Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular epidemiology of Ornithobacterium rhinotracheale

Ornithobacterium rhinotracheale is a recently described gram-negative rod-shaped bacterium associated with respiratory tract infections in poultry. In order to determine the molecular epidemiology of this bacterium, we characterized 55 O. rhinotracheale isolates from eight countries on four continents by multilocus enzyme electrophoresis (MLEE), repetitive sequence based-PCR (rep-PCR), and 16S rRNA gene sequencing. MLEE discriminated the O. rhinotracheale isolates into six electrophoretic types (ETs), of which only three ETs were recovered from domesticated poultry. The 16S rRNA gene sequence and rep-PCR analyses confirmed the results obtained by MLEE and indicated limited heterogeneity among isolates of O. rhinotracheale recovered from poultry. Taken together, the results of our analysis demonstrate that the majority of O. rhinotracheale isolates recovered from domesticated poultry throughout the world are represented by a small group of closely related clones and suggest that the bacterium was recently introduced to domesticated poultry from wild bird populations.
Gene Circuit Analysis of the Terminal Gap Gene huckebein

The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb) on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb) domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network.
OXA-163, an OXA-48-Related Class D β-Lactamase with Extended Activity Toward Expanded-Spectrum Cephalosporins

ABSTRACT Two blaOXA-48-like-positive isolates (Klebsiella pneumoniae and Enterobacter cloacae) were recovered in Argentina in 2008 as part of a large-scale survey focused on multidrug resistance in Enterobacteriaceae. In both cases, sequencing identified β-lactamase OXA-163, differing from OXA-48 by a single amino substitution and a 4-amino-acid deletion. OXA-163 hydrolyzed penicillins, ceftazidime, and cefotaxime, whereas OXA-48 did not. However, OXA-163 had a much lower ability to hydrolyze carbapenems than OXA-48, therefore barely being considered a carbapenemase. In both isolates, the blaOXA-163 gene was located on plasmids that differed in structure and size. However, a detailed genetic analysis revealed a similar genetic context in those isolates, with the blaOXA-163 gene being bracketed by novel transposase genes, making this genetic environment different from that reported for the blaOXA-48 gene. This study identified the first class D β-lactamase compromising both extended-spectrum cephalosporin and carbapenem activities.
Absence of an N-Linked Glycosylation Motif in the Glycoprotein of the Live-Attenuated Argentine Hemorrhagic Fever Vaccine, Candid #1, Results in Its Improper Processing, and Reduced Surface Expression

Junin virus (JUNV), a highly pathogenic New World arenavirus, is the causative agent of Argentine hemorrhagic fever (AHF). The live-attenuated Candid #1 (Can) strain currently serves as a vaccine for at-risk populations. We have previously shown that the Can glycoprotein (GPC) gene is the primary gene responsible for attenuation in a guinea pig model of AHF. However, the mechanisms through which the GPC contributes to the attenuation of the Can strain remain unknown. A more complete understanding of the mechanisms underlying the attenuation and immunogenicity of the Can strain will potentially allow for the rational design of additional safe and novel vaccines. Here, we provide a detailed comparison of both RNA and protein expression profiles between both inter- and intra-segment chimeric JUNV recombinant clones expressing combinations of genes from the Can strain and the pathogenic Romero (Rom) strain. The recombinant viruses that express Can GPC, which were shown to be attenuated in guinea pigs, displayed different RNA levels and GPC processing patterns as determined by Northern and Western blot analyses, respectively. Analysis of recombinant viruses containing amino acid substitutions selected at different mouse brain passages during the generation of Can revealed that altered Can GPC processing was primarily due to the T168A substitution within G1, which eliminates an N-linked glycosylation motif. Incorporation of the T168A substitution in the Rom GPC resulted in a Can-like processing pattern of Rom GPC. In addition, JUNV GPCs containing T168A substitution were retained within the endoplasmic reticulum (ER) and displayed significantly lower cell surface expression than wild-type Rom GPC. Interestingly, the reversion A168T in Can GPC significantly increased GPC expression at the cell surface. Our results demonstrate that recombinant JUNV (rJUNV) expressing Can GPC display markedly different protein expression and elevated genomic RNA expression when compared to viruses expressing Rom GPC. Additionally, our findings indicate that the N-linked glycosylation motif at amino acid positions 166–168 is important for trafficking of JUNV GPC to the cell surface, and the elimination of this motif interferes with the GPC release from the ER.
A proximate-time-optimal-control design and its application to a hard disk drive dual-stage actuator system

We propose a compensator-based strategy for design of a track-seeking and track-following control system for a dual-stage servo actuator in hard disk drives. A well-known decoupling structure is employed to disconnect the control of the primary voice coil motor (VCM) actuator from the loop for a secondary high-bandwidth actuator. The compensator is placed in the secondary loop and suitably combined with a saturation nonlinearity in order to obtain actuator signal boundedness. The design procedure consists of four steps: 1) design of an established nonlinear seek-settle-track following controller for the VCM; 2) design of a linear track following controller for the secondary actuator; 3) observer design; and 4) design of a compensator to retain global stability and to improve performance. The proposed control system improves performance of both long-span seeking (proximate-time-optimal controller) and short-span seeking. In addition, it achieves high-bandwidth track following performance. The experimental results show good track-following performance, and short-span/long-span-seeking performance with fast settling time. The overshoot during track seeking can be made negligible for a suitably tuned VCM-actuator control loop.
Information, Divergence and Risk for Binary Experiments

We unify f-divergences, Bregman divergences, surrogate regret bounds, proper scoring rules, cost curves, ROC-curves and statistical information. We do this by systematically studying integral and variational representations of these objects and in so doing identify their representation primitives which all are related to cost-sensitive binary classification. As well as developing relationships between generative and discriminative views of learning, the new machinery leads to tight and more general surrogate regret bounds and generalised Pinsker inequalities relating f-divergences to variational divergence. The new viewpoint also illuminates existing algorithms: it provides a new derivation of Support Vector Machines in terms of divergences and relates maximum mean discrepancy to Fisher linear discriminants.
Effects of Exercise Training Intensity on Pancreatic β-Cell Function

OBJECTIVE Insulin resistance and β-cell dysfunction both are important contributors to the pathogenesis of type 2 diabetes. Exercise training improves insulin sensitivity, but its effects on β-cell function are less well studied. RESEARCH DESIGN AND METHODS Sedentary, overweight adults were randomized to control or one of three 8-month exercise programs: 1) low amount/moderate intensity, 2) low amount/vigorous intensity, or 3) high amount/vigorous intensity. Of 387 randomized, 260 completed the study and 237 had complete data. Insulin sensitivity (Si), acute insulin response to glucose (AIRg), and the disposition index (DI = Si × AIRg) were modeled from an intravenous glucose tolerance test. RESULTS Compared with control subjects, all three training programs led to increases in DI. However, the moderate-intensity group experienced a significantly larger increase in DI than either of the vigorous-intensity groups and through a different mechanism. The high-amount/vigorous-intensity group improved Si and had a compensatory reduction in AIRg, whereas the moderate-intensity group had a similar improvement in Si but almost no reduction in AIRg. Importantly, the inactive control group experienced a significant increase in fasting glucose. CONCLUSIONS To the extent that the DI accurately reflects β-cell function, we observed that both moderate- and vigorous-intensity exercise training improved β-cell function, albeit through distinct mechanisms. It is not clear which of these mechanisms is preferable for maintenance of metabolic health. While moderate-intensity exercise led to a larger improvement in DI, which may reflect a transition toward a more normal DI, longer-term investigations would be necessary to determine which was more effective at reducing diabetes risk.
Mid-infrared Variability of Changing-look AGNs

It is known that some active galactic nuclei (AGNs) transit from Type 1 to Type 2 or vice versa. There are two explanations for the so-called changing-look AGNs: one is the dramatic change of the obscuration along the line of sight, and the other is the variation of accretion rate. In this Letter, we report the detection of large amplitude variations in the mid-infrared luminosity during the transitions in 10 changing-look AGNs using the Wide-field Infrared Survey Explorer (WISE) and newly released Near-Earth Object WISE Reactivation data. The mid-infrared light curves of 10 objects echo the variability in the optical band with a time lag expected for dust reprocessing. The large variability amplitude is inconsistent with the scenario of varying obscuration, rather it supports the scheme of dramatic change in the accretion rate.
Addition of Boron Based Compound in the LVL Glueline: Effect on the Mechanical Properties and the Leaching of Boron

Summary This study aims at the optimization of the durability of Laminated Veneer Lumber (LVL) panels by adding borates to the gluing formulation. Poplar veneers measuring 2.6 mm thickness were used for the manufacture of LVL by Isoroy, a French company located in Lisieux. The melamine-urea-formaldehyde (M.U.F.) glue formulations were mixed with various concentrations of boric acid. A 0.8% retention of boron was measured in the LVL panel after intensive water leaching. The mechanical properties of finished LVL panels and their bonding strength properties were evaluated. The influence of the glue bonding on leaching was also evaluated. The amount of boron in LVL was measured by spectrocolorimetry using the CIELAB system. Results demonstrated that the incorporation of boron in the glueline may improve LVL durability.
Cyclin D1 proteolysis: a retinoid chemoprevention signal in normal, immortalized, and transformed human bronchial epithelial cells.

BACKGROUND Retinoids (derivatives of vitamin A) are reported to reduce the occurrence of some second primary cancers, including aerodigestive tract tumors. In contrast, beta-carotene does not reduce the occurrence of primary aerodigestive tract cancers. Mechanisms explaining these effective retinoid and ineffective carotenoid chemoprevention results are poorly defined. Recently, the all-trans-retinoic acid (RA)-induced proteolysis of cyclin D1 that leads to the arrest of cells in G1 phase of the cell cycle was described in human bronchial epithelial cells and is a promising candidate for such a mechanism. In this study, we have investigated this proteolysis as a common signal used by carotenoids or receptor-selective and receptor-nonselective retinoids. METHODS We treated cultured normal human bronchial epithelial cells, immortalized human bronchial epithelial cells (BEAS-2B), and transformed human bronchial epithelial cells (BEAS-2BNNK) with receptor-selective or receptor-nonselective retinoids or with carotenoids and studied the effects on cell proliferation by means of tritiated thymidine incorporation and on cyclin D1 expression by means of immunoblot analysis. We also examined whether calpain inhibitor I, an inhibitor of the 26S proteasome degradation pathway, affected the decline (i.e., proteolysis) of cyclin D1. RESULTS Receptor-nonselective retinoids were superior to the carotenoids studied in mediating the decline in cyclin D1 expression and in suppressing the growth of bronchial epithelial cells. Retinoids that activated retinoic acid receptor beta or retinoid X receptor pathways preferentially led to a decrease in the amount of cyclin D1 protein and a corresponding decline in growth. The retinoid-mediated degradation of cyclin D1 was blocked by cotreatment with calpain inhibitor I. CONCLUSIONS Retinoid-dependent cyclin D1 proteolysis is a common chemoprevention signal in normal and neoplastic human bronchial epithelial cells. In contrast, carotenoids did not affect cyclin D1 expression. Thus, the degradation of cyclin D1 is a candidate intermediate marker for effective retinoid-mediated cancer chemoprevention in the aerodigestive tract.
The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae)

The complete mitochondrial genome (mitogenome) of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae) was determined. The genome is a circular molecule 15 481 bp long. It presents a typical gene organization and order for completely sequenced lepidopteran mitogenomes, but differs from the insect ancestral type for the placement of tRNAMet. The nucleotide composition of the genome is also highly A + T biased, accounting for 80.38%, with a slightly positive AT skewness (0.010), indicating the occurrence of more As than Ts, as found in the Noctuoidea species. All protein-coding genes (PCGs) are initiated by ATN codons, except for COI, which is tentatively designated by the CGA codon as observed in other lepidopterans. Four of 13 PCGs harbor the incomplete termination codon, T or TA. All tRNAs have a typical clover-leaf structure of mitochondrial tRNAs, except for tRNASer(AGN), the DHU arm of which could not form a stable stem-loop structure. The intergenic spacer sequence between tRNASer(AGN) and ND1 also contains the ATACTAA motif, which is conserved across the Lepidoptera order. The H. cunea A+T-rich region of 357 bp is comprised of non-repetitive sequences, but harbors several features common to the Lepidoptera insects, including the motif ATAGA followed by an 18 bp poly-T stretch, a microsatellite-like (AT)8 element preceded by the ATTTA motif, an 11 bp poly-A present immediately upstream tRNAMet. The phylogenetic analyses support the view that the H. cunea is closerly related to the Lymantria dispar than Ochrogaster lunifer, and support the hypothesis that Noctuoidea (H. cunea, L. dispar, and O. lunifer) and Geometroidea (Phthonandria atrilineata) are monophyletic. However, in the phylogenetic trees based on mitogenome sequences among the lepidopteran superfamilies, Papillonoidea (Artogeia melete, Acraea issoria, and Coreana raphaelis) joined basally within the monophyly of Lepidoptera, which is different to the traditional classification.
Clinical research.

Coronary heart disease Carotid intima-media thickness by B-mode ultrasound as surrogate of coronary atherosclerosis: correlation with quantitative coronary angiography and coronary intravascular ultrasound findings Aims Although well supported by postmortem studies, the reliability of carotid atherosclerosis as surro-gate marker of coronary atherosclerosis has been put in doubt by in vivo studies showing a poor correlation between carotid intima-media thickness (IMT) detected by external carotid ultrasound (ECU) and coronary stenosis assessed by quantitative coronary angiography (QCA). In the present study, we have investigated whether a stronger in vivo correlation between the two arteries can be obtained by using homogeneous variables such as carotid and coronary IMT, detected by ECU and intravascular ultrasound (IVUS), respectively. Methods and results ECU, QCA, and IVUS measurements were made in 48 patients. Carotid IMT was correlated with both angiographic and IVUS findings. A significant but weak correlation was observed between ECU and QCA variables (r % 0.35, P , 0.05); the correlation between ECU and IVUS measurements of IMT was higher, with correlation coefficients ranging from 0.49 to 0.55. In patients with a QCA diagnosis of normal/intermediate coronary atherosclerosis, the presence of a carotid-IMT mean. 1 mm was associated with an 18-fold increase in risk of having a positive IVUS test (OR = 17.99, 95% CI 1.83–177.14, P = 0.013) and with a seven-fold increased risk of having a significant IVUS coronary stenosis (OR = 7.4, 95% CI 1.27–44.0, P = 0.028). Conclusion Carotid atherosclerosis correlates better with coronary atherosclerosis when both circulations are investigated by the same technique (ultrasound) using the same parameter (IMT). This supports the concept that carotid IMT is a good surrogate marker of coronary atherosclerosis.
Risk factors for sedentary behavior in young adults: similarities in the inequalities

Physical activity is a known protective factor, with benefits for both metabolic and psychological aspects of health. Our objective was to verify early and late determinants of physical activity in young adults. A total of 2063 individuals from a birth cohort in Ribeirão Preto, Brazil, were studied at the age of 23–25 years. Poisson regression was performed using three models: (1) early model considering birth weight, gestational age, maternal income, schooling and smoking; (2) late model considering individual’s gender, schooling, smoking and body mass index; and (3) combined (early + late) model. Physical activity was evaluated using the International Physical Activity Questionnaire, stratifying the individuals into active or sedentary. The general rate of sedentary behavior in the sample was 49.6%. In the early model, low birth weight (relative risk (RR) = 1.186, confidence interval (95%CI) 1.005–1.399) was a risk factor for sedentary activity. Female gender (RR = 1.379, 95%CI = 1.259–1.511) and poor schooling (RR = 1.126, 95%CI = 1.007–1.259) were associated with sedentary behavior in the late model. In the combined model, only female gender and participant’s schooling remained significant. An interaction between birth weight and individual’s schooling was found, in which sedentary behavior was more prevalent in individuals born with low birth weight only if they had higher educational levels. Variables of early development and social insertion in later life interact to determine an individual’s disposition to practice physical activities. This study may support the theoretical model ‘Similarities in the inequalities’, in which opposed perinatal backgrounds have the same impact over a health outcome in adulthood when facing unequal social achievement during the life-course.
To Snake or Not to Snake in the Planar Swift-Hohenberg Equation

We investigate the bifurcation structure of stationary localized patterns of the two-dimensional Swift–Hohenberg equation on an infinitely long cylinder and on the plane. On cylinders, we find localized roll, square, and stripe patches that exhibit snaking and nonsnaking behavior on the same bifurcation branch. Some of these patterns snake between four saddle-node limits; in this case, recent analytical results predict the existence of a rich bifurcation structure to asymmetric solutions, and we trace out these branches and the PDE spectra along these branches. On the plane, we study the bifurcation structure of fully localized roll structures, which are often referred to as worms. In all the above cases, we use geometric ideas and spatial-dynamics techniques to explain the phenomena that we encounter.
Adaptive Allocation of Attentional Gain

Humans are adept at distinguishing between stimuli that are very similar, an ability that is particularly crucial when the outcome is of serious consequence (e.g., for a surgeon or air-traffic controller). Traditionally, selective attention was thought to facilitate perception by increasing the gain of sensory neurons tuned to the defining features of a behaviorally relevant object (e.g., color, orientation, etc.). In contrast, recent mathematical models counterintuitively suggest that, in many cases, attentional gain should be applied to neurons that are tuned away from relevant features, especially when discriminating highly similar stimuli. Here we used psychophysical methods to critically evaluate these “ideal observer” models. The data demonstrate that attention enhances the gain of the most informative sensory neurons, even when these neurons are tuned away from the behaviorally relevant target feature. Moreover, the degree to which an individual adopted optimal attentional gain settings by the end of testing predicted success rates on a difficult visual discrimination task, as well as the amount of task improvement that occurred across repeated testing sessions (learning). Contrary to most traditional accounts, these observations suggest that the primary function of attentional gain is not to enhance the representation of target features per se, but instead to optimize performance on the current perceptual task. Additionally, individual differences in gain suggest that the operating characteristics of low-level attentional phenomena are not stable trait-like attributes and that variability in how attention is deployed may play an important role in determining perceptual abilities.