cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Molybdopterin biosynthesis pathway contributes to the regulation of SaeRS two-component system by ClpP in Staphylococcus aureus
Creators: name: Zhao, Na
name: Wang, Yanan
name: Liu, Junlan
name: Yang, Ziyu
name: Jian, Ying
name: Wang, Hua
name: Ahmed, Mahmoud
name: Li, Min
name: Bae, Taeok
name: Liu, Qian
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: In Staphylococcus aureus, the SaeRS two-component system is essential for the bacterium’s hemolytic activity and virulence. The Newman strain of S. aureus contains a variant of SaeS sensor kinase, SaeS L18P. Previously, we showed that, in the strain Newman, SaeS L18P is degraded by the membrane-bound protease FtsH. Intriguingly, the knockout mutation of clpP, encoding the cytoplasmic protease ClpP, greatly reduces the expression of SaeS L18P. Here, we report that, in the strain Newman, the positive regulatory role of ClpP on the SaeS L18P expression is due to its destabilizing effect on FtsH and degradation of MoeA, a molybdopterin biosynthesis protein. Although the transcription of ftsH was not affected by ClpP, the expression level of FtsH was increased in the clpP mutant. The destabilizing effect appears to be indirect because ClpXP did not directly degrade FtsH in an in vitro assay. Through transposon mutagenesis, we found out that the moeA gene, encoding the molybdopterin biosynthesis protein A, suppresses the hemolytic activity of S. aureus along with the transcription and expression of SaeS L18P. In a proteolysis assay, ClpXP directly degraded MoeA, demonstrating that MoeA is a substrate of the protease. In a murine bloodstream infection model, the moeA mutant displayed reduced virulence and lower survival compared with the WT strain. Based on these results, we concluded that ClpP positively controls the expression of SaeS L18P in an FtsH and MoeA-dependent manner, and the physiological role of MoeA outweighs its suppressive effect on the SaeRS TCS during infection.
KiDS-450: Tomographic Cross-Correlation of Galaxy Shear with {\it Planck} Lensing
Creators: name: Harnois-Déraps, Joachim
name: Tröster, Tilman
name: Chisari, Nora Elisa
name: Heymans, Catherine
name: van Waerbeke, Ludovic
name: Asgari, Marika
name: Bilicki, Maciej
name: Choi, Ami
name: Hildebrandt, Hendrik
name: Hoekstra, Henk
name: Joudaki, Shahab
name: Kuijken, Konrad
name: Merten, Julian
name: Miller, Lance
name: Robertson, Naomi
name: Schneider, Peter
name: Viola, Massimo
Publisher: name: arXiv
Year: 2017
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present the tomographic cross-correlation between galaxy lensing measured in the Kilo Degree Survey (KiDS-450) with overlapping lensing measurements of the cosmic microwave background (CMB), as detected by Planck 2015. We compare our joint probe measurement to the theoretical expectation for a flat $Λ$CDM cosmology, assuming the best-fitting cosmological parameters from the KiDS-450 cosmic shear and Planck CMB analyses. We find that our results are consistent within $1σ$ with the KiDS-450 cosmology, with an amplitude re-scaling parameter $A_{\rm KiDS} = 0.86 \pm 0.19$. Adopting a Planck cosmology, we find our results are consistent within $2σ$, with $A_{\it Planck} = 0.68 \pm 0.15$. We show that the agreement is improved in both cases when the contamination to the signal by intrinsic galaxy alignments is accounted for, increasing $A$ by $\sim 0.1$. This is the first tomographic analysis of the galaxy lensing -- CMB lensing cross-correlation signal, and is based on five photometric redshift bins. We use this measurement as an independent validation of the multiplicative shear calibration and of the calibrated source redshift distribution at high redshifts. We find that constraints on these two quantities are strongly correlated when obtained from this technique, which should therefore not be considered as a stand-alone competitive calibration tool.
description: 14 pages, 11 figures
Development of a novel solar thermal process using magnification
Creators: name: Martin, Tyler
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: This thesis intends to develop a novel solar thermal magnification system using lenses, to provide higher efficiencies and power generation than currently implemented concentrated solar thermal power (CSP) systems. Currently, CSP systems cannot compete with fossil fuel generated power due to their low efficiencies and high required land use, increasing the cost of the system, as well as the fact that solar power generates only during the day time, unable to effectively provide power throughout the night without thermal storage systems. This report looks into the current state of the renewable energy industry in Australia, primarily solar systems, which has shown the potential for an effective CSP system, such as the novel system, to provide base load power to the grid and overcome the limitations of of existing CSP technologies , reducing the need for fossil fuel generated power. Experimental testing using various sized biconvex lenses has been completed, which showed strong potential for use in the novel system. A parabolic dish reflector was also tested and compared to the biconvex lens, with all sizes of the biconvex lenses exceeding the energy collection of the parabolic dish reflector, one of the highest efficiency CSP systems currently used. Overall, the extensive experimental testing and analysis has allowed for the creation of several conceptual models. These models are presented so that they can provide a useful base in the further development of the system into a functional prototype.
Dinuclear copper sulfate-based square lattice topology network with high alkyne selectivity
Creators: name: Andaloussi, Yassin.H
name: Sensharma, Debobroto
name: Bezrukov, Andrey
A.
name: Castell, Dominic C
name: He, Tao
name: Darwish, Shaza
name: ZAWOROTKO, MICHAEL
Publisher: name: University of Limerick
Year: 2024
Subjects: classificationCode: 34
subject: Chemical sciences
subject: FOS: Chemical sciences

description: ABSTRACT: Porous coordination networks (PCNs) sustained by inorganic anions that serve as linker ligands can offer high selectivity toward specific gases or vapors in gas mixtures. Such inorganic anions are best exemplified by electron-rich fluorinated anions, e.g., SiF6 2−, TiF6 2−, and NbOF5 2−, although sulfate anions have recently been highlighted as inexpensive and earth-friendly alternatives. Herein, we report the use of a rare copper sulfate dimer molecular building block to generate two square lattice, sql, coordination networks which can be prepared via solvent layering or slurrying, CuSO4(1,4-bib)1.5, 1, (1,4-bib = 1,4-bisimidazole benzene) and CuSO4(1,4-bin)1.5, 2, (1,4-bin = 1,4-bisimidazole naphthalene). Variable-temperature SCXRD and PXRD experiments revealed that both sql networks underwent reversible structural transformations due to linker rotations or internetwork displacements. Gas sorption studies conducted upon the narrow-pore phase of CuSO4(1,4-bin)1.5, 2np, found a high calculated 1:99 selectivity for C2H2 over C2H4 (33.01) and CO2 (15.18), as well as strong breakthrough performance. Across-the-board, C3H4 selectivity vs C3H6, CO2, and C3H8 was also observed. Sulfate-based PCNs, although still understudied, appear increasingly likely to offer utility in gas and vapor separations.
ЭФФЕКТЫ ВЗАИМНОГО ВЛИЯНИЯ СВЕРХПРОВОДИМОСТИ И МАГНЕТИЗМА В АНОМАЛЬНЫХ ДЖОЗЕФСОНОВСКИХ ПЕРЕХОДАХ
Creators: name: Ю. М. Шукринов
name: Е. Коваленко
name: К. В. Куликов
name: J. Tekic
name: M. Nashaat
Publisher: name: 39-е Совещание по физике низких температур (Международная конференция), посвященное 300-летию Российской академии наук
Year: 2024
Subjects: Физика низких температур

description: Обсуждаются эффекты проявления и взаимного влияния сверхпроводимости и магнетизма в джозефсоновском 𝞿0 переходе, где реализуется прямая связь джозефсоновской фазы и намагниченности
Carta Geologica d'Italia alla scala 1:50.000, F. 221 Bologna
Creators: name: Servizio Geologico D'Italia
Publisher: name: INFN Open Access Repository
Year: 2024
Subjects: carta geologica, Bologna, Emilia-Romagna, Pianura Padana, CARG, geological map

description: Foglio geologico alla scala 1:50.000 basato su rilevamenti alla scala 1:10.000 e 1:25.000 (eseguiti tra il 1988 e il 1998) comprensivo di legenda, schemi a cornice, sezioni geologiche.
Additional file 2: Table S2. of Renoprotective RAAS inhibition does not affect the association between worse renal function and higher plasma aldosterone levels
Creators: name: Gant, Christina
name: Gozewijn Laverman
name: Liffert Vogt
name: Slagman, Maartje
name: Hiddo Heerspink
name: Waanders, Femke
name: Hemmelder, Marc
name: Navis, Gerjan
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Multivariate analysis on the determinants of the plasma aldosterone concentration during placebo and during losartan treatment. In this table we illustrate the association between creatinine clearance and the plasma aldosterone concentration during placebo and losartan treatment, while adjusting for age and gender. (DOCX 13Â kb)
New hard X-ray sources discovered in the ongoing INTEGRAL Galactic Plane survey after 14 years of observations
Creators: name: Krivonos, Roman
name: Tsygankov, Sergey
name: Mereminskiy, Ilya
name: Lutovinov, Alexander
name: Sazonov, Sergey
name: Sunyaev, Rashid
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The International Gamma-Ray Astrophysics Laboratory (INTEGRAL) continues to successfully work in orbit after its launch in 2002. The mission provides the deepest ever survey of hard X-ray sources throughout the Galaxy at energies above 20 keV. We report on a catalogue of new hard X-ray source candidates based on the latest sky maps comprising 14 years of data acquired with the IBIS telescope onboard INTEGRAL in the Galactic Plane (|b|<17.5 deg). The current catalogue includes in total 72 hard X-ray sources detected at S/N>4.7 sigma and not known to previous INTEGRAL surveys. Among them, 31 objects have also been detected in the on-going all-sky survey by the BAT telescope of the Swift observatory. For 26 sources on the list, we suggest possible identifications: 21 active galactic nuclei, two cataclysmic variables, two isolated pulsars or pulsar wind nebulae, and one supernova remnant; 46 sources from the catalogue remain unclassified.
description: 7 pages, 2 figures, 2 tables. Submitted to MNRAS Letters, comments welcome
Additional file 7: Figure S7. of Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring
Creators: name: Díaz-Cárdenas, Carolina
name: López, Gina
name: Alzate-Ocampo, José David
name: González, Laura
name: Shapiro, Nicole
name: Woyke, Tanja
name: Kyrpides, Nikos
name: Restrepo, Silvia
name: Baena, Sandra
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Multiple alignment of the Putative DEAD/DEAH box helicase proteins. CSIs previously reported in this protein were not found. The analysis was done using Mafft. (DOCX 46 kb)
Classifying Radio Galaxies with Convolutional Neural Network
Creators: name: Aniyan, Arun
name: Thorat, Kshitij
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We present the application of deep machine learning technique to classify radio images of extended sources on a morphological basis using convolutional neural networks. In this study, we have taken the case of Fanaroff-Riley (FR) class of radio galaxies as well as radio galaxies with bent-tailed morphology. We have used archival data from the Very Large Array (VLA) - Faint Images of the Radio Sky at Twenty Centimeters (FIRST) survey and existing visually classified samples available in literature to train a neural network for morphological classification of these categories of radio sources. Our training sample size for each of these categories is approximately 200 sources, which has been augmented by rotated versions of the same. Our study shows that convolutional neural networks can classify images of the FRI and FRII and bent-tailed radio galaxies with high accuracy (maximum precision at 95%) using well-defined samples and fusion classifier, which combines the results of binary classifications, while allowing for a mechanism to find sources with unusual morphologies. The individual precision is highest for bent-tailed radio galaxies at 95% and is 91% and 75% for the FRI and FRII classes, respectively, whereas the recall is highest for FRI and FRIIs at 91% each, while bent-tailed class has a recall of 79%. These results show that our results are comparable to that of manual classification while being much faster. Finally, we discuss the computational and data-related challenges associated with morphological classification of radio galaxies with convolutional neural networks.
description: 20 Pages, 10 figures, Submitted to ApJS
Temperature dependence of shear viscosity of $SU(3)$--gluodynamics within lattice simulation
Creators: name: Astrakhantsev, Nikita
name: Braguta, Viktor
name: Kotov, Andrey
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: In this paper we study the shear viscosity temperature dependence of $SU(3)$--gluodynamics within lattice simulation. To do so, we measure the correlation functions of energy-momentum tensor in the range of temperatures $T/T_c\in [0.9, 1.5]$. To extract the values of shear viscosity we used two approaches. The first one is to fit the lattice data with some physically motivated ansatz for the spectral function with unknown parameters and then determine shear viscosity. The second approach is to apply the Backus-Gilbert method which allows to extract shear viscosity from the lattice data nonparametrically. The results obtained within both approaches agree with each other. Our results allow us to conclude that within the temperature range $T/T_c \in [0.9, 1.5]$ SU(3)--gluodynamics reveals the properties of a strongly interacting system, which cannot be described perturbatively, and has the ratio $η/s$ close to the value ${1}/{4π}$ in $N = 4$ Supersymmetric Yang-Mills theory.
description: Typos in references are corrected and the acknowledgements are modified
Genomic and phenotypic comparison of Prevotella intermedia strains possessing different virulence in vivo
Creators: name: Kwack, Kyu Hwan
name: Jang, Eun-Young
name: Bin Yang, Seok
name: Lee, Jae-Hyung
name: Moon, Ji-Hoi
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Prevotella intermedia readily colonizes healthy dental biofilm and is associated with periodontal diseases. The viscous exopolysaccharide (EPS)-producing capability is known as a major virulence factor of P. intermedia 17 (Pi17). However, the inter-strain difference in P. intermedia regarding virulence-associated phenotype is not well studied. We compared in vivo virulence and whole genome sequences using five wild-type strains: ATCC 49046 (Pi49046), ATCC 15032 (Pi15032), ATCC 15033 (Pi15033), ATCC 25611 (Pi25611), and Pi17. Non-EPS producing Pi25611 was the least virulent in insect and mammalian models. Unexpectedly, Pi49046 did not produce viscous EPS but was the most virulent, followed by Pi17. Genomes of the five strains were quite similar but revealed subtle differences such as copy number variations and single nucleotide polymorphisms. Variations between strains were found in genes encoding glycosyltransferases and genes involved in the acquisition of carbohydrates and iron/haem. Based on these genetic variations, further analyses were performed. Phylogenetic and structural analyses discovered phosphoglycosyltransferases of Pi49046 and Pi17 have evolved to contain additional loops that may confer substrate specificity. Pi17, Pi15032, and Pi15033 displayed increased growth by various carbohydrates. Meanwhile, Pi49046 exhibited the highest activities for haemolysis and haem accumulation, as well as co-aggregation with Porphyromonas gingivalis harbouring fimA type II, which is more tied to periodontitis than other fimA types. Collectively, subtle genetic differences related to glycosylation and acquisition of carbohydrates and iron/haem may contribute to the diversity of virulence and phenotypic traits among P. intermedia strains. These variations may also reflect versatile strategies for within-host adaptation of P. intermedia.
Jumping spiders as a model system for comparative visual cognition
Creators: name: Peckmezian, Tina
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Uncertainty is a common feature of the natural world. Associative learning, which enables animals to form predictive relationships between contingent events, reduces uncertainty and equips animals to respond adaptively. Associative learning is widespread across the animal kingdom, and has been particularly well characterized in a few key invertebrate model taxa. Invertebrates exhibit a broad repertoire of associative learning abilities, have significant molecular overlap with vertebrate systems, and are considerably more amenable to analyses at cellular and behavioural levels. Jumping spiders (Salticidae) - and arachnids as a whole - have been underrepresented in the comparative cognition literature but possess many traits that make them suitable and interesting models. The principle aim of this thesis was to begin to bridge the gap between spiders and traditional invertebrate model taxa. To do so, I developed methods that permitted rigorous and repeatable analysis of cognitive processes, and assessed how salticids integrate different sources of information during learning and meVmory. My research focuses on an Australian salticid, Servaea incana, but the methods and principles developed here should be relevant to other cursorial arachnids or invertebrates in which vision is well developed. I develop a novel method to produce electric shock platforms that is precise, easy to use, and highly repeatable, and isolate the changes in mobility and behaviour that are dependent on shock. Additionally, to overcome the constraints of commonly used playback methods, I develop an immersive, closed-loop virtual reality system tailored for studies of salticid cognition. Using passive and active avoidance conditioning assays coupled with the aversive electric shock stimulus, and a change detection paradigm in virtual reality, I characterize the critical determinants of learning and memory in salticids. These experiments reveal that the ecological relevance, or ‘salience’ of available visual cues, together with hunger level and the temporal nature of the training protocol, play a significant role in determining performance. At the same time, when spiders are provided with a number of cues predicting an aversive event, they learn an operant escape response while ignoring reliable visual information. These results are very surprising given the extent to which vision is known to mediate behaviour and decision making in jumping spiders.
Ergodic-nonergodic transition in tapped granular systems: The role of persistent contacts
Creators: name: Gago, Paula A.
name: Maza, Diego
name: Pugnaloni, Luis A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Static granular packs have been studied in the last three decades in the frame of a modified equilibrium statistical mechanics that assumes ergodicity as a basic postulate. The canonical example on which this framework is tested consists in the series of static configurations visited by a granular column subjected to taps. By analyzing the response of a realistic model of grains, we demonstrate that volume and stress variables visit different regions of the phase space at low tap intensities in different realizations of the experiment. We show that the tap intensity beyond which sampling by tapping becomes ergodic coincides with the forcing necessary to break all particle-particle contacts during each tap. These results imply that the well-known "reversible" branch of tapped granular columns is only valid at relatively high tap intensities.
description: 7 pages, 5 figures
Specific associations between fungi and bacteria in broncho-alveolar aspirates from mechanically ventilated intensive care unit patients
Creators: name: Shajiei, Arezoo
name: Liu, Lei
name: Seinen, Jolien
name: Dieperink, Willem
name: Hammerschmidt, Sven
name: van Dijl, Jan Maarten
name: Harmsen, Hermie J.M.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: The detection of fungi in the human respiratory tract may represent contamination, colonization or a respiratory infection. To develop effective management strategies, a more accurate and comprehensive understanding of the lung fungal microbiome is required. Therefore, the objective of the present study was to define the “mycobiome” of mechanically ventilated patients admitted to an intensive care unit (ICU) using broncho-alveolar aspirate (“sputum”) samples and correlate this with clinical parameters and the bacterial microbiota. To this end, the mycobiome of 33 sputum samples was analyzed by Internal Transcribed Spacer2 (ITS2) amplicon sequencing of the ribosomal operons. The results show that in the investigated sputa of mechanically ventilated patients Candida spp. were most frequently detected, independent of pneumonia or antimicrobial therapy. The presence of Candida excluded in most cases the presence of Malassezia, which was the second most-frequently encountered fungus. Moreover, a hierarchical clustering of the sequence data indicated a patient-specific mycobiome. Fungi detected by culturing (Candida and Aspergillus) were also detected through ITS2 sequencing, but other yeasts and fungi were only detectable by sequencing. While Candida showed no correlations with identified bacterial groups, the presence of Malassezia and Rhodotorula correlated with oral bacteria associated with periodontal disease. Likewise, Cladosporium correlated with other oral bacteria, whereas Saccharomyces correlated more specifically with dental plaque bacteria and Alternaria with the nasal-throat-resident bacteria Neisseria, Haemophilus and Moraxella. In conclusion, ITS2 sequencing of sputum samples uncovered patient-specific lung mycobiomes, which were only partially detectable by culturing, and which could be correlated to specific nasal-oral-pharyngeal niches.
Alternative splicing regulation of doublesex gene by RNA-binding proteins in the silkworm Bombyx mori
Creators: name: Zheng, Zeng-Zhang
name: Sun, Xia
name: Zhang, Bei
name: Pu, Jia
name: Jiang, Ze-Yu
name: Li, Muwang
name: Fan, Yu-Jie
name: Xu, Yong-Zhen
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Doublesex is highly conserved and sex-specifically spliced in insect sex-determination pathways, and its alternative splicing (AS) is regulated by Transformer, an exonic splicing activator, in the model system of Drosophila melanogaster. However, due to the lack of a transformer gene, AS regulation of doublesex remains unclear in Lepidoptera, which contain the economically important silkworm Bombyx mori and thousands of agricultural pests. Here, we use yeast three-hybrid system to screen for RNA-binding proteins that recognize sex-specific exons 3 and 4 of silkworm doublesex (Bm-dsx); this approach identified BxRBP1/Lark binding to the exon 3, and BxRBP2/TBPH and BxRBP3/Aret binding to the exon 4. Investigation of tissues shows that BxRBP1 and BxRBP2 have no sex specificity, but BxRBP3 has – three of its four isoforms are expressed with a sex-bias. Using novel sex-specific silkworm cell lines, we find that BxRBP1 and BxRBP3 directly interact with each other, and cooperatively function as splicing repressors. Over-expression of BxRBP1 and BxRBP3 isoforms efficiently inhibits splicing of the exons 3 and 4 in the female-specific cells and generates the male-specific isoform of Bm-dsx. We also demonstrate that the sex-determination upstream gene Masc regulates alternatively transcribed BxRBP3 isoforms. Thus, we identify a new regulatory mechanism of doublesex AS in the silkworm, revealing an evolutionary divergence in insect sex-determination.
Additional file 6: Figure S6. of Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring
Creators: name: Díaz-Cárdenas, Carolina
name: López, Gina
name: Alzate-Ocampo, José David
name: González, Laura
name: Shapiro, Nicole
name: Woyke, Tanja
name: Kyrpides, Nikos
name: Restrepo, Silvia
name: Baena, Sandra
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Multiple alignment of a conserved region of the e tRNA modification GTPase TrmE protein. The multiple alignment contained a 1 aa insertion that is specific for Dethiosulfovibrio, Jonquetella and Pyramidobacter clade. The analysis was done using Mafft. (DOCX 34 kb)
Characterisation of a gimbal's response when attached to a drone to roll, pitch and yaw movements of a drone
Creators: name: Silk, Oliver Aston George
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: With the increased capability of drones, comes the increased need for the ability to attach level sensitive packages and fly whilst these packages remain in a horizontal and leveled position. This thesis looks into the characteristic response of a horizontal and leveling gimbal device when used with a sensor suite consisting of two pairs of vector magnetometers. The project centres on the idea of using the gimbal to keep a sensor suite of vector magnetometers leveled, while connected to a low flying drone for meteorite detection. However, the scope of this device goes beyond that, looking into its applications in UXO detection and forensic geoscience. The project incorporates testing methods with the goal of analysing and commenting on the characteristic responses of a gimbal. To accomplish this, a mechanical lever apparatus was constructed to simulate a step input change of the drone's roll movement for the reason of testing a gimbal's response. The response of the gimbal was captured using a high speed camera and then analysed over a sequence of frames using image processing software. The effect of the amplitude of the input angle change and added centralised mass onto the gimbal camera mount are explored through the comparison of the gimbal response's Overshoot , Settling Time (Tˢ), and Steady State Error (SSE) during testing.
Social dysfunction is transdiagnostically associated with default mode network dysconnectivity in schizophrenia and Alzheimer’s disease
Creators: name: Saris, Ilja M. J.
name: Aghajani, Moji
name: Reus, Lianne M.
name: Visser, Pieter-Jelle
name: Pijnenburg, Yolande
name: van der Wee, Nic J. A.
name: Bilderbeck, Amy C.
name: Raslescu, Andreea
name: Malik, Asad
name: Mennes, Maarten
name: Koops, Sanne
name: Arrango, Celso
name: Ayuso-Mateos, Jose Luis
name: Dawson, Gerard R.
name: Marston, Hugh
name: Kas, Martien J.
name: Penninx, Brenda W. J. H.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: Mental Health

description: Social dysfunction is one of the most common signs of major neuropsychiatric disorders. The Default Mode Network (DMN) is crucially implicated in both psychopathology and social dysfunction, although the transdiagnostic properties of social dysfunction remains unknown. As part of the pan-European PRISM (Psychiatric Ratings using Intermediate Stratified Markers) project, we explored cross-disorder impact of social dysfunction on DMN connectivity. We studied DMN intrinsic functional connectivity in relation to social dysfunction by applying Independent Component Analysis and Dual Regression on resting-state fMRI data, among schizophrenia (SZ; N = 48), Alzheimer disease (AD; N = 47) patients and healthy controls (HC; N = 55). Social dysfunction was operationalised via the Social Functioning Scale (SFS) and De Jong-Gierveld Loneliness Scale (LON). Both SFS and LON were independently associated with diminished DMN connectional integrity within rostromedial prefrontal DMN subterritories (pcorrected range = 0.02–0.04). The combined effect of these indicators (Mean.SFS + LON) on diminished DMN connectivity was even more pronounced (both spatially and statistically), independent of diagnostic status, and not confounded by key clinical or sociodemographic effects, comprising large sections of rostromedial and dorsomedial prefrontal cortex (pcorrected=0.01). These findings pinpoint DMN connectional alterations as putative transdiagnostic endophenotypes for social dysfunction and could aid personalised care initiatives grounded in social behaviour.
Additional file 1: Table S1. of Renoprotective RAAS inhibition does not affect the association between worse renal function and higher plasma aldosterone levels
Creators: name: Gant, Christina
name: Gozewijn Laverman
name: Liffert Vogt
name: Slagman, Maartje
name: Hiddo Heerspink
name: Waanders, Femke
name: Hemmelder, Marc
name: Navis, Gerjan
Publisher: name: figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Patient characteristics. This Table depicts the patients characteristics of patients included in the study. (DOCX 19Â kb)
Competition between electron pairing and phase coherence in superconducting interfaces
Creators: name: Singh, G.
name: Jouan, A.
name: Benfatto, L.
name: Couedo, F.
name: Kumar, P.
name: Dogra, A.
name: Budhani, R.
name: Caprara, S.
name: Grilli, M.
name: Lesne, E.
name: Barthelemy, A.
name: Bibes, M.
name: Feuillet-Palma, C.
name: Lesueur, J.
name: Bergeal, N.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The large diversity of exotic electronic phases displayed by two-dimensional superconductors confronts physicists with new challenges. These include the recently discovered quantum Griffith singularity in atomic Ga films, topological phases in proximized topological insulators and unconventional Ising pairing in transition metal dichalcogenide layers. In LaAlO3/SrTiO3 heterostructures, a gate tunable superconducting electron gas is confined in a quantum well at the interface between two insulating oxides. Remarkably, the gas coexists with both magnetism and strong Rashba spin-orbit coupling and is a candidate system for the creation of Majorana fermions. However, both the origin of superconductivity and the nature of the transition to the normal state over the whole doping range remain elusive. Missing such crucial information impedes harnessing this outstanding system for future superconducting electronics and topological quantum computing. Here we show that the superconducting phase diagram of LaAlO3/SrTiO3 is controlled by the competition between electron pairing and phase coherence. Through resonant microwave experiments, we measure the superfluid stiffness and infer the gap energy as a function of carrier density. Whereas a good agreement with the Bardeen-Cooper-Schrieffer (BCS) theory is observed at high carrier doping, we find that the suppression of Tc at low doping is controlled by the loss of macroscopic phase coherence instead of electron pairing as in standard BCS theory. We find that only a very small fraction of the electrons condenses into the superconducting state and propose that this corresponds to the weak filling of a high-energy dxz/yz band, more apt to host superconductivity
Association of follicular helper T and follicular regulatory T cells with severity and hyperglycemia in hospitalized COVID-19 patients
Creators: name: Zahran, Asmaa M.
name: Abdel-Rahim, Mona H.
name: Nasif, Khalid A.
name: Hussein, Safinaz
name: Hafez, Rania
name: Ahmad, Ahmad Bahieldeen
name: Saad, Khaled
name: Elhoufey, Amira
name: Hussein, Hosni A. M.
name: Thabet, Ali A.
name: El-Badawy, Omnia
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Hematology

description: We aimed to determine the levels of follicular helper T (Tfh) and follicular regulatory T (Tfr) cells in COVID-19 patients and determine whether their levels correlated with disease severity and presence of hyperglycemia. This study was carried out in 34 hospitalized COVID-19 patients and 20 healthy controls. Levels of total circulating Tfh, inducible T-cell costimulator (ICOS)+ activated Tfh, and Tfr cells were assessed in all participants by flow cytometry. Total CD4+CXCR5+ Tfh cells and ICOS+Foxp3-activated Tfh cells increased and ICOS+Foxp3+ Tfr cells decreased in COVID-19 patients, especially in diabetic patients and those with severe disease. Activated ICOS+ Tfh cells were directly correlated with lactate dehydrogenase, D-dimer, ferritin, and respiratory rate and inversely correlated with the partial pressure of carbon dioxide. COVID-19 is associated with marked activation of Tfh cells and a profound drop in Tfr cells, especially in severe and diabetic patients. Future studies on expanded cohorts of patients are needed to clarify the relationship between SARS-CoV-2 and acute-onset diabetes.
Deep Learning-Based Behavioral Quantification of Upper Limb Rehabilitation Dose in a Rat Model of Ischemic Stroke
Creators: name: Vanterpool, Zanna
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2022
Subjects: stroke
rats
stroke rehabilitation
DeepLabCut
upper limb
skilled reaching
dose

description: Seventy percent of stroke survivors experience loss of upper limb function after stroke and rehabilitative therapy is the only option to reduce impairments. However, uncertainty remains as to the optimal dose of therapy that should be prescribed. It has been suggested to report multiple parameters of dose, to increase standardization within the field, and to gain a better understanding of the dose-response relationship. This study investigated the automatic quantification of multiple dose parameters in a rat model of ischemic stroke, with rehabilitation paradigms whereby rats repeatedly grasp for food pellets to train their forelimb function. Starting 7 days post-stroke, groups of rats received 4, 8, or 12 rehabilitative training sessions for 10 days, practicing either high-quality (precision practice) or less skilled (mass practice) reaching movements. Pellet consumption was measured after each session and various metrics were analyzed using deep learning-based software (DeepLabCut, DLC) to represent parameters of dose intensity (number of reaches, paw path length) and session density (time on task). Functional outcome was assessed with the Montoya staircase task. Computer algorithms were validated against human analysis, demonstrating reach detection accuracy and reliability >80%. Interestingly, the number of training sessions did not alter the accumulated movement practice across rehabilitation, in either task. However, the number of sessions inversely affected training intensity, resulting in more forelimb use per session in rats with 4 sessions compared to 12 sessions. We found strong positive correlations between the number of reaches, time on task, paw path length, and pellets consumed in the precision practice, but only between reaches and pellets consumed in mass practice. This work demonstrates the quantification of multiple dose parameters using deep learning software and shows subtle differences between the two commonly used forelimb training tasks. Moreover, our data suggest that rehabilitative training at a frequency that is too high may negatively impact performance per session.
Social Dysfunction is Transdiagnostically Associated with Default Mode Network Dysconnectivity in Schizophrenia and Alzheimer’s Disease
Creators: name: Saris, Ilja M. J.
name: Aghajani, Moji
name: Reus, Lianne M.
name: Visser, Pieter-Jelle
name: Pijnenburg, Yolande
name: van der Wee, Nic J. A.
name: Bilderbeck, Amy C.
name: Raslescu, Andreea
name: Malik, Asad
name: Mennes, Maarten
name: Koops, Sanne
name: Arrango, Celso
name: Ayuso-Mateos, Jose Luis
name: Dawson, Gerry R.
name: Marston, Hugh
name: Kas, Martien J.
name: Penninx, Brenda W. J. H.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: Mental Health

description: Objectives Social dysfunction is one of the most common signs of major neuropsychiatric disorders. The Default Mode Network (DMN) is crucially implicated in both psychopathology and social dysfunction, although the transdiagnostic properties of social dysfunction remains unknown. As part of the pan-European PRISM (Psychiatric Ratings using Intermediate Stratified Markers) project, we explored cross-disorder impact of social dysfunction on DMN connectivity. Methods We studied DMN intrinsic functional connectivity in relation to social dysfunction by applying Independent Component Analysis and Dual Regression on resting-state fMRI data, among Schizophrenia (SZ; N = 48), Alzheimer Disease (AD; N = 47) patients and healthy controls (HC; N = 55). Social dysfunction was operationalized via the Social Functioning Scale (SFS) and De Jong-Gierveld Loneliness Scale (LON). Results Both SFS & LON were independently associated with diminished DMN connectional integrity within rostromedial prefrontal DMN subterritories (pcorrected range =0.02-0.04). The combined effect of these indicators (Mean.SFS + LON) on diminished DMN connectivity was even more pronounced (both spatially and statistically), independent of diagnostic status, and not confounded by key clinical or sociodemographic effects, comprising large sections of rostromedial and dorsomedial prefrontal cortex (pcorrected
=0.01). Conclusions These findings pinpoint DMN connectional alterations as putative transdiagnostic endophenotypes for social dysfunction, and could aid personalized care initiatives grounded in social behavior.
Additional file 5: Figure S5. of Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring
Creators: name: Díaz-Cárdenas, Carolina
name: López, Gina
name: Alzate-Ocampo, José David
name: González, Laura
name: Shapiro, Nicole
name: Woyke, Tanja
name: Kyrpides, Nikos
name: Restrepo, Silvia
name: Baena, Sandra
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Multiple alignment of a conserved region of the 1-acyl-sn-glycerol-3- phosphate acyltransferase protein. The multiple alignment contained a 1 aa insertion that is specific for Dethiosulfovibrio, Jonquetella and Pyramidobacter clade. The analysis was done using Mafft. (DOCX 36 kb)
Additional file 2: of PORTAF – postoperative radiotherapy of non-small cell lung cancer: accelerated versus conventional fractionation – study protocol for a randomized controlled trial
Creators: name: R. Bütof
name: M. Simon
name: S. Löck
name: E. Troost
name: S. Appold
name: M. Krause
name: M. Baumann
Publisher: name: figshare
Year: 2017
Subjects: subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: SPIRIT figure. (DOC 49 kb)
Driving the formation of the RbCs dimer by a laser pulse. A nonlinear dynamics approach
Creators: name: Chandre, Cristel
name: Mahecha, J
name: Salas, J
Publisher: name: arXiv
Year: 2017
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We study the formation of the RbCs molecule by an intense laser pulse using nonlinear dynamics. Under the Born-Oppenheimer approximation, the system is modeled by a two degree of freedom rovibrational Hamiltonian, which includes the ground electronic potential energy curve of the diatomic molecule and the interaction of the molecular polarizability with the electric field of the laser. As the laser intensity increases, we observe that the formation probability first increases and then decreases after reaching a maximum. We show that the analysis can be simplified to the investigation of the long-range interaction between the two atoms. We conclude that the formation is due to a very small change in the radial momentum of the dimer induced by the laser pulse. From this observation, we build a reduced one dimensional model which allows us to derive an approximate expression of the formation probability as a function of the laser intensity.
Social dysfunction is transdiagnostically associated with default mode network dysconnectivity in schizophrenia and Alzheimer’s disease
Creators: name: Saris, Ilja M. J.
name: Aghajani, Moji
name: Reus, Lianne M.
name: Visser, Pieter-Jelle
name: Pijnenburg, Yolande
name: van der Wee, Nic J. A.
name: Bilderbeck, Amy C.
name: Raslescu, Andreea
name: Malik, Asad
name: Mennes, Maarten
name: Koops, Sanne
name: Arrango, Celso
name: Ayuso-Mateos, Jose Luis
name: Dawson, Gerard R.
name: Marston, Hugh
name: Kas, Martien J.
name: Penninx, Brenda W. J. H.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: Mental Health

description: Social dysfunction is one of the most common signs of major neuropsychiatric disorders. The Default Mode Network (DMN) is crucially implicated in both psychopathology and social dysfunction, although the transdiagnostic properties of social dysfunction remains unknown. As part of the pan-European PRISM (Psychiatric Ratings using Intermediate Stratified Markers) project, we explored cross-disorder impact of social dysfunction on DMN connectivity. We studied DMN intrinsic functional connectivity in relation to social dysfunction by applying Independent Component Analysis and Dual Regression on resting-state fMRI data, among schizophrenia (SZ; N = 48), Alzheimer disease (AD; N = 47) patients and healthy controls (HC; N = 55). Social dysfunction was operationalised via the Social Functioning Scale (SFS) and De Jong-Gierveld Loneliness Scale (LON). Both SFS and LON were independently associated with diminished DMN connectional integrity within rostromedial prefrontal DMN subterritories (pcorrected range = 0.02–0.04). The combined effect of these indicators (Mean.SFS + LON) on diminished DMN connectivity was even more pronounced (both spatially and statistically), independent of diagnostic status, and not confounded by key clinical or sociodemographic effects, comprising large sections of rostromedial and dorsomedial prefrontal cortex (pcorrected=0.01). These findings pinpoint DMN connectional alterations as putative transdiagnostic endophenotypes for social dysfunction and could aid personalised care initiatives grounded in social behaviour.