Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent additions and improvements to the Onto-Tools

The Onto-Tools suite is composed of an annotation database and six seamlessly integrated, web-accessible data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner and Pathway-Express. The Onto-Tools database has been expanded to include various types of data from 12 new databases. Our database now integrates different types of genomic data from 19 sequence, gene, protein and annotation databases. Additionally, our database is also expanded to include complete Gene Ontology (GO) annotations. Using the enhanced database and GO annotations, Onto-Express now allows functional profiling for 24 organisms and supports 17 different types of input IDs. Onto-Translate is also enhanced to fully utilize the capabilities of the new Onto-Tools database with an ultimate goal of providing the users with a non-redundant and complete mapping from any type of identification system to any other type. Currently, Onto-Translate allows arbitrary mappings between 29 types of IDs. Pathway-Express is a new tool that helps the users find the most interesting pathways for their input list of genes. Onto-Tools are freely available at .
The Determinants of Goal Commitment

The concept and measurement of commitment to goals, a key aspect of goal-setting theory, are discussed. The strength of the relationship between commitment and performance is asserted to depend on the amount of variance in commitment. Three major categories of determinants of commitment are discussed: external factors (authority, peer influence, external rewards), interactive factors (participation and competition), and internal factors (expectancy, internal rewards). Applications of these ideas are made and new research directions are suggested.
The outcome of Leishmania major experimental infection in BALB / c mice can be modulated by exogenously delivered iron

We previously established that Leishmania promastigotes express a transferrin receptor and that iron chelators inhibit promastigote growth in vitro. Thus, we were interested in modulating the vertebrate host iron pool and to monitor whether such changes will affect the outcome of L. major infection in BALB / c mice, inoculated in the footpad with 106 stationary phase promastigotes. Treatment of mice with desferrioxamine resulted in a slight delay of the development of cutaneous lesions. In contrast and unexpectedly, systemic iron delivery, at early time points of parasite delivery, significantly limited footpad pathology. Accordingly, parasite loads at the site of parasite delivery, the draining lymph node, liver and spleen were significantly reduced in iron‐loaded mice. Importantly, the "protective" effect of iron delivery correlated with the presence, at the site of inoculation, of lower levels of IL‐4 and IL‐10 transcripts while both IFN‐γ and inducible nitric oxide synthase transcripts were at higher levels. The presence of more type 1 cytokine transcripts was further supported by the increased levels of IgG2a in their sera. These data strongly suggest that susceptibility to L. major as assessed in the footpad model is modifiable by interventions that alter the iron status of the host at early time points of parasite delivery.
Cytopathic effect of coccoid forms of Helicobacter pylori in Albino rats and Swiss mice

The effect of coccoid forms of a vaculating cytotoxin A positive Helicobacter pylori strain on Mus musculus (Swiss mice) and Rattus norvegicus (Albino rats) was studied. Two groups of Swiss mice and Albino rats were used. The first group of mice and rats was orally inoculated with coccoid forms of Helicobacter pylori, whereas, the second group of mice and rats were untreated and used as a control. The animals that had been orally inoculated with a total count of 7.0x10 bacterial cell / ml died after 5-7 days of inoculation (mice), whereas, rats died after 7-9 days. Symptoms of mouth ulcers, darkening of the ventral part and peripheries and loss of weight were apparent, in addition to slow movement and general weakness compared to the control group. Histological examination of the stomach of the inoculated animals showed marked degeneration of the epithelial lining membrane and dark dense bodies most probably coccoid forms inside gastric glands. In addition dialated blood vessel, degenerated, vacuolated fused cells with coccoid forms and intravascular haemolysis were observed. These findings may indicate the toxicity of coccoid forms of Helicobacter pylori and hence their possible pathogenic role in humans. [Rajaa M. Milyani. Cytopathic effect of coccoid forms of Helicobacter pylori in Albino rats and Swiss mice. Journal of American Science 2011; 7(6):1087-1092]. (ISSN: 1545-1003). http://www.americanscience. org.
Induction of immune responses and break of tolerance by DNA against the HIV-1 coreceptor CCR5 but no protection from SIVsm challenge.

An inactivating mutation in the human CCR5 gene reduces the risk of HIV-1 infection in individuals with homozygous alleles. We explored whether genetic immunization would induce an immune response directed to CCR5 structures and if immunological tolerance toward endogenous CCR5 could be broken. We also studied whether this immunization approach could protect cynomolgus monkeys from an infection, with SIVsm, which primarily uses CCR5 as a coreceptor. Epidermal but not intramuscular delivery of the CCR5 gene to mice elicited strong IgG antibody binding responses to CCR5. Intramucosal immunization of cynomolgus macaques with CCR5 DNA followed by boosts with CCR5 peptides induced prominent IgG and IgA antibody responses in serum and vaginal washings. The CCR5-specific antibodies neutralized the infectivity of primary human R5 HIV-1 strains, and the macaque SIVsm but not that of a tissue culture-adapted X4 HIV-1 strain. The consecutive CCR5 gene and CCR5 peptide immunizations induced B- and T-cell responses to peptides representing both human and macaque amino acid sequences of the respective CCR5 proteins. This indicates that tolerance was broken against endogenous macaque CCR5, which has a 98% homology to the human CCR5 gene. After the final boost, the vaccinated monkeys together with two control monkeys were challenged with SIVsm. Neither protection against nor enhancement of SIVsm infection was achieved.
Changing University Logos and Evolving Values in Finnish Higher Education

Faculty of Social Sciences Laitos – Institution – Department Political Science Tekijä – Författare – Author Lindsey Kerber Työn nimi – Arbetets titel – Title Changing University Logos and Evolving Values in Finnish Higher Education Oppiaine – Läroämne – Subject Higher Education (HEEM) Työn laji – Arbetets art – Level Master’s Aika – Datum – Month and year May 2015 Sivumäärä – Sidoantal – Number of pages 70 Tiivistelmä – Referat – Abstract
An adaptive floating tangents fitting with helices method for image-based hair modeling

Currently, hair geometry is mostly represented as sequences of 3D points. It is difficult to simulate hair directly from this representation. This paper proposes a novel approach to convert hair geometry model into helices, which could be easily plugged into dynamic hair simulation. We construct a hair model from a hybrid orientation field. Then we use adaptive floating tangents fitting algorithm to convert this hair geometry model into a physics-based hair model. We simulate dynamic hair by Lagrange equations. Results show that this approach can preserve structural details of 3D hair models, and can be applied to simulate various hair geometries.
Tuning Context Features with Genetic Algorithms

In this paper we present an approach to tuning of context features acquired from corpora. The approach is based on the idea of a genetic algorithm (GA). We analyse a whole population of contexts surrounding related linguistic entities in order to find a generic property characteristic of such contexts. Our goal is to tune the context properties so as not to lose any correct feature values, but also to minimise the presence of ambiguous values. The GA implements a crossover operator based on dominant and recessive genes, where a gene corresponds to a context feature. A dominant gene is the one that, when combined with another gene of the same type, is inevitably reflected in the offspring. Dominant genes denote the more suitable context features. In each iteration of the GA, the number of individuals in the population is halved, finally resulting in a single individual that contains context features tuned with respect to the information contained in the training corpus. We illustrate the general method by using a case study concerned with the identification of relationships between verbs and terms complementing them. More precisely, we tune the classes of terms that are typically selected as arguments for the considered verbs in order to acquire their semantic features. * This research is a part of the BioPATH research project coordinated by LION BioScience (http://www.lionbioscience.com) and funded by German Ministry of Research
Fundamental Limitations in Domain-Specific Modeling Language Evolution

In this paper we address language engineering issues surrounding domain-specific modeling languages (DSMLs). By definition, such languages track the domain, meaning that changes to the domain require changes to the DSML in order to provide an intuitive specification of domain-specific models. For this work, our primary focus is on fundamental limitations that affect the preservation of semantics during domain model evolution. We specifically address fundamental limitations in semantics-preserving transformations, and/or the implementation of algorithms that specify such transformations. This work has implications for language engineers who are planning for the maintenance of models, or designing model transformations for the purpose of preserving semantics. We provide a brief representative example from the discipline of hybrid systems, where such results can be interpreted.
Balancing Reuse Opportunities and Performance Gains with Subblock Value Reuse

The fact that instructions in programs often produce repetitive results has motivated researchers to explore various techniques, such as value prediction and value reuse, to exploit this behavior. Value prediction improves the available instruction-level parallelism (ILP) in superscalar processors by allowing dependent instructions to be executed speculatively after predicting the values of their input operands. Value reuse, on the other hand, tries to eliminate redundant computation by storing the previously produced results of instructions and skipping the execution of redundant instructions. Previous value reuse mechanisms use a single instruction or a naturally formed instruction group, such as a basic block, a trace, or a function, as the reuse unit. These naturally-formed instruction groups are readily identifiable by the hardware at runtime without compiler assistance. However, the performance potential of a value reuse mechanism depends on its reuse detection time, the number of reuse opportunities, and the amount of work saved by skipping each reuse unit. Since larger instruction groups typically have fewer reuse opportunities than smaller groups, but they provide greater benefit for each reuse-detection process, it is very important to find the balance point that provides the largest overall performance gain. We propose a new mechanism called subblock reuse. Subblocks are created by slicing basic blocks either dynamically or with compiler guidance. The dynamic approaches use the number of instructions, numbers of inputs and outputs, or the presence of store instructions to determine the subblock boundaries. The compiler-assisted approach slices basic blocks using data-flow considerations to balance the reuse granularity and the number of reuse opportunities.
Institute for Empirical Pedagogy and Pedagogical Psychology

This report presents the evaluation of the computer-based simulation SPACE – Simulating Project Auditing & Controlling Excellence – which is an interactive multiedia business simulation developed in partnership by Andersen Consulting and Siemens AG. The aims of SPACE are fostering self-directed learning and the acquisition of applicable knowledge in the economic domain regarding construction and solution projects of US GAAP. The evaluation was conducted in cooperation with the Institute of Educational Psychology at the Ludwig-Maximilians-University in Munich. The aim of the evaluation was to compare the effectiveness of SPACE with a traditional classroom instruction. Therefore, a problem-based transfer task was designed which assessed learning gains with respect to applicable knowledge in the following areas: (1) strategic knowledge and problem-solving skills, that means selection of appropriate information and strategies to solve a realistic business problem, (2) basic skills to calculate POC and (3) conceptual knowledge, i.e. an understanding of principles and interconnections of concepts in the domain. 38 students of business administration participated in the evaluation. 19 students learned eight hours with SPACE, the other 19 students received a traditional classroom instruction lasting also eight hours in the same subject area of US GAAP. Results show that SPACE was significantly better with regard to strategic knowledge and applying problem solving skills. In other words, the study showed that SPACE is superior to classroom instruction in this area of knowledge acquisition and application. In the other areas of basic skills to calculate POC and conceptional knowledge, differences were not significant between the classroom instruction and SPACE. When SPACE is employed under realistic conditions, i.e. in business, it can be assumed that SPACE is even more superior to classroom instruction. eingesetzt wird.
KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure

Comparative genomics of virulent Tannerella forsythia ATCC 43037 and a close health-associated relative, Tannerella BU063, revealed, in the latter, the absence of an entire array of genes encoding putative secretory proteases that possess a nearly identical C-terminal domain (CTD) that ends with a -Lys-Leu-Ile-Lys-Lys motif. This observation suggests that these proteins, referred to as KLIKK proteases, may function as virulence factors. Re-sequencing of the loci of the KLIKK proteases found only six genes grouped in two clusters. All six genes were expressed by T. forsythia in routine culture conditions, although at different levels. More importantly, a transcript of each gene was detected in gingival crevicular fluid (GCF) from periodontitis sites infected with T. forsythia indicating that the proteases are expressed in vivo. In each protein, a protease domain was flanked by a unique N-terminal profragment and a C-terminal extension ending with the CTD. Partially purified recombinant proteases showed variable levels of proteolytic activity in zymography gels and toward protein substrates, including collagen, gelatin, elastin, and casein. Taken together, these results indicate that the pathogenic strain of T. forsythia secretes active proteases capable of degrading an array of host proteins, which likely represents an important pathogenic feature of this bacterium.
AVS2 speech and audio coding scheme for high quality at low bitrates

With the increasing number of portable and wireless devices and the expanding of wireless network bandwidth, there is a growing demand for high quality and low bitrate speech and audio codec. This paper presents a speech and audio codec, which is based upon AVS P10. In our presented codec, ACELP and TCX technology is adopted, and also presents a hybrid bandwidth extension to coding high band signal. The paper gives an overview of the codec architecture and presents results of formal listening tests, objective test, and complicity of algorithm comparing this new codec with ITU-T G.718 and AVS P10. This result shows a comparable performance and forms the basis of the reference model in the ongoing AVS standardization activity for AVS2 speech and audio coding.
Trace Amine-Associated Receptor 1 Modulates Dopaminergic Activity

The recent identification of the trace amine-associated receptor (TAAR)1 provides an opportunity to dissociate the effects of trace amines on the dopamine transporter from receptor-mediated effects. To separate both effects on a physiological level, a Taar1 knockout mouse line was generated. Taar1 knockout mice display increased sensitivity to amphetamine as revealed by enhanced amphetamine-triggered increases in locomotor activity and augmented striatal release of dopamine compared with wild-type animals. Under baseline conditions, locomotion and extracellular striatal dopamine levels were similar between Taar1 knockout and wild-type mice. Electrophysiological recordings revealed an elevated spontaneous firing rate of dopaminergic neurons in the ventral tegmental area of Taar1 knock-out mice. The endogenous TAAR1 agonist p-tyramine specifically decreased the spike frequency of these neurons in wild-type but not in Taar1 knockout mice, consistent with the prominent expression of Taar1 in the ventral tegmental area. Taken together, the data reveal TAAR1 as regulator of dopaminergic neurotransmission.
Morphological alterations of cell wall concomitant with protein release in a protein-producing bacterium, Bacillus brevis 47

Bacillus brevis 47 secreted vast amounts of protein into the medium and had a characteristic three-layered cell wall. The three layers are designated, from the outermost to the innermost layer, as the outer wall (4.2 nm), the middle wall(8.5 nm), and the inner wall (2.1-3.7 nm). The inner wall might be a peptidoglycan layer. The fine cell wall structure was morphologically altered to various extents, depending on the growth period. At the early stationary phase of growth, cells began to shed the outer two layers of a limited area of the surface. This shedding was complete after further cell growth. The morphological alterations in the cell wall occurred concomitantly with a prominent increase in protein excretion. When protein secretion was severely inhibited by growing cells with Mg2+, morphological alterations in the cell wall were not observed, even at the late stationary phase of growth. This was also the case with a nonprotein-producing mutant, strain 47-5-25. When cells were incubated in buffers, the outer two layers of the cell wall were specifically removed, leaving cells surrounded only by the inner wall layer. The layers removed by incubation were recovered by high-speed centrifugation. This fraction consisted of two layers resembling the outer and middle wall layers. Protein secreted by B. brevis 47-5 consisted mainly of two proteins with approximate molecular weights of 150,000 and 130,000. Proteins released by incubating cells in buffers and proteins in the outer- and middle-wall-enriched fraction were also composed mainly of two proteins with the same molecular weights as those secreted into the medium. Therefore, we conclude that B. brevis 47 secretes proteins derived from the outer two layers of cell wall and these components are synthesized even after the shedding of the outer two layers.
Complex formation of MukB, MukE and MukF proteins involved in chromosome partitioning in Escherichia coli

mukF, mukE and mukB genes are essential for the process of chromosome partitioning in Escherichia coli. We have studied protein–protein interactions among MukB, MukE and MukF proteins by co‐immunoprecipitation and sucrose gradient sedimentation experiments, using mukFEB null cells harboring plasmids carrying the wild‐type or mutant‐type mukFEB operon. MukB forms a complex with MukF and MukE. Analysis of mutant MukB proteins suggested that MukF and MukE bind the C‐terminal globular domain of MukB. MukF is indispensable for an interaction between MukB and MukE; however, MukF itself is able to associate with MukB even in the absence of MukE. We have also found that MukF has a Ca2+‐binding activity. Although purified MukF was able to make a complex either with MukE or MukB, a complex consisting of the three Muk proteins was barely detected in vitro. However, increasing the Ca2+ or Mg2+ concentration in the reaction partially restored complex formation. This suggests that Ca2+ or Mg2+ may be required for the formation of a complex consisting of the three Muk proteins, and thus may participate in a particular step during chromosome partitioning.
‘It’s not something I’m proud of but it’s … just how I feel’: local surfer perspectives of localism

This article focuses on a defining concept of modern surfing: localism. Using a qualitative ethnographic approach, the data for this study were collected using participant observation, field notes and interviews between 2008 and 2009 with a significant population of local surfers in a village location in Cornwall, South West of England, UK. Developing Bennett’s definition of localism, data suggested a benign form of localism and in conveying this, we make a number of associated observations. Our analysis considers how a process of Othering led to the construction of Established Insiders based primarily on location, rather than gender. These Established Insiders saw the need to protect their community and its way of life from Outsiders. The focal point for protection was the liminal space/phase that opened up on ‘their’ local waves, as it was through temporal space that communitas was generated and thus community sustained. We illustrate how benign localism was exacerbated by overcrowding and how local surfers’ experiences of localism made them aware of their becoming Outsiders in other surfing localities, modifying their behaviour accordingly. The paper also suggests that debates about localism need to view the concept as a continuum of attitudes and behaviours ranging from the benign to the heavy, and that attention needs paying to how localism varies between contexts and the ways in which localism may share social antecedents. Lastly, we highlight the utility of viewing the beach and wave as liminal spaces that give rise to communitas for those who surf it together regularly.
A first step towards text-independent voice conversion

So far, all conventional voice conversion approaches are text-dependent, i.e., they need equivalent training utterances of source and target speaker. Since several recently proposed applications call for renouncing this requirement, in this paper, we present an algorithm which finds corresponding time frames within text-independent training data. The performance of this algorithm is tested by means of a voice conversion framework based on linear transformation of the spectral envelope. Experimental results are reported on a Spanish cross-gender corpus utilizing several objective error measures.