Miracle-dz/UniFAR-FTUs huggingface dataset:
The Epstein-Barr virus Zta transactivator: a member of the bZIP family with unique DNA-binding specificity and a dimerization domain that lacks the characteristic heptad leucine zipper motif

Introduction of the zta gene of Epstein-Barr virus into latently infected B cells leads to induction of the entire lytic cycle program of the virus. The Zta gene product is a sequence-specific DNA-binding protein of 35 kilodaltons that behaves as a specific transcriptional transactivator in transient cotransfection assays. All known Zta-responsive target promoters contain one or more members of a family of consensus-binding sites known as ZREs. On the basis of the presence of limited amino acid similarity within a basic carboxy-terminal domain, Zta has been proposed to be a highly divergent member of the c-Jun/c-Fos/GCN4 family of AP-1-binding proteins. We show here that in vitro-translated Zta and the Jun:Fos proteins have overlapping but distinct target DNA-binding specificies; both recognize canonical AP-1 sites, but only Zta recognizes ZRE sites and only Jun:Fos recognizes CRE sites. The relative binding affinity of Zta for oligonucleotides containing the 7-base-pair c-Fos AP-1 site TGAGTCA was twofold greater than that for the ZRE core motifs TGAGCAA, TG TGCAA, and TGAGTAA, but 10-fold greater than that for TGTGTCA, as measured by gel mobility retardation and competition DNA-binding assays. Cross-linking and cotranslational heterodimerization assays showed that like GCN4, Zta forms a stable homodimer in both its DNA-bound and unbound forms. Furthermore, we show that a potential coiled-coil helical domain adjacent to the basic domain of Zta can substitute for the leucine zipper of c-Fos to produce a DNA-binding protein that has a very stringent target DNA specificity and can only recognize symmetric 9-base-pair AP-1 sites (ATGAGTCAT). Therefore, despite the absence of the repeated heptad leucine zipper motifs, the Zta protein retains the characteristic features of a juxtaposed basic region and an exactly aligned coiled-coil alpha-helical dimerization domain of the bZIP class of transcriptional regulatory factors.
Removal of Heavy Metals from Aqueous Solution Using Novel Nanoengineered Sorbents: Self‐Assembled Carbamoylphosphonic Acids on Mesoporous Silica

Self‐assembled monolayers of carbamoylphosphonic acids (acetamide phosphonic acid and propionamide phosphonic acid) on mesoporous silica supports were studied as potential absorbents for heavy and transition metal ions in aqueous wastes. The adsorption capacity, selectivity, and kinetics of the materials in sequestering metal ions, including Cd2 +, Co2 +, Cu2 +, Cr3 +, Pb2 +, Ni2 +, Zn2 +, and Mn2 +, were measured in batch experiments with excess sodium ion. The solution pH ranged from 2.2 to 5.5. The kinetics study shows that the adsorption reached equilibrium in seconds, indicating that there is little resistance to mass transfer, intraparticle diffusion, and surface chemical reaction. The competitive adsorption study found the phosphonic acid‐SAMMS to have an affinity for divalent metal ions in decreasing order of Pb2 + > Cu2 + > Mn2 + > Cd2 + > Zn2 + > Co2 + > Ni2 +. The measured Cd2 +adsorption isotherm was of the Langmuirian type and had a saturation binding capacity of 0.32 mmol/g.
Speech recognition using weighted HMM and subspace projection approaches

A weighted hidden Markov model (HMM) algorithm and a subspace projection algorithm are proposed to address the discrimination and robustness issues for HMM-based speech recognition. A robust two-stage classifier is also proposed to incorporate these two approaches to further improve the performance. The weighted HMM enhances its discrimination power by first jointly considering the state likelihoods of different word models, then assigning a weight to the likelihood of each state, according to its contribution in discriminating words. The robustness of this model is then improved by increasing the likelihood difference between the top and the second candidates. The subspace projection approach discards unreliable observations on the basis of maximizing the divergence between different word pairs. To improve robustness, the mean of each cluster is then adjusted to obtain maximum separation different clusters. The performance was evaluated with a highly confusable vocabulary consisting of the nine English E-set words. The test was conducted in a multispeaker (100 talkers), isolated-word mode. The 61.7% word accuracy for the original HMM-based system was improved to 74.9% and 76.6%, respectively, by using the weighted HMM and the subspace projection methods. By incorporating the weighted HMM in the first stage and the subspace projection in the second stage, the two-stage classifier achieved a word accuracy of 79.4%. >
Une famille de matrices sparses pour une modélisation multi-échelle par blocs

Résumé. La sériation est une technique d’analyse de données qui ordonne les observations directement à partir de leur tableau de valeurs afin de révéler une structure intrinsèque à ces données. Une telle approche présente de nombreux avantages de visualisation mais dès lors que les données sont bruitées ou que les groupes se superposent, la visualisation de toute structure devient difficile. Pour faire face à ces problèmes, nous introduisons de la parcimonie dans les données à travers une famille de matrices indicatrices de voisins communs. Celles-ci sont ordonnées selon un algorithme de type branch and bound et la matrice révélant la meilleure structure au sens de "diagonale par blocs" est sélectionnée au moyen d’un critère dérivé des problématiques de compression de données. Cet outil de partitionnement identifie des sous-ensembles de données relatifs aux clusters tout en écartant celles qui sont bruitées ou extrêmes ce qui permet de visualiser la structure globale intrinsèque aux données. Cependant, une trop grande sparsité des données amène parfois à l’éviction de données sous-représentées; nous proposons à cet effet, une approche multi-échelle combinant différents niveaux de sparsité dans une même visualisation.
Fast nonlinear time alignment for isolated word recognition

A fast nonlinear time alignment method is presented, which is based on a preprocessing of the normalized speech spectrogram by means of a segmentation of the trace in the spectral feature space. After such trace segmentation the patterns have a fixed format and allow for a subsequent classification with a distance measure which is obtained from conventional dynamic programming with extreme constraints. Since, due to the trace segmentation preprocessing, these extreme constraints can be applied without performance degradation, the described method offers savings in computing time by a factor of 10 or more as compared to conventional dynamic programming. As a side benefit, reference pattern memory savings by a factor of 3 or more are obtained.
Particle-based Gaussian process optimization for input design in nonlinear dynamical models

We propose a novel approach to input design for identification of nonlinear state space models. The optimal input sequence is obtained by maximizing a scalar cost function of the Fisher information matrix. Since the Fisher information matrix is unavailable in closed form, it is estimated using particle methods. In addition, we make use of Gaussian process optimization to find the optimal input and to mitigate the problem of a large computational cost incurred by the particle method, as the method reduces the number of functional evaluations. Numerical examples are provided to illustrate the performance of the resulting algorithm.
Exploring computational thinking assessment in introductory programming courses

Several instruments have been used for assessing Computational Thinking (CT) abilities. In this exploratory and preliminary study, we investigate how appropriate the Bebras challenge is as an instrument to assess and measure CT abilities. Bebras is an international challenge whose goal is to promote Computer Science and CT. The test can be answered without any prior knowledge on computer science. Our broad research question is whether we can evolve Bebras into a full fledged instrument to assess and measure CT abilities. In this paper, we instantiate a few more specific research questions: Is Bebras performance a good predictor of success for students within programming courses? Is there any correlation between Bebras performance and students' grades? Do students improve their performance in Bebras tests when exposed to the contents of a programming course? Our dataset consists of the grades of 138 students who attended introductory programming courses at two Brazilian universities and their performance in two simulated Bebras tests. The first test was applied at the beginning of the term and therefore before any exposition to programming classes. The second one was applied at the end of the term. The results suggest that the performance on Bebras is only moderately correlated to the student grades. We conclude that it is not very likely that CT measures can be derived from the Bebras test as it is currently designed. While further research is needed on how we can leverage the Bebras effort to extend it into a CT assessment instrument, we performed a preliminary study on the use of Item Response Theory (IRT) as a means to improve the selection of questions and the design of the test. We expect the results of this research can contribute both to the development and discussion on CT assessment as well as to the Bebras effort to educate CT.
Radiative quark and lepton masses through soft supersymmetry breaking.

A supersymmetric extension of the standard strong and electroweak gauge model has the property that light quarks and leptons acquire radiative masses as the result of the breaking of a chiral symmetry by soft supersymmetry-breaking terms. This radiative mechanism is then extended to include all known quarks and leptons in the context of a supersymmetric SU(3) x SU(2) x U(1) x U(1)' gauge model based on E/sub 6/ particle content as the possible low-energy limit of a superstring theory.
What happens when clients are evaluated online? Exploring apparatuses of valuation in the individual transportation sector

The article discusses the importance of two-way online rating systems as one of the pillars of the sharing-economy, transforming strangers into trustable providers and customers. The article ́s objective is to apply the concepts and practice based lens developed by Orlikowski and Scott (2014) to a two-way rating system by adding the provider evaluation of their clients. The article also explores the case study of usage of the rating systems by Uber driders (the combination of drivers and riders in São Paulo, Brazil. By conducting semi-structured interviews, a practical usage of rating was explored focusing on its usage, importance, effects on driders, unveiling some unexpected usages of it.
On the architecture and performance of an FFT-based spread-spectrum downlink RAKE receiver

This paper describes a spread-spectrum downlink RAKE receiver that computes data detection in the frequency domain. We assume a pilot signal is transmitted with data signals for channel sounding. The pilot signal does not degrade the receiver bit error rate (BER) performance because the receiver estimates the pilot signal and subtracts the estimated pilot signal from the received signal before data detection. A spreading code matched filter, a channel matched filter, and a sounding receiver are implemented by fast Fourier transform (FFT)-based matched filtering and integrated in a unified architecture. Monte Carlo simulation is used to evaluate the receiver BER performance in both a static channel and a mobile radio channel. Simulation results show that the RAKE receiver performs well in both kinds of channels.
T1-weighted dual-echo MRI for fat quantification in pediatric nonalcoholic fatty liver disease.

AIM To determine in obese children with nonalcoholic fatty liver disease (NAFLD) the accuracy of magnetic resonance imaging (MRI) in assessing liver fat concentration. METHODS A case-control study was performed. Cases were 25 obese children with biopsy-proven NAFLD. Controls were 25 obese children matched for age and gender, without NAFLD at ultrasonography and with normal levels of aminotransferases and insulin. Hepatic fat fraction (HFF) by MRI was obtained using a modification of the Dixon method. RESULTS HFF ranged from 2% to 44% [mean, 19.0% (95% CI, 15.1-27.4)] in children with NAFLD, while in the controls this value ranged from 0.08% to 4.69% [2.0% (1.3-2.5), P < 0.0001]. HFF was highly correlated with histological steatosis (r = 0.883, P < 0.0001) in the NAFLD children. According to the histological grade of steatosis, the mean HFF was 8.7% (95% CI, 6.0-11.6) for mild, 21.6% (15.3-27.0) for moderate, and 39.7% (34.4-45.0) for severe fatty liver infiltration. With a cutoff of 4.85%, HFF had a sensitivity of 95.8% for the diagnosis of histological steatosis ≥ 5%. All control children had HFF lower than 4.85%; thus, the specificity was 100%. After 12 mo, children with weight loss displayed a significant decrease in HFF. CONCLUSION MRI is an accurate methodology for liver fat quantification in pediatric NAFLD.
Gender Identification in Younger and Older Adults: Use of Spectral and Temporal Cues in Noise-Vocoded Speech

Objective: The aim of this study was to investigate potential effects of age on the ability of normal-hearing (NH) adult listeners to utilize spectral and temporal cues when performing a voice gender identification task. Design: Ten younger and 10 older NH adult listeners were measured on their ability to correctly identify the speaker gender of six different vowel tokens (H-/vowel/-D) when spoken by eight speakers (four male and four female). Spectral (number of channels) and temporal cues (low-pass cut-off frequency for temporal envelope extraction) were systematically manipulated using noiseband vocoding techniques; stimuli contained 1, 4, 8, 16, or 32 spectral channels, while the low-pass cut-off frequency of the temporal envelope filter was 20, 50, 100, 200, or 400 Hz. Furthermore, the fundamental frequencies (F0s) of the vowel tokens were manipulated to create two conditions: “Expanded” (large range of F0 values) and “Compressed” (small range of F0 values). Results: In general, younger listeners performed better than the older listeners but only when stimuli were spectrally degraded. For both the Expanded and Compressed conditions, the overall performance of the younger listeners was better than that of the older listeners, suggesting age-related deficits in both spectral and temporal processing. Furthermore, a significant interaction between age group and temporal envelope cues revealed that older listeners received less benefit from increasing temporal envelope information compared with the benefit observed among younger listeners. In particular, the performance of the younger NH group (collapsed across number of channels), but not the older NH group, improved as the temporal envelope cut-off frequency was increased from 50 to 400 Hz. Conclusions: The results reported here support previous findings of senescent declines in perceiving spectrally reduced speech and temporal amplitude modulation processing. These results suggest that when F0 values are similar to one another, younger listeners can use temporal cues alone to glean voice-pitch information but older listeners exhibit a lessened ability to use such cues. Previous studies have demonstrated the importance of temporal envelope cues in periodicity perception (e.g., gender recognition) by cochlear implant listeners. The results of this study suggest that aging affects the use of such cues, and consequently gender recognition might be poorer among older cochlear implant recipients.
Towards a comprehensive model of the cognitive process and mechanisms of individual sensemaking

This review introduces a comprehensive model of the cognitive process and mechanisms of individual sensemaking to provide a theoretical basis for: empirical studies that improve our understanding of the cognitive process and mechanisms of sensemaking and integration of results of such studies; education in critical thinking and sensemaking skills; the design of sensemaking assistant tools that support and guide users.
In vitro influence of Mycoplasma penetrans on activation of peripheral T lymphocytes from healthy donors or human immunodeficiency virus-infected individuals

Mycoplasma penetrans is a mycoplasma species newly isolated from the urine of human immunodeficiency virus (HIV)-infected individuals and presents the only case in which an association has been found between antibodies against a mycoplasma and HIV infection. To further explore the effects of M. penetrans on the immune system, we studied the influence of this mycoplasma on peripheral blood mononuclear cells (PBMCs) from healthy donors and HIV-infected individuals. M. penetrans induced, in addition to blastogenesis of PBMCs, a significant proliferative response associated with the expression of some activation markers such as CD69, HLA-DR, and CD25. This M. penetrans-dependent lymphocyte activation was observed not only in healthy donors but also in HIV-infected persons at different stages of the disease. In addition, our study revealed that both CD4+ and CD8+ T lymphocytes were responsive to M. penetrans. Interestingly, the mitogenic activity of M. penetrans was associated with mycoplasma cells but not with the supernatants of mycoplasma culture. The potent stimulating activity of M. penetrans on T lymphocytes from HIV-infected individuals is of particular interest in view of the supposed contribution of immune activation to HIV replication and disease progression.
Calcium supplementation of the diet: justified by present evidence.

BrMedJ 1990;300:1056-60 In a recent review Kanis and Passmore concluded that there was no case for supplementation of the diet with calcium for the prevention or treatment of osteoporosis.1 We consider that present evidence, taken as a whole, points to a different conclusion. We consider the matter under five main headings: experimental calcium deficiency; human calcium requirements; the relation between calcium intake, bone mass, and bone loss; the relation between calcium and hip fracture; and the role of calcium in established osteoporosis.
Performance Evaluation of a DHT-based Approach to Resource Discovery in Mobile Ad Hoc Networks

Recently, approaches to DHT-style key-based routing explicitly designed for the use in mobile ad hoc networks (MANETs) have been proposed. However, as DHTs are usually no applications as such, a very practical distributed application running on top of such mobile DHTs could be resource discovery. Therefore, in this paper, a DHT-based approach to resource discovery – MAPNaS – will be described in detail and thoroughly evaluated through simulations. We aim at gaining a first insight into the question under which network conditions it is meaningful to perform DHT-based resource discovery and when it would be more advisable to opt for a less complex – e.g. a simple broadcast-based – approach instead. Index Terms – DHT, MANETs, Peer-to-Peer, Service discovery
A novel crosstalk between BRCA1 and poly (ADP-ribose) polymerase 1 in breast cancer

BRCA mutations are the main known hereditary factor for breast cancer. Notably, poly (ADP-ribose) polymerase 1 (PARP1) expression status plays a critical role in breast cancer progression and the clinical development of PARP1 inhibitors to treat BRCA-mutated breast cancer has advanced rapidly. However, dynamic crosstalk between BRCA1 and PARP1 remains largely unknown. Here, we showed that: (i) BRCA1 inactivation events (mutation, promoter methylation, or knockdown) were accompanied by increased PARP1 and nicotinamide adenine dinucleotide (NAD) levels, and a subsequent increase in NAD-dependent PARP1 activity in MDA-MB-231 and primary breast cancer cells; (ii) the overexpression of BRCA1 resulted in decreased PARP1 and NAD levels, and a subsequent impairment in NAD-dependent PARP1 activity in MDA-MB-231 and primary breast cancer cells; and (iii) intracellular NAD levels were largely responsible for regulating PARP1 activity in breast cancer cells, and NAD levels were positively correlated with PARP1 activity in human breast cancer specimens (R = 0.647, P < 0.001). Interestingly, the high efficiency of PARP1 triggered by BRCA1 inactivation may further inhibit BRCA1 transcription by NAD depletion. These results highlight a novel interaction between BRCA1 and PARP1, which may be beneficial for the dynamic balance between BRCA1 and PARP1-related biologic processes, especially for maintaining stable DNA repair ability. All of this may improve our understanding of the basic molecular mechanism underlying BRCA1- and PARP1-related breast cancer progression.
Design and control of stiffness coordination between knee and ankle joints for a hopping legged robot

In order to improve the energy efficiency for the legged robot, we developed a one-legged robot which is inspired by biology to explore the locomotion principle of the legged robot. In this paper, one method is proposed for the stiffness coordination between the knee and ankle joints. We first defined the coordination and the evaluating indicator, and used the PSO algorithm to search the best optimal solution of the ankle spring. Then the control strategies were described for the hopping control, and realized the the continuous hopping by injecting extra energy to the knee joint. Finally, The experiments were implemented on the robot Tigger, whose ankle is just equipped with passive springs while the hip and knee are under actuation, and the effectiveness of our methods were validated through the experiments.