Miracle-dz/UniFAR-FTUs huggingface dataset:
Tissue-specific expression of Sarcoplasmic / Endoplasmic Reticulum Calcium ATPases ( ATP 2 A / SERCA ) 1 , 2 , 3 during Xenopus laevis development

1567-133X/$ see front matter 2010 Elsevier B.V. doi:10.1016/j.gep. 2010.10. 006 Abbreviation: SERCA, sarcoplasmic and endoplasm ⇑ Corresponding author. Tel. : +33 1 69 86 71 52. E-mail address: anne-helene.monsoro-burq@curie Calcium-ATPase pumps are critical in most cells, to sequester calcium into intracytoplasmic stores and regulate general calcium signalling. In addition, cell-specific needs for calcium signals have been described and employ a diversity of calcium ATPases in adult tissues and oocytes. A major family of such calcium pumps is ATP2A/SERCA family, for Sarcoplasmic/Endoplasmic Reticulum Calcium ATPases. Although largely studied in adults, the developmental expression of the atp2a/serca genes remains unknown. Here, we provide genome organisation in Xenopus laevis and tropicalis and phylogeny of atp2a/serca genes in craniates. We detail embryonic expression for the three X. laevis atp2a/serca genes. We found that the three atp2a/serca genes are strongly conserved among vertebrates and display complementary and tissue-specific expression in embryos. These expression patterns present variations when compared to the data reported in adults. Atp2a1/serca1 is expressed as soon as the end of gastrulation in a subset of the myod-positive cells, and later labels prospective slow muscle cells in the superficial part of the somite. In contrast atp2a2/serca2 is found in a larger subset of cells, but is not ubiquitous as reported in adults. Notably, atp2a2/serca2 is prominently expressed in the neural-related tissues, i.e. the neural plate, cement gland, but is excluded from premigratory neural crest. Finally, atp2a3/serca3 expression is restricted to the ectoderm throughout development. 2010 Elsevier B.V. All rights reserved.
Inhibition in Simple Cell Receptive Fields Is Broad and OFF-Subregion Biased

Inhibition in thalamorecipient layer 4 simple cells of primary visual cortex is believed to play important roles in establishing visual response properties and integrating visual inputs across their receptive fields (RFs). Simple cell RFs are characterized by nonoverlapping, spatially restricted subregions in which visual stimuli can either increase or decrease the firing rate of the cell, depending on contrast. Inhibition is believed to be triggered exclusively from visual stimulation of individual RF subregions. However, this view is at odds with the known anatomy of layer 4 interneurons in visual cortex and differs from recent findings in mouse visual cortex. Here we show with in vivo intracellular recordings in cats that while excitation is restricted to RF subregions, inhibition spans the width of simple cell RFs. Consequently, excitatory stimuli within a subregion concomitantly drive excitation and inhibition. Furthermore, we found that the distribution of inhibition across the RF is stronger toward OFF subregions. This inhibitory OFF-subregion bias has a functional consequence on spatial integration of inputs across the RF. A model based on the known anatomy of layer 4 demonstrates that the known proportion and connectivity of inhibitory neurons in layer 4 of primary visual cortex is sufficient to explain broad inhibition with an OFF-subregion bias while generating a variety of phase relations, including antiphase, between excitation and inhibition in response to drifting gratings. SIGNIFICANCE STATEMENT The wiring of excitatory and inhibitory neurons in cortical circuits is key to determining the response properties in sensory cortex. In the visual cortex, the first cells that receive visual input are simple cells in layer 4. The underlying circuitry responsible for the response properties of simple cells is not yet known. In this study, we challenge a long-held view concerning the pattern of inhibitory input and provide results that agree with current known anatomy. We show here that inhibition is evoked broadly across the receptive fields of simple cells, and we identify a surprising bias in inhibition within the receptive field. Our findings represent a step toward a unified view of inhibition across different species and sensory systems.
Step Activity and 6-Minute Walk Test Outcomes When Wearing Low-Activity or High-Activity Prosthetic Feet

Objective To determine changes in average daily step count (ADSC) and 6-minute walk test (6MWT) due to use of low-activity feet (LA) and high-activity energy-storage-and-return (ESAR) feet, and examine the sensitivity of these measures to properly classify different prosthetic feet. Design Individuals with transtibial amputations (n = 28) participated in a 6-week, randomized crossover study. During separate 3-week periods, participants wore either a LA foot (eg, solid-ankle-cushioned-heel) or an ESAR foot. Differences in 6MWT and ADSC at the end of the 3-week period were recorded. Results Subjects performed similarly in the 6MWT with the LA and ESAR foot (P = 0.871) and ADSC (P = 0.076). The correct classification of ESAR is only 51.9% and 61.5% with 6MWT and ADSC, respectively. For the LA foot, correct classification is less than 50% for both tests. Conclusions Neither ADSC or 6MWT are responsive to changes in prosthetic feet. The pitfalls and shortcomings of these instruments with regard to their ability to detect differences in prosthetic feet are outlined. Based on these results, it is not recommended that the 6MWT and ADSC are used as a means to assess outcomes for different prosthetic feet.
Evolving Future Internet Clean-Slate Entity Title Architecture with Quality-Oriented Control Plane Extensions

Due to the technological evolution, growth and various new service demands requiring new solutions to support novel usage scenarios, current Internet has been confronted with new requirements in terms of network mobility, quality and scalability, among others. New Future Internet approaches targeting Information Centric Networking, such as the Entity Title Architecture (ETArch), provide new services and optimizations for these scenarios, using novel mechanisms leveraging the Software Defined Networking (SDN) concept. However, the current ETArch approach is equivalent to the best-effort capability of current Internet, which limits achieving reliable communications. In this work, we evolved ETArch with both quality-oriented mobility and resilience functions following the super-dimensioning paradigm to achieve advanced network resource allocation integrated with OpenFlow. The resulting framework, called Support of Mobile Sessions with High Transport Network Resource Demand (SMART), allows the network to semantically define the quality requirements of each session to drive network Quality of Service control seeking to keep best Quality of Experience. The results of the preliminary performance evaluation of SMART were analyzed using Mininet, showing that it allowed the support of mobile multimedia applications with high transport network resource and quality demand over time, as well as efficiently dealing with both mobility and resilience events. Keywords–Future Internet; SDN; ICN; QoS and QoE.
Shock-index as a novel predictor of long-term outcome following primary percutaneous coronary intervention

Early identification of higher risk patients presenting with ST-elevation myocardial infarction (STEMI) and undergoing primary percutaneous coronary intervention (PPCI) will allow a more aggressive strategy and approach. The aim of this study was to evaluate the shock index (ratio of heart rate/systolic blood pressure on admission) as a predictor of mortality post PPCI in addition to other parameters. Methods: We analysed prospectively collected data on 3049 STEMI patients treated with PPCI in a large tertiary centre between March 2008–December 2011, out of which 2424 patients were aged up to 75 years (young) and 625 patients were older than 75 years (elderly). Results: Compared to younger patients, in-hospital mortality rates were four-fold higher in the elderly (11.5% vs 2.8%, odds ratio (OR) 3.5, 95% confidence interval (CI) 2.0–5.9). Cardiogenic shock (OR 8.7 (5.1–14.6)), non-TIMI3 (Thrombosis In Myocardial Infarction) flow post percutaneous coronary intervention (PCI) (OR 5.0 (3.1–7.9)), age over 75 (OR 3.5 (2.3–5.3)) and a positive shock index pre PPCI (OR 3.5 (2.0–5.9)) were the strongest independent predictors of in-hospital mortality. For long-term outcome (median follow-up period 454 days) we excluded 141 (4.6%) patients that died during the initial hospital stay. Previous angina (hazard ratio (HR) 2.9), and previous cerebrovascular events (HR 3.7) were predictors of adverse outcome in the younger patients, while previous myocardial infarction (HR 2.0) and a positive shock index (HR 2.3) were predictors in the elderly. Cardiogenic shock prior to PPCI was not able to predict long-term outcome for in-hospital survivors. Conclusion: Mortality rates following PPCI were higher in elderly patients although remained acceptable. Invasively measured shock index before PPCI is the strongest independent predictor of long-term outcome in elderly patients. In addition, predictors of in-hospital mortality were similar across different age groups but differed significantly in relation to longer-term mortality.
Extraction of Cell-Wall Polysaccharide Antigen from Streptococci

Slade, Hutton D. (Northwestern University Medical School, Chicago, Ill., and Max-Planck Institut für Immunbiologie, Freiburg, Germany). Extraction of cell-wall polysaccharide antigen from streptococci. J. Bacteriol. 90:667–672. 1965. —The carbohydrate grouping antigens in the cell walls of streptococci belonging to groups A, E, G, L, and T were extracted with 5% trichloroacetic acid at 90 C. The antigens were removed also from dry whole cells by extraction with trichloroacetic acid followed by treatment with phenol-water. Details of the methods are presented. The antigens obtained by use of either of these procedures were suitable for studies on immunological specificity and chemical structure. Quantitative enzymatic and chemical analyses of two group E antigens and one group T preparation showed the presence of l-rhamnose (22 to 44%), d-glucose (7 to 22%), d-galactose (T antigen only, 26%), glucosamine (2 to 16%), and galactosamine (T antigen only, 3%). In addition, analyses of A and G antigen preparations are presented. The protein and phosphate content of the A and E antigens were about 1% each. Quantitative precipitin curves of these antigens are presented.
Liver metastases from rectal carcinoma: Disease progression during chemotherapy despite loss of arterial‐phase hypervascularity on real‐time contrast‐enhanced harmonic sonography at low acoustic energy

We used a new sonographic technique, real‐time contrast‐enhanced harmonic sonography at low acoustic energy, to evaluate liver perfusion and liver metastases from colorectal cancer in a 73‐year‐old woman after chemotherapy. After 6 weeks of chemotherapy, liver metastases that had been clearly visible on conventional sonography before chemotherapy were no longer detectable on conventional sonography but were still evident on contrast‐enhanced sonography. At about 6 months after initiation of chemotherapy, the lesions were all visible again on conventional sonography and had become significantly larger, although some no longer showed contrast enhancement during the arterial phase. In this case, changes in arterial perfusion over time did not parallel the response of liver metastases to chemotherapy. © 2003 Wiley Periodicals, Inc. J Clin Ultrasound 31:387–391, 2003
Hybrid Gate-Level Leakage Model for Monte Carlo Analysis on Multiple GPUs

This paper proposes a hybrid gate-level leakage model for the use with the Monte Carlo (MC) analysis approach, which combines a lookup table (LUT) model with a first-order exponential-polynomial model (first-order model, herein). For the process parameters having strong nonlinear relationships with the logarithm of leakage current, the proposed model uses the LUT approach for the sake of modeling accuracy. For the other process parameters, it uses the first-order model for increased efficiency. During the library characterization for each type of logic gates, the proposed approach determines the process parameters for which it will use the LUT model. And, it determines the number of LUT data points, which can maximize analysis efficiency with acceptable accuracy, based on the user-defined threshold. The proposed model was implemented for gate-level MC leakage analysis using three graphic processing units. In experiments, the proposed approach exhibited the average errors of ¡5% in both mean and standard deviation with reference to SPICE-level MC leakage analysis. In comparison, MC analysis with the first-order model exhibited more than 90% errors. In CPU times, the proposed hybrid approach took only two to five times longer runtimes. In comparison with the full LUT model, the proposed hybrid model was up to one hundred times faster while increasing the average errors by only 3%. Finally, the proposed approach completed a leakage analysis of an OpenSparc T2 core of 4.5 million gates with a runtime of .
Achieving Optional Android Permissions without Operating System Modifications

Since the release of the open-source Android operating system in 2009, considerable research has been carried out into various factors affecting the security and privacy of user data. As these devices become more widespread in usage, such as in vehicles with the announcement of Android Auto, the need for users to have control over the data available to applications is becoming important. A recurring theme from other works into this topic is that a more granular permissions model for Android applications would be beneficial, allowing users to understand which permissions their apps actually need, and to make decisions, rather than be forced to accept all of the requested permissions. A number of effective solutions have been presented, but these have required modifications be made to the core operating system, to enforce the existence of these new, optional permissions. We present an approach which permits an application developer to add optional permissions to their application, without any modifications being made to the underlying operating system. By not requiring rooting or other modifications to the device, this technique makes use of native Android functionality, and thus should remain operative between Android versions (which are increasingly difficult to gain root access on), unlike alternative techniques.
Risk factors of myasthenic crisis after thymectomy in 178 generalized myasthenia gravis patients in a five-year follow-up study

Purpose: The aims of this study were to assess the clinical characteristics of patients with postoperative myasthenic crisis (PMC) and to identify the risk factors affecting the occurrence of PMC. Method: Extended thymectomy was performed on 178 patients with generalized MG with a mean onset age of 36.8 years. The potentially risk factors were analyzed by binary logistic regression analysis. Result: During the over five-year follow-up, 44 patients (24.7%) experienced 58 episodes of PMC. The mean interval between surgery and the first episodes of PMC was 13.8 months, and for 81.8% of the patients it occurred within the first 2 years after thymectomy. Nine of 16 patients (56.3%) with a history of preoperative MC had recurrent crises. Respiratory tract infection was the most common precipitant of PMC. Univariate analysis showed that age at onset, preoperative MGFA class, preoperative MC, presence of bulbar symptoms, operation duration, amount of intraoperative blood loss, and the presence of thymoma were significantly associated with the occurrence of PMC. However, multivariate logistic regression analysis revealed that a history of preoperative MC (OR = 2.845, p = 0.044), presence of bulbar symptoms (OR = 3.062, p = 0.027), and longer operation duration (OR = 1.026, p = 0.009) were the independent risk factors for PMC. Conclusion: The important risk factors for developing PMC in generalized MG patients include the presence of bulbar symptoms, history of preoperative MC, and longer operation duration. Optimization of the preoperative evaluation and proper perioperative care of MG patients may decrease the frequency of PMC.
Identification and Characterization of a Novel Cytokine, THANK, aTNF Homologue That ActivatesApoptosis, Nuclear Factor-κB, and c-Jun NH2-Terminal Kinase*

By using the amino acid sequence motif of tumor necrosis factor (TNF), we searched the expressed sequence tag data base and identified a novel full-length cDNA encoding 285 amino acid residues and named it THANK. THANK is a type II transmembrane protein with 15–20% overall amino acid sequence homology to TNF, LT-α, FasL, and LIGHT, all members of the TNF family. The mRNA for THANK was expressed at high levels by peripheral blood leukocytes, lymph node, spleen, and thymus and at low levels by small intestine, pancreas, placenta, and lungs. THANK was also prominently expressed in hematopoietic cell lines. The recombinant purified protein expressed in the baculovirus system had an approximate molecular size 20 kDa with amino-terminal sequence of AVQGP. Treatment of human myeloid U937 cells with purified THANK activated nuclear transcription factor-κB (NF-κB) consisting of p50 and p65. Activation was time- and dose-dependent, beginning with as little as a 1 pm amount of the cytokines and as early as 15 min. Under the same conditions, THANK also activated c-jun NH2-terminal kinase (JNK) in U937 cells. THANK also strongly suppressed the growth of tumor cell lines and activated caspase-3. Although THANK had all the activities and potency of TNF, it did not bind to the TNF receptors. Thus our results indicate that THANK is a novel cytokine that belongs to the TNF family and activates apoptosis, NF-κB, and JNK through a distinct receptor.
A Comparison of the Efficacy, Relapse Rate and Side Effects among Three Modalities of Systemic Corticosteroid Therapy for Alopecia Areata

Background: Systemic corticosteroids are one of the most commonly used therapeutic modalities for patients with extensive alopecia areata (AA), although they entail several drawbacks. Objective: To determine the best modality for systemic corticosteroid use in terms of their efficacy, relapse rate, and side effects. Methods: Fifty-one patients with single or multiple AA (AA/multiplex) and 38 patients with alopecia totalis or AA universalis (AA totalis/universalis) were enrolled in this open study. They were randomly divided into three groups depending on the time of their initial visit. They were administered (1) oral dexamethasone (Dex) 0.5 mg/day for 6 months (Dex group), (2) intramuscular triamcinolone acetonide (imTA) 40 mg once a month for 6 months followed by 40 mg once every 1.5 months for 1 year (imTA group), and (3) pulse therapy (PT) using oral predonine 80 mg for 3 consecutive days once every 3 months (PT group). After the treatment, each treatment modality was evaluated by the response rate, relapse rate, and side effect profile. Results: The response rate of AA/multiplex was significantly better in the imTA group than in the Dex group. The overall relapse rate and that of AA totalis/universalis were significantly better in the PT group than in the Dex group. Dysmenorrhea was the most common and problematic side effect. Impairment of the adrenocortical reserve was seen in 7% of the PT group and 23% of the imTA group, which was recov ered without any further medical treatment. Conclusion: imTA or pulse therapy is effective for AA and has an acceptable level of side effects. The development of a new strategy to reduce the relapse rate is needed.
Sex differences in genomics in lupus: girls with systemic lupus have high interferon gene expression while boys have high levels of tumour necrosis factor-related gene expression

Objectives: Systemic lupus erythematosus (SLE) is a chronic disease occurring up to 15 times more frequently in females than males. This bias extends to possible differences in disease flares and response to therapy. This study was initiated to investigate the differences between girls and boys with childhood-onset SLE (cSLE) at the molecular level. Method: We analysed the Gene Expression Omnibus National Center for Biotechnology Information (GEO NCBI) microarray data available for 88 girls and 16 boys with treatment-naïve cSLE and compared the results to those from healthy controls. Transcriptional profiles were generated using the platforms of Affymetrix U133A and U133B gene chips and Bioconductor/R programming packages were used to process and compare the data. Results: Girls with cSLE overexpressed an interferon (IFN)-α signature that was absent in boys. Boys with cSLE were observed to overexpress tumour necrosis factor-related genes that were absent in girls. Both boys and girls were observed to overexpress several genes related to granulopoeisis. Conclusions: Our results suggest a potential application of genomics to differentially predict response to therapy between females and males with SLE.
Education Interrupted: Enrollment, Attainment, and Dropout of Syrian Refugees in Jordan

Abstract The children affected by the Syrian conflict, including the large population of Syrian refugee children hosted in neighboring countries, are at risk of becoming a ‘lost generation’ due to interruptions in their schooling. This paper examines how educational outcomes of Syrian refugees in Jordan have evolved from pre-conflict to during conflict and displacement. We rely on nationally representative survey data from Jordan in 2016 and in-depth interviews with Syrian refugee youth. We use discrete-time hazard models and compare dropout pre-conflict, during the conflict, and during displacement for different stages of schooling. Syrian refugees in Jordan faced disrupted schooling in Syria due to the conflict, followed by several multidimensional supply- and demand-side barriers to education in Jordan. Yet ultimately enrollment rates, at least through 2016, have recovered to pre-conflict levels for basic education among the group of Syrians in Jordan, with important lessons for other countries struggling to protect refugee children’s education. Host countries’ policy response to refugee education plays a critical role in whether and for how long refugee children resume schooling after displacement.
Robust Polarimetric SAR Despeckling Based on Nonlocal Means and Distributed Lee Filter

This paper presents a nonlocal Lee (NL-Lee) filter for polarimetric synthetic aperture radar despeckling. In the proposed NL-Lee filter, a kind of hybrid patch similarity measure is constructed by combining together the structure similarity introduced by the nonlocal means (NLM) filter and the homogeneity similarity introduced by the Lee filter, which works in a distributive way. This combination leads to two important advantages for the proposed nonlocal filter. One is the improved robustness to the NLM parameters such as patch size and search neighborhood size, since the patch regularity assumption can be enhanced by the introduced hybrid patch similarity; the other one is the better performance tradeoff between speckle removal and detail preservation, because of the good balance between structure similarity and homogeneity similarity obtained by the framework of the proposed NL-Lee filter. Experimental results are given to demonstrate its competitive denoising performance.