Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Dsg1- and Dsg3-Mediated Signaling in Pemphigus Autoantibody-Induced Loss of Keratinocyte Cohesion

Pemphigus is an autoimmune dermatosis in which mucocutaneous blisters are induced primarily by autoantibodies against Desmoglein (Dsg) 1 and 3. Pemphigus vulgaris (PV) usually is associated with autoantibodies against Dsg3 whereas pemphigus foliaceus (PF) patients present autoantibodies against Dsg1. Several signaling pathways were proposed to cause loss of keratinocyte adhesion. However, relevance of different signaling pathways and role of Dsg1 and 3 to trigger signaling are not fully understood. Here, we show that Ca2+ chelation reduced PV-IgG- and PF-IgG-mediated loss of HaCaT keratinocyte cohesion whereas EGFR inhibition did not inhibit effects of PF-IgG. PV-IgG activated EGFR in a Src-dependent manner whereas both PV-IgG and PF-IgG caused Ca2+ influx independent of EGFR. ERK activation was Src-dependent in response to PV-IgG but not PF-IgG. To delineate the roles of Dsg isoforms to trigger signaling pathways, Dsg3- and Dsg2-deficient HaCaT keratinocyte cell lines were generated using CRISPR/Cas9. Dsg3- but not Dsg2-deficient cells were protected against PV-IgG-induced loss of cell adhesion. Ca2+ influx and ERK activation in response to PF-IgG were preserved in both cell lines.
An Extensive Checklist for Building AutoML Systems

Automated Machine Learning is a research area which has gained a lot of focus in the recent past. But the required components to build an autoML system is neither properly documented nor very clear due to the differences and the recentness of researches. If the required steps are analyzed and brought under a common survey, it will assist in continuing researches. This paper presents an analysis of the components and technologies in the domains of autoML, hyperparameter tuning and meta learning and, presents a checklist of steps to follow while building an AutoML system. This paper is a part of an ongoing research and the findings presented will assist in developing a novel architecture for an autoML
Exposure to Workplace Bullying, Distress, and Insomnia: The Moderating Role of the miR-146a Genotype

Several lines of evidence show that systematic exposure to negative social acts at the workplace i.e., workplace bullying, results in symptoms of depression and anxiety among those targeted. However, little is known about the association between bullying, inflammatory genes and sleep problems. In the present study, we examined the indirect association between exposure to negative social acts and sleep through distress, as moderated by the miR-146a genotype. The study was based on a nationally representative survey of 1179 Norwegian employees drawn from the Norwegian Central Employee Register by Statistics Norway. Exposure to workplace bullying was measured with the 9-item version of Negative Acts Questionnaire – Revised (NAQ-R) inventory. Seventeen items from Hopkins Symptom Checklist (HSCL-25) was used to measure distress. Insomnia was assessed with three items reflecting problems with sleep onset, maintenance of sleep and early morning awakening. Genotyping with regard to miR-146a rs2910164, previously linked to inflammatory processes, was carried out using Taqman assay. The data revealed that individuals systematically exposed to negative social acts at the workplace reported higher levels of sleep problems than non-exposed individuals. Moreover, the relationship between distress induced by exposure to negative social acts and insomnia was significantly stronger for individuals with the miR-146a GG genotype. Thus, the miR-146a genotype moderated the association between distress and insomnia among individuals exposed to negative social acts. The present report support the hypothesis that inflammation could play a role in stress-induced insomnia among individuals exposed to workplace bullying.
Enhancing Industry-Based Dissemination of an Occupational Sun Protection Program with Theory-Based Strategies Employing Personal Contact

Purpose. Industry-based strategies for dissemination of an evidence-based occupational sun protection program, Go Sun Smart (GSS), were tested. Design. Two dissemination strategies were compared in a randomized trial in 2004–2007. Setting. The North American ski industry. Subjects. Ski areas in the United States and Canada (n = 69) and their senior managers (n = 469). Intervention. Employers received GSS through a basic dissemination strategy (BDS) from the industry's professional association that included conference presentations and free starter kits. Half of the areas also received the enhanced dissemination strategy (EDS), in which project staff met face-to-face with managers and made ongoing contacts to support program use. Measures. Observation of program materials in use and managers' reports on communication about sun protection. Analysis. The effects of two alternative dissemination strategies were compared on program use using PROC MIXED in SAS, adjusted for covariates using one-tailed p values. Results. Ski areas receiving the EDS used more GSS materials (x̄ = 7.36) than those receiving the BDS (x̄ = 5.17; F = 7.82, p < .01). Managers from more areas receiving the EDS reported communicating about sun protection in employee newsletters/flyers (x̄ = .97, p = .04), in guest e-mail messages (x̄ = .75, p = .02), and on ski area Web sites (x̄ = .38, p = .02) than those receiving the BDS (x̄ = .84, .50, .15, respectively). Conclusion. Industry professional associations play an important role in disseminating prevention programs; however, active personal communication may be essential to ensure increased implementation fidelity.
In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential

We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp. MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments.
Development and Quality of Barley Husk Adhesion Correlates With Changes in Caryopsis Cuticle Biosynthesis and Composition

The caryopses of barley become firmly adhered to the husk during grain development through a cuticular cementing layer on the caryopsis surface. The degree of this attachment varies among cultivars, with poor quality adhesion causing “skinning”, an economically significant grain quality defect for the malting industry. Malting cultivars encompassing a range of husk adhesion qualities were grown under a misting treatment known to induce skinning. Development of the cementing layer was examined by electron microscopy and compositional changes of the cementing layer were investigated with gas-chromatography followed by mass spectroscopy. Changes in gene expression during adhesion development were examined with a custom barley microarray. The abundance of transcripts involved early in cuticular lipid biosynthesis, including those encoding acetyl-CoA carboxylase, and all four members of the fatty acid elongase complex of enzymes, was significantly higher earlier in caryopsis development than later. Genes associated with subsequent cuticular lipid biosynthetic pathways were also expressed higher early in development, including the decarbonylation and reductive pathways, and sterol biosynthesis. Changes in cuticular composition indicate that lowered proportions of alkanes and higher proportions of fatty acids are associated with development of good quality husk adhesion, in addition to higher proportions of sterols.
The Long-Term Reuse of Text in the Finnish Press, 1771-1920

This paper is based on the study of text reuse in the Finnish press from 1771–1920. In the Computational History and the Transformation of Public Discourse in Finland (COMHIS) project, we found 61 million occurrences of similarity, which formed 13.8 million clusters of reuse. This material also included strikingly slow processes of repetition, and the longest reuse cases were almost as long as the time span of the project. In sum, 2.03 million clusters, 15 per cent of the total amount, were longer than 12 months. As well, 76,259 clusters spanned over 20 years or more. The longest span was 146 years. The paper explores the volume and nature of this long-term text reuse in the Finnish press and analyses three distinctive features of slow repetition: newspapers as a site of memory, newspapers as an archive and the political ramifications of reuse. The paper argues that the habit of reprinting old texts aimed to bridge the gap between past and present, emphasising the continuity between old and new. On the other hand, there were cases where past texts were activated precisely for the opposite purposes, to obscure the past and to show how different the bygone
Elaborating a Web Interface Personalization Process

This paper builds the required conceptual model for implementing adaptation systems intended to provide a personalized navigation experience for any user. To this end, aspects such as the users' needs, preferences, and navigational behaviour are taken into account in order to select the adaptation techniques to be applied for each particular user. The validity of the proposed conceptual model to provide the necessary components and mechanisms for implementing suitable web personalization systems is shown by means of a case study.
UML in der Hochschullehre: Eine kritische Reflexion (UML in Higher Education: A Critical Reflection)

Trotz ihrer hohen Bekanntheit und Verbreitung ist die Unified Modelling Language (UML) 20 Jahre nach der Vorstellung ihrer ersten Version in der Softwaretechnik nicht unumstritten. Ein wesentlicher Grund ist ihre unklare Nutzung in der Praxis die u.a. durch Ausdifferenzierung von Softwareproduktarten, agilen Entwicklungsansätzen sowie Microservices als Architekturstil mit reduzierter Komplexität beeinflusst wird. Diese Trends befördern eine Abkehr von klassischen Top-DownAnsätzen mit sequenziellem Vorgehen, das umfangreiche Spezifikationen der Anforderungen und des Entwurfs erfordert. Für die Lehre (insbesondere auf Bachelorniveau) stellt sich daher die Frage, ob wir UML überhaupt noch brauchen und wenn ja, wofür und in welchem Umfang. Ziel dieses Beitrags ist es, empirische Belege zur Relevanz der UML zusammenzutragen und daraus Schlussfolgerungen für mögliche Kompetenzziele in der Softwaretechnikausbildung zu ziehen. Unser Ziel ist es, eine aktuelle Sicht auf die praktische Relevanz der UML zu liefern und damit die Diskussion über die Ausgestaltung der Lehre im Fach Softwaretechnik anzuregen. Abstract
Contribution of Maize Polyamine and Amino Acid Metabolism Toward Resistance Against Aspergillus flavus Infection and Aflatoxin Production

Polyamines (PAs) are ubiquitous polycations found in plants and other organisms that are essential for growth, development, and resistance against abiotic and biotic stresses. The role of PAs in plant disease resistance depends on the relative abundance of higher PAs [spermidine (Spd), spermine (Spm)] vs. the diamine putrescine (Put) and PA catabolism. With respect to the pathogen, PAs are required to achieve successful pathogenesis of the host. Maize is an important food and feed crop, which is highly susceptible to Aspergillus flavus infection. Upon infection, the fungus produces carcinogenic aflatoxins and numerous other toxic secondary metabolites that adversely affect human health and crop value worldwide. To evaluate the role of PAs in aflatoxin resistance in maize, in vitro kernel infection assays were performed using maize lines that are susceptible (SC212) or resistant (TZAR102, MI82) to aflatoxin production. Results indicated significant induction of both PA biosynthetic and catabolic genes upon A. flavus infection. As compared to the susceptible line, the resistant maize lines showed higher basal expression of PA metabolism genes in mock-inoculated kernels that increased upon fungal infection. In general, increased biosynthesis and conversion of Put to Spd and Spm along with their increased catabolism was evident in the resistant lines vs. the susceptible line SC212. There were higher concentrations of amino acids such as glutamate (Glu), glutamine (Gln) and γ-aminobutyric acid (GABA) in SC212. The resistant lines were significantly lower in fungal load and aflatoxin production as compared to the susceptible line. The data presented here demonstrate an important role of PA metabolism in the resistance of maize to A. flavus colonization and aflatoxin contamination. These results provide future direction for the manipulation of PA metabolism in susceptible maize genotypes to improve aflatoxin resistance and overall stress tolerance.
Concolic Testing of Full-Stack JavaScript Applications

Recent years have seen the rise of so-called full-stack JavaScript web applications, where both the client and the server side of the web application are developed in JavaScript. Both sides communicate with each other via asynchronous messages, as enabled by e.g., WebSockets. Traditionally, automated whitebox testing of web applications involves testing both sides of the application in isolation from each other. However, this approach lacks a holistic overview of the entire web application under test. This leads to inaccuracies in the types of program bugs that are reported by the tester, and makes it more difficult for developers to understand how the behaviour of the client may affect the behaviour of the server, and vice versa. An interesting side-effect of the evolution towards full-stack applications is that a single automated tester can be developed that observes the execution of both parts of the system simultaneously, thereby remedying the aforementioned issues. In this paper, we examine the benefits and design challenges in employing such a holistic approach towards testing full-stack applications, and we demonstrate STACKFUL, the first concolic tester for full-stack JavaScript applications.
Base Station Downlink DTX Designs for Interference Mitigation in High-Performance LTE Networks

To evolve the LTE network to cope with ever and rapidly increasing demand for mobile broadband services and traffic volumes, interference avoidance designs have been identified as one major area to address in the next LTE release. In both traditional homogeneous macro network and heterogeneous network with mix of macro and small cells, intercell interference can be substantially reduced by temporarily halting unneeded downlink transmission. In this paper, we analyze several design aspects of such base station downlink discontinuous transmission (DTX) operations. We provide extensive performance evaluation results and analysis on (1) the time scale of such DTX operations; and (2) whether the DTX operations should be restricted to the small cells only. The results provide guideline for an ideal combination of these design dimensions.
Channel Shortening by Large Multiantenna Precoding in OFDM

A channel delay spread larger than the cyclic prefix (CP) creates inter-carrier/symbol interference (ISI/ICI) in orthogonal frequency-division multiplexing (OFDM). Recent interests in low-latency applications have motivated the usage of shorter OFDM symbols where one can either downscale the CP at the cost of interference, or maintain it but with larger overhead. Alternatively, this paper studies channel shortening methods exploiting the properties of large multi-antenna precoding in order to steer the transmitted signal energy toward channel paths inside an insufficient CP. It is shown that ISI/ICI can asymptotically be canceled by conventional subcarrier-based precoding with an infinite number of antennas. This is achieved by introducing time-delay selectivity inside frequency-selective precoders in order to remove undesired delayed signals, providing a trade-off between interference mitigation and multi-path combining gains, and leading to subsequent gains in high SNR. This frequency-domain precoding method, coined time-frequency (TF) precoding, is compared to time-reversal (TR) filtering whose asymptotic rate is optimal but introduces post-modulation processing with channel-dependent signal distortion. In addition to maintain the legacy precoded multi-antenna OFDM structure, finite-size analysis shows that TF-precoding converges faster to its asymptotic rate than TR-filtering, so that TF-precoding can outperform TR-filtering in the high-SNR regime with not-so-many antennas.
On algorithms for and computing with the tensor ring decomposition

Tensor decompositions such as the canonical format and the tensor train format have been widely utilized to reduce storage costs and operational complexities for high‐dimensional data, achieving linear scaling with the input dimension instead of exponential scaling. In this paper, we investigate even lower storage‐cost representations in the tensor ring format, which is an extension of the tensor train format with variable end‐ranks. Firstly, we introduce two algorithms for converting a tensor in full format to tensor ring format with low storage cost. Secondly, we detail a rounding operation for tensor rings and show how this requires new definitions of common linear algebra operations in the format to obtain storage‐cost savings. Lastly, we introduce algorithms for transforming the graph structure of graph‐based tensor formats, with orders of magnitude lower complexity than existing literature. The efficiency of all algorithms is demonstrated on a number of numerical examples, and in certain cases, we demonstrate significantly higher compression ratios when compared to previous approaches to using the tensor ring format.
PNA Length Restriction of Antibacterial Activity of Peptide-PNA Conjugates in Escherichia coli Through Effects of the Inner Membrane

Peptide Nucleic Acid (PNA)-peptide conjugates targeting essential bacterial genes are showing promise as antisense antimicrobials in drug discovery. Optimization has focused on selection of target genes and exact localization around the ribosome binding site, but surprisingly a length optimum around 10–12 nucleobases has been found. Addressing this observation, we have investigated the relationship between PNA-length, PNA–RNA duplex stability and antimicrobial activity in E. coli in more detail. For PNAs of identical length of ten nucleobases the expected reverse correlation between the thermal stability (Tm) of the PNA–RNA duplex and the MIC for single mismatched PNAs was found. Also the expected direct correlation between the length of the PNA and the PNA–RNA duplex stability was found. Nonetheless, 10-mer PNAs [in a 6–18 mer extension series of (KFF)3K- and (RXR)4 conjugates] were the most active as antisense antimicrobials in both wild type E. coli MG1655 and AS19, suggesting that the size constraint is related to the bacterial uptake of PNA-peptide conjugates. This conclusion was supported by flow cytometry data showing higher bacterial uptake of shorter PNA fluorophore labeled conjugates. Interestingly, the size-limited uptake seems independent on outer membrane integrity (AS19), and thus the results suggest that the inner membrane limits the molecular size for peptide-PNA passage.
The Role of Temporal Acoustic Exaggeration in High Variability Phonetic Training: A Behavioral and ERP Study

High variability phonetic training (HVPT) has been found to be effective in helping adult learners acquire non-native phonetic contrasts. The present study investigated the role of temporal acoustic exaggeration by comparing the canonical HVPT paradigm without involving acoustic exaggeration with a modified adaptive HVPT paradigm that integrated key temporal exaggerations in infant-directed speech (IDS). Sixty native Chinese adults participated in the training of the English /i/ and /i/ vowel contrast and were randomly assigned to three subject groups. Twenty were trained with the typical HVPT paradigm (the HVPT group), twenty were trained under the modified adaptive approach with acoustic exaggeration (the HVPT-E group), and twenty were in the control group. Behavioral tasks for the pre- and post- tests used natural word identification, synthetic stimuli identification, and synthetic stimuli discrimination. Mismatch negativity (MMN) responses from the HVPT-E group were also obtained to assess the training effects in within- and across- category discrimination without requiring focused attention. Like previous studies, significant generalization effects to new talkers were found in both the HVPT group and the HVPT-E group. The HVPT-E group, by contrast, showed greater improvement as reflected in larger progress in natural word identification performance. Furthermore, the HVPT-E group exhibited more native-like categorical perception based on spectral cues after training, together with corresponding training-induced changes in the MMN responses to within- and across- category differences. These data provide the initial evidence supporting the important role of temporal acoustic exaggeration with adaptive training in facilitating phonetic learning and promoting brain plasticity at the perceptual and pre-attentive neural levels.