Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting periodicities with Gaussian processes

We consider the problem of detecting and quantifying the periodic component of a function given noise-corrupted observations of a limited number of input/output tuples. Our approach is based on Gaussian process regression, which provides a flexible non-parametric framework for modelling periodic data. We introduce a novel decomposition of the covariance function as the sum of periodic and aperiodic kernels. This decomposition allows for the creation of sub-models which capture the periodic nature of the signal and its complement. To quantify the periodicity of the signal, we derive a periodicity ratio which reflects the uncertainty in the fitted sub-models. Although the method can be applied to many kernels, we give a special emphasis to the Matern family, from the expression of the reproducing kernel Hilbert space inner product to the implementation of the associated periodic kernels in a Gaussian process toolkit. The proposed method is illustrated by considering the detection of periodically expressed genes in the arabidopsis genome.
Corrosion Behaviour of Al (6063) Alloy (As-Cast and Age Hardened) in H2SO4 Solution

The heat treatment and corrosion of aluminum 6063 alloy was investigated. The aim of this work was to determine the effect of heat treatment on the microstructure and the corrosion of aluminum 6063 alloy using weight loss method. The samples conditions were; as-cast, solution treated, supersaturated and age hardened condition. They were soaked in a 10 molar solution of sulphuric acid and monitored with time. The corrosion rate was calculated for various immersion periods. The result shows that the corrosion rate of the alloy was due to the nature of heat treatment given to the samples. Similarly, it was also found that the corrosion rate of the Al(6063) alloy was higher in the as-cast sample compared to the heat treated alloy. The passivation on the heat treated Al(6063) alloy was a little more stable therefore reducing the corrosion rate after 35 days of immersion for the aged hardened samples.
Encoding of phonology in a recurrent neural model of grounded speech

We study the representation and encoding of phonemes in a recurrent neural network model of grounded speech. We use a model which processes images and their spoken descriptions, and projects the visual and auditory representations into the same semantic space. We perform a number of analyses on how information about individual phonemes is encoded in the MFCC features extracted from the speech signal, and the activations of the layers of the model. Via experiments with phoneme decoding and phoneme discrimination we show that phoneme representations are most salient in the lower layers of the model, where low-level signals are processed at a fine-grained level, although a large amount of phonological information is retain at the top recurrent layer. We further find out that the attention mechanism following the top recurrent layer significantly attenuates encoding of phonology and makes the utterance embeddings much more invariant to synonymy. Moreover, a hierarchical clustering of phoneme representations learned by the network shows an organizational structure of phonemes similar to those proposed in linguistics.
Insights into Substrate Specificity and Metal Activation of Mammalian Tetrahedral Aspartyl Aminopeptidase*

Background: Structural determinants of aspartyl aminopeptidase (DNPEP) enzymatic activity have not yet been elucidated. Results: DNPEP contains a binuclear metal active site and forms a tetrahedral homo-dodecamer in solution. Conclusion: Manganese binding at the active site stimulates DNPEP activity. The tetrahedral assembly restricts peptide access to the active site. Significance: This study provides a structural and biochemical basis for understanding DNPEP physiology. Aminopeptidases are key enzymes involved in the regulation of signaling peptide activity. Here, we present a detailed biochemical and structural analysis of an evolutionary highly conserved aspartyl aminopeptidase called DNPEP. We show that this peptidase can cleave multiple physiologically relevant substrates, including angiotensins, and thus may play a key role in regulating neuron function. Using a combination of x-ray crystallography, x-ray absorption spectroscopy, and single particle electron microscopy analysis, we provide the first detailed structural analysis of DNPEP. We show that this enzyme possesses a binuclear zinc-active site in which one of the zinc ions is readily exchangeable with other divalent cations such as manganese, which strongly stimulates the enzymatic activity of the protein. The plasticity of this metal-binding site suggests a mechanism for regulation of DNPEP activity. We also demonstrate that DNPEP assembles into a functionally relevant tetrahedral complex that restricts access of peptide substrates to the active site. These structural data allow rationalization of the enzyme's preference for short peptide substrates with N-terminal acidic residues. This study provides a structural basis for understanding the physiology and bioinorganic chemistry of DNPEP and other M18 family aminopeptidases.
Political Attitudes Develop Independently of Personality Traits

The primary assumption within the recent personality and political orientations literature is that personality traits cause people to develop political attitudes. In contrast, research relying on traditional psychological and developmental theories suggests the relationship between most personality dimensions and political orientations are either not significant or weak. Research from behavioral genetics suggests the covariance between personality and political preferences is not causal, but due to a common, latent genetic factor that mutually influences both. The contradictory assumptions and findings from these research streams have yet to be resolved. This is in part due to the reliance on cross-sectional data and the lack of longitudinal genetically informative data. Here, using two independent longitudinal genetically informative samples, we examine the joint development of personality traits and attitude dimensions to explore the underlying causal mechanisms that drive the relationship between these features and provide a first step in resolving the causal question. We find change in personality over a ten-year period does not predict change in political attitudes, which does not support a causal relationship between personality traits and political attitudes as is frequently assumed. Rather, political attitudes are often more stable than the key personality traits assumed to be predicting them. Finally, the results from our genetic models find that no additional variance is accounted for by the causal pathway from personality traits to political attitudes. Our findings remain consistent with the original construction of the five-factor model of personality and developmental theories on attitude formation, but challenge recent work in this area.
Some aspects of forces and fields in atomic models of crack tips

This paper examines the stresses and displacement gradients in atomistic models of cracks based on an EAM potential devised for aluminum. Methods for computing these quantities are described. Results are presented for two models differing in terms of the orientations of the crack relative to the crystal, a [100] (010) orientation that behaves in a brittle fashion and a [111] (110) orientation that emits partial dislocations prior to extending. Both models display lattice trapping. The stresses in the brittle crack model are compared with the linear elastic prediction and found to be in remarkably good agreement to within distances of about one lattice parameter of the crack tip and at the free surface where contributions from sources other than strain energy (e.g., surface tension) influence the results. Similar results are observed for the ductile model until dislocation emission occurs. The largest stresses that develop just prior to crack extension or dislocation emission are used to estimate the ratio of theoretical tensile strength to shear strength in this material. Eshelby’s conservation integrals, F and M , are also computed. F is found to be essentially contour independent and in agreement with the linear elastic prediction in both models until dislocation emission occurs, at which point a large screening contribution arises from the emitted partials. The contour size dependence of M reveals some interesting features of the crack tip including a slight wobble of the crack tip inside its potential well with changing applied K and the existence of forces acting to move the crack faces apart as blunting occurs.
Overcoming immunosuppressive mechanisms.

Clinical trials have demonstrated from time to time that cancer vaccines can elicit effective antitumour cellular immunity that may translate to clinical benefit for cancer patients. Additionally, several monoclonal antibodies currently used for treating cancer patients mediate their effects through mechanisms like antibody-dependent cellular cytotoxicity (ADCC) and therefore rely on an effective immune system. Patients with advanced tumours, however, are known to have aberrations in their immune function. Improving the clinical effectiveness of immunotherapy therefore depends on having a better understanding of the mechanisms and developing novel strategies to overcome tumour-specific immune suppression.
VHL Mutations Linked to Type 2C von Hippel-Lindau Disease Cause Extensive Structural Perturbations in pVHL*

pVHL (von Hippel-Lindau tumor suppressor protein) is the substrate recognition subunit of the CBCVHL ubiquitin ligase complex promoting the degradation of hypoxia-inducible factor subunits, HIF-1/2α. Mutational inactivation of pVHL causes the hereditary von Hippel-Lindau tumor syndrome, which predisposes affected individuals to hemangioblastomas, renal cell carcinomas, and pheochromocytomas. Whereas the development of hemangioblastomas and renal cell carcinomas has been attributed to impaired HIF-1/2α down-regulation by pVHL mutant proteins, the molecular defects underlying the development of pheochromocytomas are still unknown. Here, we present a detailed biochemical analysis of pVHL mutant proteins linked to type 2C (pheochromocytoma only) von Hippel-Lindau disease. Type 2C-associated mutations caused extensive structural perturbations of pVHL, as revealed by the reduced stability, increased proteolytic susceptibility, and dramatically altered NMR spectrum of recombinant, mutant pVHL-ElonginC-ElonginB complexes in vitro. In human cell lines, type 2C-linked mutations destabilized the CBCVHL ubiquitin ligase complex and resulted in reduced cellular pVHL levels. Together, our data reveal unexpectedly strong structural defects of type 2C-associated pVHL mutant proteins that are likely to affect both HIF-1/2α-related and -unrelated pVHL functions in the pathogenesis of pheochromocytomas.
Phosphodiesterases 3 and 4 Differentially Regulate the Funny Current, If, in Mouse Sinoatrial Node Myocytes

Cardiac pacemaking, at rest and during the sympathetic fight-or-flight response, depends on cAMP (3′,5′-cyclic adenosine monophosphate) signaling in sinoatrial node myocytes (SAMs). The cardiac “funny current” (If) is among the cAMP-sensitive effectors that drive pacemaking in SAMs. If is produced by hyperpolarization-activated, cyclic nucleotide-sensitive (HCN) channels. Voltage-dependent gating of HCN channels is potentiated by cAMP, which acts either by binding directly to the channels or by activating the cAMP-dependent protein kinase (PKA), which phosphorylates them. PKA activity is required for signaling between β adrenergic receptors (βARs) and HCN channels in SAMs but the mechanism that constrains cAMP signaling to a PKA-dependent pathway is unknown. Phosphodiesterases (PDEs) hydrolyze cAMP and form cAMP signaling domains in other types of cardiomyocytes. Here we examine the role of PDEs in regulation of If in SAMs. If was recorded in whole-cell voltage-clamp experiments from acutely-isolated mouse SAMs in the absence or presence of PDE and PKA inhibitors, and before and after βAR stimulation. General PDE inhibition caused a PKA-independent depolarizing shift in the midpoint activation voltage (V1/2) of If at rest and removed the requirement for PKA in βAR-to-HCN signaling. PDE4 inhibition produced a similar PKA-independent depolarizing shift in the V1/2 of If at rest, but did not remove the requirement for PKA in βAR-to-HCN signaling. PDE3 inhibition produced PKA-dependent changes in If both at rest and in response to βAR stimulation. Our results suggest that PDE3 and PDE4 isoforms create distinct cAMP signaling domains that differentially constrain access of cAMP to HCN channels and establish the requirement for PKA in signaling between βARs and HCN channels in SAMs.
Increasing oxidative stress with molsidomine increases blood pressure in genetically hypertensive rats but not normotensive controls.

Spontaneously hypertensive rats (SHR) have a higher level of oxidative stress and exhibit a greater depressor response to a superoxide scavenger, tempol, than normotensive Wistar-Kyoto rats (WKY). This study determined whether an increase in oxidative stress with a superoxide/NO donor, molsidomine, would amplify the blood pressure in SHR. Male SHR and WKY were given molsidomine (30 mg.kg(-1). day(-1)) or vehicle (0.01% ethanol) for 1 wk, and blood pressure, renal hemodynamics, nitrate and nitrite excretion (NOx), renal superoxide production, and expression of renal antioxidant enzymes, Mn- and Cu,Zn-SOD, catalase, and glutathione peroxidase (GPx), were measured. Renal superoxide and NOx were higher in control SHR than in WKY. Molsidomine increased superoxide by approximately 35% and NOx by 250% in both SHR and WKY. Mean arterial blood pressure (MAP) was also higher in control SHR than WKY. Molsidomine increased MAP by 14% and caused renal vasoconstriction in SHR but reduced MAP by 16%, with no effect on renal hemodynamics, in WKY. Renal expression of Mn- and Cu,Zn-SOD was not different between SHR and WKY, but expression of catalase and GPx were approximately 30% lower in kidney of SHR than WKY. The levels of Mn- and Cu,Zn-SOD were not increased with molsidomine in either WKY or SHR. Renal catalase and GPx expression was increased by 300-400% with molsidomine in WKY, but there was no effect in SHR. Increasing oxidative stress elevated blood pressure further in SHR but not WKY. WKY are likely protected because of higher bioavailable levels of NO and the ability to upregulate catalase and GPx.
The reliability and sensitivity of indices related to cardiovascular fitness evaluation

Determining the recovery heart rate (RHR) index after various submaximal exercises is a popular and practical way for a population’s cardiovascular fitness evaluation. These evaluations are based on the regression among RHR, load intensity, and maximal oxygen uptake. However, little work has been done to 1) explore the influences of body weight and height on these tests’ reliability and sensitivity, and 2) compare the reliability among the tests. As a result, practitioners often choose tests without the appropriate criteria. This study researched the mentioned two aspects by evaluating 30 male college students via three common tests – 30 cm step test, 40 cm step test and squat-up-down test. The results showed that the reliability and sensitivity of the three tests were remarkably different. Adding body weight into the evaluation would improve both reliability and sensitivity. Considering all the influence factors, 30 cm step test was the best one. These findings suggested that applying the relative RHR index (normalized by body weight) should be considered for a population’s cardiovascular fitness evaluation in the future.
The DigiHome Service‐Oriented Platform

Nowadays, the computational devices are everywhere. In malls, offices, streets, cars, and even homes, we can find devices providing and consuming functionality to improve the user satisfaction. These devices include sensors that provide information about the environment state (e.g., temperature, occupancy, light levels), service providers (e.g., Internet TVs, GPS), smartphones (that contain user preferences), and actuators that act on the environment (e.g., closing the blinds, activating the alarm, changing the temperature). Although these devices exhibit communication capabilities, their integration into a larger monitoring system remains a challenging task, partly because of the strong heterogeneity of technologies and protocols. Therefore, in this article, we focus on home environments and propose a middleware solution, called DigiHome, that applies the Service Component Architecture (SCA) component model to integrate data and events generated by heterogeneous devices in this kind of environments. DigiHome exploits the SCA extensibility to incorporate the REpresentational State Transfer (REST) architectural style and, in this way, leverages on the integration of multiscale systems‐of‐systems (from wireless sensor networks to the Internet). Additionally, the platform applies Complex Event Processing technology that detects application‐specific situations. We claim that the modularization of concerns fostered by DigiHome and materialized in a service‐oriented architecture, makes it easier to incorporate new services and devices in smart home environments. The benefits of the DigiHome platform are demonstrated on smart home scenarios covering home automation, emergency detection, and energy saving situations. Copyright © 2011 John Wiley & Sons, Ltd.
Improved Approximation for the Number of Hamiltonian Cycles in Dense Digraphs

We propose an improved algorithm for counting the number of Hamiltonian cycles in a directed graph. The basic idea of the method is sequential acceptance/rejection, which is successfully used in approximating the number of perfect matchings in dense bipartite graphs. As a consequence, a new bound on the number of Hamiltonian cycles in a directed graph is proved, by using the ratio of the number of 1-factors. Based on this bound, we prove that our algorithm runs in expected time of $O(n^{8.5})$ for dense problems. This improves the Markov chain method, the most powerful existing method, a factor of at least $n^{4.5}(\log n)^{4}$ in running time. This class of dense problems is shown to be nontrivial in counting, in the sense that it is $#$P-Complete.
Formation of a Functional Maize Centromere after Loss of Centromeric Sequences and Gain of Ectopic Sequences[C][W]

A new centromere is formed using sequences from a chromosome arm. Sequences at the CENH3 binding region, like native centromeres, have higher DNA methylation than average in the genome, and two DNA sequence motifs are abundant in the new binding region and at native centromeres. The maize (Zea mays) B centromere is composed of B centromere–specific repeats (ZmBs), centromere-specific satellite repeats (CentC), and centromeric retrotransposons of maize (CRM). Here we describe a newly formed B centromere in maize, which has lost CentC sequences and has dramatically reduced CRM and ZmBs sequences, but still retains the molecular features of functional centromeres, such as CENH3, H2A phosphorylation at Thr-133, H3 phosphorylation at Ser-10, and Thr-3 immunostaining signals. This new centromere is stable and can be transmitted to offspring through meiosis. Anti-CENH3 chromatin immunoprecipitation sequencing revealed that a 723-kb region from the short arm of chromosome 9 (9S) was involved in the formation of the new centromere. The 723-kb region, which is gene poor and enriched for transposons, contains two abundant DNA motifs. Genes in the new centromere region are still transcribed. The original 723-kb region showed a higher DNA methylation level compared with native centromeres but was not significantly changed when it was involved in new centromere formation. Our results indicate that functional centromeres may be formed without the known centromere-specific sequences, yet the maintenance of a high DNA methylation level seems to be crucial for the proper function of a new centromere.
Co-regularized Multi-view Spectral Clustering

In many clustering problems, we have access to multiple views of the data each of which could be individually used for clustering. Exploiting information from multiple views, one can hope to find a clustering that is more accurate than the ones obtained using the individual views. Often these different views admit same underlying clustering of the data, so we can approach this problem by looking for clusterings that are consistent across the views, i.e., corresponding data points in each view should have same cluster membership. We propose a spectral clustering framework that achieves this goal by co-regularizing the clustering hypotheses, and propose two co-regularization schemes to accomplish this. Experimental comparisons with a number of baselines on two synthetic and three real-world datasets establish the efficacy of our proposed approaches.
GABAA receptors and plasticity of inhibitory neurotransmission in the central nervous system

GABAA receptors (GABAARs) are ligand‐gated Cl− channels that mediate most of the fast inhibitory neurotransmission in the central nervous system (CNS). Multiple GABAAR subtypes are assembled from a family of 19 subunit genes, raising the question of the significance of this heterogeneity. In this review, we discuss the evidence that GABAAR subtypes represent distinct receptor populations with a specific spatio‐temporal expression pattern in the developing and adult CNS, being endowed with unique functional and pharmacological properties, as well as being differentially regulated at the transcriptional, post‐transcriptional and translational levels. GABAAR subtypes are targeted to specific subcellular domains to mediate either synaptic or extrasynaptic transmission, and their action is dynamically regulated by a vast array of molecular mechanisms to adjust the strength of inhibition to the changing needs of neuronal networks. These adaptations involve not only changing the gating or kinetic properties of GABAARs, but also modifying the postsynaptic scaffold organised by gephyrin to anchor specific receptor subtypes at postsynaptic sites. The significance of GABAAR heterogeneity is particularly evident during CNS development and adult neurogenesis, with different receptor subtypes fulfilling distinct steps of neuronal differentiation and maturation. Finally, analysis of the specific roles of GABAAR subtypes reveals their involvement in the pathophysiology of major CNS disorders, and opens novel perspectives for therapeutic intervention. In conclusion, GABAAR subtypes represent the substrate of a multifaceted inhibitory neurotransmission system that is dynamically regulated and performs multiple operations, contributing globally to the proper development, function and plasticity of the CNS.
TnT – A Statistical Part-of-Speech Tagger

Trigrams'n'Tags (TnT) is an efficient statistical part-of-speech tagger. Contrary to claims found elsewhere in the literature, we argue that a tagger based on Markov models performs at least as well as other current approaches, including the Maximum Entropy framework. A recent comparison has even shown that TnT performs significantly better for the tested corpora. We describe the basic model of TnT, the techniques used for smoothing and for handling unknown words. Furthermore, we present evaluations on two corpora.