Miracle-dz/UniFAR-FTUs huggingface dataset:
Depolarization evokes different patterns of calcium signals and exocytosis in bovine and mouse chromaffin cells: the role of mitochondria

This study was planned on the assumptions that different high‐voltage activated calcium channels and/or the ability of mitochondria to take up Ca2+ could be responsible for different cytosolic Ca2+ concentrations ([Ca2+]c) and catecholamine release responses in adrenal chromaffin cells of bovine and mouse species. Short K+ pulses (2–5 s, 70 mm K+) increased [Ca2+]c to a peak of about 1 µm; however, in bovine cells the decline was slower than in mouse cells. Secretory responses were faster in mouse but were otherwise quantitatively similar. Upon longer K+ applications (1 min), elevations of [Ca2+]c and secretion were prolonged in bovine cells; in contrast [Ca2+]c in mouse cells declined three‐fold faster and failed to sustain a continued secretion. Confocal [Ca2+]c imaging following a 50‐ms depolarizing pulse showed a similar Ca2+ entry, but a rate of [Ca2+]c increase and a maximum peak significantly higher in bovine cells; the rate of dissipation of the Ca2+ wave was faster in the mouse. The mitochondrial protonophore CCCP (2 µm) halved the K+‐evoked [Ca2+]c and secretory signals in mouse cells, but had little affect on bovine responses. We conclude that the relative densities of L (15% in bovine and 50% in mouse) and P/Q Ca2+ channels (50% in bovine and 15% in mouse) do not contribute to the observed differences; rather, the different intracellular distribution of Ca2+, which is strongly influenced by mitochondria, is responsible for a more sustained secretory response in bovine, and for a faster and more transient secretory response in mouse chromaffin cells. It seems that mitochondria near the plasmalemma sequester Ca2+ more rapidly and efficiently in the mouse than in the bovine chromaffin cell.
Opening the Black Box of Practice-Based Learning: Human- Centred Design of Learning Analytics

© Copyright 2016 for this paper by its authors. Practice-based learning activities are an important aspect of education, particularly for science, technology, engineering and mathematics (STEM) subjects. Their immense importance to STEM curricula is unequivocal and so are the teachers' and students' need for support during those activities. However, considering the open-ended and hands-on nature of practice-based learning activities, designing, deploying and validating learning analytics visualisations remains as a significant challenge for the stateof-the-art learning analytics. In this paper, we present our human-centered contextual enquiry approach for generating requirements and its preliminary results in the form of visualisations that have the potential to support facilitators and learners. Although there have been certain attempts to provide learning analytics for increasing awareness, supporting reflection and facilitating decision-making and intervention, to our knowledge, our research presented is the first attempt to provide such information regarding students' progress during practice-based learning activities.
Memorization strategies of atonal music

Background in music psychology. Musicians may use their knowledge about the music structure in order to memorize the music, by segmenting the piece according to the structure. Observational studies, testing experts and non expert pianists have shown that the more experienced pianists segmented the piece according to the formal structure (Chaffin and Imreh, 2001, Williamon and Valentine, 2002), relying on highly ordered retrieval structures confirming the Long Term-Working Memory Theory (Ericsson and Kintsch, 1995).
Comparison of In Vitro- and Chorioallantoic Membrane (CAM)-Culture Systems for Cryopreserved Medulla-Contained Human Ovarian Tissue

At present, there are three ways to determine effectively the quality of the cryopreservation procedure using ovarian tissue before the re-implantation treatment: evaluation of follicles after post-thawing xenotransplantation to SCID mouse, in-vitro culture in a large volume of culture medium under constant agitation and culture on embryonic chorio-allantoic membrane within a hen's eggs. The aim of this study was to compare the two methods, culture in vitro and culture on embryonic chorioallantoic membrane (CAM) of cryopreserved human ovarian medulla-contained and medulla-free cortex. Ovarian fragments were divided into small pieces (1.5–2.0×1.0–1.2×0.8–1.5) of two types, cortex with medulla and medulla-free cortex, frozen, thawed and randomly divided into the following four groups. Group 1: medulla-free cortex cultured in vitro for 8 days in large volume of medium with mechanical agitation, Group 2: medulla-containing cortex cultured in vitro, Group 3: medulla-free cortex cultured in CAM-system for 5 days, Group 4: medulla-containing cortex cultured in CAM-system. The efficacy of the tissue culture was evaluated by the development of follicles and by intensiveness of angiogenesis in the tissue (von Willebrand factor and Desmin). For Group 1, 2, 3 and 4, respectively 85%, 85%, 87% and 84% of the follicles were morphologically normal (P>0.1). The immunohistochemical analysis showed that angiogenesis detected by von Willebrand factor was lower in groups 1 and 3 (medulla-free cortex). Neo-vascularisation (by Desmin) was observed only in ovarian tissue of Group 4 (medulla-contained cortex after CAM-culture). It appears that the presence of medulla in ovarian pieces is beneficial for post-thaw development of cryopreserved human ovarian tissue. For medical practice it is recommended for evaluation of post-warming ovarian tissue to use the CAM-system as a valuable alternative to xenotransplantation and for cryopreservation of these tissues to prepare ovarian medulla-contained strips.
A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat1[OPEN]

ODDSOC2/TaAGL33 functions in vernalization-responsive flowering of Poaceae in a similar but unique manner compared to its Arabidopsis homolog, FLOWERING LOCUS C. Winter cereals require prolonged cold to transition from vegetative to reproductive development. This process, referred to as vernalization, has been extensively studied in Arabidopsis (Arabidopsis thaliana). In Arabidopsis, a key flowering repressor called FLOWERING LOCUS C (FLC) quantitatively controls the vernalization requirement. By contrast, in cereals, the vernalization response is mainly regulated by the VERNALIZATION genes, VRN1 and VRN2. Here, we characterize ODDSOC2, a recently identified FLC ortholog in monocots, knowing that it belongs to the FLC lineage. By studying its expression in a diverse set of Brachypodium accessions, we find that it is a good predictor of the vernalization requirement. Analyses of transgenics demonstrated that BdODDSOC2 functions as a vernalization-regulated flowering repressor. In most Brachypodium accessions BdODDSOC2 is down-regulated by cold, and in one of the winter accessions in which this down-regulation was evident, BdODDSOC2 responded to cold before BdVRN1. When stably down-regulated, the mechanism is associated with spreading H3K27me3 modifications at the BdODDSOC2 chromatin. Finally, homoeolog-specific gene expression analyses identify TaAGL33 and its splice variant TaAGL22 as the FLC orthologs in wheat (Triticum aestivum) behaving most similar to Brachypodium ODDSOC2. Overall, our study suggests that ODDSOC2 is not only phylogenetically related to FLC in eudicots but also functions as a flowering repressor in the vernalization pathway of Brachypodium and likely other temperate grasses. These insights could prove useful in breeding efforts to refine the vernalization requirement of temperate cereals and adapt varieties to changing climates.
The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope

Significance We present an atomic-resolution structure of the M13 filamentous bacteriophage capsid, one of many filamentous viruses that play important roles in many areas of research. The model was obtained by combining magic-angle spinning NMR and Rosetta modeling, used for the first time, to our knowledge, to derive the atomic structure of an intact virus capsid. The structure is made up of thousands of identical helical subunits stabilized by repeating hydrophobic pockets, which serve as a locking motif, suggesting a direct role in phage particle assembly. Analysis of various phage sequences suggests the presence of a conserved design principle for helical capsids. Because the current method does not rely on any particular preparation procedure, it can be applied to other viral capsids and molecular assemblies. Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6–16.7 Å and a tilt of 36.1–36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies.
Cellulose Synthesis Is Coupled to Cell Cycle Progression at G1 in the Dinoflagellate Crypthecodinium cohnii

Cellulosic deposition in alveolar vesicles forms the “internal cell wall” in thecated dinoflagellates. The availability of synchronized single cells, the lack of secondary deposition, and the absence of cellulosic cell plates at division facilitate investigation of the possible roles of cellulose synthesis (CS) in the entire cell cycle. Flow cytograms of cellulosic contents revealed a stepwise process of CS in the dinoflagellate cell cycle, with the highest rate occurring at G1. A cell cycle delay in G1, but not G2/M, was observed after inhibition of CS. A cell cycle inhibitor of G1/S, but not G2/M, was able to delay cell cycle progression with a corresponding reduction of CS. The increase of cellulose content in the cell cycle corresponded well to the expected increase of surface area. No differences were observed in the cellulose to surface area ratio between normal and fast-growing G1 cells, implicating the significance of surface area in linking CS to the coupling of cell growth with cell cycle progression. The coupling of CS to G1 implicates a novel link between CS and cell cycle control, and we postulate that the coupling mechanism might integrate cell wall integrity to the cell size checkpoint.
Exploiting thermal energy storage to reduce data center capital and operating expenses

Power shaving has recently been proposed to dynamically shave the power peaks of a data center with energy storage devices (ESD), such that more servers can be safely hosted. In addition to the reduction of capital investment (cap-ex), power shaving also helps cut the electricity bills (op-ex) of a data center by reducing the high utility tariffs related to peak power. However, existing work on power shaving focuses exclusively on electrical ESDs (e.g., UPS batteries) to shave the server-side power demand. In this paper, we propose TE-Shave, a generalized power shaving framework that exploits both UPS batteries and a new knob, thermal energy storage (TES) tanks equipped in many data centers. Specifically, TE-Shave utilizes stored cold water or ice to manipulate the cooling power, which accounts for 30-40% of the total power cost of a data center. Our extensive evaluation with real-world workload traces shows that TE-Shave saves cap-ex and op-ex up to $2,668/day and $825/day, respectively, for a data center with 17,920 servers. Even for future data centers that are projected to have more efficient cooling and thus a smaller portion of cooling power, e.g., a quarter of today's level, TE-Shave still leads to 28% more savings than existing work that focuses only on the server-side power. TE-Shave is also coordinated with traditional TES solutions for further reduced op-ex.
A Parametric Empirical Bayesian Framework for the EEG/MEG Inverse Problem: Generative Models for Multi-Subject and Multi-Modal Integration

We review recent methodological developments within a parametric empirical Bayesian (PEB) framework for reconstructing intracranial sources of extracranial electroencephalographic (EEG) and magnetoencephalographic (MEG) data under linear Gaussian assumptions. The PEB framework offers a natural way to integrate multiple constraints (spatial priors) on this inverse problem, such as those derived from different modalities (e.g., from functional magnetic resonance imaging, fMRI) or from multiple replications (e.g., subjects). Using variations of the same basic generative model, we illustrate the application of PEB to three cases: (1) symmetric integration (fusion) of MEG and EEG; (2) asymmetric integration of MEG or EEG with fMRI, and (3) group-optimization of spatial priors across subjects. We evaluate these applications on multi-modal data acquired from 18 subjects, focusing on energy induced by face perception within a time–frequency window of 100–220 ms, 8–18 Hz. We show the benefits of multi-modal, multi-subject integration in terms of the model evidence and the reproducibility (over subjects) of cortical responses to faces.
A Novel Core Genome-Encoded Superantigen Contributes to Lethality of Community-Associated MRSA Necrotizing Pneumonia

Bacterial superantigens (SAg) stimulate T-cell hyper-activation resulting in immune modulation and severe systemic illnesses such as Staphylococcus aureus toxic shock syndrome. However, all known S. aureus SAgs are encoded by mobile genetic elements and are made by only a proportion of strains. Here, we report the discovery of a novel SAg staphylococcal enterotoxin-like toxin X (SElX) encoded in the core genome of 95% of phylogenetically diverse S. aureus strains from human and animal infections, including the epidemic community-associated methicillin-resistant S. aureus (CA-MRSA) USA300 clone. SElX has a unique predicted structure characterized by a truncated SAg B-domain, but exhibits the characteristic biological activities of a SAg including Vβ-specific T-cell mitogenicity, pyrogenicity and endotoxin enhancement. In addition, SElX is expressed by clinical isolates in vitro, and during human, bovine, and ovine infections, consistent with a broad role in S. aureus infections of multiple host species. Phylogenetic analysis suggests that the selx gene was acquired horizontally by a progenitor of the S. aureus species, followed by allelic diversification by point mutation and assortative recombination resulting in at least 17 different alleles among the major pathogenic clones. Of note, SElX variants made by human- or ruminant-specific S. aureus clones demonstrated overlapping but distinct Vβ activation profiles for human and bovine lymphocytes, indicating functional diversification of SElX in different host species. Importantly, SElX made by CA-MRSA USA300 contributed to lethality in a rabbit model of necrotizing pneumonia revealing a novel virulence determinant of CA-MRSA disease pathogenesis. Taken together, we report the discovery and characterization of a unique core genome-encoded superantigen, providing new insights into the evolution of pathogenic S. aureus and the molecular basis for severe infections caused by the CA-MRSA USA300 epidemic clone.
A Tutorial on Canonical Correlation Methods

Canonical correlation analysis is a family of multivariate statistical methods for the analysis of paired sets of variables. Since its proposition, canonical correlation analysis has, for instance, been extended to extract relations between two sets of variables when the sample size is insufficient in relation to the data dimensionality, when the relations have been considered to be non-linear, and when the dimensionality is too large for human interpretation. This tutorial explains the theory of canonical correlation analysis, including its regularised, kernel, and sparse variants. Additionally, the deep and Bayesian CCA extensions are briefly reviewed. Together with the numerical examples, this overview provides a coherent compendium on the applicability of the variants of canonical correlation analysis. By bringing together techniques for solving the optimisation problems, evaluating the statistical significance and generalisability of the canonical correlation model, and interpreting the relations, we hope that this article can serve as a hands-on tool for applying canonical correlation methods in data analysis.
Clinicopathological significance of β -tubulin isotype III gene expression in breast cancer patients.

BACKGROUND The molecular classification of breast cancer mainly focuses on estrogen receptor (ER), Progesterone receptor (PgR), and Human Epidermal Growth Factor Receptor 2(HER2/Neu) status detected by immunohistochemistry (IHC) analysis. The β -tubulin isotype III (TUBB3) gene was thought to be a marker of taxane resistance or cancer aggressiveness. METHODS To evaluate the clinicopathological significance of TUBB3 expression in breast cancer patients, we measured TUBB3 mRNA levels in 92 breast cancer patients by Quantitative reverse transcription-polymerase chain reaction (qRT-PCR), and examined their correlation with ER, PgR, and HER2 status detected by IHC. RESULTS We observed a significant positive correlation between the TUBB3 mRNA expression and the immunohistochemical positivity of both PgR (p= 0.000) and HER2 (p= 0.001). In addition, TUBB3 mRNA expression was associated with lymph nodes status (P= 0.008) and tumor stages (0.029), but no correlation was found with other clinicopathological features, such as age, pathohistological grades and tumor size. CONCLUSIONS In conclusion, TUBB3 expression correlated significantly with molecular markers of breast cancer, such as PgR and HER2, suggesting that TUBB3 mRNA level facilitate the identification of a subset of patients who respond to Taxane treatment in addition to hormonal therapy and trastuzumab.
Trajectory-tracking and path-following controllers for constrained underactuated vehicles using Model Predictive Control

This paper addresses the design of Model Predictive Control (MPC) laws to solve the trajectory-tracking problem and the path-following problem for constrained underactuated vehicles. By allowing an arbitrarily small asymptotic tracking error, we derive MPC laws where the size of the terminal set is only limited by the size of the system constraints. In fact, for the case of unconstrained inputs, the terminal set can be neglected and the resulting MPC controllers provide a global solution to the addressed constrained motion control problems. Simulation results are presented where the proposed MPC controllers are applied to 2-D and to 3-D moving vehicles.
Timely detection of Coordination Requirements to support collaboration among software developers

Work dependencies often exist between the developers of a software project. These dependencies frequently result in a need for coordination between the involved developers. However, developers are not always aware of these Coordination Requirements. Current methods which detect the need to coordinate rely on information which is available only after development work has been completed. This does not enable developers to act on their coordination needs. I have investigated a more timely method to determine Coordination Requirements in a software development team as they emerge.
‘ Me Too ’ 2 . 0 : An Analysis of Viral Retweets on the Twittersphere

We propose an analysis of retweets and their propagation through Twitter. A retweet allows Twitter users to rebroadcast specific tweets of interest by incorporating all or part of the original tweet into their own. We hypothesize that retweets play a role in introducing new connections to a network, so that individuals who do not follow an individual may see retweets of their tweets and eventually become followers. We characterize the retweet trees as defined strictly by RT: @ tags. We also perform cursory analyses on social networks that give rise to popularly-retweeted individuals and compare them to popular individuals (by follower count). Analyzing the nature of the network represented by active tweeting/retweeting can give us additional insights to how users use the service and how ideas and information spread across the network. Author
Dissociable Modulation of Overt Visual Attention in Valence and Arousal Revealed by Topology of Scan Path

Emotional stimuli have evolutionary significance for the survival of organisms; therefore, they are attention-grabbing and are processed preferentially. The neural underpinnings of two principle emotional dimensions in affective space, valence (degree of pleasantness) and arousal (intensity of evoked emotion), have been shown to be dissociable in the olfactory, gustatory and memory systems. However, the separable roles of valence and arousal in scene perception are poorly understood. In this study, we asked how these two emotional dimensions modulate overt visual attention. Twenty-two healthy volunteers freely viewed images from the International Affective Picture System (IAPS) that were graded for affective levels of valence and arousal (high, medium, and low). Subjects' heads were immobilized and eye movements were recorded by camera to track overt shifts of visual attention. Algebraic graph-based approaches were introduced to model scan paths as weighted undirected path graphs, generating global topology metrics that characterize the algebraic connectivity of scan paths. Our data suggest that human subjects show different scanning patterns to stimuli with different affective ratings. Valence salient stimuli (with neutral arousal) elicited faster and larger shifts of attention, while arousal salient stimuli (with neutral valence) elicited local scanning, dense attention allocation and deep processing. Furthermore, our model revealed that the modulatory effect of valence was linearly related to the valence level, whereas the relation between the modulatory effect and the level of arousal was nonlinear. Hence, visual attention seems to be modulated by mechanisms that are separate for valence and arousal.