Miracle-dz/UniFAR-FTUs huggingface dataset:
InfoGAN: Interpretable Representation Learning by Information Maximizing Generative Adversarial Nets

This paper describes InfoGAN, an information-theoretic extension to the Generative Adversarial Network that is able to learn disentangled representations in a completely unsupervised manner. InfoGAN is a generative adversarial network that also maximizes the mutual information between a small subset of the latent variables and the observation. We derive a lower bound to the mutual information objective that can be optimized efficiently, and show that our training procedure can be interpreted as a variation of the Wake-Sleep algorithm. Specifically, InfoGAN successfully disentangles writing styles from digit shapes on the MNIST dataset, pose from lighting of 3D rendered images, and background digits from the central digit on the SVHN dataset. It also discovers visual concepts that include hair styles, presence/absence of eyeglasses, and emotions on the CelebA face dataset. Experiments show that InfoGAN learns interpretable representations that are competitive with representations learned by existing fully supervised methods.
Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases

RNA cleavage by RNA polymerase (RNAP) is the central step in co-transcriptional RNA proofreading. Bacterial RNAPs were proposed to rely on the same mobile element of the active site, the trigger loop (TL), for both nucleotide addition and RNA cleavage. RNA cleavage can also be stimulated by universal Gre factors, which should replace the TL to get access to the RNAP active site. The contributions of the TL and Gre factors to RNA cleavage reportedly vary between RNAPs from different bacterial species and, probably, different types of transcription complexes. Here, by comparing RNAPs from Escherichia coli, Deinococcus radiodurans, and Thermus aquaticus, we show that the functions of the TL and Gre factors in RNA cleavage are conserved in various species, with important variations that may be related to extremophilic adaptation. Deletions of the TL strongly impair intrinsic RNA cleavage by all three RNAPs and eliminate the interspecies differences in the reaction rates. GreA factors activate RNA cleavage by wild-type RNAPs to similar levels. The rates of GreA-dependent cleavage are lower for ΔTL RNAP variants, suggesting that the TL contributes to the Gre function. Finally, neither the TL nor GreA can efficiently activate RNA cleavage in certain types of backtracked transcription complexes, suggesting that these complexes adopt a catalytically inactive conformation probably important for transcription regulation.
Human enteric viruses in a wastewater treatment plant: evaluation of activated sludge combined with UV disinfection process reveals different removal performances for viruses with different features

This study assess the quality of wastewater through the detection and quantification of important viruses causing gastroenteritis at different stages of the wastewater treatment process in an activated‐sludge wastewater treatment plant with ultraviolet disinfection. Ten sampling events were carried out in a campaign along a period of 18 months collecting wastewater samples from the influent, after the activated‐sludge treatment, and after the final disinfection with UV radiation. Samples were concentrated through ultracentrifugation and analysed using retro‐transcription, PCR and real time quantitative PCR protocols, for detection and quantification of Group A Rotavirus (RVA), Human Astrovirus (HAstV), Norovirus Genogroup II (NoV GII) and Human Adenovirus (HAdV). HAdV (100%), NoV GII (90%), RVA (70%) and HAstV (60%) were detected in influent samples with concentration from 1·4 (NoV GII) to 8·0 (RVA) log10 gc l−1. Activated‐sludge treatment reached well quality effluents with low organic material concentration, although nonstatistical significant differences were registered among influent and postactivated sludge treatment samples, regarding the presence and concentration for most viruses. All post‐UV samples were negative for NoV GII and HAstV, although RVA and HAdV were detected in 38% and 63% of those samples respectively, with concentration ranging from 2·2 to 5·5 and 3·1 to 3·4 log10 gc l−1.
A Near Real-Time Algorithm for Autonomous Identification and Characterization of Honeypot Attacks

Monitoring communication networks and their traffic is of essential importance for estimating the risk in the Internet, and therefore designing suited protection systems for computer networks. Network and traffic analysis can be done thanks to measurement devices or honeypots. However, analyzing the huge amount of gathered data, and characterizing the anomalies and attacks contained in these traces remain complex and time consuming tasks, done by network and security experts using poorly automatized tools, and are consequently slow and costly. In this paper, we present an unsupervised algorithm - called UNADA for Unsupervised Network Anomaly Detection Algorithm - for identification and characterization of security related anomalies and attacks occurring in honeypots. This automatized method does not need any attack signature database, learning phase, or labeled traffic. This corresponds to a major step towards autonomous security systems. This paper also shows how it is possible from anomalies characterization results to infer filtering rules that could serve for automatically configuring network routers, switches or firewalls. The performances of UNADA in terms of attacks identification accuracy are evaluated using honeypot traffic traces gathered on the honeypot network of the University of Maryland. The time latency for producing such accurate results are also presented, especially showing how the parallelization capabilities of the algorithm help reducing this latency.
Comparative performance of double‐digest RAD sequencing across divergent arachnid lineages

Next‐generation sequencing technologies now allow researchers of non‐model systems to perform genome‐based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double‐digest restriction‐site‐associated DNA sequencing (ddRADseq) by generating reduced representation genome‐wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non‐model arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6‐base pair cutter EcoRI combined with methylated site‐specific 4‐base pair cutter MspI produced, on average, the greatest numbers of intra‐individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non‐linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many arachnid taxa where reference genomes, even from closely related species, are unavailable.
Rapid Identification of Different Escherichia coli Sequence Type 131 Clades

ABSTRACT Escherichia coli sequence type 131 (ST131) is a pandemic clonal lineage that is responsible for the global increase in fluoroquinolone resistance and extended-spectrum-β-lactamase (ESBL) producers. The members of ST131 clade C, especially subclades C2 and C1-M27, are associated with ESBLs. We developed a multiplex conventional PCR assay with the ability to detect all ST131 clades (A, B, and C), as well as C subclades (C1-M27, C1-nM27 [C1-non-M27], and C2). To validate the assay, we used 80 ST131 global isolates that had been fully sequenced. We then used the assay to define the prevalence of each clade in two Japanese collections consisting of 460 ESBL-producing E. coli ST131 (2001-12) and 329 E. coli isolates from extraintestinal sites (ExPEC) (2014). The assay correctly identified the different clades in all 80 global isolates: clades A (n = 12), B (n = 12), and C, including subclades C1-M27 (n = 16), C1-nM27 (n = 20), C2 (n = 17), and other C (n = 3). The assay also detected all 565 ST131 isolates in both collections without any false positives. Isolates from clades A (n = 54), B (n = 23), and C (n = 483) corresponded to the O serotypes and the fimH types of O16-H41, O25b-H22, and O25b-H30, respectively. Of the 483 clade C isolates, C1-M27 was the most common subclade (36%), followed by C1-nM27 (32%) and C2 (15%). The C1-M27 subclade with blaCTX-M-27 became especially prominent after 2009. Our novel multiplex PCR assay revealed the predominance of the C1-M27 subclade in recent Japanese ESBL-producing E. coli isolates and is a promising tool for epidemiological studies of ST131.
Resident responses to after‐hours otolaryngology patient phone calls: An overlooked aspect of residency training?

Otolaryngology residents are often responsible for triaging after‐hours patient calls. However, residents receive little training on this topic. Data are limited on the clinical content, reporting, and management of otolaryngology patient calls. This study aimed to characterize the patient concerns residents handle by phone and their subsequent management and reporting.
Strain Induced Modifications of Valence Band Features in Fe3O4 Epitaxial Heterostructures

We report systematic investigations of lattice mismatch strain and the strain relaxation induced modifications on the valence band electronic structure of the epitaxial Fe3O4/Si (100) and Fe3O4/MgO (100) heterostructures. The Fe3O4 films on Si (100) and MgO (100) substrates were investigated though the angle-integrated photoemission spectroscopy (AIPES) at room temperature in the energy range 45-65 eV. Depending on the strain state of the films, the Raman modes and the Verwey transition temperature show deviations from the corresponding bulk values. The valence band feature at 2.7 eV (3.5 eV) shifts towards (away) the Fermi level with an increase (decrease) in strain resulting in decrease (increase) of density of states (DOS) of the minority spin Fe(A) 3d-eg band (majority spin Fe(B) 3d-t2g band). The effect is more pronounced in the case of films on MgO (100) substrate in comparison to the films on Si (100) substrate.
Cutaneous Complications Related to Tattoos: 31 Cases from Finland

Background: Cutaneous complications related to permanent tattoos affect 2-30% of those patients who have tattooed their skin. Little is known about the cases of tattoo complications in Finland. Objective: The aim of this study was to conduct a retrospective review of a series of Finnish patients with cutaneous tattoo reactions. Methods: We collected cases of tattoo reactions from the Department of Dermatology at Helsinki University Central Hospital, from members of the Finnish dermatological society and from various other sources (author's private practice, tattooists, professional internet forum). We analysed the demographics, clinical presentation, diagnosis, and microscopic findings on the skin biopsies, and evaluated the therapeutic outcome. Results: Thirty-one patients (16 men and 15 women, mean age 37.8) were included from 9 cities, mainly from Helsinki. Fifty-two percent (16/31) presented with an allergic tattoo reaction mainly against the red colour (75%, 12/16). Reactions were clinically polymorph ranging from scattered papules or nodules to complete infiltration of a colour. Lesions were itchy and sometimes painful. The reactions were lichenoid, granulomatous, pseudolymphomatous or less specific with a dermal lympho-histiocytic or plasmocytic infiltrate. Other diagnoses included tattoo blow-out (13%), melanoma within a tattoo, naevi within a tattoo (10% each), lichen planus (6%), granulomatous reaction with uveitis, sarcoidosis and dermatofibroma (3% each). Allergic tattoo reactions were mainly treated with local corticosteroid (CS) ointments, CS infiltration or surgical removal. Conclusion: This review is the largest series of tattoo complications in the Baltic area. It illustrates the wide spectrum of complications. Prospective, controlled therapeutic studies are necessary to assess the best treatment protocols for tattoo allergies and tattoo reaction management in general.
Cosmology with the Large Synoptic Survey Telescope: an overview

The Large Synoptic Survey Telescope (LSST) is a high étendue imaging facility that is being constructed atop Cerro Pachón in northern Chile. It is scheduled to begin science operations in 2022. With an ( effective) aperture, a novel three-mirror design achieving a seeing-limited field of view, and a 3.2 gigapixel camera, the LSST has the deep-wide-fast imaging capability necessary to carry out an survey in six passbands (ugrizy) to a coadded depth of over 10 years using of its observational time. The remaining of the time will be devoted to considerably deeper and faster time-domain observations and smaller surveys. In total, each patch of the sky in the main survey will receive 800 visits allocated across the six passbands with exposure visits. The huge volume of high-quality LSST data will provide a wide range of science opportunities and, in particular, open a new era of precision cosmology with unprecedented statistical power and tight control of systematic errors. In this review, we give a brief account of the LSST cosmology program with an emphasis on dark energy investigations. The LSST will address dark energy physics and cosmology in general by exploiting diverse precision probes including large-scale structure, weak lensing, type Ia supernovae, galaxy clusters, and strong lensing. Combined with the cosmic microwave background data, these probes form interlocking tests on the cosmological model and the nature of dark energy in the presence of various systematics. The LSST data products will be made available to the US and Chilean scientific communities and to international partners with no proprietary period. Close collaborations with contemporaneous imaging and spectroscopy surveys observing at a variety of wavelengths, resolutions, depths, and timescales will be a vital part of the LSST science program, which will not only enhance specific studies but, more importantly, also allow a more complete understanding of the Universe through different windows.
Addressing clinician-client mismatch: a preliminary intervention study with a bilingual Vietnamese-English preschooler.

PURPOSE This project examined receptive vocabulary treatment outcomes in the two languages of a bilingual preschooler with moderate to severe language impairment. METHOD A series of single-subject experimental designs was used to compare English-only (EO) and bilingual (BI) approaches to receptive vocabulary treatment. The participant, Nam, was a boy age 3;11 (years;months) who was learning Vietnamese as a first language at home and English in his early childhood education program. Treatment was implemented by an EO interventionist using a computer interface and prerecorded audio files in Vietnamese and English. The dependent measure was the percentage of items that were correctly identified in each language. RESULTS Combined studies revealed that the BI approach increased Nam's attention to task and was as effective as the EO approach for increasing his receptive vocabulary in English. Nam made vocabulary gains in both treatment conditions; receptive vocabulary gains were evident in both Vietnamese and English. CONCLUSION This project showed that it is feasible for an EO clinician to promote gains in both the home and school languages of a BI child through creative collaborations with BI colleagues and the use of technology. Replication with additional participants and treatment activities is needed to make further generalizations.
Profiling users in a 3g network using hourglass co-clustering

With widespread popularity of smart phones, more and more users are accessing the Internet on the go. Understanding mobile user browsing behavior is of great significance for several reasons. For example, it can help cellular (data) service providers (CSPs) to improve service performance, thus increasing user satisfaction. It can also provide valuable insights about how to enhance mobile user experience by providing dynamic content personalization and recommendation, or location-aware services. In this paper, we try to understand mobile user browsing behavior by investigating whether there exists distinct "behavior patterns" among mobile users. Our study is based on real mobile network data collected from a large 3G CSP in North America. We formulate this user behavior profiling problem as a "co-clustering" problem, i.e., we group both users (who share similar browsing behavior), and browsing profiles (of like-minded users) simultaneously. We propose and develop a scalable co-clustering methodology, Phantom, using a novel hourglass model. The proposed hourglass model first reduces the dimensions of the input data and performs divisive hierarchical co-clustering on the lower dimensional data; it then carries out an expansion step that restores the original dimensions. Applying Phantom to the mobile network data, we find that there exists a number of prevalent and distinct behavior patterns that persist over time, suggesting that user browsing behavior in 3G cellular networks can be captured using a small number of co-clusters. For instance, behavior of most users can be classified as either homogeneous (users with very limited set of browsing interests) or heterogeneous (users with very diverse browsing interests), and such behavior profiles do not change significantly at either short (30-min) or long (6 hour) time scales.
Disrupted anabolic and catabolic processes may contribute to alcohol-accentuated SAIDS-associated wasting.

BACKGROUND Alcohol abuse is a comorbid factor in many human immunodeficiency virus (HIV)-infected patients. Previously, we demonstrated that chronic binge alcohol accentuates loss of body mass at terminal stage of simian immunodeficiency virus (SIV) infection. The purpose of this study was to investigate changes in pathways that may contribute to muscle wasting in chronic binge alcohol-fed SIV-infected macaques. METHODS The impact of chronic binge alcohol during SIV infection on insulin signaling and the ubiquitin (Ub)-proteasome system-regulators of protein synthesis and degradation-was examined in SIV-infected macaques. RESULTS SIV infection induced an inflammatory and pro-oxidative milieu in skeletal muscle, which was associated with decreased insulin-stimulated phosphatidylinositol 3-kinase (PI-3k) activity and upregulated gene expression of mTOR and atrogin-1, and protein expression of Ub-proteasome system 19S base. Chronic binge alcohol accentuated the skeletal muscle pro-oxidative milieu and 19S base expression. Additionally, chronic binge alcohol increased skeletal muscle protein expression of protein-tyrosine phosphatase 1B (a negative regulator of insulin signaling) and 19S proteasome regulator non-ATPase (Rpn) 6 subunit and Rpn12, and suppressed PI-3K activity. Animals that were alcohol-fed and SIV-infected for >15 months had increased Ub-proteasome system activity. CONCLUSIONS These data suggest negative modulation of insulin signaling coupled with enhanced Ub-proteasome system activity may be central mechanisms underlying chronic binge alcohol-induced accentuation of SIV-associated muscle wasting.
Effective thermal conductivity of polymer composites: a review of analytical methods

ABSTRACT Polymer composites are widely used in different areas such as the aircraft industry, automotive industry, electronic industry and packaging industry etc. Polymer composites should have various physical, mechanical and thermal properties, within various thermal properties thermal conductivity is an important parameter to simulate heat transfer process and mechanisms in composite materials. This paper deals with various analytical methods and models for determining the effective thermal conductivity of different polymer composite materials for various applications. There are basic models, modified models and semi-empirical models to determine thermal conductivity analytically, which are discussed in brief. After that, the comparison between different models is investigated. Finally different conductive fillers, the effect of their shape, size and volume fraction on the effective thermal conductivity of composite materials are discussed.
Additively Manufactured Open-Cell Porous Biomaterials Made from Six Different Space-Filling Unit Cells: The Mechanical and Morphological Properties

It is known that the mechanical properties of bone-mimicking porous biomaterials are a function of the morphological properties of the porous structure, including the configuration and size of the repeating unit cell from which they are made. However, the literature on this topic is limited, primarily because of the challenge in fabricating porous biomaterials with arbitrarily complex morphological designs. In the present work, we studied the relationship between relative density (RD) of porous Ti6Al4V EFI alloy and five compressive properties of the material, namely elastic gradient or modulus (Es20–70), first maximum stress, plateau stress, yield stress, and energy absorption. Porous structures with different RD and six different unit cell configurations (cubic (C), diamond (D), truncated cube (TC), truncated cuboctahedron (TCO), rhombic dodecahedron (RD), and rhombicuboctahedron (RCO)) were fabricated using selective laser melting. Each of the compressive properties increased with increase in RD, the relationship being of a power law type. Clear trends were seen in the influence of unit cell configuration and porosity on each of the compressive properties. For example, in terms of Es20–70, the structures may be divided into two groups: those that are stiff (comprising those made using C, TC, TCO, and RCO unit cell) and those that are compliant (comprising those made using D and RD unit cell).
Role of GPCR (mu-opioid)–receptor tyrosine kinase (epidermal growth factor) crosstalk in opioid-induced hyperalgesic priming (type II)

Abstract Repeated stimulation of mu-opioid receptors (MORs), by an MOR-selective agonist DAMGO induces type II priming, a form of nociceptor neuroplasticity, which has 2 components: opioid-induced hyperalgesia (OIH) and prolongation of prostaglandin-E2 (PGE2)-induced hyperalgesia. We report that intrathecal antisense knockdown of the MOR in nociceptors, prevented the induction of both components of type II priming. Type II priming was also eliminated by SSP-saporin, which destroys the peptidergic class of nociceptors. Because the epidermal growth factor receptor (EGFR) participates in MOR signaling, we tested its role in type II priming. The EGFR inhibitor, tyrphostin AG 1478, prevented the induction of prolonged PGE2-induced hyperalgesia, but not OIH, when tested out to 30 days after DAMGO. However, even when repeatedly injected, an EGFR agonist did not induce hyperalgesia or priming. A phosphopeptide, which blocks the interaction of Src, focal adhesion kinase (FAK), and EGFR, also prevented DAMGO-induced prolongation of PGE2 hyperalgesia, but only partially attenuated the induction of OIH. Inhibitors of Src and mitogen-activated protein kinase (MAPK) also only attenuated OIH. Inhibitors of matrix metalloproteinase, which cleaves EGF from membrane protein, markedly attenuated the expression, but did not prevent the induction, of prolongation of PGE2 hyperalgesia. Thus, although the induction of prolongation of PGE2-induced hyperalgesia at the peripheral terminal of peptidergic nociceptor is dependent on Src, FAK, EGFR, and MAPK signaling, Src, FAK, and MAPK signaling is only partially involved in the induction of OIH.