Miracle-dz/UniFAR-FTUs huggingface dataset:
Joint Robust Voicing Detection and Pitch Estimation Based on Residual Harmonics

This paper focuses on the problem of pitch tracking in noisy conditions. A method using harmonic information in the residual signal is presented. The proposed criterion is used both for pitch estimation, as well as for determining the voicing segments of speech. In the experiments, the method is compared to six state-of-the-art pitch trackers on the Keele and CSTR databases. The proposed technique is shown to be particularly robust to additive noise, leading to a significant improvement in adverse conditions. Index Terms: fundamental frequency, pitch tracking, pitch estimation, voicing decisions
A User Preference Guided Approach to Conflict Resolution in Rule-Based Expert Systems

An approach to conflict resolution in rule-based expert systems that incorporates a behaviorally relevant generalization of multiattri-bute utility theory is proposed. The intent of this approach is to take into account preferential knowledge, specific to the user and/or situation, in rule selection. This knowledge will enhance the user's perception of the system's capability and hence the system's acceptability.
From Regular to Context Free to Mildly Context Sensitive Tree Rewriting Systems: The Path of Child Language Acquisition

Current syntactic theory limits the range of grammatical variation so severely that the logical problem of grammar learning is trivial. Yet, children exhibit characteristic stages in syntactic development at least through their sixth year. Rather than positing maturational delays, I suggest that acquisition difficulties are the result of limitations in manipulating grammatical representations. I argue that the genesis of complex sentences reflects increasing generative capacity in the systems generating structural descriptions: conjoined clauses demand only a regular tree rewriting system; sentential embedding uses a context-free tree substitution grammar; modification requires TAG, a mildly context-sensitive system.
Minimal Residual Disease in Hairy Cell Leukemia Patients Assessed by Clone-Specific Polymerase Chain Reaction

Cladribine induces long-term complete remission in hairy cell leukemia (HCL) patients but does not clear minimal residual disease (MRD) according to high-sensitivity PCR assays. To quantify MRD in patients after anti-CD22 recombinant immunotoxin BL22 and other agents, we used a relative quantitative PCR (RQ-PCR) assay using a primer and probe, both patient specific for the immunoglobulin heavy chain rearrangement. Using this method, we were able to detect one Bonna 12 HCL cell in either 106 Jurkat cells or in 106 normal mononuclear cells. We studied 84 samples from 10 patients, taken before or after treatment with BL22 and other agents. Patient-specific RQ-PCR was much more sensitive than flow cytometry, which in turn was (as recently reported) more sensitive than PCR using consensus primers. RQ-PCR was positive in 62 of 62 (100%) flow-positive samples in 10 patients and in 20 of 22 (91%) flow-negative samples in six patients. The relative level of MRD as quantified by RQ-PCR correlated with disease status and remission. Thus, patient-specific RQ-PCR is the most sensitive test for MRD in HCL patients and could be used to determine maximal response in patients obtaining multiple cycles of nonmyelotoxic biological treatment for this disease.
Short‐Term Clinical Exposure Evaluation of a Second‐Generation Electrically Heated Cigarette Smoking System

This randomized, controlled, forced‐switching, open‐label, parallel‐group study in 100 adult male and female smokers of conventional cigarettes evaluated 8 biomarkers of tobacco smoke exposure. After baseline exposure determinations, adult smokers were switched to a second‐generation electrically heated cigarette smoking system (EHCSS) for 8 days in a clinical setting. After 8 days of smoking the EHCSS biomarkers of exposure decreased by 43% to 85% compared to baseline. After correction for residual effects (carryover effects due to long elimination half‐life and non‐tobacco‐confounding sources of exposure), reductions in exposure ranged from 59% to 97%. Results from this short‐term clinical exposure study indicate that switching from a conventional cigarette to a second‐generation electrically heated cigarette smoking system substantially reduced the exposure to several measured potentially harmful constituents of tobacco smoke.
Peptide alarmone signalling triggers an auto‐active bacteriocin necessary for genetic competence

The induction of genetic competence is a strategy used by bacteria to increase their genetic repertoire under stressful environmental conditions. Recently, Streptococcus pneumoniae has been shown to co‐ordinate the uptake of transforming DNA with fratricide via increased expression of the peptide pheromone responsible for competence induction. Here, we document that environmental stress‐induced expression of the peptide pheromone competence‐stimulating peptide (CSP) in the oral pathogen Streptococcus mutans. We showed that CSP is involved in the stress response and determined the CSP‐induced regulon in S. mutans by microarray analysis. Contrary to pneumococcus, S. mutans responds to increased concentrations of CSP by cell lysis in only a fraction of the population. We have focused on the mechanism of cell lysis and have identified a novel bacteriocin as the ‘death effector’. Most importantly, we showed that this bacteriocin causes cell death via a novel mechanism of action: intracellular action against self. We have also identified the cognate bacteriocin immunity protein, which resides in a separate unlinked genetic locus to allow its differential regulation. The role of the lytic response in S. mutans competence is also discussed. Together, these findings reveal a novel autolytic pathway in S. mutans which may be involved in the dissemination of fitness‐enhancing genes in the oral biofilm.
ROSeAnn: Reconciling Opinions of Semantic Annotators

Named entity extractors can be used to enrich both text and Web documents with semantic annotations. While originally focused on a few standard entity types, the ecosystem of annotators is becoming increasingly diverse, with recognition capabilities ranging from generic to specialised entity types. Both the overlap and the diversity in annotator vocabularies motivate the need for managing and integrating semantic annotations: allowing users to see the results of multiple annotations and to merge them into a unified solution.We demonstrate ROSEANN, a system for the management of semantic annotations. ROSEANN provides users with a unified view over the opinion of multiple independent annotators both on text and Web documents. It allows users to understand and reconcile conflicts between annotations via ontology-aware aggregation. ROSEANN incorporates both supervised aggregation, appropriate when representative training data is available, and an unsupervised method based on the notion of weighted-repair.
Body Mass Index: Effects on Overt Behaviors and Perceived Reward

The incidence of obesity, defined as a BMI [body mass index] of over 30, has increased by 50% in the past 20 years (Carlson, 2004). Some notable behavioral differences as a function of weight have been identified, including the findings that individuals with obesity participate less often in physical activities, and spend more time engaging in sedentary behaviors. Using a daily-dairy assessment method as completed by undergraduate college students (n=99), the current study examined the impact of BMI on the duration of time spent and pleasure experienced within 13 behavioral domains: 1) Social, 2) Physical, 3) Health/Hygiene, 4) Spiritual, 5) Educational, 6) Sedentary, 7) Sexual, 8) Employment or Volunteering, 9) Hobbies and Recreation, 10) Eating Alone 11) Eating with Others, 12) Travel, and 13) Other. Controlling for depression, anxiety, and locus of control, both univariate and multivariate statistics suggested non-significant relationships between BMI and duration and reward level of behaviors. Study limitations and future directions are discussed. BMI, ACTIVITY, AND REWARD v Table of
Continuous Tracking Control for a Compliant Actuator With Two-Stage Stiffness

Emerging applications of robots with direct physical interactions with humans have led to the development of a variety of series elastic actuators (SEAs) which are compliant, force controllable, and back drivable. The performance of current SEAs is mainly dependent on the specific stiffness of the spring. In our previous work, a compliant actuator with two-stage stiffness has been designed to overcome the performance limitations in current SEAs. The key novelty is that a low-stiffness spring and a high-stiffness spring are employed instead of a single spring in current SEAs, which has the advantages of high fidelity, low output impedance, and also large force range and bandwidth. In this paper, a tracking control scheme is proposed for the compliant actuator with two-stage stiffness. Although the overall stiffness is discontinuous, the proposed controller is continuous by integrating different control modes for two springs into a single one. The transition between control modes is smooth and embedded inside the controller, and it is also automatically realized by monitoring the output force of the actuator. The stability and convergence of the closed-loop system are analyzed, and experimental results are presented to demonstrate the effectiveness of the proposed control scheme.Note to Practitioners—An SEA is developed by placing an elastic element into the actuator; this elasticity gives SEAs several unique properties including low mechanical output impedance, tolerance to impact loads, and passive mechanical energy storage, which makes it suitable for human–robot interaction. The performance of existing SEAs is highly dependent on the stiffness of a single spring. To overcome the limitations, a novel SEA with two-stage stiffness was proposed in our previous work. This paper suggests a continuous tracking control method for the proposed compliant actuator. Although the overall stiffness is discontinuous, the transition between different control modes for two springs is smooth and automatically realized. Experimental results show that the output force of the actuator is bounded. In future research, uncertainties in actuator dynamics will be considered, such that system identification or calibration is not required.
Methods for the Design and Analysis of Sedimentation Velocity and Sedimentation Equilibrium Experiments with Proteins

Analytical ultracentrifugation experiments play an integral role in the solution phase characterization of recombinant proteins and other biological macromolecules. This unit discusses the design of sedimentation velocity and sedimentation equilibrium experiments performed with a Beckman Optima XL‐A or XL‐I analytical ultracentrifuge. Optimal instrument settings and experimental design considerations are explained, and strategies for the analysis of experimental data with the UltraScan data analysis software package are presented. Special attention is paid to the strengths and weaknesses of the available detectors, and guidance is provided on how to extract maximum information from analytical ultracentrifugation experiments. Curr. Protoc. Protein Sci. 60:7.13. 1‐7.13. 24. © 2010 by John Wiley & Sons, Inc.
Santa: Faster Packet Delivery for Commonly Wished Replies

Increasing network speeds challenge the packet processing performance of networked systems. This can mainly be attributed to processing overhead caused by the split between the kernel-space network stack and user-space applications. To mitigate this overhead, we propose Santa, an application agnostic kernel-level cache of frequent requests. By allowing user-space applications to offload frequent requests to the kernel-space, Santa offers drastic performance improvements and unlocks the speed of kernel-space networking for legacy server software without requiring extensive changes.
Benchmarking a reduced multivariate polynomial pattern classifier

A novel method using a reduced multivariate polynomial model has been developed for biometric decision fusion where simplicity and ease of use could be a concern. However, much to our surprise, the reduced model was found to have good classification accuracy for several commonly used data sets from the Web. In this paper, we extend the single output model to a multiple outputs model to handle multiple class problems. The method is particularly suitable for problems with small number of features and large number of examples. The basic component of this polynomial model boils down to construction of new pattern features which are sums of the original features and combination of these new and original features using power and product terms. A linear regularized least-squares predictor is then built using these constructed features. The number of constructed feature terms varies linearly with the order of the polynomial, instead of having a power law in the case of full multivariate polynomials. The method is simple as it amounts to only a few lines of Matlab code. We perform extensive experiments on this reduced model using 42 data sets. Our results compared remarkably well with best reported results of several commonly used algorithms from the literature. Both the classification accuracy and efficiency aspects are reported for this reduced model.
Neural-Network-Based Online HJB Solution for Optimal Robust Guaranteed Cost Control of Continuous-Time Uncertain Nonlinear Systems

In this paper, the infinite horizon optimal robust guaranteed cost control of continuous-time uncertain nonlinear systems is investigated using neural-network-based online solution of Hamilton-Jacobi-Bellman (HJB) equation. By establishing an appropriate bounded function and defining a modified cost function, the optimal robust guaranteed cost control problem is transformed into an optimal control problem. It can be observed that the optimal cost function of the nominal system is nothing but the optimal guaranteed cost of the original uncertain system. A critic neural network is constructed to facilitate the solution of the modified HJB equation corresponding to the nominal system. More importantly, an additional stabilizing term is introduced for helping to verify the stability, which reinforces the updating process of the weight vector and reduces the requirement of an initial stabilizing control. The uniform ultimate boundedness of the closed-loop system is analyzed by using the Lyapunov approach as well. Two simulation examples are provided to verify the effectiveness of the present control approach.
The Problem of Computing the Most Probable Tree in Data-Oriented Parsing and Stochastic Tree Grammars

We deal with the question as to whether there exists a polynomial time algorithm for computing the most probable parse tree of a sentence generated by a data-oriented parsing (DOP) model. (Scha, 1990; Bod, 1992, 1993a). Therefore we describe DOP as a stochastic tree-substitution grammar (STSG). In STSG, a tree can be generated by exponentially many derivations involving different elementary trees. The probability of a tree is equal to the sum of the probabil i t ies of all its derivations. We show that in STSG, in contrast with stochastic context-free grammar, the Viterbi algorithm cannot be used for computing a most probable tree of a string. We propose a simple modification of Viterbi which allows by means of a " s e l e c t r a n d o m " search to es t ima te the most probable tree of a string in polynomial time. Experiments with DOP on ATIS show that only in 68% of the cases, the most probable derivation of a string generates the most probable tree of that string. Therefore, the parse accuracy obtained by the most probable trees (96%) is dramatically higher than the parse accuracy obtained by the most probable derivations (65%). It is still an open question whether the mos t p robab le tree of a string can be deterministically computed in polynomial time. 1 Data-Oriented Parsing A Data-Oriented Parsing model (Scha, 1990; Bod, 1992, 1993a) is characterized by a corpus of analyzed language utterances, together with a set of operations that combine sub-analyses from the corpus into new analyses. We will limit ourselves in this paper to corpora with purely syntactic annotations. For the semantic dimension of DOP, the reader is referred to (van den Berg et al., 1994). Consider the imaginary example corpus consisting of only two trees in figure 1. We will assume one operation for combining subtrees. This operation is called "composition", and is indicated by the infix operator o. The composition of t and u, tou, yields a copy of t in which its leftmost nonterminal leaf node has been identified with the roof node of u (i.e., u is subs t i tu ted on the leftmost nonterminal leaf node of t). For reasons of simplicity we will write in the following (tou)ov as:
Mutagenesis-generated mouse models of human infertility with abnormal sperm.

BACKGROUND The aetiology of human male fertility, with impairment of sperm number, motility and morphology (oligoasthenoteratozoospermia), has been difficult to understand, partly for lack of animal models. METHODS An ethylnitrosourea (ENU) mutagenesis strategy has been successful in producing heritable gene mutations with phenotypes similar to human male infertility, and here, we describe three independent ENU-induced mutations that cause a phenotype of oligoasthenoteratozoospermia in mice. RESULTS The loci identified by these three mutations are designated swm2, repro2 and repro3. All mutant males were characterized by low sperm concentration, poor sperm morphology and negligible motility, but the infertile males were apparently normal in other respects. Sperm from mutant males failed to fertilize oocytes in vitro. Ultrastructural analyses revealed varied abnormalities apparent in both testicular spermatids and epididymal sperm. Genetic mapping placed the swm2 gene on chromosome 7, the repro2 gene on chromosome 5 and the repro3 gene on chromosome 10. CONCLUSION The single-gene mutations caused complex and non-specific sperm pathologies, a point with important implications for managing cases of human male infertility. The ultimate identification of the loci for the mutations causing these phenotypes will clarify aetiology of complex syndromes of infertility with sperm abnormalities consistent with oligoasthenoteratozoospermia.
Season-dependent Postembryonic Maturation of the Diurnal Rhythm of Melatonin Biosynthesis in the Chicken Pineal Gland

Previously, we have demonstrated that the timing of the nocturnal peak of activity of the pineal arylalkylamine-N-acetyltransferase – a key enzyme in the melatonin biosynthesis pathway – in 3-wk-old chickens kept from the day of hatch under controlled laboratory conditions (L:D 12:12) varies depending on the season of hatch (summer vs. winter). The present study was undertaken to answer the following questions: (1) are season-related differences seen in the level of transcription of genes encoding enzymes of the melatonin biosynthesis pathway? (2) Does the pineal content of the main precursor (serotonin) and the final product (melatonin) exhibit age- and season-related changes? (3) At which step in postembryonic development are these season-related variations in pineal gland function most pronounced? Male Hy-line chickens hatched in the summer or winter, from eggs laid by hens held on L:D 16:8, were kept from the day of hatch under L:D 12:12 conditions. At the age of 2, 9, or 16 d, chickens were sacrificed every 2 h over a 24-h period and their pineal glands, isolated under dim red light, were processed for the measurement of (i) the level of Aanat and Asmt (acetylserotonin O-methyltransferase) mRNAs encoding the two last enzymes involved in melatonin biosynthesis, (ii) the activity of these enzymes, and (iii) the pineal content of serotonin and melatonin. Circadian rhythmicity of all the measured parameters was evaluated by the cosinor method. The levels of Aanat mRNA, AANAT enzymatic activity, and the pineal melatonin content changed during postembryonic development in a manner that was dependent on the season of hatch. Furthermore, the diurnal profile of Asmt mRNA was elevated during the light phase. In “winter” birds, the pattern and amplitude of the diurnal rhythm of accumulation of this transcript did not change with age, while in “summer” birds it increased in an age-related way. In contrast, the enzymatic activity of hydroxyindole-O-methyltransferase (HIOMT; encoded by the Asmt gene) did not change rhythmically, although it increased with age in a season-related way. In “winter” chickens, the pineal serotonin content was low, regardless of age, and did not change rhythmically, whereas in “summer” individuals the serotonin rhythm was already well established by day 2, with the amplitude increasing with age. These results confirm the existence of a “seasonal memory” operating within the chicken pineal gland, although the mechanism(s) underlying this phenomenon have yet to be characterized.
Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use

Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools, keeping in mind the minimum interaction information a researcher would need, in comparison to manual analysis has not been carried out. We compared data generated using some of the selected NLP tools with manually curated protein interaction data (PathArt and IMaps) to comparatively determine the recall and precision rate. The rates were found to be lower than the published scores when a normalized definition for interaction is considered. Each data point captured wrongly or not picked up by the tool was analyzed. Our evaluation brings forth critical failures of NLP tools and provides pointers for the development of an ideal NLP tool.
Spectral Analysis of the Transition Operator and Its Applications to Smoothness Analysis of Wavelets

This paper investigates spectral properties of the transition operator associated to a multivariate vector refinement equation and their applications to the study of smoothness of the corresponding refinable vector of functions. Let $\Phi=(\phi_1,\ldots,\phi_r)^T$ be an $r \times 1$ vector of compactly supported functions in $L_2(\Rs)$ satisfying $\,\Phi = \sum_{\ga\in\Zs} a(\ga) \Phi({M\kern .1em \cdot}-\ga)$, where M is an expansive integer matrix. The smoothness of $\Phi$ is measured by the Sobolev critical exponent $\gl (\Phi) := \sup \bigl\{ \gl: \int_{\Rs} |\hat \phi_j(\xi)|^2(1+|\xi|^\gl)^2\,d\xi<\infty, \, 1 \le j\le r \bigr\}$. Suppose %the mask $a$ is finitely supported, i.e., %the set $M$ is similar to %a diagonal matrix $\hbox{diag}(\gs_1,\ldots,\gs_s)$ with $|\gs_1|=\cdots=|\gs_s|$ and $\supp a := \{\ga\in\Zs: a(\ga) \ne 0\}$ is finite. For $\mu=(\mu_1,\ldots,\mu_s)\in\NN_0^s$, define $\gs^{-\mu} := \gs_1^{-\mu_1} \cdots \gs_s^{-\mu_s}$. Let $A := \sum_{\ga\in\Zs} a(\ga)/|\det M|$ and $b(\ga) := \sum_{\gb\in\Zs} \overline{a(\gb)} \otimes a(\ga+\gb)/|\det M|$, $\ga\in\Zs$, where $\,\otimes\,$ denotes the (right) Kronecker product. Suppose that the highest total degree of polynomials reproduced by $\Phi$ is $k-1$ and $\spec(A)$ (the spectrum of $A$) is $\{\eta_1,\eta_2, \ldots,\eta_r\}$ with $\eta_1=1$ and $\eta_j \ne 1, 2\le j\le r$. Set $$ E_k := \{ \eta_j \overline{\gs^{-\mu}}, \overline{\eta_j} \gs^{-\mu}: |\mu|