditions and the expression of reproductive traits. This link allows us to generate predictions on how reproductive traits vary in large geographic scales. Here we formalize this macroecological framework, present some general predictions, and explore empirical examples using harvestmen as study organisms. Our results show that the length of breeding season in harvestmen is primarily influenced by the number of warm months and that precipitation plays a secondary role in modulating the period devoted to reproduction. Moreover, we show that the probability of resource defense polygyny increases with longer breeding seasons and that the presence of this type of mating system positively affects the magnitude of sexual dimorphism in harvestmen. Finally, the presence of postovipositional parental care is also influenced by the length of breeding season but not by actual evapotranspiration, which is our proxy for the intensity of biotic interactions. We argue that the macroecological framework proposed here may be a fruitful field of investigation, with important implications for our understanding of sexual selection and the evolution of reproductive traits in both animals and plants.
Associations Between Sleep Hygiene and Sleep Problems in Adolescents With ADHD: A Cross-Sectional Study

Objective: To determine whether self-reported sleep hygiene practices are associated with self- and parent-reported behavioral sleep problems in adolescents with ADHD. Method: Participants included 79 adolescents with ADHD (13-17 years) and their parents. Adolescents were asked to report on their sleep hygiene (Adolescent Sleep Hygiene Scale) and sleep (Adolescent Sleep Wake Scale). Parents also reported on their adolescent’s sleep (Sleep Disturbance Scale for Children). Results: Poorer sleep hygiene was associated with higher total self-reported behavioral sleep problems and most self-reported sleep problems: falling asleep, reinitiating sleep, and returning to wakefulness. The association was also apparent for total parent-reported behavioral sleep problems, problems with initiating and maintaining sleep, and excessive somnolence. Conclusion: This study demonstrates small-to-moderate relationships between poor sleep hygiene practices and sleep problems in adolescents with ADHD, by both self- and parent-report.
Fast Subspace Clustering Based on the Kronecker Product

Subspace clustering is a useful technique for many computer vision applications in which the intrinsic dimension of high-dimensional data is often smaller than the ambient dimension. Spectral clustering, as one of the main approaches to subspace clustering, often takes on a sparse representation or a low-rank representation to learn a block diagonal self-representation matrix for subspace generation. However, existing methods require solving a large scale convex optimization problem with a large set of data, with computational complexity reaches $O$(N3) for $N$ data points. Therefore, the efficiency and scalability of traditional spectral clustering methods can not be guaranteed for large scale datasets. In this paper, we propose a subspace clustering model based on the Kronecker product. Due to the property that the Kronecker product of a block diagonal matrix with any other matrix is still a block diagonal matrix, we can efficiently learn the representation matrix which is formed by the Kronecker product of $k$ smaller matrices. By doing so, our model significantly reduces the computational complexity to O(kN3/k). Furthermore, our model is general in nature, and can be adapted to different regularization based subspace clustering methods. Experimental results on two public datasets show that our model significantly improves the efficiency compared with several state-of-the-art methods. Moreover, we have conducted experiments on synthetic data to verify the scalability of our model for large scale datasets.
A Cumulative Risk Model of Child Physical Maltreatment Potential: Findings From a Community-Based Study

Previous studies have identified the predictive risk factors of child physical maltreatment (CPM). However, a significant number of these studies assessed risk factors in isolation. The cumulative risk hypothesis postulates that health problems are caused by the accumulation of risk factors, independently of the presence or absence of specific risk indicators. Few studies examined the effect of cumulative risk on CPM potential. This study aimed to test two concurrent models of cumulative risk of CPM potential by investigating whether CPM potential was better predicted by a threshold cumulative risk model or a linear cumulative risk model. Data from the National Representative Study of Psychosocial Context of Child Abuse and Neglect in Portugal were used. Parents of school-age children (N = 796) answered to self-report measures regarding sociodemographic variables, history of child maltreatment, psychological distress, and CPM potential. A cumulative risk index was computed, comprising 10 dichotomized risk factors. Evidence for a threshold cumulative effect was found. Additional bivariate logistic regressions revealed that the odds for high-potential CPM were dramatically higher for those parents with six or more risk factors when compared with parents with any one risk factor. By testing and confirming a threshold cumulative effect on CPM potential, it was possible to find a “trigger point” from which a dramatic increase in child physical maltreatment potential occurs.
Evolutionary Pets: Offspring Numbers Reveal Speciation Process in Domesticated Chickens

Since Darwin, the nature of the relationship between evolution and domestication has been debated. Evolution offers different mechanisms of selection that lead to adaptation and may end in the origin of new species as defined by the biological species concept. Domestication has given rise to numerous breeds in almost every domesticated species, including chickens. At the same time, so-called artificial selection seems to exclude mechanisms of sexual selection by the animals themselves. We want to forward the question to the animal itself: With whom do you reproduce successfully? This study focused on the sexual behavior of the domestic chicken Gallus gallus f.dom. , particularly the White Crested Polish breed. Experiments on mate choice and the observation of fertilization and hatching rates of mixed-breeding groups revealed breed-specific preferences. In breeding groups containing White Crested Polish and a comparative breed, more purebred chicks hatched than hybrids (number of eggs collected: 1059). Mating was possible in equal shares, but in relation to the number of eggs collected, purebred offspring (62.75%±7.10%, M±SE) hatched to a greater extend compared to hybrid offspring (28.75%±15.32%, M±SE). These data demonstrate that the mechanism of sexual selection is still present in domestic chicken breeds, which includes the alteration of gene frequencies typical for domestication and evolutionary speciation. Due to selection and mate choice we state that breeding in principle can generate new species. Therefore, we see domestication as an evolutionary process that integrates human interests of animal breeding with innate mate choice by the animal.
Penguin Chicks Benefit from Elevated Yolk Androgen Levels under Sibling Competition

Crested penguins (genus Eudyptes) have a peculiar hatching pattern, with the first-laid egg (A-egg) hatching after the second-laid egg (B-egg) and chicks from A-eggs typically having a much lower survival probability. Maternal yolk androgens have been suggested to contribute to the competitive superiority of the B-chick in southern rockhopper penguins Eudyptes chrysocome, given their important role in mediating sibling competition in other species. We therefore increased the yolk androgen levels in freshly-laid eggs and examined the consequences for sibling competition - via effects on embryonic developmental times, chick growth and early survival. We placed one androgen-treated egg and one control egg into each foster nest, matching them for mass, laying date and laying order. The androgen treatment did not significantly affect embryonic developmental times or chick measurements at hatching. However, elevated yolk androgen levels benefitted chick growth in interaction with the number of siblings in a brood. Chicks from androgen-treated eggs had faster growth in the presence of a sibling than chicks from control eggs. Under these circumstances they also had a higher survival probability. Thus maternal androgens appear to reinforce the observed hatching pattern, facilitating brood reduction. This contrasts to most previous studies in other species where yolk androgens have been shown to compensate for the negative consequences of delayed hatching within the brood hierarchy.
The Short-Term Effectiveness of Non-Surgical Treatment in Reducing Levels of Interleukin-1β and Proteases in Gingival Crevicular Fluid From Patients With Type 2 Diabetes Mellitus and Chronic Periodontitis.

BACKGROUND This study aimed to compare the effectiveness of non-surgical periodontal treatment in improving periodontal status and reducing gingival crevicular fluid (GCF) levels of interleukin (IL)-1β and IL-18, elastase activity, and matrix metalloproteinase (MMP)--8 and --9 in periodontitis patients with and without type 2 diabetes mellitus (T2DM). METHODS Twenty-three patients with T2DM (diabetes group) and 26 systemically healthy subjects (control group) with chronic periodontitis participated in this study. The clinical examination included visible plaque index, gingival bleeding index, probing depth, clinical attachment level, and bleeding on probing. GCF samples were collected from five or six deep sites to evaluate the levels of IL-1β and -18, elastase, and MMP-8 and -9. Shallow sites were analyzed for IL-1β and elastase. The glycemic control was analyzed by the concentration of glycated hemoglobin (HbA1c). The subjects received non-surgical periodontal treatment and were reexamined 90 days later. RESULTS All clinical parameters showed a significant improvement after treatment, which was accompanied by a significant reduction in IL-1β, elastase activity, and MMP-8 and -9 levels in deep sites. The shallow sites also showed significant reductions in IL-1β and elastase activity levels. Treatment did not significantly reduce HbA1c concentrations in patients with T2DM. CONCLUSIONS Non-surgical periodontal treatment was effective in reducing the levels of IL-1β, elastase activity, and MMP-8 and -9 in GCF from diabetes and control groups. Patients with T2DM showed less reduction only in elastase activity in shallow sites compared to controls. This reduction was associated with improvement of the clinical periodontal status.
Software for MR image overlay guided needle insertions: the clinical translation process

PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.
Fibroblast Growth Factor 22 Is Not Essential for Skin Development and Repair but Plays a Role in Tumorigenesis

Fibroblast Growth Factors play critical roles during development, tissue homeostasis and repair by controlling cell proliferation, survival, migration and differentiation. Of the 22 mammalian FGFs, FGF22, a member of the FGF7/10/22 subfamily, has been shown to have a clear role in synaptogenesis, but its roles in other tissues have not been studied. We have investigated the in vivo functions of FGF22 in mice. Fgf22 null animals were viable, fertile and did not display any obvious abnormalities. Despite the known expression profile of FGF22 in the skin, no differences in either skin or pelage were observed, demonstrating that FGF22 is dispensable during embryogenesis and in unchallenged adult skin. Mice lacking FGF22 were able to heal acute wounds just as efficiently as wild type mice. However, classical two-step skin carcinogenesis challenge revealed that FGF22 null mice developed fewer papillomas than wild type controls, suggesting a potential pro-oncogenic role for FGF22 in the skin.
Vitamin D Responsive Elements within the HLA-DRB1 Promoter Region in Sardinian Multiple Sclerosis Associated Alleles

Vitamin D response elements (VDREs) have been found in the promoter region of the MS-associated allele HLA-DRB1*15∶01, suggesting that with low vitamin D availability VDREs are incapable of inducing *15∶01 expression allowing in early life autoreactive T-cells to escape central thymic deletion. The Italian island of Sardinia exhibits a very high frequency of MS and high solar radiation exposure. We test the contribution of VDREs analysing the promoter region of the MS-associated DRB1 *04∶05, *03∶01, *13∶01 and *15∶01 and non-MS-associated *16∶01, *01, *11, *07∶01 alleles in a cohort of Sardinians (44 MS patients and 112 healthy subjects). Sequencing of the DRB1 promoter region revealed a homozygous canonical VDRE in all *15∶01, *16∶01, *11 and in 45/73 *03∶01 and in heterozygous state in 28/73 *03∶01 and all *01 alleles. A new mutated homozygous VDRE was found in all *13∶03, *04∶05 and *07∶01 alleles. Functionality of mutated and canonical VDREs was assessed for its potential to modulate levels of DRB1 gene expression using an in vitro transactivation assay after stimulation with active vitamin D metabolite. Vitamin D failed to increase promoter activity of the *04∶05 and *03∶01 alleles carrying the new mutated VDRE, while the *16∶01 and *03∶01 alleles carrying the canonical VDRE sequence showed significantly increased transcriptional activity. The ability of VDR to bind the mutant VDRE in the DRB1 promoter was evaluated by EMSA. Efficient binding of VDR to the VDRE sequence found in the *16∶01 and in the *15∶01 allele reduced electrophoretic mobility when either an anti-VDR or an anti-RXR monoclonal antibody was added. Conversely, the Sardinian mutated VDRE sample showed very low affinity for the RXR/VDR heterodimer. These data seem to exclude a role of VDREs in the promoter region of the DRB1 gene in susceptibility to MS carried by DRB1* alleles in Sardinian patients.
Multiscale Adaptive Local Directional Texture Pattern for Facial Expression Recognition

This work presents a novel facial descriptor, which is named as multiscale adaptive local directional texture pattern (MALDTP) and employed for expression recognition. We apply an adaptive threshold value to encode facial image in different scales, and concatenate a series of histograms based on the MALDTP to generate facial descriptor in term of Gabor filters. In addition, some dedicated experiments were conducted to evaluate the performance of the MALDTP method in a person-independent way. The experimental results demonstrate that our proposed method achieves higher recognition rate than local directional texture pattern (LDTP). Moreover, the MALDTP method has lower computational complexity, fewer storage space and higher classification accuracy than local Gabor binary pattern histogram sequence (LGBPHS) method. In a nutshell, the proposed MALDTP method can not only avoid choosing the threshold by experience but also contain much more structural and contrast information of facial image than LDTP.