Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective Ablation of Ctip2/Bcl11b in Epidermal Keratinocytes Triggers Atopic Dermatitis-Like Skin Inflammatory Responses in Adult Mice

Background Ctip2 is crucial for epidermal homeostasis and protective barrier formation in developing mouse embryos. Selective ablation of Ctip2 in epidermis leads to increased transepidermal water loss (TEWL), impaired epidermal proliferation, terminal differentiation, as well as altered lipid composition during development. However, little is known about the role of Ctip2 in skin homeostasis in adult mice. Methodology/Principal Findings To study the role of Ctip2 in adult skin homeostasis, we utilized Ctip2ep−/− mouse model in which Ctip2 is selectively deleted in epidermal keratinocytes. Measurement of TEWL, followed by histological, immunohistochemical, and RT-qPCR analyses revealed an important role of Ctip2 in barrier maintenance and in regulating adult skin homeostasis. We demonstrated that keratinocytic ablation of Ctip2 leads to atopic dermatitis (AD)-like skin inflammation, characterized by alopecia, pruritus and scaling, as well as extensive infiltration of immune cells including T lymphocytes, mast cells, and eosinophils. We observed increased expression of T-helper 2 (Th2)-type cytokines and chemokines in the mutant skin, as well as systemic immune responses that share similarity with human AD patients. Furthermore, we discovered that thymic stromal lymphopoietin (TSLP) expression was significantly upregulated in the mutant epidermis as early as postnatal day 1 and ChIP assay revealed that TSLP is likely a direct transcriptional target of Ctip2 in epidermal keratinocytes. Conclusions/Significance Our data demonstrated a cell-autonomous role of Ctip2 in barrier maintenance and epidermal homeostasis in adult mice skin. We discovered a crucial non-cell autonomous role of keratinocytic Ctip2 in suppressing skin inflammatory responses by regulating the expression of Th2-type cytokines. It is likely that the epidermal hyperproliferation in the Ctip2-lacking epidermis may be secondary to the compensatory response of the adult epidermis that is defective in barrier functions. Our results establish an initiating role of epidermal TSLP in AD pathogenesis via a novel repressive regulatory mechanism enforced by Ctip2.
Data-based filtering for replicated high-throughput transcriptome sequencing experiments

Motivation: RNA sequencing is now widely performed to study differential expression among experimental conditions. As tests are performed on a large number of genes, stringent false-discovery rate control is required at the expense of detection power. Ad hoc filtering techniques are regularly used to moderate this correction by removing genes with low signal, with little attention paid to their impact on downstream analyses. Results: We propose a data-driven method based on the Jaccard similarity index to calculate a filtering threshold for replicated RNA sequencing data. In comparisons with alternative data filters regularly used in practice, we demonstrate the effectiveness of our proposed method to correctly filter lowly expressed genes, leading to increased detection power for moderately to highly expressed genes. Interestingly, this data-driven threshold varies among experiments, highlighting the interest of the method proposed here. Availability: The proposed filtering method is implemented in the R package HTSFilter available on Bioconductor. Contact: andrea.rau@jouy.inra. fr Supplementary information: Supplementary data are available at Bioinformatics online.
A new improved fruit fly optimization algorithm for traveling salesman problem

Traveling salesman problem (TSP) which is a classic combinational optimization problem has a wide range of applications in many areas. Many researchers focus on this problem and propose several algorithms. However, it was proved to be NP-hard, which is very difficult to be solved. No algorithm can solve any types of this problem effectively. In order to propose an effective algorithm for TSP, this paper improves the fruit fly optimization algorithm (FOA) proposed recently. As far as we know, the FOA has not yet been applied to solve TSP. Therefore, several modifications of FOA have to be made to meet the characteristics of TSP. Based on the whole search framework and the essence of FOA, some operations of particle swarm optimization (PSO) have been introduced into this method. In the smell search phase, the cluster mechanism of the fruit flies has been used to copy flies to one point and the mutation operation of genetic algorithm is used as the method of information exchanging among fruit flies for random search. In the visual search phase, the generalized PSO is applied to balance the global search and local search abilities of proposed algorithm. To evaluate the performance of proposed algorithm, some experiments and comparisons with other reported algorithms have been conducted. The results show the feasibility and effectiveness of proposed algorithm in solving TSP.
Privacy Preserving Provable Data Possession for Cloud Based Electronic Health Record System

The cloud computing technology offers many important features in electronic health record (EHR) system. But the patient has no control over their health record, once the data are stored in the cloud server. So ensuring the possession of correct EHR data is essential. The issue has become a challenge as the possession of data need to be verified while maintaining the privacy of EHR against the auditor. In this paper, a cloud based EHR system supporting privacy preserving provable data possession is proposed. Further, we extend our scheme to achieve important cloud based public auditing properties like data dynamics and batch auditing. The analysis results conform that our proposed scheme is secure and efficient.
Gene Ontology Annotations and Resources

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new ‘phylogenetic annotation’ process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
Cache probabilistic modeling for basic sparse algebra kernels involving matrices with a non-uniform distribution

A probabilistic model to estimate the number of misses on a set associative cache with an LRU replacement algorithm is introduced. Such modeling has been used by our group in previous work for sparse matrices with a uniform distribution of the non-zero elements. We present some new results focusing on different types of distributions that usually appear in some well-known real matrices suites, such as the Harwell-Boeing or NEP.
Family Dinner Frequency Interacts With Dinnertime Context in Associations With Child and Parent BMI Outcomes

For youth and parents, frequent family meals have been consistently associated with positive dietary outcomes but less consistently associated with lower body mass index (BMI). Researchers have speculated dinnertime context (dinnertime routines, parent dinnertime media use) may interact with family meal frequency to impact associations with BMI. The present study evaluates the associations and interactions between dinnertime context measures and family dinner frequency with parent and child BMI. This cross-sectional study uses baseline data from the Healthy Home Offerings via the Mealtime Environment (HOME) Plus randomized control trial that aimed to prevent childhood obesity. Participants (160 parent–child dyads) completed psychosocial surveys and were measured for height and weight. General linear models tested associations and interactions between dinnertime context measures and family dinner frequency with parent and child BMI, adjusted for race and economic assistance. Lower parent dinnertime media use and higher dinnertime routines were significantly associated with lower child BMI z scores but not parent BMI scores. Interaction–moderation findings suggest higher family dinner frequency amplifies the healthful impact of the dinnertime context on child BMI z scores. Additionally, findings emphasize that promoting frequent family meals along with consistent routines and reduction in parent dinnertime media use may be important for the prevention of childhood obesity.
Touch, pain and tickling: an electro‐physiological investigation on cutaneous sensory nerves

IN 1933 Blair and Erlanger demonstrated that the recorded spike heights of axone potentials from a phalangeal nerve preparation of the frog varied as their rate of conduction. On the assumption that the intrinsic potential is independent of fibre size the recorded spike heights vary as the diameters squared. Their result offers the possibility of computing the relative rate of axone potentials recorded from sensory nerves in response to various stimuli applied to their receptors. Such a procedure was adopted in some recent investigations on the lingual nerve [Zotterman, 1936]. The present research was started in order to study the response of the thinnest afferent fibres to various stimuli applied to the skin. When records of axone potentials from the thinnest nerve fibres had been obtained attempts were made to measure their rate of conduction directly. This was possible for fibres conducting at rates down to 10 m. / sec. Slower potentials than these, however, could not be measured. Although direct measurements of the slowest rates have not yet been made, the present data concerning the larger fibres provide some fixed points for the correlation of results from different experiments.
Japanese Named Entity Recognition based on a Simple Rule Generator and Decision Tree Learning

Named entity (NE) recognition is a task in which proper nouns and numerical information in a document are detected and classified into categories such as person, organization, location, and date. NE recognition plays an essential role in information extraction systems and question answering systems. It is well known that hand-crafted systems with a large set of heuristic rules are difficult to maintain, and corpus-based statistical approaches are expected to be more robust and require less human intervention. Several statistical approaches have been reported in the literature. In a recent Japanese NE workshop, a maximum entropy (ME) system outperformed decision tree systems and most hand-crafted systems. Here, we propose an alternative method based on a simple rule generator and decision tree learning. Our experiments show that its performance is comparable to the ME approach. We also found that it can be trained more efficiently with a large set of training data and that it improves readability.
Absence of Vitamin K-Dependent γ-Carboxylation in Human Periostin Extracted from Fibrotic Lung or Secreted from a Cell Line Engineered to Optimize γ-Carboxylation

Periostin (PN, gene name POSTN) is an extracellular matrix protein that is up-regulated in bronchial epithelial cells and lung fibroblasts by TH-2 cytokines. Its paralog, TGF-β-induced protein (βig-h3, gene name TGFBI), is also expressed in the lung and up-regulated in bronchial myofibroblasts by TGF-β. PN and βig-h3 contain fasciclin 1 modules that harbor putative recognition sequences for γ-glutamyl carboxylase and are annotated in UniProt as undergoing vitamin K-dependent γ-carboxylation of multiple glutamic acid residues. γ-carboxylation profoundly alters activities of other proteins subject to the modification, e.g., blood coagulation factors, and would be expected to alter the structure and function of PN and βig-h3. To analyze for the presence of γ-carboxylation, proteins extracted from fibrotic lung were reacted with monoclonal antibodies specific for PN, βig-h3, or modification with γ-carboxyglutamic acid (Gla). In Western blots of 1-dimensional gels, bands stained with anti-PN or -βig-h3 did not match those stained with anti-Gla. In 2-dimensional gels, anti-PN-positive spots had pIs of 7.0 to >8, as expected for the unmodified protein, and there was no overlap between anti-PN-positive and anti-Gla-positive spots. Recombinant PN and blood coagulation factor VII were produced in HEK293 cells that had been transfected with vitamin K 2, 3-epoxide reductase C1 to optimize γ-carboxylation. Recombinant PN secreted from these cells did not react with anti-Gla antibody and had pIs similar to that found in extracts of fibrotic lung whereas secreted factor VII reacted strongly with anti-Gla antibody. Over 67% coverage of recombinant PN was achieved by mass spectrometry, including peptides with 19 of the 24 glutamates considered targets of γ-carboxylation, but analysis revealed no modification. Over 86% sequence coverage and three modified glutamic acid residues were identified in recombinant fVII. These data indicate that PN and βig-h3 are not subject to vitamin K-dependent γ-carboxylation.
Title Stata.com Mfp — Multivariable Fractional Polynomial Models

Syntax Menu Description Options Remarks and examples Stored results Acknowledgments References Also see Syntax mfp , options : regression cmd yvar 1 yvar 2 xvarlist if in weight , regression cmd options options Description Model 2 sequential use the Royston and Altman model-selection algorithm; default uses closed-test procedure cycles(#) maximum number of iteration cycles; default is cycles(5) dfdefault(#) default maximum degrees of freedom; default is dfdefault(4) center(cent list) specification of centering for the independent variables alpha(alpha list) p-values for testing between FP models; default is alpha(0.05) df(df list) degrees of freedom for each predictor powers(numlist) list of FP powers to use; default is powers(-2-1(.5)1 2 3) Adv. model xorder(+ |-| n) order of entry into model-selection algorithm; default is xorder(+) select(select list) nominal p-values for selection on each predictor xpowers(xp list) FP powers for each predictor zero(varlist) treat nonpositive values of specified predictors as zero when FP transformed catzero(varlist) add indicator variable for specified predictors all include out-of-sample observations in generated variables Reporting level(#) set confidence level; default is level(95) display options control column formats and line width regression cmd options Description Adv. model regression cmd options options appropriate to the regression command in use All weight types supported by regression cmd are allowed; see [U] 11.1. 6 weight. See [U] 20 Estimation and postestimation commands for more capabilities of estimation commands. fp generate may be used to create new variables containing fractional polynomial powers. See [R] fp.
Toward An Understanding of Public School Politics

Mounting concern over the aims and achievements of American public schools emphasizes the need for continuing analysis of how the schools are run and who runs them. The general theory is simple enough: schools are objects of local control, the people of a local school district exercise that control through an elected school board, and the board appoints a superintendent to act as the chief executive of the district. There are variations from this pattern—in some places school boards are appointed rather than elected, in others the school system is formally a part of the city government, and in a few districts other officials, such as a business manager or building superintendent, share the top executive authority—but it is by far the most common arrangement among the nation's approximately 50,000 school districts.
Peripety in an R&D Drama: Capturing a Turnaround in Project Dynamics

This article examines the process dynamics of a complex R&D project, which for a long period of time had suffered from little technical progress, then abruptly became highly structured and effective. The article examines the mechanisms behind this dramatic turnaround and discusses its implications for research and practice. Drawing on the dramaturgical concept of ‘peripety’ (‘moment of sudden change’), the article captures how the turnaround came about due to the emergence of the participants’ shared conceptualization of the project mission. The article provides insights into the process dynamics and sensemaking in complex R&D projects and demonstrates how time and evolution need to be included in the analysis of project management and temporary organizations.
Clinical characteristics of biopsy-proven allergic bronchopulmonary mycosis: variety in causative fungi and laboratory findings.

OBJECTIVE The diagnosis of allergic bronchopulmonary mycosis (ABPM) has traditionally relied widely on Rosenberg's criteria, which emphasize immunologic responses while overlooking the investigation of mucous plugs as a primary criterion. Therefore, the characteristics of biopsy-proven ABPM require further elucidation. The aim of this study was to analyze the clinical characteristics of biopsy-proven ABPM and address whether full compliance with clinical criteria, such as the presence of asthma, and certain laboratory findings is necessary to establish a diagnosis of ABPM. METHODS We retrospectively analyzed 17 patients with biopsy-proven ABPM focusing on causative fungi and laboratory findings. RESULTS Causative fungi included Aspergillus sp. in seven patients, Schizophyllum commune in four patients, Penicillium sp. in two patients and unknown in five patients. Bronchial asthma was observed in 10 patients, eosinophilia was observed in 10 patients and an increased serum immunoglobulin (Ig) E level was observed in 14 of the 17 patients. IgG for Aspergillus sp. was positive in six of the seven patients with ABPM due to Aspergillus and turned positive in the remaining patient during follow-up. Technological limitations prevented the measurement of specific IgE for S. commune and IgG for S. commune and Penicillium sp. in most patients. Computed tomography revealed central bronchiectasis, pulmonary infiltration and mucous plugs in all patients. CONCLUSION Causative fungi other than Aspergillus sp. are not uncommon, and immunological tests for other fungi should be popularized. Asthma and characteristic laboratory findings, such as peripheral blood eosinophilia, increased serum IgE and precipitating antibodies, may not always be required to diagnose ABPM. The importance of typical pathologic findings of mucous plugs for diagnosing ABPM requires reevaluation. Further studies are needed to establish more elaborate diagnostic criteria for ABPM.
A neural-network-based detection of epilepsy

Abstract Diagnosis of epilepsy is primarily based on scalp-recorded electroencephalograms (EEG). Unfortunately the long-term recordings obtained from 'ambulatory recording systems' contain EEG data of up to one week duration, which has introduced new problems for clinical analysis. Traditional methods, where the entire EEG is reviewed by a trained professional, are very time-consuming when applied to recordings of this length. Therefore, several automated diagnostic aid approaches were proposed in recent years, in order to reduce expert effort in analyzing lengthy recordings. The most promising approaches to automated diagnosis are based on neural networks. This paper describes a method for automated detection of epileptic seizures from EEG signals using a multistage nonlinear pre-processing filter in combination with a diagnostic (LAMSTAR) Artificial Neural Network (ANN). Pre-processing via multistage nonlinear filtering, LAMSTAR input preparation, ANN training and system performance (1.6% miss rate, 97.2% overall accuracy when considering both false-alarms and 'misses') are discussed and are shown to compare favorably with earlier approaches presented in recent literature.
UvA-DARE ( Digital Academic Repository ) ASCA discovery of an x-ray pulsar in the error box of SGR 1900 + 14

We present a 2–10 keV ASCA observation of the field around the soft gamma repeater SGR 1900114. One quiescent X-ray source was detected in this observation, and it was in the SGR error box. In 2–10 keV X-rays, its spectrum may be fitted by a power law with index 22.2, and its unabsorbed flux is ergs cm 212 9.6 # 10 s. We also find a clear 5.16 s period. The properties of the three well-studied soft gamma repeaters are remarkably similar to one another, and they provide evidence that all of them are associated with young, strongly magnetized neutron stars in supernova remnants. Subject headings: gamma rays: bursts — stars: neutron — supernova remnants — X-rays: stars
An Analysis of Security and Performance Concerns in Mobile Web Application Development: Challenges and Open Issues

The paper focuses on security and performance concerns in mobile web development. The approach used in the study involved surveying journal publications to identify security and performance concerns. The paper highlights some of the contemporary issues currently being faced by application developers as they create, update and maintain mobile web applications including Cross-Site Scripting, Cookie hijacking/theft, location hijacking, history theft, behaviour analysis, session hijacking, API design, security and the type of web server used considered.
Genetically based impairment in CYP2C8- and CYP2C9-dependent NSAID metabolism as a risk factor for gastrointestinal bleeding: Is a combination of pharmacogenomics and metabolomics required to improve personalized medicine?

Polymorphisms in CYP2C8 and CYP2C9 are common in all the human populations and many CYP2C8 and CYP2C9 gene variations cause decreased enzyme activity towards the NSAIDs aceclofenac, celecoxib, diclofenac, ibuprofen, indomethazine, lornoxicam, meloxicam, naproxen, piroxicam, tenoxicam and valdecoxib. This impairment in drug biodisposition alters drug pharmacokinetics, with carriers of detrimental mutations displaying increased values of AUC and decreased drug clearance. Individuals carrying the gene variants CYP2C8*3 (rs11572080; rs10509681), CYP2C9*2 (rs1799853) or CYP2C9*3 (rs1057910) show increased risk of developing acute gastro intestinal bleeding during the use of NSAID that are CYP2C8 or CYP2C9 substrates. However, it is not known whether parent drugs or products of alternative metabolic pathways are responsible for bleeding. We present an overview of the current knowledge of relevant polymorphisms of CYP2C8 and CYP2C9 genes, their association with NSAID metabolism and pharmacokinetics and a meta-analysis that confirms the clinical significance of these gene variations with regard to gastrointestinal bleeding.