Miracle-dz/UniFAR-FTUs huggingface dataset:
Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers

In order to identify patterns in bacterial community composition in freshwater habitats, we analyzed the available database of 16S rDNA sequences from freshwater plankton, including 24 new sequences from Parker River (Massachusetts, USA), 42 from Lake Soyang (South Korea) and 148 from Lake IJssel (The Netherlands). At this point, combined diversity studies using random cloning have deposited 689 bacterial and 75 plastid 16S rDNA sequences from the water column of rivers and lakes in North America, Europe and Asia. Systematic comparisons with the global data- base showed that the majority of the bacterial sequences were most closely related to other fresh- water clones or isolates, while relatively few were closest to sequences recovered from soils or marine habitats. This habitat-specific clustering suggests that the clustered 16S rDNA sequences represent species or groups of species that are indigenous to freshwater. We have discerned 34 phylogenetic clusters of closely related sequences that are either restricted to freshwater or dominated by fresh- water sequences. Of these clusters, 23 contained no cultivated organisms. These putative freshwater clusters were found among the alpha-, beta- and gamma-Proteobacteria, the Cytophaga-Flavobac- terium-Bacteroides group, the Cyanobacteria, the Actinobacteria, the Verrucomicrobia, the green non-sulfur bacteria and candidate division OP10. This study shows that rivers and lakes have a specific planktonic bacterial community distinct from bacteria in neighboring environments such as soil and sediments. It also points out that these planktonic bacteria are distributed in diverse fresh- water ecosystems around the world.
Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer

Background Studies on gut microbiota regarding colorectal carcinogenesis, including sessile serrated adenoma (SSA), have been scarce. The aim of this study is to investigate the role of mucosa-associated gut microbiota in the colorectal carcinogenesis. Methods We collected biopsy samples of normal rectal mucosa during colonoscopy from healthy control and patients with conventional adenoma, SSA, and colorectal cancer (CRC), respectively (n = 6). Pyrosequencing for 16S rRNA gene of bacteria was performed to compare gut microbiota. Results The most abundant phylum in total samples was Proteobacteria (55.6%), followed by Firmicutes (27.4%) and Bacteroidetes (11.6%). There was no significant difference in relative abundance of the phylum level among the four groups. Fusobacterium nucleatum, known to be frequently detected during colorectal carcinogenesis, was found in only one sample of patient with SSA. The rarefaction curves showed that the diversity of mucosal communities of patients with CRC is the lowest among the four groups and the diversity of mucosal communities of patients with SSA is higher than that of healthy control. Among the four groups, Shannon’s and Simpson’s index for diversity was the lowest and the highest in the patients with CRC, respectively; it did not reach statistical significance. The proportion of genus Pseudomonas was very high in the samples of patients with stage II–IV CRC compared with those with stage I CRC (59.3% vs. 0.3%, P = 0.064). Conclusions Our study suggests no significant role of mucosa-associated gut microbiota in the colorectal carcinogenesis. Further study for many samples or using fecal material could be helpful.
Forecasting Significant Societal Events Using The Embers Streaming Predictive Analytics System

Developed under the Intelligence Advanced Research Project Activity Open Source Indicators program, Early Model Based Event Recognition using Surrogates (EMBERS) is a large-scale big data analytics system for forecasting significant societal events, such as civil unrest events on the basis of continuous, automated analysis of large volumes of publicly available data. It has been operational since November 2012 and delivers approximately 50 predictions each day for countries of Latin America. EMBERS is built on a streaming, scalable, loosely coupled, shared-nothing architecture using ZeroMQ as its messaging backbone and JSON as its wire data format. It is deployed on Amazon Web Services using an entirely automated deployment process. We describe the architecture of the system, some of the design tradeoffs encountered during development, and specifics of the machine learning models underlying EMBERS. We also present a detailed prospective evaluation of EMBERS in forecasting significant societal events in the past 2 years.
Whose Reality Counts?: Putting the First Last

Abbreviations and Addresses Glossary of Meanings Preface Acknowledgements 1 The Challenge to Change 2 Normal Error 3 Professional Realities 4 The Transfer of Reality 5 All Power Deceives 6 Learning to Learn 7 What Works and Why 8 Poor People's Realities: Local, Complex, Diverse, Dynamic and Unpredictable 9 The New High Ground 10 Putting the First Last Postscript: Past and Future PRA Contacts and Sources Notes References Index
Serum cystatin C levels to predict serum concentration of digoxin in Japanese patients

Cystatin C (Cys-C) has been recently paid great attention as a better endogenous marker of the glomerular filtration rate than creatinine (Cr). In this study, the usefulness of Cys-C was compared with Cr in terms of the estimation of the steady-state serum trough concentrations of digoxin in Japanese patients. Forty patients treated with digoxin and 56 healthy elderly subjects were participated in this study. The serum levels of Cys-C and Cr in the patients were higher than those in the healthy elderly subjects, but the increase of Cys-C was more predominant in the patients. Their levels were well-correlated for both of the healthy elderly subjects (r=0.691) and patients (r=0.774), but the serum concentrations of digoxin were better correlated with those of the reciprocal values of Cr (r=0.667) than those of Cys-C (r=0.383), presumably due to the fact that digoxin and Cr were excreted via both glomerular filtration and tubular secretion. Cys-C is useful for the substratification of the patients diagnosed to have normal renal function with Cr of < 1.3 mg/dL into those with normal and pseudo-normal renal function, resulting in the corresponding serum concentrations of digoxin.
Functional Modifications of Acid-Sensing Ion Channels by Ligand-Gated Chloride Channels

Together, acid-sensing ion channels (ASICs) and epithelial sodium channels (ENaC) constitute the majority of voltage-independent sodium channels in mammals. ENaC is regulated by a chloride channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Here we show that ASICs were reversibly inhibited by activation of GABAA receptors in murine hippocampal neurons. This inhibition of ASICs required opening of the chloride channels but occurred with both outward and inward GABAA receptor-mediated currents. Moreover, activation of the GABAA receptors modified the pharmacological features and kinetic properties of the ASIC currents, including the time course of activation, desensitization and deactivation. Modification of ASICs by open GABAA receptors was also observed in both nucleated patches and outside-out patches excised from hippocampal neurons. Interestingly, ASICs and GABAA receptors interacted to regulate synaptic plasticity in CA1 hippocampal slices. The activation of glycine receptors, which are similar to GABAA receptors, also modified ASICs in spinal neurons. We conclude that GABAA receptors and glycine receptors modify ASICs in neurons through mechanisms that require the opening of chloride channels.
Serum biochemical parameters in the ring-necked pheasant (Phasianus colchicus) on breeding season

5 Abstract: The influence of sex on serum biochemical parameters was investigated in adult (52 week-old) ring-necked pheasants on reproductive activity. Statistical comparisons were made for differences in values between male and female birds. Adult females had higher values for serum total protein and albumin. Significant variations were not observed in the analyses in relation to the sex of the birds for urea, uric acid, ratio urea/uric acid and globulins. This study also aimed to determine serum biochemical values for adult ring-necked pheasants.
Early and late markers for the detection of early-onset neonatal sepsis.

INTRODUCTION In this study we tested how a combination of early and late paraclinic markers could predict early onset neonatal sepsis (EONS). METHODOLOGY The first 24 hours after the suspicion of EONS, we measured interleukine (IL)-6, IL-8, IL-10, IL-18, tumor necrosis factor-alpha (TNF-alpha), interferon gamma (INF-gamma), procalcitonin (PCT) and C-reactive protein (CRP) at 8-hour intervals on 123 neonates clinically suspected for EONS. The neonates were divided into two groups. The sepsis group: 1A with blood culture verified bacteraemia and 1B strongly suspected sepsis (29 patients). The no sepsis group: 2A treated with antibiotics (37 patients) and 2B not treated with antibiotics (57 patients). RESULTS Combined evaluation of each of the early markers with PCT > 25 ng/ml for prediction of EONS at time 0, gave the following sensitivities and specificities: IL-6 > 250 pg/ml: 71% and 88%; IL-8 > 900 pg/ml: 50% and 88%; IL-10 > 40 pg/ml: 43% and 87%; and immature/total (I/T) ratio > 0.35: 59% and 88%. The results of IL-18, TNF-alpha and IFN-gamma did not predict EONS. CONCLUSION IL-6 combined with PCT values is a fair way to evaluate EONS at the time of suspicion of infection. The "old" early marker, I/T ratio, is almost as efficient as IL-6. By combining an early and a late marker it may be possible to reduce the diagnostic "non-conclusive" period of paraclinic values.
A narrow-domain entity recognition method based on domain relevance measurement and context information

Entity recognition is the basis of text mining. With the further development of knowledge-driven applications, types of target entities are increasingly subdivided. The lack of corpus and the limited number of entity have been the main challenges of entity recognition. Based on this observation, this paper proposes a weak-supervision method for recognizing entities from a specifically narrow domain by fusing domain relevance measurement and context information. The experimental result shows that the proposed method has high efficiency and accuracy without manual participation.
Posterior Tracheopexy for Severe Tracheomalacia Associated with Esophageal Atresia (EA): Primary Treatment at the Time of Initial EA Repair versus Secondary Treatment

Purpose We review outcomes of posterior tracheopexy for tracheomalacia in esophageal atresia (EA) patients, comparing primary treatment at the time of initial EA repair versus secondary treatment. Methods All EA patients who underwent posterior tracheopexy from October 2012 to September 2016 were retrospectively reviewed. Clinical symptoms, tracheomalacia scores, and persistent airway intrusion were collected. Indication for posterior tracheopexy was the presence of clinical symptoms, in combination with severe tracheomalacia as identified on bronchoscopic evaluation, typically defined as coaptation in one or more regions of the trachea. Secondary cases were usually those with chronic respiratory symptoms who underwent bronchoscopic evaluation, whereas primary cases were those found to have severe tracheomalacia on routine preoperative dynamic tracheobronchoscopy at the time of initial EA repair. Results A total of 118 patients underwent posterior tracheopexy: 18 (15%) primary versus 100 (85%) secondary cases. Median (interquartile range) age was 2 months (1–4 months) for primary (22% type C) and 18 months (8–40 months) for secondary (87% type C) cases (p < 0.001). There were statistically significant improvements in most clinical symptoms postoperatively for primary and secondary cases, with no significant differences in any postoperative symptoms between the two groups (p > 0.1). Total tracheomalacia scores improved significantly in primary (p = 0.013) and secondary (p < 0.001) cases. Multivariable Cox regression analysis indicated no differences in persistent airway intrusion requiring reoperation between primary and secondary tracheopexy adjusting for imbalances in age and EA type (p = 0.67). Conclusion Posterior tracheopexy is effective in treating severe tracheomalacia with significant improvements in clinical symptoms and degree of airway collapse on bronchoscopy. With no significant differences in outcomes between primary and secondary treatment, posterior tracheopexy should be selectively considered at the time of initial EA repair.
Population-based incremental learning with memory scheme for changing environments

In recent years there has been a growing interest in studying evolutionary algorithms for dynamic optimization problems due to its importance in real world applications. Several approaches have been developed, such as the memory scheme. This paper investigates the application of the memory scheme for population-based incremental learning (PBIL) algorithms, a class of evolutionary algorithms, for dynamic optimization problems. A PBIL-specific memory scheme is proposed to improve its adaptability in dynamic environments. In this memory scheme the working probability vector is stored together with the best sample it creates in the memory and is used to reactivate old environments when change occurs. Experimental study based on a series of dynamic environments shows the efficiency of the memory scheme for PBILs in dynamic environments. In this paper, the relationship between the memory scheme and the multi-population scheme for PBILs in dynamic environments is also investigated. The experimental results indicate a negative interaction of the multi-population scheme on the memory scheme for PBILs in the dynamic test environments.
CantorSim: Simplifying Acceleration of Micro-architecture Simulations

Many techniques have been developed to accelerate micro-architecture simulation since it is becoming increasingly urgent as the complexity of workloads and simulated processors increases. However, most of popular techniques need profiles or trial simulations to determine parameters before real simulations. When the number of dynamic instructions of workloads such as SPEC CPU2006 is huge, the profiles or trial simulations often take a long time. What’s worse, any changes of benchmarks need to repeat the above work. This paper proposes a novel approach based on fractals to solve this problem. It employs the generation procedure of trisection Cantor Set, a classic fractal, to select instructions simulated in detail. We implement a simulator named CantorSim using the trisection Cantor fractal approach. The simulator is evaluated with benchmark programs from SPEC CPU2000 and SPEC CPU2006. We show that our approach is micro-architecture independent as the same parameter value for a single program yields similar results on processors with different configurations. The unified analytical model used to determine sampling parameters for different benchmarks indicates the proposed approach can save a lot of time for preparing parameters. On the other hand, for SPEC CPU2000 and SPEC CPU2006, CantorSim is slightly faster than SMARTSim. The validated average CPI relative errors of the SPEC CPU2000 and SPEC CPU2006 are 3.2% and 2.2% respectively. Therefore, our proposed approach can simplify acceleration of simulations significantly without sacrificing speed and accuracy. Keywords-Microarchitecture simulation; Cantor Set; Performance Evaluation
An Accurate Calculation of the Big Bang Prediction for the Abundance of Primordial Helium

Within the standard models of particle physics and cosmology we have calculated the big-bang prediction for the primordial abundance of {sup 4}He to a theoretical uncertainty of less than 0.1{percent} ({delta}Y{sub P}{lt}{plus_minus}0.0002), improving the current theoretical precision by a factor of 10. At this accuracy the uncertainty in the abundance is dominated by the experimental uncertainty in the neutron mean lifetime, {tau}{sub n}=885.4{plus_minus}2.0 sec. The following physical effects were included in the calculation: the zero and finite-temperature radiative, Coulomb and finite-nucleon-mass corrections to the weak rates; order-{alpha} quantum-electrodynamic correction to the plasma density, electron mass, and neutrino temperature; and incomplete neutrino decoupling. New results for the finite-temperature radiative correction and the QED plasma correction were used. In addition, we wrote a new and independent nucleosynthesis code designed to control numerical errors to be less than 0.1{percent}. Our predictions for the {sup 4}He abundance are presented in the form of an accurate fitting formula. Summarizing our work in one number, Y{sub P}({eta}=5{times}10{sup {minus}10})=0.2462{plus_minus}0.0004 (expt)thinsp{plus_minus}{lt}0.0002 (theory). Further, the baryon density inferred from the Burles-Tytler determination of the primordial D abundance, {Omega}{sub B}h{sup 2}=0.019{plus_minus}0.001, leads to the prediction Y{sub P}=0.2464{plus_minus}0.0005 (D/H)thinsp{plus_minus}{lt}0.0002 (theory)thinsp{plus_minus}0.0005 (expt). This {open_quotes}prediction{close_quotes} and an accurate measurement of the primeval {supmore » 4}He abundance will allow an important consistency test of primordial nucleosynthesis. {copyright} {ital 1999} {ital The American Physical Society}« less
Measuring creative performance of teams through dynamic semantic social network analysis

In this project we compare communication structure and content exchanged by members of creative, interdisciplinary teams of medical researchers, physicians, patients and caretakers with their creative output. We find that longitudinal social networking patterns and word usage predict creative performance. We collected the e-mail archives of 60 members of a community of researchers working on 12 projects improving various aspects of the daily lives of patients with Crohn’s disease. Our results indicate that more creative projects show a decrease in group density, while more actors are involved, and more e-mails are exchanged, suggesting that a more successful project attracts more attention from many different people. We also found that members of more creative projects use more outspoken language, which gets more focused over time.
Mining Aspects and Opinions from Microblog Events

Microblogging platforms have experienced great growth during the last few years. Opinions are valuable for many applications. Most researches concentrate on classifying microblog posts into different polarities, which cannot provide concise opinion information. This paper presents an opinion mining system that extracts aspect related opinions for some specific event from Microblogs. Our approach first extracts aspect words, then cluster them as aspects of the opinions. Opinions are extracted by a CRF model that trained from automatically labeled data. Experimental results verify the effectiveness of the proposed system.
On Intra-page and Inter-page Semantic Analysis of Web Pages

To make real Web information more machine processable, this paper presents a new approach to intra-page and inter-page semantic analysis of Web pages. Our approach consists of Web pages structure analysis and semantic clustering for intra-page semantic analysis, and machine learning based link semantic analysis for inter-page analysis. Based on the automatic repetitive patterns discovery in structure level and clustering in semantic level, we explore the intra-page semantic structure of Web pages and extend the processing unit from the whole page to a finer granularity, i.e., semantic information blocks within pages. After observing the various hyperlinks, we synthesize the Web inter-page semantic and define an information organizing oriented hyperlink semantic category. Considering the presentation of the hyperlink carrier and intra-page semantic structure, we propose corresponding feature selection and quantification methods, and then exploit the C4.5 decision-tree method to classify hyperlink semantic type and analyze the inter-page semantic structure. In our experiments, the results suggest that our approch is feasible for machine processing.
Introduction: Extending the conversation: Transdisciplinary approaches to social identity and intergroup attitudes in children and adolescents

Ali, then 14, and his younger brother fled Afghanistan after their parents were arrested and killed by the Taliban. They found refuge with a friend in Iran, but the anti-Afghan prejudice they encountered made them embark on their journey to the UK at the hands of people-smugglers. (The Guardian, London, 15th June 2007).
Introduction to the Volume on Psychological Testing in Child Custody Evaluations

This volume addresses the subject of testing. The articles can be divided into three sections. The first section concerns theoretical and test usage issues. The first article, by Flens, is devoted to test selection from both legal and psychological perspectives. An article by Martindale explores the possibility of bias that may interfere with the evaluator’s ability to obtain data objectively. He is followed by Gould, who describes
Young People and their Contribution to Household Work

This article considers the theoretical and empirical neglect of children's contribution to household work. It draws upon a two-stage study of the transfer of responsibility from parents to their sixteen year-olds: a questionnaire survey of 843 young people and an interview study of parents and young people in 64 households. It considers the frequency and nature of young people's contribution to housework and changes taking place between the questionnaire and the interview studies, and makes the distinction between family-care and self-care. Drawing on the interview accounts, it examines parents' general expectations of young people in respect of housework and, more specifically, the ways these negotiations work out in practice with respect to a number of criteria - gender, cultural values, age and birth order, mothers' employment and young people's employment and education. These factors were also found to structure the survey data.
On the Edge or In Between: Niche Position, Niche Overlap, and the Duration of Voluntary Association Memberships

This paper aims to explain a major barrier to societal integration: the remarkable homogeneity of voluntary associations. The explanation derives from an ecological theory of voluntary affiliation that asserts that organizations compete for members in a property space defined by the sociodemographic characteristics of members. Voluntary organizations lose fastest those members who are either atypical of the group (the niche edge hypothesis) or subject to competition from other groups (the niche overlap hypotheis). The authors analyze an event-history data set, generated by the life-history calendar approach, of 2,813 voluntary association membership pells. The results, which strongly support both the niche edge and niche overlap hypotheses, substantiate the competitive ecological model of group structure.
A method for determining B1 field inhomogeneity. Are the biases assumed in heteronuclear relaxation experiments usually underestimated?

We describe a method allowing the determination of the effective B1 field amplitude distribution in a high-resolution NMR spectrometer. This method which can be adapted to almost any sequence, essentially consists of a mutation followed by a purging B0 gradient pulse. Experimental results obtained with this approach are described in homonuclear and heteronuclear cases. The experimental distributions are used to estimate the biases induced by B1 inhomogeneity, as well as the loss of RF power on heteronuclear transverse self-relaxation rate determination. In this type of measurement, the experimental biases induced on the intensities can be as large as 5% for long mixing times.