Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences.

Lycium comprises approximately 70 species and is disjunctly distributed in temperate to subtropical regions in South America, North America, southern Africa, Eurasia, and Australia. Among them, only Lycium sandwicense A. Gray sporadically occurs widely on oceanic islands in the Pacific Ocean. To investigate phylogenetic and biogeographic relationships of the genus with emphasis on L. sandwicense, the coding region of matK, the two intergenic spacers trnT (UGU)-trnL (UAA) and trnL (UAA)-trnF (GAA), and the trnL (UAA) intron of chloroplast DNA (cpDNA) were sequenced. A strict consensus tree resulting from the phylogenetic analysis indicates the following: (1) New World species comprise a potentially paraphyletic assemblage; (2) southern African, Australian, and Eurasian species together are monophyletic; (3) southern African species are a paraphyletic assemblage; and (4) L. sandwicense is in a clade with certain New World species. The estimated biogeographic events based on the cpDNA analysis indicate that (1) Lycium originated in the New World, (2) all southern African, Australian, and Eurasian species have a common ancestor from the New World, (3) Australian and Eurasian species originated once from a southern African progenitor, and (4) L. sandwicense differentiated from the New World species.
Genetic loci involved in rubrifacine production in the walnut pathogen Brenneria rubrifaciens.

Brenneria rubrifaciens produces a unique red pigment known as rubrifacine that has been hypothesized to play a role in pathogenesis on walnut. Analysis of DNA flanking the Tn5 insertion site in 20 rubrifacine minus (pig(-)) mutants identified three regions required for rubrifacine production. The first region was homologous to nonribosomal peptide synthetases (NRPS), the second was homologous to autoinducer synthase genes (expI homologs), and the third region was homologous to the slyA gene of Candidatus blochmania and Escherichia coli. Pigment production was not necessary for elicitation of the hypersensitive response (HR) in tobacco and had little impact on virulence in tissue-cultured walnut plants. The expI-interrupted mutants exhibited reduced virulence on walnut and were HR negative on tobacco. Pigment production was restored in Br-212 when grown in the presence of wild-type B. rubrifaciens, E. coli carrying the cloned expI-like gene, or introduction of the cloned wild-type copy of the expI-like gene. Two Brenneria spp. , B. nigrifluens and B. salicis, also restored pigment production in Br-212. These results demonstrate that rubrifacine production and virulence of B. rubrifaciens on walnut are under the control of a quorum-sensing system and are sensitive to signal molecules from other Brenneria spp.
Neuronal Death Induced by Brain-Derived Human Immunodeficiency Virus Type 1 Envelope Genes Differs between Demented and Nondemented AIDS Patients

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) infection of the brain results in viral replication primarily in macrophages and microglia. Despite frequent detection of viral genome and proteins in the brains of AIDS patients with and without HIV dementia, only 20% of AIDS patients become demented. To investigate the role of viral envelope gene variation in the occurrence of dementia, we examined regions of variability in the viral envelope gene isolated from brains of AIDS patients. Brain-derived HIV-1 V1-V2 envelope sequences from seven demented and six nondemented AIDS patients displayed significant sequence differences between clinical groups, and by phylogenetic analysis, sequences from the demented group showed clustering. Infectious recombinant viruses containing brain-derived V3 sequences from both clinical groups were macrophagetropic, and viruses containing brain-derived V1, V2, and V3 sequences from both clinical groups spread efficiently in macrophages. In an indirect in vitro neurotoxicity assay using supernatant fluid from HIV-1-infected macrophages, recombinant viruses from demented patients induced greater neuronal death than viruses from nondemented patients. Thus, the HIV-1 envelope diversity observed in these patient groups appeared to influence the release of neurotoxic molecules from macrophages and might account in part for the variability in occurrence of dementia in AIDS patients.
Specific chemotherapeutic agents induce metastatic behaviour through stromal‐ and tumour‐derived cytokine and angiogenic factor signalling

Recent studies reveal that chemotherapy can enhance metastasis due to host responses, such as augmented expression of adhesion molecules in endothelial cells and increased populations of myeloid cells. However, it is still unclear how tumour cells contribute to this process. Here, we observed that paclitaxel and carboplatin accelerated lung metastasis in tumour‐bearing mice, while doxorubicin and fluorouracil did not. Mechanistically, paclitaxel and carboplatin induced similar changes in cytokine and angiogenic factors. Increased levels of CXCR2, CXCR4, S1P/S1PR1, PlGF and PDGF‐BB were identified in the serum or primary tumour tissues of tumour‐bearing mice treated by paclitaxel. The serum levels of CXCL1 and PDGF‐BB and the tissue level of CXCR4 were also elevated by carboplatin. On the other hand, doxorubicin and fluorouracil did not induce such changes. The chemotherapy‐induced cytokine and angiogenic factor changes were also confirmed in gene expression datasets from human patients following chemotherapy treatment. These chemotherapy‐enhanced cytokines and angiogenic factors further induced angiogenesis, destabilized vascular integrity, recruited BMDCs to metastatic organs and mediated the proliferation, migration and epithelial‐to‐mesenchymal transition of tumour cells. Interestingly, inhibitors of these factors counteracted chemotherapy‐enhanced metastasis in both tumour‐bearing mice and normal mice injected intravenously with B16F10–GFP cells. In particular, blockade of the SDF‐1α–CXCR4 or S1P–S1PR1 axes not only compromised chemotherapy‐induced metastasis but also prolonged the median survival time by 33.9% and 40.3%, respectively. The current study delineates the mechanism of chemotherapy‐induced metastasis and provides novel therapeutic strategies to counterbalance pro‐metastatic effects of chemo‐drugs via combination treatment with anti‐cytokine/anti‐angiogenic therapy. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Classification of Odours for Mobile Robots Using an Ensemble of Linear Classifiers

This paper investigates the classification of odours using an electronic nose mounted on a mobile robot. The samples are collected as the robot explores the environment. Under such conditions, the sensor response differs from typical three phase sampling processes. In this paper, we focus particularly on the classification problem and how it is influenced by the movement of the robot. To cope with these influences, an algorithm consisting of an ensemble of classifiers is presented. Experimental results show that this algorithm increases classification performance compared to other traditional classification methods.
Food Intake Monitoring: Automated Chew Event Detection in Chewing Sounds

The analysis of the food intake behavior has the potential to provide insights into the development of obesity and eating disorders. As an elementary part of this analysis, chewing strokes have to be detected and counted. Our approach for food intake analysis is the evaluation of chewing sounds generated during the process of eating. These sounds were recorded by microphones applied to the outer ear canal of the user. Eight different algorithms for automated chew event detection were presented and evaluated on two datasets. The first dataset contained food intake sounds from the consumption of six types of food. The second dataset consisted of recordings of different environmental sounds. These datasets contained 68 094 chew events in around 18 h recording data. The results of the automated chew event detection were compared to manual annotations. Precision and recall over 80% were achieved by most of the algorithms. A simple noise reduction algorithm using spectral subtraction was implemented for signal enhancement. Its benefit on the chew event detection performance was evaluated. A reduction of the number of false detections by 28% on average was achieved by maintaining the detection performance. The system is able to be used for calculation of the chewing frequency in laboratory settings.
Applying Kohonen Vector Quantization Networks for Profiling Customers of Mobile Telecommunication Services

Customer clustering is used to understand customers’ preferences and behaviors by examining the differences and similarities between customers. Kohonen vector quantization clustering technology is used in this research and is compared with Kmeans clustering. The data set consists of customer records obtained from a mobile telecommunications service provider. The customers are clustered using various attributes that are broadly grouped under usage, revenue, handset, and service. The clustering results are examined to see the relationships between different types of attributes. The analysis leads to the discovery of several interesting facts about customers that may be of use to mobile service providers.
Extracting Rules from Artifical Neural Networks with Distributed Representations

Although artificial neural networks have been applied in a variety of real-world scenarios with remarkable success, they have often been criticized for exhibiting a low degree of human comprehensibility. Techniques that compile compact sets of symbolic rules out of artificial neural networks offer a promising perspective to overcome this obvious deficiency of neural network representations. This paper presents an approach to the extraction of if-then rules from artificial neural networks. Its key mechanism is validity interval analysis, which is a generic tool for extracting symbolic knowledge by propagating rule-like knowledge through Backpropagation-style neural networks. Empirical studies in a robot arm domain illustrate the appropriateness of the proposed method for extracting rules from networks with real-valued and distributed representations.
Branch-and-price for the Multi-depot Pickup and Delivery Problem with Heterogeneous Fleet and Soft Time Windows

The multi-depot pickup and delivery problem with heterogeneous fleet and soft time windows (MDPDPHSTW) requires to find a minimum cost routing for a fleet vehicles with different capacities and based at different depots, satisfying a given set of customers. A customer request is associated with two locations: a source where a certain demand must be picked up and a destination where this demand must be delivered. Each route must satisfy pairing constraints (pickup and delivery of a customer must both be visited in the same route) and precedence constraints (the delivery location must be visited after the corresponding pickup location). Further, each pickup and delivery location has a time window for the service that can be violated at the cost of a linear penalty. This problem has application in various scenarios, such as urban courier services, less-than-truckload transportation, door to door transportation services.
Complete Inhibition of Tobamovirus Multiplication by Simultaneous Mutations in Two Homologous Host Genes

ABSTRACT The TOM1 gene of Arabidopsis thaliana encodes a putative multipass transmembrane protein which is necessary for the efficient multiplication of tobamoviruses. We have previously shown that mutations severely destructive to the TOM1 gene reduce tobamovirus multiplication to low levels but do not impair it completely. In this report, we subjected one of the tom1 mutants (tom1-1) to another round of mutagenesis and isolated a new mutant which did not permit a detectable level of tobamovirus multiplication. In addition to tom1-1, this mutant carried a mutation referred to as tom3-1. Positional cloning showed that TOM3 was one of two TOM1-like genes in Arabidopsis. Based on the similarity between the amino acid sequences of TOM1 and TOM3, together with the results of a Sos recruitment assay suggesting that both TOM1 and TOM3 bind tobamovirus-encoded replication proteins, we propose that TOM1 and TOM3 play parallel and essential roles in the replication of tobamoviruses.
Melatih Keterampilan Menulis Bahasa-bahasa Inggris Siswa SMA Kelas II(Analisis Wacana Tentang Penggelolaan Dirilis dalam Kegiatan Penelitian Tindakan Kelas )

Analisis wacana ini dimaksudkan untuk menawarkan cara melatih keterampilan menulis Bahasa Inggris siswa melalui Drills untuk memberdayakan kemampuan siswa SMA mengambil manfaat (beneficiary) atas informasi dan komunikasi, khususnya IPTEKS, yang disajikan dalam bahasa Inggris. Selain itu, dengan kompetensi menulis, siswa juga diharapkan mampu berperan sebagai produser informasi dan mengkomunikasikan informasi kepada dunia luar melalui bahasa inggris, mulai dari lingkup komunitas terkecil, yaitu ruang kelas. Analisis wacana ini bertujuan untuk mengintervensi metode pembelajaran konvensional sehingga penguasaan dan penggunaan bahasa inggris, khususnya untuk kompetensi dasar menulis, dapat ditingkatkan. Materi yang akan diajarkan merupakan satu inovasi untuk menyiasati isi buku pelajaran siswa. Unsur-unsur pertimbangan inovasi materi Drills menulis melalui kegiatan PTK meliputi Contextual Teaching Learning, Guided Questions to Writing dan Mapping Idea. Pertimbangan lain adalah bahwa Drills tetap harus didisain menurut kaidah KTSP dan silabus mata pelajaran bahasa inggris.
Expressive and efficient pattern languages for tree-structured data (extended abstract)

It would be desirable to have a query language for tree-structured data that is (1) as easily usable as SQL, (2) as expressive as monadic second-order logic (MSO), and (3) efficiently evaluable. The paper develops some ideas in this direction. Towards (1) the specification of sets of vertices of a tree by combining conditions on their induced subtree with conditions on their path to the root is proposed. Existing query languages allow regular expressions (hence MSO logic) in path conditions but are limited in expressing subtree conditions. It is shown that such query languages fall short of capturing all MSO queries. On the other hand, allowing a certain guarded fragment of MSO-logic in the specification of subtree conditions results in a language fulfilling (2), (3) and, anguably, (1).
Low-Load High Volume Resistance Exercise Stimulates Muscle Protein Synthesis More Than High-Load Low Volume Resistance Exercise in Young Men

Background We aimed to determine the effect of resistance exercise intensity (% 1 repetition maximum—1RM) and volume on muscle protein synthesis, anabolic signaling, and myogenic gene expression. Methodology/Principal Findings Fifteen men (21±1 years; BMI = 24.1±0.8 kg/m2) performed 4 sets of unilateral leg extension exercise at different exercise loads and/or volumes: 90% of repetition maximum (1RM) until volitional failure (90FAIL), 30% 1RM work-matched to 90%FAIL (30WM), or 30% 1RM performed until volitional failure (30FAIL). Infusion of [ring-13C6] phenylalanine with biopsies was used to measure rates of mixed (MIX), myofibrillar (MYO), and sarcoplasmic (SARC) protein synthesis at rest, and 4 h and 24 h after exercise. Exercise at 30WM induced a significant increase above rest in MIX (121%) and MYO (87%) protein synthesis at 4 h post-exercise and but at 24 h in the MIX only. The increase in the rate of protein synthesis in MIX and MYO at 4 h post-exercise with 90FAIL and 30FAIL was greater than 30WM, with no difference between these conditions; however, MYO remained elevated (199%) above rest at 24 h only in 30FAIL. There was a significant increase in AktSer473 at 24h in all conditions (P = 0.023) and mTORSer2448 phosphorylation at 4 h post-exercise (P = 0.025). Phosporylation of Erk1/2Tyr202/204, p70S6KThr389, and 4E-BP1Thr37/46 increased significantly (P<0.05) only in the 30FAIL condition at 4 h post-exercise, whereas, 4E-BP1Thr37/46 phosphorylation was greater 24 h after exercise than at rest in both 90FAIL (237%) and 30FAIL (312%) conditions. Pax7 mRNA expression increased at 24 h post-exercise (P = 0.02) regardless of condition. The mRNA expression of MyoD and myogenin were consistently elevated in the 30FAIL condition. Conclusions/Significance These results suggest that low-load high volume resistance exercise is more effective in inducing acute muscle anabolism than high-load low volume or work matched resistance exercise modes.
Analytical computation of the eigenvalues and eigenvectors in DT-MRI.

In this paper a noniterative algorithm to be used for the analytical determination of the sorted eigenvalues and corresponding orthonormalized eigenvectors obtained by diffusion tensor magnetic resonance imaging (DT-MRI) is described. The algorithm uses the three invariants of the raw water spin self-diffusion tensor represented by a 3 x 3 positive definite matrix and certain math functions that do not require iteration. The implementation requires a positive definite mask to preserve the physical meaning of the eigenvalues. This algorithm can increase the speed of eigenvalue/eigenvector calculations by a factor of 5-40 over standard iterative Jacobi or singular-value decomposition techniques. This approach may accelerate the computation of eigenvalues, eigenvalue-dependent metrics, and eigenvectors especially when having high-resolution measurements with large numbers of slices and large fields of view.
Long-Lived Volcanism on the Lunar Farside Revealed by SELENE Terrain Camera

We determined model ages of mare deposits on the farside of the Moon on the basis of the crater frequency distributions in 10-meter-resolution images obtained by the Terrain Camera on SELENE (Selenological and Engineering Explorer) (Kaguya). Most mare volcanism that formed mare deposits on the lunar farside ceased at ∼3.0 billion years ago, suggesting that mare volcanism on the Moon was markedly reduced globally during this period. However, several mare deposits at various locations on the lunar farside also show a much younger age, clustering at ∼2.5 billion years ago. These young ages indicate that mare volcanism on the lunar farside lasted longer than was previously considered and may have occurred episodically.
Power consumption in XOR-based circuits

The use of XOR gates has shown several advantages in modern circuit design, e.g. smaller representation size and better testability. In this paper we consider power consumption in XOR dominated circuits and compare such designs with traditional AND/OR logic. We investigate the suitability of using different delay models such as unit delay, fanout delay, and random delay in power estimation of XOR dominated logic. Due to different possible implementations of XOR gate, we model the XOR gate as a basic gate and a complex static CMOS gate, respectively. Power dissipation due to (charging and discharging) internal node capacitances is also considered.
Variable-Rate Channel Capacity

This paper introduces the notions of variable-to-fixed and fixed-to-variable channel capacity, without feedback. For channels that satisfy the strong converse, these notions coincide with the conventional Shannon capacity. For channels that do not behave ergodically, the conventional fixed-rate Shannon capacity only depends on least-favorable channel conditions, while the variable-rate capacity notions are able to capture the whole range of channel states and their likelihood, even in the absence of any side information about channel state at the transmitter. Particular emphasis is placed on memoryless channels that are governed by finitely valued states. We show that (single-user) variable-to-fixed channel capacity is intimately connected to the capacity region of broadcast channels with degraded message sets, and we give an expression for the fixed-to-variable capacity.
Understanding the link between body dissatisfaction and binge eating: a model comparison approach

This thesis explored the association between body dissatisfaction and binge eating by comparing three competing theoretical frameworks. Study I utilised a cross-sectional design and collectively these findings suggest the superiority of the dual pathway model (dietary restraint and negative affect) over the objectification theory and the escape model. The purpose of Study II was then to extend on the findings from Study I by further examining in real-time the model/theory that most strongly explained the body dissatisfaction-binge eating relationship. Participants were prompted at random intervals seven times daily across the course of a week to self-report their state body dissatisfaction, current mood experiences, and eating practices. Results revealed that negative mood, but not dietary restraint, significantly mediated the state body dissatisfaction-binge eating relationship. These results highlight that the dual pathway model is robust, but raise the possibility that the dietary restraint path in the model is not well operationalized. In light of the non-significant mediating effect of dietary restraint, this led the researcher to identify various modeling alternatives to further understand the mediating influences of the pathways of negative affect and dietary restraint.
An ethnographic study of music information seeking: implications for the design of a music digital library

At present, music digital library systems are being developed based on anecdotal evidence of user needs, intuitive feelings for user information seeking behavior, and a priori assumptions of typical usage scenarios. Emphasis has been placed on basic research into music document representation, efficient searching, and audio-based searching, rather than on exploring the music information needs or information behavior of a target user group. We focus on eliciting the 'native' music information strategies employed by people searching for popular music (that is, music sought for recreational or enjoyment purposes rather than to support a 'serious' or scientific exploration of some aspect of music). To this end, we conducted an ethnographic study of the searching/browsing techniques employed by people in the researchers' local communities, as they use two common sources of music: the public library and music stores. We argue that the insights provided by this type of study can inform the development of searching/browsing support for music digital libraries.