Identifying and correcting invalid citations due to DOI errors in Crossref data

This work aims to identify classes of DOI mistakes by analysing the open bibliographic metadata available in Crossref, highlighting which publishers were responsible for such mistakes and how many of these incorrect DOIs could be corrected through automatic processes. By using a list of invalid cited DOIs gathered by OpenCitations while processing the OpenCitations Index of Crossref open DOI-to-DOI citations (COCI) in the past two years, we retrieved the citations in the January 2021 Crossref dump to such invalid DOIs. We processed these citations by keeping track of their validity and the publishers responsible for uploading the related citation data in Crossref. Finally, we identified patterns of factual errors in the invalid DOIs and the regular expressions needed to catch and correct them. The outcomes of this research show that only a few publishers were responsible for and/or affected by the majority of invalid citations. We extended the taxonomy of DOI name errors proposed in past studies and defined more elaborated regular expressions that can clean a higher number of mistakes in invalid DOIs than prior approaches. The data gathered in our study can enable investigating possible reasons for DOI mistakes from a qualitative point of view, helping publishers identify the problems underlying their production of invalid citation data. Also, the DOI cleaning mechanism we present could be integrated into the existing process (e.g. in COCI) to add citations by automatically correcting a wrong DOI. This study was run strictly following Open Science principles, and, as such, our research outcomes are fully reproducible

Identifying and correcting invalid citations due to DOI errors in Crossref data

This work aims to identify classes of DOI mistakes by analysing the open bibliographic metadata available in Crossref, highlighting which publishers were responsible for such mistakes and how many of these incorrect DOIs could be corrected through automatic processes. By using a list of invalid cited DOIs gathered by OpenCitations while processing the OpenCitations Index of Crossref open DOI-to-DOI citations (COCI) in the past two years, we retrieved the citations in the January 2021 Crossref dump to such invalid DOIs. We processed these citations by keeping track of their validity and the publishers responsible for uploading the related citation data in Crossref. Finally, we identified patterns of factual errors in the invalid DOIs and the regular expressions needed to catch and correct them. The outcomes of this research show that only a few publishers were responsible for and/or affected by the majority of invalid citations. We extended the taxonomy of DOI name errors proposed in past studies and defined more elaborated regular expressions that can clean a higher number of mistakes in invalid DOIs than prior approaches. The data gathered in our study can enable investigating possible reasons for DOI mistakes from a qualitative point of view, helping publishers identify the problems underlying their production of invalid citation data. Also, the DOI cleaning mechanism we present could be integrated into the existing process (e.g. in COCI) to add citations by automatically correcting a wrong DOI. This study was run strictly following Open Science principles, and, as such, our research outcomes are fully reproducible

Identifying and correcting invalid citations due to DOI errors in Crossref data

This work aims to identify classes of DOI mistakes by analysing the open bibliographic metadata available in Crossref, highlighting which publishers were responsible for such mistakes and how many of these incorrect DOIs could be corrected through automatic processes. By using a list of invalid cited DOIs gathered by OpenCitations while processing the OpenCitations Index of Crossref open DOI-to-DOI citations (COCI) in the past two years, we retrieved the citations in the January 2021 Crossref dump to such invalid DOIs. We processed these citations by keeping track of their validity and the publishers responsible for uploading the related citation data in Crossref. Finally, we identified patterns of factual errors in the invalid DOIs and the regular expressions needed to catch and correct them. The outcomes of this research show that only a few publishers were responsible for and/or affected by the majority of invalid citations. We extended the taxonomy of DOI name errors proposed in past studies and defined more elaborated regular expressions that can clean a higher number of mistakes in invalid DOIs than prior approaches. The data gathered in our study can enable investigating possible reasons for DOI mistakes from a qualitative point of view, helping publishers identify the problems underlying their production of invalid citation data. Also, the DOI cleaning mechanism we present could be integrated into the existing process (e.g. in COCI) to add citations by automatically correcting a wrong DOI. This study was run strictly following Open Science principles, and, as such, our research outcomes are fully reproducible

Diarrhea Is a Hallmark of Inflammation in Pediatric COVID-19

: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a pathogen with enteric tropism. We compared the clinical, biochemical and radiological features of children hospitalized for acute SARS-CoV-2 infection, classified in two groups based on the presence of diarrhea. Logistic regression analyses were used to investigate the variables associated with diarrhea. Overall, 407 children were included in the study (226 males, 55.5%, mean age 3.9 ± 5.0 years), of whom 77 (18.9%) presented with diarrhea, which was mild in most cases. Diarrhea prevalence was higher during the Alpha (23.6%) and Delta waves (21.9%), and in children aged 5-11 y (23.8%). Other gastrointestinal symptoms were most commonly reported in children with diarrhea (p < 0.05). Children with diarrhea showed an increased systemic inflammatory state (higher C-reactive protein, procalcitonin and ferritin levels, p < 0.005), higher local inflammation as judged by mesenteric fat hyperechogenicity (adjusted Odds Ratio 3.31, 95%CI 1.13-9.70) and a lower chance of previous immunosuppressive state (adjusted Odds Ratio 0.19, 95%CI 0.05-0.70). Diarrhea is a frequent feature of pediatric COVID-19 and is associated with increased systemic inflammation, which is related to the local mesenteric fat inflammatory response, confirming the implication of the gut not only in multisystem inflammatory syndrome but also in the acute phase of the infection

Epithelial ovarian cancer is infiltrated by activated effector T cells co-expressing CD39, PD-1, TIM-3, CD137 and interacting with cancer cells and myeloid cells

IntroductionDespite predicted efficacy, immunotherapy in epithelial ovarian cancer (EOC) has limited clinical benefit and the prognosis of patients remains poor. There is thus a strong need for better identifying local immune dynamics and immune-suppressive pathways limiting T-cell mediated anti-tumor immunity.MethodsIn this observational study we analyzed by immunohistochemistry, gene expression profiling and flow cytometry the antigenic landscape and immune composition of 48 EOC specimens, with a focus on tumor-infiltrating lymphocytes (TILs).ResultsActivated T cells showing features of partial exhaustion with a CD137+CD39+PD-1+TIM-3+CD45RA-CD62L-CD95+ surface profile were exclusively present in EOC specimens but not in corresponding peripheral blood or ascitic fluid, indicating that the tumor microenvironment might sustain this peculiar phenotype. Interestingly, while neoplastic cells expressed several tumor-associated antigens possibly able to stimulate tumor-specific TILs, macrophages provided both co-stimulatory and inhibitory signals and were more abundant in TILs-enriched specimens harboring the CD137+CD39+PD-1+TIM-3+CD45RA-CD62L-CD95+ signature.ConclusionThese data demonstrate that EOC is enriched in CD137+CD39+PD-1+TIM-3+CD45RA-CD62L-CD95+ T lymphocytes, a phenotype possibly modulated by antigen recognition on neoplastic cells and by a combination of inhibitory and co-stimulatory signals largely provided by infiltrating myeloid cells. Furthermore, we have identified immunosuppressive pathways potentially hampering local immunity which might be targeted by immunotherapeutic approaches

Infected pancreatic necrosis: outcomes and clinical predictors of mortality. A post hoc analysis of the MANCTRA-1 international study

: The identification of high-risk patients in the early stages of infected pancreatic necrosis (IPN) is critical, because it could help the clinicians to adopt more effective management strategies. We conducted a post hoc analysis of the MANCTRA-1 international study to assess the association between clinical risk factors and mortality among adult patients with IPN. Univariable and multivariable logistic regression models were used to identify prognostic factors of mortality. We identified 247 consecutive patients with IPN hospitalised between January 2019 and December 2020. History of uncontrolled arterial hypertension (p = 0.032; 95% CI 1.135-15.882; aOR 4.245), qSOFA (p = 0.005; 95% CI 1.359-5.879; aOR 2.828), renal failure (p = 0.022; 95% CI 1.138-5.442; aOR 2.489), and haemodynamic failure (p = 0.018; 95% CI 1.184-5.978; aOR 2.661), were identified as independent predictors of mortality in IPN patients. Cholangitis (p = 0.003; 95% CI 1.598-9.930; aOR 3.983), abdominal compartment syndrome (p = 0.032; 95% CI 1.090-6.967; aOR 2.735), and gastrointestinal/intra-abdominal bleeding (p = 0.009; 95% CI 1.286-5.712; aOR 2.710) were independently associated with the risk of mortality. Upfront open surgical necrosectomy was strongly associated with the risk of mortality (p &lt; 0.001; 95% CI 1.912-7.442; aOR 3.772), whereas endoscopic drainage of pancreatic necrosis (p = 0.018; 95% CI 0.138-0.834; aOR 0.339) and enteral nutrition (p = 0.003; 95% CI 0.143-0.716; aOR 0.320) were found as protective factors. Organ failure, acute cholangitis, and upfront open surgical necrosectomy were the most significant predictors of mortality. Our study confirmed that, even in a subgroup of particularly ill patients such as those with IPN, upfront open surgery should be avoided as much as possible. Study protocol registered in ClinicalTrials.Gov (I.D. Number NCT04747990)

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Recurrent acute obstructive hydrocephalus as clinical onset of cerebral Whipple's disease.

Whipple’s disease is a rare multisystemic infection caused by the intracellular bacteria Thropheryma whippelii. Central nervous system (CNS) involvement is not rare. The most frequent CNS manifestations are cognitive and behavioural changes, sopranuclear ophtalmoplegia, myoclonus, epilepsy, ataxia, meningitis and focal cerebral palsy. We report one case of cerebral localization of Whipple’s disease with a clinical presentation of recurrent endocranic hypertension and hydrocephalus, and uncommon neurological symptoms, successfully treated by endoscopic third ventriculostomy and antibiotic therapy with ceftriaxone and Trimethoprim–Sulfamethoxazole