cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Sparse Simultaneous Signal Detection for Identifying Genetically Controlled Disease Genes
Creators: name: Sihai Dave Zhao
name: T. Tony Cai
name: Cappola, Thomas P.
name: Margulies, Kenneth B.
name: Hongzhe Li
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
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

description: Genome-wide association studies (GWAS) and differential expression analyses have had limited success in finding genes that cause complex diseases such as heart failure (HF), a leading cause of death in the United States. This article proposes a new statistical approach that integrates GWAS and expression quantitative trait loci (eQTL) data to identify important HF genes. For such genes, genetic variations that perturb its expression are also likely to influence disease risk. The proposed method thus tests for the presence of simultaneous signals: SNPs that are associated with the gene’s expression as well as with disease. An analytic expression for the p-value is obtained, and the method is shown to be asymptotically adaptively optimal under certain conditions. It also allows the GWAS and eQTL data to be collected from different groups of subjects, enabling investigators to integrate public resources with their own data. Simulation experiments show that it can be more powerful than standard approaches and also robust to linkage disequilibrium between variants. The method is applied to an extensive analysis of HF genomics and identifies several genes with biological evidence for being functionally relevant in the etiology of HF. It is implemented in the R package ssa. Supplementary materials for this article are available online.
Unsupervised Self-Normalized Change-Point Testing for Time Series
Creators: name: Zhang, Ting
name: Lavitas, Liliya
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: We propose a new self-normalized method for testing change points in the time series setting. Self-normalization has been celebrated for its ability to avoid direct estimation of the nuisance asymptotic variance and its flexibility of being generalized to handle quantities other than the mean. However, it was developed and mainly studied for constructing confidence intervals for quantities associated with a stationary time series, and its adaptation to change-point testing can be nontrivial as direct implementation can lead to tests with nonmonotonic power. Compared with existing results on using self-normalization in this direction, the current paper proposes a new self-normalized change-point test that does not require prespecifying the number of total change points and is thus unsupervised. In addition, we propose a new contrast-based approach in generalizing self-normalized statistics to handle quantities other than the mean, which is specifically tailored for change-point testing. Monte Carlo simulations are presented to illustrate the finite-sample performance of the proposed method.
Unsupervised Self-Normalized Change-Point Testing for Time Series
Creators: name: Zhang, Ting
name: Lavitas, Liliya
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: We propose a new self-normalized method for testing change points in the time series setting. Self-normalization has been celebrated for its ability to avoid direct estimation of the nuisance asymptotic variance and its flexibility of being generalized to handle quantities other than the mean. However, it was developed and mainly studied for constructing confidence intervals for quantities associated with a stationary time series, and its adaptation to change-point testing can be nontrivial as direct implementation can lead to tests with nonmonotonic power. Compared with existing results on using self-normalization in this direction, the current article proposes a new self-normalized change-point test that does not require prespecifying the number of total change points and is thus unsupervised. In addition, we propose a new contrast-based approach in generalizing self-normalized statistics to handle quantities other than the mean, which is specifically tailored for change-point testing. Monte Carlo simulations are presented to illustrate the finite-sample performance of the proposed method. Supplementary materials for this article are available online.
Image-guided breast biopsy and localisation: recommendations for information to women and referring physicians by the European Society of Breast Imaging.
Creators: name: Bick, Ulrich
name: Trimboli, Rubina M
name: Athanasiou, Alexandra
name: Balleyguier, Corinne
name: Baltzer, Pascal A T
name: Bernathova, Maria
name: Borbély, Krisztina
name: Brkljacic, Boris
name: Carbonaro, Luca A
name: Clauser, Paola
name: Cassano, Enrico
name: Colin, Catherine
name: Esen, Gul
name: Evans, Andrew
name: Fallenberg, Eva M
name: Fuchsjaeger, Michael H
name: Gilbert, Fiona J
name: Helbich, Thomas H
name: Heywang-Köbrunner, Sylvia H
name: Herranz, Michel
name: Kinkel, Karen
name: Kilburn-Toppin, Fleur
name: Kuhl, Christiane K
name: Lesaru, Mihai
name: Lobbes, Marc B I
name: Mann, Ritse M
name: Martincich, Laura
name: Panizza, Pietro
name: Pediconi, Federica
name: Pijnappel, Ruud M
name: Pinker, Katja
name: Schiaffino, Simone
name: Sella, Tamar
name: Thomassin-Naggara, Isabelle
name: Tardivon, Anne
name: Ongeval, Chantal Van
name: Wallis, Matthew G
name: Zackrisson, Sophia
name: Forrai, Gabor
name: Herrero, Julia Camps
name: Sardanelli, Francesco
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Breast
Core Needle Biopsy
Vacuum-assisted Biopsy
Breast Lesion Localisation
Fine-needle Sampling

description: We summarise here the information to be provided to women and referring physicians about percutaneous breast biopsy and lesion localisation under imaging guidance. After explaining why a preoperative diagnosis with a percutaneous biopsy is preferred to surgical biopsy, we illustrate the criteria used by radiologists for choosing the most appropriate combination of device type for sampling and imaging technique for guidance. Then, we describe the commonly used devices, from fine-needle sampling to tissue biopsy with larger needles, namely core needle biopsy and vacuum-assisted biopsy, and how mammography, digital breast tomosynthesis, ultrasound, or magnetic resonance imaging work for targeting the lesion for sampling or localisation. The differences among the techniques available for localisation (carbon marking, metallic wire, radiotracer injection, radioactive seed, and magnetic seed localisation) are illustrated. Type and rate of possible complications are described and the issue of concomitant antiplatelet or anticoagulant therapy is also addressed. The importance of pathological-radiological correlation is highlighted: when evaluating the results of any needle sampling, the radiologist must check the concordance between the cytology/pathology report of the sample and the radiological appearance of the biopsied lesion. We recommend that special attention is paid to a proper and tactful approach when communicating to the woman the need for tissue sampling as well as the possibility of cancer diagnosis, repeat tissue sampling, and or even surgery when tissue sampling shows a lesion with uncertain malignant potential (also referred to as "high-risk" or B3 lesions). Finally, seven frequently asked questions are answered.
Race and Theatre in Nineteenth-Century Britain
Creators: name: Meer, Sarah
Publisher: name: Routledge
Year: 2024
Subjects: Race
Theatre
Nineteenth-Century

description: The early nineteenth century was a formative time for the construction and establishment of racial thinking. Theatre and performance played a crucial part in this, but also at points ironised and undermined it. This was partly because stage arts depend on performance, impersonation, and illusion, and partly because older plays survived in the repertoire, in which ideas of class and natural nobility, rather than colour, determined notions of identity. Nevertheless, throughout the nineteenth century, ‘racial’ performance took on forms and conventions which helped underpin imperial ideology. For performers of colour, these conventions both provided opportunities in the theatre, and limited the roles and representations available.
Phlogothamnus acutaedeagus Li 2011
Creators: name: Hassan, Muhammad Asghar
name: Zhang, Jie
name: Xing, Jichun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Cicadellidae
Phlogothamnus
Phlogothamnus acutaedeagus

description: Phlogothamnus acutaedeagus Li, 2011
 Phlogothamnus acutaedeagus Li, 2011 in Li, Dai & Xing, 2011: 180. Type locality: China (Sichuan: Changning). Holotype male (GUGC)
 Distribution: Oriental. China (Sichuan) (Li et al. 2011; Yao et al. 2022).
description: Published as part of Hassan, Muhammad Asghar, Zhang, Jie & Xing, Jichun, 2024, Taxonomic notes on the leafhopper genus Phlogothamnus Ishihara (Hemiptera: Cicadellidae: Deltocephalinae), with description of a new species from China, pp. 289-295 in Zootaxa 5432 (2) on page 291, DOI: 10.11646/zootaxa.5432.2.8, http://zenodo.org/record/10898783
Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations.
Creators: name: Shi, Wen
name: Koo, Daniel E S
name: Kitano, Masahiro
name: Chiang, Hsiao J
name: Trinh, Le A
name: Turcatel, Gianluca
name: Steventon, Benjamin
name: Arnesano, Cosimo
name: Warburton, David
name: Fraser, Scott E
name: Cutrale, Francesco
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020

description: Hyperspectral fluorescence imaging is gaining popularity for it enables multiplexing of spatio-temporal dynamics across scales for molecules, cells and tissues with multiple fluorescent labels. This is made possible by adding the dimension of wavelength to the dataset. The resulting datasets are high in information density and often require lengthy analyses to separate the overlapping fluorescent spectra. Understanding and visualizing these large multi-dimensional datasets during acquisition and pre-processing can be challenging. Here we present Spectrally Encoded Enhanced Representations (SEER), an approach for improved and computationally efficient simultaneous color visualization of multiple spectral components of hyperspectral fluorescence images. Exploiting the mathematical properties of the phasor method, we transform the wavelength space into information-rich color maps for RGB display visualization. We present multiple biological fluorescent samples and highlight SEER's enhancement of specific and subtle spectral differences, providing a fast, intuitive and mathematical way to interpret hyperspectral images during collection, pre-processing and analysis.
A quantitative workflow for modeling diversification in material culture.
Creators: name: Gjesfjeld, Erik
name: Silvestro, Daniele
name: Chang, Jonathan
name: Koch, Bernard
name: Foster, Jacob G
name: Alfaro, Michael E
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020

description: Questions about the evolution of material culture are widespread in the humanities and social sciences. Statistical modeling of long-term changes in material culture is less common due to a lack of appropriate frameworks. Our goal is to close this gap and provide robust statistical methods for examining changes in the diversity of material culture. We provide an open-source and quantitative workflow for estimating rates of origination, extinction, and preservation, as well as identifying key shift points in the diversification histories of material culture. We demonstrate our approach using two distinct kinds of data: age ranges for the production of American car models, and radiocarbon dates associated with archaeological cultures of the European Neolithic. Our approach improves on existing frameworks by disentangling the relative contributions of origination and extinction to diversification. Our method also permits rigorous statistical testing of competing hypotheses to explain changes in diversity. Finally, we stress the value of a flexible approach that can be applied to data in various forms; this flexibility allows scholars to explore commonalities between forms of material culture and ask questions about the general properties of cultural change.
Unsupervised Self-Normalized Change-Point Testing for Time
Creators: name: Zhang, Ting
name: Lavitas, Liliya
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: We propose a new self-normalized method for testing change points in the time series setting. Self-normalization has been celebrated for its ability to avoid direct estimation of the nuisance asymptotic variance and its flexibility of being generalized to handle quantities other than the mean. However, it was developed and mainly studied for constructing confidence intervals for quantities associated with a stationary time series, and its adaptation to change-point testing can be nontrivial as direct implementation can lead to tests with nonmonotonic power. Compared with existing results on using self-normalization in this direction, the current article proposes a new self-normalized change-point test that does not require prespecifying the number of total change points and is thus unsupervised. In addition, we propose a new contrast-based approach in generalizing self-normalized statistics to handle quantities other than the mean, which is specifically tailored for change-point testing. Monte Carlo simulations are presented to illustrate the finite-sample performance of the proposed method. Supplementary materials for this article are available online.
Bayesian Nonparametric Calibration and Combination of Predictive Distributions
Creators: name: Bassetti, Federico
name: Casarin, Roberto
name: Ravazzolo, Francesco
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: We introduce a Bayesian approach to predictive density calibration and combination that accounts for parameter uncertainty and model set incompleteness through the use of random calibration functionals and random combination weights. Building on the work of Ranjan and Gneiting, we use infinite beta mixtures for the calibration. The proposed Bayesian nonparametric approach takes advantage of the flexibility of Dirichlet process mixtures to achieve any continuous deformation of linearly combined predictive distributions. The inference procedure is based on combination Gibbs and slice sampling. We provide some conditions under which the proposed probabilistic calibration converges in terms of weak posterior consistency to the true underlying density for both cases of iid and Markovian observations. This calibration property improves upon the earlier calibration approaches. We study the methodology in simulation examples with fat tails and multimodal densities and apply it to density forecasts of daily S&P returns and daily maximum wind speed at the Frankfurt airport. Supplementary materials for this article are available online.
Boosting in the Presence of Outliers: Adaptive Classification with Non-convex Loss Functions
Creators: name: Li, Alexander Hanbo
name: Bradic, Jelena
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Computational Biology

description: This paper examines the role and the efficiency of non-convex loss functions for binary classification problems. In particular, we investigate how to design adaptive and effective boosting algorithms that are robust to the presence of outliers in the data or to the presence of errors in the observed data labels. We demonstrate that non-convex losses play an important role for prediction accuracy because of the diminishing gradient properties – the ability of the losses to efficiently adapt to the outlying data. We propose a new boosting framework called ArchBoost, that utilizes diminishing gradient property directly and leads to boosting algorithms that are provably robust. Along with the ArchBoost framework, a family of non-convex losses is proposed which leads to the new robust boosting algorithms, named Adaptive Robust Boosting (ARB). Furthermore, we develop a new breakdown point analysis and a new influence function analysis that demonstrate gains in robustness. Moreover, based only on local curvatures, we establish statistical and optimization properties of the proposed ArchBoost algorithms with highly non-convex losses. Extensive numerical and real data examples illustrate theoretical properties and reveal advantages over the existing boosting methods when data is perturbed by an adversary or otherwise.
The Cu-catalyzed asymmetric conjugate addition with chiral diphosphite ligands derived from D-(-)-tartaric acid
Creators: name: Zeng-Bo Pang
name: Tian, Mi
name: Li, Hai-Feng
name: Lai-Lai Wang
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
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: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Hematology
subject: Plant Biology

description: A series of diphosphite ligands, which were derived from D-(-)-tartaric acid, have been synthesized and successfully applied in the Cu-catalyzed asymmetric conjugate addition of organozincs to enones. There was a synergic effect between the stereogenic centers of the D-(-)-tartaric acid skeleton and the axially H8-binaphthyl moieties of ligand 2c. And ligand 2c shows a comparative catalytic performance to ligand 1-N-benzylpyrrolidine-3,4-bis[(S)-1,1′-H8-binaphthyl-2,2′-diyl]phosphite-L-tartaric acid1d derived from L-(+)-tartaric acid. Therefore, for cyclic enones, both enantiomers of the addition products can be obtained in high enantioselectivity (ees up to 96%) by simply selecting ligands 1d or 2c derived from D-(-)-tartaric acid or L-(+)-tartaric acid. Moreover, the sense of enantiodiscrimination of the products was mainly determined by the configuration of the binaphthyl phosphite moieties.
Dichiarazione attività di arruolamento studio dal titolo: Efficacia della sostituzione dell'albumina e delle soluzioni Crystalloid bilanciate nello shock settico (il processo ALBIOSS-BALANCED): uno studio fattoriale 2-per-2, avviato dallo sperimentatore, in aperto, multicentrico, randomizzato, controllato.
Creators: name: Agnese, valentina
Publisher: name: Zenodo
Year: 2024

description: Si tratta di uno studio clinico interventistico randomizzato no-profit promosso dalla FONDAZIONE IRCCS CA' GRANDA OSPEDALE MAGGIORE POLICLINICO.

Lo studio è attivo da 4 anni e l' IRCCS ISMETT ha arruolato nel 2023 un totale di 4 pazienti.
Sparse simultaneous signal detection for identifying genetically controlled disease genes
Creators: name: Sihai Dave Zhao
name: T. Tony Cai
name: Cappola, Thomas P.
name: Margulies, Kenneth B.
name: Hongzhe Li
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
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

description: Genome-wide association studies (GWAS) and differential expression analyses have had limited success in finding genes that cause complex diseases such as heart failure (HF), a leading cause of death in the United States. This paper proposes a new statistical approach that integrates GWAS and expression quantitative trait loci (eQTL) data to identify important HF genes. For such genes, genetic variations that perturb its expression are also likely to influence disease risk. The proposed method thus tests for the presence of simultaneous signals: SNPs that are associated with the gene's expression as well as with disease. An analytic expression for the p-value is obtained, and the method is shown to be asymptotically adaptively optimal under certain conditions. It also allows the GWAS and eQTL data to be collected from different groups of subjects, enabling investigators to integrate public resources with their own data. Simulation experiments show that it can be more powerful than standard approaches and also robust to linkage disequilibrium between variants. The method is applied to an extensive analysis of HF genomics and identifies several genes with biological evidence for being functionally relevant in the etiology of HF. It is implemented in the R package ssa.
Synthesis of 3-geranyl- and 3-prenyl-2,4,6-trihydroxybenzophenone
Creators: name: Vuyisa Mzozoyana
name: Heerden, Fanie R. Van
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Plant Biology

description: Biologically active phenyl[3-(3,7-dimethyl-2,6-octadienyl)-2,4,6-trihydroxyphenyl]methanone (2) and phenyl[2,4,6-trihydroxy-3-(3-methyl-2-butenyl)phenyl]methanone (3) were synthesized by an efficient and convenient synthetic sequence. The reaction steps of this synthesis included methylation, Friedel-Crafts acylation, demethylation and geranylation steps.
Competencies and training of radiographers and technologists for PET/MR imaging - a study from the UK MR-PET network.
Creators: name: Mada, Marius Ovidiu
name: Hindmarch, Paula
name: Stirling, James
name: Davies, James
name: Brian, David
name: Barnes, Anna
name: Hammers, Alexander
name: Gulliver, Nick
name: Herholz, Karl
name: O'Brien, John
name: Taylor, John-Paul
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Training
Competencies
Radiographers
Pet/mri
Nuclear Medicine Technologists
Hybrid Imaging Practitioner

description: Background:After the success of PET/CT as a clinical diagnostic tool, the introduction of PET/MRI is a natural development aimed at further improving combined diagnostic imaging and reduced ionising radiation dose for half-body imaging. As with PET and CT, the combination of PET and MRI presents a series of issues that need to be addressed regarding workforce training and education. At present, there is a lack of agreement over the competencies, training requirements and educational pathways needed for PET/MRI operation. In the UK, following the establishment of the MR-PET imaging network, a task force was created to investigate the status of the workforce training, identify gaps and make recommendations regarding staff training. To do this, we ran a national survey on the status of the workforce training and the local practices across the UK's seven PET/MRI sites, reviewed the literature, and convened a panel of experts, to assess all the evidence and make recommendations regarding PET/MRI competencies and training of nuclear medicine technologists and radiographers. Results:There is limited literature available specifically on competencies and training for technologists and radiographers. The recommendations on the topic needed revisiting and adapting to the UK MR-PET network. The online survey confirmed the need for developing PET/MRI competencies and training pathways. Local organisational structures and practices were shared across the seven sites, based on models derived from experience outside the UK. The panel of experts agreed on the need for PET/MRI competencies and training strategies. Professional organisations started collaborative discussions with partners from both Nuclear Medicine and Radiography to set training priorities. Multidisciplinary collaboration and partnership were suggested as a key to a successful implementation of competencies and training. Conclusions:The report identified the need for establishing competencies for the PET/MRI workforce, particularly for technologists and radiographers. It also helped defining these competencies as well as identifying the demand for bespoke training and the development of local and national courses to be implemented to fulfil this new training need.
The Cu-Catalyzed Asymmetric Conjugate Addition with Chiral Diphosphite Ligands Derived From D-(-)-tartaric Acid
Creators: name: Zeng-Bo Pang
name: Tian, Mi
name: Li, Hai-Feng
name: Lai-Lai Wang
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
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: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Hematology
subject: Plant Biology

description: A series of diphosphite ligands, which were derived from D-(-)-tartaric acid, have been synthesized and successfully applied in the Cu-catalyzed asymmetric conjugate addition of organozincs to enones. There was a synergic effect between the stereogenic centers of the D-(-)-tartaric acid skeleton and the axially H8-binaphthyl moieties of ligand 2c. And ligand 2c show comparative catalytic performance to ligand 1-N-benzylpyrrolidine-3,4-bis[(S)-1,1′-H8- -binaphthyl-2,2′-diyl]phosphite-L-tartaric acid1d derived from L-(+)-tartaric acid. Therefore, for cyclic enones, both enantiomers of the addition products can be obtained in high enantioselectivity (ees up to 96%) by simply selecting ligands 1d or 2c derived from D-(-)-tartaric acid or L-(+)-tartaric acid. Moreover, the sense of the enantiodiscrimination of the products was mainly determined by the configuration of the binaphthyl phosphite moieties.
Beta secretase 1-dependent amyloid precursor protein processing promotes excessive vascular sprouting through NOTCH3 signalling.
Creators: name: Durrant, Claire S
name: Ruscher, Karsten
name: Sheppard, Olivia
name: Coleman, Michael P
name: Özen, Ilknur
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020

description: Amyloid beta peptides (Aβ) proteins play a key role in vascular pathology in Alzheimer's Disease (AD) including impairment of the blood-brain barrier and aberrant angiogenesis. Although previous work has demonstrated a pro-angiogenic role of Aβ, the exact mechanisms by which amyloid precursor protein (APP) processing and endothelial angiogenic signalling cascades interact in AD remain a largely unsolved problem. Here, we report that increased endothelial sprouting in human-APP transgenic mouse (TgCRND8) tissue is dependent on β-secretase (BACE1) processing of APP. Higher levels of Aβ processing in TgCRND8 tissue coincides with decreased NOTCH3/JAG1 signalling, overproduction of endothelial filopodia and increased numbers of vascular pericytes. Using a novel in vitro approach to study sprouting angiogenesis in TgCRND8 organotypic brain slice cultures (OBSCs), we find that BACE1 inhibition normalises excessive endothelial filopodia formation and restores NOTCH3 signalling. These data present the first evidence for the potential of BACE1 inhibition as an effective therapeutic target for aberrant angiogenesis in AD.
Evolution of sustainable energy policies in India since 1947: A review.
Creators: name: Bardhan, Ronita
name: Debnath, Ramit
name: Jana, Arnab
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019

description: India's Intended Nationally Determined Contributions in 2015 toward the Two-Degree Celsius climate change goal has endorsed 15% of renewable integration in the primary energy mix by 2020. The energy space is strategy to meet the target without affecting its immediate sustainable development goals. This study documents this strategic effort by tracking the historical trajectory of energy policy planning since its independence in 1947. An objective ontological approach was adopted in reviewing the evolution of energy policy into five distinct phases. Phase I (1947-1970), focused on supply adequacy with the overall thrust on infrastructure development as the pillar of Indian economy. In Phase II (the 1970s) the focus shifted in addressing the energy access crisis. Phase III (the 1980s) was based on increment, diversification, and streamlining on supplies for energy security purposes. Phase IV (the 1990s) is the period of modernization of the overall Indian electricity system. Phase V (the 2000s) is the present phase of market transformation and climate change mitigation energy policies. A co-assessment of India's policy to the international climate negotiations showed that India remained responsive to international climate goals. It became reactive in the planning for sustainable energy policy after its ratification of Kyoto Protocol in 2001. Since then, India has been instrumental in administering strict emission reduction norms and efficiency measures. This review concludes that the country needs to upgrade its inefficient transmission and distribution networks, which was broadly neglected. The subsidy allocations in domestic energy resources should be well-adjusted without compromising on its social costs.
title: Thermal comfort and childcare, Kerala, India
Creators: name: Ibrahim, Afrin
Publisher: name: University of Southampton
Year: 2023

description: This research investigates what thermal comfort means to children living in institutionalized care in Kerala by evaluating their adaptive behavior. While there are research on thermal comfort and children, there are no available data on children from vulnerable backgrounds or living in care system. Field study methods like comfort surveys, environmental measurements and semi-structured interviews were adopted. One Boys Home and one Girls Home were selected and collected total 90 responses. Some children despite mentioning the environment was hot/warm also related to it as slightly comfortable, this major finding establishes the wider tolerance range to the environment. Lack of thermal memory and no access to thermal controls resulted the children having higher thermal acceptability rate. There was disparity in responses between genders. Girls had strong preference and expectations from their environment while boys were more acceptable and tolerant of their environment even during the heat waves recorded during study.
Bayesian Nonparametric Calibration and Combination of Predictive Distributions*
Creators: name: Bassetti, Federico
name: Casarin, Roberto
name: Ravazzolo, Francesco
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: We introduce a Bayesian approach to predictive density calibration and combination that accounts for parameter uncertainty and model set incompleteness through the use of random calibration functionals and random combination weights. Building on the work of Ranjan and Gneiting (2010) and Gneiting and Ranjan (2013), we use infinite beta mixtures for the calibration. The proposed Bayesian nonparametric approach takes advantage of the flexibility of Dirichlet process mixtures to achieve any continuous deformation of linearly combined predictive distributions. The inference procedure is based on combination Gibbs and slice sampling. We provide some conditions under which the proposed probabilistic calibration converges in terms of weak posterior consistency to the true underlying density for both cases of i.i.d. and Markovian observations. This calibration property improves upon the earlier calibration approaches. We study the methodology in simulation examples with fat tails and multimodal densities and apply it to density forecasts of daily S&P returns and daily maximum wind speed at the Frankfurt airport.
title: Consumer Preferences and Market Demand for Organic Mixed Vegetables
title: Consumer preferences and market demand for organic mixed vegetables play a crucial role in shaping the production, distribution, and marketing strategies of small-scale organic farmers. This research aims to explore the factors influencing consumer choices and the market dynamics driving the demand for organic mixed vegetables. Through a combination of surveys, focus groups, and market analysis, this study investigates various dimensions of consumer preferences, including taste, health concerns, environmental considerations, and ethical values. Additionally, it examines the impact of price premiums, product attributes, labeling, and certification on consumer purchasing decisions.
titleType: AlternativeTitle
Creators: name: Verónica Joya, Verónica Sayuri Joya Rodríguez
Publisher: name: Zenodo
Year: 2021
Subjects: PRODUCTION
FARM
PRICE

description: Consumer preferences and market demand for organic mixed vegetables play a crucial role in shaping the production, distribution, and marketing strategies of small-scale organic farmers. This research aims to explore the factors influencing consumer choices and the market dynamics driving the demand for organic mixed vegetables. Through a combination of surveys, focus groups, and market analysis, this study investigates various dimensions of consumer preferences, including taste, health concerns, environmental considerations, and ethical values. Additionally, it examines the impact of price premiums, product attributes, labeling, and certification on consumer purchasing decisions.
Characterising the spatial distribution of opportunities and constraints for land sparing in Brazil.
Creators: name: Dos Santos, Juliana Silveira
name: Feltran-Barbieri, Rafael
name: Fonte, Ellen S
name: Balmford, Andrew
name: Maioli, Veronica
name: Latawiec, Agnieszka
name: Strassburg, Bernardo B N
name: Phalan, Benjamin T
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020

description: Brazil is a megadiversity country with more tropical forest than any other, and is a leading agricultural producer. The technical potential to reconcile these roles by concentrating agriculture on existing farmland and sparing land for nature is well-established, but the spatial overlap of this potential with conservation priorities and institutional constraints remains poorly understood. We mapped conservation priorities, food production potential and socio-economic variables likely to influence the success of land sparing. Pasture occupies 70% of agricultural land but contributes ≤11% of the domestic food supply. Increasing yields on pasture would add little to Brazil's food supply but - if combined with concerted conservation and restoration policies - provides the greatest opportunities for reducing land demand. Our study illustrates a method for identifying municipalities where land-sparing policies are most likely to succeed, and those where further effort is needed to overcome constraints such as land tenure insecurity, lack of access to technical advice, labour constraints, and non-compliance with environmental law.
Observation of diffraction contrast in scanning helium microscopy.
Creators: name: Bergin, M
name: Lambrick, S M
name: Sleath, H
name: Ward, D J
name: Ellis, J
name: Jardine, A P
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020

description: Scanning helium microscopy is an emerging form of microscopy using thermal energy neutral helium atoms as the probe particle. The very low energy combined with lack of charge gives the technique great potential for studying delicate systems, and the possibility of several new forms of contrast. To date, neutral helium images have been dominated by topographic contrast, relating to the height and angle of the surface. Here we present data showing contrast resulting from specular reflection and diffraction of helium atoms from an atomic lattice of lithium fluoride. The signature for diffraction is evident by varying the scattering angle and observing sharp features in the scattered distribution. The data indicates the viability of the approach for imaging with diffraction contrast and suggests application to a wide variety of other locally crystalline materials.
A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies
Creators: name: Crary-Dooley, Florence K.
name: Tam, Mitchell E.
name: Dunaway, Keith W.
name: Irva Hertz-Picciotto
name: Schmidt, Rebecca J.
name: LaSalle, Janine M.
Publisher: name: Taylor & Francis
Year: 2017
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exposures in complex diseases. Among the available methods of quantitative DNA methylation measurements, bisulfite sequencing is considered the gold standard, but whole-genome bisulfite sequencing (WGBS) has previously been considered too costly for epidemiology studies with high sample numbers. Pyrosequencing of repetitive sequences within bisulfite-treated DNA has been routinely used as a surrogate for global DNA methylation, but a comparison of pyrosequencing to WGBS for accuracy and reproducibility of methylation levels has not been performed. This study compared the global methylation levels measured from uniquely mappable (non-repetitive) WGBS sequences to pyrosequencing assays of several repeat sequences and repeat assay-matched WGBS data and determined uniquely mappable WGBS data to be the most reproducible and accurate measurement of global DNA methylation levels. We determined sources of variation in repetitive pyrosequencing assays to be PCR amplification bias, PCR primer selection bias in methylation levels of targeted sequences, and inherent variability in methylation levels of repeat sequences. Low-coverage, uniquely mappable WGBS showed the strongest correlation between replicates of all assays. By using multiplexing by indexed bar codes, the cost of WGBS can be lowered significantly to improve the accuracy of global DNA methylation assessments for human studies.
title: The use of graph databases in systems biology: a systematic review
Creators: name: Ilya Mazein
name: Adrien Rougny
name: Alexander Mazein
name: Ron Henkel
name: Lea Gütebier
name: Lea Michaelis
name: Marek Ostaszewski
name: Reinhard Schneider
name: Venkata Pardhasaradhi Satagopam
name: Lars Juhl Jensen
name: Dagmar Waltemath
name: Judith Wodke
name: Irina-Afrodita Balaur
Publisher: name: LCSB
Year: 2024

description: Being highly suitable to store and to connect complex heterogeneous data, graph databases are becoming increasingly popular across scientific disciplines. In systems biology, they are used as a backend solution for biological data repositories, ontologies, networks, and pathway databases.
In this review, we analyse publications using or mentioning graph databases retrieved from PubMed and PubMed Central full-text search. Relevant publications were categorised according to their domain and application. Focusing on the top 16 open-source GDB technologies, we detail different approaches and highlight advantages of outstanding resources, such as UniProtKB, Disease Ontology, and Reactome.
We discuss ongoing efforts of the systems biology community to standardise and harmonise knowledge graph creation and maintenance of integrated resources. Outlining prospects, including the use of GDBs as a way of communication between biological data repositories, we conclude that efficient design, querying, and maintenance of GDs will be key for knowledge generation in systems biology and other research fields with heterogeneous data.
A synthetic lipid scramblase built from DNA
Creators: name: Ohmann, Alexander
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: DNA nanotechnology
lipid scrambling
scramblases
DNA origami
synthetic biology
cholesterol

description: The programmable self-assembly facilitated by DNA nanotechnology provides unparalleled capabilities to construct functional devices at the nanoscale. Recently, DNA nanostructures have been developed to interact with biological membranes and serve as artificial counterparts of natural ion channels, or membrane bending, scaffolding, or fusion proteins. In this thesis, we design a synthetic DNA-built enzyme that facilitates rapid lipid mixing between the two leaflets of a lipid bilayer. It thereby mimics the function of yet another class of membrane proteins $--$ lipid scramblases. Characterising this DNA nanostructure with gel electrophoresis, dynamic light scattering, atomic force and transmission electron microscopy, we find that the cholesterol groups required for membrane insertion, also induce clustering. Hence, we establish an easy-to-implement strategy to control hydrophobically mediated aggregation thereby introducing a solution to a common problem of amphiphilic DNA constructs. With a combination of fluorescence microscopy experiments and molecular dynamics simulations, we identify the mechanism behind the scrambling activity. The spontaneous membrane insertion of our DNA scramblase induces a toroidal pore that is lined by the lipid headgroups. This DNA-stabilised pore connects the inner and outer bilayer leaflet thereby facilitating diffusive lipid transport that rapidly equilibrates the membrane’s lipid composition. In good agreement between experiments and simulations, we find the scrambling rate catalysed by our DNA-made enzyme to exceed 10$^7$ lipids per second, orders of magnitude faster than natural scramblase proteins. We thereby pioneer the use of self-assembled DNA nanostructures for controlling the lipid composition of biological membranes, opening new avenues for applications of membrane-interacting DNA systems in biophysical research and medicine.
description: Engineering and Physical Sciences Research Council (EPSRC), Cambridge Trust Vice Chancellor's Award
Phlogothamnus circinatus Yao, Zhang & Xing 2022
Creators: name: Hassan, Muhammad Asghar
name: Zhang, Jie
name: Xing, Jichun
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Cicadellidae
Phlogothamnus
Phlogothamnus circinatus

description: Phlogothamnus circinatus Yao, Zhang & Xing, 2022
 Phlogothamnus circinatus Yao, Zhang & Xing, 2022: 424. Type locality: China (Guizhou: Jiangkou County, Fanjingshan). Holotype male (GUGC).
 Distribution: Oriental. China (Guizhou) (Yao et al. 2022).
description: Published as part of Hassan, Muhammad Asghar, Zhang, Jie & Xing, Jichun, 2024, Taxonomic notes on the leafhopper genus Phlogothamnus Ishihara (Hemiptera: Cicadellidae: Deltocephalinae), with description of a new species from China, pp. 289-295 in Zootaxa 5432 (2) on page 291, DOI: 10.11646/zootaxa.5432.2.8, http://zenodo.org/record/10898783
Exploiting a novel organotypic model of SOX2-driven early squamous lung cancer to identify potential routes to chemoprevention
Creators: name: Barry, Philip Simon
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: lung cancer
SOX2
squamous
AKT3
chemoprevention
squamous cell lung cancer

description: Lung cancer is a devastating disease and is the leading cause of cancer related death globally. Squamous cell lung cancer (SQC) accounts for around 25% of all lung cancer diagnoses. Better strategies for the early detection, prevention and treatment of lung cancer are urgently needed. Using a novel in vitro model of SOX2-driven early SQC I performed a screen using tool compounds and compounds in late phase clinical development for potential efficacy in chemoprevention. I combined this approach with targeted genetic ablation studies to identify/characterise targets that may be key to the progression of SOX2-driven squamous cell carcinomas. In particular I highlight an AKT isoform dependence in SQC that could be exploited in future clinical chemoprevention studies.
The impact of COVID-19 on the financial performance of Moroccan banks: a post-covid analysis
Creators: name: Mesrar Rida
name: Maach Rime
Publisher: name: Zenodo
Year: 2024

description: The health crisis in Morocco has triggered a palpable macroeconomic and microeconomic shock, which deeply affected all sectors of the national economy. Despite playing a crucial role as intermediaries for the transmission of monetary and fiscal policies to manage economic crises, banks were not spared the devastating effects of the crisis. Banks faced significant financial and operational pressures attributable to various factors such as market volatility, increased credit risk, rise in doubtful debts, liquidity strains, and a significant decline in financial results. This research aimed to specifically examine the repercussions of the pandemic on the profitability and financial performance of banks. To achieve this, a descriptive analysis methodology was adopted while focusing on two key indicators: Return on Assets (ROA) and Return on Equity (ROE). These indicators could potentially assess the profitability of banks and provide a meaningful overview of their financial performance before, during, and after the crisis to better understand the specific effects of the pandemic on the Moroccan banking sector.