Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain. " Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.
Guanylate Binding Proteins Regulate Inflammasome Activation in Response to Hyperinjected Yersinia Translocon Components

ABSTRACT Gram-negative bacterial pathogens utilize virulence-associated secretion systems to inject, or translocate, effector proteins into host cells to manipulate cellular processes and promote bacterial replication. However, translocated bacterial products are sensed by nucleotide binding domain and leucine-rich repeat-containing proteins (NLRs), which trigger the formation of a multiprotein complex called the inflammasome, leading to secretion of interleukin-1 (IL-1) family cytokines, pyroptosis, and control of pathogen replication. Pathogenic Yersinia bacteria inject effector proteins termed Yops, as well as pore-forming proteins that comprise the translocon itself, into target cells. The Yersinia translocation regulatory protein YopK promotes bacterial virulence by limiting hyperinjection of the translocon proteins YopD and YopB into cells, thereby limiting cellular detection of Yersinia virulence activity. How hyperinjection of translocon proteins leads to inflammasome activation is currently unknown. We found that translocated YopB and YopD colocalized with the late endosomal/lysosomal protein LAMP1 and that the frequency of YopD and LAMP1 association correlated with the level of caspase-1 activation in individual cells. We also observed colocalization between YopD and Galectin-3, an indicator of endosomal membrane damage. Intriguingly, YopK limited the colocalization of Galectin-3 with YopD, suggesting that YopK limits the induction or sensing of endosomal membrane damage by components of the type III secretion system (T3SS) translocon. Furthermore, guanylate binding proteins (GBPs) encoded on chromosome 3 (GbpChr3), which respond to pathogen-induced damage or alteration of host membranes, were necessary for inflammasome activation in response to hyperinjected YopB/-D. Our findings indicate that lysosomal damage by Yersinia translocon proteins promotes inflammasome activation and implicate GBPs as key regulators of this process.
Allocation of Rehabilitation Services for Older Adults in the Ontario Home Care System

Background: Physiotherapy and occupational therapy services can play a critical role in maintaining or improving the physical functioning, quality of life, and overall independence of older home care clients. Despite their importance, however, there is limited understanding of the factors that influence how rehabilitation services are allocated to older home care clients. The aim of this pilot study was to develop a preliminary understanding of the factors that influence decisions to allocate rehabilitation therapy services to older clients in the Ontario home care system, as perceived by three stakeholder groups. Methods: Semi-structured interviews were conducted with 10 key informants from three stakeholder groups: case managers, service providers, and health system policymakers. Results: Drivers of the allocation of occupational therapy and physiotherapy for older adults included functional needs and postoperative care. Participants identified challenges in providing home care rehabilitation to older adults, including impaired cognition and limited capacity in the home care system. Conclusions: Considering the changing demands for home care services, knowledge of current practices across the home care system can inform efforts to optimize rehabilitation services for the growing number of older adults. Further research is needed to advance the understanding of, and optimize rehabilitation service allocation to, older frail clients with multiple morbidities. Developing novel decision-support mechanisms and standardized clinical care pathways for older client populations may be beneficial.
The effect of ultrasonication on the immunomodulatory activity of low‐quality ginseng

This study investigated the effects of ultrasonication extraction (UE) on the immunomodulatory activity of low‐quality ginseng. The results indicate that the optimal conditions for extracting low‐quality ginseng are ultrasonication at 60 kHz and 85°C for 60 min. The extraction yield from the UE was 20% higher than that of the water extraction (WE) at 100°C. The low quality ginseng obtained from the UE exhibited relatively low cytotoxicity toward normal human cells, with an observed toxicity of 15–18% at a concentration of 1.0 mg/mL. The ginseng product obtained following UE induced human B and T cells growth and resulted in concentrations of up to 9.33 × 104 cells/mL and 15.33 × 104 cells/mL, respectively. The ginseng extract also increased the secretion of interleukin‐6 and tumor necrosis factor‐α from these cells by up to 35%, and natural killer/ cell growth was also improved by up to 30%. The UE effectively released 2‐ to 3‐fold higher levels of ginsenosides than the WE. Specifically, the obtained levels of Rb1, Re, and Rg1, which are likely immunomodulatory factors, were approximately three times higher after ultrasonication than after WE. These results were further supported by the finding that UE product‐treated macrophages produced higher levels of nitric oxide (21 μM) than macrophages treated with the WE product or with standard ginsenosides. These results demonstrate that this optimized ultrasonication process effectively destroyed the more rigid cell walls of low‐quality ginseng and released high levels of ginsenosides. This work is the first to correlate extraction parameters with both extraction yields and biological activity. The use of low‐quality ginseng can thus be expanded by utilizing a low‐temperature ultrasonic extraction process. © 2012 American Institute of Chemical Engineers Biotechnol. Prog. , 2013
Using Taint Analysis for Threat Risk of Cloud Applications

Most existing approaches to developing cloud applications using threat analysis involve program vulnerability analyses for identifying the security holes associated with malware attacks. New malware attacks can bypass firewall-based detection by bypassing stack protection and by using Hypertext Transfer Protocol logging, kernel hacks, and library hack techniques, and to the cloud applications. In performing threat analysis for unspecified malware attacks, software engineers can use a taint analysis technique for tracking information flows between attack sources (malware) and detect vulnerabilities of targeted network applications. This paper proposes a threat risk analysis model incorporating an improved attack tree analysis scheme for solving the mobile security problem, in the model, Android programs perform taint checking to analyse the risks posed by suspicious applications. In probabilistic risk analysis, defence evaluation metrics are used for each attack path for assisting a defender simulate the attack results against malware attacks and estimate the impact losses. Finally, a case of threat analysis of a typical cyber security attack is presented to demonstrate the proposed approach.
Anxiety and burnout in young athletes: The mediating role of cognitive appraisal

This study tested the relationship between trait anxiety, cognitive appraisal, and athletes’ burnout proposing two hypotheses: (a) there is a direct relationship between athletes’ trait anxiety and cognitive appraisal and burnout, and (b) cognitive appraisal mediates the relationship between trait anxiety and burnout, and this mediation occurs despite the competitive level and sport records of athletes. The study included 673 young athletes and provided measures of trait anxiety, cognitive appraisal, and burnout. Structural equation modeling indicated that cognitive appraisal mediates the relationship between trait anxiety and burnout, confirming hypothesis 2, and this model provided better fit than the direct model of hypothesis 1. However, the mediation also indicated that the direct relationship between trait anxiety and burnout should be considered. The mediating model was invariant according to competitive levels and sport records. In conclusion, cognitive appraisal is an important variable in explaining athletes’ burnout.
A Decision Support System for Global Software Development

Global Software Development (GSD) research has reached a level ofmaturity. Paper-based solutions and guidelines are readily availableto solve many known distributed software development problems. Thelarge number of recommendations can present a confusing picture to thepractitioner. The Global Teaming Model (GTM), captures key globalsoftware processes and recommendations by drawing on the large andgrowing corpus of empirical research on GSD. This paper introducesthe Global Teaming Decision Support System (GT-DSS), that is designedto help software managers navigate through the many recommendations inthe GSD literature and the GTM. The interactive GT-DSS capturesdetails about the development organization, and tailors GTM practicesto fit specific business and organizational needs. A prototype of theGTM-DSS has been evaluated by industry experts in GSD, with favorableresults.
STUDY ON STATISTICAL DAMAGE MODEL OF TRIAXIAL CREEP OF CONCRETE

In order to investigate the triaxial creep characteristic of concrete,a triaxial compression test and a triaxial creep test of concrete were carried out with a SAM-2000 triaxial electronic-hydraulic serve system controlled by a computer.And the results show that the confining pressure can significantly increase the carrying capacity of concrete.The greater the confining pressure is,the higher the axial carrying capacity of concrete would be,while the creep deformation volume and deformation rate change to be smaller,conversely.Assuming that the damage of concrete is caused by the damage accumulation of its internal micro-elements,and there exists a certain relationship P[e] between the failure probability of micro-elements and the strain of concrete,and the failure obeys the Weibull distribution,the statistical damage variable can be worked out by the triaxial compression test results.Based on the rheological model of Burgers,the statistical damage model of triaxial creep of concrete is established through introducing the damage variable.The model parameters are fitted by MATLAB software,and after a comparative analysis,the fitting results of model curves and test curves come to be more satisfied,and the greater the main deviatoric stress is,the more accurate the fitting results are.This model can be used for a later reference.
Performance Weighted Deploying and Scheduling Strategy Research for Virtual Machine on Clouds

A performance weighted deploying and scheduling strategy for virtual machine on clouds (PWDSS) is introduced in this paper concerning users’ requests of virtual resources and cloud load balancing. This approach follows three stages: first to use a monitor toolkits to collect the cloud performance data from the virtual machines and physical machines of cloud, and to standardize them; Second, to propose a cloud platform load balancing measurement model, in which the weighted vectors and matrix are set according to the customer requirements; Third, to give an algorithm to select the best appropriate physical machine in the measuring model obtained in stage 2, and then to deploy the new virtual machine, forecasting the load balancing value of every physical machine when the new virtual machine is deployed on it. The experimental results demonstrate that the proposed PWDSS can achieve better effects of system load balancing. At the same time, it can also meet the user requirements better. Keywordscloud computing;load balancing;virtual machine; deploying;
High field gradient targeting of magnetic nanoparticle-loaded endothelial cells to the surfaces of steel stents

A cell delivery strategy was investigated that was hypothesized to enable magnetic targeting of endothelial cells to the steel surfaces of intraarterial stents because of the following mechanisms: (i) preloading cells with biodegradable polymeric superparamagnetic nanoparticles (MNPs), thereby rendering the cells magnetically responsive; and (ii) the induction of both magnetic field gradients around the wires of a steel stent and magnetic moments within MNPs because of a uniform external magnetic field, thereby targeting MNP-laden cells to the stent wires. In vitro studies demonstrated that MNP-loaded bovine aortic endothelial cells (BAECs) could be magnetically targeted to steel stent wires. In vivo MNP-loaded BAECs transduced with adenoviruses expressing luciferase (Luc) were targeted to stents deployed in rat carotid arteries in the presence of a uniform magnetic field with significantly greater Luc expression, detected by in vivo optical imaging, than nonmagnetic controls.
Genome-Wide Estimates of Coancestry and Inbreeding in a Closed Herd of Ancient Iberian Pigs

Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain). Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a useful alternative to genealogical information for measuring and maintaining genetic diversity.
Heritability of major depressive and comorbid anxiety disorders in multi‐generational families at high risk for depression

Family studies have shown that MDD is highly transmittable but have not studied its heritability. Twin studies show heritability of about 40% and do not include anxiety disorders. We assessed heritability of MDD and comorbid anxiety disorders in a multigenerational study of family members at high risk for MDD. In addition, we tested the hypothesis that examined clinical subtypes of MDD defined by early and late age of onset would be under relatively stronger genetic control than broadly defined DSM‐IV MDD. The first generation with moderate to severe MDD was recruited from an ambulatory psychiatric treatment setting, and their descendants in the second, third, and fourth generation, were interviewed by clinicians up to six times during a 30‐year period. Lifetime rates of MDD and anxiety disorders were collected for 545 participants from 65 multigenerational families. The heritability (h2) of MDD in this high risk sample was estimated at 67%. Anxiety and sequential comorbidity of anxiety disorders and MDD revealed h2 of 49% and 53%, respectively, and strong positive genetic correlation (rhog = 0.92, P = 7.3 × 10−7). Early onset MDD did not appear to be under greater genetic control than broadly defined DSM‐IV MDD. Individuals who are direct descendants of subjects ascertained for moderate to severe MDD have strong genetic vulnerability to develop anxiety or MDD. Our findings support family based studies as appropriate and useful design to understand the heritability of common disorders such as MDD. © 2016 Wiley Periodicals, Inc.
Wives and Mothers at Risk: The Role of Marital and Maternal Status in Criminal Activity and Incarceration

As the numbers of women entering prison are increasing, more attention is being paid to the social circumstances of criminally involved women. Crime research has highlighted the familial roles of women more than men, focusing on the social and personal roles of women. This study examines a cross-sectional sample of 423 women in one state, assessing the associations of motherhood and intimate partnership with criminal activity. The study finds that criminal activity, particularly economic crime, is highly related to motherhood. Economic crime is predicted by having a higher number of young children, while both economic and violent crimes are predicted by a woman's history of victimization; marriage does not reduce these risks.
A computational method for identification of disease-associated non-coding SNPs in human genome

Accurate identification of functionally relevant variants against the ubiquitous background genetic variations is a significant challenge facing bioinformatics researchers and the challenge becomes more severe for non-coding variants. In this study, a novel computational method to identify candidate disease-associated non-coding single nucleotide polymorphisms (SNPs) of human genome is presented. To characterize SNPs, an extensive range of features, such as sequence context, DNA structure, evolutionary conservation and histone modification signals etc. are extracted. Then random forest is adopted to build the classifier model together with an ensemble method to deal with unbalanced data. 10-fold cross-validation result shows that the proposed method can achieve accuracy with the area under ROC curve (AUC) of 0.74. All the original data and the source matlab codes involved are available at https://sourceforge.net/projects/dissnp-predict/.
Using Multiple Membership Multilevel Models to Examine Multilevel Networks in Networked Organizations

As the network structures of work and community have grown more complex, multilevel networks have emerged as the main structural feature in organizational settings. Stressing the importance of the affiliation ties of the meso-level network, we propose a conceptualization of multilevel networks within networked organizations. To examine such networks, researchers have used both hierarchical linear models (HLMs), and exponential random graph models (ERGMs) and both show strengths and weaknesses. HLMs have focused on the effects of group characteristics on individual level nodes, and assumed that each node is affiliated with only one group. Thus they are unable to analyze the complexity of the cross-cutting ties in multievel network data from networked organizations. ERGMs, on the other hand, have been used for analyzing such networks and are able to show if the presence of certain ties shapes the development of others. However, these models assume that networks are self-organizing systems of endogenous ties and, as a result, exogenous factors are excluded from them. In this paper, we propose a new method of multiple membership multilevel models that reveal the complexity of the network at the meso-level, i.e., multiple ties between one individual-level node and multiple group-level nodes. To accomplish this we offer an examination of the Canadian research organization, GRAND NCE (Graphics, Animation, New Media and Design Network of Centers of Excellence).
Small RNAs in cell‐to‐cell communications during bacterial infection

&NA; Intercellular communication is a widespread phenomenon in all domains of life. Bacteria have developed many ways of communicating with one another and with other species, either prokaryotic or eukaryotic. RNA has been a key molecule since the beginning of life on Earth, and is one of the carriers of information. Given the current antibiotic crisis, understanding the way in which pathogens communicate can lead towards improved ways to control infections when antimicrobial therapy is not possible. Different subspecies of RNA, non‐coding, and of small size, designated here as ncRNAs, have been in recent years the subject of a great research effort, and results have contributed to a growing field of knowledge. This review focuses on four different aspects of ncRNA involvement in cell‐to‐cell communications during bacterial infections: pathogen recognition by the host, alteration of host microRNA profiles, production of domestic and secreted forms of ncRNAs and subversion of the host responses. The current review article focuses on the most recent discoveries in the field and gives an integrative idea based on the discussed studies.
Pattern Databases

The efficiency of A* searching depends on the quality of the lower bound estimates of the solution cost. Pattern databases enumerate all possible subgoals required by any solution, subject to constraints on the subgoal size. Each subgoal in the database provides a tight lower bound on the cost of achieving it. For a given state in the search space, all possible subgoals are looked up in the pattern database, with the maximum cost over all lookups being the lower bound. For sliding tile puzzles, the database enumerates all possible patterns containing N tiles and, for each one, contains a lower bound on the distance to correctly move all N tiles into their correct final location. For the 15‐Puzzle, iterative‐deepening A* with pattern databases(N ="8) reduces the total number of nodes searched on a standard problem set of 100 positions by over 1000‐fold.