cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 4: of
                     Drosophila pachea asymmetric lobes are part of a grasping device and stabilize one-sided mating
Creators: name: Rhebergen, Flor
name: Courtier-Orgogozo, Virginie
name: Dumont, Julien
name: Schilthuizen, Menno
name: Lang, Michael
Publisher: name: Figshare
Year: 2016
Subjects: subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology

description: Supplementary method. Description of the laser ablation chamber. (PDF 681 kb)
Additional file 1: Table S1. of Effect of alirocumab on specific lipoprotein non-high-density lipoprotein cholesterol and subfractions as measured by the vertical auto profile method: analysis of 3 randomized trials versus placebo
Creators: name: Toth, Peter
name: Hamon, Sara
name: Jones, Steven
name: Martin, Seth
name: Parag Joshi
name: Krishnaji Kulkarni
name: Poulabi Banerjee
name: Hanotin, Corinne
name: Roth, Eli
name: McKenney, James
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Marine Biology
subject: Computational Biology

description: Changes from baseline in lipids and lipoproteins as measured using conventional methods in the parent studies. Table S2. Change from baseline in apoB/apoAI ratio. Table S3. Changes from baseline in ratios of apoCII/VLDL-C and apoCIII/VLDL-C. Table S4. Pooled data from across the three studies (565, 566, 1003) for changes from baseline in cholesterol content of lipoprotein subfractions, apoB/apoA1 ratio, and levels of apo CII and CIII. (DOCX 45 kb)
title: Il mondo scardinato. Dispositivi poietici, dinamiche e rappresentazioni degli stati di eccezionalità
Creators: name: Fabiani, Lorenzo
name: Pollicino, Simona
name: Zanot, Irene
Publisher: name: Roma Tre University
publisherIdentifier: https://ror.org/05vf0dg29
publisherIdentifierScheme: ROR
Year: 2024

description:

Questo volume raccoglie alcuni dei contributi presentati al convegno internazionale "Il mondo scardinato. Dispositivi poietici, dinamiche e rappresentazioni degli stati di eccezionalità", tenutosi a Roma e Zagarolo dal 5 al 7 ottobre 2023. L'obiettivo delle giornate di studio era di indagare le implicazioni sociali, culturali ed etiche della rappresentazione del fatto eccezionale, attraverso la varietà dei discorsi (letterario, filosofico, politico, giornalistico) e delle immagini (arti visive, arti performative, cinema), come pure la loro capacità di scardinare generi e forme tradizionali prospettando modelli innovativi. Si è potuto riflettere, per questo, sulle diverse reazioni dell’uomo di fronte alle avversità del mondo attuale, esplorando la funzione allegorica connessa all’evento straordinario, nonché le specificità ideologiche ed estetiche delle rappresentazioni che ne scaturiscono con tutta la loro forza creatrice e performativa.
Additional file 1: of Similar efficacy of broad-range ITS PCR and conventional fungal culture for diagnosing fungal infections in non-immunocompromised patients
Creators: name: Rampini, Silvana
name: Zbinden, Andrea
name: Speck, Roberto
name: Bloemberg, Guido
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Ecology
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: MCRO-D-16-00030 R2 Supplemental data Rampini et al. The supplemental data consist of four tables. Table S1. Compilation of false positive PCR results categorized as contaminants; these specimens did not produce a distinct PCR fragment on polyacrylamide gel electrophoresis and identification pointed to known microbiological (environmental) contaminants. Table S2. Fungal ITS PCR compared to conventional cultures (n = 251). Four microscopy- and PCR-negative but culture positive specimens as included in Table 2, were categorized as culture-negative since cultures were only positive by a single fungal colony or only after enrichment culture; thus, microbiological contamination was highly likely. Table S3. Compilation of the patients with fungal infection (n = 54), including microbiological data, clinical situation and antifungal therapy. Table S4. Overview of culture negative fungal infections subdivided in (1) culture negative, broad-range fungal PCR positive fungal infections and (2) culture negative, broad-range fungal PCR negative fungal infections, including clinical information and antifungal therapy. (DOCX 63 kb)
Agrilus nigroauratus Hespenheide
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus nigroauratus

description: Agrilus nigroauratus Hespenheide
GRO, 14 km W Iguala, 21-VII-87, FSCA; PUE, 5 km NW Petlalcingo, 18°04’, 97°58’, 1400 m, 5-VII-92, CLBC.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 18, DOI: 10.5281/zenodo.273645
title: "La Cattura di Cristo", Cesari Giuseppe detto Cavalier d'Arpino, inv. 356 (ITA/EN)
title: Scheda catalogo digitale Borghese
titleType: AlternativeTitle
Creators: name: Puddu, Pier Ludovico
name: Galleria Borghese
Publisher: name: Galleria Borghese
Year: 2024

description: Pubblicazione delle schede delle opere conservate nel museo ed estratte dal catalogo digitale di Galleria Borghese, nelle due versioni esistenti online, in italiano e inglese.

Collegamento al catalogo digitale:

ITA: https://www.collezionegalleriaborghese.it/

EN: https://www.collezionegalleriaborghese.it/en
Additional file 1: Figure S1. of Detection of Mycobacterium ulcerans by real-time PCR with improved primers
Creators: name: Shinoda, Noriko
name: Nakamura, Hajime
name: Watanabe, Mineo
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Microbiology
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: Developmental Biology
subject: 60506 Virology

description: Sequence alignment of the IS2404 elements from the genome of M. ulcerans strain Agy99. (PDF 1040 kb)
Additional file 1: Table S1 of Mesenchymal stem cells in cardiac regeneration: a detailed progress report of the last 6 years (2010–2015)
Creators: name: Aastha Singh
name: Abhishek Singh
name: Dwaipayan Sen
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Pharmacology
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: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Clinical trials executed during 2010–2015 which used MSCs to treat heart diseases. (DOCX 36 kb)
Agrilus nodifrons Waterhouse
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus nodifrons

description: Agrilus nodifrons Waterhouse
MEX, 2.4 km SE Zuluapan, 1412 m, 21-VIII-91, CLBC.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 18, DOI: 10.5281/zenodo.273645
Agrilus obolinus LeConte
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus obolinus

description: Agrilus obolinus LeConte
COAH, 20 mi SE Saltillo, 6000’, rt 0 15, 20-21-VI-71, CMNC.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 18, DOI: 10.5281/zenodo.273645
Development of containment FOAM towards LW-SMR analyses
Creators: name: Vázquez-Rodríguez, Carlos
name: Kelm, Stephan
Publisher: name: Forschungzentrum Jülich
Year: 2024

description: SASPAM-SA Open Workshop, Roses, France, 17 Oct 2024 - 18 Oct 2024
description: see attached
Agrilus obscurilineatus Vogt
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus obscurilineatus

description: Agrilus obscurilineatus Vogt
NL, Hwy. 58, 32 mi W Linares, 6000’, 11-IX-82, RLWE; SLP, 4.1 mi E Cd. de Maíz, 11- VI-87, FSCA.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 18, DOI: 10.5281/zenodo.273645
Additional file 3: Figure S1. of Identification of Ixodes ricinus blood meals using an automated protocol with high resolution melting analysis (HRMA) reveals the importance of domestic dogs as larval tick hosts in Italian alpine forests
Creators: name: Collini, Margherita
name: Albonico, Francesca
name: RosĂ, Roberto
name: Tagliapietra, Valentina
name: Arnoldi, Daniele
name: Conterno, Lorenza
name: Rossi, Chiara
name: Mortarino, Michele
name: Annapaola Rizzoli
name: Hauffe, Heidi
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Sequence alignment of mtDNA control region amplicons generated with the Muroidea primer set. (PDF 307 kb)
Additional file 5: Figure S4. of Developmental delay in motor skill acquisition in Niemann-Pick C1 mice reveals abnormal cerebellar morphogenesis
Creators: name: Caporali, Paola
name: Bruno, Francesco
name: Palladino, Giampiero
name: Dragotto, Jessica
name: Petrosini, Laura
name: Mangia, Franco
name: Erickson, Robert
name: Canterini, Sonia
name: Fiorenza, Maria
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Developmental Biology
subject: Plant Biology
subject: Computational Biology

description: CD treatment fully rescued VGluT2 puncta reduction of Npc1 nmf164 mice. A Immunostaining with antibodies directed to VGluT2 (brown) of PN15 wt and Npc1 nmf164 , either sham- or CD-treated mouse cerebella. Representative fields of parasagittal sections are shown in the figure. Upper panels, arrows indicate VGluT2-positive synapses of internal granule layer glomeruli; scale bars: 20 μm. Bottom panels, higher magnifications of selected areas. Arrowheads indicate VGluT2 positive puncta; scale bars: 5 μm. B Histograms indicate VGluT2-positive puncta densities in the outer and inner molecular layers (mean ± SEM of all sections examined; N = 4 mice/genotype/treatment; 3–4 sections/mouse) of wt and Npc1 nmf164 mice, either sham- or CD-treated. Asterisks indicate statistically significant differences (two-way ANOVA, * p
Additional file 1: Figure S1. of Competitive males have higher quality sperm in a monogamous social bee
Creators: name: Sheina Koffler
name: Hiara Meneses
name: Kleinert, Astrid
name: Jaffé, Rodolfo
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Arrival of mature Scaptotrigona aff. depilis males in aggregations, according to male age (days after emergence). Emerging males from three colonies were paint-marked in the thorax (each colony identified with a different color) and returned to their origin colonies (number of marked males: blue 206, beige 162, and green 60). Male aggregations were then inspected daily for marked males, which were counted when observed. (DOCX 12 kb)
Agrilus obtusus Horn
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus obtusus

description: Agrilus obtusus Horn
NL, 10 mi W Linares, 21-IX-63, EMEC (new record, Mexico).
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 18, DOI: 10.5281/zenodo.273645
Additional file 4: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
Creators: name: Preston, Jessica
name: Royall, Ariel
name: Randel, Melissa
name: Sikkink, Kristin
name: Phillips, Patrick
name: Johnson, Eric
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
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: Cancer

description: Control SNPs detected with PELE-Seq, standard DNA-Seq, and the ORP method. Rare alleles present at 0.42 % frequency in a control E. coli spike-in library were sequenced with PELE-Seq, the ORP method, and the standard DNA-Seq method at 10,000× OPE depth of coverage per barcode (24,000× depth per barcode of non-overlapped reads). PELE-Seq and the ORP method are 100 % specific and the standard DNA-Seq method is 75 % specific. This data is also included as a spreadsheet in Additional file 3. (PDF 1109 kb)
Storytelling and gamification in E-learning – An empirical study to educate Swiss microenterprises in data protection
Creators: name: Schneider, Bettina
name: Bontempo Salgueiro, Nathalia
name: Asprion, Petra
name: Habbabeh, Ali
Publisher: name: Fachhochschule Nordwestschweiz FHNW
Year: 2020
Subjects: subject: 330 - Wirtschaft

Abstract
Additional file 3: Figure S2. of Developmental delay in motor skill acquisition in Niemann-Pick C1 mice reveals abnormal cerebellar morphogenesis
Creators: name: Caporali, Paola
name: Bruno, Francesco
name: Palladino, Giampiero
name: Dragotto, Jessica
name: Petrosini, Laura
name: Mangia, Franco
name: Erickson, Robert
name: Canterini, Sonia
name: Fiorenza, Maria
Publisher: name: Figshare
Year: 2016
Subjects: Biochemistry
Cell Biology
Molecular Biology
Neuroscience
Developmental Biology

description: A Western blot analysis of GFAP protein expression in cerebella of PN11 wt and Npc1 nmf164 mice. B Histograms indicate the abundance (mean ± SEM) of each isoform determined by densitometry of protein bands obtained in at least 3 independent experiments taking β-actin as internal reference. (PDF 95 kb)
Additional file 2: Figure S1. of Developmental delay in motor skill acquisition in Niemann-Pick C1 mice reveals abnormal cerebellar morphogenesis
Creators: name: Caporali, Paola
name: Bruno, Francesco
name: Palladino, Giampiero
name: Dragotto, Jessica
name: Petrosini, Laura
name: Mangia, Franco
name: Erickson, Robert
name: Canterini, Sonia
name: Fiorenza, Maria
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Evolutionary Biology
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Npc1 nmf164 mice display a reduced density of GNs in the external granule layer (EGL), which is due to reduced proliferation of GN precursors. A Representative sections are shown in the figure. Higher magnification fields of EGL base or crown of lobules II and X on the right of low magnification fields show that the EGL of PN15 Npc1 nmf164 mice is thinner than that of age-matched wt mice. Scale bar indicate 250 μm (panels) and 50 μm (insets). B Histograms represent GN densities (mean ± SEM of all sections examined; N = 4 mice/genotype; 3–4 sections/mouse) determined in 100 μm2 regions of the crowns of wt and Npc1 nmf164 mice anterior (I-V) and posterior (VI-X) lobules. C A representative field showing BrdU-positive cells (red) of fissure between lobules II and III of PN13 wt and Npc1 nmf164 mice. Scale bar indicates 50 μm. D Histograms represent the number of BrdU-positive cells (mean ± SEM; 4 mice/genotype; 3–4 sections/mouse) determined in 100 μm2 regions corresponding to the bases and crowns of PN13 and PN15 wt and Npc1 nmf164 mice anterior (I–V) and posterior (VI–X) lobules. Asterisks indicate statistically significant differences (unpaired two-tailed Student’s t test, ** p
Agrilus olivaceoaeneus Hespenheide
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus olivaceoaeneus

description: Agrilus olivaceoaeneus Hespenheide
PUE, 20 km E Acatlán, 5-7-VII-92, ZMAS.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 19, DOI: 10.5281/zenodo.273645
Can Query Expansion Improve Generalization of Strong Cross-Encoder Rankers?
Creators: name: Li, Minghan
name: Zhuang, Honglei
name: Hui, Kai
name: Qin, Zhen
name: Lin, Jimmy
name: Jagerman, Rolf
name: Wang, Xuanhui
name: Bendersky, Michael
Publisher: name: arXiv
Year: 2023
Subjects: subject: Information Retrieval (cs.IR)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Query expansion has been widely used to improve the search results of first-stage retrievers, yet its influence on second-stage, cross-encoder rankers remains under-explored. A recent work of Weller et al. [44] shows that current expansion techniques benefit weaker models such as DPR and BM25 but harm stronger rankers such as MonoT5. In this paper, we re-examine this conclusion and raise the following question: Can query expansion improve generalization of strong cross-encoder rankers? To answer this question, we first apply popular query expansion methods to state-of-the-art cross-encoder rankers and verify the deteriorated zero-shot performance. We identify two vital steps for cross-encoders in the experiment: high-quality keyword generation and minimal-disruptive query modification. We show that it is possible to improve the generalization of a strong neural ranker, by prompt engineering and aggregating the ranking results of each expanded query via fusion. Specifically, we first call an instruction-following language model to generate keywords through a reasoning chain. Leveraging self-consistency and reciprocal rank weighting, we further combine the ranking results of each expanded query dynamically. Experiments on BEIR and TREC Deep Learning 2019/2020 show that the nDCG@10 scores of both MonoT5 and RankT5 following these steps are improved, which points out a direction for applying query expansion to strong cross-encoder rankers.
Additional file 2: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
Creators: name: Preston, Jessica
name: Royall, Ariel
name: Randel, Melissa
name: Sikkink, Kristin
name: Phillips, Patrick
name: Johnson, Eric
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Sequencing reads from the pure W3110 and Rel606 E. coli substrains. The purity of the original DNA samples was verified through sequencing by aligning the sequencing reads from both E. coli substrains to the Rel606 genome. The “true positive” SNPs were found to be present at 100 % frequency in the W3110 DNA, and all other positions contained reference bases at 100 % frequency. (PDF 604 kb)
Stability estimates for an inverse boundary value problem for biharmonic operators with first order perturbation from partial data
Creators: name: Liu, Boya
Publisher: name: arXiv
Year: 2023
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35R30, 35J40

description: In this paper we study an inverse boundary value problem for the biharmonic operator with first order perturbation. Our geometric setting is that of a bounded simply connected domain in the Euclidean space of dimension three or higher. Assuming that the inaccessible portion of the boundary is flat, and we have knowledge of the Dirichlet-to-Neumann map on the complement, we prove logarithmic type stability estimates for both the first and the zeroth order perturbation of the biharmonic operator.
Agrilus ometauhtli Fisher
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus ometauhtli

description: Agrilus ometauhtli Fisher
GTO, 2 mi W Dolores Hidalgo, 5-VII-85; NL, 9 mi W Iturbide, 3-VII-74, TAMU; PUE, 51 mi E Puebla, 6800’, 7-VI-56; SLP, 16 mi S Sta. María de Río, 6500’, 29-VI-71, RLWE; TAMPS, 75 mi SW Cd. Victoria, 16-VI-83, FSCA, RLWE.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 19, DOI: 10.5281/zenodo.273645
Additional file 5: Figure S5. of Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods
Creators: name: Lloyd-Lewis, Bethan
name: Davis, Felicity
name: Harris, Olivia
name: Hitchcock, Jessica
name: Lourenco, Filipe
name: Pasche, Mathias
name: Watson, Christine
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology

description: De-noising of 3D image sequences. DAPI staining (top panel) and E-cadherin immunostaining (bottom panel) in lactating mammary tissue before and after a de-noising algorithm was applied to minimise Poisson-Gaussian noise in the 3D image stacks. De-noising does not greatly alter the outward appearance of the image sequence, but rather aids downstream computer-assisted analyses. See Additional file 18 for a high resolution version of these PDFs. (PDF 4 mb)
Realization of a programmable multi-purpose photonic quantum memory with over-thousand qubit manipulations
Creators: name: Zhang, Sheng
name: Shi, Jixuan
name: Cui, Zhaibin
name: Wang, Ye
name: Wu, Yukai
name: Duan, Luming
name: Pu, Yunfei
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Emerging Technologies (cs.ET)
subject: Optics (physics.optics)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Quantum networks can enable various applications such as distributed quantum computing, long-distance quantum communication, and network-based quantum sensing with unprecedented performances. One of the most important building blocks for a quantum network is a photonic quantum memory which serves as the interface between the communication channel and the local functional unit. A programmable quantum memory which can process a large stream of flying qubits and fulfill the requirements of multiple core functions in a quantum network is still to-be-realized. Here we report a high-performance quantum memory which can simultaneously store 72 optical qubits carried by 144 spatially separated atomic ensembles and support up to a thousand consecutive write or read operations in a random access way, two orders of magnitude larger than the previous record. Due to the built-in programmability, this quantum memory can be adapted on-demand for several functions. As example applications, we realize quantum queue, stack, and buffer which closely resemble the counterpart devices for classical information processing. We further demonstrate the synchronization and reshuffle of 4 entangled pairs of photonic pulses with probabilistic arrival time and arbitrary release order via the memory, which is an essential requirement for the realization of quantum repeaters and efficient routing in quantum networks. Realization of this multi-purpose programmable quantum memory thus constitutes a key enabling building block for future large-scale fully-functional quantum networks.
description: 17 pages, 19 figures
Pholoe Johnston 1839
Creators: name: Ravara, Ascensão
name: Cunha, Marina R.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Annelida
Polychaeta
Phyllodocida
Pholoidae
Pholoe

description: Genus Pholoe Johnston, 1839
Pholoe Johnston 1839, p. 437.
Type species. Pholoe inornata Johnston, 1839.
Diagnosis. Body small, with up to 90 segments. Elytra on segments 2, 4, 5, 7, alternating to 23, then on every segment to end of body. Elytra delicate, with border and sometimes also surface papillae. Dorsal cirri and branchiae absent. Prostomium triangular or rounded to bilobed. Median antennae inserted on anterior notch without auricles. Lateral antennae present or absent. Palps stout, emerging ventrolaterally to tentaculophores. Eyes present or absent. Tentacular segment fused to prostomium, with two pairs of subequal tentacular cirri, without chaetae. Parapodia biramous; acicular lobes conical with or without papillae, ventral much longer than dorsal. Notochaetae capillary, lightly spinulose, straight or geniculate. Neurochaetae compound, with subdistally spinose shafts and falcate blades. Pygidium with a pair of anal cirri.
description: Published as part of Ravara, Ascensão & Cunha, Marina R., 2016, Two new species of scale worms (Polychaeta: Aphroditiformia) from deep-sea habitats in the Gulf of Cadiz (NE Atlantic), pp. 442-450 in Zootaxa 4097 (3) on page 446, DOI: 10.11646/zootaxa.4097.3.12, http://zenodo.org/record/258754
Repeated exposure of the oral mucosa over 12 months with cold plasma is not carcinogenic in mice
Creators: name: Evert, Katja
name: Kocher, Thomas
name: Schindler, Andrea
name: Müller, Manuel
name: Müller, Karolina
name: Pink, C.
name: Holtfreter, Birte
name: Schmidt, Alexander
name: Dombrowski, Frank
name: Schubert, Andrea
name: von Woedtke, Thomas
name: Rupf, Stefan
name: Calvisi, Diego F.
name: Bekeschus, S.
name: Jablonowski, L.
Publisher: name: Universität Regensburg
Year: 2021
Subjects: subject: SQUAMOUS-CELL CARCINOMA; ATMOSPHERIC PLASMA; OSTEOBLAST GROWTH; JET; EXPRESSION
subject: 610 Medizin

description: Peri-implantitis may result in the loss of dental implants. Cold atmospheric pressure plasma (CAP) was suggested to promote re-osseointegration, decrease antimicrobial burden, and support wound healing. However, the long-term risk assessment of CAP treatment in the oral cavity has not been addressed. Treatment with two different CAP devices was compared against UV radiation, carcinogen administration, and untreated conditions over 12 months. Histological analysis of 406 animals revealed that repeated CAP exposure did not foster non-invasive lesions or squamous cell carcinoma (SCCs). Carcinogen administration promoted non-invasive lesions and SCCs. Molecular analysis by a qPCR screening of 144 transcripts revealed distinct inflammatory profiles associated with each treatment regimen. Interestingly, CAP treatment of carcinogen-challenged mucosa did not promote but instead left unchanged or reduced the proportion of non-invasive lesions and SCC formation. In conclusion, repeated CAP exposure of murine oral mucosa was well tolerated, and carcinogenic effects did not occur, motivating CAP applications in patients for dental and implant treatments in the future.
Additional file 10: Figure S9. of Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods
Creators: name: Lloyd-Lewis, Bethan
name: Davis, Felicity
name: Harris, Olivia
name: Hitchcock, Jessica
name: Lourenco, Filipe
name: Pasche, Mathias
name: Watson, Christine
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: Plant Biology

description: Compatibility of CUBIC clearing with genetically encoded FPs and recovery for histological sections. a CUBIC clearing of tissue from R26-Confetti mice with reporter expression (nuclear GFP, cytosolic YFP and cytosolic RFP) induced at very low, sporadic levels. Membranous CFP was not observed with any clearing protocol and may be technical; however, this FP is also reportedly underrepresented in mammary tissue from R26-Confetti mice. b Tissue from lactating R26-Tdtomato mice induced at very high levels. c CUBIC-cleared tissue was rehydrated in PBS prior to standard processing, paraffin embedding and sectioning. Immunostaining for E-cadherin (luminal) and SMA (basal) markers confirm the compatibility of CUBIC clearing with tissue recovery and immunostaining. See Additional file 18 for a high resolution version of these PDFs. (PDF 126 mb)
title: Utilizing the ball lens effect for astigmatism particle tracking velocimetry
Creators: name: Brockmann, Philipp
name: Kazerooni, Hamid Tabaei
name: Brandt, Luca
name: Hussong, Jeanette
Publisher: name: Springer
Year: 2024

description: In the present study, a simple method is developed to apply astigmatism particle tracking velocimetry (APTV) to transparent particles utilizing backlight illumination. Here, a particle acts as ball lens and bundles the light to a focal point, which is used to determine the particle’s out-of-plane position. Due to the distance between focal point and particle, additional features have to be considered in ball lens astigmatism particle tracking velocimetry (BLAPTV) compared to conventional APTV. We describe required calibration steps and perform parameter studies to show how the autocorrelation coefficient and the light exposure affect the accuracy of the method. It is found that the accuracy and robustness of the Euclidean calibration approach as also used in conventional APTV (Cierpka et al. in Meas Sci Technol 22(1):015401, 2010a) can be increased if an additional calibration curve for the light intensity of the particle’s focal point is considered. In addition, we study the influence of the particle diameter and the refractive index jump between liquid and particles on the calibration curves and the accuracy. In this way, particles of the same size, but different material, can be distinguished by their calibration curve. Furthermore, an approach is presented to account for shape changes of the calibration curve along the depth of the measurement volume. Overall, BLAPTV provides high out-of-plane particle reconstruction accuracies with respect to the particle diameter. In test cases, position uncertainties down to 1.8% of the particle diameter are achieved for particles of dp=124μm. The measurement technique is validated for a laminar flow in a straight rectangular channel with a cross-sectional area of 2.3×30 mm². Uncertainties of 0.75% for the in-plane and 2.29% for out-of-plane velocity with respect to the maximum streamwise velocity are achieved.
Phononic dynamical axion in magnetic Dirac insulators
Creators: name: Lhachemi, M. Nabil Y.
name: Garate, Ion
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: In cosmology, the axion is a hypothetical particle that is currently considered as candidate for dark matter. In condensed matter, a counterpart of the axion (the "axion quasiparticle") has been predicted to emerge in magnetoelectric insulators with fluctuating magnetic order and in charge-ordered Weyl semimetals. To date, both the cosmological and condensed-matter axions remain experimentally elusive or unconfirmed. Here, we show theoretically that ordinary lattice vibrations can form an axion quasiparticle in Dirac insulators with broken time- and space-inversion symmetries, even in the absence of magnetic fluctuations. The physical manifestation of the phononic axion is a magnetic-field-induced phonon effective charge, which can be probed in optical spectroscopy. By replacing magnetic fluctuations with lattice vibrations, our theory widens the scope for the observability of the axion quasiparticle in condensed matter.
description: 12 pages, 4 figures, Published version
Agrilus delicatulus Waterhouse
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus delicatulus

description: Agrilus delicatulus Waterhouse
NAY, 5.7 mi NE San Blas, 21-VII-63, RLWE.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 12, DOI: 10.5281/zenodo.273645
Exploding AI Power Use: an Opportunity to Rethink Grid Planning and Management
Creators: name: Lin, Liuzixuan
name: Wijayawardana, Rajini
name: Rao, Varsha
name: Nguyen, Hai
name: Gnibga, Wedan Emmanuel
name: Chien, Andrew A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Systems and Control (eess.SY)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The unprecedented rapid growth of computing demand for AI is projected to increase global annual datacenter (DC) growth from 7.2% to 11.3%. We project the 5-year AI DC demand for several power grids and assess whether they will allow desired AI growth (resource adequacy). If not, several "desperate measures" -- grid policies that enable more load growth and maintain grid reliability by sacrificing new DC reliability are considered.
 We find that two DC hotspots -- EirGrid (Ireland) and Dominion (US) -- will have difficulty accommodating new DCs needed by the AI growth. In EirGrid, relaxing new DC reliability guarantees increases the power available to 1.6x--4.1x while maintaining 99.6% actual power availability for the new DCs, sufficient for the 5-year AI demand. In Dominion, relaxing reliability guarantees increases available DC capacity similarly (1.5x--4.6x) but not enough for the 5-year AI demand. New DCs only receive 89% power availability. Study of other US power grids -- SPP, CAISO, ERCOT -- shows that sufficient capacity exists for the projected AI load growth.
 Our results suggest the need to rethink adequacy assessment and also grid planning and management. New research opportunities include coordinated planning, reliability models that incorporate load flexibility, and adaptive load abstractions.
description: Accepted by ACM e-Energy '24: the 15th ACM International Conference on Future and Sustainable Energy Systems
Tenomodulin knockout mice exhibit worse late healing outcomes with augmented trauma-induced heterotopic ossification of Achilles tendon
Creators: name: Delgado Caceres, Manuel
name: Angerpointner, Katharina
name: Galler, Michael
name: Lin, Dasheng
name: Michel, Philipp A.
name: Brochhausen, Christoph
name: Lu, Xin
name: Varadarajan, Adithi R.
name: Warfsmann, Jens
name: Stange, Richard
name: Alt, Volker
name: Pfeifer, Christian G.
name: Docheva, Denitsa
Publisher: name: Universität Regensburg
Year: 2021
Subjects: subject: INJURY; MUSCLE; CELLS; CALCIFICATIONS; HOMOLOGY; IDENTIFY; GENE;
subject: 610 Medizin

description: Heterotopic ossification (HO) represents a common problem after tendon injury with no effective treatment yet being developed. Tenomodulin (Tnmd), the best-known mature marker for tendon lineage cells, has important effects in tendon tissue aging and function. We have reported that loss of Tnmd leads to inferior early tendon repair characterized by fibrovascular scaring and therefore hypothesized that its lack will persistently cause deficient repair during later stages. Tnmd knockout (Tnmd(-/-)) and wild-type (WT) animals were subjected to complete Achilles tendon surgical transection followed by end-to-end suture. Lineage tracing revealed a reduction in tendon-lineage cells marked by ScleraxisGFP, but an increase in alpha smooth muscle actin myofibroblasts in Tnmd(-)(/-) tendon scars. At the proliferative stage, more pro-inflammatory M1 macrophages and larger collagen II cartilaginous template were detected in this group. At the remodeling stage, histological scoring revealed lower repair quality in the injured Tnmd(-/-) tendons, which was coupled with higher HO quantified by micro-CT. Tendon biomechanical properties were compromised in both groups upon injury, however we identified an abnormal stiffening of non-injured Tnmd(-/)(-) tendons, which possessed higher static and dynamic E-moduli. Pathologically thicker and abnormally shaped collagen fibrils were observed by TEM in Tnmd(-/-) tendons and this, together with augmented HO, resulted in diminished running capacity of Tnmd(-/-) mice. These novel findings demonstrate that Tnmd plays a protecting role against trauma-induced endochondral HO and can inspire the generation of novel therapeutics to accelerate repair.
Additional file 1 of Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints
Creators: name: Fiedler, Anna
name: Raeth, Sebastian
name: Theis, Fabian
name: Hausser, Angelika
name: Hasenauer, Jan
Publisher: name: Figshare
Year: 2016
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Supporting Information S1. This document provides a detailed description of the stability proof and the derivation of the different pathway models. Furthermore, the parameter and bounds are listed, the influence of the retraction factor on convergence and run time as well as the behavior of the proposed methods in the presence of multiple steady states and bifurcations is illustrated. (PDF 577 kb)
Prognostic markers in hepatocellular carcinoma
Creators: name: Harrod, Elizabeth Claire Brookes
Publisher: name: University of Surrey
Year: 2024
Subjects: Hepatocellular carcinoma

description: Hepatocellular carcinoma (HCC) is the 6th leading cause of cancer-related mortality, with a poor prognosis in patients diagnosed in the later stages. Further understanding of HCC and its genetics may improve our ability to develop new diagnostic, prognostic and treatment strategies.There is a known association between type 2 diabetes mellitus (T2DM) and several cancers, including HCC. This proof-of-concept study investigates the association between HCC and T2DM in 113 patients with HCC in a UK tertiary centre. The presence of T2DM and alpha-fetoprotein (aFP) positivity were compared with overall survival data but this dataset was not sufficiently powered to reach significance in most areas.A larger cohort of 1407 patients from Germany was then reviewed, demonstrating that patients with T2DM were less likely to be aFP positive. aFP is a tumour marker with both diagnostic and prognostic implications but is not present in all cases of hepatocellular carcinoma. aFP lost its poor prognostic significance in patients with T2DM when assessing surrogate markers of prognosis, in the absence of survival data. A meta-analysis of the two cohorts showed consistency with these observed associations despite an alternative aFP threshold for positivity. Patients at higher risk of developing HCC presently undergo biannual surveillance ultrasound and aFP assessment to identify these tumours at early stages. This surveillance system may disadvantage patients with T2DM as aFP is less likely to be positive in these cases.Alongside the clinical assessment of HCC, our understanding of the genetic landscape of HCC and their prognostic implications is evolving, with various novel therapies now available which may ultimately allow precision medicine. The immune subclass is characterised by more aggressive tumours, and immunofluorescent assessment of 75 tumour samples in this thesis demonstrate an increase of PDL1, PD1 and CD8 in this genetic subclass.Improving our understanding of the clinical and genetic basis of HCC may aid in our diagnostic capability, prognostication and ultimately treatment strategies.
Additional file 5: of High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
Creators: name: Preston, Jessica
name: Royall, Ariel
name: Randel, Melissa
name: Sikkink, Kristin
name: Phillips, Patrick
name: Johnson, Eric
Publisher: name: Figshare
Year: 2016
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: PCR errors that result in false positive SNPs when using unfiltered ORP data. Overlapping paired-end read libraries sequenced to 10,000Ă  OPE depth contained 109 false positive SNPs when rare variants were called with Lofreq, using default parameters with no minimum allele frequency cutoff. These putative PCR errors are predominately Câ  >â  T transitions are are found in distinct clusters throughout the genome. This data is also included as a spreadsheet in Additional file 3. (PDF 18 kb)
Understanding biological networks Systems Biology approaches to study Cell Cycle and Metabolism
Creators: name: Rojas Lopez, Maria Alejandra
Publisher: name: University of Surrey
Year: 2024
Subjects: Autoimmunity
Cell Cycle
Metabolism
Systems Biology

description: This thesis is written in publication format and comprises the work done in two main research lines: Study of the Cell Cycle regulation (Chapters 1-3) and The Integration of Metabolism and immunity (Chapters 4-7). Chapter 1 is a review article that collects relevant information on regulatory structures present in biological networks, using a Systems and Synthetic Biology approach. Chapter 2 analyses a minimal cell cycle network using the System Design Space (SDS) methodology, establishing under which conditions (parameter values) the network can exhibit bistability and oscillations. Chapter 3 uses the SDS approach to characterise the cell cycle cyclin waves in budding yeast mutant stains. Using mutant budding yeast frequency in population data provided by collaborators at the Imperial College London, it was possible to analyse how the deletion of key cell cycle genes affects the capacity of the cell to exhibit sustained oscillations and the shape of the cyclin waves. Chapter 4 is an editorial article reflecting on the importance of the balance of T cell phenotypes on health and disease, serving as the transition to the Metabolism and Immunity part of the thesis. Chapter 5 shows the use of Flux Balance Analysis (FBA) simulations to understand the response towards an experimental HIV vaccine. Starting from untargeted metabolomic data from patient serum samples, provided by collaborators at the University of Rochester it was possible to find metabolic pathways involved in the early reaction to the vaccine. Chapter 6 shows the analysis of the Priority Index Database for gene targets in autoimmune disorders, using the ranking of target genes as an input to establish similarities among autoimmune disorders and finding opportunities for drug repurposing. Finally, Chapter 7 is a perspective article that discusses the importance of addressing the metabolism when studying immune disorders, particularly the link between metabolism inflammation and ageing.
Agrilus impressicollis Gory
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus impressicollis

description: Agrilus impressicollis Gory
OAX, 5 km NE Tezoatlán, 17°42’, 97°46’, 1672 m, 29-VI-96; GRO, Hwy. 134, 6.9 km NE jct. Hwy. 200, 14-VII-85, CLBC.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 15, DOI: 10.5281/zenodo.273645
Agrilus opacipennis Waterhouse
Creators: name: Westcott, Richard L.
name: Hespenheide, Henry A.
Publisher: name: Zenodo
Year: 2006
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Buprestidae
Agrilus
Agrilus opacipennis

description: Agrilus opacipennis Waterhouse
OAX, 10 km NE Huajuapan de León, 1680 m; 5.2 km SE Huitzo (26 km NW Oaxaca), 1680 m, 9-VII-92; PUE, 6 km S Teontepec, 18°28’34” N, 97°34’30” W, 1890 m, 25-VI- 97, all beating Celtis spp., RLWE.
description: Published as part of Westcott, Richard L. & Hespenheide, Henry A., 2006, The description of a new species of Agrilus Curtis, with distributional records, and taxonomic and biological notes for Agrilinae and Trachyinae (Coleoptera: Buprestidae) of Mexico and Central America, pp. 1-35 in Zootaxa 1367 on page 19, DOI: 10.5281/zenodo.273645