cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Supplementary Information for "Linking continuous and discrete models of cell birth and migration" from Linking discrete and continuous models of cell birth and migration
Creators: name: Martinson, William
name: Volkening, Alexandria
name: Schmidtchen, Markus
name: Venkataraman, Chandrasekhar
name: Carrillo, Jose
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 490199
subject: Applied mathematics not elsewhere classified

description: This PDF document provides additional detail pertaining to the derivation of the models used in the main text of the paper, the numerical algorithms used to simulate the models, the initial conditions used, and additional results from our estimation procedure for melanophores and xanthophores that were mentioned in the main text but could not be included due to space limitations.
Additional file 4: Figure S2. of Mapping a major QTL responsible for dwarf architecture in Brassica napus using a single-nucleotide polymorphism marker approach
Creators: name: Yankun Wang
name: Wenjing Chen
name: Chu, Pu
name: Shubei Wan
name: Yang, Mao
name: Mingming Wang
name: Rongzhan Guan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary 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: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Polymorphism identification of the SSR markers. (DOCX 1028Â kb)
Additional file 1: Table S1. of New multiplex real-time PCR approach to detect gene mutations for spinal muscular atrophy
Creators: name: Zhidai Liu
name: Penghui Zhang
name: Xiaoyan He
name: Liu, Shan
name: Tang, Shi
name: Zhang, Rong
name: Xinbin Wang
name: Junjie Tan
name: Peng, Bin
name: Jiang, Li
name: Siqi Hong
name: Zou, Lin
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology

description: The guideline for SMA diagnosis and typing. (DOC 34Â kb)
Variational models for the interaction of surfactants with curvature – existence and regularity of minimizers in the case of flexible curves
Creators: name: Brand, Christopher
name: Dolzmann, Georg
name: Pluda, Alessandra
Publisher: name: Universität Regensburg
Year: 2021
Subjects: subject: 510 Mathematik

description: Existence and regularity of minimizers for a geometric variational problem is shown. The variational integral models an energy contribution of the interface between two immiscible fluids in the presence of surfactants and includes a Helfrich type contribution, a Frank type contribution and a coupling term between the orientation of the surfactants and the curvature of the interface. Analytical results are proven in a one–dimensional situation for curves.
Recovering seldom-used theorems of vector calculus and their application to problems of electromagnetism
Creators: name: Perez-Garrido, Antonio
Publisher: name: arXiv
Year: 2023
Subjects: subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: In this paper, we use differential forms to prove a number of theorems of integral vector calculus that are rarely found in textbooks. Two of them, as far as the author knows, have not been published before. Some possible applications to problems in physics are shared including a general approach for computing net forces and torques on current-carrying loops that yields insights that are not evident from the standard approach.
description: To be published in American Journal of Physics
Additional file 4: of Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Creators: name: Jiang, Yue
name: Xuejian Xiong
name: Danska, Jayne
name: Parkinson, John
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Venn diagram illustrating overlap of genera defined by putative 16S rRNA and mRNA reads for five metatranscriptomic datasets. Numbers indicate the number of genera defined by each type of sequence data. (PDF 112 kb)
Bootstrapping Smooth Conformal Defects in Chern-Simons-Matter Theories
Creators: name: Gabai, Barak
name: Sever, Amit
name: Zhong, De-liang
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The expectation value of a smooth conformal line defect in a CFT is a conformal invariant functional of its path in space-time. For example, in large $N$ holographic theories, these fundamental observables are dual to the open string partition function in AdS. In this paper, we develop a bootstrap method for studying them and apply it to conformal line defects in Chern-Simons matter theories. In these cases, the line bootstrap is based on three minimal assumptions -- conformal invariance of the line defect, large $N$ factorization, and the spectrum of the two lowest-lying operators at the end of the line. On the basis of these assumptions, we solve the one-dimensional CFT on the line and systematically compute the defect expectation value in an expansion around the straight line. We find that the conformal symmetry of a straight defect is insufficient to fix the answer. Instead, imposing the conformal symmetry of the defect along an arbitrary curved line leads to a functional bootstrap constraint. The solution to this constraint is found to be unique.
description: 33 pages. v2: Typos corrected. JHEP version
MOESM1 of Census-derived migration data as a tool for informing malaria elimination policy
Creators: name: Ruktanonchai, Nick
name: Bhavnani, Darlene
name: Sorichetta, Alessandro
name: Bengtsson, Linus
name: Carter, Keith
name: CĂłrdoba, Roberto
name: Menach, Arnaud Le
name: Lu, Xin
name: Wetter, Erik
name: Erbach-Schoenberg, Elisabeth Zu
name: Tatem, Andrew
Publisher: name: Figshare
Year: 2016
Subjects: subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
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: Science Policy

description: Additional file 1. Supplementary analysis of mobile phone data. This analysis shows some possible biases in the mobile phone data from Haiti and discusses briefly their possible implications.
Additional file 13: of Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Creators: name: Jiang, Yue
name: Xuejian Xiong
name: Danska, Jayne
name: Parkinson, John
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Marine Biology
subject: Computational Biology

description: Taxonomic contributions to select hydrogenase modules as defined through protein-interaction networks for the four well sampled datasets. Each network indicates the taxonomic representation of components of hydrogenases as defined through protein-interaction networks for four metatranscriptome datasets: mouse, kimchi, cow and deep sea. Pie charts indicate genes, with coloured sectors indicating the relative contribution to gene expression for each taxon, size of pie chart indicates relative expression (see key). (PDF 190 kb)
Construction of Initial Data Sets for Lorentzian Manifolds with Lightlike Parallel Spinors
Creators: name: Ammann, Bernd
name: Kröncke, Klaus
name: Müller, Olaf
Publisher: name: Universität Regensburg
Year: 2021
Subjects: subject: DIRAC OPERATOR; HOLONOMY; STABILITY;
subject: 510 Mathematik

description: Lorentzian manifolds with parallel spinors are important objects of study in several branches of geometry, analysis and mathematical physics. Their Cauchy problem has recently been discussed by Baum, Leistner and Lischewski, who proved that the problem locally has a unique solution up to diffeomorphisms, provided that the intial data given on a space-like hypersurface satisfy some constraint equations. In this article we provide a method to solve these constraint equations. In particular, any curve (resp. closed curve) in the moduli space of Riemannian metrics on M with a parallel spinor gives rise to a solution of the constraint equations on M x (a, b) (resp. M x S-1).
Additional file 1: of A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis
Creators: name: Huang, Yong
name: Shwu-Fan Ma
name: Vij, Rekha
name: Oldham, Justin
name: Herazo-Maya, Jose
name: Broderick, Steven
name: Strek, Mary
name: White, Steven
name: D. Hogarth
name: Sandbo, Nathan
name: Lussier, Yves
name: Gibson, Kevin
name: Kaminski, Naftali
name: Garcia, Joe
name: Noth, Imre
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
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: Computational Biology

description: Additional Methods and Tables. (DOCX 103 kb)
The spectrum of simplicial volume of non-compact manifolds
Creators: name: Heuer, Nicolaus
name: Löh, Clara
Publisher: name: Universität Regensburg
Year: 2021
Subjects: subject: Simplicial volume; Non-compact manifolds
subject: 510 Mathematik

description: We show that, in dimension at least 4, the set of locally finite simplicial volumes of oriented connected open manifolds is [0, infinity]. Moreover, we consider the case of tame open manifolds and some low-dimensional examples.
Linear bosonic quantum field theories arising from causal variational principles
Creators: name: Dappiaggi, Claudio
name: Finster, Felix
name: Oppio, Marco
Publisher: name: Universität Regensburg
Year: 2022
Subjects: subject: DYNAMICS; Causal variational principles; Algebraic quantum field theory; Causal fermion systems
subject: 510 Mathematik
subject: 49S05-49Q20-81T05-81T20

description: It is shown that the linearized fields of causal variational principles give rise to linear bosonic quantum field theories. The properties of these field theories are studied and compared with the axioms of local quantum physics. Distinguished quasi-free states are constructed.
Bose-enhanced relaxation of driven atom-molecule condensates
Creators: name: Pimenov, Dimitri
name: Mueller, Erich J.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: Motivated by recent experiments we study the interconversion between ultracold atomic and molecular condensates, quantifying the resulting oscillations and their slow decay. We find that near equilibrium the dominant damping source is the decay of condensed molecules into non-condensed pairs, with a pair kinetic energy that is resonant with the frequency of the oscillating atom-molecule interconversions. The decay, however, is non-exponential, as strong population of the resonant pairs leads to Bose enhancement. Introducing an oscillating magnetic field, which periodically modulates the molecular binding energy, enhances the oscillations at short times. However, the resulting enhancement of the pair-production process results in an accelerated decay which rapidly cuts off the initial oscillation growth.
description: journal version
Leveraging Large Language Models for Generating Labeled Mineral Site Record Linkage Data
Creators: name: Pyo, Jiyoon
name: Chiang, Yao-Yi
Publisher: name: arXiv
Year: 2024
Subjects: subject: Information Retrieval (cs.IR)
subject: Artificial Intelligence (cs.AI)
subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Record linkage integrates diverse data sources by identifying records that refer to the same entity. In the context of mineral site records, accurate record linkage is crucial for identifying and mapping mineral deposits. Properly linking records that refer to the same mineral deposit helps define the spatial coverage of mineral areas, benefiting resource identification and site data archiving. Mineral site record linkage falls under the spatial record linkage category since the records contain information about the physical locations and non-spatial attributes in a tabular format. The task is particularly challenging due to the heterogeneity and vast scale of the data. While prior research employs pre-trained discriminative language models (PLMs) on spatial entity linkage, they often require substantial amounts of curated ground-truth data for fine-tuning. Gathering and creating ground truth data is both time-consuming and costly. Therefore, such approaches are not always feasible in real-world scenarios where gold-standard data are unavailable. Although large generative language models (LLMs) have shown promising results in various natural language processing tasks, including record linkage, their high inference time and resource demand present challenges. We propose a method that leverages an LLM to generate training data and fine-tune a PLM to address the training data gap while preserving the efficiency of PLMs. Our approach achieves over 45\% improvement in F1 score for record linkage compared to traditional PLM-based methods using ground truth data while reducing the inference time by nearly 18 times compared to relying on LLMs. Additionally, we offer an automated pipeline that eliminates the need for human intervention, highlighting this approach's potential to overcome record linkage challenges.
description: 11 pages, 10 figures
Cornucistela Campbell 1980
Creators: name: Novák, Vladimír
name: Nabozhenko, Maxim
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Tenebrionidae
Cornucistela

description: Genus Cornucistela Campbell, 1980
Cornucistela Campbell, 1980: 133 (type species Cornucistela serrata Campbell, 1980; by original designation).
description: Published as part of Novák, Vladimír & Nabozhenko, Maxim, 2019, A new species of Cornucistela Campbell, 1980 (Coleoptera: Tenebrionidae: Alleculinae: Gonoderina) from Iran, pp. 267-274 in Zootaxa 4612 (2) on page 268, DOI: 10.11646/zootaxa.4612.2.9, http://zenodo.org/record/3234357
Cornucistela serrata Campbell 1980
Creators: name: Novák, Vladimír
name: Nabozhenko, Maxim
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Tenebrionidae
Cornucistela
Cornucistela serrata

description: Cornucistela serrata Campbell, 1980
(Figs 8–11)
Cornucistela serrata Campbell, 1980: 135.
Type locality. Saudi Arabia, Wadi Khumra, 700 m.
Type material. Paratype specimen: wl: Wadi Khumra / 24.VIII.1978 / 700 m [hb]// SAUDI ARABIA / W. Buttiker [hb]//yl: PARATYPE [pb]/ Cornucistela serrata [hb]/ J. M. Campbell / CNC No. [pb] 16091 [hb]; (CNC).
Distribution. Saudi Arabia.
description: Published as part of Novák, Vladimír & Nabozhenko, Maxim, 2019, A new species of Cornucistela Campbell, 1980 (Coleoptera: Tenebrionidae: Alleculinae: Gonoderina) from Iran, pp. 267-274 in Zootaxa 4612 (2) on page 272, DOI: 10.11646/zootaxa.4612.2.9, http://zenodo.org/record/3234357
Modelling the performance and sustainability of urban vegetation as Nature-based Solutions in current and future climate
Creators: name: Zhang, Ziyan
Publisher: name: Imperial College London
Year: 2022

description: Urbanization has become a concern due to a need in development for an increasing population. Climate change due to elevated global carbon emissions is predicted to increase the severity of extreme weather events, and will amplify urban-related risks such as surface flooding and urban heat island effects. Vegetation as the key component of urban Nature-based Solutions has been identified as an effective tool to provide a resilient and sustainable urban environment. However, its performance and sustainability in different countries and under climate change has not been fully understood yet. The main aim of this PhD study is to examine and understand the performance of urban vegetation in flood control, heat mitigation and carbon sequestration across multiple major cities. To do so, I implemented the state-of-the-art ecohydrological model T&C for an urban set-up, and used and further developed urban ecohydrological model UT&C for multiple cities at a global scale. First, I focused on London, UK, and tested the performance of urban parks and grassed swales in urban flood control with different urban drainage designs. I found a clear improvement in performance of urban parks and grassed swales in urban flood control when urban green spaces are integrated with urban drainage systems. Then, I identified the key drivers to urban heat island intensities and investigated the role of vegetation and its irrigation in heat mitigation across multiple Northern Hemispheric cities. Lastly, I designed a plausible urban street-level greening scenario supported by local rainwater harvesting (RWH) systems. I examined the long-term performance and co-benefits of urban greening and RWH under the extreme climate change scenario RCP8.5. The outcome of this thesis can provide a vital guidance on urban planning for different cities in order to reduce surface flooding, mitigate urban heat and offset urban carbon emission especially under climate change.
Additional file 1: Table S1. of Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
Creators: name: Yang, Bo
name: Wang, Yong
name: Qian, Pei-Yuan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Plant Biology
subject: Computational Biology

description: Conserved Markers used to identify sub-regions. (DOCX 12Â kb)
Towards a Density Preserving Objective Function for Learning on Point Sets
Creators: name: Jayasinghe, Haritha
name: Brilakis, Ioannis
Publisher: name: Apollo - University of Cambridge Repository
Year: 2024

description: Accurate measurement of the discrepancy between point sets is crucial for point cloud learning tasks. Chamfer distance (CD) is favoured over more effective loss metrics such as Earth Mover's Distance (EMD) for this purpose due to its computational efficiency. Previous investigations into loss function improvements almost exclusively focus on 3D losses as static metrics, and ignore their dynamic behaviour during training. We show that directly modifying the correspondence criteria can prevent clustering of points during training, and lead to more uniform point distributions. We propose UniformCD, a novel 3D distance metric that prioritises matching the relative local densities of point neighbourhoods when assigning correspondences. Experiments demonstrate that the proposed loss function improves performance on a variety of tasks such as cloud completion, parametric model optimisation, as well as downstream task performance when used for self-supervised learning, achieving SOTA EMD results among point set objective functions. We show that the proposed method exploits local density information to converge towards globally optimum density distributions, narrowing the disparity between CD and EMD. Source code will be publicly released.
Samichus Attems 1911
Creators: name: Korsós, Zoltán
name: Read, Helen J.
Publisher: name: Zenodo
Year: 2012
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Spirostreptida
Iulomorphidae
Samichus

description: Samichus Attems, 1911
attemsii Verhoeff, 1944 (pp. 44–45, Figs 13 –19): Western Australia decoratus Attems, 1911 (p. 198, Figs 85–91): Western Australia
Stenjulomorpha Schubart, 1966 (was considered as a subgenus of Iulomorpha by Jeekel 1971, 2004, but as a full genus by Hamer 1998, and Shelley et al. 2000)
concors (Attems, 1928) (p. 318, Figs 260–264): South Africa (from Iulomorpha concors: Schubart 1966) rixosa (Attems, 1928) (p. 318–319, Figs 243–246): South Africa (from Iulomorpha rixosa: Schubart 1966) panda Schubart, 1966 (p. 192, Figs 187–190): South Africa
penicillata Schubart, 1966 (p. 194, Figs 191–194): South Africa
Thaumaceratopus Verhoeff, 1924
cervinus Verhoeff, 1924 (pp. 86–87, Figs 40, 55–58): Queensland, Australia elongatus Verhoeff, 1924 (pp. 87–88, Fig. 59): Queensland, Australia
Victoriocambala Verhoeff, 1944
bidentata Jeekel, 2009 (pp. 35–38, Figs 6–9): Victoria, Australia
buffalensis Verhoeff, 1944 (pp. 42–43, Figs 9–12): Victoria, Australia (Jeekel 2009: pp. 38–40, Figs 10–13)
Zinagon Chamberlin, 1957
chilensis (Silvestri, 1903): Chile (from Iulomorpha chinensis: Jeekel 2004, = Nannolene nigrescens Attems, 1903: Silvestri 1904, 1905, Chamberlin 1957, = Dimerogonus chilensis: Silvestri 1904, 1905, = Zinagon osorno Chamberlin, 1957 syn. n.)
description: Published as part of Korsós, Zoltán & Read, Helen J., 2012, Redescription of Zinagon chilensis (Silvestri, 1903) from Chile, with a species list of Iulomorphidae from the Southern Hemisphere (Diplopoda: Spirostreptida: Epinannolenidea), pp. 39-48 in Zootaxa 3493 on page 46, DOI: 10.5281/zenodo.282448
The relationship between SV2A density and measures of brain function at rest and during cognitive tasks in schizophrenia
Creators: name: Shatalina, Ekaterina
Publisher: name: Imperial College London
Year: 2023

description: Schizophrenia is a common and disabling neuropsychiatric disorder associated with cognitive dysfunction. The latest in vivo data suggests patients with schizophrenia have lower synaptic terminal levels in the frontal cortex and in the anterior cingulate cortex, as well as in other brain regions. Functional magnetic resonance imaging (fMRI) studies of cognitive function show that aberrant activation of these and other regions is associated with cognitive dysfunction, both during cognitive tasks and at rest in people with schizophrenia. Given that fMRI signal has been shown to have a synaptic origin, this thesis focussed on testing a set of hypotheses around the potential link between synaptic terminal levels, measured by [11C]UCB-J positron emission tomography (PET), and brain function during cognitive tasks and at rest, measured by fMRI in patients with schizophrenia and controls. I additionally tested whether [11C]UCB-J distribution volume ratio (DVRCS), which measures synaptic vesicle protein 2A (SV2A) levels, was associated with task performance during task switching and during a working memory N-Back task. The main contributions of this thesis to the field are that aberrant brain function in schizophrenia at rest, during working memory and during task switching is not associated with interindividual differences in SV2A levels/synaptic density in controls or in patients with schizophrenia. In healthy controls, I found that working memory performance is associated with SV2A levels/synaptic density in a working memory specific prefrontal cortex region, but not with the magnitude of activation of this region under working memory load. In addition, in healthy controls switch cost is associated with SV2A/synaptic density in the parietal cortex, but not with brain activity during task switching. Importantly, neither relationship between cognitive function and SV2A levels was seen in patients with schizophrenia. Possible explanations for this may be that despite having comparable SV2A levels, patients with schizophrenia have different types of synapses contributing to total synaptic density, excitatory-inhibitory imbalance, or other factors that disrupt this relationship. At rest, associations between amplitude of low frequency fluctuations and SV2A levels were significantly different between patients with schizophrenia and control subjects, further supporting that schizophrenia may be associated with synaptic changes that are not captured by a general measure of synaptic density.
Additional file 1: of Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development
Creators: name: Dong, Qian
name: Mingxu Fang
name: Roychowdhury, Sugata
name: Bauer, Carl
Publisher: name: Figshare
Year: 2015
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Table S1. A table of all genes that are indirectly up and down regulated by CgrA. (PDF 159 kb)
Additional file 1: of
                     Mycoplasma ovipneumoniae induces sheep airway epithelial cell apoptosis through an ERK signalling-mediated mitochondria pathway
Creators: name: Yanan Li
name: Zhongjia Jiang
name: Xue, Di
name: Guangcun Deng
name: Li, Min
name: Xiaoming Liu
name: Yujiong Wang
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Original images of immunoblots for Figure 4B and Figure 5A. (PDF 860Â kb)
Hybrid skyrmion and anti-skyrmion phases in polar $C_{\rm 4v}$ systems
Creators: name: Hayami, Satoru
Publisher: name: arXiv
Year: 2024
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate the stability of the skyrmion crystal phase in a tetragonal polar system with the Dzyaloshinskii-Moriya interaction by focusing on the symmetry of ordering wave vectors forming the skyrmion crystal. Our analysis is based on numerical simulations for an effective spin model, which is derived from the weak-coupling regime in the Kondo lattice model on a polar square lattice. We show that a hybrid square skyrmion crystal consisting of Bloch and Néel spin textures emerges even under polar $C_{\rm 4v}$ symmetries when the ordering wave vectors correspond to low-symmetric wave vectors in momentum space, which is in contrast to the expectation from the Lifshitz invariants. We also show the instability toward the anti-skyrmion crystal and rhombic skyrmion crystal depending on the direction of the Dzyaloshinskii-Moriya vector in momentum space. Furthermore, we show that the regions of the skyrmion crystal phases are affected by taking into account the symmetric anisotropic exchange interaction. Our results open the potential direction of engineering the hybrid skyrmion crystal and anti-skyrmion crystal phases in polar magnets.
description: 10 pages, 9 figures
Broadband Cavity-Enhanced Absorption Spectroscopy (BBCEAS) Coupled with an Interferometer for On-Band and Off-Band Detection of Glyoxal
Creators: name: Flowerday, Callum E.
name: Thalman, Ryan
name: Asplund, Matthew C.
name: Hansen, Jaron C.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: Glyoxal CHOCHO is a trace gas in the atmosphere, often used as an indicator of biogenic emissions. It is frequently compared to formaldehyde concentrations, which serve as indicators of anthropogenic emissions, to gain insights into the characteristics of the environmental source. This study employed broadband cavity-enhanced absorption spectroscopy to detect gaseous CHOCHO, methylglyoxal, and $\mathrm{NO_2}$. Two different detection methods are compared. Spectrograph and CCD Detection: This approach involves coupling the system to a spectrograph with a charge-coupled device (CCD) detector. It achieved a 1 min 1-$σ$ detection limit of $2.5 \times 10^8$ molecules/cm$^3$, or 10 parts per trillion (ppt). Methylglyoxal and $\mathrm{NO_2}$ achieved 1 min 1-$σ$ detection limits of 34 ppt and 22 ppt, respectively. Interferometer and PMT Detection: In this method, an interferometer is used in conjunction with a photomultiplier tube (PMT) detector. It resulted in a 2 min 1-$σ$ detection limit of $1.5 \times 10^{10}$ molecules/cm$^3$, or 600 ppt. The $\mathrm{NO_2}$ 2 min 1-$σ$ detection limit was determined to be 900 ppt. Concentrations of methylglyoxal were difficult to determine using this method, as they appeared to be below the detection limit of the instrument. This study discusses the advantages and limitations of each of these detection methods.
Strictly one dimensional behavior emerging from dispersive two dimensional system: implications on metallic nanowires on semiconducting substrates
Creators: name: Sony, Keshab
name: Abdelwahab, Anas
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We studied single and two Su-Shreiffer-Heeger wires on a simple cubic semiconducting substrate. The wire-wire coupling is either perpendicular or diagonal hopping respecting the particle-hole and time-reversal symmetries. The hybridization to the substrate renormalizes the model parameters of the wires towards the hopping parameter of the substrate without changing the basic nature of perpendicular or diagonal coupling and it can mediate effective perpendicular hopping but not diagonal hopping in the absence of direct wire-wire coupling. This justifies the investigation of multi uniform tight binding wires with perpendicular or diagonal hopping parameters while neglecting the substrate. Perpendicularly coupled uniform wires reveal an anisotropic two dimensional band dispersion. Diagonally coupled uniform wires reveal strictly one dimensional bands parallel to the wires direction if the intra-wire hopping parameter is larger than twice the diagonal hopping parameter despite strong dispersion perpendicular to the wires. Otherwise, they reveal strictly one dimensional bands parallel and perpendicular to the wires direction simultaneously. We established the possibility of realizing strictly one dimensional properties emerging from dispersive two dimensional systems if time-reversal and particle-hole symmetries are respected. This can facilitate the investigations of Luttinger liquid in the Au/Ge(001) and Bi/InSb(001) surface reconstructions.
description: 15 pages, 10 figures
Management of macula-on giant retinal tear detachments– outcome of pars-plana-vitrectomy with silicone oil versus gas tamponade
Creators: name: Barth, Teresa
name: Radeck, Viola
name: Gamulescu, Maria-Andreea
name: Helbig, Horst
name: Märker, David
Publisher: name: Universität Regensburg
Year: 2024
Subjects: subject: Giant retinal tear, Rhegmatogenous retinal detachment, Pars-plana-vitrectomy, Endotamponade, Silicone oil, Gas tamponade
subject: 610 Medizin

description: Background To compare the outcome of eyes with a macula-on giant retinal tear (GRT) detachment treated with
pars-plana-vitrectomy (PPV) depending on the used endotamponade.
Methods All consecutive cases with a macula-on GRT-associated rhegmatogenous retinal detachment
(RRD) managed with PPV between 2007 and 2022 were retrospectively assessed depending on the selected
endotamponade. By reviewing medical charts and surgical protocols the pre- and intraoperative parameters were
analysed in detail. The number of vitreoretinal (VR) procedures needed for reattachment, the redetachment rate and
the functional outcome were evaluated. Eyes treated with primary silicone oil (SO) tamponade were compared to
eyes with primary gas tamponade. Cases with pre-existing conditions affecting outcome e.g. macula-off situation,
history of trauma, status after complicated cataract surgery, former VR surgery or proliferative vitreoretinopathy grade
C or higher were excluded.
Results Overall, 51 eyes of 45 patients with a macula-on GRT detachment were treated with PPV and SO (n = 32;
63%) or gas (n = 19; 37%) endotamponade in the observed period. Eyes with primary SO tamponade underwent on
average 2.3 (SD 0.8) VR procedures and had a redetachment rate of 13% (n = 4). Eyes with gas tamponade showed
a higher redetachment rate of 32% (n = 6) with a mean number of 1.6 (SD 1.0) PPV procedures. Postoperative bestcorrected
visual acuity (BCVA) was significantly better in eyes with primary gas tamponade (mean logMAR BCVA 0.32;
SD 0.30) compared to eyes with SO (mean logMAR BCVA 0.60; SD 0.42; p = 0.008).
Conclusions Surgical management of GRT-associated RRDs is complex. In clinical routine often SO is used as
endotamponade. Because of known disadvantages (second procedure necessary for SO removal, unexplained
SO-related visual loss, secondary glaucoma, SO emulsification) some VR surgeons prefer a gas tamponade. In
our cohort, eyes with a gas compared to SO tamponade showed higher redetachment rates. However, the final
postoperative BCVA was significantly better in eyes with gas compared to SO tamponade.
Sophonia Walker 1870
Creators: name: Gou, Guangli
name: Xing, Jichun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Cicadellidae
Sophonia

description: Genus Sophonia Walker, 1870
Sophonia Walker, 1870: 327; Li et al., 2020: 398. Type species: Sophonia rufitelum Walker, 1870.
Pseudonirvana Baker, 1923: 386. Type species: Pseudonirvana sandakanensis Baker, 1923
Quercinirvana Ahmed & Mahmood, 1970: 260. Type species: Quercinirvana longicephala Ahmed & Mahmood, 1970. Synonymised by Webb & Viraktamath, 2004: 4.
Description. Body medium-sized. Predominant color usually bright yellow with red, white or brown markings often including median longitudinal dorsal stripe, oblique lines near forewing costal margin and false eyespot near forewing apex.
Head including eyes narrower than greatest width of pronotum. Crown extended forward, usually subequal to or longer than width between eyes. Ocelli located at lateral edge of crown anterad of eyes. Frontoclypeus distinctly longer than width, with a median longtudinal ridge near dorsal margin. Forewing with four apical cells, appendix small. Hind wing with three apical cells. Hind femur apical setal formula 2+1+1. Hind tibia flattened and nearly straight, row PD with approximately 21–23 macrosetae; row AD with approximately 12–14 long stout setae and 1–3 shorter stout setae between each long seta.
Male genitalia. Male pygofer with strong apical setae, usually with one or more spinelike apical processes. Subgenital plate broad and long, with 3–8 strong setae. Aedeagus usually with paired or unpaired processes on shaft or atrium, or both; shaft usually curved dorsad. Connective Y-shaped, stem longer than arms. Style apex usually footlike, preapical lobe strongly produced.
Remarks. This genus is similar to Nirvana Kirkaldy, 1900 in external appearance including coloration, but can be distinguished by the male pygofer side usually with a distal process; the aedeagus with complex processes; and the subgenital plate relatively broad.
Distribution. Oriental Region, Palaearctic Region, Nearctic Region,Australian Region (adventive in continental USA, Hawaii, Spain and Portugal).
description: Published as part of Gou, Guangli & Xing, Jichun, 2024, Description of a new leafhopper species of the genus Sophonia Walker (Hemiptera: Cicadellidae: Evacanthinae) from China, pp. 411-421 in Zootaxa 5405 (3) on page 414, DOI: 10.11646/zootaxa.5405.3.4, http://zenodo.org/record/10603554
Exploring the genetic and epigenetic mechanisms underlying the evolution of oestrogen-receptor positive breast cancer
Creators: name: Ivanoiu, Mihaela Diana
Publisher: name: Imperial College London
Year: 2023

description: Up to 40% of patients treated for oestrogen-receptor positive breast cancer (ERBC) relapse with resistant tumours. Studies failed to identify driver mutations of relapse in at least 60% of patients, so I investigated the underlying genetic and epigenetic mechanisms. I analysed mutational signatures throughout ERBC evolution. Using published primary and metastatic cohorts, we showed that patients can be stratified based on mutational signatures. Using novel patient and in vitro datasets, we found that mutational signatures play a significant role in ERBC: APOBEC SBS2 and SBS13 are enriched at enhancers, clock-like SBS5 is enriched at expressed regions, and SBS2 is associated with top ERBC driver PIK3CA. We also showed that mutational signatures are context dependent, as they are shaped by genomic location, cellular lineage, endocrine therapy, and microenvironment. Last, we provided clues towards the aetiology of SBS2, SBS13 and SBS5. I analysed drivers of resistance to endocrine treatment. In a large-scale in vitro whole genome sequencing experiment, I failed to find recurrent mutations among known ERBC coding and non-coding drivers, while in a targeted sequencing analysis of two other cohorts I also failed to find novel coding drivers. I investigated the mechanism of Yin-Yang 1 (YY1) recruitment to chromatin. YY1 transcription factor is a major player in ER+ breast cancer biology, found at bona fide enhancers. We tested a model for YY1 binding to chromatin: a stimulus such as oestradiol induces changes in histone modifications, that in a combinatorial mode recruit YY1, which leads to chromatin remodelling mediated by its interactors. We found that YY1 is not inducible, while data on its recruitment by the histone code is more difficult to disentangle. SILAC nucleosome affinity purification revealed that YY1 binds to a combination of H3K and H4K acetylation, while loss of H4K16ac did not lead to loss of YY1 binding.
THE EFFECT OF ORGANIZATIONAL ATTRIBUTES ON THE FINANCIAL PERFORMANCE OF LISTED DEPOSIT MONEY BANKS IN NIGERIA
Creators: name: Nkechi Oluchukwu, Adebayo
Publisher: name: keith journal
Year: 2025
Subjects: Firm size, Board gender diversity, EPS

description: This study investigated the impact of firm attribute on performance of listed Deposit money banks in Nigeria from (2011-2020). Two research questions and corresponding two hypotheses were formulated for the study. Ex-post facto research design was employed in the study. The population of the study included all Deposit money banks quoted on the Nigerian Exchange Group (NXG) (NSE) as at 31st December 2020 with a sample size of Twelve (12) Deposit money banks selected from the population. The study relied on secondary sources of data which was obtained from Annual reports of sampled companies as provided by individual companies,

Nigerian              Exchange            Group   (NXG)   website                and        Machame            Database

(www.machameratios.company.site). Amongst other preliminary analysis and tests, the panel least square regression analysis was done in validating the hypotheses. The study found that firm size and board gender diversity has a statistically significant impact on performance. Consequent on the findings emanating from the study, the study recommended amongst others that there should be a reasonable mix of the board of directors and risk committee to recognize female directors as this will have direct impact on the firms’ image and goodwill. Also, the study recommends that, the managements of banks should find ways to improve and acquire the optimal utilization of their assets, while making maximum use of their resources during the operation processes as this would help them in improving their earnings.
MOESM2 of Effects of two kinds of imidazolium-based ionic liquids on the characteristics of steroid-transformation Arthrobacter simplex
Creators: name: Yanbing Shen
name: Lifang Wang
name: Jingting Liang
name: Tang, Rui
name: Wang, Min
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Plant Biology

description: Additional file 2. The identification of the [PrMIm]BF4-treated cells proteins.
Sophonia furcata Gou & Xing 2024, sp. nov.
Creators: name: Gou, Guangli
name: Xing, Jichun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Cicadellidae
Sophonia
Sophonia furcata

description: Sophonia furcata sp. nov.
Figs. 1–16
Description. Color pattern of anterior dorsum and face as in Figs. 1–4. Body yellow with orange-red halo around ocellus; eyes yellow dorsally, black ventrally; face yellow; frontoclypeus with yellow transverse carinae on both sides of longitudinal ridge; median longitudinal dorsal stripe absent; preapical brown spot of forewing very large. Head relatively short, crown slightly shorter than width between eyes. Other external features as in generic description.
Male genitalia. Pygofer side base broad, narrowed distad, lobe with forked distal process with short ventral and long dorsal branch weakly divergent; 13 macrosetae apically (Fig. 5). Subgenital plate long and broad, with 3 long macrosetae in the middle and several long and thin setae on distal area (Fig. 6). Aedeagus with preatrium well developed, atrium V-shaped in posterior view with each lateral arm bearing a short, sharply pointed medial and lateral projection distally; shaft relatively broad in lateral view, evenly curved dorsad, with pair of long, slender preapical processes extended laterad, apex tapered to blunt point in posterior view (Figs. 7–9). Connective 2.5x longer than basal width across arms. Style with basal half slender and broadening to the middle, apical foot relatively slender, elongate and arched.
Female genitalia. Pygofer with ventroposterior margin slightly incurved (Fig. 11). Female seventh sternite as broad as long at base, posterior margin roundly produced with slight median notch (Fig. 12). First valvula of ovipositor gradually broadened over most of length, then tapered to acute apex; sculpture strigate dorsally, granulose ventrally (Figs. 13, 14). Second valvulae toothed area confined to distal third, with ~14 small conical teeth somewhat irregularly spaced, gradually becoming smaller distally, apex pointed (Figs. 15, 16).
Measurement. Length (including tegmen): ♂, 5.4–5.8 mm; ♀, 5.9–6.2 mm.
Type Material. Holotype: ♂, CHINA: Sichuan Prov., Menghuocheng, 1 August 2022, coll. Lan Zhang (GUGC). Paratypes: 1♂ 2♀♀, same data as holotype; 15♂♂, Sichuan Prov., Longcanggou, 29 July 2022, coll. Lan Zhang (GUGC).
Remarks. This new species is similar to Sophonia fuscomarginata Li & Wang, 1991, but can be distinguished from the latter by the aedeagus with a pair of forked processes and the male pygofer side with a forked apical processes.
Etymology. The new species name is a modification of the Latin word “furca” (fork), referring to the male pygofer side and aedeagus with a pair of forked processes.
description: Published as part of Gou, Guangli & Xing, Jichun, 2024, Description of a new leafhopper species of the genus Sophonia Walker (Hemiptera: Cicadellidae: Evacanthinae) from China, pp. 411-421 in Zootaxa 5405 (3) on page 415, DOI: 10.11646/zootaxa.5405.3.4, http://zenodo.org/record/10603554
Additional file 2: of Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development
Creators: name: Dong, Qian
name: Mingxu Fang
name: Roychowdhury, Sugata
name: Bauer, Carl
Publisher: name: Figshare
Year: 2015
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
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: Marine Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Table S2. A table of all called CgrA ChIP-seq peaks and their locations on the genome. (PDF 286 kb)
Additional file 1: Figure S1. of Regulation of STEP61 and tyrosine-phosphorylation of NMDA and AMPA receptors during homeostatic synaptic plasticity
Creators: name: Jang, Sung-Soo
name: Royston, Sara
name: Xu, Jian
name: Cavaretta, John
name: Vest, Max
name: Lee, Kwan
name: Seungbae Lee
name: Jeong, Han
name: Lombroso, Paul
name: Chung, Hee
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases

description: Membrane-permeable TAT-STEP WT or C/S proteins alter STEP61–dependent Tyr-phosphorylation of GluN2B and GluA2. (A) Permeabilized immunostaining of cultured hippocampal neurons at 12 days in vitro that were incubated for 30 min with no fusion proteins (None), TAT-myc, TAT-STEP WT, or TAT-STEP C/S. Scale bars are 20 μm. (B) Background subtracted, mean intensity of myc fluorescence (n = 10–19 images per treatment). AU, arbitrary unit. (C–D) Quantification of the levels of Tyr1472–phosphorylated GluN2B (GluN2B-pY1472) and the level of GluA2 that were phosphorylated at Tyr 869, Tyr 873, and Tyr 876 (GluA2-p3Y) in CTL-treated neurons (from Fig. 4b–e) that were incubated with TAT-fusion proteins for 30 min. (C) TAT-STEP WT decreases basal Tyr-phosphorylation of GluN2B and GluA2, confirming that TAT-STEP WT increases STEP activity. (D) TAT-STEP C/S increases basal Tyr-phosphorylation of GluN2B and GluA2, confirming its ability to block dephosphorylation of STEP substrates. Data shown represent the mean ± SEM (*p