Miracle-dz/UniFAR-FTUs huggingface dataset:
Two Distinct Patterns of Clostridium difficile Diversity Across Europe Indicating Contrasting Routes of Spread

Whole-genome sequencing of Clostridium difficile across Europe demonstrates 2 distinct transmission patterns. Healthcare-associated ribotypes showed genetic clustering by country and region, and widespread fluoroquinolone resistance. However, multiple common ribotypes showed no within-country clustering, consistent with Europe-wide dissemination via nonhealthcare routes/sources.
Response of small ruminants to diets containing reed forage either as fresh, silage or hay versus berseem hay.

This study started by nutritional evaluation (digestion coefficients and feeding value) of reed forage collected from three locations using Rahmani sheep. The best one was used in the second part of the study to compare effect of feeding reed in three forms as fresh, silage or hay on goat’s milk production, compositions and quality ending by economic efficiency. Reed collected from Manzalla is relatively the best but with insignificant difference compared to others. Feeding trials lasted for 20 weeks where four groups were assigned to receive the four experimental rations. All groups were fed on restricted amount of concentrate feed mixture, to cover 50% of the requirements recommended by NRC (1981) while reed, in the three forms, offered ad lib. Results show that reed silage had the highest digestion estimates, followed by berseem hay then fresh reed and lastly reed hay. Similarly, TDN and DCP were significantly (P<0.05) higher with RS and RF compared to RH and BH (berseem hay as control) rations. TVA's, measured at 4 hrs post feeding in rumen fluid, had no significant differences among the four tested rations. However, microbial protein values were significantly (P<0.05) higher with RS and RF compared to RH and BH rations. Daily milk was significantly (P<0.05) higher for RS and RF compared to RH and BH rations. The highest milk yield was recorded with RS (1.23, Kg) while the lowest for RH (1.01Kg). Milk fat was superior with the three reed forms than berseem hay. Milk quality parameters were not differed significantly among all groups. The feed intake, kg dry matter, was better with reed silage (1.19 kg) and reed forage (1.22 kg) compared with reed hay (1.37 kg) and berseem hay (1.35 kg) . Reed silage (RS) recorded the highest economic return followed by RF then RH rations while, the lowest was obtained by BH. It is concluded that reed silage recorded the best feeding values, milk production and quality beside the economic factor.
2 4 M ar 2 01 8 Surface Pressure of Charged Colloids at the Air / Water Interface

Charged colloidal monolayers at the interface between water and air (or oil) are used in a large number of chemical, physical and biological applications. Although a considerable experimental and theoretical effort has been devoted in the past few decades to investigate such monolayers, some of their fundamental properties are not yet fully understood. In this paper, we model charged colloidal monolayers as a continuum layer of finite thickness, with separate charge distribution on the water and air sides. The electrostatic surface free-energy and surface pressure are calculated via the charging method and within the Debye-Hückel approximation. We obtain the dependence of surface pressure on several system parameters: the monolayer thickness, its distinct dielectric permittivity, and the ionic strength of the aqueous subphase. The surface pressure scaling with the area, A, is found to be between A in the close-packing limit, and A in the loose-packing limit. In general, it is found that the surface-pressure is strongly influenced by charges on the air-side of the colloids. However, when the larger charge resides on the water-side, a more subtle dependence on salt concentration emerges. This corrects a common assumption that the charges on the water-side can always be neglected due to screening. Finally, using a single fit parameter, our theory is found to fit well the experimental data for strong to intermediate strength electrolytes.
Predator-Induced Cyclical Changes in Lateral Plate Frequencies of Gasterosteus

This study investigates ecological aspects to intrapopulation variability in the lateral plates of threespine stickleback (Gasterosteus aculeatus) at a coastal lake in western Canada. The frequency distribution of the plates, which was slightly skewed to the right and leptokurtic, varied spatially and seasonally. Cyclical frequency changes in plates were most pronounced on sub-adult size classes and these closely tracked (multiple r = 0.77) seasonal differences in the relative proportion of the two major predator groups, trout and diving birds. Trout predation was correlated with an increase in plate number while bird predation was correlated with a reduction in plate number. Such divergent selection pressures, which are probably common in natural populations, would account for the presence of multiple phenotypes and allow for rapid shifts in defensive morphology among different populations where predation regime differs.
Dissimilatory Fe(III) Reduction by the Marine Microorganism Desulfuromonas acetoxidans

The ability of the marine microorganism Desulfuromonas acetoxidans to reduce Fe(III) was investigated because of its close phylogenetic relationship with the freshwater dissimilatory Fe(III) reducer Geobacter metallireducens. Washed cell suspensions of the type strain of D. acetoxidans reduced soluble Fe(III)-citrate and Fe(III) complexed with nitriloacetic acid. The c-type cytochrome(s) of D. acetoxidans was oxidized by Fe(III)-citrate and Mn(IV)-oxalate, as well as by two electron acceptors known to support growth, colloidal sulfur and malate. D. acetoxidans grew in defined anoxic, bicarbonate-buffered medium with acetate as the sole electron donor and poorly crystalline Fe(III) or Mn(IV) as the sole electron acceptor. Magnetite (Fe3O4) and siderite (FeCO3) were the major end products of Fe(III) reduction, whereas rhodochrosite (MnCO3) was the end product of Mn(IV) reduction. Ethanol, propanol, pyruvate, and butanol also served as electron donors for Fe(III) reduction. In contrast to D. acetoxidans, G. metallireducens could only grow in freshwater medium and it did not conserve energy to support growth from colloidal S0 reduction. D. acetoxidans is the first marine microorganism shown to conserve energy to support growth by coupling the complete oxidation of organic compounds to the reduction of Fe(III) or Mn(IV). Thus, D. acetoxidans provides a model enzymatic mechanism for Fe(III) or Mn(IV) oxidation of organic compounds in marine and estuarine sediments. These findings demonstrate that 16S rRNA phylogenetic analyses can suggest previously unrecognized metabolic capabilities of microorganisms.
Accumulation of follicular CD8+ T cells in pathogenic SIV infection

LN follicles constitute major reservoir sites for HIV/SIV persistence. Cure strategies could benefit from the characterization of CD8+ T cells able to access and eliminate HIV-infected cells from these areas. In this study, we provide a comprehensive analysis of the phenotype, frequency, localization, and functionality of follicular CD8+ T cells (fCD8+) in SIV-infected nonhuman primates. Although disorganization of follicles was a major factor, significant accumulation of fCD8+ cells during chronic SIV infection was also observed in intact follicles, but only in pathogenic SIV infection. In line with this, tissue inflammatory mediators were strongly associated with the accumulation of fCD8+ cells, pointing to tissue inflammation as a major factor in this process. These fCD8+ cells have cytolytic potential and can be redirected to target and kill HIV-infected cells using bispecific antibodies. Altogether, our data support the use of SIV infection to better understand the dynamics of fCD8+ cells and to develop bispecific antibodies as a strategy for virus eradication.
Defective and Clustered Graph Colouring

Consider the following two ways to colour the vertices of a graph where the requirement that adjacent vertices get distinct colours is relaxed. A colouring has "defect" $d$ if each monochromatic component has maximum degree at most $d$. A colouring has "clustering" $c$ if each monochromatic component has at most $c$ vertices. This paper surveys research on these types of colourings, where the first priority is to minimise the number of colours, with small defect or small clustering as a secondary goal. List colouring variants are also considered. The following graph classes are studied: outerplanar graphs, planar graphs, graphs embeddable in surfaces, graphs with given maximum degree, graphs with given maximum average degree, graphs excluding a given subgraph, graphs with linear crossing number, linklessly or knotlessly embeddable graphs, graphs with given Colin de Verdi\`ere parameter, graphs with given circumference, graphs excluding a fixed graph as an immersion, graphs with given thickness, graphs with given stack- or queue-number, graphs excluding $K_t$ as a minor, graphs excluding $K_{s,t}$ as a minor, and graphs excluding an arbitrary graph $H$ as a minor. Several open problems are discussed.
Approaching Neural Grammatical Error Correction as a Low-Resource Machine Translation Task

Previously, neural methods in grammatical error correction (GEC) did not reach state-of-the-art results compared to phrase-based statistical machine translation (SMT) baselines. We demonstrate parallels between neural GEC and low-resource neural MT and successfully adapt several methods from low-resource MT to neural GEC. We further establish guidelines for trustable results in neural GEC and propose a set of model-independent methods for neural GEC that can be easily applied in most GEC settings. Proposed methods include adding source-side noise, domain-adaptation techniques, a GEC-specific training-objective, transfer learning with monolingual data, and ensembling of independently trained GEC models and language models. The combined effects of these methods result in better than state-of-the-art neural GEC models that outperform previously best neural GEC systems by more than 10% M² on the CoNLL-2014 benchmark and 5.9% on the JFLEG test set. Non-neural state-of-the-art systems are outperformed by more than 2% on the CoNLL-2014 benchmark and by 4% on JFLEG.
Evolution of DNMT2 in drosophilids: Evidence for positive and purifying selection and insights into new protein (pathways) interactions

Abstract The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the DNA methyltransferase family. Nevertheless, its substrate specificity is still controversial and elusive. The genomic role and determinants of DNA methylation are poorly understood in invertebrates, and several mechanisms and associations are suggested. In Drosophila, the only known DNMT gene is Dnmt2. Here we present our findings from a wide search for Dnmt2 homologs in 68 species of Drosophilidae. We investigated its molecular evolution, and in our phylogenetic analyses the main clades of Drosophilidae species were recovered. We tested whether the Dnmt2 has evolved neutrally or under positive selection along the subgenera Drosophila and Sophophora and investigated positive selection in relation to several physicochemical properties. Despite of a major selective constraint on Dnmt2, we detected six sites under positive selection. Regarding the DNMT2 protein, 12 sites under positive-destabilizing selection were found, which suggests a selection that favors structural and functional shifts in the protein. The search for new potential protein partners with DNMT2 revealed 15 proteins with high evolutionary rate covariation (ERC), indicating a plurality of DNMT2 functions in different pathways. These events might represent signs of molecular adaptation, with molecular peculiarities arising from the diversity of evolutionary histories experienced by drosophilids.
HYDRUS: Model Use, Calibration, and Validation

The HYDRUS numerical models are widely used for simulating water flow and solute transport in variably saturated soils and groundwater. Applications involve a broad range of steady-state or transient water flow, solute transport, and/or heat transfer problems. They include both short-term, one-dimensional laboratory column flow or transport simulations, as well as more complex, long-duration, multi-dimensional field studies. The HYDRUS models can be used for both direct problems when the initial and boundary conditions for all involved processes and corresponding model parameters are known, as well as inverse problems when some of the parameters need to be calibrated or estimated from observed data. The approach to model calibration and validation may vary widely depending upon the complexity of the application. Model calibration and inverse parameter estimation can be carried out using a relatively simple, gradient-based, local optimization approach based on the Marquardt-Levenberg method, which is directly implemented into the HYDRUS codes, or more complex global optimization methods, including genetic algorithms, which need to be run separately from HYDRUS. In this article, we provide a brief overview of the HYDRUS codes, discuss which HYDRUS parameters can be estimated using internally built optimization routines and which type of experimental data can be used for this, and review various calibration approaches that have been used in the literature in combination with the HYDRUS codes.
Efficient and Hysteresis-Free Field Effect Modulation of Ambipolarly Doped Vanadium Dioxide Nanowires

Xingyue Peng, Yiming Yang, Yasen Hou, Henry C. Travaglini, Luke Hellwig, Sahar Hihath, Klaus van Benthem, Kathleen Lee, Weifeng Liu, and Dong Yu Department of Physics, University of California, Davis, California 95616, USA Department of Physics, Bard College, New York 12504, USA Department of Physics, Carleton College, Northfield, Minnesota 55057, USA Department of Materials Science and Engineering, University of California, Davis, California 95616, USA Department of Chemistry, University of California, Davis, California 95616, USA Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China (Received 22 December 2015; revised manuscript received 14 March 2016; published 12 May 2016)
Performance loss analysis and design space optimization of perovskite solar cells

While the performance enhancement witnessed in the field of perovskite solar cells over the recent years has been impressive, it is now evident that further optimization beyond the existing literature would require detailed analysis of various loss mechanisms. Here we address the same through detailed numerical simulations of optical and electrical characteristics. We quantify the various losses like optical losses (5-6%), recombination losses (3-4%), and resistive losses against the Auger limited practical efficiency limits. Moreover, we illustrate the schemes that result in reduction of these losses and eventual increase in efficiency. In addition, we extend the analyses to identify the optimum thickness of perovskite and the factors affecting the optimum thickness have been discussed in detail.
Subcycle interference upon tunnel ionization by counter-rotating two-color fields

We report on three-dimensional (3D) electron momentum distributions from single ionization of helium by a laser pulse consisting of two counterrotating circularly polarized fields (390 nm and 780 nm). A pronounced 3D low energy structure and sub-cycle interferences are observed experimentally and reproduced numerically using a trajectory based semi-classical simulation. The orientation of the low energy structure in the polarization plane is verified by numerical simulations solving the time dependent Schr\"odinger equation.
The Quarterly Journal of Experimental Psychology Window to the Wandering Mind: Pupillometry of Spontaneous Thought While Reading Window to the Wandering Mind: Pupillometry of Spontaneous Thought While Reading Pupillometry and Mind-wandering 2 Introduction

Disclaimer: This is a version of an unedited manuscript that has been accepted for publication. As a service to authors and researchers we are providing this version of the accepted manuscript (AM). Copyediting, typesetting, and review of the resulting proof will be undertaken on this manuscript before final publication of the Version of Record (VoR). During production and pre-press, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal relate to this version also. Taylor & Francis makes every effort to ensure the accuracy of all the information (the " Content ") contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content. Abstract Mind-wandering is both pervasive and detrimental to task performance. As such, identifying covert physiological measures that are associated with this off-task state could inform theories of mind-wandering and lead to interventions that improve task focus. Although previous work suggests that pupil dilation (PD) may vary between on-and off-task states, no studies have examined whether PD systematically varies within a subject as they report becoming disengaged from a task; a key step in developing useful mind-wandering prediction algorithms. In the present study, PD was measured while participants advanced through a passage one word at a time. Spontaneous mind-wandering was assessed during reading using standard thought probe methodology. Results revealed higher PD prior to off-task compared to on-task reading. This newly discovered relationship between momentary fluctuations of attention and PD offers promise for future innovations that use these systematic changes in PD to predict and better control mind-wandering.
Gender Differences in the Consequences of Divorce: A Multiple-Outcome Comparison of Former Spouses

This study examined gender differences in the consequences of divorce for multiple measures of psychological, economic, and domestic well-being. I used household panel data from the German SOEP, retaining the link between initially married couples (N = 755) to compare both spouses over a period of up to four years before and after divorce. Findings showed that men were more vulnerable to short-term declines in subjective measures of well-being, whereas women experienced longer-term disadvantages in objective economic status. Taken together, these results suggest that women’s disproportionate income strain is chronic, whereas men’s disproportionate psychological and domestic strain is not.
Butein activates p53 in hepatocellular carcinoma cells via blocking MDM2-mediated ubiquitination

Introduction In this study, we aimed to investigate the effect of butein on p53 in hepatocellular carcinoma (HCC) cells and the related molecular mechanisms by which p53 was activated. Methods MTS assay and clonogenic survival assay were used to examine the antitumor activity of butein in vitro. Reporter gene assay was adopted to evaluate p53 transcriptional activity. Flow cytometry and western blotting were performed to study apoptosis induction and protein expression respectively. Xenograft model was applied to determine the in vivo efficacy and the expression of p53 in tumor tissue was detected by immunohistochemistry. Results HCC cell proliferation and clonogenic survival were significantly inhibited after butein treatment. With the activation of cleaved-PARP and capsase-3, butein induced apoptosis in HCC cells in a dose-dependent manner. The transcriptional activity of p53 was substantially promoted by butein, and the expression of p53-targeted gene was increased accordingly. Mechanism studies demonstrated that the interaction between MDM2 and p53 was blocked by butein and MDM2-mediated p53 ubiquitination was substantially decreased. Short-hairpin RNA experiment results showed that the sensitivity of HCC cells to butein was substantially impaired after p53 was knocked down and butein-induced apoptosis was dramatically decreased. In vivo experiments validated substantial antitumor efficacy of butein against HepG2 xenograft growth, and the expression of p53 in butein-treated tumor tissue was significantly increased. Conclusion Butein demonstrated potent antitumor activities in HCC by activating p53, and butein or its analogs had therapeutic potential for HCC management.
Noninvasive analysis of motor unit behavior in pathological tremor

A robust surface EMG decomposition tool, referred to as tremor-optimized Convolution Kernel Compensation (CKC) technique, is described. This technique modifies and extends the previously published CKC method in order to circumvent the typical assumption on regularity and asynchrony of motor unit firings in normal condition and adapt to the discharge patterns in pathological tremor. The results on synthetic and experimental surface EMG signals demonstrate high performance of decomposition. In the case of simulated surface EMG with 20 dB SNR, excitation level of 20% maximum voluntary contraction (MVC) and simulated tremor frequency of 8 Hz, the newly proposed method identified 8 ± 2 motor units with sensitivity of motor unit discharge identification > 95 % and false alarm and miss rates < 5%. The performance worsened with increasing noise power, with 5 ± 2 motor units identified at 10 dB SNR and 3 ± 1 at 0 dB SNR. In 24 recordings of high-density surface EMG signals from four tremor-affected patients, the modified CKC technique identified 134 motor units (6 ± 4 motor units per contraction).
A whole brain longitudinal study in the YAC128 mouse model of Huntington’s disease shows distinct trajectories of neurochemical, structural connectivity and volumetric changes

Huntington's disease (HD) is a neurodegenerative disorder causing cognitive and motor impairments, evolving to death within 15-20 years after symptom onset. We previously established a mouse model with the entire human HD gene containing 128 CAG repeats (YAC128) which accurately recapitulates the natural history of the human disease. Defined time points in this natural history enable the understanding of longitudinal trajectories from the neurochemical and structural points of view using non-invasive high-resolution multi-modal imaging. Accordingly, we designed a longitudinal structural imaging (MRI and DTI) and spectroscopy (1H-MRS) study in YAC128, at 3, 6, 9 and 12 months of age, at 9.4 T. Structural analysis (MRI/DTI), confirmed that the striatum is the earliest affected brain region, but other regions were also identified through connectivity analysis (pre-frontal cortex, hippocampus, globus pallidus and thalamus), suggesting a striking homology with the human disease. Importantly, we found for the first time, a negative correlation between striatal and hippocampal changes only in YAC128. In fact, the striatum showed accelerated volumetric decay in HD, as opposed to the hippocampus. Neurochemical analysis of the HD striatum suggested early neurometabolic alterations in neurotransmission and metabolism, with a significant increase in striatal GABA levels, and specifically anticorrelated levels of N-acetyl aspartate and taurine, suggesting that the later is homeostatically adjusted for neuroprotection, as neural loss, indicated by the former, is progressing. These results provide novel insights into the natural history of HD and prove a valuable role for longitudinal multi-modal panels of structural and metabolite/neurotransmission in the YAC128 model.