Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of the Cobalt/Nickel Efflux Operon dmeRF in Agrobacterium tumefaciens and a Link between the Iron-Sensing Regulator RirA and Cobalt/Nickel Resistance

ABSTRACT The Agrobacterium tumefaciens C58 genome harbors an operon containing the dmeR (Atu0890) and dmeF (Atu0891) genes, which encode a transcriptional regulatory protein belonging to the RcnR/CsoR family and a metal efflux protein belonging to the cation diffusion facilitator (CDF) family, respectively. The dmeRF operon is specifically induced by cobalt and nickel, with cobalt being the more potent inducer. Promoter-lacZ transcriptional fusion, an electrophoretic mobility shift assay, and DNase I footprinting assays revealed that DmeR represses dmeRF transcription through direct binding to the promoter region upstream of dmeR. A strain lacking dmeF showed increased accumulation of intracellular cobalt and nickel and exhibited hypersensitivity to these metals; however, this strain displayed full virulence, comparable to that of the wild-type strain, when infecting a Nicotiana benthamiana plant model under the tested conditions. Cobalt, but not nickel, increased the expression of many iron-responsive genes and reduced the induction of the SoxR-regulated gene sodBII. Furthermore, control of iron homeostasis via RirA is important for the ability of A. tumefaciens to cope with cobalt and nickel toxicity. IMPORTANCE The molecular mechanism of the regulation of dmeRF transcription by DmeR was demonstrated. This work provides evidence of a direct interaction of apo-DmeR with the corresponding DNA operator site in vitro. The recognition site for apo-DmeR consists of 10-bp AT-rich inverted repeats separated by six C bases (5′-ATATAGTATACCCCCCTATAGTATAT-3′). Cobalt and nickel cause DmeR to dissociate from the dmeRF promoter, which leads to expression of the metal efflux gene dmeF. This work also revealed a connection between iron homeostasis and cobalt/nickel resistance in A. tumefaciens.
Motion initiated music ensemble with sensors for motor rehabilitation

Advances in inertial sensors technology used in smartwatches make it possible for movement-based therapies to be both therapeutic and evaluative at the same time. Therapeutic Instrumental Music Performance (TIMP) uses instrument playing for motor rehabilitation. However, applications of TIMP are not generalizable to a variety of motor disabilities and do not often consider the benefits of social interaction. To address the missing opportunities and potential strengths of an integrated technological and therapeutic application, we introduce MIMES (Motion Initiated Music Ensemble with Sensors). MIMES uses commercially available smartwatches and hand gesture recognition techniques to trigger instrumental sounds with simple hand gestures and support multiple users. We developed this system to provide rehabilitation programs and music therapy for a variety of individuals with motor impairments to improve both physical and mental health outcomes. We discuss MIMES system architecture, gesture recognition algorithm, future experimental design and a self-evaluation module to test the efficacy of the technology for rehabilitation.
Meeting Report on the ASM Conference on Mechanisms of Interbacterial Cooperation and Competition

ABSTRACT The American Society for Microbiology Conference on Mechanisms of Interbacterial Cooperation and Competition was held in Washington, DC, from 1 to 4 March 2017. The conference provided an international forum for sociomicrobiologists from different disciplines to present and discuss new findings. The meeting covered a wide range of topics, spanning molecular mechanisms, ecology, evolution, computation, and manipulation of interbacterial interactions, and encompassed social communities in medicine, the natural environment, and industry. This report summarizes the presentations and emerging themes.
Oxidative Stress Markers and Metal Ions are Correlated With Cognitive Function in Alzheimer’s Disease

We investigated oxidative stress markers and metal ions in patients with Alzheimer’s disease (AD). The serum levels of ceruloplasmin (CER), C-reactive protein (CRP), uric acid (UA), homocysteine (Hcy), copper, iron, and zinc were determined in 125 patients with AD (mild, n = 2 8; moderate, n = 42; and severe, n = 55) and 40 healthy control (HC) participants. Compared to HC, CER and UA levels were significantly lower in moderate and severe AD groups, whereas CRP and Hcy levels were significantly higher in the severe AD group. Copper level was significantly higher in moderate and severe AD groups than the other groups. Compared to HC, iron level was significantly higher in patients with AD, whereas zinc level was significantly lower in patients with AD. In patients with AD, the severity of cognitive impairment was positively correlated with CER, UA, and zinc levels, whereas it was negatively correlated with copper level. Taken together, our findings provide a novel approach to assess AD progression.
How Interpersonal Coordination Affects Individual Behavior (and Vice Versa): Experimental Analysis and Adaptive HKB Model of Social Memory

ABSTRACT How one behaves after interacting with a friend may not be the same as before the interaction. The present study investigated which spontaneous coordination patterns formed between 2 persons and whether a remnant of the interaction remained (“social memory”). Pairs of people sat face-to-face and continuously flexed index fingers while vision between partners was manipulated to allow or prevent information exchange. Trials consisted of 3 successive 20-s intervals: without vision, with vision, and again without vision. Steady, transient, or absent phase coupling was observed during vision. In support of social memory, participants tended to remain near each other's movement frequency after the interaction ended. Furthermore, the greater the stability of interpersonal coordination, the more similar partners' postinteractional frequencies became. Proposing that social memory resulted from prior frequency adaptation, a model based on Haken–Kelso–Bunz (HKB) oscillators reproduced the experimental findings, even for patterns observed on individual trials. Parametric manipulations revealed multiple routes to social memory through the interplay of adaptation and other model parameters. The experimental results, model, and interpretation motivate potential future research and therapeutic applications.
Stiffness and Damage Identification with Model Reduction Technique

For structural health monitoring, it is impractical to use full measurement to identify the unknown parameters. When one attempts to retrieve second-order parameters from the identified state space model, various methodologies impose different restrictions on the number of sensors and actuators employed, assuming that all the modes of the structure can be successfully identified. This paper explores the possibility of performing this inverse vibration problem without minimal restriction on the number of the measurements. Based on the numerical analysis of measured response due to known excitation, structural parameters such as stiffness values are identified and compared with the intended design values for damage detection. The proposed methodology is based on the Eigensystem Realization Algorithm (ERA) and the Observer/Kalman Filter Identification (OKID) approach to identify a first-order state space model. The first-order model is then transformed into a second-order model in order to evaluate the system stiffness. The focus is on estimation of all stiffness values from the condensed stiffness matrices by model reduction making use of System Equivalent Reduction Expansion Process (SEREP). The required optimization is accomplished by the Genetic Algorithm (GA). The efficiency of the proposed technique is shown by numerical examples for multi-storey shear building subjected to random excitation, taking into consideration the effects of noisy data. The results indicate that the proposed methodology offers reasonably accurate identification in terms of locating and quantifying damage.
Grazing Incidence Small Angle X-Ray Scattering as a Tool for In- Situ Time-Resolved Studies

With the advent of third-generation synchrotron sources and the development of fast two-dimensional X-ray detectors, X-ray scattering has become an invaluable tool for insitu time-resolved experiments. In the case of thin films, grazing incidence small angle X-ray scattering (GISAXS) constitutes a powerful technique to extract morphological information not only of the thin film surface but also of buried structures with statistical relevance. Thus, recently in-situ GISAXS experiments with subsecond time resolution have enabled investigating the self-assembly processes during vacuum deposition of metallic and organic thin films as well as the structural changes of polymer and colloidal thin films in the course of wet deposition. Moreover, processing of thin films has also been investigated in-situ employing GISAXS. In this chapter, we review the current trends of time-resolved GISAXS studies. After an introduction to the GISAXS techni‐ que, we present exemplary results of metallic and organic thin film preparation, wet deposition of polymer thin films and self-assembly of colloidal thin films, as well as examples of thin film modification in, e.g., microfluidic channels and within working devices. Finally, an overview of the future perspectives in the field is provided.
A pr 2 01 9 Anisotropic upper critical field of pristine and proton-irradiated single crystals of the magnetically ordered superconductor

M. P. Smylie, 2, ∗ A. E. Koshelev, K. Willa, 3 R. Willa, 4 W. -K. Kwok, J.-K. Bao, D. Y. Chung, M. G. Kanatzidis, 5 J. Singleton, F. F. Balakirev, H. Hebbeker, P. Niraula, E. Bokari, A. Kayani, and U. Welp Materials Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439 Department of Physics and Astronomy, Hofstra University, Hempstead, New York 11549 Institute for Solid-State Physics, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany Institute for Theory of Condensed Matter, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, USA National High Magnetic Field Laboratory, Los Alamos National Laboratory, MS-E536, Los Alamos, New Mexico 87545 Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008 (Dated: April 17, 2019)
Height dependent TOA ranging error model for near ground localization applications

Near ground localization is a special type of localization scenario that is widely considered in both academic and industry. A proper way to describe time-of-arrival (TOA) ranging error for near ground localization applications has been in a strong demand since early 2010s. In this paper, we proposed a mathematical model for near ground TOA ranging error based on empirical measurement. According to investigation and analysis on the empirical data, the TOA ranging error can be modeled as a Gaussian random variable and its mean and variance depends on both the antenna height and the distance between reference node and target node. To further emphasize the value of this model, Cramer-Rao Lower Bound for two dimensional (2D) near ground localization has been calculate using the proposed error model as a typical case study. It is shown that the near ground TOA ranging error model is essential for algorithm design and system performance evaluation.
A note on the expected value of the Rand index

Two expectations of the adjusted Rand index (ARI) are compared. It is shown that the expectation derived by Morey and Agresti (1984, Educational and Psychological Measurement, 44, 33) under the multinomial distribution to approximate the exact expectation from the hypergeometric distribution (Hubert & Arabie, 1985, Journal of Classification, 2, 193) provides a poor approximation, and, in some cases, the difference between the two expectations can increase with the sample size. Proofs concerning the minimum and maximum difference between the two expectations are provided, and it is shown through simulation that the ARI can differ significantly depending on which expectation is used. Furthermore, when compared in a hypothesis testing framework, multinomial approximation overly favours the null hypothesis.
1 0 M ay 2 01 8 Dust modification of the plasma conductivity in the mesosphere

Relative transverse drift (with respect to the ambient magnetic field) between the weakly magnetized electrons and the unmagnetized ions at the lower altitude (< 80 km) and between the weakly magnetized ions and unmagnetized dust at the higher altitude (< 90 km) gives rise to the finite Hall conductivity in the Earthś mesosphere. If, on the other hand, the number of free electrons is sparse in the mesosphere and most of the negative charge resides on the weakly magnetized, fine, nanometre sized dust powder and positive charge on the more massive, micron sized, unmagnetized dust, the sign of the Hall conductivity due to their relative transverse drift will be opposite to the previous case. Thus the sign of the Hall effect not only depends on the direction of the local magnetic field but also on the nature of the charge carrier in the partially ionized dusty medium. As the Hall and the Ohm diffusion are comparable below 80 km, the low frequency (∼ 10 − 10 s) long wavelength (∼ 10 − 10 km) waves will be damped at this altitude with the damping rate typically of the order of few minutes. Therefore, the ultra–low frequency magnetohydrodynamic waves can not originate below 80 km in the mesosphere. However, above 80 km since Hall effect dominates Ohm diffusion the mesosphere can host the ultra–low frequency waves which can propagate across the ionosphere ∗Corresponding author Email addresses: birendra.pandey@mq.edu. au (B.P. Pandey), sergey.vladimirov@sydney.edu. au (S.V. Vladimirov) Preprint submitted to JATP May 11, 2018 with little or, no damping.
Blind Deconvolution by a Steepest Descent Algorithm on a Quotient Manifold

In this paper, we propose a Riemannian steepest descent method for solving a blind deconvolution problem. We prove that the proposed algorithm with an appropriate initialization will recover the exact solution with high probability when the number of measurements is, up to log-factors, the information-theoretical minimum scaling. The quotient structure in our formulation yields a simpler penalty term in the cost function compared to [LLSW16], which eases the convergence analysis and yields a natural implementation. Empirically, the proposed algorithm has better performance than the Wirtinger gradient descent algorithm and an alternating minimization algorithm in the sense that i) it needs fewer operations, such as DFTs and matrix-vector multiplications, to reach a similar accuracy, and ii) it has a higher probability of successful recovery in synthetic tests. An image deblurring problem is also used to demonstrate the efficiency and effectiveness of the proposed algorithm.
Performance of an in situ activated carbon treatment to reduce PCB availability in an active harbor

In situ amendment of surface sediment with activated carbon is a promising technique for reducing the availability of hydrophobic organic compounds in surface sediment. The present study evaluated the performance of a logistically challenging activated carbon placement in a high‐energy hydrodynamic environment adjacent to and beneath a pier in an active military harbor. Measurements conducted preamendment and 10, 21, and 33 months (mo) postamendment using in situ exposures of benthic invertebrates and passive samplers indicated that the targeted 4% (by weight) addition of activated carbon (particle diameter ≤74 µm) in the uppermost 10 cm of surface sediment reduced polychlorinated biphenyl availability by an average (± standard deviation) of 81 ± 11% in the first 10 mo after amendment. The final monitoring event (33 mo after amendment) indicated an approximate 90 ± 6% reduction in availability, reflecting a slight increase in performance and showing the stability of the amendment. Benthic invertebrate census and sediment profile imagery did not indicate significant differences in benthic community ecological metrics among the preamendment and 3 postamendment monitoring events, supporting existing scientific literature that this approximate activated carbon dosage level does not significantly impair native benthic invertebrate communities. Recommendations for optimizing typical site‐specific assessments of activated carbon performance are also discussed and include quantifying reductions in availability and confirming placement of activated carbon. Environ Toxicol Chem 2018;37:1767–1777. Published 2018 Wiley Periodicals, Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
A DIFFERENTIAL GEOMETRIC APPROACH FOR VISUAL NAVIGATION IN INDOOR SCENES

Visual perception of the environment provides a detailed scene representation which contributes to improve motion planning and obstacle avoidance navigation for wheelchairs in non-structured indoor scenes. In this work we develop a mobile representation of the scene based on perspective maps for the automatic navigation in absence of previous information about the scene. Images are captured with a passive low-cost video camera. The main feature for visual navigation in this work is a map of quadrilaterals with apparent motion. From this mobile map, perspective maps are updated following hierarchical grouping in quadrilaterals maps given by pencils of perspective lines through vanishing points. Egomotion is interpreted in terms of maps of mobile quadrilaterals. The main contributions of this paper are the introduction of Lie expansion/contraction operators for quadrilateral/cuboid and the adaptation of Kalman filtering for moving quadrilaterals to estimate and predict the egomotion of a mobile platform. Our approach is enough modular and flexible for adapting to indoor and outdoor scenes provided at least four homologue cuboids be present in the scene between each pair of sampled views of a video sequence.
ORGANIZATIONAL CULTURE IN U . S . CONSTRUCTION COMPANIES

Organizational culture has gained importance in the increasingly internationalized and globalized construction business. The dynamics of the construction business have become more dependent than ever on the cultural characteristics of construction companies. It has become clear that sustained profitability and high financial returns are not enough to survive and remain successful in highly competitive markets because there is considerable evidence of conflicts and misunderstandings caused by cultural differences. Consequently, firms need to understand their own and other firms’ organizational culture and need to adjust their ways and traditions while conducting business with other firms, organizations or individuals with different cultural values. Although there is a substantial amount of research demonstrating the importance of cultural issues in the construction industry, the divergence between countries is yet to be explored. This study is a part of an international project initiated by CIB’s TG23 (TaskGroup 23 of the International Council for Research and Innovation in Building and Construction), and aims to investigate the cultural features of U.S. construction companies. Data are collected by means of a questionnaire based on OCAI (Organizational Culture Assessment Instrument), a well-known and widely used measurement tool developed by Cameron and Quinn. The survey is administered to the top 400 contractors listed by Engineering News-Record.
Determinants of working until retirement compared to a transition to early retirement among older workers with and without chronic diseases: Results from a Dutch prospective cohort study

Aim: The ageing society and recent policy changes may lead to an increase of older workers with chronic diseases in the workforce. To date, it is unclear whether workers with chronic diseases have specific needs while employed. The aim of this study is to explore the differences in determinants of working until retirement compared to a reference group who have transitioned to early retirement among workers with and without chronic diseases. Methods: Dutch workers aged 57–62 years (n = 2445) were selected from an existing prospective cohort study, ‘STREAM’. The potential determinants were categorized into: individual, health, work-related and social factors. Logistic regression analyses were performed to determine the associations between these determinants and working until retirement – once for workers with and once for those without chronic diseases. To test differences, we included an interaction term between the determinant and the covariate ‘having a chronic disease yes/no’ in the analyses of the total population. Results: In total, 1652 (68%) persons were employed from 2011 to 2013. The majority of the determinants appeared to be similar for workers with or without a chronic disease; the interaction terms for these determinants and the covariate ‘having a chronic disease’ showed a p-value higher than 0.05, except for one individual factor (i.e. mastery) and one work-related factor (i.e. autonomy), which showed a p-value below 0.05. Higher mastery and higher autonomy were statistically significantly associated with working until retirement for those with chronic diseases, whereas they were not for those without chronic diseases. Conclusions: Differences between workers with and without chronic diseases may exist for working until a statutory retirement age. Interventions aimed at encouraging work participation of older workers should make a distinction between the two groups. Autonomy at work and mastery were found to be factors that may promote work participation until higher age, specifically for older workers with chronic diseases.
Reduced selective learning in patients with fibromyalgia vs healthy controls

Abstract Impaired selective fear learning has been advanced as a core mechanism involved in excessive spreading of protective responses such as pain-related fear and avoidance leading to disability in chronic pain conditions. Using the litmus test for selective learning effects, the blocking procedure, we tested the hypothesis that patients with fibromyalgia (FM) show less selective threat learning than healthy controls (HCs). We introduce a novel selective learning task based around a clinical diary scenario. On a trial-by-trial basis, participants rated whether they expected certain situations (A, B, Z, and X) in the diary of a fictive FM patient would trigger pain in that patient. The procedure did not involve any experimental pain induction because the verbal outcomes “pain” or “no pain” were used. During the elemental acquisition phase, one situation was followed by “pain” (A+, eg, “Kim slept badly, and reports pain”), whereas another situation was followed by “no pain” (Z−, eg, “Kim was stressed, and reports no pain”). During the compound acquisition phase, another situation (X), referred to as the blocked stimulus, was presented in compound with a previously pain-eliciting situation and also paired with “pain” (AX+, eg, Kim slept badly” and “Kim has vacuumed,” and reports pain). Simultaneously, a novel situation was introduced and also followed by “pain” (B+). Within-group comparisons showed blocking (ie, significant difference between B and X) in the HCs, but not in the patients with FM. This study is the first in directly assessing differences in selective learning between patients with FM and HCs using a blocking procedure.