NCube/papyrus huggingface dataset:
Factors influencing clinicians’ referral or admission decisions for post-acute stroke
or traumatic brain injury rehabilitation : a scoping review

Demand for post-acute stroke and traumatic brain injury (TBI) rehabilitation outweighs resource availability. Every day, clinicians face the challenging task of deciding which patient will benefit or not from rehabilitation. The objectives of this scoping review were to map and compare factors reported by clinicians as influencing referral or admission decisions to post-acute rehabilitation for stroke and TBI patients, to identify most frequently reported factors and those perceived as most influential. We searched four major databases for articles published between 1946 and January 2021. Articles were included if they reported clinicians' perceptions, investigated referral or admission decisions to post-acute rehabilitation, and focused on patients with stroke or TBI. Twenty articles met inclusion criteria. The International Classification of Functioning, Disability and Health framework was used to guide data extraction and summarizing. Patient-related factors most frequently reported by clinicians were age, mental status prior to stroke or TBI, and family support. The two latter were ranked among the most influential by clinicians working with stroke patients, whereas age was ranked of low importance. Organizational factors were reported to influence decisions (particularly the availability of post-acute care services) as well as clinicians' characteristics (eg, knowledge). Moreover, clinicians' prediction of patient outcome ranked among the most important driver of referral or admission decisions by clinicians working with stroke patients. Findings highlight the complex nature of decision-making regarding patient selection for rehabilitation and provide insight on important factors that frontline clinicians need to consider when having to make rapid decisions in high-pressured acute care environments.

Keyphrases: Stroke, Traumatic brain injury, Rehabilitation, Clinical decision-making, Referral and consultation, Health services accessibility
The Plan S Rights Retention
Strategy is an administrative and
legal burden, not a sustainable open
access solution

The Plan S Rights Retention Strategy (RRS) requires authors who are submitting to subscription journals to inform publishers that the author accepted manuscript (AAM) will be made available under a Creative Commons Attribution (CC BY) licence. The laudable stated aim of the RRS is to achieve immediate open access to research outputs, while preserving journal choice for authors. However, proponents of the RRS overlook the significant administrative and legal burdens that the RRS places on authors and readers. Even though compliance with existing green open access (self-archiving) policies is poor at best, the RRS is likely to rely on authors to successfully execute the CC licensing of their work in the face of publisher resistance. The complexity of copyright law and CC licensing gives many reasons to doubt the legal validity of an RRS licence grant, which creates legal risk for authors and their institutions. The complexity of RRS CC BY licensing also creates legal risk for readers, who may not be able to fully rely on the reuse rights of a CC BY licence on the AAM. However, cOAlition S has released no legal advice that explains why the RRS is valid and legally binding. Publishers of legacy subscription journals have already begun implementing strategies that ensure they can protect their revenue streams. These actions may leave authors having to choose between paying publication fees and complying with their funding agreements. The result is that the RRS increases the complexity of the copyright and licensing landscape in academic publishing, creates legal risk and may not avoid author fees. Unless increased complexity and conflict between authors and publishers drives open access, the RRS is not fit for its stated purpose as an open access strategy.

Keyphrases: Open access, Rights retention, Plan S, Creative Commons, Licence, Copyright
Connected speech markers of amyloid burden in primary progressive aphasia

INTRODUCTION Positron emission tomography (PET) amyloid imaging has become an important part of the diagnostic workup for patients with primary progressive aphasia (PPA) and uncertain underlying pathology. Here, we employ a semi-automated analysis of connected speech (CS) with a twofold objective. First, to determine if quantitative CS features can help select primary progressive aphasia (PPA) patients with a higher probability of a positive PET amyloid imaging result. Second, to examine the relevant group differences from a clinical perspective.  METHODS 117 CS samples from a well-characterised cohort of PPA patients who underwent PET amyloid imaging were collected. Expert consensus established PET amyloid status for each patient, and 40% of the sample was amyloid positive.  RESULTS Leave-one-out cross-validation yields 77% classification accuracy (sensitivity: 74%, specificity: 79%).  DISCUSSION Our results confirm the potential of CS analysis as a screening tool. Discriminant CS features from lexical, syntactic, pragmatic, and semantic domains are discussed.

Keyphrases: Primary progressive aphasia, Biomarkers, Connected speech, Natural language processing, Alzheimer’s disease, Differential diagnosis, Telemedicine
The role of point-of-care ultrasound monitoring in cardiac surgical patients with acute kidney injury

The approach to the patient with acute kidney injury (AKI) after cardiac surgery involves multiple aspects. These include the rapid recognition of reversible causes, the accurate identification of patients who will progress to severe stages of AKI and the subsequent management of complications resulting from severe renal dysfunction. Unfortunately, the inherent limitations of physical examination and laboratory parameters results are often responsible for a sub-optimal clinical management. In this review article, we explore how Point-Of-Care ultrasound, including renal and extra-renal ultrasound, can be used to complement all aspects of the care of cardiac surgery patients with AKI, from the initial approach of early AKI to fluid balance management during renal replacement therapy. The current evidence is reviewed including knowledge gaps and future areas of research.

Keyphrases: Acute kidney injury, Cardiac surgery, Point-Of-Care ultrasound, Doppler ultrasound
High postoperative portal venous flow pulsatility indicates right ventricular dysfunction and predicts complications in cardiac surgery patients

Background Right ventricular failure after cardiac surgery is associated with morbidity and mortality. Right ventricular dysfunction results in hepatic venous congestion, which impacts the portal circulation. We aimed to determine whether an increased portal flow pulsatility fraction was associated with right ventricular dysfunction in cardiac surgery patients. We also aimed to describe the haemodynamic factors and postoperative complications associated with an increased portal pulsatility in this setting.  Methods We conducted a prospective single-centre cohort study, recruiting adults undergoing cardiac surgery. Portal flow was assessed before, during, and after surgery by Doppler ultrasound. A detailed haemodynamic and echocardiographic assessment was performed at the same time points.  Results A total of 115 patients were included. Both systolic and diastolic right ventricular dysfunction were associated with a higher portal pulsatility fraction (P=0.008 and <0.001, respectively). A positive association was present between portal pulsatility fraction and measurements representative of venous pressure (central venous pressure, inferior vena cava diameter). A post-procedural portal pulsatility fraction ≥50% measured in the operating room was present in 21 (18.3%) patients and was associated with an increased risk of major complications (odds ratio=5.83, confidence interval, 2.04–16.68, P=0.001). The addition of portal flow assessment to a predictive model including EuroSCORE II and systolic right ventricular dysfunction improved prediction of postoperative complications.  Conclusions High portal flow pulsatility fraction is associated with right ventricular dysfunction, signs of venous congestion and decreased perfusion, and an increased risk of major complications. Portal vein Doppler ultrasound appears to be promising for risk assessment in the perioperative period.

Keyphrases: Cardiac surgery, Echocardiography, Ventricular dysfunction, right, Thoracic surgery, Ultrasonography, Doppler, Ventricular function
Les Chambres extraordinaires au sein des tribunaux cambodgiens : réussites, défis et limites

Les Chambres extraordinaires au sein des tribunaux cambodgiens (CETC) ont été mises en oeuvre en 2005, environ 30 ans après la fin du régime Khmer Rouge. Ce tribunal hybride fut le résultat de longues négociations entre le Gouvernement cambodgien et l’ONU. Les tribunaux hybrides ont récemment pris de l’importance comme l’un des développements politiques les plus importants en matière de justice transitionnelle. Cependant, l’impact de ces tribunaux sur les sociétés qui ont subits des violences de masse n’est pas tout à fait clair et peu de textes actuels ont été publiés sur le sujet. Par conséquent, notre étude de cas vise à accroître les connaissances sur le fonctionnement des CETC, sur les défis que le tribunal a rencontrés, sur ses avantages, ainsi que ses limites. Pour ce faire, des entretiens semi-dirigés avec des acteurs des CETC et de DC- Cam ont été réalisés. En explorant la perception des participants concernant l’atteinte des objectifs du tribunal, il a été possible d’analyser la portée du rôle du tribunal. La présente étude s’est concentrée sur les difficultés liées à l’ingérence politique, qui s’avère être une des causes des blocages judiciaires dans les dossiers 003 et 004. Il est également ressorti des entretiens que l’équilibre entre la paix et la justice est un enjeu important. Juger davantage d’anciens soldats khmers rouges pourrait avoir comme conséquence d’engendrer de nouveaux conflits sociaux. Par ailleurs, ne pas mener à terme les dossiers 003 et 004 pourrait, selon certains de nos interviewés, nuire à l’héritage du tribunal pour le renforcement de l’État de droit. De plus, l’objectif de réconciliation nationale, qui passe par la recherche de la vérité et un travail de mémoire est une limite importante des CETC. Heureusement, des mécanismes de justice transitionnelle tels que les projets d’éducation et de mémoire réalisés par DC-Cam permettent de combler cette limite. Finalement, cette étude démontre que l’influence du tribunal sur les cours nationales pour le renforcement d’une justice équitable est freinée par le manque d’intérêt de la part du gouvernement d’apporter une réelle réforme judiciaire.

Keyphrases: Chambres extraordinaires au sein des tribunaux cambodgiens, Cambodge, Justice transitionnelle, Droit pénal international, Nations Unies, DC-Cam, Khmer rouge, Ingérence politique, Paix, Réconciliation, Justice, Vérité
Electronic absorption spectroscopy

Absorption spectroscopy in the ultraviolet, visible and near-infrared (UV-VIS-NIR) wavelength ranges is one of the oldest and most often used characterization methods in coordination chemistry. This overview illustrates examples ranging from four-coordinate and six-coordinate complexes of d-block elements to modern lanthanide complexes.

Keyphrases: Absorption bands, Absorption intensity, Absorption wavelength, d-d Absorption bands, Electronic origin transitions, f-f Absorption bands, Near-infrared wavelength, Ultraviolet wavelength, Visible wavelength
Resiniferatoxin hampers the nocifensive response of Caenorhabditis elegans to noxious heat, and pathway analysis revealed that the Wnt signaling pathway is involved

Resiniferatoxin (RTX) is a metabolite extracted from Euphorbia resinifera. RTX is a potent capsaicin analog with specific biological activities resulting from its agonist activity with the transient receptor potential channel vanilloid subfamily member 1 (TRPV1). RTX has been examined as a pain reliever, and more recently, investigated for its ability to desensitize cardiac sensory fibers expressing TRPV1 to improve chronic heart failure (CHF) outcomes using validated animal models. Caenorhabditis elegans (C. elegans) expresses orthologs of vanilloid receptors activated by capsaicin, producing antinociceptive effects. Thus, we used C. elegans to characterize the antinociceptive properties and performed proteomic profiling to uncover specific signaling networks. After exposure to RTX, wild-type (N2) and mutant C. elegans were placed on petri dishes divided into quadrants for heat stimulation. The thermal avoidance index was used to phenotype each tested C. elegans experimental group. The data revealed for the first time that RTX can hamper the nocifensive response of C. elegans to noxious heat (32 – 35 °C). The effect was reversed 6 h after RTX exposure. Additionally, we identified the RTX target, the C. elegans transient receptor potential channel OCR-3. The proteomics and pathway enrichment analysis results suggest that Wnt signaling is triggered by the agonistic effects of RTX on C. elegans vanilloid receptors.

Keyphrases: Caenorhabditis elegans, Transient receptor potential channels, Proteomics, Mass spectrometry, Resiniferatoxin, Nociception, Wnt signaling pathway
Informatisation incrémentale ou de rupture? : le cas du dossier patient hospitalier

Au niveau international, l’informatisation de la production des soins hospitaliers ne se développe que lentement. Un terme souvent utilisé dans la littérature pour expliquer ce phénomène est celui des "facteurs organisationnels", mais sans, la plupart du temps, que ce terme soit précisé. L’article, à partir d’une recherche observationnelle multi-sites, analyse sur le cas français les évolutions organisationnelles des unités cliniques consécutives à l’implantation d’un Dossier Patient Informatisé (DPI). Il montre que le système en place n’a subi que peu de transformations, au prix d’accommodements avec l’outil informatique. Une telle situation peut paraitre satisfaisante aux yeux des tutelles qui promeuvent l’innovation technologique, mais pose la question de la création de valeur organisationnelle, c’est-à-dire la possibilité pour les professionnels de soins de se saisir de l’outil dans une optique de transformation et d’amélioration à terme des différentes composantes de la performance. At the international level, the computerization of hospital care production develops only slowly. Past research has often used the term "organizational factors" to explain this phenomenon, but without specification so far. This article builds on results from an empirical research led in multiple French hospitals to investigate the organizational evolutions of clinical units due to the implementation of an Electronic Patient Record. It shows that the extant organizational system underwent only few transformations, thanks to local adjustments with the IT tool. Such a situation may be satisfactory for the eyes of the supervising structures which promote the technological innovation, but raises the issue of true organizational value creation.

Keyphrases: Dossier Patient Informatisé, Hôpital, Changements organisationnels, Valeur organisationnelle, Hospital, Electronic Health Record, Hospital, Organizational change, Organizational value
Improving reproducibility in machine learning research : a report from the NeurIPS 2019 reproducibility program

One of the challenges in machine learning research is to ensure that presented and published results are sound and reliable. Reproducibility, that is obtaining similar results as presented in a paper or talk, using the same code and data (when available), is a necessary step to verify the reliability of research findings. Reproducibility is also an important step to promote open and accessible research, thereby allowing the scientific community to quickly integrate new findings and convert ideas to practice. Reproducibility also promotes the use of robust experimental workflows, which potentially reduce unintentional errors. In 2019, the Neural Information Processing Systems (NeurIPS) conference, the premier international conference for research in machine learning, introduced a reproducibility program, designed to improve the standards across the community for how we conduct, communicate, and evaluate machine learning research. The program contained three components: a code submission policy, a community-wide reproducibility challenge, and the inclusion of the Machine Learning Reproducibility checklist as part of the paper submission process. In this paper, we describe each of these components, how it was deployed, as well as what we were able to learn from this initiative.

Keyphrases: Reproducibility, NeurIPS 2019
Mapping the biomedical sciences using Medical Subject Headings : a comparison between MeSH coassignments and MeSH citation pairs

Objective: This study compares two maps of biomedical sciences using Medical Subject Headings (MeSH) term coassignments versus MeSH terms of citing/cited articles and reveals similarities and differences between the two approaches. Methods: MeSH terms assigned to 397,475 journal articles published in 2015, as well as their 4,632,992 cited references, were retrieved from Web of Science and MEDLINE databases, respectively, which formed over 7 million MeSH co-assignments and nearly 18 million direct citation pairs. We generated six network visualizations of biomedical science at three levels using Gephi software based on these MeSH co-assignments and citation pairs. Results: The MeSH co-assignment map contained more nodes and edges, as MeSH co-assignments cover all medical topics discussed in articles. By contrast, the MeSH citation map contained fewer but larger nodes and wider edges, as citation links indicate connections to two similar medical topics. Conclusion: These two types of maps emphasize different aspects of biomedical sciences, with MeSH co-assignment maps focusing on the relationship between topics in different categories and MeSH direct citation maps providing insights into relationships between topics in the same or similar category.

Keyphrases: MeSH, Citation, Co-assignment, Map of life sciences, Gephi
Investigating the division of scientific labor using the Contributor Roles Taxonomy (CRediT)

Contributorship statements were introduced by scholarly journals in the late 1990s to provide more details on the specific contributions made by authors to research papers. After more than a decade of idiosyncratic taxonomies by journals, a partnership between medical journals and standards organizations has led to the establishment, in 2015, of the Contributor Roles Taxonomy (CRediT), which provides a standardized set of 14 research contributions. Using the data from Public Library of Science (PLOS) journals over the 2017–2018 period (N = 30,054 papers), this paper analyzes how research contributions are divided across research teams, focusing on the association between division of labor and number of authors, and authors’ position and specific contributions. It also assesses whether some contributions are more likely to be performed in conjunction with others and examines how the new taxonomy provides greater insight into the gendered nature of labor division. The paper concludes with a discussion of results with respect to current issues in research evaluation, science policy, and responsible research practices.

Keyphrases: Authorship, Contributorship, CRediT, Gender, Public Library of Science
Textual analysis of artificial intelligence manuscripts reveals features associated with peer review outcome

We analyzed a data set of scientific manuscripts that were submitted to various conferences in artificial intelligence. We performed a combination of semantic, lexical, and psycholinguistic analyses of the full text of the manuscripts and compared them with the outcome of the peer review process. We found that accepted manuscripts scored lower than rejected manuscripts on two indicators of readability, and that they also used more scientific and artificial intelligence jargon. We also found that accepted manuscripts were written with words that are less frequent, that are acquired at an older age, and that are more abstract than rejected manuscripts. The analysis of references included in the manuscripts revealed that the subset of accepted submissions were more likely to cite the same publications. This finding was echoed by pairwise comparisons of the word content of the manuscripts (i.e., an indicator of semantic similarity), which were more similar in the subset of accepted manuscripts. Finally, we predicted the peer review outcome of manuscripts with their word content, with words related to machine learning and neural networks positively related to acceptance, whereas words related to logic, symbolic processing, and knowledge-based systems negatively related to acceptance.

Keyphrases: Artificial intelligence, Peer review, Readability
Researchers’ perceptions of ethical authorship distribution in collaborative research teams

Authorship is commonly used as the basis for the measurement of research productivity. It influences career progression and rewards, making it a valued commodity in a competitive scientific environment. To better understand authorship practices amongst collaborative teams, this study surveyed authors on collaborative journal articles published between 2011 and 2015. Of the 8364 respondents, 1408 responded to the final open-ended question, which solicited additional comments or remarks regarding the fair distribution of authorship in research teams. This paper presents the analysis of these comments, categorized into four main themes: (1) disagreements, (2) questionable behavior, (3) external influences regarding authorship, and (4) values promoted by researchers. Results suggest that some respondents find ways to effectively manage disagreements in a collegial fashion. Conversely, others explain how distribution of authorship can become a "blood sport" or a "horror story" which can negatively affect researchers' wellbeing, scientific productivity and integrity. Researchers fear authorship discussions and often try to avoid openly discussing the situation which can strain team interactions. Unethical conduct is more likely to result from deceit, favoritism, and questionable mentorship and may become more egregious when there is constant bullying and discrimination. Although values of collegiality, transparency and fairness were promoted by researchers, rank and need for success often overpowered ethical decision-making. This research provides new insight into contextual specificities related to fair authorship distribution that can be instrumental in developing applicable training tools to identify, prevent, and mitigate authorship disagreement.

Keyphrases: Authorship, Collaboration, Ethics, Misbehavior, Professional ethics