Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of In Vitro Activity of Essential Oils against Trypanosoma brucei brucei and Trypanosoma evansi

Essential oils (EOs) from Cymbopogon citratus (CC), Eucalyptus citriodora (EC), Eucalyptus camaldulensis (ED), and Citrus sinensis (CS) were obtained by hydrodistillation process. The EOs were evaluated in vitro for activity against Trypanosoma brucei brucei (Tbb) and Trypanosoma evansi (T. evansi). The EOs were found to possess antitrypanosomal activity in vitro in a dose-dependent pattern in a short period of time. The drop in number of parasite over time was achieved doses of 0.4 g/ml, 0.2 g/mL, and 0.1 g/mL for all the EOs. The concentration of 0.4 g/mL CC was more potent at 3 minutes and 2 minutes for Tbb and T. evansi, respectively. The GC-MS analysis of the EOs revealed presence of Cyclobutane (96.09%) in CS, 6-octenal (77.11%) in EC, Eucalyptol (75%) in ED, and Citral (38.32%) in CC among several other organic compounds. The results are discussed in relation to trypanosome chemotherapy.
Metabolic Profiling and Antioxidant Assay of Metabolites from Three Radish Cultivars (Raphanus sativus)

A total of 13 anthocyanins and 33 metabolites; including organic acids, phenolic acids, amino acids, organic compounds, sugar acids, sugar alcohols, and sugars, were profiled in three radish cultivars by using high-performance liquid chromatography (HPLC) and gas chromatography time-of-flight mass spectrometry (GC-TOFMS)-based metabolite profiling. Total phenolics and flavonoids and their in vitro antioxidant activities were assessed. Pelargonidins were found to be the major anthocyanin in the cultivars studied. The cultivar Man Tang Hong showed the highest level of anthocyanins (1.89 ± 0.07 mg/g), phenolics (0.0664 ± 0.0033 mg/g) and flavonoids (0.0096 ± 0.0004 mg/g). Here; the variation of secondary metabolites in the radishes is described, as well as their association with primary metabolites. The low-molecular-weight hydrophilic metabolite profiles were subjected to principal component analysis (PCA), hierarchical clustering analysis (HCA), Pearson’s correlation analysis. PCA fully distinguished the three radish cultivars tested. The polar metabolites were strongly correlated between metabolites that participate in the TCA cycle. The chemometrics results revealed that TCA cycle intermediates and free phenolic acids as well as anthocyanins were higher in the cultivar Man Tang Hong than in the others. Furthermore; superoxide radical scavenging activities and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging were investigated to elucidate the antioxidant activity of secondary metabolites in the cultivars. Man Tang Hong showed the highest superoxide radical scavenging activity (68.87%) at 1000 μg/mL, and DPPH activity (20.78%), followed by Seo Ho and then Hong Feng No. 1. The results demonstrate that GC-TOFMS-based metabolite profiling, integrated with chemometrics, is an applicable method for distinguishing phenotypic variation and determining biochemical reactions connecting primary and secondary metabolism. Therefore; this study might provide information on the relationship between primary and secondary metabolites and a synergistic antioxidant ability derived from the secondary metabolites in the radish cultivars.
Incrementally optimized decision tree for noisy big data

How to extract meaningful information from big data has been a popular open problem. Decision tree, which has a high degree of knowledge interpretation, has been favored in many real world applications. However noisy values commonly exist in high-speed data streams, e.g. real-time online data feeds that are prone to interference. When processing big data, it is hard to implement pre-processing and sampling in full batches. To solve this tradeoff, this paper proposes a new incremental decision tree algorithm so called incrementally optimized very fast decision tree (iOVFDT). The experiment evaluates the proposed algorithm in comparison to existing methods under noisy data streams environment. Result shows iOVFDT has outperformance on the aspects of higher accuracy and smaller model size.
New algorithms for efficient parallel string comparison

In this paper, we show new parallel algorithms for a set of classical string comparison problems: computation of string alignments, longest common subsequences (LCS) or edit distances, and longest increasing subsequence computation. These problems have a wide range of applications, in particular in computational biology and signal processing. We discuss the scalability of our new parallel algorithms in computation time, in memory, and in communication. Our new algorithms are based on an efficient parallel method for (min,+)-multiplication of distance matrices. The core result of this paper is a scalable parallel algorithm for multiplying implicit simple unit-Monge matrices of size <i>n</i> x <i>n</i> on <i>p</i> processors using time <i>O</i>( <i>n</i> log <i>n</i> ‾ <i>p</i>). communication <i>O</i>(<i>n</i> log <i>p</i>) ‾ <i>p</i>) and <i>O</i>(log <i>p</i>) supersteps. This algorithm allows us to implement scalable LCS computation for two strings of length <i>n</i> using time <i>O</i>(<i>n</i><sup>2</sup> ‾ <i>p</i>) and communication <i>O</i>(<i>n</i> ‾ √ <i>p</i>), requiring local memory of size <i>O</i>(<i>n</i> ‾ √ <i>p</i>) on each processor. Furthermore, our algorithm can be used to obtain the first generally work-scalable algorithm for computing the longest increasing subsequence (LIS). Our algorithm for LIS computation requires computation <i>O</i>(<i>n</i> log<sup>2</sup> <i>n</i> ‾ <i>p</i>), communication <i>O</i>(<i>n</i> log <i>p</i>)/ <i>p</i>), and <i>O</i>(log<sup>2</sup> <i>p</i>) supersteps for computing the LIS of a sequence of length <i>n</i>. This is within a log n factor of work-optimality for the LIS problem, which can be solved sequentially in time O(<i>n</i> log <i>n</i>) in the comparison-based model. Our LIS algorithm is also within a log <i>p</i>-factor of achieving perfectly scalable communication and furthermore has perfectly scalable memory size requirements of <i>O</i>(<i>n</i> ‾ <i>p</i>) per processor.
RhoA Regulates Peroxisome Association to Microtubules and the Actin Cytoskeleton

The current view of peroxisome inheritance provides for the formation of new peroxisomes by both budding from the endoplasmic reticulum and autonomous division. Here we investigate peroxisome-cytoskeleton interactions and show by proteomics, biochemical and immunofluorescence analyses that actin, non-muscle myosin IIA (NMM IIA), RhoA, Rho kinase II (ROCKII) and Rab8 associate with peroxisomes. Our data provide evidence that (i) RhoA in its inactive state, maintained for example by C. botulinum toxin exoenzyme C3, dissociates from peroxisomes enabling microtubule-based peroxisomal movements and (ii) dominant-active RhoA targets to peroxisomes, uncouples the organelles from microtubules and favors Rho kinase recruitment to peroxisomes. We suggest that ROCKII activates NMM IIA mediating local peroxisomal constrictions. Although our understanding of peroxisome-cytoskeleton interactions is still incomplete, a picture is emerging demonstrating alternate RhoA-dependent association of peroxisomes to the microtubular and actin cytoskeleton. Whereas association of peroxisomes to microtubules clearly serves bidirectional, long-range saltatory movements, peroxisome-acto-myosin interactions may support biogenetic functions balancing peroxisome size, shape, number, and clustering.
Nowhere‐Zero 5‐Flows On Cubic Graphs with Oddness 4

Tutte's 5‐flow conjecture from 1954 states that every bridgeless graph has a nowhere‐zero 5‐flow. It suffices to prove the conjecture for cyclically 6‐edge‐connected cubic graphs. We prove that every cyclically 6‐edge‐connected cubic graph with oddness at most 4 has a nowhere‐zero 5‐flow. This implies that every minimum counterexample to the 5‐flow conjecture has oddness at least 6.
The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation

The initiation of DNA replication is a key event in the cell cycle of all organisms. In bacteria, replication initiation occurs at specific origin sequences that are recognized and processed by an oligomeric complex of the initiator protein DnaA. We have determined the structure of the conserved core of the Aquifex aeolicus DnaA protein to 2.7 Å resolution. The protein comprises an AAA+ nucleotide‐binding fold linked through a long, helical connector to an all‐helical DNA‐binding domain. The structure serves as a template for understanding the physical consequences of a variety of DnaA mutations, and conserved motifs in the protein suggest how two critical aspects of origin processing, DNA binding and homo‐oligomerization, are mediated. The spatial arrangement of these motifs in DnaA is similar to that of the eukaryotic‐like archaeal replication initiation factor Cdc6/Orc1, demonstrating that mechanistic elements of origin processing may be conserved across bacterial, archaeal and eukaryotic domains of life.
Video based mobile location search with large set of SIFT points in cloud

In densely populated cities like Hong Kong, GPS alone is not sufficient in providing rich location based information services. In this work, we provide a mobile location search service by allowing users shooting a short video clip about the surrounding buildings and the Cloud will return a tagged image with a summary of the location and services available. The key technical challenges are the robustness of the SIFT based object matching in video sequences, and the computational complexity associated with the large scale of the repository. We solved this by spatio-temporal pruning of SIFT points in the video repository, and PCA projection and indexing of SIFT points in Cloud. Simulation results demonstrated the robustness of the PCAed and indexed SIFT points in building identification and overall effectiveness of the proposed solution on a small scale trial. Tagging and integration with large scale video repositories like YouTube, Tudou are underway with more interesting applications.
Changes in Inflammation and Immune Activation With Atazanavir-, Raltegravir-, Darunavir-Based Initial Antiviral Therapy: ACTG 5260s.

BACKGROUND It is unclear whether the integrase inhibitor raltegravir (RAL) reduces inflammation and immune activation compared with ritonavir-boosted protease inhibitors (PIs). METHODS In a prospective, randomized, multicenter clinical trial that included 328 human immunodeficiency type 1 (HIV-1)-infected, treatment-naive participants were randomized to receive tenofovir disoproxil fumarate-emtricitabine (TDF/FTC) plus atazanavir/ritonavir (ATV/r), darunavir/ritonavir (DRV/r), or RAL. A total of 234 participants (71%) with HIV-1 RNA levels <50 copies/mL by week 24 were included. Plasma biomarkers of inflammation and coagulation that were analysed included high-sensitivity C-reactive protein, interleukin-6 (IL-6), GlycA, D-dimer, soluble CD14 (sCD14), sCD163, and sIL-2r; blood cellular markers included %CD38+DR+ of T-cell subsets and %CD14+CD16+ and%CD14(dim)CD16+ monocyte subsets. Changes from baseline were examined at earlier (24 or 48 weeks) and later (96 weeks) time points, with 95% confidence intervals on fold-change. Pairwise treatment groups were compared using Wilcoxon rank sum tests, with P values adjusted for false discovery rate control. RESULTS Changes in biomarkers varied by regimen during the 96 weeks of follow-up as follows: hsCRP declined with ATV/r and RAL, IL-6 declined only with RAL, and GLycA decreased in all groups. D-dimer declined with ATV/r and DRV/r and was unchanged with RAL. Markers of T-cell activation and sCD163 (but not sCD14 and CD14-+CD16+) declined in all groups. CONCLUSIONS Despite some differences in specific markers of inflammation and immune activation between the antiretroviral therapy (ART) regimens, we found no consistent evidence that the reduction of inflammation and immune activation with ART initiation was different between RAL and PI-based regimens. CLINICAL TRIALS REGISTRATION NCT00811954 and NCT00851799.
Study on abrasive flow ultra-precision polishing technology of small hole

The self-designed Abrasive Flow Machine and Clamp are introduced in this paper. The technology issues of abrasive flow medium selection and process parameters settings are discussed. We conducted the experiment on the small hole with diameter of 0.15mm. Through the experiment, the best process parameters of the Abrasive Flow Machining of small hole are obtained.
Openness and economic performance in sub-Saharan Africa : evidence from time-series cross-country analysis

In a cross-country study for 1967-87, the author tests whether the finding that increased openness improves performance holds true for sub-Saharan Africa as a subgroup among developing countries. Econometric analysis - based on the augmented production function that includes labor, capital stock, and a measure of openness - shows that openness exerts a significant positive impact on economic performance of countries in sub-Saharan Africa. The relationship is especially strong in fixed-effect estimates that use annual panel data with country dummies to capture unobserved country-specific differences. The author finds the evidence of a positive link between openness and performance surprisingly robust to different measures of openness, to different periods, and to the inclusion of other policy variables. All four measures of openness, for example, are significant for 1967-87. For the shorter period, 1980-87, three are significant. Also, the size and significance of the openness coefficients do not change when one controls for macroeconomic policy.
Weight initialization methods for multilayer feedforward

In this paper, we present the results of an experimental comparison among seven different weight initialization methods in twelve different problems. The comparison is performed by measuring the speed of convergence, the generalization capability and the probability of successful convergence. It is not usual to find an evaluation of the three properties in the papers on weight initialization. The training algorithm was Backpropagation (BP) with a hyperbolic tangent transfer function. We found that the performance can be improved with respect to the usual initialization scheme.
Correlated optical/X-ray variability in the high-mass X-ray binary SAX J2103.5+4545

SAX J2103.5+4545 is the Be/X-ray binary (BeX) with the shortest orbital period. It shows extended bright and faint X-ray states that last for a few hundred days. The main objective of this work is to investigate the relationship between the X-ray and optical variability and to characterize the spectral and timing properties of the bright and faint states. We have found a correlation between the spectral and temporal parameters that fit the energy and power spectra. Softer energy spectra correspond to softer power spectra. That is to say, when the energy spectrum is soft, the power at high frequencies is suppressed. We also present the results of our monitoring of the Hα line of the optical counterpart since its discovery in 2003. There is a correlation between the strength and shape of the Hα line, originated in the circumstellar envelope of the massive companion and the X-ray emission from the vicinity of the neutron star. Hα emission, indicative of an equatorial disc around the B-type star, is detected whenever the source is bright in X-rays. When the disc is absent, the X-ray emission decreases significantly. The long-term variability of SAX J2103.5+4545 is characterized by fast episodes of disc loss and subsequent reformation. The time-scales for the loss and reformation of the disc (about 2 yr) are the fastest among BeXs.
Molecular Sciences Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia Glutinosa

Rehmannia glutinosa, one of the most widely used herbal medicines in the Orient, is rich in biologically active iridoids. Despite their medicinal importance, no molecular information about the iridoid biosynthesis in this plant is presently available. To explore the transcriptome of R. glutinosa and investigate genes involved in iridoid biosynthesis, we used massively parallel pyrosequencing on the 454 GS FLX Titanium platform to generate a substantial EST dataset. Based on sequence similarity searches against the public sequence databases, the sequences were first annotated and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) based analysis. Bioinformatic analysis indicated that the 454 assembly contained a set of genes putatively involved in iridoid biosynthesis. Significantly, homologues of the secoiridoid pathway genes that were only identified in terpenoid indole alkaloid producing plants were also identified, whose presence implied that route II iridoids and route I iridoids share common enzyme steps in the early stage of biosynthesis. The gene expression patterns of four prenyltransferase transcripts were analyzed using qRT-PCR, which shed light on their putative functions in tissues of R. glutinosa. The data explored in this study will provide valuable information for further studies concerning iridoid biosynthesis.
Models of Counterterrorism 1 Dynamic Models of a Counterterrorism Strategic Influence Campaign

This paper contrasts the tradeoffs of modeling the same dynamic problem at a micro scale and at a macro scale of analysis: discrete system simulation (DS) versus continuous system simulation or system dynamics (SD). Both are employed to model the influence of entertainment education on terrorist system decay, with implications for field application. Each method emphasizes different scales of analysis, data elements, parameters, and underlying mathematics. Whether the research served by the computer model is applied or theoretical, DS tends to be useful for understand lowlevel individual unit influences on system change over time, whereas SD tends to shine when a wide-angle focus on aggregate sociological change is required.
A Graphical Interface for Document Retrieval Based on Formal Concept Analysis

The research presented in this paper is part of a larger project of building a graphical interface for document retrieval which is based on a conceptual analysis of explicit and implicit structures among document data. Mathematical lattices, which are formalized according to Formal Concept Analysis, serve as an internal model. The lattice model is opposed to the more traditional vector space-based information retrieval models. Besides the document database a thesaurus is included in the system and also formalized as a lattice. The system obtains a high degree of flexibility, i.e. adaptability to different document databases or knowledge bases and to changing users preferences, from its modular design and from a set of lattice combination options.
Differential Roles of Cytokine Receptors in the Development of Epidermal γδ T Cells1

IL-7 and IL-15 play important roles in γδ T cell development. These receptors transmit proliferation and/or survival signals in γδ T cells. In addition, the IL-7R promotes recombination and transcription in the TCR γ locus. To clarify the role of the cytokine receptors in the development of epidermal γδ T cells, we introduced a Vγ3/Vδ1 TCR transgene, derived from Thy-1+ dendritic epidermal T cells (DETC), into IL-7Rα-deficient mice, and we found that they partly rescued γδ T cells in the adult thymus but not in the spleen. Introduction of an additional Bcl-2 transgene had a minimal effect on γδ T cells in the adult thymus of these mice. In contrast to the adult thymus, the introduction of the Vγ3/Vδ1 TCR transgene into IL-7Rα−/− mice completely restored Vγ3+ T cells in the fetal thymus and DETC in the adult skin. On the contrary, the same Vγ3/Vδ1 TCR transgene failed to rescue DETC in the skin of IL-2Rβ-deficient mice, even with the additional Bcl-2 transgene. These results suggest that the IL-2/IL-15R, rather than the IL-7R, plays an essential role in proliferation and survival of DETC in the fetal thymus and the skin. In contrast, the IL-7R is probably essential in the induction of V-J recombination of TCRγ genes. Thus, this study proves that IL-7R and IL-2/IL-15R serve differential functions in epidermal γδ T cell development.
Systemic Immune Effects of Titanium Dioxide Nanoparticles after Repeated Intratracheal Instillation in Rat

The potential immune effects of titanium dioxide nanoparticles (nano-TiO2) are raising concern. Our previous study verified that nano-TiO2 induce local immune response in lung tissue followed by intratracheal instillation administration. In this study, we aim to evaluate the systemic immune effects of nano-TiO2. Sprague Dawley rats were treated by intratracheal instillation with nano-TiO2 at doses of 0.5, 4, and 32 mg/kg body weight, micro-TiO2 with 32 mg/kg body weight and 0.9% NaCl, respectively. The exposure was conducted twice a week, for four consecutive weeks. Histopathological immune organs from exposed animals showed slight congestion in spleen, generally brown particulate deposition in cervical and axillary lymph node. Furthermore, immune function response was characterized by increased proliferation of T cells and B cells following mitogen stimulation and enhanced natural killer (NK) cell killing activity in spleen, accompanying by increased number of B cells in blood. No significant changes of Th1-type cytokines (IL-2 and INF-γ) and Th2-type cytokines (TNF-α and IL-6) were observed. Intratracheal exposure to nano-TiO2 may be one of triggers to be responsible for the systemic immune response. Further study is needed to confirm long-lasting lymphocyte responses and the potential mechanisms.
A Distributed and Provably-Efficient Joint Channel-Assignment , Scheduling and Routing Algorithm for Multi-Channel Multi-Radio Wireless Mesh Networks

Abstract The capacity of wireless mesh networks can be substantially increased by equipping each mesh network node with multiple radio interfaces that can operate on multiple nonoverlapping channels. However, new scheduling, channel-assignment, and routing algorithms are required to fully utilize the increased bandwidth in multi-channel multi-radio wireless mesh networks. In this paper, we develop a fully distributed algorithm that jointly solves the channel-assignment, scheduling and routing problem. Our algorithm is an online algorithm, i.e., it does not require prior information on the offered load to the network, and can adapt automatically to the changes in the network topology and offered load. We show that our algorithm is provably efficient. That is, even compared with the optimal centralized and offline algorithm, our proposed distributed algorithm can achieve a provable fraction of the maximum system capacity. Further, the achievable fraction that we can guarantee is larger than that of some other comparable algorithms in the literature.
Biological Evidence Management for DNA Analysis in Cases of Sexual Assault

Biological evidence with forensic interest may be found in several cases of assault, being particularly relevant if sexually related. Sexual assault cases are characterized by low rates of disclosure, reporting, prosecution, and conviction. Biological evidence is sometimes the only way to prove the occurrence of sexual contact and to identify the perpetrator. The major focus of this review is to propose practical approaches and guidelines to help health, forensic, and law enforcement professionals to deal with biological evidence for DNA analysis. Attention should be devoted to avoiding contamination, degradation, and loss of biological evidence, as well as respecting specific measures to properly handle evidence (i.e., selection, collection, packing, sealing, labeling, storage, preservation, transport, and guarantee of the chain custody). Biological evidence must be carefully managed since the relevance of any finding in Forensic Genetics is determined, in the first instance, by the integrity and quantity of the samples submitted for analysis.