Miracle-dz/UniFAR-FTUs huggingface dataset:
A Non-fluorescent, Broad Range Quencher Dye for FRET Assays

We report here a novel, water soluble, non-fluorescent dye that efficiently quenches fluorescence from a broad range of visible and near-infrared (NIR) fluorophores in Forster resonance energy transfer (FRET) systems. A model FRET-based caspase-3 assay system was used to test the performance of the quencher dye. Fluorogenic caspase-3 substrates were prepared by conjugating the quencher, IRDye ® QC-1, to a GDEVDGAK peptide in combination with fluorescein (emission maximum ~540 nm), Cy3 (~570 nm), Cy5 (~670 nm), IRDye 680 (~700 nm), IRDye 700DX (~690 nm) or IRDye 800CW (~790 nm). The Forster distance R0 values are calculated as 41 to 65 A for these dye/quencher pairs. The fluorescence quenching efficiencies of these peptides were determined by measuring the fluorescence change on complete cleavage by recombinant caspase-3, and ranged from 97.5% to 98.8%. The fold increase in fluorescence on caspase cleavage of the fluorogenic substrates ranged from 40 to 83 depending on the dye/quencher pair. Because IRDye QC-1 effectively quenches both the NIR fluorophores (e.g., IRDye 700DX, IRDye 680 and IRDye 800CW) and the visible fluorophores (e.g. fluorescein, Cy3, Cy5), it should find broad applicability in FRET assays using a wide variety of fluorescent dyes. ©2009 Elsevier Inc. All rights reserved.
Head and Neck Squamous Cell Carcinoma Mutations in TP 53 Prognostic Significance of Truncating

Purpose: TP53 is a key gene in cellular homeostasis and is frequently mutated in head and neck squamous cell carcinoma (HNSCC). There is a variety of TP53mutations, each with its own biological and clinical implication. Aim of the study was to assess the prognostic significance of TP53 mutations in HNSCCs and to identify the most relevant mutation. Experimental Design: TP53 mutation status was investigated in 141 consecutive HNSCCs treated by surgery with radiotherapy when indicated and with a known human papilloma virus status. The type of mutation was correlated with overall and progression-free survival in a multivariate two-sided Cox regression analysis with wild type as reference. Results: A TP53 mutation was found in 88 (62.4%) of the carcinomas and was not significantly associated with overall survival (HR 1⁄4 1.65, P 1⁄4 0.11). Patients with a mutation resulting in a truncated protein (n1⁄4 36, 25.5%) had a significantly worse overall survival (HR1⁄4 2.54, P1⁄4 0.008) and progressionfree survival (HR 1⁄4 2.65, P 1⁄4 0.002). Four of these mutations were at a splice site, 13 were nonsense mutations (produces stop codon), and 19 were insertions or deletions resulting in a frameshift. After multivariate analysis, a truncating mutation remained a significant prognosticator. A missense (i.e., nontruncating) mutation did not influence prognosis. Other ways of classification (disruptive vs. nondisruptive, hotspot vs. nonhotspot, and DNA binding vs. non–DNA binding) were less discriminative. Conclusion: In HNSCCs, a truncating TP53 mutation is associated with a poor prognosis. This patient group seems as a target population for adjuvant therapy with chemoradiation or viral vector–mediated TP53 gene transfer. Clin Cancer Res; 17(11); 3733–41. 2011 AACR.
Evidence for increased internal noise in migraineurs for contrast and shape processing

Aim: Increased contrast-level dependent internal noise has been reported in migraine. This study aimed to investigate whether a general increase in internal noise impacted on other tasks thought to assess functioning in cortical area V1 and was evident in global contour coding (V4). Methods: Eleven migraineurs (six with aura) and 12 headache-free controls completed three psychophysical tasks: (i) contrast detection, (ii) discrimination of the angle of a spiral path and (iii) detection of deformation from circularity. Internal noise estimates were obtained using an N-pass method that compared responses to repeated presentations of identical stimuli. Internal noise results in inconsistent responses across different runs. Results: Migraineurs had significantly higher contrast thresholds when there was high external luminance noise. There were no other significant group differences in thresholds. Increased multiplicative noise associated with contrast processing was replicated and increased additive noise, which is independent of the visual input, was found for the global form task. Conclusions: This study provides further evidence for increased multiplicative internal noise associated with contrast processing in migraineurs. However there is no generalised increase in internal noise in V1 as noise estimates for angular discrimination were normal. Increased additive internal noise was associated with the global shape task, co-occurring with increased efficiency.
The Romanian Migration: Development of the Phenomenon and the Part Played by the Immigration Policies of European Countries

The paper will explore the evolution of Romanian migration phenomenon and the influence of migration policy of European countries, in order to understand the mechanism of choosing the destination country for Romanian emigrants. What type of evolution knows the migration phenomenon from Romania? Which are the most important factors that influence the emigration from Romania? How does the mechanism of choosing the work destination country for the Romanian emigrants? We expect that during the pre-joining period the European countries with tolerant attitude towards immigrants, and frequent naturalization, or regularization procedures, to be mainly preferred by Romanian immigrants. The empirical support for these hypotheses is examined based on statistical analysis of data provided by the official organisms for statistics in Romania, the Public Opinion Barometer. Official statistics of other European countries on immigration affecting their country, including Romanian immigration, will also be studied
A hybrid approach to music playlist continuation based on playlist-song membership

Automated music playlist continuation is a common task of music recommender systems, that generally consists in providing a fitting extension to a given playlist. Collaborative filtering models, that extract abstract patterns from curated music playlists, tend to provide better playlist continuations than content-based approaches. However, pure collaborative filtering models have at least one of the following limitations: (1) they can only extend playlists profiled at training time; (2) they misrepresent songs that occur in very few playlists. We introduce a novel hybrid playlist continuation model based on what we name "playlist-song membership," that is, whether a given playlist and a given song fit together. The proposed model regards any playlist-song pair exclusively in terms of feature vectors. In light of this information, and after having been trained on a collection of labeled playlist-song pairs, the proposed model decides whether a playlist-song pair fits together or not. Experimental results on two datasets of curated music playlists show that the proposed playlist continuation model compares to a state-of-the-art collaborative filtering model in the ideal situation of extending playlists profiled at training time and where songs occurred frequently in training playlists. In contrast to the collaborative filtering model, and as a result of its general understanding of the playlist-song pairs in terms of feature vectors, the proposed model is additionally able to (1) extend non-profiled playlists and (2) recommend songs that occurred seldom or never in training playlists.
Apico-basal Polarity Determinants Encoded by crumbs Genes Affect Ciliary Shaft Protein Composition, IFT Movement Dynamics, and Cilia Length

One of the most obvious manifestations of polarity in epithelia is the subdivision of the cell surface by cell junctions into apical and basolateral domains. crumbs genes are among key regulators of this form of polarity. Loss of crumbs function disrupts the apical cell junction belt and crumbs overexpression expands the apical membrane size. Crumbs proteins contain a single transmembrane domain and localize to cell junction area at the apical surface of epithelia. In some tissues, they are also found in cilia. To test their role in ciliogenesis, we investigated mutant phenotypes of zebrafish crumbs genes. In zebrafish, mutations of three crumbs genes, oko meduzy/crb2a, crb3a, and crb2b, affect cilia length in a subset of tissues. In oko meduzy (ome), this is accompanied by accumulation of other Crumbs proteins in the ciliary compartment. Moreover, intraflagellar transport (IFT) particle components accumulate in the ciliary shaft of ome;crb3a double mutants. Consistent with the above, Crb3 knockdown in mammalian cells affects the dynamics of IFT particle movement. These findings reveal crumbs-dependent mechanisms that regulate the localization of ciliary proteins, including Crumbs proteins themselves, and show that crumbs genes modulate intraflagellar transport and cilia elongation.
Oncodriver inhibition and CD4+ Th1 cytokines cooperate through Stat1 activation to induce tumor senescence and apoptosis in HER2+ and triple negative breast cancer: implications for combining immune and targeted therapies

In patients with HER2-expressing breast cancer many develop resistance to HER2 targeted therapies. We show that high and intermediate HER2-expressing cancer cell lines are driven toward apoptosis and tumor senescence when treated with either CD4+ Th1 cells, or Th1 cytokines TNF-α and IFN-γ, in a dose dependent manner. Depletion of HER2 activity by either siRNA or trastuzumab and pertuzumab, and subsequent treatment with either anti-HER2 Th1 cells or TNF-α and IFN-γ resulted in synergistic increased tumor senescence and apoptosis in cells both sensitive and cells resistant to trastuzumab which was inhibited by neutralizing anti-TNF-α and IFN-γ. Th1 cytokines induced minimal senescence or apoptosis in triple negative breast cancer cells (TNBC); however, inhibition of EGFR in combination with Th1 cytokines sensitized those cells causing both senescence and apoptosis. TNF-α and IFN-γ led to increased Stat1 phosphorylation through serine and tyrosine sites and a compensatory reduction in Stat3 activation. Single agent IFN-γ enhanced Stat1 phosphorylation on tyrosine 701 and similar effects were observed in combination with TNF-α and EGFR inhibition. These results demonstrate Th1 cytokines and anti-oncodriver blockade cooperate in causing tumor senescence and apoptosis in TNBC and HER2-expressing breast cancer, suggesting these combinations could be explored as non-cross-reactive therapy preventing recurrence in breast cancer.
Local SGD Converges Fast and Communicates Little

Mini-batch stochastic gradient descent (SGD) is state of the art in large scale distributed training. The scheme can reach a linear speedup with respect to the number of workers, but this is rarely seen in practice as the scheme often suffers from large network delays and bandwidth limits. To overcome this communication bottleneck recent works propose to reduce the communication frequency. An algorithm of this type is local SGD that runs SGD independently in parallel on different workers and averages the sequences only once in a while. This scheme shows promising results in practice, but eluded thorough theoretical analysis. We prove concise convergence rates for local SGD on convex problems and show that it converges at the same rate as mini-batch SGD in terms of number of evaluated gradients, that is, the scheme achieves linear speedup in the number of workers and mini-batch size. The number of communication rounds can be reduced up to a factor of T^{1/2}---where T denotes the number of total steps---compared to mini-batch SGD. This also holds for asynchronous implementations. Local SGD can also be used for large scale training of deep learning models. The results shown here aim serving as a guideline to further explore the theoretical and practical aspects of local SGD in these applications.
The Influence of Attentional Focus on Balance Control over Seven Days of Training

ABSTRACT This study examined the training effect of attentional focus (external focus, internal focus, or no focus instructions) on a dynamic balance task. Participants completed baseline balance testing, seven consecutive days of dynamic balance board training, and retention testing 24 hours after the last session. The novel finding of this study was the presence of a training effect on balance control when adopting an external focus relative to an internal focus or no focus instructions. Further, we report the unique observation that more patterned behavior was adopted regardless of the focus instructions. These findings provide insight into how instructions can be altered to enhance human balance control and complement the constrained-action hypothesis.
Remote and Silent Voice Command Injection on a Smartphone through Conducted IEMI Threats of Smart IEMI for Information Security

Many papers dealing with the effects of electromagnetic attacks against critical electronics have been made publicly available. Recently, it has been demonstrated that a smart use of electromagnetic interference allows for injecting voice commands remotely through connected headsets by a front-door coupling phenomena. In this paper, we investigate the possibility of injecting voice commands on modern smartphones through a conducted propagation path exploiting the so-called back-door coupling. As an outcome, we introduce an innovative silent voice command injection technique on modern smartphones connected either to the power network or to a computer through the USB cable. This research is the continuity of the work related to radiated (front-door coupling) voice command injection technique published in 2015. Remote and Silent Voice Command Injection on a Smartphone through Conducted IEMI Threats of Smart IEMI for Information Security José Lopes Esteves and Chaouki Kasmi Wireless Security Lab French Network and Information Security Agency ANSSI
Extreme dust storm over the eastern Mediterranean in September 2015: satellite, lidar, and surface observations in the Cyprus region

Abstract. A record-breaking dust storm originating from desert regions in northern Syria and Iraq occurred over the eastern Mediterranean in September 2015. In this contribution of a series of two articles (part 1, observations; part 2, atmospheric modeling), we provide a comprehensive overview of the aerosol conditions during this extreme dust outbreak in the Cyprus region. These observations are based on satellite observations (MODIS, moderate resolution imaging spectroradiometer) of aerosol optical thickness (AOT) and Angstrom exponent, surface particle mass (PM10) concentrations measured at four sites in Cyprus, visibility observations at three airports in southern Cyprus and corresponding conversion products (particle extinction coefficient, dust mass concentrations), EARLINET (European Aerosol Research Lidar Network) lidar observations of dust vertical layering over Limassol, particle optical properties (backscatter, extinction, lidar ratio, linear depolarization ratio), and derived profiles of dust mass concentrations. Maximum 550 nm AOT exceeded values of 5.0, according to MODIS, and the mass loads were correspondingly > 10 g m−2 over Larnaca and Limassol during the passage of an extremely dense dust front on 8 September 2015. Hourly mean PM10 values were close to 8000 µg m−3 and the observed meteorological optical range (visibility) was reduced to 300–750 m at Larnaca and Limassol. The visibility observations suggest peak values of the near-surface total suspended particle (TSP) extinction coefficients of 6000 Mm−1 and thus TSP mass concentrations of 10 000 µg m−3. The Raman polarization lidar observations mainly indicated a double layer structure of the dust plumes (reaching to about 4 km height), pointing to at least two different dust source regions. Dust particle extinction coefficients (532 nm) already exceeded 1000 Mm−1 and the mass concentrations reached 2000 µg m−3 in the elevated dust layers on 7 September, more than 12 h before the peak dust front on 8 September reached the Limassol lidar station around local noon. Typical Middle Eastern dust lidar ratios around 40 sr were observed in the dense dust plumes. The particle depolarization ratio decreased from around 0.3 in the lofted dense dust layers to 0.2 at the end of the dust period (11 September), indicating an increasing impact of anthropogenic haze.
Physical Attractiveness as a Signal of Biological Quality

It has been commonly thought that standards of beauty are arbitrary cultural conventions that vary between cultures and time. In my thesis I found that it is not so. Instead, I show that attractiveness and preferred traits serve as cues to phenotypic qualities that provide selective benefits for those who choose their mates based on these criteria. In the first study I show that attractive men have a stronger antibody response to the hepatitis b vaccine and higher levels of testosterone than their less attractive peers. Men with low levels of testosterone also tend to have high levels of the stress hormone cortisol, suggesting that their immune responses may have been inhibited by stress hormones. Thus, facial attractiveness may serve as an honest cue of the strength of immune defence in men. In the second study, I show that the attractiveness of the male body is also a cue of better immunity. In addition, I show that adiposity, both in men’s faces and bodies, is a better cue of the strength of immunity and attractiveness than of masculinity. In the third study, I test the preferences of women from 13 countries for facial cues of testosterone and cortisol. I show that there is cross-cultural variation in women’s preference for cues of testosterone and cortisol in male faces. I found a relationship between the health of a nation and women’s preferences for cues of testosterone in the male face and the interaction between preferences for cues of testosterone and cortisol. I show also a relationship between preferences for cues of testosterone and a societal-level measure of parasite stress. Thus, it seems that societal-level ecological factors influence the relative value of traits as revealed by combinations of testosterone and stress hormones. In the fourth study, I show that women’s immune responsiveness (amount of antibodies produced) does not predict facial attractiveness. Instead, plasma cortisol level is negatively associated with attractiveness, indicating that stressed women look less attractive. Fat percentage is curvilinearly associated with facial attractiveness, indicating that being too thin or too fat reduces attractiveness. This study suggests that in contrast to men, facial attractiveness in women does not indicate the strength of immune defence, but is associated with other aspects of long-term health and fertility: circulating levels of the stress hormone cortisol and the percentage of body fat. In the last study I show that the attractiveness of men’s body odor is positively correlated with stress hormone levels, suggesting also that the attractiveness of body odors may signal the phenotypic quality of males to females. However, the attractiveness of men’s body odor was not associated with testosterone levels. My thesis suggests that the standard of beauty is not in the eye of the beholder. Instead, our standard of beauty is hardwired in our brains by genes that are selected by natural selection and also influenced by current environmental conditions.
A comparative study of anterior cruciate ligament reconstruction with double, single, or selective bundle techniques

Purpose: Reconstruction of the anterior cruciate ligament (ACL) is the most frequently performed reconstructive surgery in the knee. Biomechanical studies have shown that double bundle (DB) reconstruction is better than single bundle (SB) reconstruction with regard to rotational stability. It is postulated that resection of ACL fibres that remain in continuity may be counterproductive for the knee as these fibres have the capacity to produce collagen. In this study, we aimed to evaluate the efficacy among selective bundle, DB and SB ACL reconstructions over a 2-year post-operative follow-up period. Methods: A retrospective comparative study was conducted for comparison between selective bundle, DB and SB reconstructions. Between 2012 and 2014, 291 ACL reconstructions were performed. Of these, 68 patients had selective ACL reconstructions (group SLB), 147 had DB ACL reconstructions (group DB) and 76 had SB ACL reconstructions (group SB). Institutional Review Board approval was obtained, and all patients provided informed consent. Clinical results were assessed with the International Knee Documentation Committee (IKDC), Lysholm and Tegner scores. Stability was measured using Lachman, pivot shift and anterior drawer stress tests using the KT1000 at 30° of knee flexion. Results: There was no significant difference in ligament grade, function grade, IKDC grade, as well as Tegner and Lysholm means among all three groups after a 2-year follow-up period. Conclusion: Selective bundle reconstruction provides comparable results to DB and SB reconstruction techniques. It is a viable alternative for patients with partial tears.
Selfish Decentralized Computation Offloading for Mobile Cloud Computing in Dense Wireless Networks

Offloading computation to a mobile cloud is a promising solution to augment the computation capabilities of mobile devices. In this paper, we consider selfish mobile devices in a dense wireless network, in which individual mobile devices can offload computations through multiple access points or through the base station to a mobile cloud so as to minimize their computation costs. We provide a game theoretical analysis of the problem, prove the existence of pure strategy Nash equilibria, and provide an efficient decentralized algorithm for computing an equilibrium. For the case when the cloud computing resources scale with the number of mobile devices, we show that all improvement paths are finite. Furthermore, we provide an upper bound on the price of anarchy of the game, which serves as an upper bound on the approximation ratio of the proposed decentralized algorithms. We use simulations to evaluate the time complexity of computing Nash equilibria and to provide insights into the price of anarchy of the game under realistic scenarios. Our results show that the equilibrium cost may be close to optimal, and the convergence time is almost linear in the number of mobile devices.