bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cooperative driver pathways discovery by multiplex network embedding
Authors: Wang Jun , Chen Xi , Wu Zhengtian , Guo Maozu , Yu Guoxian 
Published: March 2023

Abstract
Cooperative driver pathways discovery helps researchers to study the pathogenesis of cancer. However, most discovery methods mainly focus on genomics data, and neglect the known pathway information and other related multi-omics data; thus they cannot faithfully decipher the carcinogenic process. We propose CDPMiner (Cooperative Driver Pathways Miner) to discover cooperative driver pathways by multiplex network embedding, which can jointly model relational and attribute information of multi-type molecules. CDPMiner first uses the pathway topology to quantify the weight of genes in different pathways, and optimizes the relations between genes and pathways. Then it constructs an attributed multiplex network consisting of micro RNAs, long noncoding RNAs, genes and pathways, embeds the network through deep joint matrix factorization to mine more essential information for pathway-level analysis and reconstructs the pathway interaction network. Finally, CDPMiner leverages the reconstructed network and mutation data to define the driver weight between pathways to discover cooperative driver pathways. Experimental results on Breast invasive carcinoma and Stomach adenocarcinoma datasets show that CDPMiner can effectively fuse multi-omics data to discover more driver pathways, which indeed cooperatively trigger cancers and are valuable for carcinogenesis analysis. Ablation study justifies CDPMiner for a more comprehensive analysis of cancer by fusing multi-omics data.
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade
Authors: Rabone M , Horton T , Jones D O B , Simon-Lledó E , Glover A G 
Published: March 2023

Abstract
There is an urgent need for high-quality biodiversity data in the context of rapid environmental change. Nowhere is this need more urgent than in the deep ocean, with the possibility of seabed mining moving from exploration to exploitation, but where vast knowledge gaps persist. Regions of the seabed beyond national jurisdiction, managed by the International Seabed Authority (ISA), are undergoing intensive mining exploration, including the Clarion–Clipperton Zone (CCZ) in the Central Pacific. In 2019, the ISA launched its database ‘DeepData’, publishing environmental (including biological) data. Here, we explore how DeepData could support biological research and environmental policy development in the CCZ (and wider ocean regions) and whether data are findable, accessible, interoperable and reusable (FAIR). Given the direct connection of DeepData with the regulator of a rapidly developing potential industry, this review is particularly timely. We found evidence of extensive duplication of datasets; an absence of unique record identifiers and significant taxonomic data–quality issues, compromising FAIRness of the data. The publication of DeepData records on the OBIS ISA node in 2021 has led to large-scale improvements in data quality and accessibility. However, limitations in the usage of identifiers and issues with taxonomic information were also evident in datasets published on the node, stemming from mismapping of data from the ISA environmental data template to the data standard Darwin Core prior to data harvesting by OBIS. While notable data-quality issues remain, these changes signal a rapid evolution for the database and significant movement towards integrating with global systems, through the usage of data standards and publication on the global data aggregator OBIS. This is exactly what has been needed for biological datasets held by the ISA. We provide recommendations for the future development of the database to support this evolution towards FAIR.
Database URL https://data.isa.org.jm/isa/map
Clinical outcomes in ST-segment elevation myocardial infarction patients undergoing percutaneous coronary interventions later than 48 h after symptom onset
Authors: Rohla Miklos , Temperli Fabrice , Siontis George C M , Klingenberg Roland , Gencer Baris , Rodondi Nicolas , Bär Sarah , Nanchen David , Mach Francois , Häner Jonas D , Pilgrim Thomas , Muller Olivier , Matter Christian M , Lüscher Thomas , Roffi Marco , Heg Dik , Windecker Stephan , Räber Lorenz 
Published: March 2023

Abstract

Aims
Routine revascularization in patients with ST-segment elevation myocardial infarction (STEMI) presenting &gt;48 h after symptom onset is not recommended.

Methods and results
We compared outcomes of STEMI patients undergoing percutaneous coronary intervention (PCI) according to total ischaemic time. Patients included in the Bern-PCI registry and the Multicenter Special Program University Medicine ACS (SPUM-ACS) between 2009 and 2019 were analysed. Based on symptom-to-balloon-time, patients were categorized as early (&lt;12 h), late (12–48 h), or very late presenters (&gt;48 h). Co-primary endpoints were all-cause mortality and target lesion failure (TLF), a composite of cardiac death, target vessel myocardial infarction, and target lesion revascularization at 1 year. Of 6589 STEMI patients undergoing PCI, 73.9% were early, 17.2% late, and 8.9% very late presenters. The mean age was 63.4 years, and 22% were female. At 1 year, all-cause mortality occurred more frequently in late vs. early [5.8 vs. 4.4%, hazard ratio (HR) 1.34, 95% confidence interval (CI) 1.01–1.78, P = 0.04] and very late (6.8%) vs. early presenters (HR 1.59, 95% CI 1.12–2.25, P &lt; 0.01). There was no excess in mortality comparing very late and late presenters (HR 1.18, 95% CI 0.79–1.77, P = 0.42). Target lesion failure was more frequent in late vs. early (8.3 vs. 6.5%, HR 1.29, 95% CI 1.02–1.63, P = 0.04) and very late (9.4%) vs. early presenters (HR 1.47, 95% CI 1.09–1.97, P = 0.01), and similar between very late and late presenters (HR 1.14, 95% CI 0.81–1.60, P = 0.46). Following adjustment, heart failure, impaired renal function, and previous gastrointestinal bleeding, but not treatment delay, were the main drivers of outcomes.

Conclusion
PCI &gt;12 h after symptom onset was associated with less favourable outcomes, but very late vs. late presenters did not have an excess in events. While benefits seem uncertain, (very) late PCI appeared safe.
The association between sodium intake and coronary and carotid atherosclerosis in the general Swedish population
Authors: Wuopio Jonas , Lin Yi-Ting , Orho-Melander Marju , Engström Gunnar , Ärnlöv Johan 
Published: March 2023

Abstract

Aims
A high intake of salt raises blood pressure and the risk of cardiovascular disease. Previous studies have reported on the association between salt intake and carotid stenosis, but the association with coronary atherosclerosis has not been reported. Therefore, this project aimed at studying the association between salt intake and both carotid and coronary atherosclerosis in a contemporary community-based cohort.

Methods and results
Estimated 24-h sodium excretion (est24hNa) was calculated by the Kawasaki formula for participants of two sites (Uppsala and Malmö) of the Swedish Cardiopulmonary bioImage Study, who underwent a coronary computed tomography (n = 9623) and measurement of coronary artery calcium score (CACS, n = 10 289). Carotid ultrasound was used to detect carotid plaques (n = 10 700). Ordered logistic regression was used to calculate odds ratios (OR) per 1000 mg increase in est24hNa. We also investigated potential J-formed associations using quintiles of est24hNa. Increased est24hNa was associated with increased occurrence of carotid plaques [OR: 1.09, P &lt; 0.001, confidence interval (CI): 1.06–1.12], higher CACS (OR: 1.16, P &lt; 0.001, CI: 1.12–1.19), and coronary artery stenosis (OR: 1.17, P &lt; 0.001, CI: 1.13–1.20) in minimal adjusted models. Associations were abolished when adjusting for blood pressure. When adjusting for established cardiovascular risk factors (not including blood pressure), associations remained for carotid plaques but not for coronary atherosclerosis. There was no evidence of J-formed associations.

Conclusion
Higher est24hNa was associated with both coronary and carotid atherosclerosis in minimal adjusted models. The association seemed mainly mediated by blood pressure but to some degree also influenced by other established cardiovascular risk factors.
The frequency and differential pleiotropy of phenotypic nonspecificity in Drosophila melanogaster
Authors: Percival-Smith Anthony , Cheng Sheng , Ouellette Kassie 
Published: March 2023

Abstract
The regulation of the initiation of transcription by transcription factors is often assumed to be dependent on specific recognition of DNA-binding sites and nonredundant. However, the redundant induction or rescue of a phenotype by transcription factors, phenotypic nonspecificity, challenges these assumptions. To assess the frequency of phenotypic nonspecificity in the rescue of transcription factor phenotypes, seven transcription factor phenotypes (labial, Deformed, Sex combs reduced, Ultrabithorax, fruitless, doublesex, and apterous) were screened for rescue by the expression of 12, or more, nonresident transcription factors. From 308 assessments of rescue by nonresident transcription factors, 18 rescues were identified across 6 of the 7 transcription factor phenotypes. Seventeen of the 18 rescues were with transcription factors that recognize distinct DNA-binding sites relative to the resident transcription factors. All rescues were nonuniform across pleiotropic transcription factor phenotypes suggesting extensive differential pleiotropy of the rescue. Primarily using RNAi to knockdown expression, and with the exceptions of the requirement of Bric a Brac 1 for female abdominal pigmentation and Myb oncogene-like for wing development, no evidence was found for a role of the other 16 nonresident transcription factor in the transcription factor phenotypes assessed. Therefore, these 16 rescues are likely due to functional complementation and not due to the expression of an epistatic function in the developmental/behavioral pathway. Phenotypic nonspecificity is both differentially pleiotropic and frequent, as on average 1 in 10–20 nonresident transcription factors rescue a phenotype. These observations will be important in future considerations of transcription factors function.
Inverse problems for a model of biofilm growth
Authors: Brander Tommi , Lesnic Daniel , Cao Kai 
Published: March 2023

AbstractA bacterial biofilm is an aggregate of micro-organisms growing fixed onto a solid surface, rather than floating freely in a liquid. Biofilms play a major role in various practical situations such as surgical infections and water treatment. We consider a non-linear partial differential equation (PDE) model of biofilm growth subject to initial and Dirichlet boundary conditions, and the inverse coefficient problem of recovering the unknown parameters in the model from extra measurements of quantities related to the biofilm and substrate. By addressing and analysing this inverse problem, we provide reliable and robust reconstructions of the primary physical quantities of interest represented by the diffusion coefficients of substrate and biofilm, the biomass spreading parameters, the maximum specific consumption and growth rates, the biofilm decay rate and the half saturation constant. We give particular attention to the constant coefficients involved in the leading-part non-linearity, and present a uniqueness proof and some numerical results. In the course of the numerical investigation, we have identified extra data information that enables improving the reconstruction of the eight-parameter set of physical quantities associated to the model of biofilm growth.
Combination CD200R/PD-1 blockade in a humanised mouse model
Authors: Fellermeyer Martin , Anzilotti Consuelo , Paluch Christopher , Cornall Richard J , Davis Simon J , Gileadi Uzi 
Published: March 2023

Summary
There is an increasing number of immune-checkpoint inhibitors being developed and approved for cancer immunotherapy. Most of the new therapies aim to reactivate tumour-infiltrating T cells, which are responsible for tumour killing. However, in many tumours, the most abundant infiltrating immune cells are macrophages and myeloid cells, which can be tumour-promoting as well as tumouricidal. CD200R was initially identified as a myeloid-restricted, inhibitory immune receptor, but was subsequently also found to be expressed within the lymphoid lineage. Using a mouse model humanised for CD200R and PD-1, we investigated the potential of a combination therapy comprising nivolumab, a clinically approved PD-1 blocking antibody, and OX108, a CD200R antagonist. We produced nivolumab as a murine IgG1 antibody and validated its binding activity in vitro as well as ex vivo. We then tested the combination therapy in the immunogenic colorectal cancer model MC38 as well as the PD-1 blockade-resistant lung cancer model LLC1, which is characterised by a large number of infiltrating myeloid cells, making it an attractive target for CD200R blockade. No significant improvement of overall survival was found in either model, compared to nivolumab mIgG1 monotherapy. There was a trend for more complete responses in the MC38 model, but investigation of the infiltrating immune cells failed to account for this. Importantly, MC38 cells expressed low levels of CD200, whereas LLC1 cells were CD200-negative. Further investigation of CD200R-blocking antibodies in tumours expressing high levels of CD200 could be warranted.
Finite-Dimensional Approximations and Semigroup Coactions for Operator Algebras
Authors: Clouâtre Raphaël , Dor-On Adam 
Published: March 2023

Abstract
The residual finite-dimensionality of a ${\textrm{C}}^{\ast }$-algebra is known to be encoded in a topological property of its space of representations, stating that finite-dimensional representations should be dense therein. We extend this paradigm to general (possibly non-self-adjoint) operator algebras. While numerous subtleties emerge in this greater generality, we exhibit novel tools for constructing finite-dimensional approximations. One such tool is a notion of a residually finite-dimensional coaction of a semigroup on an operator algebra, which allows us to construct finite-dimensional approximations for operator algebras of functions and operator algebras of semigroups. Our investigation is intimately related to the question of when residual finite-dimensionality of an operator algebra is inherited by its maximal ${\textrm{C}}^{\ast }$-cover, which we establish in many cases of interest.
Behavior as a rapid indicator of reintroduction and translocation success for a cryptic mammal, the New England Cottontail (Sylvilagus transitionalis)
Authors: Eline Drew V , Cohen Jonathan B , McGreevy Thomas J , Whipps Christopher M , Cheeseman Amanda E 
Published: March 2023

Abstract
Interactions between animals and their environments are reflected in behavior, which is an indicator of perceived risk and habitat quality. Behavioral studies can therefore provide a rapid assessment of conservation actions. We evaluated the behavior of reintroduced and translocated New England cottontails (Sylvilagus transitionalis)– a species for which the benefits of habitat management, reintroductions, and translocations have been difficult to demonstrate via demographic studies. We first used a random forests model to create a behavioral library for the species using triaxial accelerometers deployed on captive animals that were also monitored with video. We then applied our library to compare time-activity budgets among wild catch-and-release rabbits, wild-caught translocated rabbits, and rabbits introduced into the wild from a captive population. Our library included six behaviors (feeding, grooming, vigilant, movement, resting, and investigating) with an overall classification accuracy of 96.63% and class error rates &lt;14%. For all three groups of rabbits, resting, vigilance, and grooming were the most frequent behaviors; however, captive-bred and translocated rabbits spent significantly more time vigilant and moving than did catch-and-release rabbits. The results raise concern that time spent exploring a new environment may make reintroduced and translocated New England cottontails more vulnerable to predation than local wild rabbits and contribute to low survival rates in reintroduction programs. Our approach shows promise for developing behavioral studies as a rapid indicator of response to conservation efforts for cryptic mammals.
Facilitators and barriers to telepharmacy use among community pharmacists in the Mekong Delta, Vietnam
Authors: De Tran Van , Tran Ba Kien , Huynh Duyen Thi My , Nguyen Thanh Yen , Nguyen Thi My Thao , Pham Thi My Tien , Vo Quang Loc Duyen , Dorofeeva Valeria Valeryevna , Dewey Rebecca Susan , Pham Duy Toan 
Published: March 2023

Abstract

Objectives
Recent years have seen the development and advancement of pharmaceutical care services using telecommunications, termed telepharmacy, in a variety of countries and settings. This study investigated the motivations/facilitators and barriers to pharmacists implementing telepharmacy at pharmacies/drugstores in the Mekong Delta region, Vietnam.

Methods
A descriptive cross-sectional online survey was conducted from March to May 2022, on 747 pharmacists, at pharmacies in all 13 cities/provinces in the Mekong Delta area, Vietnam.

Key findings
Of the 747 respondents, 74% participants had experience of using telepharmacy. Having a university degree in pharmacy (aOR = 1.86; 95% CI = 1.11–3.12; P = 0.018) and a monthly income &gt;8.4 million VND (~357 USD) (aOR = 2.00; 95%CI = 1.16–3.42; P = 0.012) were factors positively associated with telepharmacy use. The factor reported as most greatly motivating telepharmacy use was its ability to provide healthcare services to people in remote/rural areas and those unable to travel (82.3%). The main barrier to telepharmacy use was cited as a lack of policies and regulations on the implementation, application and support of telepharmacy practice (76.8%). More than 75% of those without telepharmacy experience reported that they would like to use it in the future.

Conclusions
Telepharmacy use in Vietnam is familiar with the community pharmacists, although the use of telecommunications in pharmacy was only recently adopted in this country. Vietnamese government bodies and policy-makers must issue detailed regulations and instructions governing telepharmacy practice to support these advancements to the healthcare system in Vietnam.
Temporal analysis of hospital network data by hierarchical Bayesian p2 models with covariates
Authors: Bartolucci Francesco , Li Donni Paolo , Mira Antonietta 
Published: March 2023

AbstractMotivated by an application about interhospital connections, we propose a modelling approach for data referred to a temporal network. The approach may be seen as an extension of the one recently proposed in Bianchi et al. (2020) and, in turn, of the popular p1 and p2 models by Holland and Leinhardt (1981) and van Duijn et al. (2004), on which the latter is built. The proposed extension consists in the introduction of covariates and in the adoption of a hierarchical Bayesian inferential approach that shows advantages in the specific application. For Bayesian inference we rely on a Markov chain Monte Carlo algorithm that produces samples from the posterior distribution of the model parameters. The application is based on original data on patient referral relations among 127 hospitals serving a large regional community of patients in Italy from 2014 to 2018. Results indicate that interhospital collaborative behaviours are primarily local and that collaborative attitudes vary at different time occasions of the considered period and in accordance with the level of competition faced by hospital organisations.
Here We Go Again
Authors: Bowman Jason K. 
Published: March 2023

Abstract
In the United States and globally, the need for subspecialty palliative care is high and increasing. Unfortunately, there aren’t enough palliative clinicians, and even in medical systems fortunate enough to have some, they aren’t always available. Given this reality, it is vitally important for all clinicians to be trained in primary care skills, such as interdisciplinary approaches to communication, symptom management, models of care, relevant ethical and legal issues, and prognostication. Not having these skills leads to clinician distress and burnout, as well as avoidable patient suffering and care that are discordant with patient and family goals. The emergency department presents additional challenges to caring for and talking with patients facing potentially life-limiting illnesses (and their families). Yet visits to an emergency department often represent a critical point in patients’ illness trajectories. Best practices in the care of these patients require that clinicians have the ability to expertly navigate challenging conversations while also managing symptoms and/or stabilizing the patient. Successfully employing primary palliative skills in the care of emergency department patients can help avoid unnecessary physical and emotional suffering, and lead to more compassionate, holistic, and patient-aligned emergency medicine care.
Time Waits for No One
Authors: Zametkin Emily , Ouchi Kei 
Published: March 2023

Abstract
Prognostication in the emergency department is a skill necessary for medical decision-making. Serious, life-limiting diseases (incurable, with less than a 12-month predicted survival) have varying trajectories with distinct long-term survival estimates. Emergency medicine providers are in a unique position to shape the course of hospitalization and must anticipate illness trajectory when planning dispositions. Effectively communicating prognosis empowers patients and their families to make medical decisions that are consistent with their values. Tools to aid providers in both prognostication and communication are readily available. Trajectories for common serious illnesses, resources to support prognostication, and the benefits of transparent communication about survival relevant to the practice of emergency medicine are examined.
From What to How
Authors: Tan Audrey , Stansky Danielle 
Published: March 2023

Abstract
Three models of implementation that are currently described in the literature—developing generalist-level palliative care knowledge for emergency providers; facilitating consultation to a specialist palliative care service; and facilitating consultation to a dedicated palliative care service in the emergency department—are explored in this chapter. Each model is discussed in greater detail along with demonstration programs and outcomes. Palliative care and emergency medicine innovators looking for a framework onto which to develop their own programs and initiatives can adapt and implement models based on their specific resources and emergency department characteristics.