Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation cascade of £agellar expression in Gram-negative bacteria

Flagellar motility helps bacteria to reach the most favourable environments and to successfully compete with other micro-organisms. These complex organelles also play an important role in adhesion to substrates, biofilm formation and virulence process. In addition, because their synthesis and functioning are very expensive for the cell (about 2% of biosynthetic energy expenditure in Escherichia coli) and may induce a strong immune response in the host organism, the expression of flagellar genes is highly regulated by environmental conditions. In the past few years, many data have been published about the regulation of motility in polarly and laterally flagellated bacteria. However, the mechanism of motility control by environmental factors and by some regulatory proteins remains largely unknown. In this respect, recent experimental data suggest that the master regulatory protein-encoding genes at the first level of the cascade are the main target for many environmental factors. This mechanism might require DNA topology alterations of their regulatory regions. Finally, despite some differences the polar and lateral flagellar cascades share many functional similarities, including a similar hierarchical organisation of flagellar systems. The remarkable parallelism in the functional organisation of flagellar systems suggests an evolutionary conservation of regulatory mechanisms in Gram-negative bacteria. 7 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
Visual estimation of articulated motion using the expectation-constrained maximization algorithm

The estimation of articulated motion from light-intensity image sequences is a requirement for many important machine vision systems. Applications involving human subjects include video motion capture and automatic motion category recognition. This dissertation develops and experimentally verifies a new class of vision algorithms for this purpose. Subsequent to binary (foreground/background) segmentation, object pixels are incomplete in that they are not affiliated with the individual rigid-body components responsible for them. By viewing segmented images as incomplete data, a modified Expectation - Maximization (EM) procedure is introduced. as the basis of estimating articulated motion in an incremental (frame-to-frame) manner. A kinematic object model is projected atop the segmented image to define a suitable foreground mixture model. The Expectation step probabilistically associates (“completes”) foreground pixels with mixture components, and therefore model components. The Maximization step then updates model component inertial configurations so that their projections maximize a suitable objective defined over the completed foreground data. An extra processing step, based on virtual work static equilibrium conditions, integrates object kinematic structure into the EM procedure, guaranteeing the validity of computed estimates and completing the processing loop by linking the EM steps back to the kinematic model. This new procedure, called Expectation - Constrained Maximization (ECM), is uniquely practical because it provides estimates of general motion descriptions (e.g. joint angel vector sequences) from commonly available image information (approximate foreground/background images). In particular, the algorithm does not depend upon regular geometric primitives or image flow, neither of which are currently guaranteed to have the necessary fidelity outside the laboratory. Although single-observer foreground-background information is not always sufficient, the ECM framework is directly extensible by multiple observers and/or additional image information in cases where they are necessary and available. An experimental evaluation is conducted for human bipedal motion, chosen due to its importance, representativeness, and accessability to single viewpoint image data. Results from ten test sequences show average precisions of about +/–. 05 Rad. (orientation) and +/–. 5 cm. (position). Degredation in input data primarily magnifies the worst errors, only modestly affecting overall average precision.
BIN1 protein loss in Alzheimer’s disease promotes synaptic tau accumulation and disrupts tau release

Citation for published version (APA): Glennon, E. B. C. , Lau, H. W. D. , Gabriele, R. M. C. , Taylor, M. , Troakes, C. , Opie-Martin, S. , Elliott, C. L. , Killick, R. , Hanger, D. P., Gomez Perez-Nievas, B. , & Noble, W. J. (2020). Loss of BIN1 protein in Alzheimer’s disease promotes synaptic accumulation of phosphorylated tau and disrupts tau release: Tau-directed effects of BIN1 loss in AD. Brain Communications, 2(1):fcaa011. https://doi.org/10.1093/braincomms/fcaa011
Identification of Key Residues in the Amino-terminal Third of Human Interleukin- LX*

Two mutational approaches were used to perform a thorough structure-function analysis of the first 63 residues of the 159-residue cytokine human interleukin-la (hIL-la). In this study, a total of 26 deletions, 97 multiple amino acid substitutions, and 46 single amino acid substitutions were examined. A synthetic hIL-la gene with many unique restriction sites was constructed to facilitate the molecular manipulations that were performed. The mutational methods employed include: Bal-31 exonuclease-generated deletions at unique restriction sites and combinatorial cassette mutagenesis via segment replacement with synthetic DNA. The mutant hIL-la proteins were expressed at high levels in Escherichia coli and were assayed for biological activity in a mouse T cell proliferation assay. We observed that the activity of hIL-la was extraordinarily sensitive to deletion mutations. Most internal deletions of as few as 1 or 2 residues substantially reduced biological activity. Combinatorial cassette mutagenesis on residues 13-53 of hIL-la identified 16 important residue positions. Of these, 8 displayed strong preferences for residues with hydrophilic side chains, and the remainder preferred hydrophobic side chains. We found that functional hIL-la had an absolute requirement for a basic residue (Arg, Lys, or His) at either position 15 or 16, and that Leu was preferred at position 40.
HIV_A_317117 813..822

1Department of Health Information Technology, Hawassa College of Health Sciences, Hawassa, Ethiopia; 2Harvard Graduate School of Arts and Science, Boston, MA, 02138, USA Background: Human immune deficiency virus (HIV) remains one of the leading causes of infectious disease mortality and morbidity in Sub-Saharan Africa. Although remarkable progress has been made in prevention and treatment of HIV, there is a higher rate of loss to follow-up in HIV-infected children than in adults, once they enter care. Objective: To determine the incidence and identify predictors of loss to follow-up among HIV-infected children on anti-retroviral treatment in Sidama Zone, Ethiopia. Methods: A retrospective cohort study was done among children that were enrolled in ART care in Sidama Zone from September 2014 to August 2018. A total of 143 eligible children were included in this study. A structured checklist was used to extract data from patients’ medical records such as patient intake forms, electronic database, and registers. Data were entered, cleaned, coded, and analyzed by STATA version 12. Cox proportional hazards models were fitted to investigate predictors of loss to follow-up. Results: Of the 143 participants, 76 (53.15%) were female children with a median age of 7 years and interquartile range of 4–9. The incidence rate was 5 per 100 person-years and the cumulative incidence 12.59%. The median follow-up time was 2.46 years and the total time at risk was 356.06 person-years. Furthermore, 55.56% and 72.22% of those lost to follow-up were within the first and the second years of follow-up, respectively. In multivariable Cox proportional model, only the TB status of the children was significantly associated with loss to follow-up with hazard ratio 3.348 [1.174831, 9.543494] and p-value of 0.024. Conclusion: In this study, TB status of children was the significant determinant of loss to follow-up. However, the overall retention was 87.4% and a substantially higher proportion of loss was observed within the first and second years of follow-up.
QuadricSLAM: Constrained Dual Quadrics from Object Detections as Landmarks in Object-oriented SLAM

—In this paper, we use 2D object detections from multiple views to simultaneously estimate a 3D quadric surface for each object and localize the camera position. We derive a SLAM formulation that uses dual quadrics as 3D landmark representations, exploiting their ability to compactly represent the size, position and orientation of an object, and show how 2D object detections can directly constrain the quadric parameters via a novel geometric error formulation. We develop a sensor model for object detectors that addresses the challenge of partially visible objects
Design of a Low Cost EEG Headset for Educational Research

Electroencephalography signals are used widely in medical and pedagogical research because they quantitatively and non-invasively reflect brain activity. However, commercially available EEG devices are often either prohibitively expensive, or do not offer the correct capabilities such as enough electrodes. This work-in-progress study aims to address this gap through the design of a low-cost, easy-to-use, and effective EEG headset for engineering educational research studies. The current study includes a relatively small sample size (N=6); however, it does identify some preliminary trends. For example, although most participants found the authors’ current design to be more comfortable than commercially available designs, the design also had a much larger range of reported comfort levels. Additionally, no distinct conclusion could be drawn from the signal quality comparison between the current design and the commercial device due to limited sample size and large variation among collected data. This exploratory study provides a framework for future studies when more data could be collected. There is potential for such a device to provide insight into learner behavior in the remote learning environment due to its lower cost, light weight, and small size.
University of Dundee Sterol 14-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana Mwenechanya,

Amphotericin B has emerged as the therapy of choice for use against the leishmaniases. Administration of the drug in its liposomal formulation as a single injection is being promoted in a campaign to bring the leishmaniases under control. Understanding the risks and mechanisms of resistance is therefore of great importance. Here we select amphotericin B-resistant Leishmania mexicana parasites with relative ease. Metabolomic analysis demonstrated that ergosterol, the sterol known to bind the drug, is prevalent in wild-type cells, but diminished in the resistant line, where alternative sterols become prevalent. This indicates that the resistance phenotype is related to loss of drug binding. Comparing sequences of the parasites’ genomes revealed a plethora of single nucleotide polymorphisms that distinguish wild-type and resistant cells, but only one of these was found to be homozygous and associated with a gene encoding an enzyme in the sterol biosynthetic pathway, sterol 14α-demethylase (CYP51). The mutation, N176I, is found outside of the enzyme’s active site, consistent with the fact that the resistant line continues to produce the enzyme’s product. Expression of wild-type sterol 14α-demethylase in the resistant cells caused reversion to drug sensitivity and a restoration of ergosterol synthesis, showing that the mutation is indeed responsible for resistance. The amphotericin B resistant parasites become hypersensitive to pentamidine and also agents that induce oxidative stress. This work reveals the power of combining polyomics approaches, to discover the mechanism underlying drug resistance as well as offering novel insights into the selection of resistance to amphotericin B itself. PLOS Neglected Tropical Diseases | https://doi.org/10.1371/journal.pntd. 0005649 June 16, 2017 1 / 21 a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPENACCESS Citation: Mwenechanya R, Kovářová J, Dickens NJ, Mudaliar M, Herzyk P, Vincent IM, et al. (2017) Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana. PLoS Negl Trop Dis 11(6): e0005649. https://doi. org/10.1371/journal.pntd. 0005649 Editor: Jayne Raper, Hunter College, CUNY, UNITED STATES Received: January 11, 2017 Accepted: May 18, 2017 Published: June 16, 2017 Copyright: © 2017 Mwenechanya et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: The Wellcome Trust (https://wellcome.ac. uk/) funded MB through awards 104111/Z/14/Z and 105614/Z/14/Z. The European Commission (http://ec.europa.eu/research/index.cfm) funded TKS through award number 602773 and JK through award number 290080. The National Institutes of Health (https://www.nih.gov/) funded GIL though award number GM067871. The
Durenkamp, Mark and Pawlett, Mark and Ritz, Karl and Harris, Jim A. and Neal, Andrew L. and McGrath, Steve P. (2016) Nanoparticles within WWTP sludges have minimal impact on leachate quality and soil microbial community

One of the main pathways by which engineered nanoparticles (ENPs) enter the environment is through land application of waste water treatment plant (WWTP) sewage sludges. WWTP sludges, enriched with Ag and ZnO ENPs or their corresponding soluble metal salts during anaerobic digestion and subsequently mixed with soil (targeting a final concentration of 1400 and 140 mg/kg for Zn and Ag, respectively), were subjected to 6 months of ageing and leaching in lysimeter columns outdoors. Amounts of Zn and Ag leached were very low, accounting for <0.3% and <1.4% of the total Zn and Ag, respectively. No differences in total leaching rates were observed between treatments of Zn or Ag originally input to WWTP as ENP or salt forms. Phospholipid fatty acid profiling indicated a reduction in the fungal component of the soil microbial community upon metal exposure. However, overall, the leachate composition and response of the soil microbial community following addition of sewage sludge enriched either with ENPs or metal salts was very similar. © 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Deficient in NgoMI Restriction and Modification

We have cloned from Neisseria gonorrhoeae MS11 the gene encoding a methylase that modifies the sequence GCCGGC. The corresponding restriction enzyme was also encoded by this clone. Sequence analysis demonstrated that the methylase shares sequence similarities with other cytosine methylases, but the sequence organization of M.NgoMI is different from that seen for other cytosine methylases. A deletion was introduced into the chromosome of N. gonorrhoeae MS11 to produce strain MUG701, a strain that is inactivated in both the methylase and the restriction genes. Although this strain no longer methylated its DNA at the NgoMI recognition sequence, cells were viable and had no other significant phenotypic changes. Transformation data indicated that MSII does not produce enough restriction activity to block plasmid transformation in the gonococcus, even though restriction activity could be demonstrated in E. coli containing the cloned gene.
Spherical harmonic Lattice Sums for Gratings

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Spherical harmonic Lattice Sums for Gratings Brian Stout
Dynamic stall experiments on the NACA 0012 airfoil

The flow over a NACA 0012 airfoil undergoing large oscillations in pitch was experimentally studied at a Reynolds number of and over a range of frequencies and amplitudes. Hot-wire probes and surface-pressure transducers were used to clarify the role of the laminar separation bubble, to delineate the growth and shedding of the stall vortex, and to quantify the resultant aerodynamic loads. In addition to the pressure distributions and normal force and pitching moment data that have often been obtained in previous investigations, estimates of the unsteady drag force during dynamic stall have been derived from the surface pressure measurements. Special characteristics of the pressure response, which are symptomatic of the occurrence and relative severity of moment stall, have also been examined.
Preposition Selection Outside the Lexicon

1. Semantically Motivated Preposition Selection How do verbs and other predicators semantically select prepositions to head their complement PPs? 1 Some preposition selection is essentially idiosyncratic, as shown by comparing semantically similar verbs like charge vs. blame vs. accuse: charge NP WITH NP, blame NP FOR NP, accuse NP OF NP . Such verbs select their prepositions via simple lexical specifications within their complement selection features:2
Penrose limit of AdS(3) X S(3) X S(3) X S(1) and its associated sigma model

We study the Penrose limit of a supersymmetric IIB background, with non-trivial NS 3-form field strength, obtaining a solution with the smallest number of supercharges (i.e. 16) allowed; we write down explicitly the superalgebra of the theory, build the supersymmetric associated IIB string sigma model and make conjectures on the dual gauge theory.
Observations of H1426+428 with HEGRA

The HEGRA system of imaging air Cherenkov telescopes has been used to observe the BL Lac object H1426 +428 (z = 0.129) for 217.5 hours in 2002. In this data set alone, the source is detected at a confidence level of 5 . 3 σ, confirming this object as a TeV source. The overall flux level during the observations in 2002 is found to be a factor of ≈2.5 lower than during the previous observations by HEGRA in 1999 and 2000. A new spectral analysis has been carried out, improving the signal-to-noise ratio at the expense of a slightly increased systematic uncertainty and reducing the relative energy resolution to ∆E/E ≤ 12% over a wide range of energies. The new method has also been applied to the previously published data set taken in 1999 and 2000, confirming the earlier claim of a flattening of the energy spectrum between 1 and 5 TeV. The data set taken in 2002 shows again a signal at energies above 1 TeV. We combine the energy spectra as determined by the CAT and VERITAS groups with our reanalyzed result of the 1999 and 2000 data set and apply a correction to account for e ffects of absorption of high energy photons on extragalactic background light in the optical to mid infrared band. The shape of the inferred source spectrum is mostly sensitive to the characteristics of the extragalactic background light between wavelengths of 1 and 15 μm.
A correction model for variation of distortion within the photographic field

For the attainment of the highest accuracies in close-range industrial photogrammetry it is necessary to account for the variation of radial distortion within the photographic field, especially for large-format lenses. In this paper an empirical correction model is introduced which overcomes serious shortcomings in the traditionally applied geometric correction approach. The new model has been tested with success on a number of medium- and wide-angle, large-format lenses. The results of sample tests are presented, and the effectiveness and practicability of the empirical approach are discussed.
Cell Proliferation and Promoting Action in Skin Carcinogenesis1

The changes induced in the thickness, number of nu cleated cell layers, and mitotic index of mouse interfollicular epidermis by various doses of ethylphenylpropiolate (EPP) or turpentine were measured and their promoting activity was tested. Doses of EPP or turpentine able to induce marked cell proliferation and hyperplasia of the epidermis were found to have minimal or no promoting activity. Experiments in which EPP or turpentine were applied to mouse skin [weekly after four weekly applica tions of a promoting dose of 12-0-tetradecanoyl-phorbol13-acetate (TPA) or weekly 72 hr after treatment with TPA] show that, contrary to what would be expected if a summation of the effects of the promoter and the hyperplastic agents took place, EPP and turpentine have an inhibi tory effect on the promoting activity of TPA. These find ings show that induction of cell proliferation and hyper plasia of the epidermis is not sufficient to ensure skin tumor promotion or the growth of the tumor cells into clin ical neoplasms and suggest that cellular events other than cell proliferation are required to enable the expression of neoplastic transformation. A comparative study of the time sequence of the early histolÃ3gica! changes induced in mouse interfollicular epider mis by turpentine, cantharidin, and a nonpromoting dose of TPA shows that, after treatment with a nonpromoting dose of these agents, the increase in the number of nucleated cell layers of interfollicular epidermis occurs only after the increase in the mitotic index, comparable to that observed with EPP. The time sequence of these changes is clearly different from that observed after treatment with a promot ing dose of TPA, in which the increase in number of nucleated cell layers precedes the increase in mitotic index. It suggests that stimulation of cells of the upper layers of the epidermis and reversal of their differentiation induced by a promoting dose of TPA is not induced by these nonpromot ing agents, and indicates that basic differences exist between the cellular reprogramming induced by promoting and nonpromoting agents.
The influence of the equatorial QBO on the Northern hemisphere winter circulation of a GCM

The influence of a simulated equatorial quasi-biennial oscillation (QBO) on the Northern Hemisphere winter was studied by analyzing output data from a general circulation model (GCM). The differences between the 7-50 hPa equatorial QBO phases of the January March (JFM) averaged zonal wind composite exhibit a weaker polar-night jet during the easterly phase of the equatorial QBO and a stronger polar-night jet in the westerly phase. The Eliassen-Palm flux of planetary waves is stronger and more convergent in the high latitude stratosphere for the easterly phase, while it exhibits similar characteristics in the mid latitude stratosphere during the westerly phase. These results are nearly consistent with observed results. Zonal wind deceleration anomalies are located slightly north of the zonal wind anomalies. It is likely that the JFM time-mean zonal wind anomalies develop from the small zonal wind anomalies during the early winter and propagate northward with time. The anomaly pattern in the troposphere coupled with that in the stratosphere reveals a tripole structure among equatorial, middle, and high latitudes, similar to the North Atlantic oscillation (NAO) pattern.