Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacteriophages with the Ability to Degrade Uropathogenic Escherichia Coli Biofilms

Escherichia coli-associated urinary tract infections (UTIs) are among the most common bacterial infections in humans. UTIs are usually managed with antibiotic therapy, but over the years, antibiotic-resistant strains of uropathogenic E. coli (UPEC) have emerged. The formation of biofilms further complicates the treatment of these infections by making them resistant to killing by the host immune system as well as by antibiotics. This has encouraged research into therapy using bacteriophages (phages) as a supplement or substitute for antibiotics. In this study we characterized 253 UPEC in terms of their biofilm-forming capabilities, serotype, and antimicrobial resistance. Three phages were then isolated (vB_EcoP_ACG-C91, vB_EcoM_ACG-C40 and vB_EcoS_ACG-M12) which were able to lyse 80.5% of a subset (42) of the UPEC strains able to form biofilms. Correlation was established between phage sensitivity and specific serotypes of the UPEC strains. The phages’ genome sequences were determined and resulted in classification of vB_EcoP_ACG-C91 as a SP6likevirus, vB_EcoM_ACG-C40 as a T4likevirus and vB_EcoS_ACG-M12 as T1likevirus. We assessed the ability of the three phages to eradicate the established biofilm of one of the UPEC strains used in the study. All phages significantly reduced the biofilm within 2–12 h of incubation.
Learning a Nonlinear Embedding by Preserving Class Neighbourhood Structure

We show how to pretrain and ﬁne-tune a multilayer neural network to learn a nonlinear transformation from the input space to a low-dimensional feature space in which K-nearest neighbour classiﬁcation performs well. We also show how the non-linear transformation can be improved using unlabeled data. Our method achieves a much lower error rate than Support Vector Machines or standard backpropagation on a widely used version of the MNIST handwritten digit recognition task. If some of the dimensions of the low-dimensional feature space are not used for nearest neighbor classiﬁcation, our method uses these dimensions to explicitly represent transformations of the digits that do not affect their identity.
Variational modelling of extreme waves through oblique interaction of solitary waves

Abstract. In this work, we model extreme waves that occur due to Mach reflection through the intersection of two obliquely incident solitary waves. For a given range of incident angles and amplitudes, the Mach stem wave grows linearly in length and amplitude, reaching up to 4 times the amplitude of the incident waves. A variational approach is used to derive the bidirectional Benney–Luke equations, an asymptotic equivalent of the three-dimensional potential-flow equations modelling water waves. This nonlinear and weakly dispersive model has the advantage of allowing wave propagation in two horizontal directions, which is not the case with the unidirectional Kadomtsev–Petviashvili (KP) equation used in most previous studies. A variational Galerkin finite-element method is applied to solve the system numerically in Firedrake with a second-order Stormer–Verlet temporal integration scheme, in order to obtain stable simulations that conserve the overall mass and energy of the system. Using this approach, we are able to get close to the 4-fold amplitude amplification predicted by Miles.
The Current Extent and Historical Expansion of Mangroves in the Kuantu Nature Reserve, North Taiwan

ABSTRACT Hsu, L. -C. and Lee, C. -T. , 2018. The current extent and historical expansion of mangroves in the Kuantu Nature Reserve, North Taiwan. The Kandelia candel (L.) Druce mangrove forest in the Kuantu Nature Reserve, North Taiwan, has experienced rapid expansion since 1978. This study assesses the current extent and historical expansion of the mangroves by means of aerial photograph interpretation. An analysis of a time series of aerial photographs, covering the period from 1978 to 2012, has revealed major changes in the distribution of mangroves in relation to the geomorphic changes in the Kuantu Nature Reserve. The results indicate that the area-increasing rate was highest (2.27 ha/y) during the 1986–94 period, meaning the most rapid encroachment of mangroves into the habitats of Cyperus and Phragmites saltmarshes. Based on the Shannon diversity index t test, with the encroachment of Kandelia, the landscape composition in the Kuantu Nature Reserve has been dominated by the mangrove swamp of Kandelia. The geomorphic changes in the area of accretion and erosion were derived from the 0-m contour in the 1:5000 topographic maps in 1978, 1986, 1994, and 2005. Based on a review of related literature, the possible driving forces of geomorphic changes are explained by human impacts (e.g., land subsidence because of the overpumping of groundwater and collapse triggered by sand pumping) and natural forces (e.g., increased accretion induced by mangroves and headward expansion of tidal creek and typhoon-induced erosion). The complicated interplay between vegetation and landform in the Kuantu Nature Reserve is discussed from the viewpoint of biogeomorphic succession. Similar mangrove expansion cases are also examined.
Effects of optically shallow bottoms on upwelling radiances: Bidirectional reflectance distribution function effects

Radiative transfer simulations were carried out for a variety of measured and modeled benthic bidirectional reflectance distribution functions (BRDFs), incident lighting conditions, bottom depths, and water inherent optical properties. These simulations quantify the errors that occur in predictions of above‐surface remote‐sensing reflectances and in‐water upwelling radiances if non‐Lambertian ocean bottoms are replaced by Lambertian bottoms having the same irradiance reflectance. We found that when computing water‐leaving radiances, non‐Lambertian BRDFs can be replaced by a Lambertian BRDF having the same irradiance reflectance, with errors seldom greater than 10% and often much less, for considerations of above‐surface ocean‐color remote sensing by Ocean Portable Hyperspectral Imager for Low‐Light Spectroscopy (Ocean PHILLS) or similar systems using near‐nadir viewing directions. The crucial measurement to make in characterizing the reflectance properties of a benthic surface for such applications is the spectral irradiance reflectance.
Diagnosing Performance Changes by Comparing System Behaviours

Abstract : The causes of performance changes in a distributed system often elude even its developers. This paper develops a new technique for gaining insight into such changes: comparing system behaviours from two executions (e.g., of two system versions or time periods). Building on end-to-end request flow tracing within and across components, algorithms are described for identifying and ranking changes in the flow and/or timing of request processing. The implementation of these algorithms in a tool called Spectroscope is described and evaluated. Five case studies are presented of using Spectroscope to diagnose performance changes in a distributed storage system caused by code changes and configuration modifications, demonstrating the value and efficacy of comparing system behaviours.
Newly observed, deep slow slip events at the central Hikurangi margin, New Zealand: Implications for downdip variability of slow slip and tremor, and relationship to seismic structure

We present previously undocumented deep (25–45 km depth), moderate‐duration (2–3 months) slow slip events (SSEs) directly downdip of known shallow (<15 km depth), short‐term (2–3 weeks) SSEs at the central Hikurangi margin, New Zealand. The moderate‐duration SSEs produce 2–6 mm of horizontal displacement at continuous Global Positioning System stations in 2006 and 2008, similar to Cascadia SSEs. They involve 2–5 cm of slip over ~5000 km2 of the subduction interface. Tremor occurs just downdip of the deep SSE source area. We also present results from a large, shallow (<12 km) SSE in 2013 just updip of the 2006/2008 SSEs. The location of deep SSEs between shallow, short‐term SSEs and tremor indicates strong downdip variation of subduction interface slip behavior at central Hikurangi. The deep SSEs occur where Qp and Vp/Vs data suggest an accumulation of fluid‐rich underplated sediment at the interface, consistent with the idea that SSEs occur under high fluid pressure.
Relativistic dynamical friction in a collisional fluid

The dynamical friction force experienced by a body moving at relativistic speed in a gaseous medium is examined. This force, which arises due to the gravitational interaction of the body with its own gravitationally-induced wake, is calculated for straight-line motion and circular motion, generalizing previous results by several authors. Possible applications to the study of extreme mass-ratio inspirals around strongly accreting supermassive black holes are suggested.
Classification via Sparse Representation of Steerable Wavelet Frames on Grassmann Manifold: Application to Target Recognition in SAR Image

Automatic target recognition has been widely studied over the years, yet it is still an open problem. The main obstacle consists in extended operating conditions, e.g., depression angle change, configuration variation, articulation, and occlusion. To deal with them, this paper proposes a new classification strategy. We develop a new representation model via the steerable wavelet frames. The proposed representation model is entirely viewed as an element on Grassmann manifolds. To achieve target classification, we embed Grassmann manifolds into an implicit reproducing Kernel Hilbert space (RKHS), where the kernel sparse learning can be applied. Specifically, the mappings of training sample in RKHS are concatenated to form an overcomplete dictionary. It is then used to encode the counterpart of query as a linear combination of its atoms. By designed Grassmann kernel function, it is capable to obtain the sparse representation, from which the inference can be reached. The novelty of this paper comes from: 1) the development of representation model by the set of directional components of Riesz transform; 2) the quantitative measure of similarity for proposed representation model by Grassmann metric; and 3) the generation of global kernel function by Grassmann kernel. Extensive comparative studies are performed to demonstrate the advantage of proposed strategy.
Human kin recognition is self- rather than family-referential

Inclusive fitness theory predicts that organisms will tend to help close kin more than less related individuals. In a variety of birds and mammals, relatives are recognized by comparing their phenotype to an internal representation or template, which might be learned through either repeated exposure to family members or self-inspection. Mirrors are ubiquitous now, but were absent during our evolutionary history; hence it is hard to predict, and empirically unknown, whether human kin recognition is family- or self-referential. Here we put this issue to the strongest possible test by comparing nepotistic behaviour towards self- versus co-twin-resemblant individuals. Seventy monozygotic and dizygotic twins were shown same-sex faces, covertly manipulated to resemble either themselves or their co-twin, and indicated which individual they would prefer in two prosocial contexts. Self-resemblant faces were significantly preferred to twin-resemblant faces, showing that visual information about the self supersedes that about close family members in the kin-recognition template. Because, under conditions of paternal uncertainty, a reliable family-referent template could be based only on one's mother and maternal relatives, a unique advantage of self-referent phenotype matching is the possibility of (consciously or unconsciously) identifying one's father and paternal relatives as kin.
Eco-evolutionary effects on population recovery following catastrophic disturbance

Fine‐scale genetic diversity and contemporary evolution can theoretically influence ecological dynamics in the wild. Such eco‐evolutionary effects might be particularly relevant to the persistence of populations facing acute or chronic environmental change. However, experimental data on wild populations is currently lacking to support this notion. One way that ongoing evolution might influence the dynamics of threatened populations is through the role that selection plays in mediating the ‘rescue effect’, the ability of migrants to contribute to the recovery of populations facing local disturbance and decline. Here, we combine experiments with natural catastrophic events to show that ongoing evolution is a major determinant of migrant contributions to population recovery in Trinidadian guppies (Poecilia reticulata). These eco‐evolutionary limits on migrant contributions appear to be mediated by the reinforcing effects of natural and sexual selection against migrants, despite the close geographic proximity of migrant sources. These findings show that ongoing adaptive evolution can be a double‐edged sword for population persistence, maintaining local fitness at a cost to demographic risk. Our study further serves as a potent reminder that significant evolutionary and eco‐evolutionary dynamics might be at play even where the phenotypic status quo is largely maintained generation to generation.
3-D Quasi-Atomistic Model for Line Edge Roughness in Nonplanar MOSFETs

As the physical sizes of devices have been scaled down, the negative impact of process-induced random variation on device performance has increased; therefore, there is an urgent demand for advanced simulation methods for variation. In this paper, a 3-D quasi-atomistic simulation methodology for line edge roughness (LER) in nonplanar devices, such as FinFETs and gate-all-around (GAA) FETs, is proposed. In addition, a simple gate oxide layer model is proposed to analyze the impact of LER on device performance while excluding the impact of oxide thickness variation. To verify the importance of the quasi-atomistic 3-D LER model and to compare the LER-induced performance variation in a FinFET to that in a GAA FET, the case studies using the 3-D quasi-atomistic LER model for FinFETs and GAA FETs are performed.
Drivers of consumer’s adoption of innovative food

Over the last years, food safety, health and environmental issues are a few among many other reasons that force consumers to adopt new innovative food products – organic, private label, genetically modified and functional – as part of their consumption. This spectacular shift of the consumption forwards “innovative” food products attracts the interest of the analyst as it can shed new light on consumer’s behaviour and on modeling and understanding better his long-term behaviour. Thus, this study attempts to investigate the factors that influence consumer’s decision in purchasing either traditional or new innovative products and to what extend this shift between those two groups of products is related to pre-defined elements. This is achieved by employing both descriptive statistics and multivariate analysis. Two-step cluster analysis was used to explore the different levels of innovative products adoption and a categorical regression model was estimated to determine the relation between consumer’s characteristics and willingness to adopt innovative products.
A world review of fungi, yeasts, and slime molds in caves

literature on cave fungi (127 species in 59 genera) but did not include all relevant papers available at that time, and many articles have since been published. Landolt et al. (1992) summarized the few records of slime molds found in caves, but otherwise there has been no comprehensive review of the microf lora in cave habitats. Here we organize data from 225 studies dealing with fungi, yeasts, and slime molds occurring in caves, with 130 of these allowing some exploration of broader patterns of occurrence in relation to the ecology of the cave habitat. Although studies published before 1965 do provide useful records of occurrence, unfortunately many do not report their methods in suff icient detail to allow comparisons with later work. We also identify gaps in information, but most importantly, we note the need for adequately applied and consistently reported methodologies. Our hope is that the review of cave fungi presented here will prove timely and useful to both speleologists and WNS researchers.
Studies on the active components and antioxidant activities of the extracts of Mimosa pudica Linn. from southern China

Background: The total flavonoid (TF) and total phenolic (TP) contents of the ethanol extracts of the whole plant, stem, leaf, and seed of Mimosa pudica Linn belonging to the genus Mimosa (Family: Fabaceae alt. Leguminosae), which originates from the subtropical regions of southern China, were determined in this experiment. Materials and Methods: The antioxidant activity of the extracts and 5 flavonoid monomers of M. pudica Linn. were also evaluated by 2 assays, the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity and ferric reducing/antioxidant power (FRAP) assays. In addition, correlation analysis was also made in the present study. Results: The results showed that leaf extracts contained the highest amount of TF and TP, and the content was significantly higher than that found in other parts of the plant. Moreover, the sequence of antioxidant activity of the ethanol extracts was as follows: leaf > the whole plant > seed > stem; the sequence of the 5 flavonoid monomers was as follows: 5,7,3´,4´-tetrahydroxy-6-C-[β-D-apiose-(1→4)]-β-D-glycopyranosyl flavone (1) > isorientin (2) > orientin (3) > isovitexin (4) > vitexin (5), and the antioxidant activity of compound 1 is equivalent to the synthetic antioxidant trolox or a bit stronger than trolox, and significant correlations were found among the active ingredient contents and the results of antioxidant activity. Conclusion: The present study suggested that M. pudica Linn. could be a potential rich source of natural antioxidants.
Informational divergence approximations to product distributions

The minimum rate needed to accurately approximate a product distribution based on an unnormalized informational divergence is shown to be a mutual information. This result subsumes results of Wyner on common information and Han-Verdú on resolvability. The result also extends to cases where the source distribution is unknown but the entropy is known.
Prevalence, Incidence and Obstetric Factors’ Impact on Female Urinary Incontinence in Europe: A Systematic Review

Objectives: A systematic review of the published data on the prevalence, incidence and risk factors of female urinary incontinence (UI) and obstetric treatment of UI in Europe. Data Sources: Epidemiologic studies were sought via PubMed to identify articles published in English, French, Spanish, German and Italian between 2000 and September 30, 2010, in Europe. Results: The prevalence of UI ranged from 14.1 to 68.8% and increased with increasing age. Significant risk factors for UI in pregnancy were maternal age ≥35 years and initial body mass index, a family history of UI and parity. UI in women who delivered ‘at term’ ranged from 26 to 40.2%, with a remission rate of 3 months after childbirth of up to 86.4%. Pelvic floor muscle training may help to prevent postpartum UI in primiparous women without UI during pregnancy. Conclusion: UI definition, outcome measures, survey methods and validation criteria are still heterogeneous, and thus it is difficult to compare data and impossible to draw definite conclusions.
Dissociation of the N400 component between linguistic and non-linguistic processing: A source analysis study

The N400 component is commonly associated with the detection of linguistic incongruity. A few studies have shown that the N400 can also be elicited by non-linguistic stimuli. Different spatiotemporal patterns were observed between the typical Linguistic N400 and the Non-linguistic N400, suggesting distinct brain generators. The aim of this study was to investigate the presence of an N400 in response to linguistic and non-linguistic stimuli, and to specify anatomical sources of both N400s using a novel analysis method: the Bayesian Model Averaging (BMA) distributed source model. Picture-word and environmental soundpicture associations, either congruent or incongruent, were presented to ten young healthy adults while highdensity ERP recordings were made. Standard electrophysiological analyses confirmed that the N400 was not specific to linguistic incongruity but was also elicited by environmental sound-picture incongruities. Different topographic distributions were obtained for the Linguistic N400 and Non-linguistic N400. BMA analysis showed that the Linguistic N400 generators were mostly located in the left superior temporal gyrus, whereas the sources of the Non-linguistic N400 were identified mostly in the right middle and superior temporal gyri. Detection of linguistic incongruities recruited cerebral areas commonly associated with language processing, whereas non-linguistic incongruities recruited right cerebral regions usually associated with auditory processing of non-linguistic stimuli. The Linguistic and Non-linguistic N400s appear to be elicited by similar cognitive mechanisms assumed by different cerebral areas depending on the type of material to be processed. The present findings support the existence of parallel pathways for the processing of linguistic and non-linguistic incongruities.
Manipulating Heat Shock Factor-1 in Xenopus Tadpoles: Neuronal Tissues Are Refractory to Exogenous Expression

Background The aging related decline of heat shock factor-1 (HSF1) signaling may be causally related to protein aggregation diseases. To model such disease, we tried to cripple HSF1 signaling in the Xenopus tadpole. Results Over-expression of heat shock factor binding protein-1 did not inhibit the heat shock response in Xenopus. RNAi against HSF1 mRNA inhibited the heat shock response by 70% in Xenopus A6 cells, but failed in transgenic tadpoles. Expression of XHSF380, a dominant-negative HSF1 mutant, was embryonic lethal, which could be circumvented by delaying expression via a tetracycline inducible promoter. HSF1 signaling is thus essential for embryonic Xenopus development. Surprisingly, transgenic expression of the XHSF380 or of full length HSF1, whether driven by a ubiquitous or a neural specific promoter, was not detectable in the larval brain. Conclusions Our finding that the majority of neurons, which have little endogenous HSF1, refused to accept transgene-driven expression of HSF1 or its mutant suggests that HSF1 levels are strictly controlled in neuronal tissue.
Serologic analyses of cottontail rabbits for antibodies to Borrelia burgdorferi

An enzyme-linked immunosorbent assay was developed to detect antibodies to Borrelia burgdorferi in cottontail rabbits captured in Millbrook, N.Y. , and New York, N.Y. Five antigenically variable strains of B. burgdorferi were analyzed to determine the variability of serologic test results. In analyses of 79 serum samples, seropositivity ranged from 56% for a strain cultured from kidney tissues of a cottontail rabbit to 68% for a strain isolated from a larva of Ixodes dentatus, a tick that parasitized a cottontail rabbit. There were false-positive results when reference rabbit antisera to B. hermsii and Treponema pallidum were screened against B. burgdorferi. Cross-reactivity with antisera to Leptospira interrogans serovars was less pronounced. Western blot (immunoblot) analyses revealed reactivities of test sera to two or more surface or subsurface proteins of B. burgdorferi with approximate molecular masses of 18, 25 to 27, 34, 36, 41, and 59 kilodaltons. Cottontail rabbits respond immunologically to B. burgdorferi, but the observed variations in serologic test results should not be a limitation in field and laboratory investigations of Lyme borreliosis.