bluuebunny/crossref_metadata_2025_split huggingface dataset:
LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning
Authors: Martenot Vincent , Masdeu Valentin , Cupe Jean , Gehin Faustine , Blanchon Margot , Dauriat Julien , Horst Alexander , Renaudin Michael , Girard Philippe , Zucker Jean-Daniel 
Published: December 2022

Abstract
Introduction
Detecting safety signals attributed to a drug in scientific literature is a fundamental issue in pharmacovigilance. The constant increase in the volume of publications requires the automation of this tedious task, in order to find and extract relevant articles from the pack. This task is critical, as serious Adverse Drug Reactions (ADRs) still account for a large number of hospital admissions each year.

Objectives
The aim of this study is to develop an augmented intelligence methodology for automatically identifying relevant publications mentioning an established link between a Drug and a Serious Adverse Event, according to the European Medicines Agency (EMA) definition of seriousness.

Methods
The proposed pipeline, called LiSA (for Literature Search Application), is based on three independent deep learning models supporting a precise detection of safety signals in the biomedical literature. By combining a Bidirectional Encoder Representations from Transformers (BERT) algorithms and a modular architecture, the pipeline achieves a precision of 0.81 and a recall of 0.89 at sentences level in articles extracted from PubMed (either abstract or full-text). We also measured that by using LiSA, a medical reviewer increases by a factor of 2.5 the number of relevant documents it can collect and evaluate compared to a simple keyword search. In the interest of re-usability, emphasis was placed on building a modular pipeline allowing the insertion of other NLP modules to enrich the results provided by the system, and extend it to other use cases. In addition, a lightweight visualization tool was developed to analyze and monitor safety signal results.

Conclusions
Overall, the generic pipeline and the visualization tool proposed in this article allows for efficient and accurate monitoring of serious adverse drug reactions from the literature and can easily be adapted to similar pharmacovigilance use cases. To facilitate reproducibility and benefit other research studies, we also shared a first benchmark dataset for Serious Adverse Drug Events detection.
Exploring the experiences of the team members in the interprofessional socialization process for becoming an interprofessional collaborator
Authors: Keshmiri Fatemeh 
Published: December 2022

Abstract
Background
The current study aimed to explore the team members’ experiences in the socialization process for becoming a collaborator in an interprofessional team.

Method
This qualitative study is conducted using an inductive qualitative content analysis approach. Participants consisted of 32 physicians (n = 16) and nurses (n = 16) who participated by purposeful sampling. Data were collected through in-depth semi-structured interviews and analyzed by Graneheim and Lundman approach.

Results
In the study, “the perceived confrontation between interprofessional professionalism and uni-professionalism in the interprofessional socialization process” is explored as the theme, including two categories: “interprofessional professionalism commitment” as a facilitator and “uni-professional centrism” as a barrier.

Conclusion
A reciprocal dimension in interprofessional socialization was explored. Interprofessional professionalism adherence and team-centered accountability among team members were explored as a facilitator. The uni-professional culture and immature interprofessional collaboration competencies of team members disrupted the interprofessional socialization process.
A comparative study of positive and negative electronic word-of-mouth on the SERVQUAL scale during the COVID-19 epidemic - taking a regional teaching hospital in Taiwan as an example
Authors: Lee Po-Chun , Liang Li-Lin , Huang Min-Hsin , Huang Ching-Yuan 
Published: December 2022

Abstract
Background
In recent years, studies have shown that electronic WOM (eWOM) directly reflects consumers’ post-purchase psychological perception and directly affects repurchase behavior. This information is valued by institutions in various fields. Within the scope of the evaluation of service characteristics, medical service is the least visible and most difficult service attribute to evaluate. Service organizations must have high trust attributes. Therefore, an eWOM review significantly influences people’s decision-making process when choosing a healthcare provider. The purpose of this research is to combine eWOM reviews with the SERVQUAL scale in a comparative study of positive and negative eWOM reviews of a regional teaching hospital in Taiwan.

Methods
This research obtained data from publicly available eWOM reviews on Google Maps of a regional teaching hospital in Taiwan over the past 10 years (from June 24, 2011, to December 31, 2021) using website scraping technology. The semantic content analysis method was used in this study to classify eWOM reviews according to the revised PZB SERVQUAL scale.

Results
Statistical analysis was conducted. During the COVID-19 pandemic, positive reviews showed a downward trend. Among the five determinants of the SERVQUAL of PZB, positive eWOM reviews performed best in “assurance” with a positive review rate of 60.00%, followed by 42.11% for “reliability”. For negative eWOM reviews, “assurance” performed the worst with a positive rate of 72.34%, followed by “responsiveness” at 28.37% and “reliability” at 26.95%.

Conclusion
Since the onset of COVID-19 in 2020, negative eWOM has increased significantly and exceeded the amount of positive eWOM. Regardless of positive and negative reviews, what patients care most about is “assurance” of the professional attitude and skills of medical staff, which urgently needs to be strengthened. In addition, good “reliability” will help to develop positive eWOM. However, “responsiveness” as indicated by poor service waiting time can easily lead to the spread of negative eWOM. Hospital management should focus on these service-oriented qualities.
Malaria transmission in Nepal under climate change: anticipated shifts in extent and season, and comparison with risk definitions for intervention
Authors: Bhattarai Shreejana , Blackburn Jason K. , Ryan Sadie J. 
Published: December 2022

AbstractBackgroundClimate and climate change affect the spatial pattern and seasonality of malaria risk. Season lengths and spatial extents of mapped current and future malaria transmission suitability predictions for Nepal were assessed for a combination of malaria vector and parasites:Anopheles stephensiandPlasmodium falciparum(ASPF) andAn. stephensiandPlasmodium vivax(ASPV) and compared with observed estimates of malaria risk in Nepal.MethodsThermal bounds of malaria transmission suitability for baseline (1960–1990) and future climate projections (RCP 4.5 and RCP 8.5 in 2030 and 2050) were extracted from global climate models and mapped for Nepal. Season length and spatial extent of suitability between baseline and future climate scenarios for ASPF and ASPV were compared using the Warren’s I metric. Official 2010 DoHS risk districts (DRDs) and 2021 DoHS risk wards (DRWs), and spatiotemporal incidence trend clusters (ITCs) were overlaid on suitability season length and extent maps to assess agreement, and potential mismatches.ResultsShifts in season length and extent of malaria transmission suitability in Nepal are anticipated under both RCP 4.5 and RCP 8.5 scenarios in 2030 and 2050, compared to baseline climate. The changes are broadly consistent across both future climate scenarios for ASPF and ASPV. There will be emergence of suitability and increasing length of season for both ASPF and ASPV and decreasing length of season for ASPV by 2050. The emergence of suitability will occur in low and no-risk DRDs and outside of high and moderate-risk DRWs, season length increase will occur across all DRD categories, and outside of high and moderate-risk DRWs. The high and moderate risk DRWs of 2021 fall into ITCs with decreasing trend.ConclusionsThe study identified areas of Nepal where malaria transmission suitability will emerge, disappear, increase, and decrease in the future. However, most of these areas are anticipated outside of the government’s current and previously designated high and moderate-risk areas, and thus outside the focus of vector control interventions. Public health officials could use these anticipated changing areas of malaria risk to inform vector control interventions for eliminating malaria from the country, and to prevent malaria resurgence.
Tumor microenvironment enriches the stemness features: the architectural event of therapy resistance and metastasis
Authors: Nallasamy Palanisamy , Nimmakayala Rama Krishna , Parte Seema , Are Abhirup C. , Batra Surinder K. , Ponnusamy Moorthy P. 
Published: December 2022

AbstractCancer divergence has many facets other than being considered a genetic term. It is a tremendous challenge to understand the metastasis and therapy response in cancer biology; however, it postulates the opportunity to explore the possible mechanism in the surrounding tumor environment. Most deadly solid malignancies are distinctly characterized by their tumor microenvironment (TME). TME consists of stromal components such as immune, inflammatory, endothelial, adipocytes, and fibroblast cells. Cancer stem cells (CSCs) or cancer stem-like cells are a small sub-set of the population within cancer cells believed to be a responsible player in the self-renewal, metastasis, and therapy response of cancer cells. The correlation between TME and CSCs remains an enigma in understanding the events of metastasis and therapy resistance in cancer biology. Recent evidence suggests that TME dictates the CSCs maintenance to arbitrate cancer progression and metastasis. The immune, inflammatory, endothelial, adipocyte, and fibroblast cells in the TME release growth factors, cytokines, chemokines, microRNAs, and exosomes that provide cues for the gain and maintenance of CSC features. These intricate cross-talks are fueled to evolve into aggressive, invasive, migratory phenotypes for cancer development. In this review, we have abridged the recent developments in the role of the TME factors in CSC maintenance and how these events influence the transition of tumor progression to further translate into metastasis and therapy resistance in cancer.
Hospitalization, death, and probable reinfection in Peruvian healthcare workers infected with SARS-CoV-2: a national retrospective cohort study
Authors: Ramos Willy , Guerrero Nadia , Napanga-Saldaña Edwin Omar , Medina José , Loayza Manuel , De La Cruz-Vargas Jhony A. , Vargas María , Ordóñez Luis , Seclén-Ubillús Yovanna , Álvarez-Antonio Carlos , Arrasco Juan 
Published: December 2022

Abstract
Background
Peru has some of the worst outcomes worldwide as a result of the SARS-CoV-2 pandemic; it is presumed that this has also affected healthcare workers. This study aimed to establish whether occupation and other non-occupational variables were risk factors for possible reinfection, hospitalization, and mortality from COVID-19 in cohorts of Peruvian healthcare workers infected with SARS-CoV-2.

Methods
Retrospective cohort study. Healthcare workers who presented SARS-CoV-2 infection between March 1, 2020, and August 6, 2021, were included. Occupational cohorts were reconstructed from the following sources of information: National Epidemiological Surveillance System, molecular tests (NETLAB), results of serology and antigen tests (SICOVID-19), National Registry of Health Personnel (INFORHUS), and National Information System of Deaths (SINADEF). The incidence of probable reinfection, hospitalization, and death from COVID-19 was obtained in the cohorts of technicians and health assistants, nursing staff, midwives, dentists, doctors, and other healthcare workers. We evaluated whether the occupation and other non-occupational variables were risk factors for probable reinfection, hospitalization, and death from COVID-19 using log-binomial and probit binomial models, obtaining the adjusted relative risk (RRAJ).

Results
90,398 healthcare workers were included in the study. Most cases were seen in technicians and health assistants (38.6%), and nursing staff (25.6%). 8.1% required hospitalization, 1.7% died from COVID-19, and 1.8% had probable reinfection. A similar incidence of probable reinfection was found in the six cohorts (1.7–1.9%). Doctors had a higher incidence of hospitalization (13.2%) and death (2.6%); however, they were also those who presented greater susceptibility linked to non-occupational variables (age and comorbidities). The multivariate analysis found that doctors (RRAJ = 1.720; CI 95: 1.569–1.886) had a higher risk of hospitalization and that the occupation of technician and health assistant was the only one that constituted a risk factor for mortality from COVID-19 (RRAJ = 1.256; 95% CI: 1.043–1.512).

Conclusions
Peruvian technicians and health assistants would have a higher risk of death from COVID-19 than other healthcare workers, while doctors have a higher incidence of death probably linked to the high frequency of non-occupational risk factors. Doctors present a higher risk of hospitalization independent of comorbidities and age; likewise, all occupations show a similar risk of probable reinfection.
Identification of biological pathways and processes regulated by NEK5 in breast epithelial cells via an integrated proteomic approach
Authors: de Castro Ferezin Camila , Lim Kam Sian Terry C. C. , Wu Yunjian , Ma Xiuquan , Chüeh Anderly C. , Huang Cheng , Schittenhelm Ralf B. , Kobarg Jörg , Daly Roger J. 
Published: December 2022

AbstractSpecific members of the Nima-Related Kinase (NEK) family have been linked to cancer development and progression, and a role for NEK5, one of the least studied members, in breast cancer has recently been proposed. However, while NEK5 is known to regulate centrosome separation and mitotic spindle assembly, NEK5 signalling mechanisms and function in this malignancy require further characterization. To this end, we established a model system featuring overexpression of NEK5 in the immortalized breast epithelial cell line MCF-10A. MCF-10A cells overexpressing NEK5 exhibited an increase in clonogenicity under monolayer conditions and enhanced acinar size and abnormal morphology in 3D Matrigel culture. Interestingly, they also exhibited a marked reduction in Src activation and downstream signalling. To interrogate NEK5 signalling and function in an unbiased manner, we applied a variety of MS-based proteomic approaches. Determination of the NEK5 interactome by Bio-ID identified a variety of protein classes including the kinesins KIF2C and KIF22, the mitochondrial proteins TFAM, TFB2M and MFN2, RhoH effectors and the negative regulator of Src, CSK. Characterization of proteins and phosphosites modulated upon NEK5 overexpression by global MS-based (phospho)proteomic profiling revealed impact on the cell cycle, DNA synthesis and repair, Rho GTPase signalling, the microtubule cytoskeleton and hemidesmosome assembly. Overall, the study indicates that NEK5 impacts diverse pathways and processes in breast epithelial cells, and likely plays a multifaceted role in breast cancer development and progression.
Incentivising public transport use for physical activity gain: process evaluation of the COVID-19 disrupted trips4health randomised controlled trial
Authors: Jose K. A. , Sharman M. J. , Stanesby O. , Greaves S. , Venn A. J. , Blizzard L. , Palmer A. , Cooper K. , Williams J. , Cleland V. J. 
Published: December 2022

Abstract
Background
Partnering with a public transport (PT) provider, state government, and local government, the single-blinded randomised controlled trial, trips4health, investigated the impact of PT use incentives on transport-related physical activity (PA) in Tasmania, Australia. The intervention involved 16-weeks of incentives (bus trip credits) for achieving weekly PT use targets, supported by weekly text messages. This study objective was to conduct a process evaluation of the COVID-19 disrupted trips4health study.

Methods
The Medical Research Council UK’s framework for complex public health interventions guided the process evaluation. Participant reach, acceptability, fidelity and feasibility were evaluated. Administrative and post-intervention survey data were analysed descriptively. Semi-structured interviews with intervention participants (n = 7) and PT provider staff (n = 4) were analysed thematically.

Results
Due to COVID-19, trips4health was placed on hold (March 2020) then stopped (May 2020) as social restrictions impacted PT use. At study cessation, 116 participants (approximately one third of target sample) had completed baseline measures, 110 were randomised, and 64 (n = 29 in the intervention group; n = 35 in the control group) completed post-intervention measures. Participants were 18 – 80 years (average 44.5 years) with females (69%) and those with tertiary education (55%) over-represented. The intervention was delivered with high fidelity with 96% of bus trip credits and 99% of behavioural text messages sent as intended. Interviewed PT staff said implementation was highly feasible. Intervention participant acceptability was high with 90% reporting bus trip incentives were helpful and 59% reporting the incentives motivated them to use PT more. From a total of 666 possible bus trip targets, 56% were met with 38% of intervention participants agreeing and 41% disagreeing that ‘Meeting the bus trip targets was easy’. Interviews and open-ended survey responses from intervention participants revealed incentives motivated bus use but social (e.g., household member commitments) and systemic (e.g., bus availability) factors made meeting bus trip targets challenging.

Conclusions
trips4health demonstrated good acceptability and strong fidelity and feasibility. Future intervention studies incentivising PT use will need to ensure a broader demographic is reached and include more supports to meet PT targets.

Trial registration
ACTRN12619001136190.
The impact of interventions in the built environment on physical activity levels: a systematic umbrella review
Authors: Zhang Yufang , Koene Marijke , Reijneveld Sijmen A. , Tuinstra Jolanda , Broekhuis Manda , van der Spek Stefan , Wagenaar Cor 
Published: December 2022

AbstractPhysical activity is good for people’s health. The relationship between the built environment and physical activity has been well documented. However, evidence is both scarce and scattered on specific urban interventions, i.e., intentional redesigns of the built environment that promote physical activity accompanied by pre- and post-effect measurement. This umbrella review aims to synthesize the findings of systematic reviews focused on these urban interventions. We followed the PRISMA 2020 and JBI umbrella review protocol guidelines and searched seven databases covering the period between Jan 2010 and April 2022 using keywords relating to the built environment, health, physical activity, and interventions. This yielded seven systematic reviews, in which we identified several urban interventions that can promote physical activity. We found positive effects of urban interventions on physical activity regarding park renovations, adding exercise equipment, introducing a (new) pocket park, improving cycling environments, improving walking & cycling environments, as well as multi-component initiatives for active travel and enhancing the availability & accessibility of destinations. The findings suggest that the urban environment can effectively promote physical activity, especially by adding various facilities and destinations and by making the environment better suitable for active use.
Beneficial effects of anti-apolipoprotein A-2 on an animal model for coronary arteritis in Kawasaki disease
Authors: Ito Fuyu , Oharaseki Toshiaki , Tsukui Daisuke , Kimura Yoshitaka , Yanagida Tamiko , Kishi Fukuko , Yamakawa Yoshio , Kameoka Yosuke , Suzuki Shoichi , Uno Kazuko , Suzuki Osamu , Miura Noriko N. , Ohno Naohito , Takahashi Kei , Kono Hajime , Suzuki Kazuo 
Published: December 2022

Abstract
Background
Kawasaki disease (KD) is usually treated with high-dose intravenous immunoglobulin (IVIg) as severe infectious and other diseases. Due to issues that are associated with immunoglobulin preparation, such as the risk of possible contamination by infectious agents and limited blood banking resources, recombinant immunoglobulins are required.
We developed a novel recombinant antibody drug candidate, “VasSF,” based on the therapeutic effects it exerted on a mouse spontaneous crescentic glomerulonephritis model (SCG/Kj). Apolipoprotein A-2 (ApoA2) has been identified as one of VasSF’s target molecules.

Methods
Here, we tested the potential of anti-apolipoprotein A-2 antibodies (anti-ApoA2) as a new therapeutic drug against KD by examining its effect on a mouse model, in which KD was induced via Candida albicans water-soluble fraction (CAWS). CAWS (2 mg/mouse) was injected intraperitoneally into C57BL/6NCrSlc mice for five consecutive days. The incidence and histological severity of vasculitis in CAWS-induced coronary arteritis in mice administered anti-ApoA2 was examined. The following experimental groups were tested: solvent (only PBS (−) injection); anti-ApoA2 antibodies at dosages of 0.05 mg, 0.1 mg, and 0.5 mg/kg/day; human IgG at 0.1 mg/kg/day.

Results
The group treated with anti-ApoA2 0.5 mg/kg/day showed a lower incidence of panvasculitis induced by CAWS, less inflammation of the coronary arteries and aortic roots, and lower levels of serum IL-6, M-CSF, and MIP-1α and 32 cytokines/chemokines compared with those in the solvent group.

Conclusions
The anti-ApoA2 treatment suppressed the development of coronary arteritis in an animal KD model and anti-ApoA2 shows potential as an effective therapeutic candidate for the treatment of KD vasculitis. The use of specific antibodies that display higher vasculitis-suppressing effects, such as anti-ApoA2, may attenuate KD as well as other infectious diseases, with less severe adverse side effects than treatment with IVIg.
Obesity-induced neuroinflammation and cognitive impairment in young adult versus middle-aged mice
Authors: Henn Rosemary E. , Elzinga Sarah E. , Glass Emily , Parent Rachel , Guo Kai , Allouch Adam M. , Mendelson Faye E. , Hayes John , Webber-Davis Ian , Murphy Geoffery G. , Hur Junguk , Feldman Eva L. 
Published: December 2022

AbstractBackgroundObesity rates are increasing worldwide. Obesity leads to many complications, including predisposing individuals to the development of cognitive impairment as they age. Immune dysregulation, including inflammaging (e.g., increased circulating cytokines) and immunosenescence (declining immune system function), commonly occur in obesity and aging and may impact cognitive impairment. As such, immune system changes across the lifespan may impact the effects of obesity on neuroinflammation and associated cognitive impairment. However, the role of age in obesity-induced neuroinflammation and cognitive impairment is unclear. To further define this putative relationship, the current study examined metabolic and inflammatory profiles, along with cognitive changes using a high-fat diet (HFD) mouse model of obesity.ResultsFirst, HFD promoted age-related changes in hippocampal gene expression. Given this early HFD-induced aging phenotype, we fed HFD to young adult and middle-aged mice to determine the effect of age on inflammatory responses, metabolic profile, and cognitive function. As anticipated, HFD caused a dysmetabolic phenotype in both age groups. However, older age exacerbated HFD cognitive and neuroinflammatory changes, with a bi-directional regulation of hippocampal inflammatory gene expression.ConclusionsCollectively, these data indicate that HFD promotes an early aging phenotype in the brain, which is suggestive of inflammaging and immunosenescence. Furthermore, age significantly compounded the impact of HFD on cognitive outcomes and on the regulation of neuroinflammatory programs in the brain.