cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 5: of The unique evolutionary pattern of the Hydroxyproline-rich glycoproteins superfamily in Chinese white pear (Pyrus bretschneideri)
Creators: name: Jiao, Huijun
name: Liu, Xing
name: Sun, Shuguang
name: Wang, Peng
name: Qiao, Xin
name: Li, Jiaming
name: Tang, Chao
name: Wu, Juyou
name: Zhang, Shaoling
name: Tao, Shutian
Publisher: name: figshare
Year: 2018
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure. S4. Heatmap of the expression levels of HRGP genes in reproductive tissues. A. The expression levels of HRGP genes in pollen. MP, HP, PT and SPT correspond to four different developmental stages: matured pollen, hydrated pollen, growing pollen tubes after three hours of hydration and stopped growing pollen tubes, respectively. B. The expression levels of HRGP genes in the pistils of â Jinzhuiâ pollinated with self- and non-self-pollen; JY24, JJ24, JY48, JJ48, JY72 and JJ72 refer to pollinated pistils corresponding to time after pollination. The colour scale represents log2 transformed reads per kilobase per million (RPKM) values. Light green indicates low expression and red indicates high expression. (PDF 313Â kb)
Tectonics, ore bodies, and gamma-ray logging of the Variscan basement, southern Gennargentu massif (central Sardinia, Italy)
Creators: name: Meloni, Mattia Alessio
name: Oggiano, Giacomo
name: Funedda, Antonio
name: Pistis, Marco
name: Linnemann, Ulf
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
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: Inorganic Chemistry
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: We present a structural geological map (1:14,000 scale) that covers a 100 km2 area of Variscan basement rocks exposed in central Sardinia. The mapped area is located between 39°56′20′′ N 9°04′59′′ E (northwestern corner) and 39°51′47′′ N 9°13′16′′ E (southeastern corner) on the southern slope of the Gennargentu massif, surrounding the mining village of Gadoni. This village was the hub of a mining district in central Sardinia. The region extends between the external and inner nappe zones of the Variscan orogenic wedge of Sardinia. Despite significant mining, the area lacked an up-to-date structural and stratigraphic synthesis comparable to that achieved in the southern Sardinia. This gap in knowledge was due to: (i) more complex structural deformation; (ii) slightly higher grade regional metamorphism including a late Variscan high-temperature overprint; (iii) difficulty in distinguishing terrigenous stratigraphic units that belong to different tectonic units; and (iv) the absence of key stratigraphic marker for resolve complex structures in the uppermost tectonic unit. Integration of field mapping, structural analysis, portable gamma-ray spectroscopy, and zircon U-Pb ages of intrusive rocks has enabled a new geological map and cross-sections. These contributions synthesize the collisional and postcollisional evolution of the region and its relationship with ore genesis.
Creating biological pathways for WikiPathways using PathVisio
Creators: name: Ehrhart, Friederike
name: Kutmon, Martina
name: Willighagen, Egon
name: Hanspers, Kristina
name: Pico, Alexander
name: Rieswijk, Linda
name: Nymark, Penny
Publisher: name: figshare
Year: 2017
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 100708 Nanomaterials
subject: FOS: Nanotechnology
subject: Toxicology

description: Introduction This tutorial shows users how to make a biological (or biochemical) pathway for WikiPathways using the software PathVisio. The information and images are derived from help pages of WikiPathways with some recent updates. Pathways can be created from e.g. comprehensive images in reviews showing the interactions of genes, proteins and metabolites in a good graphical way. Pathways can show molecular biological interactions like signal cascades, enzyme reactions, transport mechanisms of “healthy” pathways, drug or nanoparticle interactions, adverse outcome pathways and diseases. You can find examples for nanomaterial specific pathways and discussions in the nanomaterials portal of WikiPathways. What is WikiPathways WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a collaborative model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, WikiPathways added a custom graphical pathway editing tool and integrated identifier databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.
Additional file 6: of The unique evolutionary pattern of the Hydroxyproline-rich glycoproteins superfamily in Chinese white pear (Pyrus bretschneideri)
Creators: name: Jiao, Huijun
name: Liu, Xing
name: Sun, Shuguang
name: Wang, Peng
name: Qiao, Xin
name: Li, Jiaming
name: Tang, Chao
name: Wu, Juyou
name: Zhang, Shaoling
name: Tao, Shutian
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Figure. S5. Heatmap of the expression levels of HRGP in 6 stages of pear fruit. S1~S6 correspond to the dynamic stages of fruit development at 15 d, 36 d,80 d, 110 d, 145 d and 167 d after flowering. (PDF 388Â kb)
Additional file 7: of The unique evolutionary pattern of the Hydroxyproline-rich glycoproteins superfamily in Chinese white pear (Pyrus bretschneideri)
Creators: name: Jiao, Huijun
name: Liu, Xing
name: Sun, Shuguang
name: Wang, Peng
name: Qiao, Xin
name: Li, Jiaming
name: Tang, Chao
name: Wu, Juyou
name: Zhang, Shaoling
name: Tao, Shutian
Publisher: name: figshare
Year: 2018
Subjects: subject: Cell Biology
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: Figure. S6. Relative expression levels of HRGPs in pollinated pistils. A-C. The relative expression levels of Pbr036330.1 (A), Pbr010506.1 (B) and Pbr031110.1 (C) in different pear tissues. JY24, JJ24, JY48, JJ48, JY72 and JJ72 refer to pollinated pistils corresponding to time after pollination with ‘Yali’ and ‘Jinzhui’ pollen. (PDF 183 kb)
Visible-light photochromism of phosphomolybdic acid and polyvinyl alcohol by inorganic-organic nanocomposite multilayer films
Creators: name: Li, Zhuo-Juan
name: Zhao, Wen-Jin
name: Shi, Yan
name: Ying, Zu-Ping
name: Feng, Wei
name: Bai, Li
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: A novel visible-light photochromic inorganic-organic multilayer was constructed based on phosphomolybdic acid (PMoA) and polyvinyl alcohol (PVA) which was prepared using the layer-by-layer (LbL) assembly technique to form the multilayer film. The structures of the multilayer films were characterized via Fourier transform infrared spectra (FT-IR) and atomic force microscopy (AFM). The grown process, internal interaction, the surface topography and photochromic properties could be obviously studied through ultraviolet–visible (UV–vis) spectra and X-ray photoelectron spectra (XPS). The advantage of the structure and performance of the multilayer films prepared by layer-by-layer method could be found. It was suggested that the nearly linear growth process in peak-top absorbance in multilayer assembly. The PVA polymer substrate could disperse PMoA particles and changed the surface morphology. The polymer skeleton and PMoA particles were with strong interfacial interactions. The PMoA/PVA LbL film had wonderful visible light response. The oxygen acted a significant part during the bleaching process. According to XPS resoults, 51% of Mo6+ in the PMoA turned into Mo5+, obvious photoinduce oxidation and reduction reactions happened from PVA and PMoA through the proton transfer mechanism. A novel visible-light photochromic hybrid film composed of PMoA and PVA was prepared by the layer-by-layer (LbL) assembly technique. The photo-reduction process occurred according to the proton charge transfer mechanism.
Additional file 1: of Molecular subtyping of nasopharyngeal carcinoma (NPC) and a microRNA-based prognostic model for distant metastasis
Creators: name: Zhao, Lan
name: Fong, Alvin
name: Liu, Na
name: Cho, William
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer

description: Figure S1. Ten-miRNA expression patterns in the training (86 NPC and 18 normal) and validation (226 NPC and 18 normal) datasets. In the heatmaps, columns correspond to samples, and rows to the 10 miRNAs. Expression values are represented by different colors, red means higher expression values, and green for lower expression values. Note: IM is short for immunogenic. (PDF 53 kb)
Additional file 1: of In-utero exposure to phenols and phthalates and the intelligence quotient of boys at 5 years
Creators: name: Nakiwala, Dorothy
name: Peyre, Hugo
name: Heude, Barbara
name: Bernard, Jonathan
name: Béranger, Rémi
name: Slama, Rémy
name: Philippat, Claire
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Figure S1. Path diagram illustrating associations between phenols, phthalate metabolites and FSIQ of boys in the EDEN Cohort. Table S1. Estimated standardized factor loadings of outcome and exposure indicator variables. Table S2. Associations between the covariates included in our final SEM model and boys’ IQ. Table S3. Spearman correlation coefficients between biomarker concentrations measured in maternal urine (n = 452a). Table S4. Adjusted associations between phenols, phthalate metabolites and Full Scale IQ of boys at 5 years using SEM (N = 452). Table S5. Adjusted associations between phenols, phthalate metabolites and IQ (Manual based scales) of boys at 5 years in the EDEN cohort, using multiple linear regression (N = 452). Table S6. Adjusted associations between phenols, phthalate metabolites concentrations categorized in tertiles and IQ (Manual based scales) of boys at 5 years in the EDEN cohort, using multiple linear regression (N = 452). Table S7. Adjusted associations between phenols, phthalate metabolites and IQ of boys at 5 years in the EDEN cohort, stratified for center of recruitment. (DOCX 184 kb)
Additional file 1: of De novo mast cell leukemia without CD25 expression and KIT mutations: a rare case report in a 13-year-old child
Creators: name: Zheng, Yalin
name: Nong, Lin
name: Liang, Li
name: Wang, Wei
name: Li, Ting
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Materials and Methods. (DOCX 22 kb)
Additional file 1: of Efficacy and safety of Ding-Kun-Dan for female infertility patients with predicted poor ovarian response undergoing in vitro fertilization/intracytoplasmic sperm injection: study protocol for a randomized controlled trial
Creators: name: Ma, Saihua
name: Ma, Ruihong
name: Xia, Tian
name: Afnan, Masoud
name: Song, Xueru
name: Xu, Fengqin
name: Hao, Guimin
name: Zhu, Fangfang
name: Han, Jingpei
name: Zhao, Zhimei
Publisher: name: figshare
Year: 2018
Subjects: subject: Cell Biology
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: SPIRIT Checklist. The SPIRIT Checklist document. (DOC 135Â kb)
Additional file 1: of Herbal formula Huang Qin Ge Gen Tang enhances 5-fluorouracil antitumor activity through modulation of the E2F1/TS pathway
Creators: name: Liu, Haizhou
name: Liu, Hui
name: Zhou, Zhiyi
name: Parise, Robert
name: Chu, Edward
name: Schmitz, John
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Table S1. Components of Chinese herbal formulations. Table S2. Tumor doubling time. (DOCX 25 kb)
Stability analysis of the flow past a low-pressure turbine blade
Creators: name: Abdessemed, Nadir
Publisher: name: Imperial College London
Year: 2020

description: Results are presented of BiGlobal linear stability analysis of incompressible flow over a row of T-106/300 aircraft Low Pressure Turbine (LPT) blades. In particular the three-dimensional stability of two-dimensional steady and periodic states is investigated for Reynolds numbers below 10,000, where the primary two-dimensional instability leading the flow through a Hopf-bifurcation from steady to periodic has been identified to be at a chord Reynolds number of Rec = 905 ± 1. Structured and unstructured meshes have been used while variation of the polynomial order of the numerical methods as well as extension of the domain under consideration has ensured numerical convergence. Furthermore, consistency between linear stability analysis and full Navier-Stokes solution is shown. The leading Floquet- and eigenvalues of the LPT flow are observed at a range of Reynolds and span-wise wavenumber parameters. They show that the instability depends on the imposed periodicity in the two-dimensional plane of the computational model. Neglecting subharmonic effects the flow undergoes a three-dimensional transition caused by three-dimensional long wavelength disturbances immediately after its two-dimensional instability. The associated unstable mode is related to the wake of the basic state. A second short wavelength stable mode has been identified to be associated to the separation bubble at the trailing edge. A pseudospectra analysis has also been performed showing sensitivity of the eigenvalue problem and the associated potential for transient growth due to the non-orthogonal properties of the eigenmodes. Three-dimensional direct numerical simulation (DNS) shows that three-dimensional transition is susceptible to the modes identified. Finally, a subsequent two-dimensional optimum growth analysis based on a newly developed method related to the computation of the singular values of the eigenvalue problem has been performed for flow past a cylinder and the LPT flow. Optimum modes that exhibit strong energy growth were identified and compared with the adjoint modes as found in the literature. The maximum energy associated to sensitivity regions is located around the separation bubble at the trailing edge of the blade as they grow downstream. Demonstrating the potential of the developed method based on singular values, the purely two-dimensional results as presented in this work serve as a basis for future three-dimensional analyses.
Science & Digital Technologies : what is changing ?
Creators: name: Mooc Scinum
Publisher: name: figshare
Year: 2017
Subjects: subject: Science Policy
subject: 100599 Communications Technologies not elsewhere classified
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: Information Systems
subject: FOS: Computer and information sciences

description: Graphics from the "MOOC Digital Technologies and research in health and life sciences"

MOOC
Syllabus here
Additional file 1: Table S1. of Disease-related determinants are associated with mortality in dementia due to Alzheimerâ s disease
Creators: name: Rhodius-Meester, Hanneke
name: Liedes, Hilkka
name: Koene, Ted
name: Lemstra, Afina
name: Teunissen, Charlotte
name: Barkhof, Frederik
name: Scheltens, Philip
name: van Gils, Mark
name: LĂśtjĂśnen, Jyrki
name: van der Flier, Wiesje
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Mathematical Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Cox proportional hazard models using nonimputed data; influence of baseline characteristics and medical history on survival status. Table S2. Cox proportional hazard models based on nonimputed data; influence of CSF and MRI on survival status. (DOCX 26 kb)
Additional file 1: of Cooperative p16 and p21 action protects female astrocytes from transformation
Creators: name: Kfoury, Najla
name: Sun, Tao
name: Yu, Kwanha
name: Rockwell, Nathan
name: Tinkum, Kelsey
name: Qi, Zongtai
name: Warrington, Nicole
name: McDonald, Peter
name: Roy, Anuradha
name: Weir, Scott
name: Mohila, Carrie
name: Deneen, Benjamin
name: Rubin, Joshua
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Computational Biology

description: Table S1. Real-time quantitative PCR primers and CRISPR guide RNA sequences. Table S2. Antibody details. Figure S1. Female and male CRISPR-IUE gliomas exhibit differences in histology. Figure S2. Sex differences in p21 and p27 expression in the CRISPR-IUE glioma model. Figure S3. Metaphase spreads from male and female GBM astrocytes grown under control (DMSO treated) conditions revealed aneuploidy. Figure S4. Western blot demonstration of p16, p21 and p27 deletion in Cas-9 expressing male and female GBM astrocytes expressing (+) or not expressing (â ) the appropriate guide RNAs (gRNAs) as indicated. (PDF 3121Â kb)
Androgens and cardiovascular disease in men
Creators: name: Dockery, Frances
Publisher: name: Imperial College London
Year: 2020

description: Endogenous testosterone appears to be protective of certain cardiovascular risk factors in men. Suppression of endogenous testosterone is a widely used form of therapy in men with prostate cancer but the cardiovascular adverse effects of this therapy if any, are unknown. Anti-androgen drugs are often continued for years as the optimal treatment of prostate cancer is unclear. Arterial stiffness is an emerging marker of cardiovascular risk over and above that of other traditional risk factors. Using this measure a series of studies were conducted in men with prostate cancer to look at the effects of anti-androgen drugs on this cardiovascular risk factor. It was demonstrated that testosterone-deprived men have increased arterial stiffness compared to controls, and that following androgen suppression arterial stiffness is increased compared to controls. It was found that endogenous testosterone in older men is inversely correlated with arterial stiffness independently of other cardiovascular risk factors including age and blood pressure. It was also demonstrated that both testosterone suppression and androgen receptor-blockade have the same adverse effect on arterial stiffness, though the effects were not sustained in the latter situation, which might be attributable to a beneficial increase in oestradiol levels. The latter drug however led to an increase in B-type natriuretic peptide (BNP) levels - another independent marker of cardiovascular risk. This increase was not explained by changes in left ventricular function. It may also be related to the rise in oestradiol, as this BNP increase has been observed in women following oestrogen therapy. In conclusion both testosterone suppression and androgen receptor-blockade have an adverse effect on arterial stiffness in men with prostate cancer. This appears to be sustained with suppression therapy but not receptor blockade. Receptor blockade however leads to a sustained increase in BNP levels which may also imply an adverse cardiovascular effect. The different effect of the two drugs on the sex-hormone profile might account for these findings. This may have therapeutic implications for the increasing number of prostate cancer cases being treated, and long-term randomised trials are required to investigate whether or not androgen-receptor blockade is to be preferred to testosterone suppression or to no intervention for cancer, cardiovascular and quality of life outcomes.
A new natural hybrid in the genus Petasites: P. japonicus × P. pyrenaicus (Asteraceae)
Creators: name: Desjardins, Stuart D.
name: Hoare, Arthur G.
name: Stace, Clive A.
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
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: A large clone of a Petasites found growing at Borde Hill, East Sussex in 2014, which had been identified as female P. pyrenaicus (P. fragrans), otherwise unknown in Europe as far as we are aware, has been shown by morphological and molecular studies to be the hybrid female P. japonicus × male P. pyrenaicus. The origin of this hybrid, new to science, is unknown, but it has evidently been growing at Borde Hill for several decades, and has now escaped into the wild beside an adjacent footpath.
Additional file 1: Table S1. of Ablation of caspase-1 protects against TBI-induced pyroptosis in vitro and in vivo
Creators: name: Liu, Wei
name: Chen, Yuhua
name: Meng, Jiao
name: Wu, Minfei
name: Bi, Fangfang
name: Chang, Cuicui
name: Li, Hua
name: Zhang, Liangjun
Publisher: name: figshare
Year: 2018
Subjects: Biochemistry
Medicine
Cell Biology
Molecular Biology
Biological Sciences not elsewhere classified
Developmental Biology
Marine Biology
Cancer
Hematology

description: Primers of caspase-1 for RT-qPCR. (DOCX 15Â kb)
Additional file 2: Figure S1. of Ablation of caspase-1 protects against TBI-induced pyroptosis in vitro and in vivo
Creators: name: Liu, Wei
name: Chen, Yuhua
name: Meng, Jiao
name: Wu, Minfei
name: Bi, Fangfang
name: Chang, Cuicui
name: Li, Hua
name: Zhang, Liangjun
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Caspase-1 mRNA expression level in the primary neuron. The primary neuron was infected with caspase-1 shRNA (m) lentiviral particles (Santa Cruz, sc-29922-V) according to the manufacturer’s protocol (Santa Cruz Biotechnology, Inc.). At 72 h after infection, The RNAi efficiency was determined by qRT-PCR. Caspase-1 mRNA was significantly reduced by RNAi. Data were represented as means ± SEM, one representative experiment of four was shown. ***p < 0.001, versus control. (DOCX 24 kb)
Optimal control, piecewise-deterministic processes and viscosity solutions
Creators: name: Farid, Mohammad
Publisher: name: Imperial College London
Year: 2020

description: Piecewise-Deterministic Markov Processes (PDPs) are a general class of non- diffusion stochastic system models. A PDP is a Markov process that follows deterministic trajectories between random jumps, the latter occurs either spontaneously, in a Poisson-like fashion, or when the process hits the boundary of its state space. This formulation includes a wide variety of applied problems in engineering, operations research, management science and economics; examples include queueing systems, optimal exploration and consumption of renewable or non-renewable resources, capacity expansion, Permanent Health Insurance (PHI), insurance analysis, target tracking and fault detection in process systems. As a preliminary example of piecewise-deterministic processes, an iterative computational method for determining the value function of an optimal control problem, related to target tracking, was obtained. The target is assumed to be located in a fixed known position in space but its identity (hostile or friendly) is only known with a prior probability. An observation of the target can be made at any location and its error has position-dependent probability. The objective was finding the optimal navigation and observation strategy which leads to a final decision (i.e. the target is friendly or hostile). The value function was shown to be the unique viscosity solution of some variational inequality and in addition the unique fixed point of a non-decreasing concave operator. The strong boundary condition in the theory of PDPs (introduced by Vermes [Ver85]) which states that all trajectories in the vicinity of the boundary must steer towards the boundary, was relaxed and under some weaker assumptions it was proved that the associated value function is the unique viscosity solution of some Dirichlet type HJB equation. The stochastic optimal control problem reduces to a deterministic exit-time optimal control problem with an unusual boundary condition and an iterative computational method can be used for finding the value function and optimal control; in fact the value function is the unique fixed point of some two-stage contraction operator and hence the convergence of the algorithm is guaranteed. As a final example, the optimal consumption and exploration of non-renewable resources, e.g. oil, is considered. The objective is to find the optimal consumption and exploration rates under uncertain exploration. The policy maker determines the consumption and exploration rates both measured in Pounds per unit time. It is shown that the exploration policy is of “bang-bang” type, i.e. either explore at the maximum rate or not at all. Some simulation results obtained via the iterative computational method are presented.
Additional file 3: Figure S2. of Ablation of caspase-1 protects against TBI-induced pyroptosis in vitro and in vivo
Creators: name: Liu, Wei
name: Chen, Yuhua
name: Meng, Jiao
name: Wu, Minfei
name: Bi, Fangfang
name: Chang, Cuicui
name: Li, Hua
name: Zhang, Liangjun
Publisher: name: figshare
Year: 2018
Subjects: Biophysics
Biochemistry
Medicine
Cell Biology
Molecular Biology
Developmental Biology
Cancer
Computational Biology

description: Uncropped blots for the pro-form and cleaved fragments of caspase-1 in figures. (DOCX 877Â kb)
Additional file 4: Figure S3. of Ablation of caspase-1 protects against TBI-induced pyroptosis in vitro and in vivo
Creators: name: Liu, Wei
name: Chen, Yuhua
name: Meng, Jiao
name: Wu, Minfei
name: Bi, Fangfang
name: Chang, Cuicui
name: Li, Hua
name: Zhang, Liangjun
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Hematology
subject: Plant Biology
subject: FOS: Biological sciences

description: VX-765 neurotoxicity detected by CKK8 assay. In order to demonstrate the reduction in the pro-form of caspase-1 levels by VX-765 was not an artifact due to direct VX-765 neurotoxicity, a VX-765 alone and a vehicle control for VX-765 treated with neuron. The primary neuron was seeded in 96-well according to the primary neuronal cultures. At 10 days, cells were supplied with a fresh medium and treated with VX-765 (0, 1, 5, and 10 μM). After 24 h of cultivation respectively, then 10 μl of the CCK8 reaction solution (Dojindo Laboratories) was added to each well. After 4 h incubation at 37 °C in the 5% CO2 incubator, the absorbance at 450 nm was measured by Thermo MK3 (Thermo Scientific). The primary neuron was supplied with a fresh medium and treated with VX-765 at 0, 1, 5, and 10 μM (DMSO as the menstruum). After 24 h of cultivation respectively, neurotoxicity was detected by CCK8 assay. Data were represented as means ± SEM, one representative experiment of five was shown. (DOCX 43 kb)
Additional file 1: Table S1. of Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer’s disease
Creators: name: Chung, Jaeyoon
name: Zhang, Xiaoling
name: Allen, Mariet
name: Wang, Xue
name: Ma, Yiyi
name: Beecham, Gary
name: Montine, Thomas
name: Younkin, Steven
name: Dickson, Dennis
name: Golde, Todd
name: Price, Nathan
name: Ertekin-Taner, Nilüfer
name: Lunetta, Kathryn
name: Mez, Jesse
name: Mayeux, Richard
name: Haines, Jonathan
name: Pericak-Vance, Margaret
name: Schellenberg, Gerard
name: Jun, Gyungah
name: Farrer, Lindsay
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified

description: Sample characteristics. Table S2. Association P values of Alzheimer disease loci previously established by GWAS in univariate and pleiotropy association tests of neuropathological features. Table S3. Association of cis-eQTL for HDAC9 in the Mayo Clinic brain expression genome-wide association study (eGWAS). rs79524815 was not available in the Mayo Clinic brain eGWAS, so proxy SNPs that are in LD (D′ > 0.90) with rs79524815 were used for the eQTL test with HDAC9 expression. Table S4. Association of expression of SNPs for TRAPPC12-AS1 and ADI1 with neuropathological traits and gene expression in the GTEx portal database. Table S5. Association results from the trivariate pleiotropy model of neuritic plaque (NP), neurofibrillary tangles (NFT), and cerebral amyloid angiopathy (CAA) for study-wide significant SNPs in the bivariate pleiotropy model. Table S6. Results of differential gene expression analysis by brain region among AD cases and controls for AD loci previously established by GWAS in RNA-Seq and microarray analysis. Figure S1. Quantile-quantile plots of observed (y-axis) vs. expected (x-axis) P values of all SNPs (black dots) and after excluding SNPs in APOE region (blue dots) for the pleiotropy analysis of (a) NP and NFT, (b) NP and CAA, and (c) NFT and CAA using the O’Brien method [10]. Figure S2. Manhattan plots showing genome-wide pleiotropy analyses of (a) NP and NFT, (b) NP and CAA, and (c) NFT and CAA using the O’Brien method [10]. Red dashed line represents the genome-wide significance threshold of P < 5.0 × 10−−8. Loci achieving genome-wide significance are highlighted in red, and known AD genes that attained at least a moderate significance level (P < 10−−4) are highlighted in gold. Figure S3. Regional association plots of genes, including TRAPPC12, TRAPPC12-AS1, and ADI1, on chromosome 2 from the joint model of NFT and CAA. Figure S4. Genome-wide trivariate pleiotropy analysis of NP, NFT, and CAA. (a) Quantile-quantile plot. (b) Manhattan plot. (DOCX 1028 kb)
Additional file 2: of FAK-ERK activation in cell/matrix adhesion induced by the loss of apolipoprotein E stimulates the malignant progression of ovarian cancer
Creators: name: Lai, Huiling
name: Zhao, Xuejiao
name: Qin, Yu
name: Ding, Yi
name: Chen, Ruqi
name: Li, Guannan
name: Labrie, Marilyne
name: Ding, Zhiyong
name: Zhou, Jianfeng
name: Hu, Junbo
name: Ma, Ding
name: Fang, Yong
name: Gao, Qinglei
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Table S1. The quantification of secreted factors in the cytokine profiling arrays. (DOC 210 kb)
AK47 3D from The benefit of a tough skin: bullet holes, weathering and the preservation of heritage
Creators: name: Mol, Lisa
name: M. Gomez-Heras
name: C. Brassey
name: O. Green
name: T. Blenkinsop
Publisher: name: The Royal Society
Year: 2017
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences
subject: 40399 Geology not elsewhere classified
subject: 30399 Macromolecular and Materials Chemistry not elsewhere classified
subject: FOS: Chemical sciences

description: Projectile damage to building stone is a widespread phenomenon. Sites damaged 100 years ago during First World War still see daily use, while in a more contemporary setting numerous reports show the damage to buildings in Babylon, Mosul and Palmyra. While research has been carried out on the long-term effects of conflict such as fire damage, little is known about the protracted damage sustained through the impact of bullets, shrapnel and other metal projectiles outside of the field of engineering focused on ceramics and metals. To investigate alterations to mineral structure caused by projectile damage, impacts were created in medium grained, well-compacted, mesoporous sandstone samples using 0.22 calibre lead bullets shot at a distance of 20 m. Half these samples were treated with a surface consolidant (Wacker OH 100), to mimic natural cementation of the rock surface. These samples were then tested for changes to surface hardness and moisture movement during temperature cycles of 15–65°C. Petrographic thin section analysis was carried out to investigate the micro-scale deformation associated with high speed impact. The results surprisingly show that stress build-up behind pre-existing cementation of the surface, as found in heritage sites that have been exposed to moisture and temperature fluctuations for longer periods of time, can be alleviated with a bullet impact. However, fracture networks and alteration of the mineral matrices still form a weak point within the structure, even at a relatively low impact calibre. This initial study illustrates the need for geomorphologists, geologists, engineers and heritage specialists to work collectively to gain further insights into the long-term impact of higher calibre armed warfare on heritage deterioration.
Free surface flow simulations using high order algorithms
Creators: name: Robertson, Iain
Publisher: name: Imperial College London
Year: 2020

description: The aim of this work is to formulate a computational algorithm to simulate the motion of a viscous fluid with a free surface boundary undergoing oscillations of sufficient amplitude to induce nonlinearities. To achieve this aim stability complications caused by the spatial discretisation of a two dimensional fluid domain are investigated by analysing the eigenspectrum of the semi-discrete, linear, inviscid solution system. The conditions for stability are established and procedures to overcome instability are formulated and tested. Unsteady, inviscid flows with nonlinear boundary conditions are then examined. Free surface flows of a viscous, incompressible fluid undergoing unsteady motion are computationally generated using a high order temporal and spatial discretisation scheme to solve the arbitrary Lagrangian-Eulerian Navier-Stokes and continuity equations. The discretisation concepts are presented and the governing equations for fluid flow within a moving frame of reference are formulated. The suitability of differing free surface boundary conditions is investigated by simulating forced and free oscillations of a contained body of fluid for increasing Reynolds number. The flow structures they promote are compared and the effect of Reynolds number is investigated, in terms of the general flow characteristics and the choice of boundary condition. The dissipative nature of the boundary conditions are compared with analytically predicted decay rates for the oscillation of a free surface under the force of gravity [37]. Various models to overcome the moving free surface contact point and no-slip boundary conditions are devised and their respective merits studied by observing the production of contact wall boundary layers and advected vorticity layers. The additional dissipation generated by the introduction of the formulated contact wall boundary conditions is assessed and compared with analytically predicted decay rates of a freely oscillating bounded fluid [35]. Preliminary three dimensional results are given for free surface flow within a container undergoing forced oscillations. Three dimensional effects are investigated for uni-directional and bi-directional horizontal motion of the containing tank for Re = 111.
Actualización y reflexiones en Sexología
Creators: name: Villena-Moya, Alejandro
name: Muñoz-Montesinos, Fernando
name: Tolosa, Iris
name: Serrano, Gabriel
name: Ruiz, Bárbara
name: Miren Ciaurriz, Amaia
name: Chenoll, Gema
name: Galarreta, Andrea
name: Ladrón De Guevara, Andrea Lucía
name: Mestre-Bach, Gemma
name: Chiclana-Actis, Carlos
Publisher: name: Psicosomàtica y Psiquiatría
Year: 2024

description: Se presenta en esta sección una revisión de los artículos científicos de mayor impacto publicados entre septiembre y noviembre del 2023 en las revistas internacionales sobre Sexología con mayor reconocimiento a nivel nacional e internacional (Journal of Sexual Medicine; International Journal of Sexual Health; Archives of Sexual Behavior; Sex roles; Sexual Health & Compulsivity, Psychology and Sexuality; Culture, Health and Sexuality; DeSexología, Psicología de la orientación sexual y la diversidad, American Journal of Sexual Education, Journal of Sex & Marital Therapy y Violence Against Woman).



 
description: Psicosomàtica y Psiquiatría, Núm. 28 (2024): enero-febrero-marzo
From h to p efficiently : optimising the implementation of spectral/hp element methods
Creators: name: Vos, Peter Edward Julia
Publisher: name: Imperial College London
Year: 2020

description: Various aspects that may help to enhance the implementation of the spectral/hp element method have been considered. A first challenge encountered is to implement the method and the corresponding algorithms in a digestible, generic and coherent manner. Therefore, we first of all demonstrate how the mathematical structure of a spectral/ hp element discretisation can be encapsulated in an object-oriented environment, leading to a generic and flexible spectral/hp software library. Secondly, we present a generic framework for time-stepping partial differential equations. Based upon the unifying concept of General Linear Methods, we have designed an object-oriented framework that allows the user to apply a broad range of time-stepping schemes in a unified fashion. The spectral/hp element method can be considered as bridging the gap between the - traditionally low-order - finite element method on one side and spectral methods on the other side. Consequently, a second challenge which arises in implementing the spectral/hp element methods is to design algorithms that perform efficiently for both low- and high-order spectral/hp discretisations, as well as discretisations in the intermediate regime. In this thesis, we describe how the judicious use of different implementation strategies for the evaluation of spectral/hp operators can be employed to achieve high efficiency across a wide range of polynomial orders. Furthermore, we explain how the multi-level static condensation technique can be applied as an efficient direct solution technique for solving linear systems that arise in the spectral/hp element method. Finally, based upon such an efficient implementation of the spectral/hp element method, we analyse which spectral/hp discretisation (that is, which specific combination of mesh size h and polynomial order P) minimises the computational cost to solve an elliptic problem up to a predefined level of accuracy. We investigate this question for a set of both smooth and non-smooth problems.
Non-invasive characterization of user behavior in high-performance computing systems: The case of the Santos Dumont supercomputer
Creators: name: Juan, H. L. Fabian
name: Antônio, T. A. Gomes
Publisher: name: Zenodo
Year: 2024
Subjects: User behavior characterization
High-performance computing systems
Resource management

description: User behavior characterization is a key step towards increasing system utilization and user satisfaction in HPC systems. Different variables can be used for characterizing user behavior, including job geometry, dependency between jobs, and think time. In this work, we propose a non-invasive characterization methodology centered around the distribution of different job types in distinct user groups. The methodology is defined as non-invasive because it relies solely on accounting information made available by resource managers, without resorting to the monitoring of the applications’ execution. We used the Santos Dumont supercomputer at the National Laboratory for Scientific Computing (LNCC) in Brazil as a case study for our methodology. We made a cohort of the accounting logs of Santos Dumont’s resource manager (Slurm) during the period from 01/01/2023 to 07/31/2023. We identified 6 different job types and a distinctive distribution of them for different projects—the hierarchical organization of the supercomputer users in groups—, emphasizing the use of different strategies to explore the available capability of the supercomputer, as well as different styles of under-utilization of its resources. We believe such a methodology can help in identifying opportunities for improving resource allocation and reducing queue waiting times in HPC systems like the Santos Dumont supercomputer.
description: This poster received the "Best Poster Award" during the 11th Edition of the Latin American Conference on High Performance Computing (CARLA). September 30 to October 4 in Santiago, Chile.
Table S2 from A statistical model for brain networks inferred from large-scale electrophysiological signals
Creators: name: Obando, Catalina
name: Fallani, Fabrizio De Vico
Publisher: name: The Royal Society
Year: 2017
Subjects: Computational Biology

description: Network science has been extensively developed to characterize structural properties of complex systems, including brain networks inferred from neuroimaging data. As a result of the inference process, networks estimated from experimentally obtained biological data, represent one instance of a larger number of realizations with similar intrinsic topology. A modelling approach is therefore needed to support statistical inference on the bottom-up local connectivity mechanisms influencing the formation of the estimated brain networks. Here, we adopted a statistical model based on exponential random graphs (ERGM) to reproduce brain networks, or connectomes, estimated by spectral coherence between high-density electroencephalographic (EEG) signals. ERGMs are made up by different local graph metrics, whereas the parameters weight the respective contribution in explaining the observed network. We validated this approach in a dataset of N = 108 healthy subjects during eyes-open (EO) and eyes-closed (EC) resting-state conditions. Results showed that the tendency to form triangles and stars, reflecting clustering and node centrality, better explained the global properties of the EEG connectomes as compared to other combinations of graph metrics. In particular, the synthetic networks generated by this model configuration replicated the characteristic differences found in the real brain networks, with EO eliciting significantly higher segregation in the alpha frequency band (8–13 Hz) as compared to EC. Furthermore, the fitted ERGM parameter values provided complementary information showing that clustering connections are significantly more represented from EC to EO in the alpha range, but also in the beta band (14–29 Hz), which is known to play a crucial role in cortical processing of visual input and externally oriented attention. Taken together, these findings support the current view of the brain functional segregation and integration in terms of modules and hubs, and provide a statistical approach to extract new information on the (re)organizational mechanisms in healthy and diseased brains.
MOESM1 of Computational analysis identifies putative prognostic biomarkers of pathological scarring in skin wounds
Creators: name: Nagaraja, Sridevi
name: Chen, Lin
name: DiPietro, Luisa
name: Reifman, Jaques
name: Mitrophanov, Alexander
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Virology
subject: Computational Biology

description: Additional file 1. Description of the univariate and multivariate analysis of model-identified prognostic biomarkers of pathological scarring, list of modeled cell types and proteins, and Table S1 showing the logistic regression model coefficients, odds ratios, and AUCs.
MOESM2 of Computational analysis identifies putative prognostic biomarkers of pathological scarring in skin wounds
Creators: name: Nagaraja, Sridevi
name: Chen, Lin
name: DiPietro, Luisa
name: Reifman, Jaques
name: Mitrophanov, Alexander
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Virology

description: Additional file 2. Original data from six published experimental studies that were used to derive the protein fold change values shown in Fig.Â 3g.