cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 6 of Cdk5 regulatory subunit-associated protein 1 knockout mice show hearing loss phenotypically similar to age-related hearing loss
Creators: name: Miwa, Toru
name: Fan-Yan Wei
name: Tomizawa, Kazuhito
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 6. Metabolome principal-component analysis.
Forest Products Trade Flow Discrepancies--Unintentional and International Errors
Creators: name: Janse, Gerben
name: Janse, Gerben
Publisher: name: Unknown
Year: 2004
Subjects: subject: Agribusiness
subject: International Relations/Trade
subject: Land Economics/Use
subject: EU
subject: Asia
subject: import and export reports
subject: reporting errors
subject: illegal forest products trade.

description: Forest products trade flow data consists of two observations for each trade flow. The first observation is made by an exporting country A(concerning exports to importing country B) and the second observation is made by the importing country B(concerning imports from the previously mentioned, exporting country, A). The existence of these two different observations regarding the same trade flow allows for some rather than interesting investigations. Looking at trade flow statistics one often sees that reports on opposite ends of the same trade flow are contradictory. In this paper a number of possible explanations will be given. Furthermore, some suggestions will be given that might help to distinguish between unintentional and intentional data reporting faults, because the latter can be an indication for the occurrence of illegal activities.
Additional file 1 of Prevalence of IGFBP3, NOS3 and TCF7L2 polymorphisms and their association with hypertension: a population-based study with Brazilian women of African descent
Creators: name: Neto, Abel Barbosa Lira
name: Vasconcelos, Nancy Borges Rodrigues
name: Santos, Tamara Rodrigues Dos
name: Duarte, Luisa Elvira Cavazzani
name: Assunção, Monica Lopes
name: De Sales-Marques, Carolinne
name: Da Silva Ferreira, Haroldo
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Table S1. Distribution of systemic arterial hypertension the according to socioeconomic, demographic, lifestyle, anthropometric, and biochemical variables in women of African descent in the state of Alagoas (n = 1021). Table S2. Prevalence of arterial hypertension (%) and systolic blood pressure (mean ± SD; median and interquartile range), according to the genotypic frequencies for NOS3 rs1799983, TCF7L2 rs7903146, and IGFBP3 rs11977526 genes. Brazilian women descended from African descent, 2018.
Chemical localization
Creators: name: Gantmakher, V. F.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Analysis of experimental data shows that the metal--insulator transition is possible in materials composed of atoms of only metallic elements. Such a transition may occur in spite of the high concentration of valence electrons. It requires stable atomic configurations to act as deep potential traps absorbing dozens of valence electrons. This means in essence that bulk metallic space transforms into an assembly of identical quantum dots. Depending on the parameters, such a material either does contain delocalized electrons (metal) or does not contain such electrons (insulator). The degree of disorder is one of these parameters. Two types of substances with such properties are discussed: liquid binary alloys with both components being metallic, and thermodynamically stable quasicrystals.
description: 12 pages, 15 figures
Managing the Sawmill with Product Costs - A Simulation Study
Creators: name: Jhansson, Mats
name: Jhansson, Mats
Publisher: name: Unknown
Year: 2004
Subjects: subject: Agribusiness
subject: Agricultural Finance
subject: Land Economics/Use
subject: joint cost
subject: product costing
subject: linear programming
subject: sawmilling
subject: lumber costing
subject: sales management

description: This paper analyzes the effects of using product costs derived from an LP-model for managing the salesmen's efforts at a sawmill company. The salesmen are not controlled by sales quota, as is usual, but assessed by the accounting profit they generate. The analysis is realized by a computer simulation experiments under various assumptions on sales response and the mill's flexibility in purchasing timber. The cost figures are recalculated in each period. The results indicate that the success of the approach decreases with the length of the recalculation period, and increases strongly with the mill's flexibility in purchasing timber.
Additional file 5 of Cdk5 regulatory subunit-associated protein 1 knockout mice show hearing loss phenotypically similar to age-related hearing loss
Creators: name: Miwa, Toru
name: Fan-Yan Wei
name: Tomizawa, Kazuhito
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 5. Heatmap analysis of the metabolome results.
2d Material Inks for Printed Electronics
Creators: name: Ng, Leonard
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: 2d materials
graphene
printing
large-scale fabrication
h-BN
Dielectrics
Conductive ink
Conformal printing

description: Functional printing is a tried and tested method of low-cost and high-throughput production. Combining 2d materials with printing is an emerging, cost-effective and large-scale fabrication strategy of their devices. However, successful scale-up and adoption of printing as an ubiquitous fabrication method has been limited due to the lack of diversity in the available printing methods and materials. Since 2012, the majority of the 2d material printing demonstrations have been with inkjet. Methods such as blade coating, screen printing and flexography have received less attention despite having notable advantages. Also, the majority of 2d material printing research has focused on conducting (e.g. graphene) and semiconducting (e.g. black phosphorus) 2d materials and less emphasis has been placed on dielectric layers using wide bandgap 2d materials like hexagonal boron nitride (h-BN), which represent an important material in printed electronics applications, for example, in parallel plate capacitors and thin film transistors. Similarly, 2d material printing has thus far been demonstrated on flat surfaces, and little work has been done to print on conformal 3d objects. Conformal printing is an attractive and emerging field, which can enable the deposition of specific electronic features, such as sensors and circuits, directly on to 3d objects. Functional ink deposition on 3d structures is not a trivial process due to uneven and sometimes, complex topography. My PhD dissertation focuses on these key aspects of 2d material inks, I first present the formulation of conductive 2d material inks for screen printing. I begin to tackle the issues outlined above by using the screen inks to fabricate simple devices. I then combine screen printing with a water-based technique utilising a sacrificial layer that is capable of printing on to 3D objects. Next, I demonstrate and evaluate the feasibility of using flexographic printing as a means of large-scale fabrication via the high-speed printing of graphene-modified flexographic ink on a commercial press. Lastly, I investigate the use of h-BN as a dielectric nanofiller to enhance the dielectric properties of an existing dielectric polymer, polyurethane (PU). The work I present on conformal printing and in the formulation of dielectric inks in my thesis is my novel contribution to the research field. My research, therefore, addresses existing shortcomings of 2d material inks towards their large-scale exploitation.
Synalpheus mcclendoni Coutiere 1910
Creators: name: Hultgren, Kristin M.
name: Macdonald Iii, Kenneth S.
name: Duffy, J. Emmett
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Malacostraca
Decapoda
Alpheidae
Synalpheus
Synalpheus mcclendoni

description: Synalpheus mcclendoni Coutière, 1910
(Pls. 5B–C)
 Material examined. Curaçao: 2 non-ov. individuals (VIMS 08CU3002–3), Caracas Baai, from the canals of Agelas cf. clathrodes. 2 ov. females, 2 non-ov. individuals (VIMS 08CU12401, 13002), Eastpunt, from the canals of A. cf. clathrodes. 1 individual (VIMS 08CU12203), Eastpunt, from the canals of Hyattella intestinalis. 1 ov. female, 1 non-ov. individual (VIMS 08CU504–5), Piscadera Baai, from the canals of H. intestinalis. 1 ov. female, 2 non-ov. individuals (VIMS 08CU9801), Piscadera Baai east, from the canals of Aiolochroia crassa. 1 individual (VIMS 08CU8203), Scary Steps, from the canals of A. cf. clathrodes. 1 individual (VIMS 08CU2801), St. Michiel Baai, from the canals of A. crassa. 1 ov. female (VIMS 08CU5608), 1 non-ov. individual (VIMS 08CU5609), Westpunt, from the canals of H. intestinalis. Largest ov. female, CL 3.1, largest non-ov. individual, CL 3.9 mm.
 Color. Individuals found in Curaçao typically had a brightly colored major chela, with distal red tips, a white crescent, and the rest of the chela proximal to the white crescent blue (Plate 5B). This “red white and blue” color morph has also been described from specimens collected from Belize and Caribbean Panama (Rios & Duffy 2007). Ovigerous females tended to have more drab coloration on the major chela, and had yellowish-green embryos.
 Hosts and ecology. In Curaçao, S. mcclendoni was typically found in equal sex ratios and occurred in low frequencies across three different sponge hosts (Agelas cf. clathrodes, Hyattella intestinalis, and Aiolochroia crassa).
 Distribution. Florida (Coutière 1910); Bahamas (Dardeau 1984); Cuba (Martínez Iglesias & García Raso 1999); Yucatan peninsula of Mexico (Chace 1972); Caribbean Panamá (Duffy 1992), Belize (Rios & Duffy 2007), Jamaica (Macdonald et al. 2009); Curaçao (this study).
 Remarks. S. mcclendoni can be distinguished from its morphologically closest relative (S. sanctithomae) on the basis of its curved major chela fingers (not curved in S. sanctithomae) and the broad fan of plumose setae on the distal margin of the telson (typically containing <6 setae in S. sanctithomae).
description: Published as part of Hultgren, Kristin M., Macdonald Iii, Kenneth S. & Duffy, J. Emmett, 2010, Sponge-dwelling snapping shrimps of Curaçao, with descriptions of three new species *, pp. 221-262 in Zootaxa 2372 (1) on pages 245-246, DOI: 10.11646/zootaxa.2372.1.20, http://zenodo.org/record/5306751
paperChain - FACTSHEET CC1b - "GLDs and Grits containing Asphalt pavements"
Creators: name: Oleaga, Asier
Publisher: name: Zenodo
Year: 2022
Subjects: Asphalt
Pavement
Grits
GLDs
Mixtures

description: This factsheet has been extracted from D07.3 "Guidelines for the implementation of the Circular Economy models" CC1b: GLDs and Grits in Asphalt pavements: GLDs and Grits can replace partially standard fillers and aggregates in the production of asphalt pavements. Circular Case 1b is focused on the use of treated Grits and Green Liquor Dregs (GLDs) as fillers and aggregates on the elaboration of a bituminous mixture of type AC 14 on a road surface layer in an industrial site, substituting standard raw materials: 1) standard bituminous mixture, 2) section with fine aggregates were partially replaced by grits, 3) section where the fine aggregates were partially replaced by GLD, and 4) section where the fine aggregates were partially replaced by grits and GLDs. Waste pre-treatment consisting on drying, sieving, and, also salts washing. Technical and environmental performance achieved user requirements. CC1b CEM has a high replicability potential. THE NAVIGATOR COMPANY (PPI) produced GLDs and grits wastes were managed by DILUMEX carrying out the material transportation and waste pre-treatment. Elaboration of the asphalt mixture by MEGAVIA (Constructor). UNIVERSITY OF AVEIRO (UAVR) collaborated with DILUMEX and NAVIGATOR in this Circular Case, for technical support. Figure 1 shows the CC1 Circular Case in Portugal integrating the CC1a (see factsheet CC1a), and CC1b, Figures 2 to 4 show the industrial scale pilot demonstration, and Tables 1 and 2 show CC main items, key factors and lessons learnt.
What Drives, Hinders, and Enables Internationalization among Swedish Furniture Producers?
Creators: name: Snygg, Asa
name: Snygg, Asa
Publisher: name: Unknown
Year: 2004
Subjects: subject: Agribusiness
subject: International Development
subject: International Relations/Trade
subject: SMEs
subject: Key Decision Maker
subject: Internal Organization
subject: External Environment.

description: The internalization of small and medium sized companies has recently received an increased amount of attention. However, no existing model or theory manages to satisfactory explain this process, which is indicated by the varying results from empirical studies. The prime interest of this study is to investigate what drives, hinders, and enables the internationalization of Swedish furniture producers. Thus, the focus is not directly on the internalization outcomes or activities, but rather on the influencers and their impact on the process. The influencers refer to a firm's key decision maker, the internal organization, and the external environment of the firm. All three influencers simultaneously impact the process by driving it, hindering it, or enabling the firm to overcome the barriers. The empirical material will be collected among small and medium sized Swedish furniture producers. Multiple case studies will be complimented by an industry wide survey.
Quantum correlations versus Multisimultaneity: an experimental test
Creators: name: Stefanov, Andre
name: Gisin, Nicolas
name: Suarez, Antoine
name: Zbinden, Hugo
Publisher: name: arXiv
Year: 2001
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Multisimultaneity is a causal model of relativistic quantum physics which assigns a real time ordering to any set of events, much in the spirit of the pilot-wave picture. Contrary to standard quantum mechanics, it predicts a disappearance of the correlations in a Bell-type experiment when both analysers are in relative motion such that, each one in its own inertial reference frame, is first to select the output of the photons. We tested this prediction using acousto-optic modulators as moving beam-splitters and interferometers separated by 55 m. We didn't observe any disappearance of the correlations, thus refuting Multisimultaneity.
description: 4 pages, 3 figures, RevTex 4 version
Monitoring trace levels of ctDNA using integration of variant reads
Creators: name: Wan, Jonathan Chee Ming
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: liquid biopsy
circulating tumour DNA
ctDNA
cancer genomics
bioinformatics
cancer
melanoma
circulating nucleic acids

description: In patients with early-stage cancer, ctDNA detection rates can be low due to the presence of few or no copies of any individual mutation in each sample. Sensitivity may be increased by collecting larger plasma volumes, but this is not feasible in practice. Although cancers typically have thousands of mutations in their genome, previous analyses measured only individual or up to 32 tumour-specific mutations in plasma. Here, we demonstrate that sensitivity can be greatly enhanced for any given input DNA mass by analysing a large number of mutations via sequencing. We sequenced in plasma 10^2-10^4 mutated loci per patient, using custom capture panels, whole exome (WES) or whole genome sequencing (WGS). We developed a method for INtegration of VAriant Reads (INVAR) that aggregates reads carrying tumour mutations across multiple mutant loci, and assigns confidence to error-suppressed reads based on mutation context, fragment length and tumour representation. This workflow combines a number of concepts in a novel approach in order to quantify ctDNA with maximal sensitivity. We applied INVAR to plasma sequencing data from 45 patients with stage II-IV melanoma and 26 healthy individuals. ctDNA was detected to 1 mutant molecule per million, and tumour volumes of ~1cm^3. We show that this algorithm is applicable across targeted and untargeted sequencing methods. In patients with stage II-III melanoma who relapsed after resection, ctDNA was detected within 6 months post-surgery and prior to relapse in 50% of cases, compared to 16% in a similar cohort analysed with digital PCR. In addition, INVAR may enhance detection of ctDNA in samples with limited input or sequencing coverage by aggregating signal across a large number of mutations. Using low-depth WGS (0.6x), ctDNA was detected to 1 mutant per 10,000 molecules. Given that 60 genome copies of cfDNA may be obtained from 1 drop of blood (50-75μL), we suggest that INVAR may enable cancer monitoring from limited samples volumes. As tumour sequencing becomes more widespread allowing identification of a large number of mutations per patient, this method has potential to quantify ctDNA with enhanced sensitivity, and to enable routine cancer monitoring using low-depth sequencing, potentially from low-volume blood samples that might be self-collected.
description: Cancer Research UK
Additional file 4 of Cdk5 regulatory subunit-associated protein 1 knockout mice show hearing loss phenotypically similar to age-related hearing loss
Creators: name: Miwa, Toru
name: Fan-Yan Wei
name: Tomizawa, Kazuhito
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 4. Lipofuscin detection using H&E staining of the middle cochlear turn in Cdk5rap1-KO and CNT mice at different ages. (a) OC, (b) SGCs, (c) SV and SLi. Black arrows indicate lipofuscin. Scale bar = 100 µm.
Cascading Hybrid Bandits: Online Learning to Rank for Relevance and Diversity
Creators: name: Li, Chang
name: Feng, Haoyun
name: de Rijke, Maarten
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Information Retrieval (cs.IR)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Relevance ranking and result diversification are two core areas in modern recommender systems. Relevance ranking aims at building a ranked list sorted in decreasing order of item relevance, while result diversification focuses on generating a ranked list of items that covers a broad range of topics. In this paper, we study an online learning setting that aims to recommend a ranked list with $K$ items that maximizes the ranking utility, i.e., a list whose items are relevant and whose topics are diverse. We formulate it as the cascade hybrid bandits (CHB) problem. CHB assumes the cascading user behavior, where a user browses the displayed list from top to bottom, clicks the first attractive item, and stops browsing the rest. We propose a hybrid contextual bandit approach, called CascadeHybrid, for solving this problem. CascadeHybrid models item relevance and topical diversity using two independent functions and simultaneously learns those functions from user click feedback. We conduct experiments to evaluate CascadeHybrid on two real-world recommendation datasets: MovieLens and Yahoo music datasets. Our experimental results show that CascadeHybrid outperforms the baselines. In addition, we prove theoretical guarantees on the $n$-step performance demonstrating the soundness of CascadeHybrid.
MOESM1 of A phase Ib study of capecitabine and ziv-aflibercept followed by a phase II single-arm expansion cohort in chemotherapy refractory metastatic colorectal cancer
Creators: name: Strickler, John
name: Rushing, Christel
name: Niedzwiecki, Donna
name: McLeod, Abigail
name: Altomare, Ivy
name: Uronis, Hope
name: S. Hsu
name: S. Zafar
name: Morse, Michael
name: Chang, David
name: Wells, James
name: Blackwell, Kimberly
name: P. Marcom
name: Arrowood, Christy
name: Bolch, Emily
name: Haley, Sherri
name: Rangwala, Fatima
name: Ace Hatch
name: Nixon, Andrew
name: Hurwitz, Herbert
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 1: Table S1. Taqman Gene Expression Primers and Table S2. Association of angiogenic ligand expression with clinical outcomes.
Additional file 3 of Cdk5 regulatory subunit-associated protein 1 knockout mice show hearing loss phenotypically similar to age-related hearing loss
Creators: name: Miwa, Toru
name: Fan-Yan Wei
name: Tomizawa, Kazuhito
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Additional file 3. Magnified images of SA-β-gal assay of middle cochlear turn in Cdk5rap1-KO and CNT mice at different ages. (a) OC, (b) SGCs, (c) SV and SLi. Scale bar = 100 µm.
Additional file 1 of The impact of chest pain center on treatment delay of STEMI patients: a time series study
Creators: name: Sun, Xiaolin
name: Yao, Bo
name: Shi, Kexin
name: Xue, Yajiong
name: Liang, Huigang
Publisher: name: figshare
Year: 2021
Subjects: Medicine
Cell Biology
Biological Sciences not elsewhere classified
Science Policy
Computational Biology

description: Additional file 1: Appendix A. Sample characteristics. Table A1. STEMI patient characteristics. Table A2. Frequency of clinical symptoms among STEMI patients. Appendix B. Illustration of segmented regression analysis. Figure B1. Analysis logic of SRA.
title: Investigating the role of 70 bp repeats and VSGs in formation of DNA double strand breaks in Trypanosoma brucei bloodstream expression sites
Creators: name: Salthouse, Holly Rebecca
Publisher: name: University of Glasgow
Year: 2025

description: Trypanosoma brucei are protozoan parasites, which evade the immune system by antigenic variation with the use of a variant surface glycoprotein (VSG). A double strand DNA break (DSB) has been proposed as the first step in VSG switching and it has previously been demonstrated that when DNA breaks arise in the active expression site, this leads to accumulation of RNA-DNA hybrids, R-loops, however, there is still uncertainty of how and where the double stranded breaks form. Mapping of DNA breaks in the expression site by BLISS has implicated two key features in the formation of the breaks: the VSG 3’ end where the break is found and in the 70 bp repeats. This project aimed to examine the relative contribution of both the VSG 3’ end and the 70 bp repeats to the formation of a DNA break and VSG switching. To address this, bloodstream form T. brucei cell lines with alterations in the active bloodstream expression site (BES) were generated using CRISPR/Cas9. Two regions of 70 bp repeats were successfully removed and a distinct VSG sequence (VSG121) was relocated to two other locations within the active BES. In addition, a plasmid containing the VSG of the active expression site in this cell line (VSG221) was successfully generated. To confirm alterations to the active BES PCR screening, VSG immunofluorescence, and Oxford Nanopore sequencing were performed. It was identified by Oxford Nanopore sequencing that when the large section of 70 bp repeats was removed, the smaller section of 70 bp repeats expanded. In future work, these cell lines will allow for investigation of R-loops and double strand breaks by comparison of DRIP-seq and INDUCE-seq/BLISS data with the natural organisation of the active BES and so, give an insight into whether the 70 bp repeats and/or VSG sequence drive R-loop and DNA DSB formation and if they are necessary for break formation linked to VSG switching.
Revised Stellar Temperatures for Magellanic Cloud O Supergiants from FUSE and VLT-UVES Spectroscopy
Creators: name: Crowther, P. A.
name: Hillier, D. J.
name: Evans, C. J.
name: Fullerton, A. W.
name: De Marco, O.
name: Willis, A. J.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We have undertaken quantitative analysis of four LMC and SMC O4--9.7 extreme supergiants using far-ultraviolet FUSE, ultraviolet IUE/HSTand optical VLT UVES spectroscopy. Extended, non-LTE model atmospheres that allow for the consistent treatment of line blanketing are used to analyse wind & photospheric spectral features simultaneously. Using Halpha to constrain dM/dt, HeI-II photospheric lines reveal T_eff's which are systematically (5-7.5kK) & substantially (15-20%) lower than previously derived from unblanketed, plane-parallel, non-LTE photospheric studies. We have confidence in these revisions, since derived T_eff's generally yield consistent fits across the entire 912-7000Ang observed spectral range. In particular, we are able to resolve previous UV-optical T_eff discrepancies. `Of' classification criteria are directly linked to (strong) nitrogen enrichment (via NIII 4097) & (weak) carbon depletion (via CIII 4647-51), providing evidence for mixing of unprocessed and CNO processed material at their stellar surfaces. Oxygen abundances are more difficult to constrain, except via OII lines in the O9.7 supergiant for which it is also found to be somewhat depleted. The effect of wind clumping is also investigated, for which PV 1118-28 potentially provides a useful diagnostic in O-star winds. Revised stellar properties affect existing calibrations of (i) Lyman continuum photons - a factor of two lower for the O4 supergiant; and (ii) kinetic energy released into the ISM by O supergiants. Our results also have importance for the calibration of the wind momentum-luminosity relationship for OB stars.
description: Submitted to ApJ. 36 pages, 19 figures (mostly in color). Version with ps figures is available at ftp://ftp.star.ucl.ac.uk/pub/pac/osuper.ps.gz
Additional file 1 of Amaranth leaf extract protects against hydrogen peroxide induced oxidative stress in Drosophila melanogaster
Creators: name: Ndinawe Johnmark
name: Kinyi, Hellen W.
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file1. Supplementary file: Detailed Materials and Methods.
Characterising the early aggregation events of human lysozyme using single-molecule microscopy
Creators: name: Bernardo Gancedo, Ana
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Aggregation
lysozyme
single-molecule
amyloid
Alexa
fluorophore
laser
clusterin
oligomer
human

description: Human lysozyme (HuL) is a widely characterised protein whose mutational variants misfold, forming amyloid fibrils that are associated with a rare systemic amyloidosis. Given that a number of proteins, including lysozyme, can misfold and give rise to disorders such as Alzheimer’s disease, Parkinson’s disease, and type II diabetes, it is vital to understand the mechanistic features by which this process occurs, in order to attempt to cure or regulate these diseases. Work on lysozyme and other globular proteins has revealed that they require a process of global or partial unfolding to initiate protein aggregation, which is different from the natively unfolded proteins known as intrinsically disordered proteins (IDPs). Although the processes of folding and fibril formation for HuL have been well studied, the details of the early events leading to aggregation have proven difficult to study. Recent advances in site-specific labelling of HuL have made it possible to introduce Alexa fluorophores into the I59T variant of HuL without perturbing the process of in vitro fibril formation as compared to the unlabelled protein. Using this fluorescently labelled protein, we have used single-molecule fluorescence microscopy techniques including two-colour coincidence detection (TCCD) and fluorescence resonance energy transfer (FRET) to determine the oligomer population distributions present during the aggregation of HuL. Our data showed that HuL populates disordered small low-FRET oligomers (<10 monomers) which in turn can undergo a conformational change to form more stable and structured high-FRET oligomers over the course of the aggregation. The second type of oligomers can then grow to form amyloid fibrils. We fitted our data from the early stages of the aggregation reaction to an early-time kinetic model, in which the monomer concentration can be assumed constant during the selected period of time. Using this model, we calculated the different rate constants associated with the microscopic steps along the aggregation pathway that we were able to monitor using SM techniques. In addition, the interactions between HuL oligomers and the extracellular chaperone clusterin were investigated. Previous studies have shown that clusterin inhibits I59T HuL aggregation by interacting with species formed early in the aggregation pathway. Here, we show that clusterin enhances the population of small high-FRET oligomers, trapping them and preventing their growth into larger aggregates over the time-course of our analysis. These results allow us to directly compare the mechanism of protein aggregation in a globular system versus that of IDPs, providing potential insight into targeting these pathways for therapeutic interventions.
Additional file 1 of Population genetic considerations for using biobanks as international resources in the pandemic era and beyond
Creators: name: Carress, Hannah
name: Lawson, Daniel John
name: Elhaik, Eran
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Text S1. concepts used in the study. Table S1. A summary of the advantages and limitations of seven of the most popular global genomic ancestry tools, as discussed in this review. Table S2. A summary of the advantages and limitations of the five of the most popular selected local ancestry inference tools. Table S3. A summary of the advantages and limitations of the six most popular of the selected relatedness inference tools, as discussed in this review. Figure S1. The popularity (normalised number of citations) of the different GAI software, separated into model-based (red) and non-parametric (blue) tools. The tools were found using existing review papers and free search, using the search engines ‘Google,’ ‘Google Scholar’ and the journal ‘Bioinformatics’ to search for keywords including: ‘software,’ ‘tools,’ ‘inference,’ ‘biogeographic,’ ‘ancestry,’ ‘kinship’ and ‘haplotype.’ The number of citations for the paper proposing the tool, taken from ‘Google Scholar,’ were compared for each tool within each domain. To account for the differences in the number of years since publication, the number of citations was normalised by dividing the number of citations by the number of years since publication. Figure S2. The popularity (normalised number of citations) of the different LAI software, separated into their technologies: Hidden Markov Model (HMM) (green), Chromosome Painting (red) and Statistical Learning Algorithm (SLA) (blue). Finding the tools and calculating the normalised citation number was done as in Figure S1. Figure S3. The popularity (normalised number of citations) of the different kinship inference software, separated into their software strategies: Identity-By-Descent (IBD) detection (red) and Kinship Coefficient Estimation (blue). Finding the tools and calculating the normalised citation number was done as in Figure S1
Structural determinants of mutability across cancer genomes
Creators: name: Georgakopoulos-Soares, Ilias
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Cancer
Mutability
Genomes
DNA structures

description: Cancer is a group of diseases which are characterised and actuated by somatic mutations. In cancer the distribution of mutations across the genome is inhomogeneous, with genomic and epigenomic features influencing mutational patterns. Previous studies have indicated that chromatin organization and replication time domains are correlated with and thus predictive of this variation. Here the role of alternative DNA structures was investigated across a multitude of whole-genome sequenced cancers. Sequences that are predisposed to fold in alternative DNA structures can be identified by the primary DNA sequence of the human genome and are collectively known as non-B DNA motifs. More specifically, these include Z-DNA, G-quadruplexes, inverted repeats that can fold in cruciforms and hairpins, direct and short tandem repeats that can mediate the formation of slipped structures and a subset of mirror repeats that fold in intramolecular triple stranded DNA also known as H-DNA. A systematic investigation of the association between each of those non-B DNA motifs and mutability was performed across thousands of whole genome sequenced tumours from different tissues. Non-B DNA motifs were more mutable than the surrounding regions and were found to be determinants of mutability across cancer types. Additionally, they could be used to predict variation in mutational density genome-wide. Exposed structural components and physical properties of non-B DNA motifs influenced the likelihood of mutagenesis, indicating that secondary structures are possibly causally implicated in mutagenesis. Furthermore, non-B DNA motifs increased the likelihood of recurrent mutations in the genome, which has direct implications for the identification of driver mutations in non-coding regions. A detailed characterisation of indel mutagenesis was performed across the different cancer types. The analysis indicated the roles of different non-B DNA motif categories as well as sequence homologies in indel mutagenesis. In particular, sequence characteristics of a subset of non-B DNA motifs significantly influenced their relative mutational enrichment at specific indel categories. Finally, a method was developed to quantify replication and transcription strand asymmetries at indels systematically for the first time. As a result, mutational processes that are causally implicated in strand asymmetries at indels were identified and analysed. These included mismatch repair and transcription-coupled nucleotide excision repair both of which contributed to the observed transcriptional strand asymmetries for indels.
description: Wellcome Trust
Static elastic cloaking, low frequency elastic wave transparency and neutral inclusions
Creators: name: Norris, Andrew N.
name: Parnell, William J.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Classical Physics (physics.class-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: New connections between static elastic cloaking, low frequency elastic wave scattering and neutral inclusions are established in the context of two dimensional elasticity. A cylindrical core surrounded by a cylindrical shell is embedded in a uniform elastic matrix. Given the core and matrix properties, we answer the questions of how to select the shell material such that (i) it acts as a static elastic cloak, and (ii) it eliminates low frequency scattering of incident elastic waves. It is shown that static cloaking (i) requires an anisotropic shell, whereas scattering reduction (ii) can be satisfied more simply with isotropic materials. Implicit solutions for the shell material are obtained by considering the core-shell composite cylinder as a neutral elastic inclusion. Two types of neutral inclusion are distinguished, \textit{weak} and \textit{strong} with the former equivalent to low frequency transparency {and the classical Christensen and Lo generalised self-consistent result for in-plane shear from 1979. Our introduction of the \textit{strong neutral inclusion} is an important extension of this result in that we show that standard anisotropic shells can act as perfect static cloaks, contrasting previous work that has employed "unphysical" materials.} The relationships between low frequency transparency, static cloaking and neutral inclusions provide the material designer with options for achieving elastic cloaking in the quasi-static limit.
description: 30 pages, 2 figures
MOESM2 of What happened and why? A programme theory-based qualitative evaluation of a healthcare-academia partnership reform in primary care
Creators: name: HĂĽkan Uvhagen
name: Hasson, Henna
name: Hansson, Johan
name: Knorring, Mia Von
Publisher: name: figshare
Year: 2019
Subjects: subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer

description: Additional file 2: Interview guide.
A Critical Examination of Li Pollution and Giant Planet Consumption by a Host Star
Creators: name: Sandquist, Eric L.
name: Dokter, Jon J.
name: Lin, D. N. C.
name: Mardling, Rosemary A.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We examine the overall likelihood that the consumption of a giant planet could pollute its host star. First, we show that the detection of 6Li in SWPs could be used to distinguish between giant planet formation theories, and can be used to detect the consumption of giant planets independent of planet mass. Second, we examine the probability that giant planets between 1 and 3 M_J could be destroyed in the outer convection zone of stars slightly more massive than the Sun, finding that heated giant planets would be efficiently destroyed near the surface of the star, while the cores of cold giant planets may be able to survive to the base of the star's convection zone. Third, we examine the tidal interaction between a planet and its host star, showing that this interaction can lead to tidal disruption of the planet and accretion of its material, or orbital decay followed by hydrodynamical interaction. Throughout, we consider the case of HD 82943, a star known to have two planets and having a preliminary detection of 6Li. Using stellar models including diffusion, we estimate the mass of the HD 82943 to be about 1.2 M_sun and its age to be about 0.5-1.5 Gyr. The observed 7Li abundance for HD 82943 is consistent with stars of similar T_eff and age in the open cluster NGC 752. We describe a possible dynamical history for a hypothetical planet in the presence of the two resonant planets currently known. (abridged)
description: 33 pages, 3 figures, accepted for ApJ
Semiclassical dynamics for torsional Newton-Cartan strings
Creators: name: Roychowdhury, Dibakar
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We explore \emph{folded} spinning string configurations over torsional Newton Cartan (TNC) geometry with $ R\times S^2 $ topology within the semiclassical approximation. We consider the large $ c $ and/or nonrelativistic (NR) limit associated with the world-sheet d.o.f. and compute the one loop stringy corrections to the energy spectrum in the dual Spin Matrix Theory (SMT) theory in the limit of strong ($ \mathtt{g}\gg 1 $) coupling.
description: Latex, 10 pages, Version accepted in Nucl. Phys. B
Charmonium Production in $e^+e^-$ Annihilation at $\sqrt{s}=10.6GeV$
Creators: name: Chao, Kuang-Ta
name: Hao, Li-Kun
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We review the charmonium production in $e^+e^-$ annihilation at $\sqrt{s}=10.6GeV$. NRQCD predictions for the $J/ψ$ production are compared with the recent measurements by BaBar and Belle. A NRQCD calculation for the $D$-wave charmonium production is reported to further test the color-octet mechanism and detect the $J^{PC}=2^{--}$ state. The issue of double $c \bar c$ production in $e^+e^-$ annihilation observed by Belle is also discussed.
description: 4 pages, 2 figures, talk given at 5th International Conference on Hyperons, Charm and Beauty Hardons (BEACH 2002), Vancouver, Canada, June 25-29
paperChain - FACTSHEET CC2 - "Construction: roads with WPFA based HRB binders"
Creators: name: Oleaga, Asier
Publisher: name: Zenodo
Year: 2022
Subjects: Soil Cement
Stabilisation
Leaching
Binder
Roads

description: This factsheet has been extracted from D07.3 "Guidelines for the implementation of the Circular Economy models" CC2: Wastepaper Fly ash (WPFA) for Hydraulic Road Binders (HRBs) production: CC2 is focused on Wastepaper Fly Ash (WPFA) based hydraulic road binder (HRB) production for soil stabilization in road construction sector. ACCIONA (Constructor) and SAICA (PPI waste valoriser) that generates the WPFA, cooperated in PAPERCHAIN to find an alternative and sustainable solution for the use of fly ash waste other than landfilling. In CC2 ash replaces standard binder (cement) typically employed in the stabilization of soils S-EST2, S-EST3 type layers (according to local standards PG3) in rural roads, and a soil-cement layer in highway. 3 Pilots successfully completed in Spain: a) unpaved rural road (Ejea de los Caballeros, Zaragoza), b) paved peri urban road (Villamayor de Gállego, Zaragoza); c) A31 highway (La Font de la Figuera, Valencia). UPC (University), and TECNALIA (Research Center) have supported CC2 in product design, and the technical and environmental performance monitoring. Process must be adapted to the characteristics of WPFA to avoid problems of low density, mixing-compaction and generation of dust when mixing on site (stabilized soils approach). WPFA quality monitoring is focused on its salts and heavy metals content and variability. CC2 CEM has a high replicability potential. A technical Conformity (TC) document for its certification as product in progress.Figure 1 shows the CC2 Circular Case in Spain, Figures 2-4 show the industrial scale pilot demonstration, and Tables 1 and 2 show the CC main items, Key factors and lessons learnt.
Scattering of particles bounded to an infinite planar curve
Creators: name: Dittrich, J.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 81Q10, 81U99, 47B10

description: Non-relativistic quantum particles bounded to a curve in R^2 by attractive contact $δ$-interaction are considered. The interval between the energy of the transversal bound state and zero is shown to belong to the absolutely continuous spectrum, with possible embedded eigenvalues. The existence of the wave operators is proved for the mentioned energy interval using the Hamiltonians with the interaction supported by the straight lines as the free ones. Their completeness is not proved. The curve is assumed C^3-smooth, non-intersecting, unbounded, asymptotically approaching two different half-lines (non-parallel or parallel but excluding the "U-case"). Physically, the system can be considered as a model of long nanostructural channel.
description: 43 pages
Additional file 1 of A model-agnostic approach for understanding heart failure risk factors
Creators: name: Miran, Seyed M.
name: Nelson, Stuart J.
name: Zeng-Treitler, Qing
Publisher: name: figshare
Year: 2021
Subjects: subject: Artificial Intelligence and Image Processing
subject: FOS: Computer and information sciences

description: Additional file1: Table S1 Patient characteristics.
Saddles and dynamics in a solvable mean-field model
Creators: name: Angelani, L.
name: Ruocco, G.
name: Zamponi, F.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We use the saddle-approach, recently introduced in the numerical investigation of simple model liquids, in the analysis of a mean-field solvable system. The investigated system is the k-trigonometric model, a k-body interaction mean field system, that generalizes the trigonometric model introduced by Madan and Keyes [J. Chem. Phys. 98, 3342 (1993)] and that has been recently introduced to investigate the relationship between thermodynamics and topology of the configuration space. We find a close relationship between the properties of saddles (stationary points of the potential energy surface) visited by the system and the dynamics. In particular the temperature dependence of saddle order follows that of the diffusivity, both having an Arrhenius behavior at low temperature and a similar shape in the whole temperature range. Our results confirm the general usefulness of the saddle-approach in the interpretation of dynamical processes taking place in interacting systems.
description: 7 pages, 8 figures
Additional file 1 of Bayesian belief network modelling of household food security in rural South Africa
Creators: name: Eyre, Robert W.
name: House, Thomas
name: F. Xavier Gómez-Olivé
name: Griffiths, Frances E.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy

description: Additional file 1. Bayesian belief network modelling of household food security in rural South Africa - supplementary material. Further details on the variable selection literature search, as well as further results for both the simulations of established food security interventions and the interventional inferences.