Miracle-dz/UniFAR-FTUs huggingface dataset:
FoxO and Stress Responses in the Cnidarian Hydra vulgaris

Background In the face of changing environmental conditions, the mechanisms underlying stress responses in diverse organisms are of increasing interest. In vertebrates, Drosophila, and Caenorhabditis elegans, FoxO transcription factors mediate cellular responses to stress, including oxidative stress and dietary restriction. Although FoxO genes have been identified in early-arising animal lineages including sponges and cnidarians, little is known about their roles in these organisms. Methods/Principal Findings We have examined the regulation of FoxO activity in members of the well-studied cnidarian genus Hydra. We find that Hydra FoxO is expressed at high levels in cells of the interstitial lineage, a cell lineage that includes multipotent stem cells that give rise to neurons, stinging cells, secretory cells and gametes. Using transgenic Hydra that express a FoxO-GFP fusion protein in cells of the interstitial lineage, we have determined that heat shock causes localization of the fusion protein to the nucleus. Our results also provide evidence that, as in bilaterian animals, Hydra FoxO activity is regulated by both Akt and JNK kinases. Conclusions These findings imply that basic mechanisms of FoxO regulation arose before the evolution of bilaterians and raise the possibility that FoxO is involved in stress responses of other cnidarian species, including corals.
PCR Improves Diagnostic Yield from Lung Aspiration in Malawian Children with Radiologically Confirmed Pneumonia

Background Accurate data on childhood pneumonia aetiology are essential especially from regions where mortality is high, in order to inform case-management guidelines and the potential of prevention strategies such as bacterial conjugate vaccines. Yield from blood culture is low, but lung aspirate culture provides a higher diagnostic yield. We aimed to determine if diagnostic yield could be increased further by polymerase chain reaction (PCR) detection of bacteria (Streptococcus pneumoniae and Haemophilus influenzae b) and viruses in lung aspirate fluid. Methods A total of 95 children with radiological focal, lobar or segmental consolidation had lung aspirate performed and sent for bacterial culture and for PCR for detection of bacteria, viruses and Pneumocystis jirovecii. In children with a pneumococcal aetiology, pneumococcal bacterial loads were calculated in blood and lung aspirate fluid. Results Blood culture identified a bacterial pathogen in only 8 patients (8%). With the addition of PCR on lung aspirate samples, causative pathogens (bacterial, viral, pneumocystis) were identified singly or as co-infections in 59 children (62%). The commonest bacterial organism was S.pneumoniae (41%), followed by H. influenzae b (6%), and the commonest virus identified was adenovirus (16%), followed by human bocavirus (HBoV) (4%), either as single or co-infection. Conclusions In a select group of African children, lung aspirate PCR significantly improves diagnostic yield. Our study confirms a major role of S.pneumoniae and viruses in the aetiology of childhood pneumonia in Africa.
Lightweight Intrusion Detection of Rootkit with VMI-Based Driver Separation Mechanism

Intrusion detection techniques based on virtual machine introspection (VMI) provide high temper-resistance in comparison with traditional in-host anti-virus tools. However, the presence of semantic gap also leads to the performance and compatibility problems. In order to map raw bits of hardware to meaningful information of virtual machine, detailed knowledge of different guest OS is required. In this work, we present VDSM, a lightweight and general approach based on driver separation mechanism: divide semantic view reconstruction into online driver of view generation and offline driver of semantics extraction. We have developed a prototype of VDSM and used it to do intrusion detection on 13 operation systems. The evaluation results show VDSM is effective and practical with a small performance overhead.
Listing Maximal Subgraphs in Strongly Accessible Set Systems

Algorithms for listing the subgraphs satisfying a given property (e.g.,being a clique, a cut, a cycle, etc.) fall within the general framework of set systems. A set system (U, F) uses a ground set U (e.g., the network nodes) and an indicator F, subset of 2^U, of which subsets of U have the required property. For the problem of listing all sets in F maximal under inclusion, the ambitious goal is to cover a large class of set systems, preserving at the same time the efficiency of the enumeration. Among the existing algorithms, the best-known ones list the maximal subsets in time proportional to their number but may require exponential space. In this paper we improve the state of the art in two directions by introducing an algorithmic framework that, under standard suitable conditions, simultaneously (i) extends the class of problems that can be solved efficiently to strongly accessible set systems, and (ii) reduces the additional space usage from exponential in |U| to stateless, thus accounting for just O(q) space, where q <= |U| is the largest size of a maximal set in F
Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen

Research conducted The phytohormone ethylene impacts secondary stem growth in plants by stimulating cambial activity, xylem development and fiber over vessel formation. Here we report the effect of ethylene on secondary cell wall formation and the molecular connection between ethylene signaling and wood formation. Methods We applied exogenous ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to wild type and ethylene insensitive hybrid aspen trees (Populus tremula x tremuloides) and studied secondary cell wall anatomy, chemistry and ultrastructure. We furthermore analyzed the transcriptome (RNA Seq) after ACC application to wild type and ethylene insensitive trees. Key results We demonstrate that ACC and ethylene induce gelatinous-layers (G-layers) and alter the fiber cell wall cellulose microfibril angle. G-layers are tertiary wall layers rich in cellulose, typically found in tension wood of aspen trees. A vast majority of transcripts affected by ACC are downstream of ethylene perception and include a large number of transcription factors (TFs). Motif-analyses reveal potential connections between ethylene TFs (ERFs, EIN3/EIL1) and wood formation. Conclusion G-layer formation upon ethylene application suggests that the increase in ethylene biosynthesis observed during tension wood formation is important for its formation. Ethylene-regulated TFs of the ERF and EIN3/EIL1 type could transmit the ethylene signal.
Identification of influencing factors and strategies to improve communication between general practitioners and community nurses: a qualitative focus group study

Background As the number of patients with complex healthcare needs grows, inter-professional collaboration between primary care professionals must be constantly optimized. General practitioners (GPs) and community nurses (CNs) are key professions in primary care; however, poor GP-CN communication is common, and research into the factors influencing its quality is limited. Objective To explore patient-related GP-CN communication and facilitating and hindering factors, and to identify strategies to enhance this communication. Method A qualitative focus group design was used to identify the facilitating and hindering factors and strategies for improvement. In a Dutch primary care setting, 6 mono-professional focus group interviews (3 meetings of 13 GPs; 3 meetings of 18 CNs) were organized between June 2015 and April 2016, recorded and transcribed verbatim. Two independent researchers performed the coding of these interviews, identifying their categories and themes. Results Results show that, despite the regular contact between GPs and CNs, communication was generally perceived as poor in effectiveness and efficiency by both professions. Mutual trust was considered the most important facilitating factor for effective communication. Profession-specific factors (e.g. differences in responsibility and profession-specific language) and organizational factors (e.g. lack of shared care plans, no in-person communication, lack of time) may be of influence on communication. Participants' suggestions for improvement included organizing well-structured and reimbursed team meetings and facilitating face-to-face contact. Conclusion GP-CN patient-related communication benefits most from trusting inter-personal relationships. Inter-professional training programmes should address both professional and organizational factors and should be evaluated for their effect on quality of care.
European Multicenter Study on Analytical Performance of Veris HIV-1 Assay

ABSTRACT The analytical performance of the Veris HIV-1 assay for use on the new, fully automated Beckman Coulter DxN Veris molecular diagnostics system was evaluated at 10 European virology laboratories. The precision, analytical sensitivity, performance with negative samples, linearity, and performance with HIV-1 groups/subtypes were evaluated. The precision for the 1-ml assay showed a standard deviation (SD) of 0.14 log10 copies/ml or less and a coefficient of variation (CV) of ≤6.1% for each level tested. The 0.175-ml assay showed an SD of 0.17 log10 copies/ml or less and a CV of ≤5.2% for each level tested. The analytical sensitivities determined by probit analysis were 19.3 copies/ml for the 1-ml assay and 126 copies/ml for the 0.175-ml assay. The performance with 1,357 negative samples demonstrated 99.2% with not detected results. Linearity using patient samples was shown from 1.54 to 6.93 log10 copies/ml. The assay performed well, detecting and showing linearity with all HIV-1 genotypes tested. The Veris HIV-1 assay demonstrated analytical performance comparable to that of currently marketed HIV-1 assays. (DxN Veris products are Conformité Européenne [CE]-marked in vitro diagnostic products. The DxN Veris product line has not been submitted to the U.S. FDA and is not available in the U.S. market. The DxN Veris molecular diagnostics system is also known as the Veris MDx molecular diagnostics system and the Veris MDx system.)
Microbiological safety of processed meat products formulated with low nitrite concentration — A review

Nitrite plays a major role in inhibiting the growth of foodborne pathogens, including Clostridium botulinum (C. botulinum) that causes botulism, a life-threatening disease. Nitrite serves as a color-fixing agent in processed meat products. However, N-nitroso compounds can be produced from nitrite, which are considered as carcinogens. Thus, consumers desire processed meat products that contain lower concentrations (below conventional concentrations of products) of nitrite or no nitrite at all, although the portion of nitrite intake by processed meat consumption in total nitrite intake is very low. However, lower nitrite levels might expose consumers to risk of botulism poisoning due to C. botulinum or illness caused by other foodborne pathogens. Hence, lower nitrite concentrations in combination with other factors such as low pH, high sodium chloride level, and others have been recommended to decrease the risk of food poisoning. In addition, natural compounds that can inhibit bacterial growth and function as color-fixing agents have been developed to replace nitrite in processed meat products. However, their antibotulinal effects have not been fully clarified. Therefore, to have processed meat products with lower nitrite concentrations, low pH, high sodium chloride concentration, and others should also be applied together. Before using natural compounds as replacement of nitrite, their antibotulinal activities should be examined.
Hello: A generic flexible protocol for neighbor discovery

Neighbor discovery is crucial for both wireless sensor networks and mobile computing applications. The crux of the problem is to achieve energy efficiency, which has been demonstrated to be difficult by prior work. In this paper we propose Hello, a generic flexible protocol for neighbor discovery. With an unrestricted parameter, it serves as a generic framework that incorporates existing deterministic protocols. Under the framework, we expose optimal parameters for either symmetric or asymmetric duty cycles, which is the first to our knowledge. As a result, it exhibits great flexibility by adjusting itself to any configuration that best meets application demands. Besides, several techniques are applied to removing redundant discoveries without sacrificing the worst-case latency. We evaluate Hello through extensive simulation and real-world sensor experiments. The results show that Hello is highly energy-efficient under symmetric and asymmetric duty cycles. In particular, it is two times better than the state of the art in terms of the worst-case latency under asymmetric duty cycles.
Ropinirole and Pramipexole Promote Structural Plasticity in Human iPSC-Derived Dopaminergic Neurons via BDNF and mTOR Signaling

The antiparkinsonian ropinirole and pramipexole are D3 receptor- (D3R-) preferring dopaminergic (DA) agonists used as adjunctive therapeutics for the treatment resistant depression (TRD). While the exact antidepressant mechanism of action remains uncertain, a role for D3R in the restoration of impaired neuroplasticity occurring in TRD has been proposed. Since D3R agonists are highly expressed on DA neurons in humans, we studied the effect of ropinirole and pramipexole on structural plasticity using a translational model of human-inducible pluripotent stem cells (hiPSCs). Two hiPSC clones from healthy donors were differentiated into midbrain DA neurons. Ropinirole and pramipexole produced dose-dependent increases of dendritic arborization and soma size after 3 days of culture, effects antagonized by the selective D3R antagonists SB277011-A and S33084 and by the mTOR pathway kinase inhibitors LY294002 and rapamycin. All treatments were also effective in attenuating the D3R-dependent increase of p70S6-kinase phosphorylation. Immunoneutralisation of BDNF, inhibition of TrkB receptors, and blockade of MEK-ERK signaling likewise prevented ropinirole-induced structural plasticity, suggesting a critical interaction between BDNF and D3R signaling pathways. The highly similar profiles of data acquired with DA neurons derived from two hiPSC clones underpin their reliability for characterization of pharmacological agents acting via dopaminergic mechanisms.
The complete chloroplast genome sequence of Schefflera octophylla

Abstract The complete chloroplast genome sequence of Schefflera octophylla, a critical Chinese medicine was reported here. The complete chloroplast genome of Schefflera octophylla is 156 685 bp in length with 37.93% overall GC content. A pair of IRs (inverted repeats) of 25 965 bp were separated by LSC (86 609 bp) and SSC (18 146 bp). The phylogenetic analysis of 17 taxa showed a strong sister relationship with Schefflera delavayi. Furthermore the Araliaceae was separated into two major groups.
Restriction of HIV-1 Genotypes in Breast Milk Does Not Account for the Population Transmission Genetic Bottleneck That Occurs following Transmission

Background Breast milk transmission of HIV-1 remains a major route of pediatric infection. Defining the characteristics of viral variants to which breastfeeding infants are exposed is important for understanding the genetic bottleneck that occurs in the majority of mother-to-child transmissions. The blood-milk epithelial barrier markedly restricts the quantity of HIV-1 in breast milk, even in the absence of antiretroviral drugs. The basis of this restriction and the genetic relationship between breast milk and blood variants are not well established. Methodology/Principal Findings We compared 356 HIV-1 subtype C gp160 envelope (env) gene sequences from the plasma and breast milk of 13 breastfeeding women. A trend towards lower viral population diversity and divergence in breast milk was observed, potentially indicative of clonal expansion within the breast. No differences in potential N-linked glycosylation site numbers or in gp160 variable loop amino acid lengths were identified. Genetic compartmentalization was evident in only one out of six subjects in whom contemporaneously obtained samples were studied. However, in samples that were collected 10 or more days apart, six of seven subjects were classified as having compartmentalized viral populations, highlighting the necessity of contemporaneous sampling for genetic compartmentalization studies. We found evidence of CXCR4 co-receptor using viruses in breast milk and blood in nine out of the thirteen subjects, but no evidence of preferential localization of these variants in either tissue. Conclusions/Significance Despite marked restriction of HIV-1 quantities in milk, our data indicate intermixing of virus between blood and breast milk. Thus, we found no evidence that a restriction in viral genotype diversity in breast milk accounts for the genetic bottleneck observed following transmission. In addition, our results highlight the rapidity of HIV-1 env evolution and the importance of sample timing in analyses of gene flow.
Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

ABSTRACT To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.
Agreeing to Interact: Understanding Interaction as Human-Robot Goal Conflicts

In human-robot interaction (HRI) people have studied user preferable robot actions in various social situations. The role of the robot is often designed, and situations are assumed that the robot will interact with the human. However, there are also situations where either the human or robot may not be willing to interact. In such situations, the human and robot are under a goal conflict and must first agree to begin an interaction. In this paper, we re-explore interaction beginnings and endings as a confliction and agreement between human and robot goals - the willingness of whether to interact or not. Through our discussion, we categorize conflict/agreement interactions into nine situations. Using a probabilistic analysis approach and 93 HRI recordings, we evaluate the different human behaviors in different interaction situations. We further question whether learning from typical existing HRI would benefit other scenarios when a robot has physical task capabilities. We conclude that the benefits of understanding different agreement situations would largely depend on a robot»s task capability as well as the human»s expectation toward these capabilities; however, conflict and agreement should not be neglected when applying interaction capability to physical-task-capable robots. Our research also suggests the probabilistic drawbacks of robot speech in situations where both the human and robot are not willing to interact.
Towards Intelligent Autonomous Controllers: Architecture for Industrial Distributed System

In industrial production systems, operators and engineers develop, on a daily basis, a degree of knowledge about some processes that, giving enough time, they become experts in the systems which themselves operate. In order to take advantage of this knowledge and experience, a knowledge-based system (KBS) can be employed to model and store the inference as well as the ways of decision-making of the operators in their working procedures. This article considers that in a setting of higher autonomy, a KBS could be embedded, such as for example, coupled in a programmable logic controller (PLC), which would adjust the controller as well as take control actions in a closed loop system without the direct intervention from the operators. Thus, as a possible application, such systems can be developed for the task of automatic tuning of proportional-integral-derivative (PID) parameters of a conventional controller, an important activity in process control operational routines. The study includes a conceptual proposal for developing this application and emphasizes the importance of artificial intelligence technologies for obtaining a higher degree of autonomy.
Phylogenetic studies of Anas clypeata (Anatidae: Anas) based on complete mitochondrial DNA sequences

Abstract Northern shoveler (Anas clypeata) is a middle-sized duck living in an extremely geographical range in northern hemisphere. Here, the complete mitochondrial genome of A. clypeata (16 599 bp in length) has been analyzed for building the database. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Overall base composition of the complete mitochondrial DNA is A (29.4%), G (15.7%), C (32.5%) and T (22.4%), the percentage of A and T (51.8%) is slightly higher than G and C (48.2%). All the genes in A. clypeata were distributed on the H-strand, except for the ND6 subunit gene and 9 tRNA genes which were encoded on the L-strand. The phylogenetic relationships of 12 Anatidae species were reconstructed based on the complete mtDNA sequences using the Bayesian inference method.