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Book ; Online: The fortedata R package

Atkins, Jeff W. / Agee, Elizabeth / Barry, Alexandra / Dahlin, Kyla M. / Dorheim, Kalyn / Grigri, Maxim S. / Haber, Lisa T. / Hickey, Laura J. / Kamoske, Aaron G. / Mathes, Kayla / McGuigan, Catherine / Paris, Evan / Pennington, Stephanie C. / Rodriguez, Carly / Shafer, Autym / Shiklomanov, Alexey / Tallant, Jason / Gough, Christopher M. / Bond-Lamberty, Ben

eISSN: 1866-3516

open-science datasets from a manipulative experiment testing forest resilience

2021

Abstract: The fortedata R package is an open data notebook from the Forest Resilience Threshold Experiment ...

Abstract	The fortedata R package is an open data notebook from the Forest Resilience Threshold Experiment (FoRTE) – a modeling and manipulative field experiment that tests the effects of disturbance severity and disturbance type on carbon cycling dynamics in a temperate forest. Package data consist of measurements of carbon pools and fluxes and ancillary measurements to help analyze and interpret carbon cycling over time. Currently the package includes data and metadata from the first three FoRTE field seasons, serves as a central, updatable resource for the FoRTE project team, and is intended as a resource for external users over the course of the experiment and in perpetuity. Further, it supports all associated FoRTE publications, analyses, and modeling efforts. This increases efficiency, consistency, compatibility, and productivity while minimizing duplicated effort and error propagation that can arise as a function of a large, distributed and collaborative effort. More broadly, fortedata represents an innovative, collaborative way of approaching science that unites and expedites the delivery of complementary datasets to the broader scientific community, increasing transparency and reproducibility of taxpayer-funded science. The fortedata package is available via GitHub: https://github.com/FoRTExperiment/fortedata (last access: 19 February 2021), and detailed documentation on the access, used, and applications of fortedata are available at https://fortexperiment.github.io/fortedata/ (last access: 19 February 2021). The first public release, version 1.0.1 is also archived at https://doi.org/10.5281/zenodo.4399601 (Atkins et al., 2020b). All data products are also available outside of the package as .csv files: https://doi.org/10.6084/m9.figshare.13499148.v1 (Atkins et al., 2020c).
Subject code	333
Language	English
Publishing date	2021-03-12
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The fortedata R package

J. W. Atkins / E. Agee / A. Barry / K. M. Dahlin / K. Dorheim / M. S. Grigri / L. T. Haber / L. J. Hickey / A. G. Kamoske / K. Mathes / C. McGuigan / E. Paris / S. C. Pennington / C. Rodriguez / A. Shafer / A. Shiklomanov / J. Tallant / C. M. Gough / B. Bond-Lamberty

Earth System Science Data, Vol 13, Pp 943-

open-science datasets from a manipulative experiment testing forest resilience

2021 Volume 952

Abstract: The fortedata R package is an open data notebook from the Forest Resilience Threshold Experiment ...

Abstract	The fortedata R package is an open data notebook from the Forest Resilience Threshold Experiment (FoRTE) – a modeling and manipulative field experiment that tests the effects of disturbance severity and disturbance type on carbon cycling dynamics in a temperate forest. Package data consist of measurements of carbon pools and fluxes and ancillary measurements to help analyze and interpret carbon cycling over time. Currently the package includes data and metadata from the first three FoRTE field seasons, serves as a central, updatable resource for the FoRTE project team, and is intended as a resource for external users over the course of the experiment and in perpetuity. Further, it supports all associated FoRTE publications, analyses, and modeling efforts. This increases efficiency, consistency, compatibility, and productivity while minimizing duplicated effort and error propagation that can arise as a function of a large, distributed and collaborative effort. More broadly, fortedata represents an innovative, collaborative way of approaching science that unites and expedites the delivery of complementary datasets to the broader scientific community, increasing transparency and reproducibility of taxpayer-funded science. The fortedata package is available via GitHub: https://github.com/FoRTExperiment/fortedata (last access: 19 February 2021), and detailed documentation on the access, used, and applications of fortedata are available at https://fortexperiment.github.io/fortedata/ (last access: 19 February 2021). The first public release, version 1.0.1 is also archived at https://doi.org/10.5281/zenodo.4399601 (Atkins et al., 2020b). All data products are also available outside of the package as .csv files: https://doi.org/10.6084/m9.figshare.13499148.v1 (Atkins et al., 2020c).
Keywords	Environmental sciences ; GE1-350 ; Geology ; QE1-996.5
Subject code	333
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Copernicus Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: R&D and productivity

Bond, Stephen R / Guceri, Irem

Economics of innovation and new technology Vol. 26, No. 1/2 , p. 108-120

evidence from large UK establishments with substantial R&D activities

2017 Volume 26, Issue 1, Page(s) 108–120

Author's details	Stephen R. Bond and Irem Guceri
Keywords	R&D ; productivity
Language	English
Dates of publication	2017-9999
Publisher	Routledge, Taylor & Francis Group
Publishing place	Abingdon
Document type	Article
ZDB-ID	1067565-6 ; 2069648-6
ISSN	1476-8364 ; 1043-8599
ISSN (online)	1476-8364
ISSN	1043-8599
Database	ECONomics Information System

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Article ; Online: William R. Brinkley (1936–2020)

Howard H. Garrison / Bettie Sue Masters / Judith Bond

FASEB BioAdvances, Vol 3, Iss 4, Pp 280-

2021 Volume 281

Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Efficacy and safety of baricitinib or ravulizumab in adult patients with severe COVID-19 (TACTIC-R): a randomised, parallel-arm, open-label, phase 4 trial.

Hall, Frances C / Cheriyan, Joseph / Cope, Andrew P / Galloway, James / Wilkinson, Ian / Bond, Simon / Norton, Sam / Banham-Hall, Edward / Bayes, Hannah / Kostapanos, Michalis / Nodale, Marianna / Petchey, William G / Sheeran, Thomas / Underwood, Jonathan / Jayne, David R

The Lancet. Respiratory medicine

2023 Volume 11, Issue 12, Page(s) 1064–1074

Abstract: ... dysregulation and complement activation in severe disease. In the TACTIC-R trial, we evaluated the efficacy and ... hospitalised with COVID-19.: Methods: TACTIC-R was a phase 4, randomised, parallel-arm, open-label platform ...

Abstract	Background: From early in the COVID-19 pandemic, evidence suggested a role for cytokine dysregulation and complement activation in severe disease. In the TACTIC-R trial, we evaluated the efficacy and safety of baricitinib, an inhibitor of Janus kinase 1 (JAK1) and JAK2, and ravulizumab, a monoclonal inhibitor of complement C5 activation, as an adjunct to standard of care for the treatment of adult patients hospitalised with COVID-19. Methods: TACTIC-R was a phase 4, randomised, parallel-arm, open-label platform trial that was undertaken in the UK with urgent public health designation to assess the potential of repurposing immunosuppressants for the treatment of severe COVID-19, stratified by a risk score. Adult participants (aged ≥18 years) were enrolled from 22 hospitals across the UK. Patients with a risk score indicating a 40% risk of admission to an intensive care unit or death were randomly assigned 1:1:1 to standard of care alone, standard of care with baricitinib, or standard of care with ravulizumab. The composite primary outcome was the time from randomisation to incidence (up to and including day 14) of the first event of death, invasive mechanical ventilation, extracorporeal membrane oxygenation, cardiovascular organ support, or renal failure. The primary interim analysis was triggered when 125 patient datasets were available up to day 14 in each study group and we included in the analysis all participants who were randomly assigned. The trial was registered on ClinicalTrials.gov (NCT04390464). Findings: Between May 8, 2020, and May 7, 2021, 417 participants were recruited and randomly assigned to standard of care alone (145 patients), baricitinib (137 patients), or ravulizumab (135 patients). Only 54 (39%) of 137 patients in the baricitinib group received the maximum 14-day course, whereas 132 (98%) of 135 patients in the ravulizumab group received the intended dose. The trial was stopped after the primary interim analysis on grounds of futility. The estimated hazard ratio (HR) for reaching the composite primary endpoint was 1·11 (95% CI 0·62-1·99) for patients on baricitinib compared with standard of care alone, and 1·53 (0·88-2·67) for ravulizumab compared with standard of care alone. 45 serious adverse events (21 deaths) were reported in the standard-of-care group, 57 (24 deaths) in the baricitinib group, and 60 (18 deaths) in the ravulizumab group. Interpretation: Neither baricitinib nor ravulizumab, as administered in this study, was effective in reducing disease severity in patients selected for severe COVID-19. Safety was similar between treatments and standard of care. The short period of dosing with baricitinib might explain the discrepancy between our findings and those of other trials. The therapeutic potential of targeting complement C5 activation product C5a, rather than the cleavage of C5, warrants further evaluation. Funding: UK Medical Research Council, UK National Institute for Health Research Cambridge Biomedical Research Centre, Eli Lilly and Company, Alexion Pharmaceuticals, and Addenbrooke's Charitable Trust.
MeSH term(s)	Humans ; Adult ; Adolescent ; COVID-19 ; SARS-CoV-2 ; Pandemics ; COVID-19 Drug Treatment ; Complement C5 ; Treatment Outcome
Chemical Substances	ravulizumab (C3VX249T6L) ; baricitinib (ISP4442I3Y) ; Complement C5
Language	English
Publishing date	2023-11-14
Publishing country	England
Document type	Randomized Controlled Trial ; Clinical Trial, Phase IV ; Journal Article
ZDB-ID	2686754-0
ISSN	2213-2619 ; 2213-2600
ISSN (online)	2213-2619
ISSN	2213-2600
DOI	10.1016/S2213-2600(23)00376-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG

Aho, Ken / Kriloff, Cathy / Godsey, Sarah E. / Ramos, Rob / Wheeler, Chris / You, Yaqi / Warix, Sara / Derryberry, DeWayne / Zipper, Sam / Hale, Rebecca L. / Bond, Charles T. / Kuehn, Kevin A.

Environmental Modelling and Software. 2023 Sept., v. 167 p.105775-

2023

Abstract: ... a large number of graph theoretic metrics, and introduce a new R package, streamDAG that codifies ...

Abstract	Many conventional stream network metrics are poorly suited to non-perennial streams, which can vary substantially in space and time. To address this issue, we considered non-perennial stream networks as directed acyclic graphs (DAGs). DAG metrics allow: 1) summarization of important non-perennial stream characteristics (e.g., complexity, connectedness, and nestedness) from both local (individual segment) and global stream network perspectives, and 2) tracking of these features as networks expand and contract. We review a large number of graph theoretic metrics, and introduce a new R package, streamDAG that codifies approaches we feel are most useful. The streamDAG package contains procedures for handling water presence data, and functions for both local and global analyses of both unweighted and weighted stream DAGs. We demonstrate streamDAG using two North American non-perennial streams: Murphy Creek, a simple drainage system in the Owyhee Mountains of southwestern Idaho, and Konza Prairie, a relatively complex network in central Kansas.
Keywords	computer software ; drainage systems ; nestedness ; space and time ; streams ; Idaho ; Kansas ; Non-perennial stream ; Graph theory ; Directed acyclic graph ; Network analysis ; Hydrologic connectivity ; R computational software
Language	English
Dates of publication	2023-09
Publishing place	Elsevier Ltd
Document type	Article ; Online
ISSN	1364-8152
DOI	10.1016/j.envsoft.2023.105775
Database	NAL-Catalogue (AGRICOLA)

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Article: rpsftm: An R Package for Rank Preserving Structural Failure Time Models.

Allison, Annabel / White, Ian R / Bond, Simon

The R journal

2018 Volume 9, Issue 2, Page(s) 342–353

Abstract: Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard ... ...

Abstract	Treatment switching in a randomised controlled trial occurs when participants change from their randomised treatment to the other trial treatment during the study. Failure to account for treatment switching in the analysis (i.e. by performing a standard intention-to-treat analysis) can lead to biased estimates of treatment efficacy. The rank preserving structural failure time model (RPSFTM) is a method used to adjust for treatment switching in trials with survival outcomes. The RPSFTM is due to Robins and Tsiatis (1991) and has been developed by White et al. (1997, 1999). The method is randomisation based and uses only the randomised treatment group, observed event times, and treatment history in order to estimate a causal treatment effect. The treatment effect,
Language	English
Publishing date	2018-01-31
Publishing country	United States
Document type	Journal Article
ISSN	2073-4859
ISSN	2073-4859
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Automated detection of atrial fibrillation using R-R intervals and multivariate-based classification.

Kennedy, Alan / Finlay, Dewar D / Guldenring, Daniel / Bond, Raymond R / Moran, Kieran / McLaughlin, James

Journal of electrocardiology

2016 Volume 49, Issue 6, Page(s) 871–876

Abstract: ... from existing sources. R-R intervals were then analyzed using four previously described R-R irregularity ... outputs from all four R-R irregularity measurements, RF and k-nn models were trained. RF classification ...

Abstract	Automated detection of AF from the electrocardiogram (ECG) still remains a challenge. In this study, we investigated two multivariate-based classification techniques, Random Forests (RF) and k-nearest neighbor (k-nn), for improved automated detection of AF from the ECG. We have compiled a new database from ECG data taken from existing sources. R-R intervals were then analyzed using four previously described R-R irregularity measurements: (1) the coefficient of sample entropy (CoSEn), (2) the coefficient of variance (CV), (3) root mean square of the successive differences (RMSSD), and (4) median absolute deviation (MAD). Using outputs from all four R-R irregularity measurements, RF and k-nn models were trained. RF classification improved AF detection over CoSEn with overall specificity of 80.1% vs. 98.3% and positive predictive value of 51.8% vs. 92.1% with a reduction in sensitivity, 97.6% vs. 92.8%. k-nn also improved specificity and PPV over CoSEn; however, the sensitivity of this approach was considerably reduced (68.0%).
Language	English
Publishing date	2016-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	410286-1
ISSN	1532-8430 ; 0022-0736
ISSN (online)	1532-8430
ISSN	0022-0736
DOI	10.1016/j.jelectrocard.2016.07.033
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Feasibility of high-dose methotrexate administered on day 1 of (R)CHOP in aggressive non-Hodgkin lymphomas.

Fleming, Megan / Huang, Ying / Dotson, Emily / Bond, David A / Reneau, John / Epperla, Narendranath / Alinari, Lapo / Brammer, Jonathan / Christian, Beth A / Baiocchi, Robert A / Maddocks, Kami / Sawalha, Yazeed

Blood advances

2021 Volume 6, Issue 2, Page(s) 460–472

Abstract: The optimal timing for administering high-dose methotrexate (HDMTX) when combined with (R)CHOP ... that the administration of prophylactic HDMTX before day 10 of R- CHOP may lead to fewer treatment delays. Herein ... we report our experience with HDMTX administered on day 1 of (R)CHOP in patients with aggressive ...

Abstract	The optimal timing for administering high-dose methotrexate (HDMTX) when combined with (R)CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone, with/without rituximab) is unclear. Recent data showed that the administration of prophylactic HDMTX before day 10 of R- CHOP may lead to fewer treatment delays. Herein, we report our experience with HDMTX administered on day 1 of (R)CHOP in patients with aggressive non-Hodgkin lymphoma (NHL). We identified 140 patients treated with ≥1 cycle of HDMTX combined with (R)CHOP for prophylaxis against (n = 84) or treatment of (n = 56) central nervous system (CNS) involvement. Overall, (R)CHOP treatment delays ≥7 days (4% of cycles, 13% of patients), doxorubicin, and/or cyclophosphamide dose reductions (1% of cycles, 6% of patients) or (R)CHOP discontinuations due to toxicity (4% of patients) were uncommon. Neutropenic fever (NF) occurred in 7% of cycles and 24% of patients and was more common during HDMTX-containing cycles. Acute kidney injury (AKI) occurred in 19% of cycles but was mostly grade ≤2. Grade ≥3 hepatotoxicity and mucositis were uncommon (each 2% of cycles). In the prophylaxis cohort, the rates of NF and grade ≥2 AKI were lower in patients who initiated HDMTX with cycle 2 or later (11% vs 30%, P = .03 and 16% vs 39%, P = .03, respectively). Our data show that HDMTX administration on day 1 of (R)CHOP may improve the deliverability of (R)CHOP and the overall safety of the regimen compared with historical data of HDMTX administration on day 10 or later of R-CHOP. Delaying prophylactic HDMTX beyond cycle 1 of (R)CHOP may reduce the risk of NF and AKI.
MeSH term(s)	Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Cyclophosphamide/adverse effects ; Doxorubicin/adverse effects ; Feasibility Studies ; Humans ; Lymphoma, Large B-Cell, Diffuse/pathology ; Lymphoma, Non-Hodgkin/drug therapy ; Methotrexate/adverse effects ; Prednisone/adverse effects ; Rituximab/adverse effects ; Vincristine/adverse effects
Chemical Substances	Rituximab (4F4X42SYQ6) ; Vincristine (5J49Q6B70F) ; Doxorubicin (80168379AG) ; Cyclophosphamide (8N3DW7272P) ; Prednisone (VB0R961HZT) ; Methotrexate (YL5FZ2Y5U1)
Language	English
Publishing date	2021-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2021005999
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Article: Outcomes of patients with diffuse large B-cell and high-grade B-cell lymphomas with synchronous CNS and systemic involvement at diagnosis treated with high-dose methotrexate and R-CHOP: a single-center retrospective study.

Fleming, Megan / Huang, Ying / Dotson, Emily / Bond, David A / Reneau, John / Epperla, Narendranath / Alinari, Lapo / Brammer, Jonathan / Christian, Beth / Baiocchi, Robert A / Maddocks, Kami / Sawalha, Yazeed

Therapeutic advances in hematology

2022 Volume 13, Page(s) 20406207221112900

Abstract: ... not well defined. High-dose methotrexate administered concurrently with R-CHOP (RM-CHOP) is a commonly ...

Abstract	Background: The optimal treatment of patients with systemic diffuse large B-cell (DLBCL) or high-grade B-cell (HGBL) lymphomas with synchronous central nervous system (CNS) involvement at diagnosis is not well defined. High-dose methotrexate administered concurrently with R-CHOP (RM-CHOP) is a commonly used regimen, but data on outcomes achieved with this regimen are limited. Objective: To report our experience with RM-CHOP in patients with systemic DLBCL or HGBL with synchronous CNS involvement at diagnosis. Design: A single-center retrospective analysis. Methods: We identified consecutive patients with systemic DLBCL or HGBL with synchronous CNS involvement at diagnosis who were treated with RM-CHOP from January 2012 to January 2021. Results: Fifty patients were included with a median age of 62 years; 82% had DLBCL ( Conclusion: CNS involvement in aggressive B-cell non-Hodgkin lymphoma at diagnosis dictates clinical outcomes and requires more effective treatment options.
Language	English
Publishing date	2022-07-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2585183-4
ISSN	2040-6215 ; 2040-6207
ISSN (online)	2040-6215
ISSN	2040-6207
DOI	10.1177/20406207221112900
Database	MEDical Literature Analysis and Retrieval System OnLINE

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