Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated Unmixing of Complex Protein Subcellular Location Patterns

Many proteins and macromolecules exhibit complex subcellular distributions, which may include localizing in more than one organelle and varying in location depending on the cell physiology. Estimating fraction of fluorescence in each pattern of subcellular location is essential to quantitatively understand protein dynamics such as synthesis, degradation and relocation. Previously the only available method to access such information relies on using colocalization with other fluorescent markers. However, this technique is limited by the probes’ specificity, availability and spectral overlap, rendering automated analysis of protein localization difficult with this strategy. We therefore developed both supervised and unsupervised learning methods to quantify the fractions of a fluorescent marker in different organelles in automated fashion. The principle of these methods is representing the protein distribution into distinct object types combined with the assumption that mixed patterns were formed by additive combinations of object types. The supervised method then uses fundamental patterns of organelles to unmix the mixed patterns by linear regression or multinomial inference; while the unsupervised method, which assumes no pre-knowledge of fundamental patterns available, discloses the fundamental patterns from the mixed patterns and fractional composition of each image set with graphical model learning strategy. To test our approaches, cells were tagged by combinations of two organelle specific probes that had the same fluorescent properties and imaged to simulate multiple patterns of subcellular localization. The results indicate that we can unmix the complex subcellular distribution with reasonably high accuracy using both supervised and unsupervised methods.
POLITECNICO DI TORINO Repository ISTITUZIONALE K-Band GaAs MMIC Doherty Power Amplifier for Microwave Radio With Optimized Driver /

In this paper, a Doherty power amplifier for Kband point-to-point microwave radio, developed in TriQuint GaAs 0. 15μm PWR pHEMT monolithic technology, is presented. Highly efficient driver stages on both the main and auxiliary branches have been designed and optimized to boost gain with minimal impact on power added efficiency. The selected architecture enables a modular combination to reach higher power levels. Matching network structures have been designed, according to simple equivalent circuit approaches, to obtain the desired 10% fractional bandwidth. The fabricated power amplifier exhibits, at 24 GHz in continuous wave conditions, an output power of 30.9 dBm, with a power added efficiency of 38% at saturation and 20% at 6 dB of output power back-off, together with a gain of 12.5 dB. System level characterization at 24 GHz, in very demanding conditions, with 28 MHz channel, 7.5 dB peakto-average ratio modulated signal, showed full compliance with the standard emission mask, adopting a simple predistorter, with average output power of 23.5 dBm, and average efficiency above 14%. The measured performance favorably compare with other academic and commercial K-band power amplifiers for similar applications.
Protein Kinase D Isoforms Differentially Modulate Cofilin-Driven Directed Cell Migration

Background Protein kinase D (PKD) enzymes regulate cofilin-driven actin reorganization and directed cell migration through both p21-activated kinase 4 (PAK4) and the phosphatase slingshot 1L (SSH1L). The relative contributions of different endogenous PKD isoforms to both signaling pathways have not been elucidated, sufficiently. Methodology/Principal Findings We here analyzed two cell lines (HeLa and MDA-MB-468) that express the subtypes protein kinase D2 (PKD2) and protein kinase D3 (PKD3). We show that under normal growth conditions both isoforms can form a complex, in which PKD3 is basally-active and PKD2 is inactive. Basal activity of PKD3 mediates PAK4 activity and downstream signaling, but does not significantly inhibit SSH1L. This signaling constellation was required for facilitating directed cell migration. Activation of PKD2 and further increase of PKD3 activity leads to additional phosphorylation and inhibition of endogenous SSH1L. Net effect is a dramatic increase in phospho-cofilin and a decrease in cell migration, since now both PAK4 and SSH1L are regulated by the active PKD2/PKD3 complex. Conclusions/Significance Our data suggest that PKD complexes provide an interface for both cofilin regulatory pathways. Dependent on the activity of involved PKD enzymes signaling can be balanced to guarantee a functional cofilin activity cycle and increase cell migration, or imbalanced to decrease cell migration. Our data also provide an explanation of how PKD isoforms mediate different effects on directed cell migration.
Concentration of moxifloxacin in plasma and tonsillar tissue after multiple administration in adult patients.

OBJECTIVES The antibacterial spectrum of moxifloxacin includes all the major respiratory pathogens, and its pharmacokinetics demonstrate high peak concentrations in plasma as well as at respiratory sites. Nevertheless, tonsillar tissue concentrations have never been investigated. In this study we determined the moxifloxacin concentrations in plasma and tonsillar tissue after the administration of three doses of moxifloxacin 400 mg to adult patients with chronic or recurrent tonsillitis undergoing tonsillectomy. METHODS This was an uncontrolled, open-label, randomized, parallel group study including 35 patients assigned randomly to five groups of 7 patients each, depending on the time between the last dose of moxifloxacin and plasma and tissue sampling. Moxifloxacin was given orally once daily for 3 days; its concentrations were measured using a validated HPLC assay and fluorescence detection. Each sample was analysed twice and the mean value obtained used for the statistical analysis. Pharmacokinetic data were analysed by presenting descriptive statistics of moxifloxacin concentrations in plasma and tonsillar tissue. RESULTS C(max) occurred at 3 h in tonsillar tissue (mean 8.96 mg/L) and in plasma (mean 3.20 mg/L), the tissue/plasma concentration ratios (mean values) being constantly >2, ranging between 2.37 (after 2 h) and 2.93 (after 24 h), which indicates a prolonged maintenance of moxifloxacin concentration in tonsillar tissue compared with plasma. Variability among patients was present at 6 h, with the tonsillar tissue/plasma concentration ratio ranging between 0.8 and 3.4. CONCLUSIONS Moxifloxacin achieves a good penetration in tonsillar tissue, which compares favourably with that reported for other fluoroquinolones. The moxifloxacin concentrations we observed exceed the MICs for the usual respiratory tract pathogens.
Role of p53 and CDKN2A Inactivation in Human Squamous Cell Carcinomas

p53 tumor suppressor gene is the most commonly mutated gene in human and mouse cancers. Disruption of the p53 and Rb pathways is a fundamental trend of most human cancer cells. Inactivation of CDKN2A can lead to deregulation of these two pathways. Genetic abnormalities in CDKN2A gene have been well documented in human melanoma but their involvement in human nonmelanoma skin cancer (NMSC) and in particular in squamous cell carcinoma (SCC) is less clear. Several studies have shown that human SCCs harbour unique mutations in the p53 gene as well as inactivation of the CDKN2A gene. While mutations in the p53 gene are induced by UV radiation and represent tumor initiating events, the majority of alterations detected in the CDKN2A gene do not appear to be UV-dependent. In conclusion, in addition to p53 mutations, silencing of the CDKN2A gene might play a significant role in SCC development.
Performance-oriented DevOps: A Research Agenda

DevOps is a trend towards a tighter integration between development (Dev) and operations (Ops) teams. The need for such an integration is driven by the requirement to continuously adapt enterprise applications (EAs) to changes in the business environment. As of today, DevOps concepts have been primarily introduced to ensure a constant flow of features and bug fixes into new releases from a functional perspective. In order to integrate a non-functional perspective into these DevOps concepts this report focuses on tools, activities, and processes to ensure one of the most important quality attributes of a software system, namely performance. Performance describes system properties concerning its timeliness and use of resources. Common metrics are response time, throughput, and resource utilization. Performance goals for EAs are typically defined by setting upper and/or lower bounds for these metrics and specific business transactions. In order to ensure that such performance goals can be met, several activities are required during development and operation of these systems as well as during the transition from Dev to Ops. Activities during development are typically summarized by the term Software Performance Engineering (SPE), whereas activities during operations are called Application Performance Management (APM). SPE and APM were historically tackled independently from each other, but the newly emerging DevOps concepts require and enable a tighter integration between both activity streams. This report presents existing solutions to support this integration as well as open research challenges in this area.
HOW WE VIEW THOSE WHO DEROGATE: PERCEPTIONS OF FEMALE COMPETITOR DEROGATORS

Past research on intrasexual competition for mates has revealed at least four strategies that people may deploy. One of the most frequently used strategies is competitor derogation, such that people derogate potential rivals with respect to their appearance and personality. What remains unknown is how those who derogate rivals are perceived by others. Here we examine how female derogators are viewed by men (i.e., potential mates) and women (i.e., potential rivals), and investigate whether the form of derogation matters. We used a pre-post research design to document changes in perceptions of derogators who made negative statements about other women’s appearance, personality or sexuality. Overall, men significantly decreased their evaluations of the derogator’s friendliness, kindness, trustworthiness and overall desirability as a mate. Women mirrored these results, but also significantly decreased their views of the derogator’s fitness as a parent and her physical attractiveness, and in the case of appearance derogations, her promiscuity. We examine these results within the framework of women’s intrasexual competition for mates.
Impatience vs. Incentives

This paper studies the long-run dynamics of Pareto-optimal self-enforcing contracts in a repeated principal-agent framework with differential discounting. Impatience concerns encourage contracts to favor the more patient player in the long run, and incentives concerns encourage contracts to favor the agent in the long run. When the agent is relatively impatient, the impatience and incentives forces are in conflict. If the conflict is strong, we show that optimal contracts oscillate between favoring the principal and favoring the agent as a way to cater to both forces in the long-run. This occurs in the absence of uncertainty or any need to randomize. When the impatience and incentives forces are aligned or one force dominates the other, we show that every optimal contract converges to a steady state in the long run in a well-behaved way. The results of Ray (2002) and Lehrer and Pauzner (1999) can be recovered as limiting cases.
The structure of negative emotion scales: generalization over contexts and comprehensiveness

In this article, we tested whether a four‐dimensional individual‐difference structure of negative emotions (Sadness, Fear, Anger, Shame) as described e.g. by Diener, Smith and Fujita can be found in self‐report data when the emotions are explicitly linked to three different specific contexts. In addition, we check the comprehensiveness of the structure by adding terms people spontaneously use to directly express negative affect. A situational questionnaire was constructed, based on the emotion terms from Diener et al., and it was administered to 161 participants. The structure we obtained was five dimensional instead of four dimensional: the Shame scale turned out to be two dimensional, with guilt and regret defining one factor, and shame and embarrassment defining another factor. Between these two, there is a moderate positive correlation. The structure is shown to be nearly identical for all three situations. The minor differences we found do contextualize the meaning of the emotional responses. The newly added terms could be captured quite well by the factor Anger. No separate factor was needed, meaning that the obtained five‐dimensional structure may be considered comprehensive enough for the field of negative emotions. Copyright © 2002 John Wiley & Sons, Ltd.
Going general: Responding to yes–no questions in informational webinars for prospective grant applicants

While research on question–answer sequences has yielded important insights into the structures of responses and the actions they implement, the advising literature has illuminated how advice-giving may be resisted or avoided in certain institutional contexts. In this study, we examine the audio-recorded Q&A sections of applicant webinars delivered by a major philanthropic foundation in the United States, with a particular focus on the foundation representatives’ complex responses to audience members’ yes–no questions that seek specificity. Within a conversation analytic framework, we show how the practice of going general is engaged to manage the demands of being helpful to the individual questioner without appearing to guarantee a particular outcome while foregrounding the foundation’s principles and priorities for the broader audience. Findings of this study may be useful for formulating recommendations for foundation representatives tasked with communicating effectively with potential grantees.
Simulating probability learning and probabilistic reversal learning using the attention-gated reinforcement learning (AGREL) model

In a probability learning task, participants estimate the probabilistic reward contingencies, and this task has been used extensively to study instrumental conditioning with partial reinforcement. In the probabilistic reversal learning task, the probabilistic reward contingencies are reversed between options in the middle of the experiment to measure how well people adapt to new contingency situations. In this work, we used the attention-gated reinforcement learning (AGREL) model (Roelfsema & Van Ooyen, 2005) to simulate how people learn the probabilistic relationship between stimulus-reward pairs in probability and reversal learning tasks. AGREL algorithm put forward two important aspects of a learning phenomenon together in a neural network scheme: (1) the effect of unexpected outcomes on learning and (2) the effect of top-down (selective) attention on updating weights. Contrary to its importance in the learning literature, AGREL has not yet been tested with these well known learning tasks. The results of the first simulation showed that in a binary choice probability learning experiment an AGREL model can simulate different learning strategies, such as probability matching and maximizing. Secondly, we simulated a probabilistic reversal learning experiment with the same AGREL model, and the results showed that the AGREL model dynamically adapted to new contingency situations. Furthermore, we also evaluated effects of learning rate on the model's adaption to reversal contingency by plotting the inter-phase dynamics. These results showed that AGREL model simulates the traditional findings observed in probability and reversal learning experiments, and it can be further developed to understand the role of dopamine in learning and it can be used in model-based fMRI research.
Turf algae-mediated coral damage in coastal reefs of Belize, Central America

Many coral reefs in the Caribbean experienced substantial changes in their benthic community composition during the last decades. This often resulted in phase shifts from scleractinian coral dominance to that by other benthic invertebrate or algae. However, knowledge about how the related role of coral-algae contacts may negatively affect corals is scarce. Therefore, benthic community composition, abundance of algae grazers, and the abundance and character of coral-algae contacts were assessed in situ at 13 Belizean reef sites distributed along a distance gradient to the Belizean mainland (12–70 km): Mesoamerican Barrier Reef (inshore), Turneffe Atoll (inner and outer midshore), and Lighthouse Reef (offshore). In situ surveys revealed significantly higher benthic cover by scleractinian corals at the remote Lighthouse Reef (26–29%) when compared to the other sites (4–19%). The abundance of herbivorous fish and the sea urchin Diadema antillarum significantly increased towards the offshore reef sites, while the occurrence of direct coral-algae contacts consequently increased significantly with decreasing distance to shore. About 60% of these algae contacts were harmful (exhibiting coral tissue damage, pigmentation change, or overgrowth) for corals (mainly genera Orbicella and Agaricia), particularly when filamentous turf algae were involved. These findings provide support to the hypothesis that (turf) algae-mediated coral damage occurs in Belizean coastal, near-shore coral reefs.
The influence of gas on the structure of merger remnants

We present a large set of merger simulations of early-type disc galaxies with mass ratios of 1:1 and 3:1 and 10 per cent of the total disc mass in gas. The internal orbital structure and the kinematic and photometric properties of the remnants are analysed in detail and compared to pure stellar mergers. In contrast to the collisionless case, equal-mass mergers with gas do not result in very boxy remnants which is caused by the suppression of box orbits and the change of the projected shape of minor-axis tube orbits in the more axisymmetric remnants. The isophotal shape of 3:1 remnants and the global kinematic properties of 1:1 and 3:1 remnants are only weakly affected by the presence of gas. 1:1 remnants are slowly rotating, whereas 3:1 remnants are fast rotating and discy. The shape of the stellar line-of-sight velocity distributions (LOSVDs) is strongly influenced by gas. Within the effective radius, the LOSVDs of collisionless remnants have broad leading wings while their gaseous counterparts show steep leading wings, more consistent with observations of elliptical galaxies. We show that this change is also caused by the suppressed populating of box orbits and it is amplified by the formation of extended gas discs in the merger remnants which might eventually turn into stars. If elliptical galaxies have formed from mergers, our results indicate that massive, slowly rotating boxy elliptical galaxies cannot have formed from dissipative mergers of discs. Pure stellar (dry) mergers are the more likely candidates. On the other hand, lower mass, fast rotating and discy ellipticals can have formed from dissipative (wet) mergers of early-type discs. So far, only unequal-mass disc mergers with gas can successfully explain their observed substructure. This is consistent with the revised morphological classification scheme of increasing importance of gas dissipation when moving from boxy to discy ellipticals and then to spiral galaxies, proposed by Kormendy & Bender.
Evolutionary paths to and from the red sequence: star formation and H i properties of transition galaxies at z∼ 0

We investigate the properties of galaxies between the blue and the red sequence (i.e. the transition region, 4.5 < NUV - H < 6 mag) by combining ultraviolet (UV) and near-infrared imaging to 21-cm H I line observations for a volume-limited sample of nearby galaxies. We confirm the existence of a tight relation between colour and H I fraction across all the range of colours, although outside the blue cloud this trend becomes gradually weaker. Transition galaxies are divided into two different families, according to their atomic hydrogen content. 'HI-deficient' galaxies are the majority of transition galaxies in our sample. They are found in high-density environments and all their properties are consistent with a quenching of the star formation via gas stripping. However, while the migration from the blue cloud is relatively quick (i.e. ≲ 1 Gyr), a longer amount of time (a few Gyr at least) seems required to completely suppress the star formation and reach the red sequence. At all masses, migrating 'H I-deficient' galaxies are mainly discs, implying that the mechanism responsible for today's migration in clusters cannot have played a significant role in the creation of the red sequence at high redshift. Conversely, 'HI-normal' transition galaxies are a more heterogeneous population. A significant fraction of these objects show star formation in ring-like structures and evidence for accretion/minor-merging events suggesting that at least part of the H I reservoir has an external origin. The detailed evolution of such systems is still unclear, but our analysis suggests that, in at least two cases, galaxies might have migrated back from the red sequence after accretion events. Interestingly, the H I available may be sufficient to sustain star formation at the current rate for several billion years. Our study clearly shows the variety of evolutionary paths leading to the transition region and suggests that the transition galaxies may not be always associated with systems quickly migrating from the blue to the red sequence.
Evaluation of stress distributions in peri-implant and periodontal bone tissues in 3- and 5-unit tooth and implant-supported fixed zirconia restorations by finite elements analysis

Objective: In this study, it is aimed to compare the distribution of stress on periodontal and peri-implant bone tissues in 3- and 5-unit-dental and implant-supported zirconia restorations using finite element analysis. Materials and Methods: Stress distribution formed in periodontal and peri-implant bone tissues as a result of chewing forces was analyzed in dental and implant-supported three-dimensional (3D) finite element models of zirconia restoration with 5-unit placed on the numbers of 43, 44, 45, 46, and 47 and with 3-unit placed on the number of 45, 46, and 47. Four different loading conditions were used. 200 Nforce was applied in 30° from the buccal inclination of number 43, 45, and 47 restorations separately and totally 850 Nforce was applied in 30° from the buccal inclination of whole restoration. The study was performed through static nonlinear analysis with the 3D finite element analysis method. Results: Stress accumulation in bone tissues in the tooth-supported model was found less than in implant-supported models. Stress accumulation was observed in the cervical portion of the implant in implant-supported models, and stress accumulation was observed surrounding bone of roots in tooth-supported models. The highest stress values were occurred in 5 unit implant-supported model in all loadings. Conclusion: In posterior restorations increased in the number of supported teeth and implant can reduce the destructive forces on periodontal and peri-implant bone tissues and may allow longer period retention of the restorations in the mouth.
Do Power Consumption Data Tell the Story? - Electricity Intensity and Hidden Economy in Post-Socialist Countries

The paper disputes the frequently presented and quoted statement that in post-socialist economies data on power consumption are better indicators for aggregate output changes than data on official GDP. Attempt is made to show that the variation of electricity intensities in post-socialist countries does not necessarily reflect the growth of the hidden parts of the economy. Statistical and econometric analysis of data for 18 post-socialist economies show that in this region, the differences in measured and registered structural changes are more important factors explaining the differences in the changes of electricity intensity than the changing size of the unofficial economy.