cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The plaster texts from Kuntillet ʻAjrud and Deir ʻAlla : an inductive approach to the emergence of northwest Semitic literary texts in the first millennium B.C.E.
Creators: name: Wearne, Gareth James
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: This study examines the emergence of literary texts from the primarily oral milieux of the southern Levant during the first millennium B.C.E. The question of textualisation has received considerable attention in the last two decades, with particular emphasis given to the origins of the Hebrew Bible. But whereas earlier studies have tended to work heuristically––beginning at the level of the received biblical text and attempting to develop explanatory models––, the present study proceeds inductively––beginning with a particular instantiation of the phenomenon of literary text production, namely plaster wall inscriptions, and extrapolating conclusions based on these specific examples. Working within the paradigm of an oral-literate continuum, the research focusses on two roughly contemporary case studies: the 8th century B.C.E. plaster texts from Kuntillet ʿAjrud and Deir ʿAlla. For both case studies detailed epigraphic and archaeological analyses are used to assess three core questions: What was written? Who was writing? And how were the texts experienced by their audiences? It is concluded that in the physical context of the plaster inscriptions writing served both symbolic and memorialising functions, communicating specific information to posterity and serving as a form of communal self identification and expression. Possible numinous associations of writing are also considered along the way. The final section includes a discussion of implications for the origins of the biblical text. It is argued that by the end of the 8th century B.C.E. there is evidence for the textualisation of stories and songs comparable to those found in the Hebrew Bible, and that the impulse toward literary text production was shaped within a larger pool of folk-traditions.
Improving drug sensitivity predictions in precision medicine through active expert knowledge elicitation
Creators: name: Sundin, Iiris
name: Peltola, Tomi
name: Majumder, Muntasir Mamun
name: Daee, Pedram
name: Soare, Marta
name: Afrabandpey, Homayun
name: Heckman, Caroline
name: Kaski, Samuel
name: Marttinen, Pekka
Publisher: name: arXiv
Year: 2017
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Human-Computer Interaction (cs.HC)
subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Predicting the efficacy of a drug for a given individual, using high-dimensional genomic measurements, is at the core of precision medicine. However, identifying features on which to base the predictions remains a challenge, especially when the sample size is small. Incorporating expert knowledge offers a promising alternative to improve a prediction model, but collecting such knowledge is laborious to the expert if the number of candidate features is very large. We introduce a probabilistic model that can incorporate expert feedback about the impact of genomic measurements on the sensitivity of a cancer cell for a given drug. We also present two methods to intelligently collect this feedback from the expert, using experimental design and multi-armed bandit models. In a multiple myeloma blood cancer data set (n=51), expert knowledge decreased the prediction error by 8%. Furthermore, the intelligent approaches can be used to reduce the workload of feedback collection to less than 30% on average compared to a naive approach.
description: 24 pages, 3 figures
Learning, memory and cue choice in navigating ants
Creators: name: Freas, Cody A.
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: A critical reoccurring challenge facing mobile animals is the need to reliably find goal locations (e.g. food or nest). To solve this problem, animal navigators acquire and use multiple cue sets within their environment, which designate direction and distance estimates of these locations. Navigational cues can conflict, which adds a further challenge, requiring the navigator to integrate these cues before moving. Foraging ants are expert visual navigators known to use both learned panorama cues and path integration to navigate. This thesis examines navigational memory, learning and cue choice in two Australian ant species, the diurnal ant Melophorus bagoti and the nocturnal bull ant Myrmecia midas. M. bagoti is a solitary foraging desert ant endemic to Central Australia. Foragers are shown to retain robust memories of both the nest skyline and multiple non-nest site skylines. Forager orientation performance shows evidence of retroactive interference after changes are made to the skyline at the same site. When presented with cue conflicts between the terrestrial and celestial cue sets, foragers appear to choose dynamically based on experience and cue reliability in accordance with the Temporal Weighting Rule. Foragers with directional conflicts in their inbound and outbound routes show evidence of rapid vector calibration to the inbound route.This calibration appears to have a directional limit of around 45˚. When foragers are restricted to the nest site, they are unable to extrapolate panorama cues from the nest to local sites but only require one experience of the homeward route to learn the correct nest direction. Furthermore, exposure to the outbound foraging path appears critical for efficient homeward route formation in this species. M. midas is a previously unstudied solitary foraging bull ant that forages nocturnally. Foragers show a strong reliance on terrestrial panorama cues in cue choice tests and only weak use of accumulated vectors. Foragers that are subjected to polarised light manipulations during route navigation dynamically weight the terrestrial and celestial cues during the foraging trip. M. midas foragers also navigate using the panorama while on the tree face, exhibiting similar solutions to navigational challenges on the ground and when navigating in three dimensions. Both species show heavy use of panorama learning and memory along with flexible use of navigation strategies.
A Robust Blind Watermarking Using Convolutional Neural Network
Creators: name: Mun, Seung-Min
name: Nam, Seung-Hun
name: Jang, Han-Ul
name: Kim, Dongkyu
name: Lee, Heung-Kyu
Publisher: name: arXiv
Year: 2017
Subjects: subject: Multimedia (cs.MM)
subject: FOS: Computer and information sciences

description: This paper introduces a blind watermarking based on a convolutional neural network (CNN). We propose an iterative learning framework to secure robustness of watermarking. One loop of learning process consists of the following three stages: Watermark embedding, attack simulation, and weight update. We have learned a network that can detect a 1-bit message from a image sub-block. Experimental results show that this learned network is an extension of the frequency domain that is widely used in existing watermarking scheme. The proposed scheme achieved robustness against geometric and signal processing attacks with a learning time of one day.
description: 4 pages. We are modifying this paper to submit to SPL
Comprehensive analysis of lncRNA expression profiles in cytopathic biotype BVDV-infected MDBK cells provides an insight into biological contexts of host-BVDV interactions
Creators: name: Gao, Xuwen
name: Niu, Chao
name: Wang, Zhuo
name: Jia, Shuo
name: Han, Meijing
name: Ma, Yingying
name: Guan, Xueting
name: Wang, Li
name: Qiao, Xinyuan
name: Xu, Yigang
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Bovine viral diarrhea virus (BVDV) is the causative agent of bovine viral diarrhea-mucosal disease, which significantly affects the production performance of cattle, causing serious economic losses to the cattle industries worldwide. Up to now, some mechanisms involved in host-BVDV interaction are still not fully understood. The discovery of long non-coding RNAs (lncRNAs) has provided a new perspective on gene regulation in diverse biological contexts, particularly in viral infection and host immune responses. However, little is known about the profiles and functions of lncRNAs in host cells in response to BVDV infection. Here, we utilized Illumina sequencing to explore lncRNAs profiles in cytopathic (CP) biotype BVDV-infected MDBK cells to further reveal the potential roles of lncRNAs in BVDV infection and host-BVDV interaction with integrated analysis of lncRNAs and mRNA expression profiles. A total of 1747 significantly differentially expressed genes, DEGs (156 lncRNAs and 1591 mRNAs) were obtained via RNA-seq in BVDV-infected MDBK cells compared to mock-infected cells. Next, these DE lncRNAs and mRNAs were subjected to construct lncRNAs-mRNAs co-expression network followed by the prediction of potential functions of the DE lncRNAs. Co-expression network analysis elucidated that DE lncRNAs were significant enrichment in NOD-like receptor, TNF, NF-ĸB, ErbB, Ras, apoptosis, and fatty acid biosynthesis pathways, indicating that DE lncRNAs play important roles in host-BVDV interactions. Our data give an overview of changes in transcriptome and potential roles of lncRNAs, providing molecular biology basis for further exploring the mechanisms of host-BVDV interaction.
Trace element and isotopic analyses of raw and commercial beehive products
Creators: name: Zhou, Xiaoteng
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Bees have existed on the planet for more than 100 million years and their relationship with early humans dates to the Pliocene period (5.3 million to 2.6 million years ago). As a result of recent human industrial activity, bees' foraging environments have been subject to variable levels of contamination. Consequently, bees have been used as bio-indicators to assess anthropogenic contamination. The primary product of bees is honey, a valued and popular human food. However, honey can be subject to adulteration via the addition of sugars and misleading labelling in relation to its geographic origin. Some international studies have evaluated beehive products for their authenticity and use in environmental monitoring. This study builds on existing approaches by applying multiple geochemical analytical techniques to link environmental sources to the concentrations and compositions of both raw and commercial beehive products. This thesis uses trace element analysis and isotopic techniques to: (a) evaluate the use of bees as environmental bio-indicators; (b) investigate the quality of Australian and global honey; and (c) explore a valid method to authenticate the geographic origin of honey. Trace element analysis of beehive products demonstrates that measurements of As, Pb, Mn and Zn in two bee species (Apis mellifera, European honey bees and Tetragonula carbonaria, an Australian native bee species) correlates to co-located soils and dusts. Furthermore, Pb isotopic composition analysis verifies that the contamination found in bees can be attributed to a range of local sources, specifically, current mining activities in the city of Broken Hill (NSW), former leaded petrol depositions and geogenic background according to their locations. Carbon isotopic ratios (13C/12C) and trace elements are used in this thesis to identify if commercial honey samples (from Africa, Asia, Europe, North America and Oceania) have been adulterated by synthetic sugars derived from C-4 plants. These techniques are also used to test whether the stated geographic information on the honey samples is correct. The carbon isotopic analysis demonstrates that the adulteration practice of adding C-4 sugars remains a common problem in the Australian and global market, with a 17 % and 27 % adulteration rate, respectively. Manganese, P, K and Sr concentrations are shown to be the most important trace elements for distinguishing Australian from international honey. Overall, this thesis contributes to the growing body of research that evaluates the effectiveness of bees and their respective products for use as bio-indicators of current and legacy trace element contamination. The research findings also demonstrate that isotopic composition and trace element concentrations can be used to authenticate and establish the geographic origin of honey, which has benefits for bona fide honey producers and consumers alike.
Additional file 8: of Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application
Creators: name: Zhong, Jian
name: Zhenqing Ye
name: Lenz, Samuel
name: Clark, Chad
name: Bharucha, Adil
name: Gianrico Farrugia
name: Robertson, Keith
name: Zhiguo Zhang
name: Ordog, Tamas
name: Jeong-Heon Lee
Publisher: name: figshare
Year: 2017
Subjects: subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Plant Biology

description: Overlapping percentage of peaks relative to ENCODE data. (PDF 91Â kb)
Additional file 6: of Overexpression of RNF38 facilitates TGF-β signaling by Ubiquitinating and degrading AHNAK in hepatocellular carcinoma
Creators: name: Peng, Rui
name: Zhang, Peng-Fei
name: Yang, Xuan
name: Wei, Chuan-Yuan
name: Huang, Xiao-Yong
name: Cai, Jia-Bin
name: Lu, Jia-Cheng
name: Gao, Chao
name: Sun, Hai-Xiang
name: Gao, Qiang
name: Bai, Dou-Sheng
name: Shi, Guo-Ming
name: Ke, Ai-Wu
name: Fan, Jia
Publisher: name: figshare
Year: 2019
Subjects: Medicine
Cell Biology
Biological Sciences not elsewhere classified
Developmental Biology
Cancer
Science Policy

description: Figure S4. Clinical relevance of RNF38 and/or AHNAK expression. A. The correlation between RNF38 and AHNAK were assessed by the Pearson correlation. B. RNF38 and AHNAK IOD relative value of 102 patients had negative correlation. C. HCC patients with low AHNAK had the lowest survival rate and the highest recurrence rate. D. HCC patients with high RNF38 and low AHNAK had the most unfavorable prognosis including the OS and recurrence. Group 1, patients of RNF38 low and AHNAK high (n = 30). Group 2, patients of both RNF38 and AHNAK low or high (n = 36), Group 3, patients of RNF38 high and AHNAK low (n = 36). (PDF 132 kb)
Helicobacter pylori GmhB enzyme involved in ADP-heptose biosynthesis pathway is essential for lipopolysaccharide biosynthesis and bacterial virulence
Creators: name: Chiu, Sue-Fen
name: Teng, Kai-Wen
name: Wang, Po-Chuan
name: Chung, Hsin-Yu
name: Wang, Chun-Jen
name: Cheng, Hui-Chun
name: Kao, Mou-Chieh
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Helicobacter pylori infection is linked to serious gastric-related diseases including gastric cancer. However, current therapies for treating H. pylori infection are challenged by the increased antibiotic resistance of H. pylori. Therefore, it is in an urgent need to identify novel targets for drug development against H. pylori infection. In this study, HP0860 gene from H. pylori predicted to encode a D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) involved in the synthesis of ADP-L-glycero-D-manno-heptose for the assembly of lipopolysaccharide (LPS) in the inner core region was cloned and characterized. We reported HP0860 protein is monomeric and functions as a phosphatase by converting D-glycero-D-manno-heptose-1,7-bisphosphate into D-glycero-D-manno-heptose-1-phosphate with a preference for the β-anomer over the α-anomer of sugar phosphate substrates. Subsequently, a HP0860 knockout mutant and its complementary mutant were constructed and their phenotypic properties were examined. HP0860 knockout mutant contained both mature and immature forms of LPS and could still induce significant IL-8 secretion after gastric AGS cell infection, suggesting other enzymatic activities in HP0860 knockout mutant might be able to partially compensate for the loss of HP0860 activity. In addition, HP0860 knockout mutant was much more sensitive to antibiotic novobiocin, had decreased adherence abilities, and caused less classic hummingbird phenotype on the infected AGS cells, indicating H. pylori lacking HP0860 is less virulent. Furthermore, the disruption of HP0860 gene altered the sorting of cargo proteins into outer membrane vesicles (OMVs). The above findings confirm the importance of HP0860 in LPS core biosynthesis and shed light on therapeutic intervention against H. pylori infection.
The NANOGrav Nine-Year Data Set: Measurement and Interpretation of Variations in Dispersion Measures
Creators: name: Jones, M. L.
name: McLaughlin, M. A.
name: Lam, M. T.
name: Cordes, J. M.
name: Levin, L.
name: Chatterjee, S.
name: Arzoumanian, Z.
name: Crowter, K.
name: Demorest, P. B.
name: Dolch, T.
name: Ellis, J. A.
name: Ferdman, R. D.
name: Fonseca, E.
name: Gonzalez, M. E.
name: Jones, G.
name: Lazio, T. J. W.
name: Nice, D. J.
name: Pennucci, T. T.
name: Ransom, S. M.
name: Stinebring, D. R.
name: Stairs, I. H.
name: Stovall, K.
name: Swiggum, J. K.
name: Zhu, W. W.
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We analyze dispersion measure (DM) variations of 37 millisecond pulsars in the 9-year NANOGrav data release and constrain the sources of these variations. Variations are significant for nearly all pulsars, with characteristic timescales comparable to or even shorter than the average spacing between observations. Five pulsars have periodic annual variations, 14 pulsars have monotonically increasing or decreasing trends, and 13 pulsars show both effects. Several pulsars show correlations between DM excesses and lines of sight that pass close to the Sun. Mapping of the DM variations as a function of the pulsar trajectory can identify localized ISM features and, in one case, an upper limit to the size of the dispersing region of 13.2 AU. Finally, five pulsars show very nearly quadratic structure functions, which could be indicative of an underlying Kolmogorov medium. Four pulsars show roughly Kolmogorov structure functions and another four show structure functions less steep than Kolmogorov. One pulsar has too large an uncertainty to allow comparisons. We discuss explanations for apparent departures from a Kolmogorov-like spectrum, and show that the presence of other trends in the data is the most likely cause.
description: 20 pages, 13 figures, submitted to ApJ
Vagus nerve plays a pivotal role in CD4+ T cell differentiation during CVB3-induced murine acute myocarditis
Creators: name: Yue-Chun, Li
name: Gu, Xiao-Hong
name: Li-Sha, Ge
name: Zhou, De-Pu
name: Xing, Chao
name: Guo, Xiao-Ling
name: Pan, Lu-Lu
name: Song, Shi-Yang
name: Yu, Li-Li
name: Chen, Guang-Yi
name: Lin, Jia-Feng
name: Chu, Mao-Ping
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Cell Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Abnormalities in CD4+ T cell (Th cell) differentiation play an important role in the pathogenesis of viral myocarditis (VMC). Our previous studies demonstrated that activation of the cholinergic anti-inflammatory pathway (CAP) alleviated the inflammatory response. In addition, we observed that right cervical vagotomy aggravates VMC by inhibiting CAP. However, the vagus nerve’s effect on differentiation of CD4+ T cells has not been studied in VMC mice to date. In this study, we investigated the effects of cervical vagotomy and the α7nAChR agonist pnu282987 on CD4+ T cell differentiation in a murine myocarditis model (BALB/c) infected with coxsackievirus B3 (CVB3). Splenic CD4+ T cells from CVB3-induced mice obtained and cultured to investigate the potential mechanism of CD4+ T cell differentiation. Each Th cell subset was analyzed by flow cytometry. Our results showed that right cervical vagotomy increased proportions of Th1 and Th17 cells and decreased proportions of Th2 and Treg cells in the spleen. Vagotomy-induced upregulation of T-bet, Ror-γ, IFN-γ, and IL-17 expression while downregulating the expression of Gata3, Foxp3, and IL-4 in the heart. In addition, we observed upregulated levels of proinflammatory cytokines, aggravated myocardial lesions and cellular infiltration, and worsened cardiac function in VMC mice. Pnu282987 administration reversed these outcomes. Furthermore, vagotomy inhibited JAK2-STAT3 activation and enhanced NF-κB activation in splenic CD4+ T cells. The CD4+ T cell differentiation was related to JAK2-STAT3 and NF-κB signal pathways. In conclusion, vagus nerve modulates the inflammatory response by regulating CD4+ T cell differentiation in response to VMC.
title: ADCO, Ordre cistercien : comptes (1499-1515) (11 H 1162), f. 00466
Creators: name: de la Côte-d'Or, Archives départementales
name: Petot, Frédéric
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CBMA/CG21/F.PETOT/2019
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: comptes
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Ordre cistercien : comptes (1499-1515), Archives départementales de la Côte-d'Or, (11 H 1162). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Ordre cistercien : comptes (1499-1515), Archives départementales de la Côte-d'Or, (11 H 1162), f. 00466, in Projet CBMA - Corpus Burgundiae Medii Aevi \[Ressource en ligne\], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
Histoire de la Guerre d'Espagne et des Brigades internationales_5
Creators: name: Marty, André
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2015

description: Correspondance, notes, documents de travail, brochures, témoignages et récits, lettres d’antifascistes espagnols déportés ou emprisonnés
Additional file 2: of Discriminative ability of quality of life measures in multiple sclerosis
Creators: name: Fiest, Kirsten
name: Greenfield, Jamie
name: Luanne Metz
name: Patten, Scott
name: JettĂŠ, Nathalie
name: Marrie, Ruth Ann
Publisher: name: figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Figure S1. Mean score on HRQOL measures according to the number of comorbidities. (DOCX 29 kb)
Emperor Decius' 249 CE edict commanding sacrifice to the gods
Creators: name: Worboys, Kerrie
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: A terrible choice faced Christi an Romans in 249 C.E: offer sacrifice to the gods, considered an anathema, or be martyred , as some were, but many more succumbed and sacrificed. Decius has left us no record of his reasons. The only extant sources are either Christian or sympathetic, and they say that he was directly targeting Christians because he hated his predecessor Philip, who was believed to have been a Christian . Historians have challenge d this view over the last hundred years . Since the 1923 initial publication of 41 papyrus libelli (certificates of sacrifice) , academia has debated this topic and shed new light on Decius' possible reasons. This was a watershed in the history of anti - Christian persecution . Prior to Decius' Edict, religion in the empire was based on local cults which were no w weakened . T he certificate that was required as proof of sacrifice was an innovation , moreover the Egyptian papyri are dated to five months after the first arrests elsewhere. After assessing the authenticity of the extant sources , comparing these with the libelli and with what can be deduced about Decius himself , from history and coinage, I trace the arguments from modern scholarship to arrive at four assessable hypotheses The edict was: a) anti - Christian persecution; b) sacrifices to avert danger; c) sacrifices for Decius' accession as Emperor; or d) A re - celebration of Rome's Millenium. I concluded that it is most likely that Decius' edict was a stipulation of the correct way for his subjects to pray to the gods to ensure safety and security for his dynasty and the empire. It was a grand Accession Ceremony. It is also possible that Decius was motivated to include a re - celebration of Rome's Millennium in the face of fearful portents. I t was much less likely that Decius was focussed on the Christians at all. However, the recalcitrance of disobedient Christian s under Decius probably contributed to the later fiercer persecutions of Valerian and Diocletian.
Antiferromagnetic structure and electronic properties of BaCr2As2 and BaCrFeAs2
Creators: name: Filsinger, Kai A.
name: Schnelle, Walter
name: Adler, Peter
name: Fecher, Gerhard H.
name: Reehuis, Manfred
name: Hoser, Andreas
name: Hoffmann, Jens-Uwe
name: Werner, Peter
name: Greenblatt, Martha
name: Felser, Claudia
Publisher: name: arXiv
Year: 2017
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The chromium arsenides BaCr2As2 and BaCrFeAs2 with ThCr2Si2 type structure (space group I4/mmm; also adopted by '122' iron arsenide superconductors) have been suggested as mother compounds for possible new superconductors. DFT-based calculations of the electronic structure evidence metallic antiferromagnetic ground states for both compounds. By powder neutron diffraction we confirm for BaCr2As2 a robust ordering in the antiferromagnetic G-type structure at T_N = 580 K with mu_Cr = 1.9 mu_B at T = 2K. Anomalies in the lattice parameters point to magneto-structural coupling effects. In BaCrFeAs2 the Cr and Fe atoms randomly occupy the transition-metal site and G-type order is found below 265 K with mu_Cr/Fe = 1.1 mu_B. 57Fe Moessbauer spectroscopy demonstrates that only a small ordered moment is associated with the Fe atoms, in agreement with electronic structure calculations with mu_Fe ~ 0. The temperature dependence of the hyperfine field does not follow that of the total moments. Both compounds are metallic but show large enhancements of the linear specific heat coefficient gamma with respect to the band structure values. The metallic state and the electrical transport in BaCrFeAs2 is dominated by the atomic disorder of Cr and Fe and partial magnetic disorder of Fe. Our results indicate that Neel-type order is unfavorable for the Fe moments and thus it is destabilized with increasing iron content.
description: 14 pages, 14 figures, submitted to Physical Review B
The Enderstruder: An accessible open-source syringe extruder compatible with Ender series 3D printers
Creators: name: Crosby, Cody
Publisher: name: OSF Registries
Year: 2023
Subjects: subject: Polymer Chemistry
subject: Statistical, Nonlinear, and Soft Matter Physics
subject: Molecular, Cellular, and Tissue Engineering
subject: Physical Sciences and Mathematics
subject: Biomaterials
subject: Physics
subject: Chemistry
subject: Engineering
subject: Biomedical Engineering and Bioengineering
subject: 3D bioprinting
subject: bioink
subject: hydrogel
subject: open-source extruder
subject: printability
subject: screw-driven extrusion

description: A syringe extruder designed specifically for Ender 3D printers that can be printed and built for about $55. We have rigorously tested on popular biomaterial inks and pastes. Complete details will be published in an open-access article that is currently under peer review.
Downregulation of a novel flagellar synthesis regulator AsiR promotes intracellular replication and systemic pathogenicity of Salmonella Typhimurium
Creators: name: Ma, Shuangshuang
name: Jiang, Lingyan
name: Wang, Jingting
name: Liu, Xiaoqian
name: Li, Wanwu
name: Ma, Shuai
name: Feng, Lu
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: The intracellular pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) exploits host macrophage as a crucial survival and replicative niche. To minimize host immune response stimulated by flagellin, the expression of flagellar genes is downregulated during S. Typhimurium growth within host macrophages. However, the underlying mechanisms are largely unknown. In this study, we show that STM14_1285 (named AsiR), a putative RpiR-family transcriptional regulator, which is downregulated within macrophages as previously reported and also confirmed here, positively regulates the expression of flagellar genes by directly binding to the promoter of flhDC. By generating an asiR mutant strain and a strain that persistently expresses asiR gene within macrophages, we confirmed that the downregulation of asiR contributes positively to S. Typhimurium replication in macrophages and systemic infection in mice, which could be attributed to decreased flagellar gene expression and therefore reduced flagellin-stimulated secretion of pro-inflammatory cytokines IL-1β and TNF-α. Furthermore, the acidic pH in macrophages is identified as a signal for the downregulation of asiR and therefore flagellar genes. Collectively, our results reveal a novel acidic pH signal-mediated regulatory pathway that is utilized by S. Typhimurium to promote intracellular replication and systemic pathogenesis by repressing flagellar gene expression.
Recovery of mechanical pressure in a gas of underdamped active dumbbells with Brownian noise
Creators: name: Joyeux, Marc
Publisher: name: arXiv
Year: 2017
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In contrast with a gas at thermodynamic equilibrium, the mean force exerted on a wall by a gas of active particles usually depends on the confining potential, thereby preventing a proper definition of mechanical pressure. In this paper, we investigate numerically the properties of a gas of underdamped self-propelled dumbbells subject to Brownian noise of increasing intensity, in order to understand how the notion of pressure is recovered as noise progressively masks the effects of self-propulsion and the system approaches thermodynamic equilibrium. The simulations performed for a mobile asymmetric wall separating two chambers containing an equal number of active dumbbells highlight some subtle and unexpected properties of the system. First, Brownian noise of moderate intensity is sufficient to let mean forces equilibrate for small values of the damping coefficient, while much stronger noise is required for larger values of the damping coefficient. Moreover, the displacement of the mean position of the wall upon increase of the intensity of the noise is not necessarily monotonous and may instead display changes of direction. Both facts actually reflect the existence of several mechanisms leading to the rupture of force balance, which tend to displace the mean position of the wall towards different directions and display different robustness against an increase of the intensity of Brownian noise. This work therefore provides a clear illustration of the fact that driving an autonomous system towards (or away from) thermodynamic equilibrium may not be a straightforward process, but may instead proceed through the variations of the relative weights of several conflicting mechanisms.
Additional file 1: of Discriminative ability of quality of life measures in multiple sclerosis
Creators: name: Fiest, Kirsten
name: Greenfield, Jamie
name: Luanne Metz
name: Patten, Scott
name: JettĂŠ, Nathalie
name: Marrie, Ruth Ann
Publisher: name: figshare
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Hematology

description: Table S1. Comparison of Health Related Quality of Life Measures. (DOCX 12 kb)
Gyrokinetic continuum simulation of turbulence in a straight open-field-line plasma
Creators: name: Shi, E. L.
name: Hammett, G. W.
name: Stoltzfus-Dueck, T.
name: Hakim, A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: 3D2V continuum gyrokinetic simulations of electrostatic plasma turbulence in a straight, open-field-line geometry have been performed using the full-$f$ discontinuous-Galerkin code Gkeyll. These simulations include the basic elements of a fusion-device scrape-off layer: localized sources to model plasma outflow from the core, cross-field turbulent transport, parallel flow along magnetic field lines, and parallel losses at the limiter or divertor with sheath model boundary conditions. The set of sheath boundary conditions used in the model allows currents to flow through the walls. In addition to details of the numerical approach, results from numerical simulations of turbulence in the Large Plasma Device (LAPD), a linear device featuring straight magnetic field lines, are presented.
description: 22 pages, 7 figures, submitted to J. Plasma Phys
IPBES Technical Guidelines Series - Part 12A: File Naming Convention
Creators: name: Gudde, Renske
name: Krug, Rainer M.
Publisher: name: Zenodo
Year: 2024

description: These technical guidelines have been prepared by the technical support unit on knowledge and data and reviewed by the task force on knowledge and data within IPBES.
The approved version of these guidelines are available at https://ict.ipbes.net/data-management/technical-guidelines.
Part 12A of the technical guideline series, File Naming Convention, is part of the Organisation of Work guideline, and focuses on the recommended file names for IPBES products, and shows examples for different file types.
If interested, all source files are also available on our GitHub. For any questions, feedback, or suggestions for future guidelines, contact aidin.niamir@senckenberg.de.
Probing the diffractive production of Z boson pair at forward rapidities at the LHC
Creators: name: Sun, Hao
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this paper, we present the results from phenomenological analysis of Z boson pair hard diffractive production at the LHC. The calculation is based on the Regge factorization approach. Diffractive parton density functions extracted by the H1 Collaboration at DESY-HERA are used. The multiple Pomeron exchange corrections are considered through the rapidity gap survival probability factor. We give numerical predictions for single diffractive as well as double Pomeron exchange cross sections and compare with the photon-induced and non-diffractive ones. The contributions from quark-anti-quark collision and gluon-gluon fusion are displayed. Various kinematical distributions are presented. We make predictions which could be compared to future measurements at the LHC where forward proton detectors are installed and detector acceptances are considered.
description: 21 pages, 9 figures, Physics Review D. arXiv admin note: text overlap with arXiv:0705.1005, arXiv:hep-ph/0703315, arXiv:1509.05551 by other authors. Citation added
Partition musicale : pas de farandole
Creators: name: Lancelot, Francine
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020

description: Source: http://www.calames.abes.fr/pub/ms/FileId-3413
description: created: ca 1970
Additional file 7: of Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application
Creators: name: Zhong, Jian
name: Zhenqing Ye
name: Lenz, Samuel
name: Clark, Chad
name: Bharucha, Adil
name: Gianrico Farrugia
name: Robertson, Keith
name: Zhiguo Zhang
name: Ordog, Tamas
name: Jeong-Heon Lee
Publisher: name: figshare
Year: 2017
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Analysis of library complexity by Preseq package. The library complexity was estimated by Preseq package [8] for H3K4me3 and H3K27me3 ChIP-seq data from the ENCODE reference (ENB and ENw) and the corresponding datasets obtained either with standard protocol for the lab (St) or by using different purification reagents as identified in Fig. 1. (PDF 114Â kb)
H2O Southern Galactic Plane Survey (HOPS): Paper III - Properties of Dense Molecular Gas across the Inner Milky Way
Creators: name: Longmore, S. N.
name: Walsh, A. J.
name: Purcell, C. R.
name: Burke, D. J.
name: Henshaw, J.
name: Walker, D.
name: Urquhart, J.
name: Barnes, A. T.
name: Whiting, M.
name: Burton, M. G.
name: Breen, S. L.
name: Britton, T.
name: Brooks, K. J.
name: Cunningham, M. R.
name: Green, J. A.
name: Harvey-Smith, L.
name: Hindson, L.
name: Hoare, M. G.
name: Indermuehle, B.
name: Jones, P. A.
name: Lo, N.
name: Lowe, V.
name: Moore, T. J. T.
name: Thompson, M. A.
name: Voronkov, M. A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The H2O Southern Galactic Plane Survey (HOPS) has mapped 100 square degrees of the Galactic plane for water masers and thermal molecular line emission using the 22-m Mopra telescope. We describe the automated spectral-line fitting pipelines used to determine the properties of emission detected in HOPS datacubes, and use these to derive the physical and kinematic properties of gas in the survey. A combination of the angular resolution, sensitivity, velocity resolution and high critical density of lines targeted make the HOPS data cubes ideally suited to finding precursor clouds to the most massive and dense stellar clusters in the Galaxy. We compile a list of the most massive HOPS ammonia regions and investigate whether any may be young massive cluster progenitor gas clouds. HOPS is also ideally suited to trace the flows of dense gas in the Galactic Centre. We find the kinematic structure of gas within the inner 500pc of the Galaxy is consistent with recent predictions for the dynamical evolution of gas flows in the centre of the Milky Way. We confirm a recent finding that the dense gas in the inner 100pc has an oscillatory kinematic structure with characteristic length scale of ~20pc, and also identify similar oscillatory kinematic structure in the gas at radii larger than 100pc. Finally, we make all of the above fits and the remaining HOPS data cubes across the 100 square degrees of the survey available to the community.
description: 53 pages, 34 figures, 4 tables. Submitted MNRAS. Paper with full resolution images can be downloaded here: http://www.astro.ljmu.ac.uk/~snl/hops_p3.pdf
IPBES Technical Guidelines Series - Part 12A: File Naming Convention
Creators: name: Gudde, Renske
name: Krug, Rainer M.
Publisher: name: Zenodo
Year: 2023

description: These technical guidelines have been prepared by the technical support unit on knowledge and data and reviewed by the task force on knowledge and data within IPBES.
The approved version of these guidelines are available at https://ict.ipbes.net/data-management/technical-guidelines.
Part 12A of the technical guideline series, File Naming Convention, is part of the Organisation of Work guideline, and focuses on the recommended file names for IPBES products, and shows examples for different file types.
If interested, all source files are also available on our GitHub. For any questions, feedback, or suggestions for future guidelines, contact aidin.niamir@senckenberg.de.
Investigating the praxis of evaluating small-scale learning and teaching projects in higher education
Creators: name: Huber, Elaine
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Small-scale learning and teaching projects in higher education have the potential to drive innovation. However, a lack of systemic evaluation can inhibit the realisation and sustainability of these innovations and there is limited literature available to illuminate these evaluation practices. The broad aim of this study was to investigate the praxis of evaluating small-scale learning and teaching projects in higher education. A pragmatic, multiphase research design, underpinned by action research and case study methodologies was used for the study, drawing on reflection to understand what works and what does not work in small-scale project evaluation practice. The study was undertaken in three-phases across two Australian metropolitan universities using primary data. These data include the project documentation, reflective field notes, one-on-one interviews, and focus group discussions with university staff responsible for leading small-scale learning and teaching projects. My research reveals that a project leader's perception and conceptualisation of evaluation have important implications for practice. The research also highlights the need for an approach to the evaluation of small-scale learning and teaching projects that requires tailored resources including evidence-based frameworks to enable praxis. Outputs from this research include a new evidence-based evaluation-planning framework, SPELT (Small Project Evaluation in Learning and Teaching), and a set of recommendations for effective evaluation strategies for small-scale learning and teaching projects in higher education.
Models of Star-Planet Magnetic Interaction
Creators: name: Strugarek, A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Magnetic interactions between a planet and its environment are known to lead to phenomena such as aurorae and shocks in the solar system. The large number of close-in exoplanets that were discovered triggered a renewed interest in magnetic interactions in star-planet systems. Multiple other magnetic effects were then unveiled, such as planet inflation or heating, planet migration, planetary material escape, and even modification of the host star properties. We review here the recent efforts in modelling and understanding magnetic interactions between stars and planets in the context of compact systems. We first provide simple estimates of the effects of magnetic interactions and then detail analytical and numerical models for different representative scenarii. We finally lay out a series of future developments that are needed today to better understand and constrain these fascinating interactions.
description: 23 pages, 10 figures, accepted as a chapter in the Handbook of Exoplanets
Additional file 2: of Identification of prognostic signature in cancer based on DNA methylation interaction network
Creators: name: Hu, Wei-Lin
name: Xiong-Hui Zhou
Publisher: name: figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Marine Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Supplementary manuscript. This file contains the seven supplementary figures and the code for the construction of the DNA methylation interaction network. (DOCX 3703 kb)
Additional file 7: of Overexpression of RNF38 facilitates TGF-Î˛ signaling by Ubiquitinating and degrading AHNAK in hepatocellular carcinoma
Creators: name: Peng, Rui
name: Zhang, Peng-Fei
name: Yang, Xuan
name: Wei, Chuan-Yuan
name: Huang, Xiao-Yong
name: Cai, Jia-Bin
name: Lu, Jia-Cheng
name: Gao, Chao
name: Sun, Hai-Xiang
name: Gao, Qiang
name: Bai, Dou-Sheng
name: Shi, Guo-Ming
name: Ke, Ai-Wu
name: Fan, Jia
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Table S2. SILAC of differential proteins in HepG2-RNF38 and HepG2-vector (Up-regulated) (DOCX 43 kb)
Temperature, humidity and vegetation density affect eggshell pigmentation across a continent
Creators: name: L'Herpiniere, Kiara
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: The distinctive evolutionary shift from white reptilian eggs to pigmented eggs in a majority of avian species, has stimulated much thought and research, but has yet to be completely explained. Pigments in eggs may serve a variety of structural or signalling functions, which are not mutually exclusive. This research focuses on the variability of Australian Magpie (Cracticus tibicen) eggs, and the possible drivers of such variability. Using a dataset of 283 clutches from the Australian continent we used a range of methodologies to assess the degree of inter-clutch variation in egg pigmentation in relation to genetic divergence, environmental factors, and brood parasitism. We found little evidence for divergence between subspecies, however the Tasmanian subspecies did differ significantly from most of the others. The analysis of environmental parameters revealed that maximum temperature and the interactions between maximum temperature, relative humidity and leaf area cover explained variation for background colour patterning. The presence of a brood parasite in about one third of the magpie's distribution was related to a small degree, not significantly so, to the variation in colour and patterning. The results from our study add to the body of evidence that environmental drivers have an impact on pigment deposition.