Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary bacterial foraging algorithm to solve constraint numerical optimization problems

A version of Modified Bacterial Foraging Optimization Algorithm to solve Constraints Numerical Optimization is tested. The proposal uses mutation operator, skew mechanism and local search operator. To prove the effectiveness of the mechanism and adaptations proposed, 24 well-known test problems are solved along set experiments. Performance measures are used for validating results obtained by the proposal and they are compared against state-of-the-art algorithms. The results show that the proposed algorithm is able to generate feasible solutions within of feasible region with few evaluations and improves them over the generations. Moreover, the results are competitive against the comparison algorithms based on performance measures found in the literature. Bacterial foraging optimization, mutation operator, swarm intelligence, Constrained optimization, premature convergence.
SOME OBSERVATIONS ON THE STUDY OF THE INTESTINAL BACTERIA

The alimentary canal may be regarded from the point of view of bacterial processes within it, as a singularly perfect incubator; an incubator in which there is provided at different levels such a range of reaction and diversity of food that not only are the conditions suitable for the growth of the normal habituated intestinal bacteria but often also for those organisms, capable of developing at body temperature, which are ingested with the food of the host. An idea of the truly enormous daily bacterial proliferation which takes place in the intestinal tract may be obtained if one remembers that a considerable portion of the fecal mass is made up of the bodies of bacteria, dead and living. At the same time the multiplicity of types and variety of physiological requirements of this intestinal flora are indications of the excellence of the incubator and a strong reminder of the influence which the unrestrained activity of these organisms might conceivably exercise upon the general condition of the host. The possibilities of bacterial invasion through the intestinal portal of entry have not been overlooked by investigators, and, indeed, among the most brilliant chapters of medicine are those concerning the etiological relationships which have been demonstrated between certain pathogenic bacteria of exogenous origin and specific diseases of the intestinal tract, for example, typhoid, cholera and dysentery. The very importance of these discoveries has been a potent factor in diverting attention from the studies of the normal intestinal flora with its wealth of problems relating to the principles which govern the activity of these bacteria. Even at the present time the sequence of events which permits the establishment of
Spring 2014 Editorial : Development as a Complex Adaptive Field of Research

This issue of the AMD Newsletter is very special: we are celebrating its 10 years of biannual publication! It has progressively become a place of lively and inspiring scientific dialogues spanning an incredible network of topics, with the contributions of many key actors of computational developmental sciences. It has been for me a fantastic honour to be editor of the newsletter in the last seven years, and I sincerely thank all those who accepted to play the game of dialogues through my solicitations. These dialogues have vividly explored the role of intrinsic motivation and social interaction in development, the mechanisms of cumulative learning, the processes of perceptual growth and organisation, the issue of language acquisition and symbol grounding, and the application of developmental and social robotics as a tool to address developmental disorders in humans. Several dialogues also discussed the epistemological foundations of modelling development, rethinking why and how the study of robot and human development can feed each other. Most texts expose arguments that are still valid, and reading them again is a great opportunity to observe at the same time what has been achieved and what remains to be done (see http://www.cse.msu.edu/amdtc/ amdnl/). Indeed, developmental processes are probably among the most complicated phenomena under scientific inquiry, and we are just beginning to uncover them. So many great questions are still unanswered. For example, understanding how infants create meaningful and usable abstractions over their multimodal sensorimotor flow, how they build skills upon each other in an open-ended manner, how they come to participate so flexibly in complex interactions with adults without understanding many details, and how to achieve such capabilities with robots, are still largely beyond our reach. But great progress is being made, and especially in realising that development is a complex multi-scale dynamical system, the study of which requires the deep interconnec-tion between concepts and techniques coming from biology, psychology, neuroscience, physics , computer science and mathematics. The study of developmental systems is itself a complex field of research, which needs to find adaptive strategies to grow beyond the traditional disciplinary walls built within academic institutions. Over the years, the gathering of researchers of very diverse and complementary background within this newsletter, within TAMD, within ICDL-Epirob conference and within multiple workshops, shows the successes of this enterprise. Large-scale European projects and widespread research platform such as the ICub across Europe are other examples. The dialogue in this …
Enriching PubMed Related Article Search with Sentence Level Co-citations

PubMed related article links identify closely related articles and enhance our ability to navigate the biomedical literature. They are derived by calculating the word similarity between two articles, relating articles with overlapping word content. In this paper, we propose to enrich PubMed with a new type of related article link based on citations within a single sentence (i.e. sentence level co-citations or SLCs). Using different similarity metrics, we demonstrated that articles linked by SLCs are highly related. We also showed that only half of SLCs are found among PubMed related article links. Additionally, we discuss how the citing sentence of an SLC explains the connection between two articles.
Bleeding risk with dabigatran, rivaroxaban, warfarin, and antiplatelet agent in Asians with non-valvular atrial fibrillation

It is not understood if dabigatran or rivaroxaban are superior to antiplatelet agents (AA) for safety outcomes in Asians with non-valvular atrial fibrillation (NVAF). In this study we evaluated the bleeding risk of dabigatran, rivaroxaban, warfarin and AA in Asians with NVAF. This national retrospective cohort study analyzed 6,600, 3,167, 5,338 and 8,238 consecutive NVAF patients taking dabigatran, rivaroxaban, warfarin or AAs (including aspirin, clopidogrel or ticlopidine), respectively, from June 1, 2012 to December 31, 2013. Propensity-score weighting was used to balance covariates across study groups. Patients were followed until the first occurrence of any bleeding outcome or the end of the study. The CHA2DS2-VASc scores were 4.1±1.6, 4.1±1.6, 3.3±1.8 and 2.4±1.6 for the dabigatran, rivaroxaban, warfarin, and AA groups, respectively. There were 5,822 (88.2%) and 164 (5.2%) patients taking low dose dabigatran and rivaroxaban, respectively. Hazard ratios (95% confidence intervals) for dabigatran, rivaroxaban, or warfarin versus AA were: intracranial hemorrhage, 0.36 (0.23-0.57;PP=0.0037) and 1.34 (0.89-2.02;P=0.1664); gastrointestinal bleeding, 0.44 (0.32-0.59;PP=0.0189); and all hospitalized major bleeding, 0.41 (0.32-0.53;PP=0.0644) and 0.90 (0.70-1.16;P=0.4130) after adjustment. The risk reduction of all major bleeding for dabigatran versus AA persisted on subgroup analysis. In conclusion, we observed that dabiagtran was associated with a lower risk of all major bleeding in Asians with NVAF, whereas rivaroxaban had a similar risk of all major bleeding compared with antiplatelet agents after adjustment of comorbidities.
Role of lignan sources in tumour formation in multiple intestinal neoplasia mice

Abstract Plants lignans are ubiquitous compounds in plants, and some of them, such asmatairesinol and secoisolariciresinol, are converted into the mammalian lignansenterolactone and enterodiol by gut microflora. Lignans have been suggested todecrease risks of hormone-related cancers in man and to retard tumorigenesis inanimal models of cancer. Diet has a major impact on the incidence of colorectalcancer, and lignans have been proposed to prevent this form of cancer. Multipleintestinal neoplasia (Min) mice, which have an inherited mutation in the adenomatouspolyposis coli gene, and thus, a spontaneous formation of intestinal adenomas, serveas a useful experimental model in studies of diet and colon cancer.The aims of this study were to elucidate the role of lignan sources and lignanmetabolism in adenoma formation in Min mice, and to see if there is gender orgenotype based differences in these parameters. To study this, the mice were fedlignan-rich foods, such as flaxseed and rye bran, and the pure lignans 7-hydroxymatairesinol, matairesinol and secoisolariciresinol in aglycone forms.Furthermore, the role of other dietary components in flaxseed and rye bran (besideslignans) in tumour formation, and the effects of diets on levels of such cell-signallingparameters asβ-catenin, cyclooxygenase-2 and protein kinase C-ζ were alsoelucidated.The results showed that flaxseed and rye diets providing such lignans assecoisolariciresinol diglycoside and syringaresinol showed no clear anticarcinogeniceffects in Min mice. Studies with the three pure lignans yielded conflicting results; thecrude extract of 7-hydroxymatairesinol was chemopreventive, pure matairesinol hadtumour growth-favouring effects, and pure secoisolariciresinol had a neutral effect.The exact mechanism of action of these lignans was unclear, but it did not appear todepend on enterolactone formation. We found also that neither plasma enterolactonenor the intestinal enterodiol, enterolactone or secoisolariciresinol had
Efficient and Distributed Detection of Node Replication Attacks in Mobile Sensor Networks

In this paper, we study the challenging problem of node replication detection. Although defending against node replication attacks demands immediate attention, only a few solu- tions were proposed. In this paper, an Efficient and Distributed Detection (EDD) scheme and its variant, SEDD, are proposed to resist against node replication attacks in mobile sensor net- works. The characteristics possessed by EDD and SEDD include (1) Distributed Detection; (2) Efficiency and Effectiveness; (3) Individual Detection; (4) Network-Wide Revocation Avoidance. Performance comparison with known methods are provided to demonstrate the efficiency of the EDD and SEDD schemes.
Design of a Multi-mode Flight Deck Decision Support System for Airborne Conflict Management

NASA Langley has developed a multi-mode decision support system for pilots operating in a Distributed Air-Ground Traffic Management (DAG-TM) environment. An Autonomous Operations Planner (AOP) assists pilots in performing separation assurance functions, including conflict detection, prevention, and resolution. Ongoing AOP design has been based on a comprehensive human factors analysis and evaluation results from previous human-in-the-loop experiments with airline pilot test subjects. AOP considers complex flight mode interactions and provides flight guidance to pilots consistent with the current aircraft control state. Pilots communicate goals to AOP by setting system preferences and actively probing potential trajectories for conflicts. To minimize training requirements and improve operational use, AOP design leverages existing alerting philosophies, displays, and crew interfaces common on commercial aircraft. Future work will consider trajectory prediction uncertainties, integration with the TCAS collision avoidance system, and will incorporate enhancements based on an upcoming air-ground coordination experiment.
Pallidal deep-brain stimulation in primary generalized or segmental dystonia.

BACKGROUND Neurostimulation of the internal globus pallidus has been shown to be effective in reducing symptoms of primary dystonia. We compared this surgical treatment with sham stimulation in a randomized, controlled clinical trial. METHODS Forty patients with primary segmental or generalized dystonia received an implanted device for deep-brain stimulation and were randomly assigned to receive either neurostimulation or sham stimulation for 3 months. The primary end point was the change from baseline to 3 months in the severity of symptoms, according to the movement subscore on the Burke-Fahn-Marsden Dystonia Rating Scale (range, 0 to 120, with higher scores indicating greater impairment). Two investigators who were unaware of treatment status assessed the severity of dystonia by reviewing videotaped sessions. Subsequently, all patients received open-label neurostimulation; blinded assessment was repeated after 6 months of active treatment. RESULTS Three months after randomization, the change from baseline in the mean (+/-SD) movement score was significantly greater in the neurostimulation group (-15.8+/-14.1 points) than in the sham-stimulation group (-1.4+/-3.8 points, P<0.001). During the open-label extension period, this improvement was sustained among patients originally assigned to the neurostimulation group, and patients in the sham-stimulation group had a similar benefit when they switched to active treatment. The combined analysis of the entire cohort after 6 months of neurostimulation revealed substantial improvement in all movement symptoms (except speech and swallowing), the level of disability, and quality of life, as compared with baseline scores. A total of 22 adverse events occurred in 19 patients, including 4 infections at the stimulator site and 1 lead dislodgment. The most frequent adverse event was dysarthria. CONCLUSIONS Bilateral pallidal neurostimulation for 3 months was more effective than sham stimulation in patients with primary generalized or segmental dystonia. (ClinicalTrials.gov number, NCT00142259 [ClinicalTrials.gov].).
Proposta de modelo para análise da integração da cadeia de suprimentos utilizando-se índices de automação

As organizacoes reconhecem que a integracao intra e inter sistemas de manufatura e fundamental para manter-se nao apenas competitivo, mas a frente da concorrencia. O Sistema de manufatura pode ser visto como o conjunto de relacoes entre as atividades de Engenharia, Chao de Fabrica, Negocios e Suporte e suas sub atividades e, a sua Integracao, entendida como o fluxo sinergico de informacao, pode ser alcancada ao se aplicar recursos de automacao. Uma forma de analisar esta integracao e atraves de Indices de Automacao. O presente trabalho propoe o desenvolvimento de um modelo para analise de integracao da cadeia de suprimentos baseado em indices de automacao e para isto, considera a relacao entre os sistemas de manufatura da empresa foco e seus primeiro nivel de fornecedores. Sao apresentadas nove arquiteturas, divididas entre arquiteturas com capacidade de integracao e arquiteturas sem capacidade de integracao entre fornecedor e empresa. A aplicacao do modelo de integracao da cadeia de suprimento foi em uma Empresa foco do ramo de maquinas e implementos agricolas e em tres fornecedores primarios, utilizando um questionario estruturado em 12 questoes de multipla escolha, referentes ao grau de automacao das sub atividades de cada sistema de manufatura. A relacao de integracao da cadeia de suprimentos estudada se enquadra na arquitetura na qual a empresa foco nao apresenta integracao estrutural no sistema de manufatura e o primeiro nivel de fornecedores apresenta integracao estrutural das atividades no sistema de manufatura. Na conclusao, sao propostas alternativas de integracao para a cadeia de suprimentos e sugeridos trabalhos futuros Abstract
Inner mean-motion resonances with eccentric planets: a possible origin for exozodiacal dust clouds

Fondo Nacional de Desarrollo Cientifico y Tecnologico (FONDECYT) Postdoctoral Fellowships [3150106, 3140479]; Chilean Ministry of Economy [RC130007]; Millennium Nucleus 'Protoplanetary Disks'; Deutsche Forschungsgemeinschaft (DFG) [2164/15-1]; Comision Nacional de Investigacion Cientifica y Tecnologica-Chile through FONDECYT grant [1141175]; Comision Nacional de Investigacion Cientifica y Tecnologica-Chile through Basal grant [PFB0609]; VRI
Polyphonic Approximation of Change Sets

When studying the evolution of software systems, software processes and software configuration systems are the main sources of information. Ideally, these sources can be used to identify change sets: groups of changes to software entities sharing a common motivation. These change sets are typically used to identify clusters of software entities that are often changed together. The identified clusters can be used for predicting future changes and to assess the decomposition of a software system’s archive. Because of the fundamental nature of a change set for studying software evolution, we take a closer look at the notion of a change set. Precise knowledge of change sets often evaporates due to insufficient documentation. Hence we have to deal with approximations. Most studies use a single perspective only on how to approximate change sets. In this paper, we discuss different ways to approximate change sets. We argue that one needs to apply multiple approximations of change sets in parallel, since modifications are often captured differently as a result of the diversity of the executed software processes. We illustrate the benefits of multiple change set approximations in an industrial case study.
A Near-Capacity MIMO Coded Modulation Scheme for Digital Terrestrial Television Broadcasting

Multiple-input multiple-output (MIMO), which can provide ultrahigh data transmission rate, is one of the key technologies for the next generation digital terrestrial television broadcasting (DTTB) standards. This paper proposes a near-capacity MIMO bit-interleaved coded modulation scheme with either independent or iterative demapping (BICM/BICM-ID) for the DTTB system. First, the amplitude phase shift keying (APSK) constellation with Gray mapping is proposed to replace the conventional Gray quadrature amplitude modulation (QAM) counterpart. From the perspective of average mutual information analysis, Gray-APSK has certain shaping gain compared to Gray-QAM for both independent and iterative demapping schemes. Besides the APSK constellation, a novel bit interleaver named bit mapping, which takes into account the unequal error protection of both APSK constellations and low-density parity-check codes, is proposed to further improve the system performance. The tool of extrinsic information transfer chart is utilized to analyze and design the optimal bit mapping for the BICM/BICM-ID scheme. Bit error rate simulations are finally carried out to verify the superiority of the proposed MIMO coded modulation scheme.
Integrated, Genome-Wide Screening for Hypomethylated Oncogenes in Salivary Gland Adenoid Cystic Carcinoma

Purpose: Salivary gland adenoid cystic carcinoma (ACC) is a rare malignancy that is poorly understood. To look for relevant oncogene candidates under the control of promoter methylation, an integrated, genome-wide screen was conducted. Experimental Design: Global demethylation of normal salivary gland cell strains using 5-aza-2′-deoxycytidine (5-aza-dC) and trichostatin A (TSA), followed by expression array analysis was conducted. ACC-specific expression profiling was generated using expression microarray analysis of primary ACC and normal samples. Next, the two profiles were integrated to identify a subset of genes for further validation of promoter demethylation in ACC versus normal. Finally, promising candidates were further validated for mRNA, protein, and promoter methylation levels in larger ACC cohorts. Functional validation was then conducted in cancer cell lines. Results: We found 159 genes that were significantly re-expressed after 5-aza-dC/TSA treatment and overexpressed in ACC. After initial validation, eight candidates showed hypomethylation in ACC: AQP1, CECR1, C1QR1, CTAG2, P53AIP1, TDRD12, BEX1, and DYNLT3. Aquaporin 1 (AQP1) showed the most significant hypomethylation and was further validated. AQP1 hypomethylation in ACC was confirmed with two independent cohorts. Of note, there was significant overexpression of AQP1 in both mRNA and protein in the paraffin-embedded ACC cohort. Furthermore, AQP1 was upregulated in 5-aza-dC/TSA–treated SACC83. Finally, AQP1 promoted cell proliferation and colony formation in SACC83. Conclusions: Our integrated, genome-wide screening method proved to be an effective strategy for detecting novel oncogenes in ACC. AQP1 is a promising oncogene candidate for ACC and is transcriptionally regulated by promoter hypomethylation. Clin Cancer Res; 17(13); 4320–30. ©2011 AACR.
Will Pyramids Built of Nuggets Topple Over?

The present methodology for evaluating complex questions at TREC analyzes answers in terms of facts called "nuggets". The official F-score metric represents the harmonic mean between recall and precision at the nugget level. There is an implicit assumption that some facts are more important than others, which is implemented in a binary split between "vital" and "okay" nuggets. This distinction holds important implications for the TREC scoring model---essentially, systems only receive credit for retrieving vital nuggets---and is a source of evaluation instability. The upshot is that for many questions in the TREC testsets, the median score across all submitted runs is zero. In this work, we introduce a scoring model based on judgments from multiple assessors that captures a more refined notion of nugget importance. We demonstrate on TREC 2003, 2004, and 2005 data that our "nugget pyramids" address many shortcomings of the present methodology, while introducing only minimal additional overhead on the evaluation flow.
Circulating microRNAs in hepatitis B virus–infected patients

Summary. MicroRNAs (miRNAs) are stably present in human serum. The relationship between circulating miRNAs and hepatitis B virus (HBV) infected liver disease has not been previously reported. Applied Biosystems array‐based miRNA expression profiling was performed on pooled sera obtained from identified groups of chronic asymptomatic carriers (ASC), patients with chronic hepatitis B (CHB) and HBV‐associated acute‐on‐chronic liver failure (ACLF), as well as healthy controls (HC). Nine miRNAs were verified in more clinical samples by RT‐PCR. The correlation between miRNAs expression and the relationship between miRNA levels and clinical characteristics was analysed. Results showed that circulating miRNAs were detected in all disease and control samples, and their numbers increased with symptom severity, from 37 in HC, 77 in ASC, 101 in CHB, to 135 in ACLF. The expression levels of most miRNAs were also up‐regulated in HBV‐infected patients when compared to HC. Expression of the liver‐specific miR‐122 was significantly up‐regulated in HBV‐infected patients. Concomitant regulation of miRNAs not in clusters was disrupted by HBV infection. However, such disruption was not observed for miRNAs in paralogous clusters. Furthermore, the level of miRNAs in the CHB serum was up‐regulated most in hepatitis B e antigen–positive patients. The expression levels of miR‐122 and miR‐194 correlated negatively with the age of patients with CHB or ACLF. Functional analysis showed that miR‐122 could inhibit HBV replication in Huh7 and HepG2 cells. In all, our study revealed that a number of miRNAs were differentially expressed during HBV infection and underscored the potential importance of miR‐122 in the infection process.