bluuebunny/crossref_metadata_2025_split huggingface dataset:
An analysis of security vulnerabilities in container images for scientific data analysis
Authors: Kaur Bhupinder , Dugré Mathieu , Hanna Aiman , Glatard Tristan 
Published: June 2021

Abstract

Background
Software containers greatly facilitate the deployment and reproducibility of scientific data analyses in various platforms. However, container images often contain outdated or unnecessary software packages, which increases the number of security vulnerabilities in the images, widens the attack surface in the container host, and creates substantial security risks for computing infrastructures at large. This article presents a vulnerability analysis of container images for scientific data analysis. We compare results obtained with 4 vulnerability scanners, focusing on the use case of neuroscience data analysis, and quantifying the effect of image update and minification on the number of vulnerabilities.

Results
We find that container images used for neuroscience data analysis contain hundreds of vulnerabilities, that software updates remove roughly two-thirds of these vulnerabilities, and that removing unused packages is also effective.

Conclusions
We provide recommendations on how to build container images with fewer vulnerabilities.
A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Authors: Gaio Daniela , DeMaere Matthew Z , Anantanawat Kay , Eamens Graeme J , Liu Michael , Zingali Tiziana , Falconer Linda , Chapman Toni A , Djordjevic Steven P , Darling Aaron E 
Published: June 2021

Abstract

Background
Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows.

Results
Here we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of &gt;8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning.

Conclusions
This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset can be explored to assess a wide range of ecological questions with regards to antimicrobial resistance, host-associated microbial and phage communities, and their dynamics during the aging of the host.
Trends in marine survival of Atlantic salmon populations in eastern Canada
Authors: Pardo Sebastián A , Bolstad Geir H , Dempson J Brian , April Julien , Jones Ross A , Raab Dustin , Hutchings Jeffrey A 
Published: June 2021

Abstract
Declines in wild Atlantic salmon (Salmo salar) abundance throughout the north Atlantic are primarily attributed to decreases in survival at sea. However, comparing trends in marine survival among populations is challenging as data on both migrating smolts and returning adults are sparse and models are difficult to parameterize due to their varied life histories. We fit a hierarchical Bayesian maturity schedule model to data from seven populations in eastern Canada to estimate numbers of out-migrating smolts, survival in the first and second year at sea, and the proportion returning after 1 year. Trends in survival at sea were not consistent among populations; we observe positive, negative, and no correlations in these, suggesting that large-scale patterns of changes in marine survival are not necessarily representative for individual populations. Variation in return abundances was mostly explained by marine survival in the first winter at sea in all but one population. However, variation in the other components were not negligible and their relative importance differed among populations. If salmon populations do not respond in a uniform manner to changing environmental conditions throughout their range, future research initiatives should explore why.
Public Opinion and Crisis Behavior in a Nuclearized South Asia
Authors: Clary Christopher , Lalwani Sameer , Siddiqui Niloufer 
Published: June 2021

AbstractResearch on public opinion and crisis behavior has focused largely on pressures felt by leaders who have initiated a crisis, not on leaders in target states responding to adversary provocation. Our survey experiment involving 1,823 respondents in Punjab, Pakistan, finds public support for escalating rather than de-escalating in response to such provocation. It shows how public pressures can encourage conflict even in instances where a leader has engaged in no prior effort to generate audience costs following crisis onset. Survey respondents were more likely to support escalatory decisions if they were made by a military, rather than civilian, leader, although we do not find that military leaders receive more support in de-escalatory decisions. Finally, while we demonstrate that leaders can mitigate the costs of de-escalating by highlighting the dangers of conflict, they still incur opportunity costs in foregone public support when they opt to de-escalate rather than escalate a crisis.
Why National Ministries Consider the Policy Advice of International Bureaucracies: Survey Evidence from 106 Countries
Authors: Herold Jana , Liese Andrea , Busch Per-Olof , Feil Hauke 
Published: June 2021

AbstractScholars of international relations and public administration widely assume that international bureaucracies, in their role as policy advisors, directly influence countries’ domestic policies. Yet, this is not true across the board. Why do some countries closely consider the advice of international bureaucracies while others do not? This article argues that international bureaucracies’ standing as sources of expertise is crucial. We tested this argument using data from a unique survey that measured prevalent practices of advice utilization in thematically specialized policy units of national ministries in a representative sample of more than a hundred countries. Our findings show that ministries’ perceptions of international bureaucracies’ expertise, that is, specialized and reliable knowledge, are the key factor. International bureaucracies influence national ministries directly and without the support of other actors that may also have an interest in the international bureaucracies’ policy advice. Our analysis also demonstrates that the effects of alternative means of influence, such as third-party pressure and coercion, are themselves partly dependent on international bureaucracies’ reputation as experts. The findings presented in this article reinforce the emphasis on expertise as a source of international bureaucracies’ influence, and provide a crucial test of its importance.
Automation in nursing decision support systems: A systematic review of effects on decision making, care delivery, and patient outcomes
Authors: Akbar Saba , Lyell David , Magrabi Farah 
Published: June 2021

Abstract

Objective
The study sought to summarize research literature on nursing decision support systems (DSSs ); understand which steps of the nursing care process (NCP) are supported by DSSs, and analyze effects of automated information processing on decision making, care delivery, and patient outcomes.

Materials and Methods
We conducted a systematic review in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement. PubMed, CINAHL, Cochrane, Embase, Scopus, and Web of Science were searched from January 2014 to April 2020 for studies focusing on DSSs used exclusively by nurses and their effects. Information about the stages of automation (information acquisition, information analysis, decision and action selection, and action implementation), NCP, and effects was assessed.

Results
Of 1019 articles retrieved, 28 met the inclusion criteria, each studying a unique DSS. Most DSSs were concerned with two NCP steps: assessment (82%) and intervention (86%). In terms of automation, all included DSSs automated information analysis and decision selection. Five DSSs automated information acquisition and only one automated action implementation. Effects on decision making, care delivery, and patient outcome were mixed. DSSs improved compliance with recommendations and reduced decision time, but impacts were not always sustainable. There were improvements in evidence-based practice, but impact on patient outcomes was mixed.

Conclusions
Current nursing DSSs do not adequately support the NCP and have limited automation. There remain many opportunities to enhance automation, especially at the stage of information acquisition. Further research is needed to understand how automation within the NCP can improve nurses’ decision making, care delivery, and patient outcomes.
Evaluation of the Compatibility of Ethyl Glucuronide and Ethyl Sulfate Levels to Assess Alcohol Consumption in Decomposed and Diabetic Postmortem Cases
Authors: Dip Aybike , Mozayani Ashraf 
Published: June 2021

Abstract
The aim of the study is to evaluate the contribution of ethanol metabolite detection in postmortem cases by showing the connection between the presence of ethanol metabolites, which are indicators of alcohol consumption, and the detection of potential postmortem ethanol formation in decomposed and diabetic cases. Determination of ethanol consumption before death is often one of the most important questions in death investigations. Postmortem ethanol formation or degradation products in the blood make it difficult to distinguish antemortem consumption or postmortem formation of ethanol and eventually may lead to misinterpretation. Decomposed bodies and diabetic cases are vulnerable to postmortem ethanol formation due to putrefaction, fermentation or other degradations. Ethyl glucuronide (EtG) and ethyl sulfate (EtS) are two metabolites of ethanol produced only in the antemortem time interval. In this study, EtG and EtS levels in urine and vitreous humor samples of 27 postmortem cases, including diabetic and degraded bodies were compared to ethanol results of their blood, urine and vitreous humor samples. EtG and EtS in urine and vitreous humor were analyzed by liquid chromatography–tandem mass spectrometry, and ethanol was assayed by routine headspace gas chromatography–flame ionization detector. These cases were devoid of other influences from forensically relevant drugs, so ethanol and/or glucose were among the only positive findings in these cases. The results of this pilot study indicate the postmortem ethanol concentrations do not correlate with the measured EtG and EtS values but are beneficial in rulings of accidental or natural deaths. This preliminary study gives additional data to help distinguish between antemortem ethanol intake and postmortem formation. EtG and EtS were well correlated positively with antemortem ethanol use instead of forming spontaneously in samples from decedents who are decomposing or have a history of diabetic hyperglycemia.
Transmembrane protein 168 mutation reduces cardiomyocyte cell surface expression of Nav1.5 through αB-crystallin intracellular dynamics
Authors: Nguyen Le Kim Chi , Shimizu Akio , Soh Joanne Ern Chi , Komeno Masahiro , Sato Akira , Ogita Hisakazu 
Published: June 2021

Abstract
Transmembrane protein 168 (TMEM168) was found to be localized on the nuclear membrane. A heterozygous mutation (c.1616G&gt;A, p. R539Q) in TMEM168 was identified in patients with Brugada syndrome. This mutation reduced expression of cardiomyocyte sodium channel Nav1.5 via Nedd4-2 E3 ubiquitin ligase-induced ubiquitination and degradation. However, the detailed molecular mechanism provoked by the TMEM168 mutant remains unclear. Here, we demonstrated that small heat shock protein αB-crystallin, which can bind to Nav1.5 and Nedd4-2 and interfere with the association of both proteins, was strongly recruited from the cell surface to the perinuclear region because of the much higher affinity of αB-crystallin with the TMEM168 mutant than with wild-type TMEM168. Following knockdown of αB-crystallin in HL-1 cardiomyocytes, the interaction of Nav1.5 with Nedd4-2 was increased, despite the reduced expression of Nav1.5. Moreover, reduction of Nav1.5 expression by αB-crystallin knockdown was rescued in the presence of a proteasome inhibitor MG-132, suggesting the importance of the αB-crystallin-modulated ubiquitin–proteasome system for the stability of Nav1.5 expression. Collectively, the balance of molecular interactions among Nav1.5, Nedd4-2 and αB-crystallin plays a role in the regulation of cardiomyocyte cell surface expression of Nav1.5, and the TMEM168 mutant disturbs this balance, resulting in a decrease in Nav1.5 expression.
Oncologic and survival outcomes in elderly patients with locally advanced rectal cancer receiving neoadjuvant chemoradiotherapy and total mesorectal excision
Authors: He Fang , Chen Mo , Xiao Wei-Wei , Zhang Qun , Liu Yanping , Zheng Jian , Wan Xiang-Bo , Gao Yuan-Hong 
Published: June 2021

Abstract

Background
The efficacy of the addition of neoadjuvant chemotherapy to neoadjuvant chemoradiotherapy and total mesorectal excision for locally advanced rectal cancer in elderly patients has not been established.

Methods
A total of 3096 locally advanced rectal cancer patients who received neoadjuvant chemotherapy, along with neoadjuvant chemoradiotherapy and total mesorectal excision, with or without adjuvant chemotherapy, between January 2010 and December 2018, were studied retrospectively. Patients were divided into elderly (&gt;75 years) and younger (≤75 years) groups, and propensity score matching was used to balance a potentially confounding clinical bias. Overall survival, cancer-specific survival, disease-free survival, distant metastasis-free survival and local recurrence-free survival rates for the two groups were compared. Hazard ratios (HR) with 95% confidence intervals (CI) for different clinicopathological variables were calculated to determine predictors of 3-year overall survival.

Results
Mean follow-up was 39.0 (range, 5–140) months. The overall 3-year overall survival, cancer-specific survival, disease-free survival, distant metastasis-free survival and locoregional relapse-free survival rates were 86.1, 87.6, 80.0, 82.4 and 95.4%, respectively. Only 3-year overall survival rates differed significantly between the elderly (77.2%) and younger (88.9%) groups (P = 0.01). Cancer-specific survival, disease-free survival, distant metastasis-free survival and locoregional relapse-free survival rates did not differ significantly between the two groups. Significant negative independent prognostic factors for 3-year overall survival were age &gt;75 years (HR = 2.016, 95% CI 1.157–23.511, P = 0.01) and high pathologic TNM stage (yp stage III, P &lt; 0.001).

Conclusion
For elderly locally advanced rectal cancer patients who have good health and performance status, the addition of neoadjuvant chemotherapy to neoadjuvant chemoradiotherapy and total mesorectal excision can result in disease-related survival rates and oncological outcomes similar to those experienced by younger patients. The decision to use this treatment approach in elderly patients should not be based solely on chronological age.
Suicide Risk Screening and Suicide Prevention in Patients With Cancer
Authors: Gascon Bryan , Leung Yvonne , Espin-Garcia Osvaldo , Rodin Gary , Chu Dominic , Li Madeline 
Published: June 2021

Abstract

Background
Suicide rates are up to 4 times greater in cancer compared with the general population, yet best practices for institutional suicide prevention are unknown. The objective of this study was to examine the association between suicide risk screening (SRS), clinician response, and suicide mortality at a comprehensive cancer treatment center.

Methods
We conducted a naturalistic, retrospective cohort study of patients attending the Princess Margaret Cancer Centre, where routine screening for suicidal intent within the Distress Assessment and Response Tool (DART-SRS) was implemented in 2010. Inverse probability of treatment weighting was used to evaluate the impact of DART-SRS completion on suicide mortality from 2005 to 2014. Chart audits were conducted for clinician response to suicidality, and crude suicide rates over the study period were analyzed. All statistical tests were 2-sided.

Results
Among 78 650 cancer patients, 89 (0.1%) died by suicide, of whom only 4 (4.5%) had completed DART-SRS. Among DART-SRS completers (n = 14 517), 69 (0.5%) reported suicidal intent, none of whom died by suicide. DART-SRS completion was associated with increased clinician response to suicidality (17.4% vs 6.7%, P = .04), more psychosocial service usage (30.5% vs 18.3%, P &lt; .001), and lower suicide mortality (hazard ratio = 0.29, 95% confidence interval = 0.28 to 0.31). Crude suicide rates at the Princess Margaret Cancer Centre were lower in patients whose first contact year was after DART-SRS implementation.

Conclusion
DART-SRS completion is associated with lower suicide mortality and increased access to psychosocial care, but patients who did not complete DART-SRS were at highest suicide risk. Further research is needed to identify mechanisms to ensure psychosocial and suicidality assessment in cancer patients who do not complete SRS.
Patterns of HIV Self-Disclosure in the Oncology Setting
Authors: Fuzzell Lindsay N , Vadaparampil Susan T , Giuliano Anna R , Liu Yifen , Coghill Anna E 
Published: June 2021

Abstract
Higher rates of cancer treatment toxicity and uniquely poor outcomes following a cancer diagnosis have been reported for persons living with HIV (PLWH). This highlights the importance of active HIV status ascertainment in the oncology setting. Self-disclosure of HIV via electronic questionnaire at patient intake is a low-cost option that has not been thoroughly evaluated. We examined 10 years (2009-2019) of patient intake questionnaire data at Moffitt Cancer Center. Self-disclosure of an HIV diagnosis was not uniform, with 36.1% (n = 299, 95% confidence interval [CI] = 32.8% to 39.4%) of 828 patients disclosing. Identification of HIV through this method was highest for anal cancer patients (66.7%, 95% CI = 57.8% to 74.7%). Self-disclosure among patients with hematopoietic malignancies, the most common diagnosis among PLWH at our institution, was lower (19.4%, 95% CI = 14.6% to 25.0%). Patient characteristics associated with HIV self-disclosure included cancer site, natal gender, and race and ethnicity. Findings highlight gaps to motivate future efforts to increase HIV ascertainment prior to initiating cancer care.
Domestic Contestations against International Courts and Tribunals: Introduction to the Special Issue
Authors: Fromageau Edouard , Kanetake Machiko , Wittich Stephan , Gattini Andrea 
Published: June 2021

Abstract
Domestic authorities, including national courts, at times, resist accepting the decisions of international courts and tribunals. The formal division between the national and international legal orders creates space for domestic authorities to contest or avoid international binding judicial decisions. The present special issue examines domestic contestations in multiple fields of international law, including human rights and investment law. In contesting some of the international decisions, domestic authorities invoke a wide range of legal bases in resisting the effect of international decisions. The contributions in the present issue examine various such argumentative bases of contestations. The contributions also consider whether domestic resistance could give rise to the opportunity for international courts and tribunals to critically reflect on their own decisions and underlying reasoning.
Retropharyngeal Edema and Neck Pain in Multisystem Inflammatory Syndrome in Children (MIS-c)
Authors: Jenkins Elan , Sherry Whitney , Smith Alison G C , Rostad Bradley S , Rostad Christina A , Jones Kaitlin , Jaggi Preeti 
Published: June 2021

Abstract
We defined the prevalence of neck pain, trismus, or dysphagia (28.4%) and retropharyngeal edema (2.9%) among 137 patients with multisystem inflammatory syndrome in children (MIS-c). Retropharyngeal edema or phlegmon has been documented radiologically in at least 9 children. Symptoms of neck inflammation are common in MIS-c.
Recurrent pancreatitis due to intraductal papillary mucinous neoplasm in a young adult
Authors: Yang Ryan C , Abuhakmeh Yousef , Schriver John P , Nelson Daniel W 
Published: June 2021

Abstract
A young adult male presented with recurrent pancreatitis and a 2.2 cm mixed duct intraductal papillary mucinous neoplasm (IPMN) located in the pancreatic body.
Our patient presented at age 21 with his second hospitalization for acute pancreatitis within a year. A mixed duct IPMN with main ductal dilation was identified, which prompted additional workup. Based upon the findings the patient was counseled regarding the risks and benefits of surveillance versus surgery. The patient elected to undergo a robotic-assisted laparoscopic distal pancreatectomy and splenectomy. Final pathology revealed an IPMN involving branch and main pancreatic ducts with low and focally high-grade dysplasia.
IPMNs are increasingly being identified. Consensus guidelines generally propose surveillance, but management in young adults can be complex. Herein we present the second youngest reported case and highlight the continued need for consensus management guidelines.
Laser-Trélat sign improved after the resection of a tiny ground-grass nodule: a case report
Authors: Nagata Masashi , Otani Shinichi , Kanai Yoshihiko , Yamamoto Shinichi , Tsubochi Hiroyoshi , Endo Shunsuke 
Published: June 2021

Abstract
The Laser-Trélat sign refers to eruptive seborrheic keratoses accompanied by internal malignancies, mainly abdominal advanced ones. Detailed associations remain unclear, and the skin lesions do not improve with the treatment of internal malignancies in half of the patients. Herein, we report a rare case of Laser-Trélat sign that improved after resection of a 0.6-cm pulmonary ground-glass nodule: adenocarcinoma in situ. The patient requested the resection with the hopes of improving the skin lesions, though immediate resection was not indicated oncologically. With informed consent, despite possible failure in improving cutaneous diseases, thoracoscopic partial resection of the right lower lobe was performed. Fortunately, her seborrheic keratoses substantially improved after the resection, without exacerbation. To our knowledge, this is the first report describing such a clinical course. It is essential to inform patients regarding the indication of treatment for internal malignancy and its limitation in improving eruptive seborrheic keratoses.