Miracle-dz/UniFAR-FTUs huggingface dataset:
Simple, efficient location‐based routing for data center network using IP address hierarchy

Increasing demand and sophistication of applications deployed on data centers resulted in various designs for data center networks (DCNs). One of the major challenges in the design of DCNs is the design of routing protocol that scales to support millions of servers that a typical DCN hosts. Many alternative routing protocols are proposed to overcome the scalability problem of conventional routing protocols such as Open Shortest Path First and Routing Information Protocol. These alternative protocols that use topology characteristics of DCN are broadly classified as source routing and location‐based routing. In the process of fixing the scalability problem, these protocols introduced additional complexities such as large network control overhead and reprogramming of network elements. The extra control overhead in these protocols is the result of their effort to determine the relative location of the end hosts in a given topology. Further, existing location‐based routing is not entirely location based and covers only the latter half of a route. In our work, we present a new location‐based routing based on IP address hierarchy that (a) does not need any additional network control plane and management planes, (b) deployable on proven network technologies, and (c) covers entire path of the route. We establish the correlation between topology design and address assignments that helps determining the location of an end host directly from the address assigned to it. We demonstrate our proposed location‐based routing on an existing proven architecture for DCN, BCube‐IP and on our proposed architecture 4‐4, 1‐4. We give proper justification for proposing 4‐4, 1‐4, a better design for our proposed location‐based routing. Copyright © 2016 John Wiley & Sons, Ltd.
Non-Random Variability in Functional Composition of Coral Reef Fish Communities along an Environmental Gradient

Changes in the coral reef complex can affect predator-prey relationships, resource availability and niche utilisation in the associated fish community, which may be reflected in decreased stability of the functional traits present in a community. This is because particular traits may be favoured by a changing environment, or by habitat degradation. Furthermore, other traits can be selected against because degradation can relax the association between fishes and benthic habitat. We characterised six important ecological traits for fish species occurring at seven sites across a disturbed coral reef archipelago in Indonesia, where reefs have been exposed to eutrophication and destructive fishing practices for decades. Functional diversity was assessed using two complementary indices (FRic and RaoQ) and correlated to important environmental factors (live coral cover and rugosity, representing local reef health, and distance from shore, representing a cross-shelf environmental gradient). Indices were examined for both a change in their mean, as well as temporal (short-term; hours) and spatial (cross-shelf) variability, to assess whether fish-habitat association became relaxed along with habitat degradation. Furthermore, variability in individual traits was examined to identify the traits that are most affected by habitat change. Increases in the general reef health indicators, live coral cover and rugosity (correlated with distance from the mainland), were associated with decreases in the variability of functional diversity and with community-level changes in the abundance of several traits (notably home range size, maximum length, microalgae, detritus and small invertebrate feeding and reproductive turnover). A decrease in coral cover increased variability of RaoQ while rugosity and distance both inversely affected variability of FRic; however, averages for these indices did not reveal patterns associated with the environment. These results suggest that increased degradation of coral reefs is associated with increased variability in fish community functional composition resulting from selective impacts on specific traits, thereby affecting the functional response of these communities to increasing perturbations.
Self-Organization in the Nervous System

Self-organization refers to a process in which the internal organization of a system increases in complexity without guidance from the outside world. In brain development many aspects of self-organization are involved. Although development of the nervous system depends on external stimulation, pattern formation in the brain is considered to be a result of internal interactions through unsupervised learning. Self-organizing maps generally perform a projection from a high-dimensional to a low-dimensional data space. As part of the visual system, the primary visual cortex manages to reduce the complexity of input stimuli by developing spatial patterns called cortical maps. These biological maps are role models in computational research, especially in the field of artificial neural networks.
Molecular structures guide the engineering of chromatin

Abstract Chromatin is a system of proteins, RNA, and DNA that interact with each other to organize and regulate genetic information within eukaryotic nuclei. Chromatin proteins carry out essential functions: packing DNA during cell division, partitioning DNA into sub-regions within the nucleus, and controlling levels of gene expression. There is a growing interest in manipulating chromatin dynamics for applications in medicine and agriculture. Progress in this area requires the identification of design rules for the chromatin system. Here, we focus on the relationship between the physical structure and function of chromatin proteins. We discuss key research that has elucidated the intrinsic properties of chromatin proteins and how this information informs design rules for synthetic systems. Recent work demonstrates that chromatin-derived peptide motifs are portable and in some cases can be customized to alter their function. Finally, we present a workflow for fusion protein design and discuss best practices for engineering chromatin to assist scientists in advancing the field of synthetic epigenetics.
Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

Background Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular α-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). Methodology/Principal Findings We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (∼1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. Conclusion/Significance Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets.
Analysis of EGF signaling in healthy aging promotion in caenorhabditis elegans

OF THE DISSERTATION.ii ACKNOWLEDGMENTS.iv TABLE OF CONTENTS.vi LIST OF FIGURES.viii LIST OF TABLES.xi CHAPTER 1 : Introduction.1 Biology of aging.2 Sarcopenia is one of the most prevalent conditions in aging and genetic approaches toward understanding.3 The benefit of addressing aging biology in simple organisms.3 Caenorhabditis elegans – a powerful model organism for the study of aging.4 Aging in C. elegans.5 Evaluation of healthy aging in C. elegans.6 The Insulin/IGF signaling pathway.9 EGF signaling is a conserved pathway in many organisms.10 Summary of thesis work.11 CHAPTER 2 : Novel EGF pathway regulators modulate C. elegans healthspan and lifespan via EGF receptor, PLC-γ, and IP3 receptor activation.18 CHAPTER 3 : Deciphering mechanisms by which EGF signaling protects against the aging process.23 Introduction.25
Reproductive mode plasticity: Aquatic and terrestrial oviposition in a treefrog

Diversification of reproductive mode is a major theme in animal evolution. Vertebrate reproduction began in water, and terrestrial eggs evolved multiple times in fishes and amphibians and in the amniote ancestor. Because oxygen uptake from water conflicts with water retention in air, egg adaptations to one environment typically preclude development in the other. Few animals have variable reproductive modes, and no vertebrates are known to lay eggs both in water and on land. We report phenotypic plasticity of reproduction with aquatic and terrestrial egg deposition by a frog. The treefrog Dendropsophus ebraccatus, known to lay eggs terrestrially, also lays eggs in water, both at the surface and fully submerged, and chooses its reproductive mode based on the shade above a pond. Under unshaded conditions, in a disturbed habitat and in experimental mesocosms, these frogs lay most of their egg masses aquatically. The same pairs also can lay eggs terrestrially, on vegetation over water, even during a single night. Eggs can survive in both aquatic and terrestrial environments, and variable mortality risks in each may make oviposition plasticity adaptive. Phylogenetically, D. ebraccatus branches from the basal node in a clade of terrestrially breeding species, nested within a larger lineage of aquatic-breeding frogs. Reproductive plasticity in D. ebraccatus may represent a retained ancestral state intermediate in the evolution of terrestrial reproduction.
[The importance of a normal ECG in non-ST elevation acute coronary syndromes].

BACKGROUND Admission ECG has a major impact on the diagnosis and management of non-ST elevation acute coronary syndromes (ACS). OBJECTIVE To assess the impact of the admission ECG on prognosis over non-ST ACS. POPULATION prospective, continuous, observational study of 802 non-ST ACS patients from a single center. METHODS Patients were divided in 2 groups: A (n=538) - Abnormal ECG and B (n=264) - Normal ECG. Normal ECG was synonymous of sinus rhythm and no acute ischemic changes. A one-year clinical follow up was performed targeting all causes of mortality and the MACE rate. RESULTS Group A patients were older (68.7+/-11.7 vs. 63.4+/-12.7Y, p<0.001), had higher Killip classes and peak myocardial necrosis biomarkers. Furthermore, they had lower left ventricular ejection fraction (LVEF) (52.01+/-10.55 vs. 55.34+/- 9.51%, p<0.001), glomerular filtration rate, initial hemoglobin, and total cholesterol levels. Group B patients were more frequently submitted to invasive strategy (63.6 vs. 46.5%, p<0.001) and treated with aspirin, clopidogrel, beta blockers and statins. They also more often presented normal coronary anatomy (26.2 vs. 18.0%, p=0.45). There was a trend to higher in-hospital mortality in group A (4.6 vs. 1.9%, p=0.054). Kaplan-Meyer analysis showed that at one month and one year (95.1 vs. 89.5%, p=0.012) survival was higher in group B and the result remained significant on a Cox regression model (normal ECG HR 0.45 (0.21 - 0.97). There were no differences regarding the MACE rate. CONCLUSION In our non-ST elevation ACS population, a normal ECG was an early marker for good prognosis.
The Urban Policy-making and Development Dimension of Fordism and Post-Fordism: A Toronto Case Study

This paper investigates urban policy-making and development from a regulation theory perspective. It describes major Toronto urban trends of the past 50 years in order to gauge their conformity to changing regulation conditions. Results indicate that in the 1950s and 1960s, policies in Toronto were in accord with the Fordist mass consumption and welfare orientation. They also suggest a coincidence between the post-1995 period of public-sector retrenchment and the market-driven nature of post-Fordism. The intermediary period, however, was dominated by unsuccessful efforts at maintaining Fordist-type policies in a regulation context shifting towards post-Fordism. These findings confirm the non-functionalist interpretation of links between policy-making and regulation professed by regulation theory researchers. They also cast light on the role the city plays in the changing nature of regulation. Assertive metropolitan planning and socially balanced sub-divisions characteristic of the Fordist period of regulation gradually made way for market-driven development. With a reduced government presence, urban development has become less co-ordinated and more socially polarised, thus reflecting at the urban level society-wide features of post-Fordism.
Methods of assessment of selenium status in humans: a systematic review.

BACKGROUND To understand the effect of selenium intake on health, it is important to identify sensitive and population-specific biomarkers of selenium status. OBJECTIVE The objective of this systematic review was to assess the usefulness of biomarkers of selenium status in humans. DESIGN The methods included a structured search strategy on Ovid MEDLINE, EMBASE (Ovid), and Cochrane databases; formal inclusion and exclusion criteria; data extraction into an Access database; validity assessment; and meta-analysis. RESULTS The data from 18 selenium supplementation studies (of which 9 were randomized controlled trials and 1 was considered to be at low risk of bias) indicate that plasma, erythrocyte, and whole-blood selenium, plasma selenoprotein P, and plasma, platelet, and whole-blood glutathione peroxidase activity respond to changes in selenium intake. Although there is a substantial body of data for plasma selenium, more large, high-quality, randomized controlled trials are needed for this biomarker, as well as for the other biomarkers, to explore the reasons for heterogeneity in response to selenium supplementation. There was insufficient evidence to assess the usefulness of other potential biomarkers of selenium status, including urinary selenium, plasma triiodothyroxine:thyroxine ratio, plasma thyroxine, plasma total homocysteine, hair and toenail selenium, erythrocyte, and muscle glutathione peroxidase activity. CONCLUSIONS For all potentially useful biomarkers, more information is needed to evaluate their strengths and limitations in different population groups, including the effects of varying intakes, the duration of intervention, baseline selenium status, and possible confounding effects of genotype.
Conceptual feedback for semantic multimedia indexing

In this paper, we consider the problem of automatically detecting a large number of visual concepts in images or video shots. State of the art systems involve feature (descriptor) extraction, classification (supervised learning) and fusion when several descriptors and/or classifiers are used. Though direct multi-label approaches are considered in some works, detection scores are often computed independently for each target concept. We propose here a method that we call “conceptual feedback” for improving the overall detection performance that implicitly takes into account the relations between concepts. The vector of normalized detection scores is added to the pool of available descriptors. It is then processed just as the other descriptors for the normalization, optimization and classification steps. The resulting detection scores are finally fused with the already available detection scores obtained with the original descriptors. The feedback of the global detection scores in the pool of descriptors can be iterated several times. It is also compatible with the use of the temporal context that also improves the overall performance by taking into account the local homogeneity of video contents. The method has been evaluated in the context of the TRECVID 2012 semantic indexing task involving the detection of 346 visual or multimodal concepts. Combined with temporal re-scoring, the proposed method increased the global system performance (MAP) from 0.2613 to 0.3014 (+15.3% of relative improvement) while the temporal re-scoring alone increased it only from 0.2613 to 0.2691 (+3.0%).
Investigating Secondary School Leaders’ Perceptions of Performance Management

Much of the research into teacher appraisal and performance management has focused on the experience of the classroom teacher. In this article, I will: (1) concentrate on the perspectives of the senior managers in secondary schools; (2) consider their views of the purpose of performance management; (3) compare their methods of implementation of the statutory regulations; (4) reflect on their leadership ethos; and (5) review the links between their ideology and their perceptions of performance management. I have reflected on the links between performance management and strategic management—looking particularly at the work of Storey (2002) on using a balanced scorecard approach in education and Hartle et al. (2001), on leadership effectiveness and on the use of teaching and management competences. A major additional area for investigation that emerged as a result of this study is a possible link between implementation and practice of performance management in a particular school with the leadership style of the headteacher and her/his ideological relationship with the senior leader responsible for performance management.
Isolation and characterization of murine cell surface components. I. Purification of milligram quantities of Thy-1.1

The Thy-l.1 molecule was isolated from the BW5147 murine lymphoblastoid cell line. The initial step in purification was the preparation of a crude plasma membrane fraction followed by acetone precipitation. The acetone pellet was solubilized using deoxycholate (DOC) and Thy-1.1 was purified by use of a Lens culinaris lectin affinity column and an AcA-34 gel filtration column. The purified glycoprotein with Thy-1.1 activity had a mol wt of approximately 25,000 daltons. The isolation of this molecule was effected by detecting Thy-I activity utilizing rabbit anti- mouse brain serum tested on rat thymocytes. Congenic anti-Thy-l.1 serum was ineffective in detecting Thy-l.1 after DOC solubilization. An antiserum prepared in rabbits to the purified Thy-1.1 was found to be cytotoxic to mouse and rat thymocytes. The cytotoxic activity of this antisera could be completely absorbed with AKR/Jax brain and thymus but was not absorbed by liver. In addition, AKR/Jax thymocytes totally absorbed all cytotoxic activity of the rabbit anti-purified Thy-1 serum for BW5147 cells suggesting that the cell line shares identical specificities with normal thymocytes. The purified Thy-1.1 molecule was able to totally absorb the cytotoxic activity of mouse congenic anti-Thy-1. These studies serve as a model for the isolation of other murine lymphoid cell surface components in quantities for detailed structural and functional analysis.
Assessment of the Fecal Microbiota in Beef Calves

Background There is increasing interest in the fecal microbiota, but study in calves has been limited. Hypothesis/Objectives To evaluate the fecal microbiota of beef calves and cows on different farms, and to preliminarily explore the impact of antimicrobial exposure. Animals A total of 172 animals, 156 (91%) calves and 16 (9.3%) cows, were enrolled from 5 cow‐calf farms. Methods The fecal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V4 region) amplicons. Results There were significant differences in the relative abundances of numerous phyla between calves on different farms. Farms could be separated into 2 groups: 1 (farms B and C) dominated by Firmicutes and 1 (farms A, D, and E) with predominance of Proteobacteria and Actinobacteria. Richness (median 2,974 versus 1,477, P = .008), diversity (51.4 versus 29.1, P = .0029), and evenness (0.73 versus 0.68, P = .006) were higher in cows. Over‐represented operational taxonomic units (OTUs) in cows tended to be from the classes Bacilli and Bacteroidia, whereas Clostridia and Actinobacteria were most prominently over‐represented in calves. There were differences in community membership (P = .028) and structure (P = .029) in calves that had a history of antimicrobial exposure compared those that did not. Eight (89%) over‐represented OTUs in the untreated group were Firmicutes (7 from the order Clostridiales), compared to only 3 (38%) (2 Clostridiales) in the untreated group. Conclusions and Clinical Importance Interfarm variation should be investigated to determine the causes and potential implications for health and production. Antimicrobial exposure may have an impact on the fecal microbiota at individual and farm levels.