Miracle-dz/UniFAR-FTUs huggingface dataset:
The network motif architecture of dominance hierarchies

The widespread existence of dominance hierarchies has been a central puzzle in social evolution, yet we lack a framework for synthesizing the vast empirical data on hierarchy structure in animal groups. We applied network motif analysis to compare the structures of dominance networks from data published over the past 80 years. Overall patterns of dominance relations, including some aspects of non-interactions, were strikingly similar across disparate group types. For example, nearly all groups exhibited high frequencies of transitive triads, whereas cycles were very rare. Moreover, pass-along triads were rare, and double-dominant triads were common in most groups. These patterns did not vary in any systematic way across taxa, study settings (captive or wild) or group size. Two factors significantly affected network motif structure: the proportion of dyads that were observed to interact and the interaction rates of the top-ranked individuals. Thus, study design (i.e. how many interactions were observed) and the behaviour of key individuals in the group could explain much of the variations we see in social hierarchies across animals. Our findings confirm the ubiquity of dominance hierarchies across all animal systems, and demonstrate that network analysis provides new avenues for comparative analyses of social hierarchies.
Multifeature Prostate Cancer Diagnosis and Gleason Grading of Histological Images

We present a study of image features for cancer diagnosis and Gleason grading of the histological images of prostate. In diagnosis, the tissue image is classified into the tumor and nontumor classes. In Gleason grading, which characterizes tumor aggressiveness, the image is classified as containing a low- or high-grade tumor. The image sets used in this paper consisted of 367 and 268 color images for the diagnosis and Gleason grading problems, respectively, and were captured from representative areas of hematoxylin and eosin-stained tissue retrieved from tissue microarray cores or whole sections. The primary contribution of this paper is to aggregate color, texture, and morphometric cues at the global and histological object levels for classification. Features representing different visual cues were combined in a supervised learning framework. We compared the performance of Gaussian, -nearest neighbor, and support vector machine classifiers together with the sequential forward feature selection algorithm. On diagnosis, using a five-fold cross-validation estimate, an accuracy of 96.7% was obtained. On Gleason grading, the achieved accuracy of classification into low- and high-grade classes was 81.0%.
The topology of symplectic circle bundles

We consider circle bundles over compact three-manifolds with symplectic total spaces. We show that the base of such a space must be irreducible or the product of the two-sphere with the circle. We then deduce that such a bundle admits a symplectic form if and only if it admits one that is invariant under the circle action in three special cases: namely if the base is Seifert bered, has vanishing Thurston norm, or if the total space admits a Lefschetz bration.
Dynamic regression models and their applications in survival and reliability analysis

This thesis was designed to explore the dynamic regression models, assessing the sta-tistical inference for the survival and reliability data analysis. These dynamic regressionmodels that we have been considered including the parametric proportional hazards andaccelerated failure time models contain the possibly time-dependent covariates. We dis-cussed the following problems in this thesis.At first, we presented a generalized chi-squared test statisticsY2nthat is a convenient tofit the survival and reliability data analysis in presence of three cases: complete, censoredand censored with covariates. We described in detail the theory and the mechanism to usedofY2ntest statistic in the survival and reliability data analysis. Next, we considered theflexible parametric models, evaluating the statistical significance of them by usingY2nandlog-likelihood test statistics. These parametric models include the accelerated failure time(AFT) and a proportional hazards (PH) models based on the Hypertabastic distribution.These two models are proposed to investigate the distribution of the survival and reliabilitydata in comparison with some other parametric models. The simulation studies were de-signed, to demonstrate the asymptotically normally distributed of the maximum likelihood estimators of Hypertabastic’s parameter, to validate of the asymptotically property of Y2n test statistic for Hypertabastic distribution when the right censoring probability equal 0% and 20%. n the last chapter, we applied those two parametric models above to three scenes ofthe real-life data. The first one was done the data set given by Freireich et al. on thecomparison of two treatment groups with additional information about log white blood cellcount, to test the ability of a therapy to prolong the remission times of the acute leukemiapatients. It showed that Hypertabastic AFT model is an accurate model for this dataset.The second one was done on the brain tumour study with malignant glioma patients, givenby Sauerbrei & Schumacher. It showed that the best model is Hypertabastic PH onadding five significance covariates. The third application was done on the data set given by Semenova & Bitukov on the survival times of the multiple myeloma patients. We did not propose an exactly model for this dataset. Because of that was an existing oneintersection of survival times. We, therefore, suggest fitting other dynamic model as SimpleCross-Effect model for this dataset.
Automatic Recognition of Emotions from the Acoustic Speech Signal 1

This research aims at investigating several feature sets such as acoustic, lexical, and discourse features, and classification algorithms for classifying spoken utterances based on the emotional state of the speaker [1]. Besides applications in enabling natural human machine interfaces, the problem motivates development of novel classification algorithms that can operate with sparse data. Another aim is to find out the way to seamlessly combine the emotion recognition system with state-of-the-art speech recognition system, and the satisfactory dialog management of the automated call center system to better support human-computer interaction in that application.
Consistency and regularity in past-tense verb generation in healthy ageing, Alzheimer's disease, and semantic dementia

Older adults, individuals with dementia of the Alzheimer's type (DAT), and individuals with semantic dementia (SD) produced the past tense of verbs based on present-tense carrier sentences (e.g., Everyday I ding the bell. Yesterday I_____the bell). Both regularity (i.e., whether or not -ed is used for the past tense) and consistency (i.e., the degree to which verbs of similar orthography and phonology in the present tense have similar past tenses to the target) were manipulated. Participants received regular consistent (e.g., land–landed), regular inconsistent (e.g., weed–weeded), irregular consistent (e.g., sting–stung), and irregular inconsistent (e.g., light–lit) verbs. The dependent measures were overall accuracy rates and error rate types (e.g., regularizations, analogies, and other errors). Both consistency and regularity influenced performance. In addition, individuals with DAT showed a disproportionate deficit for inconsistent verbs associated with a high summed frequency of enemies, whereas SD individuals produced disproportionate breakdowns in performance on regular inconsistent, irregular consistent, and irregular inconsistent verbs. These results are consistent with the perspective that semantic/lexical processes are involved in processing the past tense of both irregular verbs and regular inconsistent verbs, and that attention is used to select appropriate responses and control inappropriate responses.
Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

Transcriptional regulation of all genes is initiated by the specific binding of regulatory proteins called transcription factors to specific sites on DNA called promoter regions. Transcription factors employ a variety of mechanisms to recognise their DNA target sites. In the last few decades, attempts have been made to describe these mechanisms by general sets of rules and associated models. We give an overview of these models, starting with a historical review of the somewhat controversial issue of a "recognition code" governing protein-DNA interaction. We then present a probabilistic framework in which advantages and disadvantages of various models can be discussed. Finally, we conclude that simplifying assumptions about additivity of interactions are sufficiently justified in many situations (and can be suitably extended in other situations) to allow a unifying concept of a "probabilistic code" for protein-DNA recognition to be defined.
Human-inspired robot navigation in unknown dynamic environments

This paper proposes a novel algorithm for mobile robot navigation in completely unknown dynamic environments involving humans. Unlike existing navigation algorithms that assume full knowledge of the environment, i.e. position, direction and velocity of all obstacles, the proposed algorithm is only based on the local sensory information. The algorithm, inspired from pedestrian studies, has a proxemics-based local reactive planner that works on a cognitive representation of the environment. It enables the robot to mimic human-like responses in navigation. The efficiency of the algorithm is studied and analyzed through extensive quantitative simulations for different complexities of the environment and the results exhibit a good performance.
A Mitogen-activated Protein Kinase Kinase Kinase Mediates Reactive Oxygen Species Homeostasis in Arabidopsis*

Mitogen-activated protein kinase kinase kinases (MAPKKKs) play key roles in intra- and extracellular signaling in eukaryotes. Here we report that the MAPKKK MEKK1 regulates redox homeostasis in Arabidopsis. We show that MEKK1-deficient plants are misregulated in the expression of a number of genes involved in cellular redox control and accumulate reactive oxygen species (ROS). Most strikingly, homozygous mekk1 mutant plants exhibit a lethal phenotype when developing true leaves. MEKK1 kinase activity and protein stability was regulated by H2O2 in a proteasome-dependent manner and mekk1 plants were compromised in ROS-induced MAPK MPK4 activation. Whereas mpk3 and mpk6 knock out plants showed no defects in development or changes in redox control genes, mpk4 null mutant shared several phenotypic and transcript profile features with mekk1 plants. In agreement with the concept that ROS negatively regulates auxin responses in plants, mekk1 and mpk4 mutants show reduced expression of several auxin-inducible marker genes. Overall, our data defines MPK4 as downstream target of MEKK1 and show that MEKK1 functions in integrating ROS homeostasis with plant development and hormone signaling.
Neon Abundances in B Stars of the Orion Association: Solving the Solar Model Problem?

We report on non-LTE Ne abundances for a sample of B-type stellar members of the Orion association. The abundances were derived by means of non-LTE fully metal-blanketed model atmospheres and extensive model atoms with updated atomic data. We find that these young stars have a very homogeneous abundance of A(Ne) = 8.11 ± 0.04. This abundance is higher by ~0.3 dex than the currently adopted solar value, A(Ne) = 7.84, which is derived from lines produced in the corona and active regions. The general agreement between the abundances of C, N, and O derived for B stars with the solar abundances of these elements derived from three-dimensional hydrodynamical models atmospheres strongly suggests that the abundance patterns of the light elements in the Sun and B stars are broadly similar. If this hypothesis is true, then the Ne abundance derived here will help to reconcile solar models with helioseismological observations.
Robust speech communication and its embedded smart robot system

This paper introduces our developed noise robust speech communication techniques and its LSI implementation. The speech communication system consists of automatic speech detection, speech recognition and speech rejection. The developed noise robust speech processing can reduce various noises in many environments. In addition to the design of noise robust speech recognition, the LSI design of this system has been introduced. By using the design of speech recognition ASIC (application specific IC), we can realize low power consumption and real time processing at the same time. As current speech recognition accuracy, the system can realize 85%-99% under 0-20 dB SNR and echo environments.
Development of a Text-Dependent Speaker Recognition System

Speaker recognition is the ability of recognizing a person based on his voice. Many modalities and techniques have been applied to achieve the task of authentication, ranging from retina scans to finger prints. This paper presents a TextDependent model for automatic Speaker Recognition. Features extractor are based on Mel-Frequency Cepstrum Coefficients (MFCCs) and Linear Predictive Coding (LPC) analysis technique which aids the translation of incoming speech into a feature value. Also, a recognizer block, employs the two techniques (MFCC and LPC) to get an hybrid features for speaker identification/verification system. An experiment was carried out on the threshold from 75% to 95% at 5% differential to know the performance of the MFCCs and LPC identification/verification system. From the experiment carried out, the result shows that LPC outperforms MFCCs and a combination. The text-dependent speaker recognition system was implemented using Java Programming Language (Java Speech Application Programming Interface (JSAPI) ). The system is developed for access control into computer systems and could be used for access control where security is considered to be of utmost important.
Semantically Enhanced Pronouns

This paper revisits the relationship between the form of referring expressions and the assumed salience of their referents. Previous work suggests that pronouns must refer to highly salient discourse entities, while descriptive noun phrases should be used to refer to less salient items. Our claim is that the referring expression itself is only part of this relationship, since it is not the only constituent that contributes semantic constraints that bear on its referent. Semantic constraints can be contributed by additional constituents, and such Semantically Enhanced pronouns may coherently refer to less salient entities, even entities not previously mentioned in the
Generalized permutation patterns and a classification of the Mahonian statistics

We introduce generalized permutation patterns, where we allow the requirement that two adjacent letters in a pattern must be adjacent in the permutation. We show that essentially all Mahonian permutation statistics in the literature can be written as linear combinations of such patterns. Almost all known Mahonian permutation statistics can be written as linear combinations of patterns of length at most 3. There are only fourteen possible such Mahonian statistics, which we list. Of these, eight are known and we give proofs for another three. The remaining three we conjecture to be Mahonian. We also give an explicit numerical description of the combinations of patterns a Mahonian statistic must have, depending on the maximal length of its patterns.
The Interplay of Work-Family Life and Psychosocial Adjustment for International Graduate Students

The purpose of this paper is to critically review the literature on the interplay of work-family life and psychosocial adjustment of married international graduate students to the United States, provide evidence for a complicated and integrated support mechanism for married international graduate students, and make specific recommendations. Empirical studies on student and expatriate work-family life and psychosocial adjustment are reviewed. Studies indicated a significant negative relationship between work-family conflict and (a) life satisfaction, (b) work satisfaction, and (c) family satisfaction. Moreover, studies signified a positive relationship between work-family balance and (a) psychological well-being and (b) sociocultural adjustment. Due to the difficulty of separating work and family domains for married international graduate students, it will be critical to find ways to support international graduate students’ work and family life in an integrated way, which would help with their psychosocial adjustment to the United States. This support could be done through organizing seminars or workshops on healthy work-family balance, having their spouses involved in the graduate student orientation program, or discussing work-family issues and their influence on married graduate students’ lives through group programs. The paper’s implications would be of value to married international graduate students who are planning to study in a foreign country by helping ease their adjustment process.
Recent results in antenna pattern measurement with UAVs

A novel antenna measurement strategy has been developed to characterize both the embedded-element and the array patterns in the real installation conditions at low frequencies (50 MHz - 650 MHz) [1]. It exploits a micro Unmanned Aerial Vehicle (UAV) as a far-field test source. The system demonstrated good performance on the copolarization radiation pattern of VHF and UHF antennas. Several results with reference antennas have been published [2, 3]. Further experiments have been performed on the Aperture Array Verification System (AAVS0) array and the Medicina Array Demonstrator (MAD), which also focus on the calibration of a small array and the beam forming. This paper presents two recent experiments performed on a log-periodic antenna at 250 MHz and 350 MHz. Significant results have been achieved for both co- and cross-polarization patterns. Moreover, the symmetry of the test-source pattern has also been demonstrated.
Upper limit on C60 and C60+ features in the ISO-SWS spectrum of the reflection nebula NGC 7023

We present here the 7.0-8.7 micron spectrum of the bright reflection nebula NGC 7023. Our observations are made with the Short Wavelength Spectrometer (SWS) on the European satellite Infrared Space Observatory (ISO). The vibrational bands of the ionized fullerene C60+ are expected at 7.11 and 7.51 microns, while those of the neutral fullerene C60 are expected at 7.0 and 8.45 microns. We estimate an upper limit in NGC 7023 for the C60+ abundance of <0.26% of the interstellar abundance of carbon, while C60 contains <0.27% of interstellar carbon.
A DATA-DRIVEN INDEXING APPROACH FOR CHINESE SPOKEN DOCUMENT RETRIEVAL

The choice of indexing features is critical to the performance of a retrieval system. Predefined, overlapping, fixed-length term sequences are widely used in many retrieval systems. However, predefined feature sets are often riddled with meaningless and non-informative terms, which unavoidably degrades retrieval performance, and explodes the feature set. In this paper we present a statistical approach to derive data-driven term segments as features. We let the data to tell which features are important and which are not. The results show that very satisfactory performance can be achieved with these data-driven indexing features while retaining very compact feature set size. This approach also has the potential to identify domain-specific terminologies or newly-generated phrases.
Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model

An RNA secondary structure is saturated if no base pairs can be added without violating the definition of secondary structure. Here we describe a new algorithm, RNAsat, which for a given RNA sequence a, an integral temperature 0 <or= T <or= 100 in degrees Celsius, and for all integers k, computes the Boltzmann partition function Z(k)(T)(a) = SigmaSepsilonSAT(k)(a) exp(-E(S)/RT), where the sum is over all saturated secondary structures of a which have exactly k base pairs, R is the universal gas constant and E(S) denotes the free energy with respect to the Turner nearest neighbor energy model. By dynamic programming, we compute Z(k)(T)simultaneously for all values of k in time O(n(5)) and space O(n(3)). Additionally, RNAsat computes the partition function Q(k)(T)(a) = SigmaSepsilonS(k)(a) exp(-E(S)/RT), where the sum is over all secondary structures of a which have k base pairs; the latter computation is performed simultaneously for all values of k in O(n(4)) time and O(n(3)) space. Lastly, using the partition function Z(k)(T) [resp. Q(k)(T)] with stochastic backtracking, RNAsat rigorously samples the collection of saturated secondary structures [resp. secondary structures] having k base pairs; for Q(k)(T) this provides a parametrized form of Sfold sampling (Ding and Lawrence, 2003). Using RNAsat, (i) we compute the ensemble free energy for saturated secondary structures having k base pairs, (ii) show cooperativity of the Turner model, (iii) demonstrate a temperature-dependent phase transition, (iv) illustrate the predictive advantage of RNAsat for precursor microRNA cel-mir-72 of C. elegans and for the pseudoknot PKB 00152 of Pseudobase (van Batenburg et al., 2001), (v) illustrate the RNA shapes (Giegerich et al., 2004) of sampled secondary structures [resp. saturated structures] having exactly k base pairs. A web server for RNAsat is under construction at bioinformatics.bc. edu/clotelab/RNAsat/.
Pirfenidone in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease without proven effective therapy. A multicentre, double-blind, placebo-controlled, randomised phase III clinical trial was conducted in Japanese patients with well-defined IPF to determine the efficacy and safety of pirfenidone, a novel antifibrotic oral agent, over 52 weeks. Of 275 patients randomised (high-dose, 1,800 mg·day−1; low-dose, 1,200 mg·day−1; or placebo groups in the ratio 2:1:2), 267 patients were evaluated for the efficacy of pirfenidone. Prior to unblinding, the primary end-point was revised; the change in vital capacity (VC) was assessed at week 52. Secondary end-points included the progression-free survival (PFS) time. Significant differences were observed in VC decline (primary end-point) between the placebo group (-0.16 L) and the high-dose group (-0.09 L) (p = 0.0416); differences between the two groups (p = 0.0280) were also observed in the PFS (the secondary end-point). Although photosensitivity, a well-established side-effect of pirfenidone, was the major adverse event in this study, it was mild in severity in most of the patients. Pirfenidone was relatively well tolerated in patients with IPF. Treatment with pirfenidone may decrease the rate of decline in VC and may increase the PFS time over 52 weeks. Additional studies are needed to confirm these findings.