cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1: of Cholelithiasis and the risk of intrahepatic cholangiocarcinoma: a meta-analysis of observational studies
Creators: name: Cai, Hao
name: Kong, Wen-Tao
name: Chao-Bo Chen
name: Shi, Guo-Ming
name: Huang, Cheng
name: Ying-Hao Shen
name: Hui-Chuan Sun
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Title of dataset: Data extracted from the studies included in the meta-analysis. NOS Newcastle-Ottawa scale, CI confidence interval, CC caseâ  control study, EHST extrahepatic bile duct stone or choledocholithiasis, GBST gallbladder stone or cholecystolithiasis, BDST bile duct stone, CLD chronic liver diseases, DM diabetes mellitus, ALD alcoholic liver disease, IBD inflammatory bowel disease, HBV hepatitis B virus. (DOC 62Â kb)
Additional file 2: Figure S1. of Comparative transcriptome profiling of two Brassica napus cultivars under chromium toxicity and its alleviation by reduced glutathione
Creators: name: Rafaqat Gill
name: Ali, Basharat
name: Cui, Peng
name: Enhui Shen
name: Farooq, Muhammad
name: Islam, Faisal
name: Shafaqat Ali
name: Bizeng Mao
name: Weijun Zhou
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Pie-chart shows the E-value, similarity and species distribution of Brassica napus L. to other plant species. Figure S2 Scattered plots shows the pair wise comparison of differentially expressed genes, ZS 758 considered as a control and Zheda 622 as a treatment under the different concentrations. In Figure, (A) represents the control, (B) as Cr 400 μM, and (C) represents the Cr 400 μM + GSH 1 mM. Figure S3 Pie-chart (A) shows the number of up-regulated and down-regulated DEGs in ZS 758/Zheda 622 and (B) Zheda 622/ZS 758, respectively. Figure S4 HemI hierarchal cluster shows stress responsive relatively differentially expressed genes (DEGs). Diagram (A) shows the DEGs among treatments i.e. Ck, Cr 400 μM, and Cr 400 μM + 1 mM GSH and (B) between cultivars such as ZS 758 and Zheda 622. Figure S5 Shows the comparative gene ontology functional classification (WEGO) by transcriptome profile analysis in ZS 758 vs Zheda 622. Former cultivar ZS 758 was taken as a control while later cultivar Zheda 622 as a treatment. Figure S6 Diagram showing the transcription factors (TFs) between cultivars and among the treatments. Numbers of each circle show the number of TFs that are uniquely (inside of non overlapping part) or commonly (inside of overlapping part) regulated. (A) diagram shows the TFs between cultivars and (B) shows the TFs among the treatments. (DOCX 1005 kb)
title: Optical and Wearable Detection of Diabetes
Creators: name: Mondal, Himadri Shekhar
Publisher: name: The Australian National University
Year: 2024

description: This thesis presents a thorough investigation into detection of diabetes, incorporating cutting-edge optical technologies alongside advanced machine learning algorithms. The emphasis centers is on the utilisation of Surface Plasmonic Resonance (SPR) and Localized Surface Plasmonic Resonance (LSPR) technologies, which have been creatively utilised to devise precise and selective approaches for the detection of diabetes biomarkers, including Glycated Albumin (GA). This study explores the potential of LSPR technology for the detection of GA, a crucial biomarker for diabetes. The research focuses on the utilisation of cost-efficiently manufactured gold nanoparticles. This methodology offers a more precise and cost-effective alternative for the detection of diabetes in contrast to conventional approaches. Furthermore, a substantial portion of the study shows the advancement and execution of machine learning models, including deep learning methodologies such as Convolutional Neural Networks (CNNs), to process intricate medical data. These models are employed for the processing and interpretation of data derived from many sources, including electrocardiogram (ECG) signals. This utilisation provides a new and innovative approach in the timely identification and treatment of diabetes. Using the physiological signal, this thesis explores the domain of wearable technologies, specifically examining the use of complex ECG signal for diabetes detection. The objective of this strategy is to improve patient adherence and convenience, hence progressing towards a healthcare management system that is more tailored and proactive. This thesis critically examines the limitations, problems, and future directions of these technologies in clinical contexts. The research reported in this study not only makes a valuable contribution to the progress of non-invasive approaches for detecting diabetes, but also establishes a foundation for potential future advancements in the field of medical diagnostics and wearable healthcare technologies.
Constraint on Lorentz invariance violation from Vela pulsar
Creators: name: Li, Hao
name: Zhu, Jie
name: Ma, Bo-Qiang
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The High Energy Stereoscopic System (H.E.S.S) Collaboration reported the discovery of a novel radiation component from the Vela pulsar by their Cherenkov telescopes. It is of great importance that gamma rays with energies of at least 20~TeV are recorded unexpectedly. The H.E.S.S Collaboration argued that such results may challenge the state-of-the-art models for the high-energy emission of pulsars. We point out in this work that these results also provide a unique opportunity to constrain certain Lorentz invariance violation parameters, leading to the realization of studying Lorentz invariance violation by using gamma-ray pulsars. The Lorentz invariance violation scale is constrained at the level of $E_{\mathrm{LV,}1}> 1.66\times 10^{17} \rm GeV$ for the linear scenario, and $E_{\mathrm{LV,}2}>3.53\times 10^{10} \rm GeV$ for the quadratic scenario. We anticipate that digging into the detailed features of the data of the Vela pulsar and analyzing potentially more very-high-energy photon data from pulsars in the future would improve the constraints on Lorentz invariance violation.
description: 3 pages, no figure
Additional file 1: of Alantolactone selectively ablates acute myeloid leukemia stem and progenitor cells
Creators: name: Yahui Ding
name: Huier Gao
name: Zhang, Yu
name: Li, Ye
name: Vasdev, Neil
name: Yingdai Gao
name: Chen, Yue
name: Zhang, Quan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: Copies of NMR, MS, HPLC spectra of alantolactone and copies of NMR spectra of DMA-alantolactone. (DOCX 533 kb)
Additional file 2. of The efficacy of QingfengGanke granule in treating postinfectious cough in pathogenic wind invading lungs syndrome: a multicenter, randomized, double-blind, placebo-controlled trial
Creators: name: Hongli Jiang
name: Mao, Bing
name: Wang, Lei
name: Ruiming Zhang
name: She, Bin
name: Faguang Jin
name: Yanling Xu
name: Ma, Jian
name: Qiuping Liu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Study protocol.
Well-posedness and qualitative behaviour of the Mullins-Sekerka problem with ninety-degree angle boundary contact
Creators: name: Abels, Helmut
name: Rauchecker, Maximilian
name: Wilke, Mathias
Publisher: name: Universität Regensburg
Year: 2020
Subjects: subject: EXISTENCE; SPACES;
subject: 510 Mathematik

description: We show local well-posedness for a Mullins-Sekerka system with ninety degree angle boundary contact. We will describe the motion of the moving interface by a height function over a fixed reference surface. Using the theory of maximal regularity together with a linearization of the equations and a localization argument we will prove well-posedness of the full nonlinear problem via the contraction mapping principle. Here one difficulty lies in choosing the right space for the Neumann trace of the height function and showing maximal L-p-L-q-regularity for the linear problem. In the second part we show that solutions starting close to certain equilibria exist globally in time, are stable, and converge to an equilibrium solution at an exponential rate.
Magnetic Field Effects and Transverse Ratchets in Charge Lattices Coupled to Asymmetric Substrates
Creators: name: Reichhardt, C. J. O.
name: Reichhardt, C.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We examine a charge lattice coupled to a one-dimensional asymmetric potential in the presence of an applied magnetic field, which induces gyrotropic effects in the charge motion. This system could be realized for Wigner crystals in nanostructured samples, dusty plasmas, or other classical charge-ordered states where gyrotropic motion and damping can arise. For zero magnetic field, an applied external ac drive can produce a ratchet effect in which the particles move along the easy flow direction of the substrate asymmetry. The zero field ratchet effect can only occur when the ac drive is aligned with the substrate asymmetry direction; however, when a magnetic field is added, the gyrotropic forces generate a Hall effect that leads to a variety of new behaviors, including a transverse ratchet motion that occurs when the ac drive is perpendicular to the substrate asymmetry direction. We show that this system exhibits commensuration effects as well as reversals in the ratchet effect and the Hall angle of the motion. The magnetic field also produces a nonmonotonic ratchet efficiency when the particles become localized at high fields.
description: 18 pages, 14 figures
Additional file 4. of The efficacy of QingfengGanke granule in treating postinfectious cough in pathogenic wind invading lungs syndrome: a multicenter, randomized, double-blind, placebo-controlled trial
Creators: name: Hongli Jiang
name: Mao, Bing
name: Wang, Lei
name: Ruiming Zhang
name: She, Bin
name: Faguang Jin
name: Yanling Xu
name: Ma, Jian
name: Qiuping Liu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: CONSORT checklist.
Additional file 1. of The efficacy of QingfengGanke granule in treating postinfectious cough in pathogenic wind invading lungs syndrome: a multicenter, randomized, double-blind, placebo-controlled trial
Creators: name: Hongli Jiang
name: Mao, Bing
name: Wang, Lei
name: Ruiming Zhang
name: She, Bin
name: Faguang Jin
name: Yanling Xu
name: Ma, Jian
name: Qiuping Liu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Informed consent.
Time-modulated near-field radiative heat transfer
Creators: name: Yu, Renwen
name: Fan, Shanhui
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We explore near-field radiative heat transfer between two bodies under time modulation by developing a rigorous fluctuational electrodynamics formalism. We demonstrate that time modulation can results in the enhancement, suppression, elimination, or reversal of radiative heat flow between the two bodies, and can be used to create a radiative thermal diode with infinite contrast ratio, as well as a near-field radiative heat engine that pumps heat from the cold to the hot bodies. The formalism reveals a fundamental symmetry relation in the radiative heat transfer coefficients that underlies these effects. Our results indicate the significant capabilities of time modulation for managing nanoscale heat flow.
On transfer maps in the algebraic K-theory of spaces
Creators: name: Raptis, George
Publisher: name: Universität Regensburg
Year: 2021
Subjects: subject: GROUP-COMPLETION; FIBRATIONS; TRACE;
subject: 510 Mathematik

description: We show that the Waldhausen trace mapTrX:A(X)-> QX(+), which defines a natural splitting map from the algebraicK-theory of spaces to stable homotopy, is natural up toweakhomotopy with respect to transfer maps in algebraicK-theory and Becker-Gottlieb transfer maps respectively.
Opamyrma hungvuong Yamane, Bui & Eguchi 2008
Creators: name: Hamer, Matthew T.
name: Weemaels, André Ibáñez
name: Fu, Yifan
name: Xuan, Liu
name: Tse, Cheung Yau Leo
name: Tang, Kit Lam
name: Guénard, Benoit
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Opamyrma
Opamyrma hungvuong

description: Opamyrma hungvuong Yamane, Bui & Eguchi, 2008 – First record for Sichuan Province.
Figure 1B; Figure 2A–F.
Opamyrma hungvuong Yamane et al., 2008: 57, figs. 1-12 (w.) VIETNAM.
description: Published as part of Hamer, Matthew T., Weemaels, André Ibáñez, Fu, Yifan, Xuan, Liu, Tse, Cheung Yau Leo, Tang, Kit Lam & Guénard, Benoit, 2024, New insights into the diversity and distribution of Leptanillinae (Formicidae) within China, pp. 99-112 in Zootaxa 5471 (1) on page 101, DOI: 10.11646/zootaxa.5471.1.6, http://zenodo.org/record/12189798
Reassessment of the Styxosaurus snowii (Williston, 1890) holotype specimen and its implications for elasmosaurid plesiosaurian interrelationships
Creators: name: SACHS, SVEN
name: LINDGREN, JOHAN
name: KEAR, BENJAMIN P.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Biological Sciences not elsewhere classified

description: The holotype (KUVP 1301) of Styxosaurus snowii—one of the earliest described elasmosaurid plesiosaurians—consists of a well-preserved cranium, mandible and articulated sequence of anterior–mid-series cervical vertebrae found in the lowermost Campanian strata of the Smoky Hill Chalk Member in the Niobrara Formation of Kansas, USA. This particular specimen has proven important for recent phylogenies of Elasmosauridae, and is integral to resulting definitions of the subfamily-level clade, Styxosaurinae. Despite this, KUVP 1301 has not been redescribed or figured in detail since its original taxonomic establishment. We, therefore, re-evaluated KUVP 1301 and assessed its phylogenetic implications. Several notable character states are pertinent for diagnosing S. snowii at genus and species level: (1) an anisodont functional dentition comprising enlarged premaxillary and dentary teeth with a pair of maxillary ‘fangs’, and elongate posterior-most dentary teeth that overlap the upper tooth row; (2) a prominent dorsomedian crest extending from the tip of the premaxillary rostrum, and expanding into a low ‘mound-like’ boss between the external bony nasal openings and orbits; (3) a pronounced convex projection on the posterolateral edge of the squamosals; and (4) platycoelous post-axial cervical vertebral centra that are substantially longer than high, and bear both lateral longitudinal ridges and ventral notches. Character state comparisons with the congeneric subfamily specifier Styxosaurus browni suggest that taxonomic distinction is possible, but equivocal. We, therefore, restrict our definition of Styxosaurus to morphologies observable in KUVP 1301. Furthermore, phylogenetic analysis of our first-hand data returns inconsistent elasmosaurid intra-clade relationships, especially with regard to Styxosaurinae. Consequently, we posit that a more targeted reassessment of Elasmosauridae is necessary to resolve both species-level topologies and higher taxonomy within the group. Sven Sachs* [sachs.pal@gmail.com] Naturkunde-Museum Bielefeld, Abteilung Geowissenschaften, Adenauerplatz 2, 33602 Bielefeld, Germany; Johan Lindgren [johan.lindgren@geol.lu.se], Department of Geology, Lund University, Sölvegatan 12, SE-223 62 Lund, Sweden; Benjamin P. Kear [benjamin.kear@em.uu.se] Museum of Evolution, Uppsala University, Norbyvägen 16, Uppsala SE-752 36, Sweden. *Also affiliated with: Im Hof 9, 51766 Engelskirchen, Germany. Received 26.5.2016; revised 13.7.2018; accepted 24.7.2018.
Large Language Models and Multimodal Retrieval for Visual Word Sense Disambiguation
Creators: name: Kritharoula, Anastasia
name: Lymperaiou, Maria
name: Stamou, Giorgos
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Visual Word Sense Disambiguation (VWSD) is a novel challenging task with the goal of retrieving an image among a set of candidates, which better represents the meaning of an ambiguous word within a given context. In this paper, we make a substantial step towards unveiling this interesting task by applying a varying set of approaches. Since VWSD is primarily a text-image retrieval task, we explore the latest transformer-based methods for multimodal retrieval. Additionally, we utilize Large Language Models (LLMs) as knowledge bases to enhance the given phrases and resolve ambiguity related to the target word. We also study VWSD as a unimodal problem by converting to text-to-text and image-to-image retrieval, as well as question-answering (QA), to fully explore the capabilities of relevant models. To tap into the implicit knowledge of LLMs, we experiment with Chain-of-Thought (CoT) prompting to guide explainable answer generation. On top of all, we train a learn to rank (LTR) model in order to combine our different modules, achieving competitive ranking results. Extensive experiments on VWSD demonstrate valuable insights to effectively drive future directions.
description: Conference on Empirical Methods in Natural Language Processing (EMNLP) 2023
Additional file 2: of Genetic manipulation of putrescine biosynthesis reprograms the cellular transcriptome and the metabolome
Creators: name: Page, Andrew
name: Cseke, Leland
name: Minocha, Rakesh
name: Swathi Turlapati
name: Gopi Podila
name: Ulanov, Alexander
name: Li, Zhong
name: Minocha, Subhash
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Methods for RNA extraction, cDNA preparation and labeling, microarray hybridization and processing, and metabolomic analysis. Supplemental data Microarrays: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79420 . Metabolomic Data: https://mynotebook.labarchives.com/share/ulav72/MjIuMXwxNzEzMTkvMTcvVHJlZU5vZGUvMzg1Mzg2MTkxNHw1Ni4x . (PDF 451 kb)
OSCAwards2024
Creators: name: Sarafoglou, Alexandra
name: Karvovskaya, Lena
Publisher: name: OSF
Year: 2024

description: Do you think a transparent research culture is important? Do you get enthusiastic about community engagement and science communication? Are you curious what projects are currently contributing to Open Science? Join us for the Open Science Community Amsterdam Awards. It’s a way to meet the community and get to know what Open Science is about.
It is the second time, that the Open Science Community Amsterdam (OSCA) is organizing the OSCAwards. Open Science is an international academic movement that makes scientific knowledge openly available, accessible and reusable for everyone. Do you want to learn about Open Science projects in Amsterdam? During this event, 10 nominations for OSCAwards will be awarded.
Several scientists, researchers, students and teachers will pitch their projects and involvement with Open Science.
title: Bank of Russia macroprudential policy
Creators: name: The Central Bank of the Russian Federation (Bank of Russia)
Publisher: name: Bank of Russia
Year: 2022
Subjects: subject: Economics and business
subject: FOS: Economics and business

description: The Bank of Russia pursues countercyclical policy in macroprudential regulation. In the conditions of the crisis in 2022 Q1, the Bank of Russia fully released the macroprudential capital buffer and significantly reduced the risk-weight add-ons for newly issued loans. This easing supported lending to the economy. After the tightening of the lending standards by banks, which is typical of the outbreak of a crisis, unsecured consumer lending (traditionally, a high-margin segment) demonstrated an emerging recovery trend and started to restore high-risk practices in recent months. Amid high uncertainty, banks might face increased risks associated with retail lending development. On the one hand, this might entail excessive growth in households’ debt burden. On the other hand, this might adversely affect the structural transformation of the Russian economy due to inadequate financing of the corporate sector and cause a rise in long-term macroeconomic risks.
Homotopy ribbon concordance and Alexander polynomials
Creators: name: Friedl, Stefan
name: Powell, Mark
Publisher: name: Universität Regensburg
Year: 2020
Subjects: subject: HOMOLOGY; Ribbon concordance; Alexander polynomial; Knot theory; Link theory
subject: 510 Mathematik

description: We show that if a linkJin the 3-sphere is homotopy ribbon concordant to a linkL, then the Alexander polynomial ofLdivides the Alexander polynomial ofJ.
Protanilla lini Terayama 2009
Creators: name: Hamer, Matthew T.
name: Weemaels, André Ibáñez
name: Fu, Yifan
name: Xuan, Liu
name: Tse, Cheung Yau Leo
name: Tang, Kit Lam
name: Guénard, Benoit
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Protanilla
Protanilla lini

description: Protanilla lini Terayama, 2009 – First record for Fujian Province and Hong Kong SAR.
Figure 1C; Figure 3A–F; Figure 4A–B; Figure 5C–D.
Protanilla lini Terayama, 2009: 126, figs. 113-118 (w.) TAIWAN. Indomalaya.
description: Published as part of Hamer, Matthew T., Weemaels, André Ibáñez, Fu, Yifan, Xuan, Liu, Tse, Cheung Yau Leo, Tang, Kit Lam & Guénard, Benoit, 2024, New insights into the diversity and distribution of Leptanillinae (Formicidae) within China, pp. 99-112 in Zootaxa 5471 (1) on page 104, DOI: 10.11646/zootaxa.5471.1.6, http://zenodo.org/record/12189798
Additional file 1: Figure S1. of Genetic manipulation of putrescine biosynthesis reprograms the cellular transcriptome and the metabolome
Creators: name: Page, Andrew
name: Cseke, Leland
name: Minocha, Rakesh
name: Swathi Turlapati
name: Gopi Podila
name: Ulanov, Alexander
name: Li, Zhong
name: Minocha, Subhash
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified

description: The pathway for the biosynthesis of polyamines and related metabolites starting from the assimilation of nitrogen (Adapted from Majumdar et al. 2016). Figure S2. (A, B) - Quality control scatter plots showing expression level for data that passed CV and dye-swap tests. Red spots indicate data that passed statistical analysis for differential expression between the control and the HP cells. Figure S3. The loading plots (S-plot) of the OPLS-DA results for the control and HP cell extracts on days 2 (A), 4 (B), and 6 (C). In the S-plot, each point represents a single metabolite (marker). The x-axis shows the variable contributions. The farther away a data point is from the 0 value, the more it contributes to sample variance. The y-axis shows the sample correlations within the same sample group. The farther away a metabolite is from the 0 value, the better is its correlation from injection to injection. As a result, the metabolites on both ends of the S-shaped curve represent the leading contributing ions from each sample group. The OPLS-DA is a multivariate analysis model which separates the systematic variation in X into two parts, one that is linearly related (and therefore predictive) to Y and one that is orthogonal to Y (unrelated); the Y-predictive/related part represents the between-class variation, the Y-orthogonal (ToPo) part constitutes the within-class variation. (DOCX 1653Â kb)
Additional file 3: Table S1. of Genetic manipulation of putrescine biosynthesis reprograms the cellular transcriptome and the metabolome
Creators: name: Page, Andrew
name: Cseke, Leland
name: Minocha, Rakesh
name: Swathi Turlapati
name: Gopi Podila
name: Ulanov, Alexander
name: Li, Zhong
name: Minocha, Subhash
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Computational Biology

description: Summary of changes in expression of genes involved in polyamine metabolism. For abbreviations see Fig. 1. Sequences for AS, CARB, DAO, NAGK, NAGPR, NAOD, NAOGAcT, ODC, OTC and SPDS were not represented on the microarray. Table S2. Functional clustering of gene models showing significant (P ≤ 0.05) differences (≥2 fold) between the HP and the control cell lines on both day 3 and day 5. Table S3. Functional clustering of gene models showing significant (P ≤ 0.05) differences (≥2 fold) between the HP and the control cell lines on day 3 only. Table S4. Functional clustering of gene models showing significant (P ≤ 0.05) differences (≥2 fold) between the HP and the control cell lines on day 5 only. Table S5. List of metabolites that were positively identified in poplar control and HP cell lines. ND = not detectable. Values that are significantly different (P ≤ 0.05) in the HP cells from the corresponding control cells on a given day are marked in bold. (DOCX 103 kb)
Optimizing numerical performance of enzymatic coagulation models: Insight into proteolysis and gelation dynamics
Creators: name: Ansari, Zeeshan
name: Rae, Mitchell
name: Kumar, Jitendra
name: Singh, Mehakpreet
Publisher: name: University of Limerick
Year: 2024
Subjects: classificationCode: 49
subject: Mathematical sciences

description: Cheese manufacturing from milk is a meticulous process that transforms casein micelles into various cheeses through enzymatic action and controlled steps. During enzymatic milk coagulation, three key processes occur: enzymatic proteolysis, coagulation, and gelation. Enzymatic proteolysis breaks down milk proteins, leading to coagulation, where the milk thickens. Gelation then forms a gel-like structure that separates curds from whey, essential for cheese production. To model the enzymatic coagulation of milk, a new mathematical frame-work is derived based on the conservative formulation of the coagulation equation. To solve this nonlinear complex model, an efficient numerical approach utilizing the finite volume scheme is developed. This method features a straightforward mathematical formulation and robustness for implementation on both uniform and nonuniform grids, enhancing its applicability across various scenarios compared to existing approaches [M. Tsagkaridis et al., “Analysis of turbulent coagulation in a jet with discretised population balance and DNS,” J. Fluid Mech. 937, A25 (2022)]. We also discuss the stability condition for the time step to ensure a positive solution. The validation of this new approach involves analyzing number density functions and their integral moments for different gelling and non-gelling kernels. Results indicate that the method captures zeroth and first-order moments with high precision while also computing second-order moments and average micelle sizes formed in the system. Additionally, the impact of the proteolysis constant on gelation is thoroughly examined. This comprehensive capability and detailed analysis provide deeper insight into the enzymatic coagulation process, facilitating its efficient optimization
Leptanilla bethyloides Griebenow 2024
Creators: name: Hamer, Matthew T.
name: Weemaels, André Ibáñez
name: Fu, Yifan
name: Xuan, Liu
name: Tse, Cheung Yau Leo
name: Tang, Kit Lam
name: Guénard, Benoit
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Leptanilla
Leptanilla bethyloides

description: Leptanilla bethyloides Griebenow, 2024
Leptanilla bethyloides Griebenow, 2024: 102, figs. 11, 12 (m.) CHINA (Hong Kong).
Material examined (n = 3)
Mainland China, Hong Kong SAR, Tai Po River; 22.4359 114.1584; 165 m a.s.l.; 3–10 May 2022; Malaise trap; Coll. M. T. Hamer; male TPR2M1 IBBL • Mainland China, Hong Kong SAR, Lantau Island, Ngong Ping; 22.25252 113.90662 ± 40m ²; 472 m a.s.l.; 29 June–24 July 2023; Malaise trap; Coll. M. T. Hamer et al; male NGP-PM2-8 IBBL • Mainland China, Hong Kong SAR, Lantau, Wong Lung Hang; 22.26964 113.95248 ± 40m ²; 265 m a.s.l.; 15 August – 05 September 2023; Malaise trap; Coll. M. T. Hamer et al; male WLHL-M1-2 IBBL • Mainland China, Hong Kong SAR, R-Farm; 22.45 114.09; 17 m a.s.l.; 16–26 July 2023; Malaise trap; Coll. A. Reshchikov; male MT000201 ZRC.
description: Published as part of Hamer, Matthew T., Weemaels, André Ibáñez, Fu, Yifan, Xuan, Liu, Tse, Cheung Yau Leo, Tang, Kit Lam & Guénard, Benoit, 2024, New insights into the diversity and distribution of Leptanillinae (Formicidae) within China, pp. 99-112 in Zootaxa 5471 (1) on page 107, DOI: 10.11646/zootaxa.5471.1.6, http://zenodo.org/record/12189798
Additional file 2: of Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map
Creators: name: Linhai Wang
name: Qiuju Xia
name: Yanxin Zhang
name: Xiaodong Zhu
name: Xiaofeng Zhu
name: Donghua Li
name: Xuemei Ni
name: Gao, Yuan
name: Haitao Xiang
name: Wei, Xin
name: Jingyin Yu
name: Zhiwu Quan
name: Xiurong Zhang
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Consists of Figures S1â  S7. Figure S1. Distributions of the interval distances between adjacent markers on the genetic map; Figure S2. Length distributions of the anchored scaffolds; Figure S3. Genetic distance vs. physical distance. The genetic position of the markers was plotted against the corresponding physical position; Figure S4. Variations in sesame plant height and the height of the first capsule-bearing node in the two parents and the RILs; Figure S5. Boxplots of sesame plant height and related traits of the population across three trial sites; Figure S6. Histograms of the segregation of sesame plant height and related traits across three trial sites; Figure S7. Distributions of the L*, a*, and b* color space values across two trial sites. (DOCX 1406 kb)
Additional file 3: Figure S3. of Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica
Creators: name: Gkarmiri, Konstantia
name: Finlay, Roger
name: Alstrรถm, Sadhna
name: Thomas, Elizabeth
name: Cubeta, Marc
name: Hรถgberg, Nils
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Physiology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Volcano plots of R. solani genes that are differentially expressed when challenged with a) S4 Serratia proteamaculans and b) AS13 Serratia plymuthica bacteria compared to growth in monoculture. Red dots represent significant and blue dots non-significant, differential expression of up- and down- regulated genes.
Additional file 13: Figure S11. of Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica
Creators: name: Gkarmiri, Konstantia
name: Finlay, Roger
name: Alstrรถm, Sadhna
name: Thomas, Elizabeth
name: Cubeta, Marc
name: Hรถgberg, Nils
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Comparison of Biological Process annotations of R. solani genes between S4 Serratia proteamaculans and AS13 Serratia plymuthica treatments. a) Bar Chart of Gene Ontology (GO) annotations between S4-AS13 upregulated genes, b) Bar Chart of GO annotations between S4-AS13 downregulated genes (Values taken from WEGO).
Injectivity results for coarse homology theories
Creators: name: Bunke, Ulrich
name: Engel, Alexander
name: Kasprowski, Daniel
name: Winges, Christoph
Publisher: name: Universität Regensburg
Year: 2020
Subjects: subject: K-THEORY; CONJECTURE; 19D50 (primary); 20F65; 20F69 (secondary)
subject: 510 Mathematik

description: We show injectivity results for assembly maps using equivariant coarse homology theories with transfers. Our method is based on the descent principle and applies to a large class of linear groups or, more generally, groups with finite decomposition complexity.
Natural frequency trees improve diagnostic efficiency in Bayesian reasoning
Creators: name: Binder, Karin
name: Krauss, Stefan
name: Schmidmaier, Ralf
name: Braun, Leah
Publisher: name: Universität Regensburg
Year: 2021
Subjects: subject: ; Bayesian reasoning; Clinical reasoning; Diagnostic efficiency; Natural frequencies; Undergraduate medical students
subject: 510 Mathematik

description: When physicians are asked to determine the positive predictive value from the a priori probability of a disease and the sensitivity and false positive rate of a medical test (Bayesian reasoning), it often comes to misjudgments with serious consequences. In daily clinical practice, however, it is not only important that doctors receive a tool with which they can correctly judge-the speed of these judgments is also a crucial factor. In this study, we analyzed accuracy and efficiency in medical Bayesian inferences. In an empirical study we varied information format (probabilities vs. natural frequencies) and visualization (text only vs. tree only) for four contexts. 111 medical students participated in this study by working on four Bayesian tasks with common medical problems. The correctness of their answers was coded and the time spent on task was recorded. The median time for a correct Bayesian inference is fastest in the version with a frequency tree (2:55 min) compared to the version with a probability tree (5:47 min) or to the text only versions based on natural frequencies (4:13 min) or probabilities (9:59 min).The score diagnostic efficiency (calculated by: median time divided by percentage of correct inferences) is best in the version with a frequency tree (4:53 min). Frequency trees allow more accurate and faster judgments. Improving correctness and efficiency in Bayesian tasks might help to decrease overdiagnosis in daily clinical practice, which on the one hand cause cost and on the other hand might endanger patients' safety.
Constructing smooth and fully faithful tropicalizations for Mumford curves
Creators: name: Jell, Philipp
Publisher: name: Universität Regensburg
Year: 2020
Subjects: subject: COHOMOLOGY; Tropical geometry; Smooth tropical curves; Mumford curves; Extended skeleta; Faithful tropicalization
subject: 510 Mathematik

description: The tropicalization of an algebraic variety X is a combinatorial shadow of X, which is sensitive to a closed embedding of X into a toric variety. Given a good embedding, the tropicalization can provide a lot of information about X. We construct two types of these good embeddings for Mumford curves: fully faithful tropicalizations, which are embeddings such that the tropicalization admits a continuous section to the associated Berkovich space X-an of X, and smooth tropicalizations. We also show that a smooth curve that admits a smooth tropicalization is necessarily a Mumford curve. Our key tool is a variant of a lifting theorem for rational functions on metric graphs.
Agrilus macroderus Abeille de Perrin 1897
Creators: name: Jendek, Eduard
name: Nakládal, Oto
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus macroderus

description: Agrilus macroderus Abeille de Perrin, 1897
Examined specimens. BULGARIA. Belotintsi; 43°32'56"N, 022°55'48"E; 6-1985; 1 ♀ (EJCB) // Burgas, Vlas; 42°42'58"N, 027°46'E; 5-1989; 1 ♂ (EJCB) // Melnik; 41°31'26"N, 023°23'30"E; 7-1989; 1 ♂ (EJCB) // Melnik, Rozhen; 41°32'01"N, 023°26'E; 6-2013; 1 (EJCB) // Sandanski; 41°34'39"N, 023°17'05"E; 6-1985; 1 (EJCB). SLOVENIA. Čmotiče; 45°33'N, 013°54'E; 6-2008; alt. 400 m; 2 (EJCB). SYRIA. Latakia. Djebel Ansariya, E of Sharkiya; 35°36'N, 036°13'E; 6-1989; alt. 1200 m; 1 ♂, 1 ♀ (EJCB).
Remarks. See note at A. pecirkai.
description: Published as part of Jendek, Eduard & Nakládal, Oto, 2019, Taxonomic, distributional and biological study of the genus Agrilus (Coleoptera: Buprestidae). Part II, pp. 401-459 in Zootaxa 4554 (2) on page 428, DOI: 10.11646/zootaxa.4554.2.5, http://zenodo.org/record/2623782
GREEMA: Proposal and Experimental Verification of Growing Robot by Eating Environmental MAterial for Landslide Disaster
Creators: name: Tsunoda, Yusuke
name: Sato, Yuya
name: Osuka, Koichi
Publisher: name: arXiv
Year: 2023
Subjects: subject: Robotics (cs.RO)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: In areas that are inaccessible to humans, such as the lunar surface and landslide sites, there is a need for multiple autonomous mobile robot systems that can replace human workers. In particular, at landslide sites such as river channel blockages, robots are required to remove water and sediment from the site as soon as possible. Conventionally, several construction machines have been deployed to the site for civil engineering work. However, because of the large size and weight of conventional construction equipment, it is difficult to move multiple units of construction equipment to the site, resulting in significant transportation costs and time. To solve such problems, this study proposes a novel growing robot by eating environmental material called GREEMA, which is lightweight and compact during transportation, but can function by eating on environmental materials once it arrives at the site. GREEMA actively takes in environmental materials such as water and sediment, uses them as its structure, and removes them by moving itself. In this paper, we developed and experimentally verified two types of GREEMAs. First, we developed a fin-type swimming robot that passively takes water into its body using a water-absorbing polymer and forms a body to express its swimming function. Second, we constructed an arm-type robot that eats soil to increase the rigidity of its body. We discuss the results of these two experiments from the viewpoint of Explicit-Implicit control and describe the design theory of GREEMA.
Numerical semigroups generated by primes
Creators: name: Hellus, Michael
name: Rechenauer, Anton
name: Waldi, Rolf
Publisher: name: Universität Regensburg
Year: 2020
Subjects: subject: ; Numerical semigroup; Diophantine Frobenius problem; Goldbach conjecture; Wilf's conjecture on numerical semigroups
subject: 510 Mathematik

description: Let p(1) = 2, p(2) = 3, p(3) = 5,. be the consecutive prime numbers, S-n the numerical semigroup generated by the primes not less than p(n) and u(n) the largest irredundant generator of S-n. We will show, that u(n) similar to 3p(n). Similarly, for the largest integer f(n) not contained in S-n, by computational evidence (https://www.uni-regensburg.de/Fakul taeten/nat_Fak_I/Hellus/table 1.pdf) we suspect that (1) f(n) is an odd number for n = 5 and (2) f(n) similar to 3p n; further (3) 4p(n) > f(n+1) for n >= 1. If f n is odd for large n, then f(n) similar to 3p(n). In case f(n) similar to 3p(n) every large even integer x is the sum of two primes. If 4p(n) > f(n+1) for n >= 1, then the Goldbach conjecture holds true. Further, Wilf's question in Wilf (Am Math Mon 85:562-565, 1978) has a positive answer for the semigroups S-n.
Additional file 14: Figure S12. of Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica
Creators: name: Gkarmiri, Konstantia
name: Finlay, Roger
name: Alström, Sadhna
name: Thomas, Elizabeth
name: Cubeta, Marc
name: Högberg, Nils
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Comparison of Molecular Function annotations of R. solani genes between the induced (log2FPKM > 0) and repressed (log2FPKM
Leptanilla japonica Baroni Urbani 1977
Creators: name: Hamer, Matthew T.
name: Weemaels, André Ibáñez
name: Fu, Yifan
name: Xuan, Liu
name: Tse, Cheung Yau Leo
name: Tang, Kit Lam
name: Guénard, Benoit
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Leptanilla
Leptanilla japonica

description: Notes on Leptanilla japonica from Hong Kong
Leptanilla sp. cf. japonica (CASENT0914941) was first recorded from Hong Kong SAR based on a worker (Wong & Guénard, 2016). In Griebenow (2024), it was stated that L. japonica occurred in Hong Kong, but communications with Z. Griebenow clarified that this specimen had not been examined. Morphological features of CASENT0914941 which differ to L.japonica include (but not limited to) a more narrow head with straight lateral margins, a wider propodeum and petiole in dorsal view, and reduced hair density across the head dorsum. We therefore redesignate this specimen as L. sp. cf. japonica, until more certifications can be made – ideally with the collection of more material. Intriguingly, multiple male specimens have been collected in Hong Kong that key to the Western Palaearctic Leptanilla tenuis Santschi, 1907 within Griebenow (2024). Such specimens differ enough from L. tenuis in their genital morphology and geographical range to be a new species (Griebenow pers. comm). Specifically, when compared to L. japonica, the gonostyli are slender and bifurcated in the Hong Kong specimens, but penial sclerites are similar. It is possible that these specimens are the male caste of L. sp. cf. japonica. We therefore postpone describing this species as new until a hopeful simultaneous collection of both workers and males, or indirect association using molecular data becomes available in the future.
description: Published as part of Hamer, Matthew T., Weemaels, André Ibáñez, Fu, Yifan, Xuan, Liu, Tse, Cheung Yau Leo, Tang, Kit Lam & Guénard, Benoit, 2024, New insights into the diversity and distribution of Leptanillinae (Formicidae) within China, pp. 99-112 in Zootaxa 5471 (1) on page 107, DOI: 10.11646/zootaxa.5471.1.6, http://zenodo.org/record/12189798
Additional file 15: Figure S13. of Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica
Creators: name: Gkarmiri, Konstantia
name: Finlay, Roger
name: Alström, Sadhna
name: Thomas, Elizabeth
name: Cubeta, Marc
name: Högberg, Nils
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Plant Biology
subject: Computational Biology

description: Comparison of Biological Process annotations of R. solani genes between the induced (log2FPKM > 0) and repressed (log2FPKM
Quest for the golden ratio universality class
Creators: name: Popkov, V.
name: Schütz, G. M.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: Cellular Automata and Lattice Gases (nlin.CG)
subject: FOS: Physical sciences

description: Using mode coupling theory the conditions for all allowed dynamical universality classes for the conserved modes in one-dimensional driven systems are presented in closed form as a function of the stationary currents and their derivatives. With a view on the search for the golden ratio universality class the existence of some families of microscopic models is ruled out a priori by using an Onsager-type macroscopic current symmetry. At equal mean densities of the conserved quantities the golden modes can only appear if the currents are antisymmetric under interchange of the conserved densities and if these densities are correlated, but not in the symmetric case where at equal densities one mode is always diffusive and the second may be either Kardar-Parisi-Zhang (KPZ), modified KPZ, 3/2-Lévy, or also diffusive. We also show that the predictions of mode coupling theory for a noisy chain of harmonic oscillators are exact.
description: 12 pages