bluuebunny/crossref_metadata_2025_split huggingface dataset:
Open Data Governance at the Canadian Open Neuroscience Platform (CONP): From the Walled Garden to the Arboretum
Authors: Bernier Alexander , Knoppers Bartha M , Bermudez Patrick , Beauvais Michael J S , Thorogood Adrian ,   CONP Consortium, Behan Brendan , Bellec Pierre , Brown Shawn , Bujold David , Cavoukian Ann , Clarkson John , Das Samir , Dessureault Emilie , Dharsee Moyez , Dickie Erin , Duchesne Simon , Dyke Stephanie , Evans Ken , Evans Alan , Flynn Jennifer , Forkert Nils , Gee Tom , Glatard Tristan , Gold Richard , Harding Rachel , Henriques Felipe , Hill Sean , Illes Judy , Karamchandani Jason , Khan Ali , Kiar Greg , Maria Knoppers Bartha , Lecours Xavier , Legault Melanie , MacFarlane Dave , Madjar Cécile , Nadler Roland , Paiva Santiago , Pavlidis Paul , Poline Jean-Baptiste , Rotenberg David , Rousseau Marc-Etienne , Stewart Walter , Stikov Nikola , Theriault Elizabeth , Evans Alan 
Published: January 2024

Abstract
Scientific research communities pursue dual imperatives in implementing strategies to share their data. These communities attempt to maximize the accessibility of biomedical data for downstream research use, in furtherance of open science objectives. Simultaneously, such communities safeguard the interests of research participants through data stewardship measures and the integration of suitable risk disclosures to the informed consent process. The Canadian Open Neuroscience Platform (CONP) convened an Ethics and Governance Committee composed of experts in bioethics, neuroethics, and law to develop holistic policy tools, organizational approaches, and technological supports to align the open governance of data with ethical and legal norms. The CONP has adopted novel platform governance methods that favor full data openness, legitimated through the use of robust deidentification processes and informed consent practices. The experience of the CONP is articulated as a potential template for other open science efforts to further build upon. This experience highlights informed consent guidance, deidentification practices, ethicolegal metadata, platform-level norms, and commercialization and publication policies as the principal pillars of a practicable approach to the governance of open data. The governance approach adopted by the CONP stands as a viable model for the broader neuroscience and open science communities to adopt for sharing data in full open access.
A multi-omics data analysis workflow packaged as a FAIR Digital Object
Authors: Niehues Anna , de Visser Casper , Hagenbeek Fiona A , Kulkarni Purva , Pool René , Karu Naama , Kindt Alida S D , Singh Gurnoor , Vermeiren Robert R J M , Boomsma Dorret I , van Dongen Jenny , ’t Hoen Peter A C , van Gool Alain J 
Published: January 2024

Abstract

Background
Applying good data management and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles in research projects can help disentangle knowledge discovery, study result reproducibility, and data reuse in future studies. Based on the concepts of the original FAIR principles for research data, FAIR principles for research software were recently proposed. FAIR Digital Objects enable discovery and reuse of Research Objects, including computational workflows for both humans and machines. Practical examples can help promote the adoption of FAIR practices for computational workflows in the research community. We developed a multi-omics data analysis workflow implementing FAIR practices to share it as a FAIR Digital Object.

Findings
We conducted a case study investigating shared patterns between multi-omics data and childhood externalizing behavior. The analysis workflow was implemented as a modular pipeline in the workflow manager Nextflow, including containers with software dependencies. We adhered to software development practices like version control, documentation, and licensing. Finally, the workflow was described with rich semantic metadata, packaged as a Research Object Crate, and shared via WorkflowHub.

Conclusions
Along with the packaged multi-omics data analysis workflow, we share our experiences adopting various FAIR practices and creating a FAIR Digital Object. We hope our experiences can help other researchers who develop omics data analysis workflows to turn FAIR principles into practice.
Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations
Authors: Shen Yizhao , Li Yan , Wu Tingting , Dong Quanbin , Deng Qiufeng , Liu Lu , Guo Yanfei , Cao Yufeng , Li Qiufeng , Shi Jing , Zou Huayiyang , Jiao Yuwen , Ding Luoyang , Li Jianguo , Gao Yanxia , Hu Shixian , Wang Yifeng , Chen Lianmin 
Published: January 2024

Abstract

Background
The rumen of neonatal calves has limited functionality, and establishing intestinal microbiota may play a crucial role in their health and performance. Thus, we aim to explore the temporal colonization of the gut microbiome and the benefits of early microbial transplantation (MT) in newborn calves.

Results
We followed 36 newborn calves for 2 months and found that the composition and ecological interactions of their gut microbiomes likely reached maturity 1 month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction of Bacteroides species, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion and antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites.

Conclusions
Our study provides a metagenomic and metabolomic atlas of the temporal development of the gut microbiome in newborn calves. MT can alter the gut microbiome of newborns, leading to improved physiological status and later milk production. The data may help develop strategies to manipulate the gut microbiota during early life, which may be relevant to the health and production of newborn calves.
Health promotion roles shaped by professional identity: an ethnographic study in the Netherlands
Authors: van Heteren F , Raaphorst N J , Bussemaker J M 
Published: January 2024

Abstract
How frontline care professionals interpret and fulfill their health promotion roles is of great importance for the health of the vulnerable clients they work with. While the literature on health promotion is limited to describing the roles of healthcare professionals, this study examines the health promotion roles held by various frontline professionals when working with clients with combined psychosocial problems and how this is associated with professional identity. Based on ethnographic data from Dutch frontline professionals in social welfare, general healthcare and mental healthcare, this article shows how various frontline professionals promote health by reframing and customizing health problems and that this is associated with how they identify as pragmatic or holistic professionals.
Distant organ metastasis patterns and prognosis of lung adenosquamous carcinoma: a SEER database analysis
Authors: Xing Hongquan , Wu Cong , Zhang Dongdong , Zhang Xinyi 
Published: January 2024

Abstract

OBJECTIVES
Our purpose is to evaluate the patterns of organ metastasis and the prognosis in lung adenosquamous carcinoma patients with organ metastasis.

METHODS
We collected the data from the surveillance epidemiology and end results database, covering the period of 2000–2018. Cox regression, Kaplan–Meier and log-rank analyses were performed.

RESULTS
Totally, 2698 patients were enrolled, comprising 851 (31.54%) patients diagnosed with organ metastasis and 2017 (68.46%) patients without organ metastasis. Patients with distant organ metastasis show a significant decrease in median overall survival. In addition to the aforementioned factors, age over 70 years, male, main bronchus, advanced T stage, larger tumour size, absence of primary tumour surgery and lack of radiotherapy have all been identified as prognostic indicators associated with a poorer outcome. In terms of treatment options, patients with organ metastasis can benefit from chemotherapy and primary tumour surgery. Moreover, in patients with organ metastasis, those who received a combination treatment of surgery, chemotherapy and radiotherapy displayed the most favourable prognosis, with a median overall survival of 17 months.

CONCLUSIONS
We identified the prognostic indicators for organ metastasis in patients with lung adenosquamous carcinoma. Highly selected patients who undergo a combination treatment of surgery, chemotherapy and radiotherapy may experience the greatest survival benefit.
Pulmonary blood flow in children with univentricular heart and unilateral diaphragmatic paralysis
Authors: Kratz Tobias , Gaukstern Lisa , Wiebe Walter , Müller Nicole , Freudenthal Noa , Breuer Johannes , Luetkens Julian , Hart Christopher 
Published: January 2024

Abstract

OBJECTIVES
Spontaneous breathing has an important effect on pulmonary arterial blood flow in patients with Glenn/Fontan circulation. Unilateral diaphragmatic paralysis (DP) is a frequent complication after heart surgery in congenital heart disease. The aim of this study was to investigate the influence of unilateral DP on blood flow distribution in the pulmonary arteries with Glenn/Fontan circulation.

METHODS
Magnetic resonance phase-contrast imaging was used to evaluate stroke volume index (SVI) in the left and right pulmonary arteries in patients with Glenn/Fontan circulation with unilateral DP. Data for 18 patients with univentricular heart and unilateral DP were analysed, 8 in the Glenn stage and 10 in the Fontan stage. Ten patients had right-sided DP, and 8 had left-sided DP. A diaphragmatic plication was performed in 7 patients. The control group consisted of 36 patients with Glenn (n = 16)/Fontan (n = 20) circulation without DP.

RESULTS
In both left- and right-sided DP, the SVI to the ipsilateral side was significantly lower than in controls [2.81 (1.45–4.50) ml/m2 left vs 11.97 (7.36–16.37) ml/m2 in controls, P &lt; 0.0002; 8.2 (4.49–12.64) ml/m2 with right vs 12.64 (9.66–16.61) ml/m2 in controls; P = 0.0284]. The SVI to the contralateral side showed a slight but non-significant increase in the presence of unilateral DP.

CONCLUSIONS
Unilateral DP in patients with Glenn/Fontan circulation has a negative impact on pulmonary arterial SVI on the side of the paralysis.
Migrant Work, Gender and the Hostile Environment: A Human Rights Analysis
Authors: Sedacca Natalie 
Published: January 2024

Abstract
This article addresses work-related and gendered harms of the ‘hostile environment’, a set of measures implemented through the Immigration Acts of 2014 and 2016, which aims to make life in the UK impossible for irregular migrants. The hostile environment criminalises work without legal status, facilitates data sharing between public bodies and immigration enforcement, and restricts access services and benefits. The article examines factors that can make women susceptible to irregularity and exposure to hostile environment measures, and distinctive forms of gendered harm such as workplace sexual harassment. It argues that the detrimental impacts of the hostile environment contravene international and regional human rights obligations. Barring certain migrants from access to the labour market may violate the socio-economic right to work and/ or the right to private and family life, while a lack of access to legal remedy or labour inspection fuelled can violate migrants’ right to decent work and undermine protections against forced labour. The UK’s recent ratification of the Council of Europe’s ‘Istanbul Convention’ and ILO Convention 190 on violence and harassment at work signifies a renewed commitment to safeguarding women regardless of migration status, but the universalistic potential of these instruments is undermined by the hostile environment’s continued operation.
Lessons from the Viral Body Politic: Borders and the Possibilities of a More-than-Human Worldmaking
Authors: Fishel Stefanie , Agius Christine 
Published: January 2024

AbstractBordering practices have been a central and controversial feature of the SARS-CoV-2 pandemic. Closed borders, lockdowns, and restrictions on movement and individual “freedoms” have revived concepts of the biopolitical “state of exception” and state control. In this article, we argue that biopolitical critiques of responses to the pandemic fail to grasp the opportunity to rethink worldmaking and instead base their critiques on a desired “return to normal” which foregrounds human-centric individualism at the expense of alternative worldmaking that accounts for the more-than-human. To do so, we bring the virus and the virome into our discussion to rethink bordering practices and how the SARS-CoV-2 virus affects bodies, worlds, and politics. We focus primarily on the Australian case, where the pandemic response began with lockdowns and then gave way to a militarized and individualistic approach. Responses to the pandemic have failed to produce a reimagining of human and more-than-human relations. Opportunities for ethical engagement have been missed, resulting in limited responses that stem from the failure of state capacity and entrenched modes of inequality that are harmful to vulnerable others, both human and more-than-human. This requires an ontological reframing of how we relate to a complex world from a more-than-human perspective.
Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents
Authors: Hu Sarah K , Anderson Rika E , Pachiadaki Maria G , Edgcomb Virginia P , Serres Margrethe H , Sylva Sean P , German Christopher R , Seewald Jeffrey S , Lang Susan Q , Huber Julie A 
Published: January 2024

Abstract
Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial eukaryotes (or protists) play a critical role in hydrothermal vent food webs as consumers and hosts of symbiotic bacteria, and as a nutritional source to higher trophic levels. We measured microbial eukaryotic cell abundance and predation pressure in low-temperature diffuse hydrothermal fluids at the Von Damm and Piccard vent fields along the Mid-Cayman Rise in the Western Caribbean Sea. We present findings from experiments performed under in situ pressure that show cell abundances and grazing rates higher than those done at 1 atmosphere (shipboard ambient pressure); this trend was attributed to the impact of depressurization on cell integrity. A relationship between the protistan grazing rate, prey cell abundance, and temperature of end-member hydrothermal vent fluid was observed at both vent fields, regardless of experimental approach. Our results show substantial protistan biomass at hydrothermally fueled microbial food webs, and when coupled with improved grazing estimates, suggest an important contribution of grazers to the local carbon export and supply of nutrient resources to the deep ocean.
Assessing the in vivo impact of novel β-lactamase inhibitors on the efficacy of their partner β-lactams against serine carbapenemase-producing Pseudomonas aeruginosa using human-simulated exposures
Authors: Ruiz Victor H , Gill Christian M , Nicolau David P 
Published: January 2024

Abstract

Objectives
To evaluate the efficacy of human-simulated regimens (HSRs) of ceftazidime, ceftazidime/avibactam, imipenem, imipenem/relebactam, meropenem and meropenem/vaborbactam in a murine thigh infection model against serine carbapenemase-producing Pseudomonas aeruginosa.

Methods
Nine P. aeruginosa clinical isolates harbouring GES-5 (n = 1), GES-20 (n = 1), GES-5/20 (n = 1), GES-19, GES-20 (n = 3) and KPC (n = 3) were evaluated. Six mice were administered HSRs of ceftazidime 2 g q8h (2 h infusion), ceftazidime/avibactam 2.5 g q8h (2 h infusion), meropenem 2 g q8h (3 h infusion), imipenem 0.5 g q6h (0.5 h infusion), imipenem/relebactam 1.25 g q6h (0.5 h infusion) and meropenem/vaborbactam 4 g q8h (3 h infusion). Change in bacterial burden relative to baseline and the percent of isolates meeting the 1 log10 kill endpoint were assessed.

Results
The addition of avibactam to ceftazidime increased the percentage of isolates meeting 1 log10 kill from 33% to 100% of GES- or KPC-harbouring isolates. Imipenem/relebactam HSR produced ≥1 log10 of kill against 83% and 100% of GES- and KPC-harbouring isolates, respectively, while imipenem alone failed to reach 1 log10 kill for any isolates. Vaborbactam resulted in variable restoration of meropenem activity as 1 log10 kill was achieved in only 33% and 66% of GES- and KPC-harbouring isolates, respectively, compared with no isolates for meropenem alone.

Conclusions
Ceftazidime/avibactam and imipenem/relebactam were active against 100% and 89% of KPC- or GES-harbouring isolates tested in vivo. The activity of meropenem/vaborbactam was variable, suggesting this may be an inferior treatment option in this setting. Further studies to evaluate clinical outcomes in GES- and KPC-producing P. aeruginosa are warranted given their increasing prevalence worldwide.
Population pharmacokinetics of posaconazole in allogeneic haematopoietic stem cell transplant patients
Authors: Selby Philip R , Heffernan Aaron J , Yeung David , Warner Morgyn S , Peake Sandra L , Hahn Uwe , Westley Ian , Shakib Sepehr , Roberts Jason A 
Published: January 2024

Abstract

Background
Invasive fungal disease (IFD) in the early post-allogeneic HSCT (alloHCT) period is associated with increased likelihood of catastrophic outcomes. The utility of oral modified release (MR) posaconazole tablets is limited by reduced drug absorption from gastrointestinal toxicity induced by cytotoxic chemotherapy, necessitating a switch to the IV posaconazole formulation.

Objectives
To describe the population pharmacokinetics of posaconazole for oral MR and IV formulations in alloHCT patients and determine dosing regimens likely to achieve therapeutic exposures.

Methods
We performed a prospective observational pharmacokinetic study in adult patients in the early post-alloHCT period requiring a change in posaconazole formulation (oral to IV). Samples were analysed using a validated LC-MS/MS method. Population pharmacokinetic analysis and Monte Carlo simulations (n = 1000) were performed using Pmetrics for R.

Results
Twenty patients aged between 21 and 70 years were included in the study. A two-compartment model, incorporating mucositis/diarrhoea to modify the bioavailability for oral administration best described the data. To achieve ≥90% PTA, simulations showed that higher than currently recommended doses of oral MR posaconazole were required for prophylaxis Cmin targets (≥0.5 and ≥0.7 mg/L), while increased doses of both formulations were required for IFD treatment PK/PD targets, with patients experiencing oral mucositis/diarrhoea unlikely to achieve these.

Conclusions
Increased doses of posaconazole should be considered for both prophylaxis and treatment of IFD to increase the proportion of alloHCT patients achieving therapeutic exposures, particularly the oral formulation in patients with mucositis and/or diarrhoea. Posaconazole therapeutic drug monitoring should be considered for all formulations in this setting.
The Multi-Dimensional Emergence of Climate-Induced Migrants in Rights-Based Litigation in the Global South
Authors: Andreolla Serraglio Diogo , Cavedon-Capdeville Fernanda de Salles , Thornton Fanny 
Published: January 2024

AbstractThe article evidences to what extent rights-based climate litigation is applied as a strategy to enhance the recognition and protection of climate-induced migrants. Adopting a deductive approach and desk review, the study, illustrates how climate-induced migration has been addressed by International Human Rights Law, with some attention also paid to the growing application of the right to a safe climate and climate justice. The study highlights the duties of both States and private actors in tackling the emerging climate crisis under the human rights agenda. Relevant responsibilities are framed in particular within the scope of rights-based litigation dealing with the topic. We present an analysis of litigation linked to climate-induced migration that was filed before distinct international, regional, and national jurisdictions and, in doing so, propose a chronology of cases—structured in three generations—of how population movements as a result of climate change have been discussed by judicial means. The first generation relates to cases that consider the issue from the perspective of protection—in both national, regional, and international jurisdictions. The second generation emerges within general climate litigation claims, involving commitments linked to the climate agenda. In addition to raising (forced) population movements as one of the expected impacts of climate change, such cases frequently call upon a rights-based approach. The third generation encompasses rights-based cases centred on climate-induced migrants per se. The strengths and limitations of rights-based litigation to respond to the topic are finally highlighted: we conclude that litigation remains a blunt but not unpromising tool to respond to climate-induced migration. Generic references to the risk of (forced) population movements largely prevail; nevertheless, strategic rights-based litigation can facilitate the visibility of climate-induced migrants to the international community, fostering the development of legal solutions in the longer term.
Developments, Opportunities, and Complexities in Global South Climate Litigation: Introduction to the Special Collection
Authors: Murcott Melanie Jean , Tigre Maria Antonia 
Published: January 2024

AbstractThis introduction presents a special collection of the Journal of Human Rights Practice, ‘Developments, Opportunities and Complexities in Global South Climate Litigation’. It conceptualizes and problematizes ‘climate litigation’ and the ‘Global South’, and brings together perspectives from a diverse range of scholars and practitioners from the Global South to advance knowledge on how climate litigation in the region has developed in recent years. The number of cases discussed, and the depth of analyses illustrate that the region is contributing to the pursuit of climate justice through litigation. The collection showcases a rich body of scholarship on climate litigation from African, Latin American, and Asian perspectives. In the face of political, cultural, and other barriers to knowledge production, contributions demonstrate nuanced, contextual engagement with climate litigation in the Global South. Therefore, this collection challenges the narrative that cases dealing with climate change and its human rights and justice implications are few and far between in the Global South. It emphasizes their relevance for the global discourse on climate litigation.