Miracle-dz/UniFAR-FTUs huggingface dataset:
Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation

Characterizing the community structure of naturally occurring microbes through marker gene amplicons has gained widespread acceptance for profiling microbial populations. The 16S ribosomal RNA (rRNA) gene provides a suitable target for most studies since (1) it meets the criteria for robust markers of evolution, e.g., both conserved and rapidly evolving regions that do not undergo horizontal gene transfer, (2) microbial ecologists have identified widely adopted primers and protocols for generating amplicons for sequencing, (3) analyses of both cultivars and environmental DNA have generated well-curated databases for taxonomic profiling, and (4) bioinformaticians and computational biologists have published comprehensive software tools for interpreting the data and generating publication-ready figures. Since the initial descriptions of high-throughput sequencing of 16S rRNA gene amplicons to survey microbial diversity, we have witnessed an explosion of association-based inferences of interactions between microbes and their environment.
Environmental effects on species richness of macrophytes in Slovak streams

The effect of 19 environmental variables on species richness of macrophytes was studied in 39 Slovak streams. The studied streams were poor in species; in total, 88 macrophyte taxa were found and the average number of macrophytes per sampling site was 4, ranging from 0 to15. The most frequently occurring macrophytes were filamentous algae (occurrence at 38.6% of sampling sites), followed by Rhynchostegium riparioides (28.4%) and Phalaris arundinacea (19.3%). The strongest environmental gradient in the sampling site detected by factor analysis (factor 1 explains more than 32% variability) is related to the portion of artificial banks, shading by woody vegetation along banks, flexuosity of stream course and the portion of natural land cover in the contact zone of the stream, and can be interpreted as a natural-anthropogenic gradient. The following variables had the highest correlations with species richness of macrophytes: shading by woody vegetation (r=−0.507), portions of artificial bank (r=0.488), flexuosity (r=−0.457) and distance from stream source (r=0.388).
Giggle: A Framework for Constructing Scalable Replica Location Services

In wide area computing systems, it is often desirable to create remote read-only copies (replicas) of files. Replication can be used to reduce access latency, improve data locality, and/or increase robustness, scalability and performance for distributed applications. We define a replica location service (RLS) as a system that maintains and provides access to information about the physical locations of copies. An RLS typically functions as one component of a data grid architecture. This paper makes the following contributions. First, we characterize RLS requirements. Next, we describe a parameterized architectural framework, which we name Giggle (for GIGa-scale Global Location Engine), within which a wide range of RLSs can be defined. We define several concrete instantiations of this framework with different performance characteristics. Finally, we present initial performance results for an RLS prototype, demonstrating that RLS systems can be constructed that meet performance goals.
DIP: The Database of Interacting Proteins: 2001 update

The Database of Interacting Proteins (DIP; http://dip.doe-mbi.ucla. edu) is a database that documents experimentally determined protein-protein interactions. Since January 2000 the number of protein-protein interactions in DIP has nearly tripled to 3472 and the number of proteins to 2659. New interactive tools have been developed to aid in the visualization, navigation and study of networks of protein interactions.
Exploring regularities and self-similarity in Internet traffic

The characterization and quantitative description of Internet traffic is becoming increasingly important in light of the rapid growth being observed in the size and usage of the network. Modeling of modern teletraffic and large telecommunications networks with fractal stochastic processes has been investigated by analyzing traffic measurements collected on the “Federico II” university WAN link to the National Research Network backbone, and using them to test the existence of fractal behavior and specific properties. A fractal character with approximate selfsimilarity and statistical long-range dependence has been observed in the Internet access traffic measurements. This approach leads to some interesting insights about whether and how regularities in Internet user behavior can be noticed and exploited. The derived characterization could be seen as a first step to a generalized parametric Internet traffic model. Key-Words: Internet traffic modeling, self-similarity, long-range dependency
The research of the entity relation extraction based on statistical model

Entity relation extraction is the important research field in many languages processing, such as the knowledge management, semantic network, information retrieval and information extraction. In this paper, some specific entity relations can be extracted in the football match domain, firstly, the definition of the five types relation had been defined. Based on the conditional random fields, aiming to each relation type, the different features were discussed. The approach is effective when evaluated on the data set.
Large-Scale Dynamic Controller Placement

The controller placement problem (CPP) is one of the key challenges of software defined networks (SDNs) to increase performance. Given the locations of <inline-formula> <tex-math notation="LaTeX">${n}$ </tex-math></inline-formula> switches, CPP consists of choosing the controller locations that minimize the latency between switches and SDN controllers. In its current form, however, CPP assumes a fixed traffic and no existing solutions adapt the placement to the load. In this paper, we have addressed the <italic>dynamic CPP</italic> that consists of: 1) determining the locations of controller modules to bound communication latencies and 2) determining the number of controllers per module to support the dynamic load. We propose an algorithm named <italic>LiDy+</italic> that runs in <inline-formula> <tex-math notation="LaTeX">${O(n^{2})}$ </tex-math></inline-formula> and combines a controller module placement algorithm with a dynamic flow management algorithm. We evaluate the number of controllers, the controller utilization, and the power consumption and the maintenance cost of <italic>LiDy+</italic> on both sparse and dense networks. Our comparison against a previous solution shows that <italic>LiDy+</italic> does not only achieve a smaller number of controllers and a higher controller utilization but also incurs less energy and maintenance costs than the previous solution. Finally, we run <italic>LiDy+</italic> in a large-scale environment where the previous solution of time complexity <inline-formula> <tex-math notation="LaTeX">$ {\Omega (n^{2} \log {n})}$ </tex-math></inline-formula> is impractical.
Arthritis patients show long-term benefits from 3 weeks intensive exercise training directly following hospital discharge.

OBJECTIVE To examine the efficacy of short-term intensive exercise training (IET) directly following hospital discharge. METHODS In the Disabled Arthritis Patients Post-hospitalization Intensive Exercise Rehabilitation (DAPPER) study, patients with rheumatoid arthritis or osteoarthritis were eligible when they needed hospitalization for either a flare-up in disease, elective hip or knee arthroplasty. The intervention group received IET for 3 weeks immediately after discharge; the control group was treated with the usual care (UC). The intensive exercise was provided in a resort. Outcomes were assessed at baseline, after 3, 13, 26 and 52 weeks. Range of motion was measured using the Escola Paulista de Medicina-Range of Motion scale (EPM-ROM), disability was measured using the HAQ and the McMaster Toronto Arthritis Patient Preference Disability Questionnaire (MACTAR), and for health-related quality of life (HRQoL), the Research and Development 36-Item Health Survey (RAND-36) was used. RESULTS The IET showed a better and faster improvement than UC on all outcome measures except for HRQoL. Up to 52 weeks after baseline, the EPM-ROM and the MACTAR remained favourable in IET compared with UC. At 3 weeks, the MACTAR improved significantly more in the IET compared with the UC: mean difference -5.5 (95% CI -8.4 to -2.2). At 26 weeks, the mean difference remained significant (-5.2; 95% CI -10.0 to -0.34). At 52 weeks, the effect was not significant; however, the mean difference in improvement between the groups can be considered clinically relevant. At 3 weeks, the IET had improved significantly more on the HAQ walking and rising subscales. CONCLUSION Intensive short-term exercise training of arthritis patients, immediately after hospital discharge results in improved regain of function. The DAPPER programme has a direct effect, which lasts up to 52 weeks.
Amyloid (cid:1) -Protein Oligomerization PRENUCLEATION INTERACTIONS REVEALED BY PHOTO-INDUCED CROSS-LINKING OF UNMODIFIED PROTEINS*

Assembly of the amyloid (cid:1) -protein (A (cid:1) ) into neurotoxic oligomers and fibrils is a seminal event in Alzheimer’s disease. Understanding the earliest phases of A (cid:1) assembly, including prenucleation and nucleation, is es-sential for the development of rational therapeutic strategies. We have applied a powerful new method, photoinduced cross-linking of unmodified proteins (PI-CUP), to the study of A (cid:1) oligomerization. Significant advantages of this method include an extremely short reaction time, enabling the identification and quantification of short lived metastable assemblies, and the fact that no pre facto structural modification of the native peptide is required. Using PICUP, the distribution of A (cid:1) oligomers existing prior to assembly was defined. A rapid equilibrium was observed involving monomer, dimer, trimer, and tetramer. A similar distribution was seen in studies of an unrelated amyloidogenic peptide, whereas nonamyloidogenic peptides yielded distributions indicative of a lack of monomer preassociation. These results suggest that simple nucleation-dependent polymerization models are insufficient to describe the dynamic equilibria associated with prenucleation phases of A (cid:1) assembly. fibrillogenesis inhibitor that stabilizes the native structure of the protein reveals that the majority of the reactive groups (such as Tyr and Trp) are either buried in the hydrophobic core of each monomer or at the “dimer interface” (53). This result is in agreement with the propensity of the protein to produce mainly “within dimer” or intramolecular cross-linking. This burial of reactive groups also accounts for the lack of oligomers higher than tetramers observed following cross-linking of native TTR. Nevertheless, these results demonstrate that PICUP is capable of distinguishing between monomeric and oligomeric states of the same protein, since the relative oligomer distributions obtained in each case were very distinct.
The Dynamic of Religious Life: A Study of Conflict and Integration of Ahmadiyah in Garut, Tasikmalaya and Kuningan, West Java

The conflict does not automatically lead to disintegration. Sociologist like Georg Simmel and Lewis Coser reinforce this assumption. Conflict can also function to strengthen social groups and restore social integration. Conflict and integration (harmony) like two sides of a coin, different but still one. This paper supports the assumption above. After the conflict between the community and Ahmadiyah’s followers in the three Regencies (Garut, Tasikmalaya and Kuningan), they live in harmony (integration). This fact in line with the argument of Georg Simmel and Lewis Coser. This study showed that the conflicts occurred in three regencies (Garut, Tasikmalaya and Kuningan), did not make the Ahmadiyah adherents disintegrated and crumbled. But on the contrary, Ahmadiyah followers increasingly integrated, solid and live co-exist with the non-Ahmadiyah community and live harmoniously.
A Pilot Study of Omalizumab in Eosinophilic Esophagitis

Eosinophilic disorders of the gastrointestinal tract are an emerging subset of immune pathologies within the spectrum of allergic inflammation. Eosinophilic Esophagitis (EoE), once considered a rare disease, is increasing in incidence, with a rate of over 1 in 10,000 in the US, for unknown reasons. The clinical management of EoE is challenging, thus there is an urgent need for understanding the etiology and pathophysiology of this eosinophilic disease to develop better therapeutic approaches. In this open label, single arm, unblinded study, we evaluated the effects of an anti-IgE treatment, omalizumab, on local inflammation in the esophagus and clinical correlates in patients with EoE. Omalizumab was administered for 12 weeks to 15 subjects with long standing EoE. There were no serious side effects from the treatment. Esophageal tissue inflammation was assessed both before and after therapy. After 3 months on omalizumab, although tissue Immunoglobulin E (IgE) levels were significantly reduced in all but two of the subjects, we found that full remission of EoE, which is defined as histologic and clinical improvement only in 33% of the patients. The decrease in tryptase-positive cells and eosinophils correlated significantly with the clinical outcome as measured by improvement in endoscopy and symptom scores, respectively. Omalizumab-induced remission of EoE was limited to subjects with low peripheral blood absolute eosinophil counts. These findings demonstrate that in a subset of EoE patients, IgE plays a role in the pathophysiology of the disease and that anti-IgE therapy with omalizumab may result in disease remission. Since this study is open label there is the potential for bias, hence the need for a larger double blind placebo controlled study. The data presented in this pilot study provides a foundation for proper patient selection to maximize clinical efficacy. Trial Registration ClinicalTrials.gov NCT01040598
Revisiting the 1976 "swine flu" vaccine clinical trials: cross-reactive hemagglutinin and neuraminidase antibodies and their role in protection against the 2009 H1N1 pandemic virus in mice.

BACKGROUND The 2009 H1N1 pandemic viruses are genetically similar to A/New Jersey/76 H1N1 virus (NJ/76), the strain selected for the 1976 "swine flu" vaccines. Approximately 45 million people in the United States were vaccinated against NJ/76 30 years ago, but the impact of this nationwide immunization on the current pandemic is largely unknown. METHODS Archived human serum samples collected during the 1976 swine flu vaccine trials were assessed for cross-reactive antibody responses to the 2009 H1N1 pandemic viruses. RESULTS Administration of an NJ/76 monovalent vaccine or the combination of a bivalent vaccine (NJ/76 H1N1 and A/Victoria/75 H3N2) plus a B/Hong Kong/72 monovalent vaccine increased hemagglutinin inhibition (HAI) and neuraminidase inhibition (NAI) antibodies cross-reacting with the 2009 H1N1 pandemic viruses. We showed that cross-reactive human HAI antibodies elicited by the 1976 swine flu vaccination played a dominant role in protecting recipient mice against the wild-type A/California/04/2009. Cross-reactive human NAI antibodies were also protective in recipient mice after a lethal challenge with a hemagglutinin mismatched virus bearing the A/California/04/2009 neuraminidase gene. Transfer of human serum samples with an original HAI titer of 43 or an original NAI titer of 472 was estimated to protect 50% of recipient mice from a lethal infection under the experimental conditions described. CONCLUSIONS The 1976 swine flu vaccination induced cross-reactive HAI and NAI antibodies that were functionally protective in mice, suggesting that this vaccination campaign might have had a positive impact on older adults (≥50 years) in the United States during the 2009 H1N1 pandemic.
Unequal Error Protection of Multiple Programs Based on Length-Variable Transport Stream Packets

Unequal Error Protection (UEP), which provides important data with more protection, has been proven to be able to produce better quality in image communication. Previous UEP schemes are mostly proposed for single-image or single-program scenarios. Yet few are developed for multiple programs. Inspired by the MPEG-2 Transport Stream (TS), in this paper we transform the conventional TS packets to be length-variable, and propose a new UEP scheme, which is suitable for multiple-program scenarios. A theoretical model for this scheme is built in this paper, and experimental results also demonstrate the effectiveness of the scheme.
English-Chinese Bi-Directional OOV Translation based on Web Mining and Supervised Learning

In Cross-Language Information Retrieval (CLIR), Out-of-Vocabulary (OOV) detection and translation pair relevance evaluation still remain as key problems. In this paper, an English-Chinese Bi-Directional OOV translation model is presented, which utilizes Web mining as the corpus source to collect translation pairs and combines supervised learning to evaluate their association degree. The experimental results show that the proposed model can successfully filter the most possible translation candidate with the lower computational cost, and improve the OOV translation ranking effect, especially for popular new words.
Non-L\'evy mobility patterns of Mexican Me'Phaa peasants searching for fuelwood

We measured mobility patterns that describe walking trajectories of individual Me'Phaa peasants searching and collecting fuelwood in the forests of "La Monta\~na de Guerrero" in Mexico. These one-day excursions typically follow a mixed pattern of nearly-constant steps when individuals displace from their homes towards potential collecting sites and a mixed pattern of steps of different lengths when actually searching for fallen wood in the forest. Displacements in the searching phase seem not to be compatible with L\'evy flights described by power-laws with optimal scaling exponents. These findings however can be interpreted in the light of deterministic searching on heavily degraded landscapes where the interaction of the individuals with their scarce environment produces alternative searching strategies than the expected L\'evy flights. These results have important implications for future management and restoration of degraded forests and the improvement of the ecological services they may provide to their inhabitants.
Application of naïve Bayes classifier in fall detection systems based on infrared depth sensors

A novel solution of the fall detection problem, based on the use of infrared depth sensors, is proposed. A methodology for acquisition of real-world data and their preprocessing is presented. The procedures for feature generation, preprocessing and selection are described. The naïve Bayes classifier is designed for the selected features and its performance is evaluated using a data set consisting of 144 sequences representative of 72 falls and 72 other human activities.
The Determinants of TFP Growth in Middle Income Economies in ASEAN: Implication of Financial Crises

Maintaining a sustained level of productivity growth is an important aspect of the economic development process, particularly in periods of economic turbulence. This paper examines the determinants of total factor productivity (TFP) growth and their behavior in five middle-income ASEAN countries during events such as the Asian Contagion and the Global Financial Crisis. In particular, this paper examines the effects on TFP of foreign direct investment (FDI), trade, the agricultural sector, government spending, human capital, and dummy variables representing the financial crises. The results show that trade, government spending, the scale of the agricultural sector, and the dummy variables have significantly influenced productivity growth. Government spending affects it positively, and the scale of the agricultural sector and the dummy variables representing the Asian Contagion influence it negatively. These empirical findings support the popular belief that trade significantly influences TFP growth, but the trend is not consistent with expectations. Despite strongly supportive theoretical arguments, this study does not find the human capital and FDI variables to be significant. Notably, there is no evidence to suggest that the Global Financial Crisis has had a significant influence when compared with the Asian Contagion.
Modulation of Caspase Activity Regulates Skeletal Muscle Regeneration and Function in Response to Vasopressin and Tumor Necrosis Factor

Muscle homeostasis involves de novo myogenesis, as observed in conditions of acute or chronic muscle damage. Tumor Necrosis Factor (TNF) triggers skeletal muscle wasting in several pathological conditions and inhibits muscle regeneration. We show that intramuscular treatment with the myogenic factor Arg8-vasopressin (AVP) enhanced skeletal muscle regeneration and rescued the inhibitory effects of TNF on muscle regeneration. The functional analysis of regenerating muscle performance following TNF or AVP treatments revealed that these factors exerted opposite effects on muscle function. Principal component analysis showed that TNF and AVP mainly affect muscle tetanic force and fatigue. Importantly, AVP counteracted the effects of TNF on muscle function when delivered in combination with the latter. Muscle regeneration is, at least in part, regulated by caspase activation, and AVP abrogated TNF-dependent caspase activation. The contrasting effects of AVP and TNF in vivo are recapitulated in myogenic cell cultures, which express both PW1, a caspase activator, and Hsp70, a caspase inhibitor. We identified PW1 as a potential Hsp70 partner by screening for proteins interacting with PW1. Hsp70 and PW1 co-immunoprecipitated and co-localized in muscle cells. In vivo Hsp70 protein level was upregulated by AVP, and Hsp70 overexpression counteracted the TNF block of muscle regeneration. Our results show that AVP counteracts the effects of TNF through cross-talk at the Hsp70 level. Therefore, muscle regeneration, both in the absence and in the presence of cytokines may be enhanced by increasing Hsp70 expression.
Application of Solution NMR Spectroscopy to Study Protein Dynamics

Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR) spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.
Multiple teams for mobile robot formation control

Formation control is one research topic among multirobot research issues. Among these formation research topics, they generally control multiple robots in only one team, and little research focuses on multi-team formation control. We use the VOMAS architecture to organize multiple teams in formation control, and the architecture has the advantages of scalability, autonomy, etc. We implement several formations in simulation, such as line, column, wedge, and platoon. We also implement a rescue mission to show the capability of multi-team control.