Miracle-dz/UniFAR-FTUs huggingface dataset:
Suppression of Red Blood Cell Autofluorescence for Immunocytochemistry on Fixed Embryonic Mouse Tissue

Autofluorescence is a problem that interferes with immunofluorescent staining and complicates data analysis. Throughout the mouse embryo, red blood cells naturally fluoresce across multiple wavelengths, spanning the emission and excitation spectra of many commonly used fluorescent reporters, including antibodies, dyes, stains, probes, and transgenic proteins, making it difficult to distinguish assay fluorescence from endogenous fluorescence. Several tissue treatment methods have been developed to bypass this issue with varying degrees of success. Sudan Black B dye has been commonly used to quench autofluorescence, but can also introduce background fluorescence. Here we present a protocol for an alternative called TrueBlack Lipofuscin Autofluorescence Quencher. The protocol described in this unit demonstrates how TrueBlack efficiently quenches red blood cell autofluorescence across red and green wavelengths in fixed embryonic tissue without interfering with immunofluorescent signal intensity or introducing background staining. We also identify optimal incubation, concentration, and multiple usage conditions for routine immunofluorescence microscopy. © 2017 by John Wiley & Sons, Inc.
Molecular profiling of malignant pleural mesothelioma and pulmonary fibrosis

5 I REVIEW OF THE LITERATURE 8 1 ASBESTOS FIBRES 8 1.1.1 Oxidative stress and antioxidant pathways 11 1.1.2 Nuclear factor-kappa B (NFB) and tumor necrosis factor(TNF) 13 1.1. 3 Epidermal growth factor receptor (EGFR) mediated pathway 14 1.1. 4 Transforming growth factor(TGF) 14 2 MALIGNANT MESOTHELIOMA (MM) 15 2.2.1 DNA copy number changes in MM 19 3 IDIOPATHIC PULMONARY FIBROSIS (IPF) 28 3.1.1 Transforming growth factor– (TGF) 31 3.1.2 Bone morphogenetic proteins (BMPs) and gremlin 32 4 HIGH-RESOLUTION PROFILING METHODS IN FINDING MARKERS FOR DETECTION OF DISEASES 35 1.1 Genes and pathways affected by asbestos fibres 9 1.2 Asbestos-related diseases 15 2.1 Histological classification of MM 17 2.2 Molecular genetics and pathology of MM 18 2.3 Diagnoses and prognosis of MM patients 23 2.4 MM therapy options, and treatment resistance 25 3.2 Diagnosis and prognosis of lung fibrosis 34 4.1 Microarray platforms 35 4.2 Asbestos associated signatures 36
Integrating element and term semantics for similarity-based XML document clustering

Structured link vector model (SLVM) is a recently proposed document representation that takes into account both structural and semantic information for measuring XML document similarity. Its formulation includes an element similarity matrix for capturing the semantic similarity between XML elements - the structural components of XML documents. In this paper, instead of applying heuristics to define the similarity matrix, we proposed to learn the matrix using pair wise similar training data in an iterative manner. In addition, we extended SLVM to SLVM-LSI by incorporating term semantics into SLVM using latent semantic indexing, with the element similarity related properties of the original SLVM preserved. For performance evaluation, we applied SLVM-LSI to similarity-based clustering of two XML datasets and the proposed SLVM-LSI was found to significantly outperform the conventional vector space model and the edit-distance based methods. The similarity matrix, obtained as a byproduct via the learning, can provide higher level knowledge about the semantic relationship between the XML elements.
RNF2 is the target for phosphorylation by the p38 MAPK and ERK signaling pathways

RNF2, a member of polycomb group (PcG) proteins, is involved in chromatin remodeling. However, mechanisms that regulate RNF2 function are unknown. To identify such mechanisms, RNF2 was expressed in HEK‐293 cells and analyzed by 2‐D electrophoresis. RNF2 was resolved into at least seven protein spots, migrating toward the lower pI from its expected pI of 6.38, suggesting that RNF2 undergoes post‐translational modifications. Western blotting indicated that majority of these RNF2 spots contained phosphoserine(s), which were completely dephosphorylated upon treatment with a phosphatase. SB203580, a specific inhibitor of p38 MAPK, inhibited RNF2 phosphorylation at one site. On the other hand, PD98059, an inhibitor of MEK1/2, inhibited majority of the phosphorylation events in RNF2. Mass spectrometry analysis identified that RNF2 expressed in Sf9 insect cells undergoes co‐translational excision of 1Met coupled to N‐acetylation of 2Ser, and phosphorylation of 41Ser. Interestingly, 41Ser is a predicted p38/MAPK phosphorylation site, consistent with the loss of phosphorylation induced by SB203580. Further analysis indicated that RNF2 phosphorylation differentially modulates the expression of transcription factors and histone 2B acetylation. These results provide first evidence for phosphorylation of RNF2, and suggest that the mitogen activated protein kinases including p38 MAPK and ERK1/2 regulate growth, stress response, differentiation and other cellular processes, through phosphorylation of RNF2.
Bias in Estimation of a Mixture of Normal Distributions

Estimating parameters in a mixture of normal distributions dates back to the 19th century when Pearson originally considered data of crabs from the Bay of Naples. Since then, many real world applications of mixtures have led to various proposed methods for studying similar problems. Among them, maximum likelihood estimation (MLE) and the continuous empirical characteristic function (CECF) methods have drawn the most attention. However, the performance of these competing estimation methods has not been thoroughly studied in the literature and conclusions have not been consistent in published research. In this article, we review this classical problem with a focus on estimation bias. An extensive simulation study is conducted to compare the estimation bias between the MLE and CECF methods over a wide range of disparity values. We use the overlapping coefficient (OVL) to measure the amount of disparity, and provide a practical guideline for estimation quality in mixtures of normal distributions. Application to an ongoing multi-site Huntington disease study is illustrated for ascertaining cognitive biomarkers of disease progression.
Brachial-Ankle Pulse Wave Velocity and the Risk Prediction of Cardiovascular Disease: An Individual Participant Data Meta-Analysis

An individual participant data meta-analysis was conducted in the data of 14 673 Japanese participants without a history of cardiovascular disease (CVD) to examine the association of the brachial-ankle pulse wave velocity (baPWV) with the risk of development of CVD. During the average 6.4-year follow-up period, 687 participants died and 735 developed cardiovascular events. A higher baPWV was significantly associated with a higher risk of CVD, even after adjustments for conventional risk factors (P for trend <0.001). When the baPWV values were classified into quintiles, the multivariable-adjusted hazard ratio for CVD increased significantly as the baPWV quintile increased. The hazard ratio in the subjects with baPWV values in quintile 5 versus that in those with the values in quintile 1 was 3.50 (2.14–5.74; P<0.001). Every 1 SD increase of the baPWV was associated with a 1.19-fold (1.10–1.29; P<0.001) increase in the risk of CVD. Moreover, addition of baPWV to a model incorporating the Framingham risk score significantly increased the C statistics from 0.8026 to 0.8131 (P<0.001) and also improved the category-free net reclassification (0.247; P<0.001). The present meta-analysis clearly established baPWV as an independent predictor of the risk of development of CVD in Japanese subjects without preexisting CVD. Thus, measurement of the baPWV could enhance the efficacy of prediction of the risk of development of CVD over that of the Framingham risk score, which is based on the traditional cardiovascular risk factors.
Eecient Cross-trees for External Memory

We describe eecient methods for organizing and maintaining large multidimensional data sets in external memory. This is particular important as access to external memory is currently several order of magnitudes slower than access to main memory, and current technology advances are likely to make this gap even wider. We focus particularly on multidimensional data sets which must be kept simultaneously sorted under several total orderings: these order-ings may be deened by the user, and may also be changed dynamically by the user throughout the lifetime of the data structures, according to the application at hand. Besides standard insertions and deletions of data, our proposed solution can perform eeciently split and concatenate operations on the whole data sets according to any ordering. This allows the user: (1) to dynamically rearrange any ordering of a segment of data, in a time that is faster than recomputing the new ordering from scratch; (2) to eeciently answer queries related to the data contained in a particular range of the current orderings. Our solution fully generalizes the notion of B-trees to higher dimensions by carefully combining space-driven and data-driven partitions. Balancing is easy as we introduce a new multidimensional data structure, the cross-tree, that is the cross product of balanced trees. As a result, the cross-tree is competitive with other popular index data structures that require linear space (including k-d trees, quad-trees, grid les, space lling curves, hB-trees, and R-trees).
An Analysis of Failure-Related Energy Waste in a Large-Scale Cloud Environment

Cloud computing providers are under great pressure to reduce operational costs through improved energy utilization while provisioning dependable service to customers; it is therefore extremely important to understand and quantify the explicit impact of failures within a system in terms of energy costs. This paper presents the first comprehensive analysis of the impact of failures on energy consumption in a real-world large-scale cloud system (comprising over 12 500 servers), including the study of failure and energy trends of the spatial and temporal environmental characteristics. Our results show that 88% of task failure events occur in lower priority tasks producing 13% of total energy waste, and 1% of failure events occur in higher priority tasks due to server failures producing 8% of total energy waste. These results highlight an unintuitive but significant impact on energy consumption due to failures, providing a strong foundation for research into dependable energy-aware cloud computing.
Interprocedural Parallelization Analysis: Preliminary Results

This paper describes a fully interprocedural automatic parallelization system for Fortran programs, and presents the results of extensive experiments obtained using this system. The system incorporates a comprehensive and integrated collection of analyses including dependence, privatization and reduction recognition for both array and scalar variables, and scalar symbolic analysis to support these. All the analyses have been implemented in the SUIF (Stanford University Intermediate Format) compiler system, with the aid of an interprocedural analysis construction tool known as FIAT. Our interprocedural analysis is uniquely designed to provide the same quality of information as if the program were analyzed as a single procedure, while managing the complexity of the analysis. We have implemented a robust system that has parallelized, completely automatically, loops containing over a thousand lines of code. This work makes possible the first comprehensive empirical evaluation of state-of-the-art automatic parallelization technology. This paper reports evaluation numbers on programs from standard benchmark suites. The results demonstrate that all the interprocedural analyses taken together can substantially advance the capability of current automatic parallelization technology.
Sex-Role Stereotyping and Individual Differences in Liking for the Physically Attractive

To examine relationships between sex-role stereotyping and attraction to the opposite sex, subjects scoring high or low on the Macho Scale estimated their liking for a person of the opposite sex who was physically attractive or unattractive. A predicted two-way interaction showed that high scorers reported greatest liking for attractive persons and least liking for unattractive persons, while the liking of low scorers was less affected by physical attractiveness. Secondary findings showed that low scorers on the Macho Scale recalled more biographical information about the persons they rated, that information recall was positively correlated with liking, and that high and low scorers differed markedly in the traits ascribed to the physically attractive.
Nonparaxial soliton refraction at optical interfaces with χ(3) and χ(5) susceptibilities

Summary form only given. In their most general form, wave-interface problems are inherently angular in nature. For instance, the interaction between light waves and material boundaries essentially defines the entire field of optics. The seminal works of Aceves et al. [1,2] considered scalar bright spatial solitons impinging on the planar interface between two Kerr-type media with different χ(3) susceptibilities. While these classic nonlinear Schrödinger models undeniably paved the way toward understanding how self-collimated light beams behave at material discontinuities, they suffer from a fundamental limitation: the assumption of slowly-varying wave envelopes means that, in the laboratory frame, angles of incidence, reflection and refraction (relative to the interface) must be near-negligibly small. This intrinsic angular restriction may be eliminated by adopting a mathematical and computational framework based on the solution of nonlinear Helmholtz equations. To date, we have considered bright [3] and dark [4] soliton refraction in dissimilar focusing and de focusing τ materials, respectively.In this presentation, we give the first detailed overview of beam refraction at the interface between materials whose nonlinear polarization has contributions from both χ(3) and χ(5) susceptibilities [5]. The governing equation is of the inhomogeneous Helmholtz class with a cubic-quintic nonlinearity, and analysis is facilitated through the exact bright soliton solutions of the corresponding homogeneous problem [6]. By respecting field continuity conditions at the interface, a universal Snell's law may be derived for describing the refractive properties of soliton beams. This compact nonparaxial law contains a supplementary multiplicative factor that captures the interplay between system nonlinearity, discontinuities in material properties, and finite beam waists. Extensive numerical calculations have tested analytical predictions, providing strong supporting evidence for the validity of our modelling approach across wide regions of a six-dimensional parameter space. Our Snell's law also provides theoretical predictions for critical angles that are in generally good agreement with full simulations of beams at linear and weakly-nonlinear interfaces. We have quantified Goos-Hänchen shifts [7] at such interfaces (see Fig. 1). Of particular interest are regimes involving external linear refraction [8], since these physical contexts have no counterpart in conventional (Schrödinger-based) theory [1]. For strongly nonlinear interfaces, new and potentially exploitable qualitative phenomena can emerge.
Using Dependency-Based Features to Take the ’Para-farce’ out of Paraphrase

As research in text-to-text paraphrase generation progresses, it has the potential to improve the quality of generated text. However, the use of paraphrase generation methods creates a secondary problem. We must ensure that generated novel sentences are not inconsistent with the text from which it was generated. We propose a machine learning approach be used to filter out inconsistent novel sentences, or False Paraphrases. To train such a filter, we use the Microsoft Research Paraphrase corpus and investigate whether features based on syntactic dependencies can aid us in this task. Like Finch et al. (2005), we obtain a classification accuracy of 75.6%, the best known performance for this corpus. We also examine the strengths and weaknesses of dependency based features and conclude that they may be useful in more accurately classifying cases of False Paraphrase.
Destabilizing the autoinhibitory conformation of Zap70 induces up-regulation of inhibitory receptors and T cell unresponsiveness

Zap70 plays a critical role in normal T cell development and T cell function. However, little is known about how perturbation of allosteric autoinhibitory mechanisms in Zap70 impacts T cell biology. Here, we analyze mice with a hypermorphic Zap70 mutation, W131A, which destabilizes the autoinhibitory conformation of Zap70, rendering the kinase in a semiactive state. W131A mutant mice with wild-type T cell receptor (TCR) repertoires exhibited relatively normal T cell development. However, crossing the W131A mutant mice to OTII TCR transgenic mice resulted in increased negative selection of OTII+ thymocytes and in increased thymic and peripheral T regulatory cells. Strikingly, increased basal TCR signaling was associated with a marked increase in inhibitory receptor expression and with T cells that were relatively refractory to TCR stimulation. PD-1 inhibitory receptor blockade partially reversed T cell unresponsiveness. Collectively, disruption of normal Zap70 autoinhibition engaged negative feedback mechanisms by which negative selection and inhibitory receptors restrain TCR signaling to enforce both central and peripheral tolerance.
Whole-Genome Sequences of Four Corynebacterium CDC Group F-1 Strains Isolated from Urine

ABSTRACT Three draft and one complete genome sequence from strains isolated from urine and consistent with Corynebacterium CDC group F-1 were assembled and studied. Genome sizes ranged between 2.3 and 2.44 Mb, with G+C content between 60.4% and 60.7%.
DEA MODELS WITH INTERVAL SCALE INPUTS AND OUTPUTS

This paper proposes an alternative approach for efficiency analysis when a set of DMUs uses interval scale variables in the productive process. To test the influence of these variables, we present a general approach of deriving DEA models to deal with the variables. We investigate a number of performance measures with unrestricted-in-sign interval and/or interval scale variables.
Investigation of the 5q33.3 longevity locus and age-related phenotypes

A large meta-analysis recently found the 5q33.3 locus to be associated with survival to ≥ 90 years and lower all-cause mortality, thus suggesting it as a third human longevity locus alongside APOE and FOXO3A. The 5q33.3 locus has previously been associated with blood pressure regulation and cardiovascular diseases in middle-aged individuals. However, part of the influence on mortality appears to be independent of cardiovascular phenotypes, and the role of the 5q33.3 locus in longevity and survival is therefore still partly unknown. We investigated the association between the longevity-associated variant rs2149954 on chromosome 5q33.3 and age-related phenotypes in two cohorts of 1,588 and 1,271 long-lived individuals (mean ages 93.1 and 95.9 years, respectively) as well as in 700 middle-aged and 677 elderly individuals (mean ages 52.5 and 78.7 years). Altogether, nominally significant associations between the rs2149954 minor allele and a decreased risk of heart attack and heart failure as well as increased physical functioning were found in the long-lived individuals. In the middle-aged and elderly individuals, rs2149954 minor allele carriers had a lower risk of hypertension. Our results thereby confirm a role of the 5q33.3 locus in cardiovascular health and, interestingly, they also suggest a role in physical functioning.
Increasing the user perceived quality for IPTV services

Currently, digital television is gradually replacing analogue TV. Although these digital TV services can be delivered via various broadcast networks (e.g., terrestrial, cable, satellite), Internet Protocol TV over broadband telecommunication networks offers much more than traditional broadcast TV. Not only can it improve the quality that users experience with this linear programming TV service, but it also paves the way for new TV services, such as video-on- demand, time-shifted TV, and network personal video recorder services, because of its integral return channel and the ability to address individual users. This article first provides an overview of a typical IPTV network architecture and some basic video coding concepts. Based on these, we then explain how IPTV can increase the linear programming TV quality experienced by end users by reducing channel-change latency and mitigating packet loss. For the latter, forward error correction and automatic repeat request techniques are discussed, whereas for the former a solution based on a circular buffer strategy is described. This article further argues that the availability of larger buffers in the network enables IPTV to better offer new services (in particular, time-shifted TV, network personal video recorder, and video-on-demand) than the competing platforms.
Achilles tendon assessed with sonoelastography: histologic agreement.

PURPOSE To compare and determine the level of agreement of findings at conventional B-mode ultrasonography (US) and sonoelastography of the Achilles tendon with findings at histologic assessment. MATERIALS AND METHODS This study was conducted with the approval of the institutional review boards, and all cadavers were in legal custody of the study institution. Thirteen Achilles tendons in 10 cadavers (four male, six female; age range, 70-90 years) were examined with B-mode US and sonoelastography. B-mode US grading was as follows: Grade 1 indicated a normal-appearing tendon with homogeneous fibrillar echotexture; grade 2, a focal fusiform or diffuse enlarged tendon; and grade 3, a hypoechoic area with or without tendon enlargement. Sonoelastography grading was as follows: Grade 1 indicated blue (hardest) to green (hard); grade 2, yellow (soft); and grade 3, red (softest). Twenty-five biopsy specimens from representative lesions of the middle and distal thirds of the Achilles tendons were evaluated histologically. The concordance of B-mode US grading compared with sonoelastographic grading was assessed by using κ analysis. RESULTS With B-mode US and sonoelastography, all 11 tendon thirds of histologically normal tendons were verified as normal (grade 1). Sonoelastography depicted 14 of 14 (100%) tendon thirds with histologic degeneration (grade 2 or 3), whereas B-mode US could depict only 12 of 14 (86%) lesions (grade 2 or 3). Only moderate agreement between B-mode US and sonoelastography was seen (κ = 0.52, P < .001). CONCLUSION Sonoelastography might help predict signs of histopathologic degeneration of Achilles tendinosis, potentially more sensitively than B-mode US.
Spiritual Development and Gratitude among Indian Emerging Adults

Gratitude, a significant Christian value, is regarded as a duty among Indians. The present study examines the role played by spiritual development in gratitude among the Indian population. The participants were emerging Indian male adults, aged between 18 and 30 years. The first sample is from 495 Catholic Indian seminarians (267 theology students and 228 philosophy students) with intensive spiritual training, and the second is from 504 Catholic Indian nonseminarians. We use the Gratitude Questionnaire-6 and the Spiritual Assessment Inventory (SAI) in the study. The results show that the factors of SAI, Awareness (of God) and Realistic Experience (of God), had medium-size correlations with gratitude in both samples. Awareness predicted gratitude in both samples and Realistic Acceptance predicted gratitude only in seminarians. The study shows that individuals with an awareness of God's presence tend to be highly grateful. Spiritually mature individuals who undergo spiritual training were also more grateful.