Miracle-dz/UniFAR-FTUs huggingface dataset:
Gonad RNA-specific qRT-PCR analyses identify genes with potential functions in schistosome reproduction such as SmFz1 and SmFGFRs

In the search for new strategies to fight schistosomiasis, the unique reproductive biology of Schistosoma mansoni has come into the focus of research. The development of the gonads and the ability of egg production are fundamental not only for continuing the life cycle but also for pathogenicity. Previous studies of schistosome biology demonstrated an influence of pairing on gonad development of the female and on gene expression profiles in both genders. Due to the limited access to specific tissues, however, most of these studies were done at the level of whole worms neglecting individual tissues that may be targets of pairing-dependent processes. Recently, we established a protocol allowing the isolation of testes and ovaries from adult S. mansoni. Here, we describe tissue-specific qRT-PCR analyses comparing transcript levels of selected genes on the basis of RNA from gonads and whole worms. Gene expression in ovary and testes was in some cases found to be significantly influenced by pairing, which was not traceable in whole worms. Among the candidate genes identified as regulated by pairing in gonads were the frizzled homolog SmFz1 and the two fibroblast growth factor receptor homologs SmFGFR-A and SmFGFR-B. First functional characterizations were done, including comparative qRT-PCR analyses, in situ-localization experiments, heterologous expression in Xenopus oocytes (SmFGFR-A/B), and inhibitor studies using the Fz/Dvl-pathway inhibitor 3289-8625, or BIBF1120 blocking FGFR-signaling. Besides confirming gonad localization and receptor functions, inhibitor-induced phenotypes were observed in vitro such as decreased egg production as well as drastic effects on gonad differentiation, morphology, embryogenesis, and survival of adult worms. In summary, these results emphasise the usefulness of tissue-specific qRT-PCRs for selection of candidate genes with important roles in reproduction, allowing subsequent studies to determine their suitability as drug targets.
A Constraint-Based Analysis of Association with Focus in Japanese

In this paper, I present an explicit analysis of association with focus in Japanese. The proposed formal analysis, basically couched in Rooth's (1985) alternative semantics supported by the syntactic devices of HPSG, captures the behaviors of focus particles in Japanese in a fairly straightforward manner. Section 1 is devoted to a survey of data and definitions of key terms and concepts in this paper. In section 2, I present my analysis and explain in detail how it accounts for the observed phenomena. 1 Focus and focus particles in Japanese The term "focus", as it is used in the context of modern generative linguistics, typically refers to some prosodic prominence which functions as indicating certain semantic and pragmatic emphasis (Rooth, 1996, 271). Since Rooth (1985), much attention has been paid to a class of function words called focus particles (FPs), representatives of which in English include only, even and also, that interact in a certain way with the phenomenon of focus (ICOnig, 1991). Typically, an FP appears with a focused phrase which is marked by a readily detectable pitch accent. The significance of the interaction between FPs and focused phrases is that it affects the truth-conditional interpretation of the sentences. Thus, the following sentences from Rooth (1985, 2) have different truth conditions although they are composed of exactly the same string of words:1 (1) a. I only introduced BillF to Sue. b. I only introduced Bill to SueF. (la) is true when I introduced Bill and no one else to Sue. ( lb), on the other hand, is true when I introduced Bill to Sue and to no one else. Under the situation where I introduced Bill and Mary to Sue and no one else to anyone else, ( la) is false while (lb) is true. It is clear that the interpretation of the sentence is crucially dependent on what is the focused phrase. That is, the focused phrase is what the FP only is interpreted with respect to. This phenomenon is termed as "association with focus" (Jackendoff, 1972; Rooth, 1985). In (la), for example, we say that the FP only associates with the focused phrase Bill. In English, association with focus is more or less a clear-cut phenomenon. What is focused in a given sentence can be largely determined by phonologically observable evidence. In Japanese, on the other hand, the situation is somewhat obscured. Phonological stress does play a role in indicating a certain kind of emphasis in a sentence. But it is far less clear, as compared to English, whether what we call "focus particles" in Japanese (perhaps so named because they most closely resemble English ones in terms of their function and meaning) interact with something that can be independently defined by 1 In this paper, I mark the focused phrase with the subscript F. The definition of the term "focus" as used in this paper is given below.
Evaluation of diverse controller Strategic for a level process

This paper proposes different tuning methods of PID controller for a level process. Four different controller tuning methods are taken. They are closed Ziegler Nicholos(ZN) method, Modified Ziegler Nicholos(M-ZN) method [without overshoot], Cohen Coon(CC) method and Model Predictive Control method(MPC). These four methods are compared and listed out in a table. Among these MPC method is the best tuning method of PID for a level process.
Structure of the rhesus monkey TRIM5α PRYSPRY domain, the HIV capsid recognition module

Tripartite motif protein TRIM5α blocks retroviral replication after cell entry, and species-specific differences in its activity are determined by sequence variations within the C-terminal B30.2/PRYSPRY domain. Here we report a high-resolution structure of a TRIM5α PRYSPRY domain, the PRYSPRY of the rhesus monkey TRIM5α that potently restricts HIV infection, and identify features involved in its interaction with the HIV capsid. The extensive capsid-binding interface maps on the structurally divergent face of the protein formed by hypervariable loop segments, confirming that TRIM5α evolution is largely determined by its binding specificity. Interactions with the capsid are mediated by flexible variable loops via a mechanism that parallels antigen recognition by IgM antibodies, a similarity that may help explain some of the unusual functional properties of TRIM5α. Distinctive features of this pathogen-recognition interface, such as structural plasticity conferred by the mobile v1 segment and interaction with multiple epitopes, may allow restriction of divergent retroviruses and increase resistance to capsid mutations.
DUBbing Cancer: Deubiquitylating Enzymes Involved in Epigenetics, DNA Damage and the Cell Cycle As Therapeutic Targets

Controlling cell proliferation is one of the hallmarks of cancer. A number of critical checkpoints ascertain progression through the different stages of the cell cycle, which can be aborted when perturbed, for instance by errors in DNA replication and repair. These molecular checkpoints are regulated by a number of proteins that need to be present at the right time and quantity. The ubiquitin system has emerged as a central player controlling the fate and function of such molecules such as cyclins, oncogenes and components of the DNA repair machinery. In particular, proteases that cleave ubiquitin chains, referred to as deubiquitylating enzymes (DUBs), have attracted recent attention due to their accessibility to modulation by small molecules. In this review, we describe recent evidence of the critical role of DUBs in aspects of cell cycle checkpoint control, associated DNA repair mechanisms and regulation of transcription, representing pathways altered in cancer. Therefore, DUBs involved in these processes emerge as potentially critical targets for the treatment of not only hematological, but potentially also solid tumors.
Symmetric Binary Random Signals With Given Spectral Properties

The usual known methods for generating signals with given marginal probability and spectral properties cannot be applied to binary signals widely used in theoretical problems and communications systems. To overcome this difficulty, we first present some structural properties of power spectral densities, enabling the precise definition of the concept of spectral properties. This allows us to introduce a new method valid for symmetric binary random signals. This method uses some specific properties of filters with random impulse responses. Results of computer simulations show clearly the good performance of this method. Some extensions by using random thinning can further improve its performance.
You Never Forget How to Drive: Driver Skilling and Deskilling in the Advent of Autonomous Vehicles

In the scope of autonomous driving, the question arises if the increased use of automated systems will have an impact on driver's skills in handling the car in the long term. In order to gain more insights on the issue of driver deskilling and how it relates to driving experience and time intervals of non-driving, we conducted an online survey (n=703) considering three driver groups. We found that initial skilling is more of an issue than deskilling after long periods of driving inactivity, i.e., while once learned driving skills seem to remain stable after longer periods of non-driving, they are much more influenced by driving experience in terms of annual mileage and frequency of use. Applied to the autonomous context, this means that drivers must be trained to a high enough skill level or require sufficient manual driving experience, in order to be able to react properly when driving themselves.
Variation in the Oral Processing of Everyday Meals Is Associated with Fullness and Meal Size; A Potential Nudge to Reduce Energy Intake?

Laboratory studies have demonstrated that experimental manipulations of oral processing can have a marked effect on energy intake. Here, we explored whether variations in oral processing across a range of unmodified everyday meals could affect post-meal fullness and meal size. In Study 1, female participants (N = 12) attended the laboratory over 20 lunchtime sessions to consume a 400-kcal portion of a different commercially available pre-packaged meal. Prior to consumption, expected satiation was assessed. During each meal, oral processing was characterised using: (i) video-recordings of the mouth and (ii) real-time measures of plate weight. Hunger and fullness ratings were elicited pre- and post-consumption, and for a further three hours. Foods that were eaten slowly had higher expected satiation and delivered more satiation and satiety. Building on these findings, in Study 2 we selected two meals (identical energy density) from Study 1 that were equally liked but maximised differences in oral processing. On separate days, male and female participants (N = 24) consumed a 400-kcal portion of either the “fast” or “slow” meal followed by an ad libitum meal (either the same food or a dessert). When continuing with the same food, participants consumed less of the slow meal. Further, differences in food intake during the ad libitum meal were not compensated at a subsequent snacking opportunity an hour later. Together, these findings suggest that variations in oral processing across a range of unmodified everyday meals can affect fullness after consuming a fixed portion and can also impact meal size. Modifying food form to encourage increased oral processing (albeit to a lesser extent than in experimental manipulations) might represent a viable target for food manufacturers to help to nudge consumers to manage their weight.
STELLAR POPULATIONS AND RADIAL MIGRATIONS IN VIRGO DISK GALAXIES

We present new stellar age profiles, derived from well-resolved optical and near-infrared images of 64 Virgo cluster disk galaxies, whose analysis poses a challenge for current disk galaxy formation models. Our ability to break the age–metallicity degeneracy and the significant size of our sample represent key improvements over complementary studies of field disk galaxies. Our results can be summarized as follows: first, and contrary to observations of disk galaxies in the field, these cluster galaxies are distributed almost equally amongst the three main types of disk galaxy luminosity profiles (I/II/III), indicating that the formation and/or survival of Type II breaks is suppressed within the cluster environment. Second, we find examples of statistically significant inversions (“U-shapes”) in the age profiles of all three disk galaxy types, reminiscent of predictions from high-resolution simulations of classically truncated Type II disks in the field. These features characterize the age profiles for only about a third (⩽36%) of each disk galaxy type in our sample. An even smaller fraction of cluster disks (∼11% of the total sample) exhibit age profiles that decrease outward (i.e., negative age gradients). Instead, flat and/or positive age gradients prevail (⩾50%) within our Type I, II, and III subsamples. These observations thus suggest that while stellar migrations and inside-out growth can play a significant role in the evolution of all disk galaxy types, other factors contributing to the evolution of galaxies can overwhelm the predicted signatures of these processes. We interpret our observations through a scenario whereby Virgo cluster disk galaxies formed initially like their brethren in the field but which, upon falling into the cluster, were transformed into their present state through external processes linked to the environment (e.g., ram-pressure stripping and harassment). Current disk galaxy formation models, which have largely focused on field galaxies, fail to reproduce these results, thus calling for adequate hydrodynamical simulations of dense galaxy environments if we are to understand cluster disks. The current paper highlights numerous constraints for such simulations. In the Appendix, we confirm the claim by Erwin et al. that Type II breaks are absent in Virgo cluster S0s and discuss the detection of Type III breaks in such galaxies.
Quantum mechanics as complex probability theory

Realistic quantum mechanics based on complex probability theory is shown to have a frequency interpretation, to coexist with Bell's theorem, to be linear, to include wavefunctions which are expansions in eigenfunctions of Hermitian operators and to describe both pure and mixed systems. Illustrative examples are given. The quantum version of Bayesian inference is discussed. Postscript version of hep-th/9307019.
Morphological and molecular characterisation of Heliconema hainanensis sp. nov. (Spirurina: Physalopteridae) from congers in the South China Sea, with a key to the species of Heliconema

Heliconema hainanensis sp. nov. collected from Uroconger lepturus (Richardson) (Anguilliformes: Congridae), Muraenesox cinereus (Forsskål) and Congresox talabonoides (Bleeker) (Anguilliformes: Muraenesocidae) in the South China Sea was described using light and scanning electron microscopy. The new species differs from its congeners by the following morphology: pseudolabia, the number and arrangement of caudal papillae (4 pairs of pedunculate precloacal papillae arranged in 2 groups of 2 and 2 pairs and 6 pairs of pedunculate postcloacal papillae arranged in 4 groups of 1, 2, 1 and 2 pairs), the length of spicules [left spicule 0.51-0.69 mm, right spicule 0.20-0.27 mm, spicule (right:left) ratio 1:2.20-2.69] and the morphology of the female tail tip. In addition, specimens of the new species collected from the three different hosts and specimens of an unidentified species of Heliconema collected from U. lepturus were characterised using molecular methods by sequencing the internal transcribed spacer (ITS) of ribosomal DNA. Analyses and comparison of the ITS sequence of H. hainanensis sp. nov. with Heliconema sp. support the validity of the new species based on morphological observations. An identification key to the species of Heliconema is also provided.
Linear Discrete-time Set-valued Pareto-nash-stackelberg Control Processes and Their Principles

Abstract Mathematical models of linear discrete-time set-valued Pareto-Nash-Stackelberg control processes are examined as extension of mono-valued Pareto-Nash-Stackelberg control models proposed by V. Ungureanu in [10]. A straightforward principle is applied to solve Pareto-Nash-Stackelberg control problems. Models and results are presented in natural order by beginning with the simplest case and, by sequential considering of more general cases, the results for the highlighted Pareto-Nash-Stackelberg set-valued control are presented. The maximum principle of Pontryagin is extended for considered control processes, too.
VOLUMES, TRACES AND ZETA FUNCTIONS

Let Q(x) be a quadratic form over R n . The Epstein zeta function associ- ated to Q(x) is a well known function in number theory. We generalize the construc- tion of the Epstein zeta function to a class of function ϕ(x) defined in R n that we call A−homogeneous, where A is a real aquare matrix of order n having each eigenvalue in the left hal space Re λ > 0. Such a class includes all the homogeneous polyno- mials (positive outside the origin) and all the norms on R n which are smooth outside the origin. As in the classical (i.e. quadratic) case we prov e that such zeta functions are obtained from the Mellin transforms of theta function of Jacobi type associated to the A−homogeneous function ϕ(x). We prove that the zeta function associated to a A−homogeneous function ϕ(x) which is positive and smooth outside the origin is an entire meromorphic function having a unique simple pole at s = α the trace of the ma- trix A with residue given by the product of the trace α and the Lebesgue volume of the unit ball associated to ϕ(x), that is the volume of the set x ∈ IR n satisfying ϕ(x) < 1. We also prove that the theta funtion associated to ϕ(x) has an asymptotic expansion near the origin. We find that the coefficients of such expansio n depend on the values that the zeta function associated to ϕ(x) assumes at the negative integers.
Non-altering time scales for aggregation of dynamic networks into series of graphs

Many dynamic networks coming from real-world contexts are link streams, i.e. a finite collection of triplets (u,v,t) where u and v are two nodes having a link between them at time t. A great number of studies on these objects start by aggregating the data on disjoint time windows of length Δ in order to obtain a series of graphs on which are made all subsequent analyses. Here we are concerned with the impact of the chosen Δ on the obtained graph series. We address the fundamental question of knowing whether a series of graphs formed using a given Δ faithfully describes the original link stream. We answer the question by showing that such dynamic networks exhibit a threshold for Δ, which we call the saturation scale, beyond which the properties of propagation of the link stream are altered, while they are mostly preserved before. We design an automatic method to determine the saturation scale of any link stream, which we apply and validate on several real-world datasets.
Hedge Detection and Scope Finding by Sequence Labeling with Procedural Feature Selection

This paper presents a system which adopts a standard sequence labeling technique for hedge detection and scope finding. For the first task, hedge detection, we formulate it as a hedge labeling problem, while for the second task, we use a two-step labeling strategy, one for hedge cue labeling and the other for scope finding. In particular, various kinds of syntactic features are systemically exploited and effectively integrated using a large-scale normalized feature selection method. Evaluation on the CoNLL-2010 shared task shows that our system achieves stable and competitive results for all the closed tasks. Furthermore, post-deadline experiments show that the performance can be much further improved using a sufficient feature selection.
Traffic control in an ATM network using fuzzy set theory

Due to the demand for high-speed and multimedia services, ATM (asynchronous transfer mode) networks have increasingly received high attention. The multimedia services in ATM networks have diverse traffic characteristics and service requirements, appropriate traffic controls of call admission and congestion are needed so as to guarantee the required quality of service (QOS) for services. Previous studies on the traffic control were based on the results of queueing analyses. In the present paper, an alternative traffic control for admission in conjunction with congestion based on fuzzy set theory are proposed for an ATM network. The performance evaluation via simulation shows the effectiveness of the proposed method in comparison with the equivalent capacity in Guerin et al. (1991); link utilization is effectively improved by 8% while keeping the QOS contract. <<ETX>>
Development of a food handling gripper considering an appetizing presentation

In recent years, industrial robots have been applied to food production because of its huge potential market. Although cooking large amount of foods are done by specially designed cooking machines, dishing up the cooked foods remains as a labor-intensive task. To solve this problem, this paper proposes a new food handling gripper which is suitable for lunch box setout considering appetizing shape of presentation. A two degree-of-freedom multi-fingered gripper with a sliding push part was developed, and evaluated by grasping experiments with noodles and simmered foods. The gripper could put the food with a circular cone shape and control the amount of grasped food.
Deletion Mutants of VPg Reveal New Cytopathology Determinants in a Picornavirus

Background Success of a viral infection requires that each infected cell delivers a sufficient number of infectious particles to allow new rounds of infection. In picornaviruses, viral replication is initiated by the viral polymerase and a viral-coded protein, termed VPg, that primes RNA synthesis. Foot-and-mouth disease virus (FMDV) is exceptional among picornaviruses in that its genome encodes 3 copies of VPg. Why FMDV encodes three VPgs is unknown. Methodology and Principal Findings We have constructed four mutant FMDVs that encode only one VPg: either VPg1, VPg3, or two chimeric versions containing part of VPg1 and VPg3. All mutants, except that encoding only VPg1, were replication-competent. Unexpectedly, despite being replication-competent, the mutants did not form plaques on BHK-21 cell monolayers. The one-VPg mutant FMDVs released lower amounts of encapsidated viral RNA to the extracellular environment than wild type FMDV, suggesting that deficient plaque formation was associated with insufficient release of infectious progeny. Mutant FMDVs subjected to serial passages in BHK-21 cells regained plaque-forming capacity without modification of the number of copies of VPg. Substitutions in non-structural proteins 2C, 3A and VPg were associated with restoration of plaque formation. Specifically, replacement R55W in 2C was repeatedly found in several mutant viruses that had regained competence in plaque development. The effect of R55W in 2C was to mediate an increase in the extracellular viral RNA release without a detectable increase of total viral RNA that correlated with an enhanced capacity to alter and detach BHK-21 cells from the monolayer, the first stage of cell killing. Conclusions The results link the VPg copies in the FMDV genome with the cytopathology capacity of the virus, and have unveiled yet another function of 2C: modulation of picornavirus cell-to-cell transmission. Implications for picornaviruses pathogenesis are discussed.