bluuebunny/crossref_metadata_2025_split huggingface dataset:
Personal development, wellbeing and empowerment gains for nutrition peer educators: a South Australian perspective
Authors: Mehta Kaye , Dent Carolyn , Middleton Georgia , Booth Sue 
Published: October 2019

Abstract
This study aimed to explore the experience of being a Community Foodies (CF) peer educator with respect to personal benefits, specifically, personal development, wellbeing and empowerment. Qualitative semi-structured telephone interviews conducted with metropolitan and country peer educators of the CF programme. The CF programme in South Australia (SA) delivers nutrition education to disadvantaged communities. Ten adult peer educators from the CF programme: seven from country SA and three from Adelaide. Phenomenon of interest is that peer educators’ perceptions of personal growth and development from involvement in the CF programme. The interviews were audiotaped and analysed thematically. The experience of being a nutrition peer educator improved personal skills and knowledge, dietary habits, self-esteem, confidence, sense of belonging and civic engagement. Peer educators felt that the CF programme was run in a straightforward, easy to understand way, with a welcoming environment and abundant support from the coordinators. Apart from benefits to themselves, peer educators appeared to be most proud of their capacity to contribute to the nutritional health of the broader community. Peer education programmes in disadvantaged communities provide policy makers with valuable and cost-effective approaches to improve health, build self-efficacy, strengthen community engagement, and, foster active participation and trust.
Flatness of the Commutator Map Over SLn
Authors: Larsen Michael , Lu Zhipeng 
Published: October 2019

AbstractLet $K$ be any field, and let $n$ be a positive integer. If we denote by $\xi _{\textrm{SL}_n}\colon \textrm{SL}_n\times \textrm{SL}_n\to \textrm{SL}_n$ the commutator morphism over $K$, then $\xi _{\textrm{SL}_n}$ is flat over the complement of the center of $\textrm{SL}_n$.
Longitudinal Antibody Responses in People Who Inject Drugs Infected With Similar Human Immunodeficiency Virus Strains
Authors: Redd Andrew D , Doria-Rose Nicole A , Weiner Joshua A , Nason Martha , Seivers Matthew , Schmidt Stephen D , Laeyendecker Oliver , Martens Craig , Bruno Daniel , Keele Brandon F , Raju Nagarajan , Georgiev Ivelin S , Lamers Susanna L , Astemborski Jacquie , Kirk Gregory D , Mascola John R , Ackerman Margaret E , Mehta Shruti H , Quinn Thomas C 
Published: October 2019

Abstract

Background
Multiple factors influence the human immunodeficiency virus (HIV) antibody response produced during natural infection, leading to responses that can vary in specificity, strength, and breadth.

Methods
People who inject drugs identified as recently infected with HIV (n = 23) were analyzed for clustering of their viral sequences (genetic distance, &lt;2%). Longitudinal antibody responses were identified for neutralizing antibody (Nab) potential, and differences in antibody subclass, specificity, and Fc receptor ligation using pseudovirus entry and multiplexed Fc array assays, respectively. Responses were analyzed for differences between subject groups, defined by similarity in the sequence of the infecting virus.

Results
Viral sequences from infected individuals were grouped into 3 distinct clusters with 7 unclustered individuals. Subjects in cluster 1 generally had lower antibody response magnitudes, except for antibodies targeting the V1/V2 region. Subjects in clusters 2 and 3 typically had higher antibody response magnitudes, with the Fv specificity of cluster 2 favoring gp140 recognition. NAb responses differed significantly between clusters for 3 of 18 pseudoviruses examined (P &lt; .05), but there were no differences in overall NAb breadth (P = .62).

Discussion
These data demonstrate that individuals infected with similar viral strains can generate partially similar antibody responses, but these do not drastically differ from those in individuals infected with relatively unrelated strains.
Evaluating a digital sepsis alert in a London multisite hospital network: a natural experiment using electronic health record data
Authors: Honeyford Kate , Cooke Graham S , Kinderlerer Anne , Williamson Elizabeth , Gilchrist Mark , Holmes Alison ,   The Sepsis Big Room, Glampson Ben , Mulla Abdulrahim , Costelloe Ceire 
Published: October 2019

AbstractObjectiveThe study sought to determine the impact of a digital sepsis alert on patient outcomes in a UK multisite hospital network.Materials and MethodsA natural experiment utilizing the phased introduction (without randomization) of a digital sepsis alert into a multisite hospital network. Sepsis alerts were either visible to clinicians (patients in the intervention group) or running silently and not visible (the control group). Inverse probability of treatment-weighted multivariable logistic regression was used to estimate the effect of the intervention on individual patient outcomes.OutcomesIn-hospital 30-day mortality (all inpatients), prolonged hospital stay (≥7 days) and timely antibiotics (≤60 minutes of the alert) for patients who alerted in the emergency department.ResultsThe introduction of the alert was associated with lower odds of death (odds ratio, 0.76; 95% confidence interval [CI], 0.70-0.84; n = 21 183), lower odds of prolonged hospital stay ≥7 days (OR, 0.93; 95% CI, 0.88-0.99; n = 9988), and in patients who required antibiotics, an increased odds of receiving timely antibiotics (OR, 1.71; 95% CI, 1.57-1.87; n = 4622).DiscussionCurrent evidence that digital sepsis alerts are effective is mixed. In this large UK study, a digital sepsis alert has been shown to be associated with improved outcomes, including timely antibiotics. It is not known whether the presence of alerting is responsible for improved outcomes or whether the alert acted as a useful driver for quality improvement initiatives.ConclusionsThese findings strongly suggest that the introduction of a network-wide digital sepsis alert is associated with improvements in patient outcomes, demonstrating that digital based interventions can be successfully introduced and readily evaluated.
The (Dis)assembling of Form: Revealing the Ideas Built Into Manchester’s Medical School
Authors: Hopkins James 
Published: October 2019

Abstract
This paper addresses a gap in our understanding of medical history - the architecture of medical schools - and demonstrates the ways in which architectural form can be used to better understand medical epistemology and pedagogy. It examines an instructive case study - the late-nineteenth-century medical school buildings in Manchester - and examines the concepts that were drawn together and expressed in the buildings. Through its exploration, the paper argues first, that medical schools and spaces for medical education should be given greater consideration as a significant category in the history of medical buildings. Second, that buildings such as its case study are an important source of evidence and means to understand the role of medicine in society and the ideas with which its contemporary practitioners and educators were concerned. Third, the paper argues that, to make best use of buildings as sources, we should view them as agents which have assembled divergent ideas and incorporated them into the built form. In this way, such buildings have woven into them an inventory of ideas which can be untangled using designs and physical evidence.
Pragmatic logics for hypotheses and evidence
Authors: Carrara Massimiliano , Chiffi Daniele , De Florio Ciro 
Published: October 2019

Abstract
The present paper is devoted to present two pragmatic logics and their corresponding intended interpretations according to which an illocutionary act of (scientific) hypothesis-making is justified by a scintilla of evidence. The paper first introduces a general pragmatic frame for assertions, expanded to hypotheses, ${\mathsf{AH}}$ and a hypothetical pragmatic logic for evidence ${\mathsf{HLP}}$. Both ${\mathsf{AH}}$ and ${\mathsf{HLP}}$ are extensions of the Logic for Pragmatics, $\mathcal{L}^P$. We compare ${\mathsf{AH}}$ and $\mathsf{HLP}$. Then, we underline the expressive and inferential richness of both systems in dealing with hypothetical judgements, especially when based on different, sometimes conflicting, evidence.
Considerations When Using Breast Cancer Risk Models for Women with Negative BRCA1/BRCA2 Mutation Results
Authors: MacInnis Robert J , Liao Yuyan , Knight Julia A , Milne Roger L , Whittemore Alice S , Chung Wendy K , Leoce Nicole , Buchsbaum Richard , Zeinomar Nur , Dite Gillian S , Southey Melissa C , Goldgar David , Giles Graham G , McLachlan Sue-Anne , Weideman Prue C , Nesci Stephanie , Friedlander Michael L , Glendon Gord ,   kConFab Investigators, Andrulis Irene L , John Esther M , Daly Mary B , Buys Saundra S , Phillips Kelly Anne , Hopper John L , Terry Mary Beth 
Published: October 2019

Abstract
The performance of breast cancer risk models for women with a family history but negative BRCA1 and/or BRCA2 mutation test results is uncertain. We calculated the cumulative 10-year invasive breast cancer risk at cohort entry for 14 657 unaffected women (96.1% had an affected relative) not known to carry BRCA1 or BRCA2 mutations at baseline using three pedigree-based models (Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm, BRCAPRO, and International Breast Cancer Intervention Study). During follow-up, 482 women were diagnosed with invasive breast cancer. Mutation testing was conducted independent of incident cancers. All models underpredicted risk by 26.3%–56.7% for women who tested negative but whose relatives had not been tested (n = 1363; 63 breast cancers). Although replication studies with larger sample sizes are needed, until these models are recalibrated for women who test negative and have no relatives tested, caution should be used when considering changing the breast cancer risk management intensity of such women based on risk estimates from these models.
Circulating Lysophosphatidylcholines, Phosphatidylcholines, Ceramides, and Sphingomyelins and Ovarian Cancer Risk: A 23-Year Prospective Study
Authors: Zeleznik Oana A , Clish Clary B , Kraft Peter , Avila-Pacheco Julian , Eliassen A Heather , Tworoger Shelley S 
Published: October 2019

AbstractBackgroundExperimental evidence supports a role of lipid dysregulation in ovarian cancer progression. We estimated associations with ovarian cancer risk for circulating levels of four lipid groups, previously hypothesized to be associated with ovarian cancer, measured 3–23 years before diagnosis.MethodsAnalyses were conducted among cases (N = 252) and matched controls (N = 252) from the Nurses’ Health Studies. We used logistic regression adjusting for risk factors to investigate associations of lysophosphatidylcholines (LPCs), phosphatidylcholines (PCs), ceramides (CERs), and sphingomyelins (SMs) with ovarian cancer risk overall and by histotype. A modified Bonferroni approach (0.05/4 = 0.0125, four lipid groups) and the permutation-based Westfall and Young approach were used to account for testing multiple correlated hypotheses. Odds ratios (ORs; 10th–90th percentile), and 95% confidence intervals of ovarian cancer risk were estimated. All statistical tests were two-sided.ResultsSM sum was statistically significantly associated with ovarian cancer risk (OR = 1.97, 95% CI = 1.16 to 3.32; P = .01/permutation-adjusted P = .20). C16:0 SM, C18:0 SM, and C16:0 CERs were suggestively associated with risk (OR = 1.95–2.10; P = .004–.01; permutation-adjusted P = .08–.21). SM sum, C16:0 SM, and C16:0 CER had stronger odds ratios among postmenopausal women (OR = 2.16–3.22). Odds ratios were similar for serous/poorly differentiated and endometrioid/clear cell tumors, although C18:1 LPC and LPC to PC ratio were suggestively inversely associated, whereas C18:0 SM was suggestively positively associated with risk of endometrioid/clear cell tumors. No individual metabolites were associated with risk when using the permutation-based approach.ConclusionsElevated levels of circulating SMs 3–23 years before diagnosis were associated with increased risk of ovarian cancer, regardless of histotype, with stronger associations among postmenopausal women. Further studies are required to validate and understand the role of lipid dysregulation in ovarian carcinogenesis.
Doppler tomography as a tool for detecting exoplanet atmospheres
Authors: Watson C A , de Mooij E J W , Steeghs D , Marsh T R , Brogi M , Gibson N P , Matthews S 
Published: October 2019

ABSTRACT
High-resolution Doppler spectroscopy is a powerful tool for identifying molecular species in the atmospheres of both transiting and non-transiting exoplanets. Currently, such data are analysed using cross-correlation techniques to detect the Doppler shifting signal from the orbiting planet. In this paper we demonstrate that, compared to cross-correlation methods currently used, the technique of Doppler tomography has improved sensitivity in detecting the subtle signatures expected from exoplanet atmospheres. This is partly due to the use of a regularizing statistic, which acts to suppress noise, coupled to the fact that all the data is fit simultaneously. In addition, we show that the technique can also effectively suppress contaminating spectral features that may arise due to overlapping lines, repeating line patterns, or the use of incorrect linelists. These issues can confuse conventional cross-correlation approaches, primarily due to aliasing issues inherent in such techniques, whereas Doppler tomography is less susceptible to such effects. In particular, Doppler tomography shows exceptional promise for simultaneously detecting multiple line species (e.g. isotopologues), even when there are high contrasts between such species – and far outperforms current cross-correlation function (CCF) in this respect. Finally, we demonstrate that Doppler tomography is capable of recovering molecular signals from exoplanets using real data, by confirming the strong detection of CO in the atmosphere of τ Boo b. We recover a signal with a planetary radial velocity semi-amplitude Kp = 109.6 ± 2.2 km s−1, in excellent agreement with the previously reported value of 110.0 ± 3.2 km s−1.
The southern stellar stream spectroscopic survey (S5): Overview, target selection, data reduction, validation, and early science
Authors: Li T S , Koposov S E , Zucker D B , Lewis G F , Kuehn K , Simpson J D , Ji A P , Shipp N , Mao Y-Y , Geha M , Pace A B , Mackey A D , Allam S , Tucker D L , Da Costa G S , Erkal D , Simon J D , Mould J R , Martell S L , Wan Z , De Silva G M , Bechtol K , Balbinot E , Belokurov V , Bland-Hawthorn J , Casey A R , Cullinane L , Drlica-Wagner A , Sharma S , Vivas A K , Wechsler R H , Yanny B ,   (S5 Collaboration)
Published: October 2019

ABSTRACT
We introduce the southern stellar stream spectroscopy survey (S5), an on-going program to map the kinematics and chemistry of stellar streams in the southern hemisphere. The initial focus of S5 has been spectroscopic observations of recently identified streams within the footprint of the dark energy survey (DES), with the eventual goal of surveying streams across the entire southern sky. Stellar streams are composed of material that has been tidally striped from dwarf galaxies and globular clusters and hence are excellent dynamical probes of the gravitational potential of the Milky Way, as well as providing a detailed snapshot of its accretion history. Observing with the 3.9 m Anglo-Australian Telescope’s 2-degree-Field fibre positioner and AAOmega spectrograph, and combining the precise photometry of DES DR1 with the superb proper motions from Gaia DR2, allows us to conduct an efficient spectroscopic survey to map these stellar streams. So far S5 has mapped nine DES streams and three streams outside of DES; the former are the first spectroscopic observations of these recently discovered streams. In addition to the stream survey, we use spare fibres to undertake a Milky Way halo survey and a low-redshift galaxy survey. This paper presents an overview of the S5 program, describing the scientific motivation for the survey, target selection, observation strategy, data reduction, and survey validation. Finally, we describe early science results on stellar streams and Milky Way halo stars drawn from the survey. Updates on S5, including future public data releases, can be found at http://s5collab.github.io.
Illuminating the Tadpole’s metamorphosis – I. MUSE observations of a small globule in a sea of ionizing photons
Authors: Reiter Megan , McLeod Anna F , Klaassen Pamela D , Guzmán Andrés E , Dale J E , Mottram Joseph C , Garay Guido 
Published: October 2019

ABSTRACT
We present new MUSE/VLT observations of a small globule in the Carina H ii region that hosts the HH 900 jet+outflow system. Data were obtained with the GALACSI ground-layer adaptive optics system in wide-field mode, providing spatially resolved maps of diagnostic emission lines. These allow us to measure the variation of the physical properties in the globule and jet+outflow system. We find high temperatures (Te ≈ 104 K), modest extinction (AV ≈ 2.5 mag), and modest electron densities (ne ≈ 200 cm−3) in the ionized gas. Higher excitation lines trace the ionized outflow; both the excitation and ionization in the outflow increase with distance from the opaque globule. In contrast, lower excitation lines that are collisionally de-excited at densities ≳104 cm−3 trace the highly collimated protostellar jet. Assuming the globule is an isothermal sphere confined by the pressure of the ionization front, we compute a Bonnor–Ebert mass of ∼3.7 M⊙. This is two orders of magnitude higher than previous mass estimates, calling into question whether small globules like the Tadpole contribute to the bottom of the initial mass function. The derived globule properties are consistent with a cloud that has been and/or will be compressed by the ionization front on its surface. At the estimated globule photoevaporation rate of ∼5 × 10−7 M⊙ yr−1, the globule will be completely ablated in ∼7 Myr. Stars that form in globules like the Tadpole will emerge into the H ii later and may help resolve some of the temporal tension between disc survival and enrichment.
Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies
Authors: Martínez Miguel Angel , Jordan-Paiz Ana , Franco Sandra , Nevot Maria 
Published: October 2019

AbstractSynthetic genome recoding is a new means of generating designed organisms with altered phenotypes. Synonymous mutations introduced into the protein coding region tolerate modifications in DNA or mRNA without modifying the encoded proteins. Synonymous genome-wide recoding has allowed the synthetic generation of different small-genome viruses with modified phenotypes and biological properties. Recently, a decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments (e.g. lambda red recombination and CRISPR-based editing) have enabled the construction of an Escherichia coli variant with a 4-Mb synthetic synonymously recoded genome with a reduced number of sense codons (n = 59) encoding the 20 canonical amino acids. Synonymous genome recoding is increasing our knowledge of microbial interactions with innate immune responses, identifying functional genome structures, and strategically ameliorating cis-inhibitory signaling sequences related to splicing, replication (in eukaryotes), and complex microbe functions, unraveling the relevance of codon usage for the temporal regulation of gene expression and the microbe mutant spectrum and adaptability. New biotechnological and therapeutic applications of this methodology can easily be envisaged. In this review, we discuss how synonymous genome recoding may impact our knowledge of microbial biology and the development of new and better therapeutic methodologies.
Systematic search for structural motifs of peptide binding to double-stranded DNA
Authors: Kolchina Nina , Khavinson Vladimir , Linkova Natalia , Yakimov Alexander , Baitin Dmitry , Afanasyeva Arina , Petukhov Michael 
Published: September 2019

Abstract
A large variety of short biologically active peptides possesses antioxidant, antibacterial, antitumour, anti-ageing and anti-inflammatory activity, involved in the regulation of neuro-immuno-endocrine system functions, cell apoptosis, proliferation and differentiation. Therefore, the mechanisms of their biological activity are attracting increasing attention not only in modern molecular biology, biochemistry and biophysics, but also in pharmacology and medicine. In this work, we systematically analysed the ability of dipeptides (all possible combinations of the 20 standard amino acids) to bind all possible combinations of tetra-nucleotides in the central part of dsDNA in the classic B-form using molecular docking and molecular dynamics. The vast majority of the dipeptides were found to be unable to bind dsDNA. However, we were able to identify 57 low-energy dipeptide complexes with peptide-dsDNA possessing high selectivity for DNA binding. The analysis of the dsDNA complexes with dipeptides with free and blocked N- and C-terminus showed that selective peptide binding to dsDNA can increase dramatically with the peptide length.
PDBe-KB: a community-driven resource for structural and functional annotations
Authors:   PDBe-KB consortium, Varadi Mihaly , Berrisford John , Deshpande Mandar , Nair Sreenath S , Gutmanas Aleksandras , Armstrong David , Pravda Lukas , Al-Lazikani Bissan , Anyango Stephen , Barton Geoffrey J , Berka Karel , Blundell Tom , Borkakoti Neera , Dana Jose , Das Sayoni , Dey Sucharita , Micco Patrizio Di , Fraternali Franca , Gibson Toby , Helmer-Citterich Manuela , Hoksza David , Huang Liang-Chin , Jain Rishabh , Jubb Harry , Kannas Christos , Kannan Natarajan , Koca Jaroslav , Krivak Radoslav , Kumar Manjeet , Levy Emmanuel D , Madeira F , Madhusudhan M S , Martell Henry J , MacGowan Stuart , McGreig Jake E , Mir Saqib , Mukhopadhyay Abhik , Parca Luca , Paysan-Lafosse Typhaine , Radusky Leandro , Ribeiro Antonio , Serrano Luis , Sillitoe Ian , Singh Gulzar , Skoda Petr , Svobodova Radka , Tyzack Jonathan , Valencia Alfonso , Fernandez Eloy Villasclaras , Vranken Wim , Wass Mark , Thornton Janet , Sternberg Michael , Orengo Christine , Velankar Sameer 
Published: October 2019

Abstract
The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages—the PDBe-KB aggregated views of structure data—which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession.