Miracle-dz/UniFAR-FTUs huggingface dataset:
Glyoxal as an alternative fixative to formaldehyde in immunostaining and super‐resolution microscopy

Paraformaldehyde (PFA) is the most commonly used fixative for immunostaining of cells, but has been associated with various problems, ranging from loss of antigenicity to changes in morphology during fixation. We show here that the small dialdehyde glyoxal can successfully replace PFA. Despite being less toxic than PFA, and, as most aldehydes, likely usable as a fixative, glyoxal has not yet been systematically tried in modern fluorescence microscopy. Here, we tested and optimized glyoxal fixation and surprisingly found it to be more efficient than PFA‐based protocols. Glyoxal acted faster than PFA, cross‐linked proteins more effectively, and improved the preservation of cellular morphology. We validated glyoxal fixation in multiple laboratories against different PFA‐based protocols and confirmed that it enabled better immunostainings for a majority of the targets. Our data therefore support that glyoxal can be a valuable alternative to PFA for immunostaining.
Adhesion and Autohesion of Rubber Compounds: Effect of Surface Roughness

Abstract Sheets of various rubber compounds were pre-molded using different mold surfaces: Mylar film, smooth steel, and roughened steel. Two sheets of the same compound were then bonded together by crosslinking them in contact. Measurements of peel strength were carried out over a range of temperatures from −40°C to + 130°C. When an uncured sheet was crosslinked in contact with a smooth fully-cured sheet, the peel strength was generally lower than the tear strength of either sheet and the degree of interlinking was inferred to be only about one-half of the degree of crosslinking. On the other hand, when a sheet was cured in contact with a rough surface the strength of adhesion was 2× to 3× higher than with a smooth surface, probably because of increased area for bonding. Thus, when a rubber compound was cured in contact with a fully-cured sheet having a roughened surface, the two effects largely cancelled out and the resultant bond was about as strong as the material itself. Examples are given for carbon.
Microkeratome-assisted preparation of ultrathin grafts for descemet stripping automated endothelial keratoplasty.

PURPOSE To compare three microkeratome-assisted techniques for the preparation of ultrathin (UT) grafts for Descemet stripping automated endothelial keratoplasty. METHODS After dissection with a 300-μm microkeratome head in 40 donor tissues, a second cut was performed with a 130-μm head either after manual stromal hydration (group A, n = 10) or osmotic hydration at the eye bank (group B, n = 10) or with a 50- or 90-μm head, depending on residual bed thickness (group C, n = 10); no further dissection was performed in the control group (group D, n = 10). Corneal thickness and endothelial cell (EC) count were determined at all appropriate stages. Statistical analysis was performed using a Fisher exact test. RESULTS Final graft thicknesses in groups A (89.1 ± 34.1μm), B (84.1 ± 18.6 μm), and C (72.1 ± 10.1 μm) were significantly lower than in group D (201.9 ± 25.3 μm) (P < 0.001). EC loss did not differ significantly among the groups. Multiple areas of Descemet detachment were seen in 4 of 10 corneas of group A. CONCLUSIONS All methods proved equally efficient in producing UT grafts, but stromal hydration induced tissue structural changes. EC loss was unaffected by the additional manipulation required to prepare UT grafts.
Flow Measurements in Turbulent Flow Fields with Magnetic Resonance Phase Velovity Mapping

Arterial stenosis (narrowing) is due to vascular disease that, if untreated, leads to death. The stenosis causes the development of complex flow which results in high energy losses and great forces between blood and tissue. Traditionally, turbulent flows lead to signal loss in magnetic resonance (MR) image acquisitions, resulting in loss of diagnostic information. With the advancement in MR hardware and software, some of the limitations of MR in turbulent flow fields may have been reduced or eliminated. This study evaluated the potential of MR phase velocity mapping (MRPVM), a clinical velocimetry technique, under turbulent flow conditions such as those developed in arterial stenosis. Specifically, the goal of this study was to determine how accurately MRPVM can quantify the flow rate in experimental models of arterial stenosis under a variety of flow conditions, ranging from laminar to turbulent. Three models were used: a non-occluded straight tube; an occluded tube with a 75% area reduction stenosis; and an occluded tube with a 94% area reduction stenosis. Flow vi experiments were conducted under steady-state flow conditions (flow rates of 1.4-10.4 L/min) inside a 1.5 Tesla whole-body clinical Siemens MR scanner. Of interest was to vary several imaging parameters which control the time of the acquisitions and the spatial resolution of the acquired images. Therefore, five different echo times (TE) (2.65-6.0 ms) and three different combinations of the field of view and matrix size, resulting in three different spatial resolutions, were studied. Axial MRPVM acquisitions were performed in all models upstream, at the throat, and downstream of the stenosis. The acquired phase images provided the velocity from which the flow rate was calculated. The MR-measured flow rates were compared with the true flow rates from rotameters to determine the accuracy of MRPVM. The results confirmed that MRPVM can measure the flow rate accurately under laminar flow conditions. In turbulent flow, the accuracy was reduced due to signal loss. Underestimation of the flow rate was observed in the most severe stenosis model, downstream of the throat, at the highest flow rate (and thus highest Reynolds number). Overall, the lower the TE was, the more accurate the flow rate measurement was. The effect of spatial resolution seemed to be much weaker than that of TE on the accuracy of the results. Additional experimental studies covering a larger range of Reynolds numbers and geometric features and clinical studies in healthy subjects and patients are necessary to provide information about the clinical potential of MRPVM to measure flow under pathologic flow conditions.
Transport-Based Pattern Theory: A Signal Transformation Approach

In many scientific fields imaging is used to relate a certain physical quantity to other dependent variables. Therefore, images can be considered as a map from a real-world coordinate system to the non-negative measurements being acquired. In this work we describe an approach for simultaneous modeling and inference of such data, using the mathematics of optimal transport. To achieve this, we describe a numerical implementation of the linear optimal transport transform, based on the solution of the Monge-Ampere equation, which uses Brenier's theorem to characterize the solution of the Monge functional as the derivative of a convex potential function. We use our implementation of the transform to compute a curl-free mapping between two images, and show that it is able to match images with lower error that existing methods. Moreover, we provide theoretical justification for properties of the linear optimal transport framework observed in the literature, including a theorem for the linear separation of data classes. Finally, we use our optimal transport method to empirically demonstrate that the linear separability theorem holds, by rendering non-linearly separable data as linearly separable following transform to transport space.
Gene expression Sequence 2 Vec : a novel embedding approach for modeling transcription factor binding affinity landscape

Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these hidden Markov models into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA datasets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods. Availability and implementation: Our program is freely available at https://github.com/ram zan1990/sequence2vec. Contact: xin.gao@kaust.edu. sa or lsong@cc.gatech. edu. Supplementary information: Supplementary data are available at Bioinformatics online.
Networking effects on cooperation in evolutionary N-person threshold games

Evolutionary game theory has been extensively employed to study the evolution of cooperation in human society. Many previous studies have shown that public cooperation can emerge from positive interactions and social diversity in structured populations. Here we study the evolution of cooperation under N-person interactions, where a minimum threshold of individuals must cooperate to produce public benefits. This is a very common phenomenon in teamwork, especially given the limited capacity of individuals. In this paper, we first present two scenarios of individual contribution mechanisms under an N-person threshold game to characterize such real-world situations. Then, we analyze the stable equilibrium for both scenarios of threshold games in well-mixed populations. Finally, we carry out simulations on three types of complex networks to evaluate the effects of both individual interactions and social diversity on the evolution of cooperation in structured populations. The analytical and simulation results in this paper offer a new insight into the evolution of cooperation in the face of threshold.
Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical dengue fever and dengue shock syndrome

Ethnic diversity has been long considered as one of the factors explaining why the severe forms of dengue are more prevalent in Southeast Asia than anywhere else. Here we take advantage of the admixed profile of Southeast Asians to perform coupled association-admixture analyses in Thai cohorts. For dengue shock syndrome (DSS), the significant haplotypes are located in genes coding for phospholipase C members (PLCB4 added to previously reported PLCE1), related to inflammation of blood vessels. For dengue fever (DF), we found evidence of significant association with CHST10, AHRR, PPP2R5E and GRIP1 genes, which participate in the xenobiotic metabolism signaling pathway. We conducted functional analyses for PPP2R5E, revealing by immunofluorescence imaging that the coded protein co-localizes with both DENV1 and DENV2 NS5 proteins. Interestingly, only DENV2-NS5 migrated to the nucleus, and a deletion of the predicted top-linking motif in NS5 abolished the nuclear transfer. These observations support the existence of differences between serotypes in their cellular dynamics, which may contribute to differential infection outcome risk. The contribution of the identified genes to the genetic risk render Southeast and Northeast Asian populations more susceptible to both phenotypes, while African populations are best protected against DSS and intermediately protected against DF, and Europeans the best protected against DF but the most susceptible against DSS.
An evaluation of IASI-NH 3 with ground-based FTIR 1 measurements 2

Global distributions of atmospheric ammonia (NH3) measured with satellite instruments such as the 27 Infrared Atmospheric Sounding Interferometer (IASI) contain valuable information on NH3 concentrations and 28 variability in regions not yet covered by ground based instruments. Due to their large spatial coverage and daily 29 observations, the satellite observations have the potential to increase our knowledge of the distribution of NH3 30 emissions, and associated seasonal cycles. However the observations remain poorly validated, with only a 31 handful of available studies often using only surface observations without any vertical information. In this study, 32 we present the first validation of the IASI-NH3 product using ground-based Fourier Transform InfraRed (FTIR) 33 observations. Using a recently developed consistent retrieval strategy, NH3 concentration profiles have been 34 retrieved using observations from nine Network for the Detection of Atmospheric Composition Change 35 (NDACC) stations around the world between 20082015. We demonstrate the importance of strict spatio36 temporal collocation criteria for the comparison. Large differences in the regression results are observed for 37 changing intervals of spatial criteria, mostly due to terrain characteristics and the short lifetime of NH3 in the 38 atmosphere. The seasonal variations of both datasets are consistent for most sites. Correlations are found to be 39 high at sites in areas with considerable NH3 levels, whereas correlations are lower at sites with low atmospheric 40 NH3 levels close to the detection limit of the IASI instrument. A combination of the observations from all sites 41 (Nobs = 547) give a MRD of -32.4 ± (56.3) %, a correlation r of 0.8 with a slope of 0.73. These results indicate 42 that the IASI-NH3 product performs better than previous upper bound estimates (-50% +100%). 43 44 Atmos. Chem. Phys. Discuss. , doi:10.5194/acp-2016-141, 2016 Manuscript under review for journal Atmos. Chem. Phys. Published: 15 March 2016 c © Author(s) 2016. CC-BY 3.0 License.
Neurophysiological Processing of an Emotional Task is Sensitive to Time-of-Day

Previous work from our laboratory has shown that a measure of attention to emotionally-charged stimuli, the late positive potential (LPP) event related potential (ERP), distinguished neutral from emotional pictures on a baseline day, but not after sleep deprivation. Here we sought to extend these findings and address the uncertainty about the effect of time-of-day on emotion processing by testing a morning group (8:00–10:00 a.m., n = 30) and an evening group (8:00–10:00 p.m., n = 30). We also examined the extent of diurnal changes in cortisol related to the emotion processing task. Results from this study mirrored those found after one night of sleep deprivation. Compared to the morning group, the LPP generated by the evening group (who had a greater homeostatic sleep drive) did not distinguish neutral from emotionally-charged stimuli. New to this study, we also found that there was a time-of-day effect on positive, but not negative pictures. While, as expected, cortisol levels were higher in the morning relative to the evening group, there was no relationship between cortisol and the LPP ERP emotion measure. In addition, neither time-of-day preference nor sleep quality was related to the LPP measure. These findings show that, similar to what occurs after sleep deprivation, increased sleep pressure throughout the day interferes with attention processing to emotional stimuli.
Are differences in population prevalence of alcohol's harm to others related to survey administration mode?

INTRODUCTION AND AIMS This study assessed the comparability of estimates of alcohol's harm to others across different administration modes in Swedish general population surveys. Harm was categorised as harm from strangers' drinking and harm from heavy drinkers known to the respondent. DESIGN AND METHODS Three surveys were conducted in 2011/2012 (n = 6841), including identical questions. One was based on self-administered postal or Web questionnaires, and two were based on computer-assisted telephone interviews of which one included a more ambitious procedure in terms of for example monetary incentives to the respondents. Pearson χ2 -tests were used to compare differences in the prevalence of harm. To estimate potential effects of survey mode, the samples were pooled, and multivariate Poisson regression models with mode as explanatory variable were used, adjusting for socio-demographic and behavioural factors. RESULTS Respondents in the two computer-assisted telephone interviews were more likely to report harm from strangers' drinking compared with respondents in the self-administered postal or Web questionnaires. However, no significant differences were found between survey modes concerning reports of harm from known people's drinking. DISCUSSION AND CONCLUSIONS A survey mode based on interviews seems to facilitate reports of harm from strangers' drinking. This does not apply to reports of harm from known people's drinking. Therefore, the comparability of estimates of alcohol's harm to others between survey modes depends on the type of harm being studied. [Sundin E, Landberg J, Galanti MR, Room R, Ramstedt M. Are differences in population prevalence of alcohol's harmto others related to survey administration mode?
Constrained Neural Style Transfer for Decorated Logo Generation

Making decorated logos requires image editing skills, without sufficient skills, it could be a time-consuming task. While there are many on-line web services to make new logos, they have limited designs and duplicates can be made. We propose using neural style transfer with clip art and text for the creation of new and genuine logos. We introduce a new loss function based on distance transform of the input image, which allows the preservation of the silhouettes of text and objects. The proposed method constrains style transfer only around the designated area. We demonstrate the characteristics of proposed method. Finally, we show the results of logo generation with various input images.
A type I IFN-dependent DNA damage response regulates the genetic program and inflammasome activation in macrophages

Macrophages produce genotoxic agents, such as reactive oxygen and nitrogen species, that kill invading pathogens. Here we show that these agents activate the DNA damage response (DDR) kinases ATM and DNA-PKcs through the generation of double stranded breaks (DSBs) in murine macrophage genomic DNA. In contrast to other cell types, initiation of this DDR depends on signaling from the type I interferon receptor. Once activated, ATM and DNA-PKcs regulate a genetic program with diverse immune functions and promote inflammasome activation and the production of IL-1β and IL-18. Indeed, following infection with Listeria monocytogenes, DNA-PKcs-deficient murine macrophages produce reduced levels of IL-18 and are unable to optimally stimulate IFN-γ production by NK cells. Thus, genomic DNA DSBs act as signaling intermediates in murine macrophages, regulating innate immune responses through the initiation of a type I IFN-dependent DDR. DOI: http://dx.doi. org/10.7554/eLife.24655. 001
Constant-factor approximation of domination number in sparse graphs

The k-domination number of a graph is the minimum size of a set X such that every vertex of G is in distance at most k from X. We give a linear time constant-factor approximation algorithm for k-domination number in classes of graphs with bounded expansion, which include e.g. proper minor-closed graph classes, classes closed on topological minors or classes of graphs that can be drawn on a fixed surface with bounded number of crossings on each edge. The algorithm is based on the following approximate min-max characterization. A subset A of vertices of a graph G is d-independent if the distance between each pair of vertices in A is greater than d. Note that the size of the largest 2k-independent set is a lower bound for the k-domination number. We show that every graph from a fixed class with bounded expansion contains a 2k-independent set A and a k-dominating set D such that |D|=O(|A|), and these sets can be found in linear time. For domination number (k=1) the assumptions can be relaxed, and the result holds for all graph classes with arrangeability bounded by a constant.
Modeling and Analysis of D2D Millimeter-Wave Networks With Poisson Cluster Processes

This paper investigates the performance of millimeter wave (mmWave) communications in clustered device-to-device (D2D) networks. The locations of D2D transceivers are modeled as a Poisson Cluster Process. In each cluster, devices are equipped with multiple antennas, and the active D2D transmitter (D2D-Tx) utilizes mmWave to serve one of the proximate D2D receivers. Specifically, we introduce three user association strategies: 1) uniformly distributed D2D-Tx model; 2) nearest D2D-Tx model; and 3) closest line-of-site (LOS) D2D-Tx model. To characterize the performance of the considered scenarios, we derive new analytical expressions for the coverage probability and area spectral efficiency (ASE). Additionally, in order to efficiently illustrating the general trends of our system, a closed-form lower bound for the special case interfered by intra-cluster LOS links is derived. We provide Monte Carlo simulations to corroborate the theoretical results and show that: 1) the coverage probability is mainly affected by the intra-cluster interference with LOS links; 2) there exists an optimum number of simultaneously active D2D-Txs in each cluster for maximizing ASE; and 3) the closest LOS model outperforms the other two scenarios but at the cost of extra system overhead.
Duloxetine Plasma Concentrations and Its Effectiveness in the Treatment of Nonorganic Chronic Pain in the Orofacial Region

Objective The purpose of this study was to examine the relationship between the pain-relieving effects of duloxetine and its plasma concentrations in patients with burning mouth syndrome and atypical odontalgia characterized by chronic nonorganic pain in the orofacial region. Methods We administered duloxetine to 77 patients diagnosed as having burning mouth syndrome or atypical odontalgia for 12 weeks. The initial dose of duloxetine was established as 20 mg/d and was increased to 40 mg/d after week 2. We evaluated pain using the visual analog scale and depressive symptoms using the Structured Interview Guide for the Hamilton Depression Rating Scale at weeks 0, 2, 4, 6, 8, 10, and 12 and measured plasma concentrations of duloxetine 12 weeks after the start of its administration. Results Visual analog scale scores were significantly lower 12 weeks after than at the start of the administration of duloxetine (paired t test, t = 6.65, P < 0.0001). We examined the relationship between the rate of decreases in visual analog scale scores and plasma concentrations of duloxetine. There was no significant linear regression or quadratic regression. Conclusions Duloxetine significantly relieved pain in patients with chronic nonorganic pain in the orofacial region. However, no relationship was observed between its pain-relieving effects and plasma concentrations.