cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 7: Figure S6. of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Creators: name: Genshaft, Alex
name: Shuqiang Li
name: Gallant, Caroline
name: Darmanis, Spyros
name: Prakadan, Sanjay
name: Ziegler, Carly
name: Lundberg, Martin
name: Fredriksson, Simon
name: Hong, Joyce
name: Regev, Aviv
name: Livak, Kenneth
name: Landegren, Ulf
name: Shalek, Alex
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology
subject: 60506 Virology

description: Additional benchmarking of a combined PEA/STA workflow: ICAM1. aâ  c Validation of protein and RNA detection in single cells using a coupled PEA/STA script on the C1 throughout a PMA perturbation time course (0 hr = purple, 24 hr = green, 48 hr = blue). a RNA-FISH and IF staining of ICAM1 was performed to validate the C1-based, high-throughput RNA and protein measurements. Cyan (left) shows cell nuclei and boundaries, magenta ICAM1 protein (middle), and yellow ICAM1 RNA (right). Scale bars indicate 25 Îźm. b Qualitative agreement between the protein and RNA data obtained in situ and on the C1. Density distributions (each with their own arbitrary units) for ICAM1 RNA (left) and protein (right) obtained via qPCR (top) or in situ (bottom) staining. c Q-Q plots showing the range over which the PEA/STA measurements of ICAM1 track linearly with IF staining or in situ hybridization for the same. (PDF 107675 kb)
Evaluating the Design Features of an Intelligent Tutoring System for Advanced Mathematics Learning
Creators: name: Fang, Ying
name: He, Bo
name: Liu, Zhi
name: Liu, Sannyuya
name: Yan, Zhonghua
name: Sun, Jianwen
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mathematical Software (cs.MS)
subject: Artificial Intelligence (cs.AI)
subject: Computers and Society (cs.CY)
subject: History and Overview (math.HO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Xiaomai is an intelligent tutoring system (ITS) designed to help Chinese college students in learning advanced mathematics and preparing for the graduate school math entrance exam. This study investigates two distinctive features within Xiaomai: the incorporation of free-response questions with automatic feedback and the metacognitive element of reflecting on self-made errors.
Polypedilum (Tripodura) procerum Zhang, Song, Wang & Wang
Creators: name: Zhang, Ruilei
name: Song, Chao
name: Qi, Xin
name: Wang, Xinhua
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Chironomidae
Polypedilum
Polypedilum procerum

description: Polypedilum (Tripodura) procerum Zhang, Song, Wang & Wang
Polypedilum (Tripodura) procerum Zhang, Song, Wang & Wang, 2015: 575.
Material examined. Holotype (BDN. 21333), male. CHINA, Guangdong Province, Fengkai County, Heishiding Natural Conserve, 12. IV. 1985, light trap, X. Wang. Paratypes: 2 males. 1 male as holotype. 1 male: Fujian Province, Fuzhou City, on campus of Fuzhou Agricultural College, 22. IV. 1993, light trap, X. Wang.
Diagnostic characters. P. (T.) procerum Zhang & Wang can be separated from other related species by the following characters: tergite IX sub-circular; anal tergite bands very short, gradually narrowed, abruptly terminating at the base of tergite IX; superior volsella S-like, bare and very long, with a crotchet-like apex; inferior volsella slender, uniformly elongated.
Key characters of male imago. Total length 2.03–2.43 mm, wing length 1.08–1.46 mm. AR 0.86–1.24. Clypeus with 8–12 setae. Wing clear without marking. R with 13–18 setae; R1 with 8–9; R4+5 with 11–16. Squama with 4–5 setae. Dorsocentrals 7–9, acrostichals 9–15, prealars 2–3. Scutellum with 3–4 setae. Terminal scale of front tibia triangular and apically pointed; fore leg ratio 2.30–2.33.
Tergite IX sub-circular; anal tergite bands very short, gradually narrowed, interrupted at a long distance from the basal area of anal point. Anal point 40–50 µm long, broad and apically rounded; the lateral projections weak, about 5–8 µm long; dorsally with a V–shaped ridge bearing 5–6 setae on each side. Superior volsella S-shaped, pointed apically, with a crotchet–like apex, nearly reaching apex of anal point and distal part of inferior volsella. Inferior volsella 95–105 µm long, slender, uniformly elongated, curved inwards on its proximal half, distal half straight and uniformly elongated, dorsally with 4–5 orally projected setae, 1 longer apical seta present apically. HR 0.71–0.78, HV 1.66–2.23.
Distribution. The species distributes in Fujian and Guangdong Province (Oriental China).
Remarks. The species is very close to P. (T.) leptovolsellae Ree, 2009 and P. (T.) pseudacifer Zorina & Makarchenko, 2001 in having long, extremely slender and apically curved superior volsella. The differences between them consult Zhang, et al. (2015: 577).
description: Published as part of Zhang, Ruilei, Song, Chao, Qi, Xin & Wang, Xinhua, 2016, Taxonomic review on the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from China with eleven new species and a supplementary world checklist, pp. 1-53 in Zootaxa 4136 (1) on page 29, DOI: 10.11646/zootaxa.4136.1.1, http://zenodo.org/record/399782
Additional file 1: of Allyl-isothiocyanate treatment induces a complex transcriptional reprogramming including heat stress, oxidative stress and plant defence responses in Arabidopsis thaliana
Creators: name: Kissen, Ralph
name: Øverby, Anders
name: Winge, Per
name: Bones, Atle
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Developmental Biology
subject: Marine Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: List of genes whose expression is significantly affected (P < 0.05 and log2 ≥ 1 or ≤ -1) by the allyl-ITC treatment at one of the three time points. (PDF 1744 kb)
X-Ray Views of Galactic Accreting Pulsars in High-Mass X-Ray Binaries
Creators: name: Weng, Shan-Shan
name: Ji, Long
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Accreting X-ray pulsars, located in X-ray binaries, are neutron stars with magnetic fields as strong as $B\sim10^{12\text{--}13}$ G. This review offers a concise overview of the accretion and radiation processes of X-ray pulsars and summarizes their rich observational features, particularly focusing on complex and variable temporal phenomena, spectral properties, and evolution, the new window for X-ray polarimetry and multi-wavelength advances. We also briefly discuss other related systems, i.e., gamma-ray binaries and pulsating ultraluminous X-ray sources.
description: Universe 2024, 10(12), 453
Mezirinae Oshanin 1908
Creators: name: Heiss, Ernst
Publisher: name: Zenodo
Year: 2013
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Aradidae

description: Subfamily Mezirinae Oshanin 1908
description: Published as part of Heiss, Ernst, 2013, Aradidae from Vietnam I. Two new genera of micropterous Mezirinae (Hemiptera: Heteroptera: Aradidae), pp. 587-595 in Zootaxa 3694 (6) on page 588, DOI: 10.11646/zootaxa.3694.6.6, http://zenodo.org/record/219853
Coupled differential-algebraic equations framework for modeling six-degree-of-freedom flight dynamics of asymmetric fixed-wing aircraft
Creators: name: Marzouk, Osama A.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Systems and Control (eess.SY)
subject: Symbolic Computation (cs.SC)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences
subject: I.6.3; I.6.5; J.2
subject: 34M15, 65L80, 70E15

description: This study presents a comprehensive mathematical framework for modeling the flight dynamics of a six-degree-of-freedom fixed-wing aircraft as a rigid body with three control surfaces: rudder, elevators, and ailerons. The framework consists of 35 differential-algebraic equations (DAEs) and requires 30 constants to be specified. It supports both direct and inverse flight dynamics analyses. In direct dynamics, the historical profiles of control inputs (deflection angles and engine thrust) are specified, and the resulting flight trajectory is predicted. In inverse dynamics, the desired flight trajectory and an additional constraint are specified to determine the required control inputs. The framework employs wind axes for linear-momentum equations and body axes for angular-momentum equations, incorporates two flight path angles, and provides formulas for aerodynamic force and moment coefficients. Key advantages include improved computational efficiency, elimination of Euler angle singularities, and independence from symmetry assumptions with regard to the aircraft's moments of inertia. The model also accounts for nonlinear air density variations with altitude, up to 20 km above mean sea level, making it suitable for accurate and efficient flight dynamics simulations.
description: 22 pages, 9 figures, 3 tables, published journal article, open access, peer-reviewed
THE COMPARATIVE ANALYSIS OF PREPOSITIONS IN ENGLISH AND RUSSIAN LANGUAGES
Creators: name: Ruzimova, Lazizabonu
Publisher: name: Zenodo
Year: 2024

description: This article explores the similarities and differences in the usage of prepositions in English and Russian. It examines the forms, functions, and grammatical nuances of prepositions in both languages, highlighting key challenges faced by learners. While English prepositions are invariant and often idiomatic, Russian prepositions are intricately linked to the case system, requiring a deeper understanding of grammatical structures. By providing a detailed comparison, the article aims to facilitate a better grasp of prepositional usage for language learners and linguists alike.
title: Strong plasmonic enhancement of biexciton emission
title: controlled coupling of a single quantum dot to a gold nanocone antenna
titleType: Subtitle
Creators: name: Matsuzaki, Korenobu
name: Vassant, Simon
name: Liu, Hsuan-Wei
name: Dutschke, Anke
name: Hoffmann, Björn
name: Chen, Xuewen
name: Christiansen, Silke H.
name: Buck, Matthew R.
name: Hollingsworth, Jennifer A.
name: Götzinger, Stephan
name: Sandoghdar, Vahid
Publisher: name: Freie Universität Berlin
Year: 2017
Subjects: subject: Multiexcitonic transitions and emission
subject: semiconductor quantum dots
subject: optoelectronics
subject: nano-optics
classificationCode: 539
subject: Moderne Physik

description: Multiexcitonic transitions and emission of several photons per excitation comprise a very attractive feature of semiconductor quantum dots for optoelectronics applications. However, these higher-order radiative processes are usually quenched in colloidal quantum dots by Auger and other nonradiative decay channels. To increase the multiexcitonic quantum efficiency, several groups have explored plasmonic enhancement, so far with moderate results. By controlled positioning of individual quantum dots in the near field of gold nanocone antennas, we enhance the radiative decay rates of monoexcitons and biexcitons by 109 and 100 folds at quantum efficiencies of 60 and 70%, respectively, in very good agreement with the outcome of numerical calculations. We discuss the implications of our work for future fundamental and applied research in nano-optics.
Secondary frequency regulation in power networks with on-off load side participation
Creators: name: Kasis, A
name: Monshizadeh, N
name: Lestas, I
Publisher: name: IEEE
Year: 2017
Subjects: 4007 Control Engineering, Mechatronics and Robotics
40 Engineering

description: © 2017 IEEE. We study the problem of secondary frequency regulation where ancillary services are provided via load-side participation. In particular, we consider on-off loads that switch when prescribed frequency thresholds are exceeded in order to assist existing secondary frequency control mechanisms. We show that system stability is not compromised despite the switching nature of the loads. However, such control policies are prone to Zeno-like behavior, which limits the practicality of these schemes. As a remedy to this problem, we propose a hysteresis on-off policy and provide stability guarantees in this setting. We provide numerical investigations of the results on a realistic power network.
title: All-silicon polarized light source based on electrically excited whispering gallery modes in inversely tapered photonic resonators
Creators: name: Schmitt, Sebastian W.
name: Schwarzburg, Klaus
name: Sarau, George
name: Christiansen, Silke H.
name: Wiesner, Sven
name: Dubourdieu, Catherine
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: Nanofabrication
subject: Purcell enhancement
subject: Light emitting diodes
subject: P-N junctions
subject: Electrical properties and parameters
subject: Electroluminescence
subject: Whispering gallery wave
subject: Etching
subject: Silicon photonics
subject: Optoelectronic properties
classificationCode: 539
subject: Moderne Physik

description: As a result of its indirect bandgap, emitting photons from silicon in an efficient way remains challenging. Silicon light emitters that can be integrated seamlessly on a CMOS platform have been demonstrated; however, none satisfies an ensemble of key requirements such as a small footprint, room-temperature operation at low voltages, and emission of narrow and polarized lines with a high spectral power density in the near-infrared range. Here, we present an all-silicon electrically driven light emitting diode that consists of an inversely tapered half-ellipsoidal silicon photonic resonator containing a p–n junction used to excite whispering gallery modes (WGMs) inside the resonator. Under low voltage operation at room temperature, such a photonic silicon light-emitting diode exhibits a band-edge emission (900–1300 nm) with a wall-plug efficiency of 10−4. The emitted spectrum is amplified in multiple WGMs and shows peaks that are polarized and have linewidths Δλ as narrow as 0.33 nm and spectral power densities as high as 8 mW cm−2 nm−1. Considering its small footprint of ∼1 µm and remarkable emission characteristics, this silicon light source constitutes a significant step ahead toward fully integrated on-chip silicon photonics.
title: Zwischen Reformen und Revolutionen¨. Die Bestimmung des Menschen im Denken von Philipp Albert Stapfer (1766-1840)
Creators: name: Theilkäs, Lorenz
Publisher: name: Universität Bern
Year: 2024
Subjects: subject: 940 History of Europe

description: Das Leben, Denken und Wirken des Berner Theologen, Philosophen und Staatsmannes Philipp Albert Stapfer (1766-1840) wurde in der Forschung stets thematisch selektiv und auf sich zum Teil widersprechende Art und Weise besprochen. Eine umfassende Untersuchung, die Stapfers gesamtes Leben abdeckt, fehlt bis dato. Die vorliegende Arbeit versucht diese Lücke zu schliessen, indem sie Stapfers Denken systematisch und über sein gesamtes Leben hinweg untersucht. Dafür wurden zwei Untersuchungszeiträume definiert und miteinander verglichen: Der erste Zeitraum ist der zwischen 1792 und 1800, in dem Stapfer als Lehrer und Professor in Bern tätig war und als erster Minister der Künste und Wissenschaften in der Helvetik amtete. Der zweite Zeitraum erstreckt sich von Stapfers Engagement im französischen Réveil ab den späten 1810er Jahren bis zu seinem Lebensende 1840. In beiden Zeiträumen liegt der Fokus der Untersuchung auf Stapfers Denken, das unter dem Leitmotiv der spätaufklärerischen Idee der Bestimmung des Menschen rekonstruiert wird. Als systembildende Idee vermag sie alle wesentlichen theologischen, philosophischen, pädagogischen und staatsphilosophischen Überzeugungen von Stapfer zu fassen. Fundiert ist die Arbeit mit den geschichtstheoretischen Arbeiten des britischen Historikers Mark Bevir. Sein Konzept des «web of beliefs» sowie seine synchronen und diachronen Erklärungsansätze menschlichen Handeln und Weltverstehens liessen mich Konstanten und Entwicklungen im Denken von Stapfer herausarbeiten. Dominierende Konstante im Denken Stapfers ist die Frage nach der Bestimmung des Menschen selbst. Zu bestimmen, was sie ist und wie sie zu realisieren sei, trieb ihn sein Leben lang um. In Anlehnung an den deutschen Philosophen Immanuel Kant meinte er die Bestimmung des Menschen in der Realisierung des Höchsten Gutes zu erkennen, das sich aus den beiden Teilgütern Sittlichkeit und Glückseligkeit zusammensetzt. Um sittlich zu werden, habe der Mensch, so Stapfer, seinen Willen nach moralischen Grundsätzen zu bestimmen. Dazu müssen sich die Menschen zu einem ethischen Gemeinwesen zusammenschliessen. Tun sie dies, so können sie darauf hoffen, dass ihnen Gott in einem Leben nach dem Tod Glückseligkeit spenden wird. Während Stapfer diese Grundüberzeugungen sein Leben lang behielt, veränderten sich auch einige seiner Auffassungen. So wandelte sich beispielsweise seine Überzeugung, mit welchen Hilfsmitteln der Mensch seinen Willen bestmöglich moralisch bestimmen kann und inwiefern er dies aus sich selbst heraus tun kann (Suffizienzfrage). Ergänzt wird die Rekonstruktion von Stapfers Denken mit Einblicken in seine Biografie sowie zwei kürzeren Darstellungen, wie er während der Helvetik und dem französischen Réveil versucht hat, seine Überzeugungen zu realisieren.
Variation in the intensity ratio at each wavelength point of the Si iv 1394/1403 Å lines. Spectral diagnostics of a bifurcated eruption
Creators: name: Zhou, Yi'an
name: Yan, Xiaoli
name: Xue, Zhike
name: Yang, Liheng
name: Wang, Jincheng
name: Xu, Zhe
Publisher: name: arXiv
Year: 2024
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Aims. This study aims to investigate the deviation of the intensity ratio of the \ion{Si}{IV} 1394 Å and 1403 Å emission lines from the expected value of 2 in the optically thin regime, as observed in many recent studies.
 Methods. We analyzed the integrated intensity ratio ($R$) and the wavelength-dependent ratio ($r(Δλ)$) in a small bifurcated eruption event observed by the Interface Region Imaging Spectrograph (IRIS).
 Results. Despite the relatively complex line profiles, most of the intensity ratio $R$ of \ion{Si}{IV} lines remained greater than 2 in the loops. The ratio $r(Δλ)$ varied in the line core and wings, changing distinctly from 2.0 to 3.3 along the wavelength. At certain positions, the \ion{Si}{IV} 1394 Å and 1403 Å lines exhibited different Doppler velocities.
 Conclusions. When diagnosing the spectra of small active region events, not only the impact of opacity but also the influence of resonance scattering should be considered. We propose that the ratio $r(Δλ)$ can serve as an indicator of the resonance scattering and opacity effect of the \ion{Si}{IV} line.
description: 8 pages, 6 figures
Additional file 2 of Why are medical students so motivated to learn ultrasound skills? A qualitative study
Creators: name: Pless, Anina
name: Hari, Roman
name: Harris, Michael
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: Supplementary Material 2
Additional file 1: of Effect of a patient decision aid (PDA) for type 2 diabetes on knowledge, decisional self-efficacy, and decisional conflict
Creators: name: Robert. Bailey
name: Pfeifer, Michael
name: Shillington, Alicia
name: Harshaw, Qing
name: Funnell, Martha
name: VanWingen, Jeffrey
name: Nanada Col
Publisher: name: Figshare
Year: 2016
Subjects: subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy
subject: 60506 Virology

description: T2DM Medication Knowledge Questions. (DOCX 16Â kb)
Additional file 9: Figure S8. of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Creators: name: Genshaft, Alex
name: Shuqiang Li
name: Gallant, Caroline
name: Darmanis, Spyros
name: Prakadan, Sanjay
name: Ziegler, Carly
name: Lundberg, Martin
name: Fredriksson, Simon
name: Hong, Joyce
name: Regev, Aviv
name: Livak, Kenneth
name: Landegren, Ulf
name: Shalek, Alex
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: PCA separation of the various time points (0 hr = purple, 24 hr = green, 48 hr = blue). a A PCA over all quantitative protein targets and the corresponding ROC curves (b) for all three time points generated from random forest decision categorization with AUC of 0.98, 0.94, and 0.86 for 0 hr, 24 hr, and 48 hr, respectively. c A PCA over all quantitative RNA targets and the corresponding ROC curves (d) for all three time points generated from random forest decision categorization with AUC of 0.81, 0.80, and 0.57 for 0 hr, 24 hr, and 48 hr, respectively. e A PCA over all quantitative protein and RNA targets and the corresponding ROC curves (f) for all three time points generated from random forest decision categorization with AUC of 0.99, 0.94, and 0.84 for 0 hr, 24 hr, and 48 hr, respectively. For a, c, e, axis labels indicate which PC was used and what percent variance it explains. (PDF 269 kb)
Additional file 1: of Fast and high temperature hyperthermia coupled with radiotherapy as a possible new treatment for glioblastoma
Creators: name: Borasi, Giovanni
name: Nahum, Alan
name: Margarethus Paulides
name: Gibin Powathil
name: Russo, Giorgio
name: Fariselli, Laura
name: Lamia, Debora
name: Cirincione, Roberta
name: Forte, Giusi
name: Borrazzo, Cristian
name: Caccia, Barbara
name: Castro, Elisabetta Di
name: Pozzi, Silvia
name: Gilardi, Maria
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer

description: Reports the results of four trials of clinical HT. (DOCX 18 kb)
title: Synthetic Image Rendering Solves Annotation Problem in Deep Learning Nanoparticle Segmentation
Creators: name: Mill, Leonid
name: Wolff, David
name: Gerrits, Nele
name: Philipp, Patrick
name: Kling, Lasse
name: Vollnhals, Florian
name: Ignatenko, Andrew
name: Jaremenko, Christian
name: Huang, Yixing
name: Christiansen, Silke H.
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: helium ion microscopy
subject: image analysis
subject: machine learning
subject: nanoparticles
subject: segmentation
subject: toxicology
classificationCode: 530
subject: Physik

description: Nanoparticles occur in various environments as a consequence of man-made processes, which raises concerns about their impact on the environment and human health. To allow for proper risk assessment, a precise and statistically relevant analysis of particle characteristics (such as size, shape, and composition) is required that would greatly benefit from automated image analysis procedures. While deep learning shows impressive results in object detection tasks, its applicability is limited by the amount of representative, experimentally collected and manually annotated training data. Here, an elegant, flexible, and versatile method to bypass this costly and tedious data acquisition process is presented. It shows that using a rendering software allows to generate realistic, synthetic training data to train a state-of-the art deep neural network. Using this approach, a segmentation accuracy can be derived that is comparable to man-made annotations for toxicologically relevant metal-oxide nanoparticle ensembles which were chosen as examples. The presented study paves the way toward the use of deep learning for automated, high-throughput particle detection in a variety of imaging techniques such as in microscopies and spectroscopies, for a wide range of applications, including the detection of micro- and nanoplastic particles in water and tissue samples.
Additional file 5: Figure S4. of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Creators: name: Genshaft, Alex
name: Shuqiang Li
name: Gallant, Caroline
name: Darmanis, Spyros
name: Prakadan, Sanjay
name: Ziegler, Carly
name: Lundberg, Martin
name: Fredriksson, Simon
name: Hong, Joyce
name: Regev, Aviv
name: Livak, Kenneth
name: Landegren, Ulf
name: Shalek, Alex
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology
subject: 60506 Virology

description: Additional benchmarking of a combined PEA/STA workflow: BIRC5. aâ  c Validation of protein and RNA detection in single cells using a coupled PEA/STA script on the C1 throughout a PMA perturbation time course (0 hr = purple, 24 hr = green, 48 hr = blue). a RNA-FISH and IF staining of BIRC5 was performed to validate the C1-based, high-throughput RNA and protein measurements. Cyan (left) shows cell nuclei and boundaries, magenta BIRC5 protein (middle), and yellow BIRC5 RNA (right). Scale bars indicate 25 Îźm. b Qualitative agreement between the protein and RNA data obtained in situ and on the C1. Density distributions (each with their own arbitrary units) for BIRC5 RNA (left) and protein (right) obtained via qPCR (top) or in situ (bottom) staining. c Q-Q plots showing the range over which the PEA/STA measurements of BIRC5 track linearly with IF staining or in situ hybridization for the same. (PDF 79799 kb)
Tunable beam splitting via photorefractive nonlinearity and its applications in chiral waveguide induction and vortex generation
Creators: name: Chen, Hechong
name: Liu, Zihan
name: Lian, Shengdi
name: Quan, Qingying
name: Malomed, Boris A.
name: Li, Shuobo
name: Zhang, Yong
name: Li, Huagang
name: Deng, Dongmei
Publisher: name: arXiv
Year: 2024
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We report experimental observation and theoretical explanation of novel propagation regimes for optical beams in an artificial nonlinear material with outstanding photorefractive properties. Nondiffractive beams, which keep their shapes invariant in the free space, feature self-splitting from the middle in two separating secondary beams, due to the light-matter interaction. The splitting degree is controlled by means of a phase-pre-modulation method. We propose applications of the self-splitting to the creation of an effectively chiral waveguide and the generation of even-order vortices.
MOESM1 of Star fruit toxicity: a cause of both acute kidney injury and chronic kidney disease: a report of two cases
Creators: name: R. Abeysekera
name: S. Wijetunge
name: N. Nanayakkara
name: A. Wazil
name: N. Ratnatunga
name: T. Jayalath
name: A. Medagama
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Computational Biology

description: Additional file 1. CARE Checklist (2013) of information to include when writing a case report.
Additional file 1: of A systematic, realist review of zooprophylaxis for malaria control
Creators: name: Blรกnaid Donnelly
name: Berrang-Ford, Lea
name: Ross, Nancy
name: Michel, Pascal
Publisher: name: Figshare
Year: 2015
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Pharmacology
subject: Developmental Biology
subject: Computational Biology

description: Articles excluded from review and reasons for exclusion.
APEX$^2$: Adaptive and Extreme Summarization for Personalized Knowledge Graphs
Creators: name: Li, Zihao
name: Fu, Dongqi
name: Ai, Mengting
name: He, Jingrui
Publisher: name: arXiv
Year: 2024
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: Databases (cs.DB)
subject: Symbolic Computation (cs.SC)
subject: FOS: Computer and information sciences

description: Knowledge graphs (KGs), which store an extensive number of relational facts, serve various applications. Recently, personalized knowledge graphs (PKGs) have emerged as a solution to optimize storage costs by customizing their content to align with users' specific interests within particular domains. In the real world, on one hand, user queries and their underlying interests are inherently evolving, requiring PKGs to adapt continuously; on the other hand, the summarization is constantly expected to be as small as possible in terms of storage cost. However, the existing PKG summarization methods implicitly assume that the user's interests are constant and do not shift. Furthermore, when the size constraint of PKG is extremely small, the existing methods cannot distinguish which facts are more of immediate interest and guarantee the utility of the summarized PKG. To address these limitations, we propose APEX$^2$, a highly scalable PKG summarization framework designed with robust theoretical guarantees to excel in adaptive summarization tasks with extremely small size constraints. To be specific, after constructing an initial PKG, APEX$^2$ continuously tracks the interest shift and adjusts the previous summary. We evaluate APEX$^2$ under an evolving query setting on benchmark KGs containing up to 12 million triples, summarizing with compression ratios $\leq 0.1\%$. The experiments show that APEX outperforms state-of-the-art baselines in terms of both query-answering accuracy and efficiency.
description: Accepted by KDD 2025. 27 pages
title: Growing Research Networks on Mycorrhizae for Mutual Benefits
Creators: name: Ferlian, Olga
name: Biere, Arjen
name: Bofante, Paola
name: Buscot, François
name: Eisenhauer, Nico
name: Fernandez, Ivan
name: Hause, Bettina
name: Hermann, Sylvie
name: Krajinski-Barth, Franziska
name: Rillig, Matthias C.
Publisher: name: Freie Universität Berlin
Year: 2018
Subjects: subject: mycorrhiza
subject: integration
subject: organizational level
subject: synergies
classificationCode: 580
subject: Pflanzen (Botanik)
classificationCode: 579
subject: Mikroorganismen, Pilze, Algen

description: Research on mycorrhizal interactions has traditionally developed into separate disciplines addressing different organizational levels. This separation has led to an incomplete understanding of mycorrhizal functioning. Integration of mycorrhiza research at different scales is needed to understand the mechanisms underlying the context dependency of mycorrhizal associations, and to use mycorrhizae for solving environmental issues. Here, we provide a road map for the integration of mycorrhiza research into a unique framework that spans genes to ecosystems. Using two key topics, we identify parallels in mycorrhiza research at different organizational levels. Based on two current projects, we show how scientific integration creates synergies, and discuss future directions. Only by overcoming disciplinary boundaries, we will achieve a more comprehensive understanding of the functioning of mycorrhizal associations.
title: Author Correction: Novel diagnostic and therapeutic techniques reveal changed metabolic profiles in recurrent focal segmental glomerulosclerosis
Creators: name: Müller-Deile, Janina
name: Sarau, George
name: Kotb, Ahmed M.
name: Jaremenko, Christian
name: Rolle-Kampczyk, Ulrike E.
name: Daniel, Christoph
name: Kalkhof, Stefan
name: Christiansen, Silke H.
name: Schiffer, Mario
Publisher: name: Freie Universität Berlin
Year: 2022
Subjects: subject: Diagnostic markers
subject: Focal segmental glomerulosclerosis
subject: Glomerular diseases
subject: Glomerulus
subject: Kidney
subject: Mass spectrometry
subject: Podocytes
subject: Raman spectroscopy
classificationCode: 539
subject: Moderne Physik

description: Idiopathic forms of Focal Segmental Glomerulosclerosis (FSGS) are caused by circulating permeability factors, which can lead to early recurrence of FSGS and kidney failure after kidney transplantation. In the past three decades, many research endeavors were undertaken to identify these unknown factors. Even though some potential candidates have been recently discussed in the literature, “the” actual factor remains elusive. Therefore, there is an increased demand in FSGS research for the use of novel technologies that allow us to study FSGS from a yet unexplored angle. Here, we report the successful treatment of recurrent FSGS in a patient after living-related kidney transplantation by removal of circulating factors with CytoSorb apheresis. Interestingly, the classical published circulating factors were all in normal range in this patient but early disease recurrence in the transplant kidney and immediate response to CytoSorb apheresis were still suggestive for pathogenic circulating factors. To proof the functional effects of the patient’s serum on podocytes and the glomerular filtration barrier we used a podocyte cell culture model and a proteinuria model in zebrafish to detect pathogenic effects on the podocytes actin cytoskeleton inducing a functional phenotype and podocyte effacement. We then performed Raman spectroscopy in the < 50 kDa serum fraction, on cultured podocytes treated with the FSGS serum and in kidney biopsies of the same patient at the time of transplantation and at the time of disease recurrence. The analysis revealed changes in podocyte metabolome induced by the FSGS serum as well as in focal glomerular and parietal epithelial cell regions in the FSGS biopsy. Several altered Raman spectra were identified in the fractionated serum and metabolome analysis by mass spectrometry detected lipid profiles in the FSGS serum, which were supported by disturbances in the Raman spectra. Our novel innovative analysis reveals changed lipid metabolome profiles associated with idiopathic FSGS that might reflect a new subtype of the disease.
Polypedilum (Tripodura) spathum Zhang & Wang
Creators: name: Zhang, Ruilei
name: Song, Chao
name: Qi, Xin
name: Wang, Xinhua
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Chironomidae
Polypedilum
Polypedilum spathum

description: Polypedilum (Tripodura) spathum Zhang & Wang
Polypedilum (Tripodura) spathum Zhang & Wang, 2007: 789.
Material examined. Holotype: male (BDN. 06753) CHINA, Yunnan Province, Menglun County, 12. IV. 1987, light trap, H. Zou. Paratypes: 13 males, as the holotype.
Diagnostic characters. The spatula-shaped superior volsella of the species is unique in the subgenus. The high fore leg ratio (2.63–2.89), high number of median setae (20–28) on tergite IX and the low number of setae (2–3) on the inferior volsella will separate the species from other members in the subgenus.
Key characters of male imago. Total length 2.59–2.92, 2.74 mm. Wing length 1.57–1.70, 1.64 mm. AR 1.32– 1.58, 1.44. Temporal setae 9–11. Clypeus with 14–22, 18 setae. Vein R with 20–25, 22 setae; R1 with 16–21, 18; R4+5 with 35–43, 39. Squama with 4–6, 5 setae. Dorsocentrals 11–17, 14; acrostichals 17–24, 20; prealars 4–5, 5. Scutellum with 12–16, 14 setae. Front leg ratio 2.63–2.89, 2.75.
Tergite IX with 20–28, 25 median setae. Laterosternite with 2–3 setae. Anal point 58–72, 65 µm long, broad and distal half transparent; lateral projection absent. Superior volsella spatula-shaped, with 2 long setae on distal margin. Inferior volsella slender, 101–112, 106 µm long, with 2–3 setae. HR 0.90–1.06, 0.97. HV 1.80–2.04, 1.97.
Distribution. The species distributes in Yunnan Province (Oriental China).
description: Published as part of Zhang, Ruilei, Song, Chao, Qi, Xin & Wang, Xinhua, 2016, Taxonomic review on the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from China with eleven new species and a supplementary world checklist, pp. 1-53 in Zootaxa 4136 (1) on page 33, DOI: 10.11646/zootaxa.4136.1.1, http://zenodo.org/record/399782
Additional file 13: Figure S12. of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Creators: name: Genshaft, Alex
name: Shuqiang Li
name: Gallant, Caroline
name: Darmanis, Spyros
name: Prakadan, Sanjay
name: Ziegler, Carly
name: Lundberg, Martin
name: Fredriksson, Simon
name: Hong, Joyce
name: Regev, Aviv
name: Livak, Kenneth
name: Landegren, Ulf
name: Shalek, Alex
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Correlation between protein and RNA: MET. Presented are the correlations of the various MET STAs with MET protein (by PEA) across time points (0 hr = purple, 24 hr = green, 48 hr = blue). We observe that the strong increase in correlation after stimulation is most noted in MET.5_R (spliced short isoform) and MET.6_R (exon 10), with the other STAs showing a modest increase in correlation at 24Â hr that becomes negative by 48Â hr. (PDF 122 kb)
Additional file 11: Figure S10. of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Creators: name: Genshaft, Alex
name: Shuqiang Li
name: Gallant, Caroline
name: Darmanis, Spyros
name: Prakadan, Sanjay
name: Ziegler, Carly
name: Lundberg, Martin
name: Fredriksson, Simon
name: Hong, Joyce
name: Regev, Aviv
name: Livak, Kenneth
name: Landegren, Ulf
name: Shalek, Alex
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Change in average, standard deviation, and frequency of expression. Density traces (each with their own arbitrary units) for change in mean, standard deviation, and frequency of expression are shown for genes quantified as both RNA (a) and protein (b). Each row depicts a time point transition (24 – 0 hr, 48 – 24 hr, 48 – 0 hr for the top, middle, and bottom rows, respectively) for every gene with at least two cells above detection in every time point for both RNA and protein (19 genes). The ticks display individual measurements from each time point transition. (PDF 508 kb)
Additional File 1:
Creators: name: Chen, Jenny
name: Shishkin, Alexander
name: Xiaopeng Zhu
name: Kadri, Sabah
name: Maza, Itay
name: Guttman, Mitchell
name: Hanna, Jacob
name: Regev, Aviv
name: Garber, Manuel
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
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: Developmental Biology

description: Supplementary figures and tables. (PDF 3.85 MB)
title: Novel diagnostic and therapeutic techniques reveal changed metabolic profiles in recurrent focal segmental glomerulosclerosis
Creators: name: Müller-Deile, Janina
name: Sarau, George
name: Kotb, Ahmed M.
name: Jaremenko, Christian
name: Rolle-Kampczyk, Ulrike E.
name: Daniel, Christoph
name: Kalkhof, Stefan
name: Christiansen, Silke H.
name: Schiffer, Mario
Publisher: name: Freie Universität Berlin
Year: 2021
Subjects: subject: Diagnostic markers
subject: Focal segmental glomerulosclerosis
subject: Glomerular diseases
subject: Glomerulus
subject: Kidney
subject: Mass spectrometry
subject: Podocytes
subject: Raman spectroscopy
classificationCode: 570
subject: Biowissenschaften; Biologie

description: Idiopathic forms of Focal Segmental Glomerulosclerosis (FSGS) are caused by circulating permeability factors, which can lead to early recurrence of FSGS and kidney failure after kidney transplantation. In the past three decades, many research endeavors were undertaken to identify these unknown factors. Even though some potential candidates have been recently discussed in the literature, “the” actual factor remains elusive. Therefore, there is an increased demand in FSGS research for the use of novel technologies that allow us to study FSGS from a yet unexplored angle. Here, we report the successful treatment of recurrent FSGS in a patient after living-related kidney transplantation by removal of circulating factors with CytoSorb apheresis. Interestingly, the classical published circulating factors were all in normal range in this patient but early disease recurrence in the transplant kidney and immediate response to CytoSorb apheresis were still suggestive for pathogenic circulating factors. To proof the functional effects of the patient’s serum on podocytes and the glomerular filtration barrier we used a podocyte cell culture model and a proteinuria model in zebrafish to detect pathogenic effects on the podocytes actin cytoskeleton inducing a functional phenotype and podocyte effacement. We then performed Raman spectroscopy in the < 50 kDa serum fraction, on cultured podocytes treated with the FSGS serum and in kidney biopsies of the same patient at the time of transplantation and at the time of disease recurrence. The analysis revealed changes in podocyte metabolome induced by the FSGS serum as well as in focal glomerular and parietal epithelial cell regions in the FSGS biopsy. Several altered Raman spectra were identified in the fractionated serum and metabolome analysis by mass spectrometry detected lipid profiles in the FSGS serum, which were supported by disturbances in the Raman spectra. Our novel innovative analysis reveals changed lipid metabolome profiles associated with idiopathic FSGS that might reflect a new subtype of the disease.
title: Ultralow‐parameter denoising: trainable bilateral filter layers in computed tomography
Creators: name: Wagner, Fabian
name: Thies, Mareike
name: Gu, Mingxuan
name: Huang, Yixing
name: Pechmann, Sabrina
name: Patwari, Mayank
name: Ploner, Stefan
name: Aust, Oliver
name: Uderhardt, Stefan
name: Schett, Georg
name: Christiansen, Silke H.
name: Maier, Andreas
Publisher: name: Freie Universität Berlin
Year: 2022
Subjects: subject: bilateral filter
subject: denoising
subject: known operator learning
subject: low-dose CT
classificationCode: 530
subject: Physik

description: Background Computed tomography (CT) is widely used as an imaging tool to visualize three-dimensional structures with expressive bone-soft tissue contrast. However, CT resolution can be severely degraded through low-dose acquisitions, highlighting the importance of effective denoising algorithms. Purpose Most data-driven denoising techniques are based on deep neural networks, and therefore, contain hundreds of thousands of trainable parameters, making them incomprehensible and prone to prediction failures. Developing understandable and robust denoising algorithms achieving state-of-the-art performance helps to minimize radiation dose while maintaining data integrity. Methods This work presents an open-source CT denoising framework based on the idea of bilateral filtering. We propose a bilateral filter that can be incorporated into any deep learning pipeline and optimized in a purely data-driven way by calculating the gradient flow toward its hyperparameters and its input. Denoising in pure image-to-image pipelines and across different domains such as raw detector data and reconstructed volume, using a differentiable backprojection layer, is demonstrated. In contrast to other models, our bilateral filter layer consists of only four trainable parameters and constrains the applied operation to follow the traditional bilateral filter algorithm by design. Results Although only using three spatial parameters and one intensity range parameter per filter layer, the proposed denoising pipelines can compete with deep state-of-the-art denoising architectures with several hundred thousand parameters. Competitive denoising performance is achieved on x-ray microscope bone data and the 2016 Low Dose CT Grand Challenge data set. We report structural similarity index measures of 0.7094 and 0.9674 and peak signal-to-noise ratio values of 33.17 and 43.07 on the respective data sets. Conclusions Due to the extremely low number of trainable parameters with well-defined effect, prediction reliance and data integrity is guaranteed at any time in the proposed pipelines, in contrast to most other deep learning-based denoising architectures.
Additional file 2: of Structuring successful collaboration: a longitudinal social network analysis of a translational research network
Creators: name: Long, Janet
name: Hibbert, Peter
name: Braithwaite, Jeffrey
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Some methodological considerations. Â Discussion of response rate, reciprocity and the high "opt out" rate. (14.4 kb)
Additional file 1: of Structuring successful collaboration: a longitudinal social network analysis of a translational research network
Creators: name: Long, Janet
name: Hibbert, Peter
name: Braithwaite, Jeffrey
Publisher: name: Figshare
Year: 2016
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Marine Biology
subject: Science Policy

description: De-identified version of collaboration survey #3. Formatting of roster style social network questions shown (Q.18 ff). (18.1 kb)Â
On the Power and Limitations of Examples for Description Logic Concepts
Creators: name: Cate, Balder ten
name: Koudijs, Raoul
name: Ozaki, Ana
Publisher: name: arXiv
Year: 2024
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences
subject: F.4.1; I.2.6; I.2.4

description: Labeled examples (i.e., positive and negative examples) are an attractive medium for communicating complex concepts. They are useful for deriving concept expressions (such as in concept learning, interactive concept specification, and concept refinement) as well as for illustrating concept expressions to a user or domain expert. We investigate the power of labeled examples for describing description-logic concepts. Specifically, we systematically study the existence and efficient computability of finite characterisations, i.e. finite sets of labeled examples that uniquely characterize a single concept, for a wide variety of description logics between EL and ALCQI, both without an ontology and in the presence of a DL-Lite ontology. Finite characterisations are relevant for debugging purposes, and their existence is a necessary condition for exact learnability with membership queries.
description: Published in the Proceedings of the 33rd International Joint Conference on Artificial Intelligence (IJCAI)