bluuebunny/crossref_metadata_2025 huggingface dataset:
bulkAnalyseR: An accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data
Authors: Moutsopoulos Ilias , Williams Eleanor C , Mohorianu Irina I
Published: December 2021

Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.

bulkAnalyseR is available on CRAN and GitHub, with extensive documentation and usage examples (https://github.com/Core-Bioinformatics/bulkAnalyseR, https://cran.r-project.org/web/packages/bulkAnalyseR/)

Contact

Irina Mohorianu iim22@cam.ac.uk
Subject-specific features of excitation/inhibition profiles in neurodegenerative diseases
Authors: Monteverdi Anita , Palesi Fulvia , Costa Alfredo , Vitali Paolo , Pichiecchio Anna , Ramusino Matteo Cotta , Bernini Sara , Jirsa Viktor , Gandini Wheeler-Kingshott Claudia A.M. , D’Angelo Egidio
Published: December 2021

Brain pathologies are based on microscopic changes in neurons and synapses that reverberate into large scale networks altering brain dynamics and functional states. An important yet unresolved issue concerns the impact of patients excitation/inhibition profiles on neurodegenerative diseases including Alzheimer’s disease, Frontotemporal Dementia and Amyotrophic Lateral Sclerosis. In this work we used a simulation platform, The Virtual Brain, to simulate brain dynamics in healthy controls and in Alzheimer’s disease, Frontotemporal Dementia and Amyotrophic Lateral Sclerosis patients. The brain connectome and functional connectivity were extracted from 3T-MRI scans and The Virtual Brain nodes were represented by a Wong-Wang neural mass model endowing an explicit representation of the excitatory/inhibitory balance. The integration of cerebro-cerebellar loops improved the correlation between experimental and simulated functional connectivity, and hence The Virtual Brain predictive power, in all pathological conditions. The Virtual Brain biophysical parameters differed between clinical phenotypes, predicting higher global coupling and inhibition in Alzheimer’s disease and stronger NMDA (N-methyl-D-aspartate) receptor-dependent excitation in Amyotrophic Lateral Sclerosis. These physio-pathological parameters allowed an advanced analysis of patients’ state. In backward regressions, The Virtual Brain parameters significantly contributed to explain the variation of neuropsychological scores and, in discriminant analysis, the combination of The Virtual Brain parameters and neuropsychological scores significantly improved discriminative power between clinical conditions. Eventually, cluster analysis provided a unique description of the excitatory/inhibitory balance in individual patients. In aggregate, The Virtual Brain simulations reveal differences in the excitatory/inhibitory balance of individual patients that, combined with cognitive assessment, can promote the personalized diagnosis and therapy of neurodegenerative diseases.
Synthesis and structure of a new bulky bis(alkoxide) ligand on a terphenyl platform
Authors: Kurup Sudheer S. , Nasser Sandra , Ward Cassandra L. , Groysman Stanislav
Published: December 2021

A new sterically bulky chelating bis(alkoxide) ligand 3,3′-([1,1′:4′,1′′-terphenyl]-2,2′′-diyl)bis(2,2,4,4-tetramethylpentan-3-ol), (H2[OO]tBu), was prepared in a two-step process as the dichloromethane monosolvate, C36H50O2·CH2Cl2. The first step is a Suzuki–Miyaura coupling reaction between 2-bromophenylboronic acid and 1,4-diiodobenzene. The resulting 2,2′′-dibromo-1,1′:4′,1′′-terphenyl was reacted with
t
BuLi and hexamethylacetone to obtain the desired product. The crystal structure of H2[OO]tBu revealed an anti conformation of the [CPh2(OH)] fragments relative to the central phenyl. Furthermore, the hydroxyl groups point away from each other. Likely because of this anti–anti conformation, the attempts to synthesize first-row transition-metal complexes with H2[OO]tBu were not successful.
Debate as a learning activity for teaching programming: a case in the subject of machine learning
Authors: Gunasilan Uma
Published: December 2021

Purpose

Debates are well known to encompass a variety of skills we would like higher education candidates to embody when they graduate.

Design/methodology/approach

Debates in a classroom with computer science as the main subject has been popular in high schools particularly with emerging issues around the area, however it does not have as an extensive similar documented outreach in tertiary education, particularly in the area of hard computer sciences and more recent concentrations of computer science, such as machine learning, artificial intelligence and cloud computing.

Findings

To explore further, the debate dataset had more methodologies applied and was split into training and testing sets, whose results were then compared by a standardized measure: Root Mean Square Error (RMSE) which is currently standard in the industry. The rationale of the approach is to quantify that debate activities have an immensely positive impact towards both the teaching and learning in technical subjects and needs to be more often and robustly used within higher education.

Originality/value

The rationale of the approach is that classroom debate activities equip students with verbal and social learning styles and an opportunity to engage with content in a way that is more comfortable than working with traditional lecture-and-laboratory style learning.
Getting students out there; using community partnerships to engage students
Authors: Cain Liz , Goldring John E. , Scott Jones Julie
Published: December 2021

Purpose

The purpose of the paper is to discuss the “Q-Step in the Community” programme, part of the Q-Step Centre based in the Sociology Department at Manchester Metropolitan University, designed to help address the skills gap in quantitative methods (QM) that is evident across parts of the UK higher-education sector. “Q-Step in the Community” is a data-driven work-based learning programme that works in partnership with local organisations to provide placement opportunities for final year undergraduates and postgraduates. Students conduct a quantitative research project, which is typically identified by the placement provider.

Design/methodology/approach

The authors use quantitative and qualitative feedback from students and placement providers, along with our own reflections on the process to evaluate the placement programme. Data were collected through a focus group and email interviews with placement providers, along with a questionnaire, which was distributed to “Q-Step in the Community” alumni.

Findings

Data-driven work-based learning opportunities allow students to develop and demonstrate their quantitative skills and support networking opportunities whilst also developing valuable soft-skills experience of the workplace that develops their career-readiness. In addition, those opportunities provide valuable research for placement providers, which support their sustainability and enhance their service delivery.

Research limitations/implications

The research focusses solely on one programme at one university offering quantitative data driven work-based learning opportunities at undergraduate and post-graduate level. It is not possible to make valid comparisons between those who do a placement with those who do not.

Originality/value

Views of key stakeholders in the process have been sought for this research, which can be useful to consider for others considering developing similar programmes for their students.
A review and content analysis of U.S. Department of Corrections end-of-life decision making policies
Authors: Helmly Victoria , Garica Marisol , Williams Brie , Howell Benjamin A.
Published: December 2021

Purpose

With a rapidly growing population of older adults with chronic illness in US prisons, the number of people who die while incarcerated is increasing. Support for patients’ medical decision-making is a cornerstone of quality care for people at the end of life (EOL). This study aims to identify, describe, and analyze existing policies regarding EOL decision-making in U.S. Departments of Corrections.

Design/methodology/approach

This study performed an iterative content analysis on all available EOL decision-making policies in US state departments of corrections and the Federal Bureau of Prisons.

Findings

This study collected and reviewed available policies from 37 of 51 prison systems (73%). Some areas of commonality included the importance of establishing health-care proxies and how to transfer EOL decision documents, although policies differed in terms of which patients can complete advance care planning documents, and who can serve as their surrogate decision-makers.

Practical implications

Many prison systems have an opportunity to enhance their patient medical decision-making policies to bring them in line with community standard quality of care. In addition, this study was unable to locate policies regarding patient decision-making at the EOL in one quarter of US prison systems, suggesting there may be quality-of-care challenges around formalized approaches to documenting patient medical wishes in some of those prison systems.

Originality/value

To the best of the authors’ knowledge, this is the first content analysis of EOL decision-making policies in US prison systems.
Low-carbon VRP for cold chain logistics considering real-time traffic conditions in the road network
Authors: Bai Qinyang , Yin Xaioqin , Lim Ming K. , Dong Chenchen
Published: December 2021

Purpose

This paper studies low-carbon vehicle routing problem (VRP) for cold chain logistics with the consideration of the complexity of the road network and the time-varying traffic conditions, and then a low-carbon cold chain logistics routing optimization model was proposed. The purpose of this paper is to minimize the carbon emission and distribution cost, which includes vehicle operation cost, product freshness cost, quality loss cost, penalty cost and transportation cost.

Design/methodology/approach

This study proposed a mathematical optimization model, considering the distribution cost and carbon emission. The improved Nondominated Sorting Genetic Algorithm II algorithm was used to solve the model to obtain the Pareto frontal solution set.

Findings

The result of this study showed that this model can more accurately assess distribution costs and carbon emissions than those do not take real-time traffic conditions in the actual road network into account and provided guidance for cold chain logistics companies to choose a distribution strategy and for the government to develop a carbon tax.

Research limitations/implications

There are some limitations in the proposed model. This study assumes that there are only one distribution and a single type of vehicle.

Originality/value

Existing research on low-carbon VRP for cold chain logistics ignores the complexity of the road network and the time-varying traffic conditions, resulting in nonmeaningful planned distribution routes and furthermore low carbon cannot be discussed. This study takes the complexity of the road network and the time-varying traffic conditions into account, describing the distribution costs and carbon emissions accurately and providing the necessary prerequisites for achieving low carbon.
Information technology investment and innovation performance: does investment paradox exist?
Authors: Ji Peinan , Yan Xiangbin , Shi Yan
Published: December 2021

Purpose

The purpose of this study is to deepen the understanding of the effects of information technology (IT) investment on firm innovation performance and examining the investment paradox effect in China.

Design/methodology/approach

Using a sample of China’ public firms IT investment data between 2010 and 2016, the authors establish a test model of IT investment and innovation performance.

Findings

The result indicates that IT investment in firms have no effect on innovation performance in the investment period. However, in the full sample and manufacturing sample, the IT investment has a significant positive effect on innovation performance in the post-investment years. In addition, this study finds that large companies and low-age companies may contribute more to innovation when firm investment in IT.

Research limitations/implications

There are several limitations in this research. First, the authors are failed to obtain a larger sample about the IT investment information data set in China, so this study was compelled to use limited sample data from China, hence, this could lead to errors of too early generalization. Second, the authors use the number of invention patent applications to represent the performance of enterprise innovation, which may not show enterprise innovation effectively. Third, the firms in the sample are all in China Listed Companies, so this may not accurately reflect the entire environment of firm innovation performance, and could possibly.

Practical implications

The research confirms that there is a paradox and time lag effect in IT investment, which enterprises should pay attention to.

Originality/value

Existing research confirms that corporate IT investments can bring new products or services. However, the authors still do not know whether IT investment has improved the company’s ability of innovation. This study will fill this gap and the industry effect and time lag effect of the influence of IT investment on innovative performance are also examined.
Assessing international students' satisfaction of a Jordanian university using the service quality model
Authors: Abu-Rumman Ayman , Qawasmeh Rasha
Published: December 2021

Purpose

Education plays a key role in socio-economic development and globalization has increased the numbers of students wanting to study abroad. Attracting international students is therefore an important objective for universities as international students open up opportunities to bring economic, cultural and academic benefits to both the universities themselves and to the countries in which they are located. This study therefore aimed to assess student satisfaction with a Jordanian university using the dimensions of quality contained within the established SERVQUAL model.

Design/methodology/approach

To achieve these goals, quantitative data was collected from international students attending one university located in Jordan via a questionnaire survey, using a randomized sample. Structural equation modeling (SEM) was used to analyze the construct validity, and correlations between student satisfaction and the different dimensions of quality were tested.

Findings

Consistent with other studies, the findings demonstrated that the five dimensions of service quality, i.e. tangibility, reliability, responsiveness, assurance and empathy, and the university of study, have a strong relationship with student satisfaction. However, there was no statistically significant correlation between country satisfaction and the tangibility and assurance sub-dimensions of quality.

Practical implications

Practical implications – The findings of this study are of interest and practical benefit to university leaders in developing their quality and student acquisition strategies.

Originality/value

This study makes a useful contribution to the growing body of evidence of service quality in higher education set within the context of a developing country.
Through the looking glass: perceiving risk and emotions toward cosmetic procedure engagement
Authors: Sood Abhinav , Quintal Vanessa Ann , Phau Ian
Published: December 2021

Purpose

This research aims to develop a user risk segmentation typology and implement a method that traces how user emotions adapt before, after and toward a next cosmetic procedure. It introduces the user risk segments to an empirical framework to explain re-engagement with the procedure.

Design/methodology/approach

A survey was self-administered to online consumer panels in the USA. The survey targeted users who had previously undertaken one of three elective procedures, namely, Botox (N = 550), hair transplant (N = 350) or liposuction (N = 350).

Findings

The typology identified timid image seekers, daring image crafters, approval-seeking socialites and mainstream image adopters. The method tracking user emotions found significant differences before, after and toward a next cosmetic procedure in the user risk segments. The framework predicted user re-engagement with the procedure for each segment.

Research limitations/implications

The typology presents more sophisticated user risk profiles. The method maps adapting user emotions toward engagement pre- and post-procedure. However, findings are limited to the USA and three cosmetic procedures.

Practical implications

The typology offers a profile of users and their risk perceptions of a behavior. The method presents an instrument that follows how user emotions adapt. The framework advances understanding of user re-engagement with the behavior.

Originality/value

Arguably, to the best of the authors’ knowledge, this is the first research to explore how perceived risk operates on emotional states and adaptation, which manifest user well-being and impact user behavior.
Value co-creation in services for animal companions
Authors: Hendricks Jennifer , Schmitz Gertrud
Published: December 2021

Purpose

As other actors in the service ecosystem often have a pivotal role in value creation for actors experiencing vulnerability, this paper aims to explore caregiving customer value co-creation in services for animal companions.

Design/methodology/approach

Study 1 follows a two-step procedure, using two different qualitative approaches (interviews and observations) to identify caregiving customer value co-creation activities. Study 2 serves to empirically test a higher-order structure of caregiving customer participation behaviour in value co-creation and test for differences regarding customer and service characteristics (questionnaire survey;n= 680).

Findings

The results reveal the existence of various value co-creation activities towards the service provider (e.g. cooperation under consideration of the animal companion’s needs) and animal companion (e.g. emotional support). Significant differences in individual caregiving customers’ activities were found regarding gender, age, type of service and animal companion. Caregiving customer value co-creation is influenced by emotional attachment and has a positive effect on value outcomes for both the caregiving customer and the animal companion.

Originality/value

This study extends and enriches customer value co-creation literature by providing innovative findings on various such caregiving activities and value outcomes in services for (non-human) actors experiencing vulnerability. It also adds knowledge by showing differences in customer value co-creation behaviour regarding specific customer and service characteristics.
Systematic and ontology-based approach to interoperable cross-domain open government data services
Authors: Masoumi Hadi , Farahani Bahar , Shams Aliee Fereidoon
Published: December 2021

Purpose

Open government data (OGD) has emerged as a radical paradigm shift and endeavor among government administrations across the world mainly due to its promises of transparency, accountability, public-private collaboration, civic participation, social innovation and data-driven value creation. Complexity, cross-cutting nature, diversity of data sets, interoperability and quality issues usually hamper unlocking the full potential value of data. To tackle these challenges, this paper aims to provide a novel solution using a top-down approach.

Design/methodology/approach

In this paper, the authors propose a systematic ontology-based approach combined with a novel architecture and its corresponding processes enabling organizations to carry out all the steps in the OGD value chain. In addition, an OGD Platform including a portal (www.iranopendata.ir) and a data management system (www.ogdms.iranopendata.ir) are developed to showcase the proposed solution.

Findings

The efficiency and the applicability of the solution are evaluated by a real-life use case on energy consumption of the buildings of the city of Tehran, Iran. Finally, a comparison was made with existing solutions, and the results show the proposed approach is able to address the existing gaps in the literature.

Originality/value

The results imply that modeling and designing the data model, as well as exploiting an ontology-based approach are critical pillars to create rich, relevant and well-described OGD data sets. Moreover, clarity on processes, roles and responsibilities are the key factors influencing the quality of the published data services. Thus, to the best of the knowledge, this is the first study that exploits and considers an ontology-based approach in a top-down manner to create OGD data sets.
Spatial variation in the biotic and abiotic filters of oyster recruitment: Implications for restoration
Authors: Esquivel‐Muelbert Juan R. , Lanham Brendan S. , Martínez‐Baena Francisco , Dafforn Katherine A. , Gribben Paul E. , Bishop Melanie J.
Published: December 2021

Attempts to restore marine ecosystems are increasing, but the success of projects remains variable. For marine invertebrates, the establishment of self‐sustaining populations requires a larval supply as well as conditions that permit recruitment.

Abiotic and biotic conditions that determine recruitment can vary across environmental gradients and have opposing or reinforcing effects. We assessed how predation and tidal inundation influence recruitment of the reef‐forming oyster, Saccostrea glomerata, at 15 sites, 5 estuaries and 8 degrees of latitude in eastern Australia.

Oysters recruited to all 15 sites, but their density displayed spatially variable effects of tidal inundation and caging. Effects of tidal inundation and caging were weakest at the two lower‐latitude estuaries where recruitment was low overall, average temperature and turbidity were high and dissolved oxygen low.

At higher‐latitude estuaries, where abiotic conditions were more favourable for recruitment, recruit density displayed tidal elevation gradients that were dependent on caging and time. Initially, recruit density decreased with tidal inundation (and exposure to finfish predators), in the uncaged but not the caged treatment. However, over time the elevation gradient disappeared, and recruitment and survival of oysters was greater in caged than uncaged treatments irrespective of elevation.

Synthesis and applications. Our results suggest that both abiotic (i.e. temperature, turbidity and dissolved oxygen) and biotic (i.e. predation) factors can negatively influence oyster recruitment and, hence, restoration success. Consequently, oyster reef restoration projects should be planned to prioritise sites with low turbidity, high dissolved oxygen and low predation unless these stressors can be mitigated. Restoration projects that are designed with knowledge of local stressors are more likely to be successful.
Insights into genetic variation and demographic history of sharpnose rays: examinations of three species of Telatrygon (Elasmobranchii, Dasyatidae) from the Indo‐West Pacific
Authors: QI Jiwei , SHI Fanglei , ZHANG Baowei , CHEN Xiao , XING Jie , FURUMITSU Keisuke , CORUSH Joel B. , YAMAGUCHI Atsuko , ZHANG Jie
Published: December 2021

Coastal and demersal chondrichthyans (sharks, rays, and skates) are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology. Population genetic studies investigating the extent to which demographic history shapes the genetic structure of these fishes are rare. Here, we combined mitochondrial DNA (Cytb and ND2) and 8 nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the 3 Indo‐West Pacific species of sharpnose rays (Telatrygon zugei, Telatrygon biasa, and Trygon crozieri). High levels of genetic variation both within and between species were identified. Phylogenetic analysis partitioned haplotypes into 2 lineages supporting divergence of T. zugei from T. crozieri and T. biasa during the Pleistocene. Furthermore, microsatellite‐based clustering analyses identified 4 genetic groups (i.e. T. zugei from Japan, T. zugei from coastal China, T. biasa from Gulf of Thailand, and T. crozieri from the Andaman Sea). Measurements of genetic differentiation also support these 4 groups. Additionally, Pleistocene demographic expansions were examined in all genetic groups. The climate oscillations and current hydrologic cycles in the Indo‐West Pacific appear to coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays. Considering the species group has, until recently, been thought to be one species, these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity.
Does size affect the prognosis of resectable thymoma beyond the eighth edition TNM?
Authors: Tseng Yen‐Chiang , Hsu Han‐Shui , Lin Yi‐Hsuan , Tseng Yen‐Han , Shu Chih‐Wen , Goan Yih‐Gang , Tseng Ching‐Jiunn
Published: December 2021

Background

Thymoma is a type of rare mediastinal tumor whose clinical characteristics and indicators of prognosis are poorly understood. This single‐institution retrospective study aimed to assess the predictive value of tumor, node, metastasis (TNM) staging incorporating tumor size in predicting the risk of thymoma recurrence after resection.

Methods

Four binary logistic regression models were developed. Models I and II included median tumor size and TNM stage, respectively. Model III included the above two variables. Model IV was model III containing these two variables and their interaction terms. All models were adjusted for WHO histological type, operational time, and adjuvant therapy.

Results

A total of 276 patients with a median age of 51.0, including 21 patients with thymoma recurrence, were included in this study. Models II or III showed a lower ‐2LogL and higher AUC (0.735 and 0.738 vs. 0.576) with significantly better discrimination than model I, and model III and model II shared similar discrimination. In model III, TNM stage was positively correlated with thymoma recurrence. The recurrence risk of patients with TNM stage IV was significantly higher than those with TNM stage I (OR of 11.03, p = 0.022). No significant correlation between the tumor size and recurrence risk (p = 0.779) and no interaction was found between medium tumor size and TNM stage in model IV.

Conclusions

This study suggests that the prediction contribution of the TNM stage combined with tumor size is similar to the TNM stage alone for tumor recurrence in patients with thymoma after surgical resection.
Host immune‐inflammatory markers to unravel the heterogeneous outcome and assessment of patients with PD‐L1 ≥50% metastatic non‐small cell lung cancer and poor performance status receiving first‐line immunotherapy
Authors: Banna Giuseppe L. , Tiseo Marcello , Cortinovis Diego L. , Facchinetti Francesco , Aerts Joachim G. J. V. , Baldessari Cinzia , Giusti Raffaele , Bria Emilio , Grossi Francesco , Berardi Rossana , Morabito Alessandro , Catino Annamaria , Genova Carlo , Mazzoni Francesca , Gelibter Alain , Rastelli Francesca , Macerelli Marianna , Chiari Rita , Gori Stefania , Mansueto Giovanni , Citarella Fabrizio , Cantini Luca , Rijavec Erika , Bertolini Federica , Cappuzzo Federico , De Toma Alessandro , Friedlaender Alex , Metro Giulio , Pensieri Maria Vittoria , Porzio Giampiero , Ficorella Corrado , Pinato David J. , Cortellini Alessio , Addeo Alfredo
Published: December 2021

Background

Patients with programmed cell death‐ligand 1 (PD‐L1) ≥50% metastatic non‐small cell lung cancer (mNSCLC) and ECOG performance status (PS) of 2 treated with first‐line immunotherapy have heterogeneous clinical assessment and outcomes.

Methods

To explore the role of immune‐inflammatory surrogates by the validated lung immuno‐oncology prognostic score (LIPS) score, including the neutrophil‐to‐lymphocyte ratio (NLR) and the pretreatment use of steroids, alongside other prognostic variables. A retrospective analysis of 128 patients with PS2 and PD‐L1 ≥50% mNSCLC treated between April 2018 and September 2019 with first‐line pembrolizumab in a real‐world setting was performed.

Results

With a median follow‐up of 15.3 months, the 1‐year overall survival (OS) and median progression‐free survival (PFS) were 32.3% (95% CI: 30.9–33.9) and 3.3 months (95% CI: 1.8–4.7), respectively. The NLR, lactate dehydrogenase (LDH) and pretreatment steroids results were the only significant prognostic factors on the univariate analysis and independent prognostic factors by the multivariate analysis on both OS and PFS. The LIPS score, including the NLR and pretreatment steroids, identified 29 (23%) favourable‐risk patients, with 0 factors, 1‐year OS of 67.6% and median PFS of 8.2 months; 57 (45%) intermediate‐risk patients, with 1 factor, 1‐year OS 32.1% and median PFS 2.7 months; 42 (33%) poor‐risk patients, with both factors, 1‐year OS of 10.7% and median PFS of 1.2 months.

Conclusions

The assessment of pre‐existing imbalance of the host immune response by combined blood and clinical immune‐inflammatory markers may represent a way to unravel the heterogeneous outcome and assessment of patients with mNSCLC and poor PS in the immune‐oncology setting.
Evaluation of a novel salaried medical officer position on service provision and performance at a rural health service: An exploratory mixed‐methods study
Authors: Bishop Jaclyn L. , Ping Sophie
Published: December 2021

Objective

The objective of this study was to determine the impact of a new salaried medical officer position on health service provision and organisational performance.

Design

Health service staff were invited to complete a survey to ascertain their overall satisfaction with the salaried medical officer position and impact on their workflow. Purposive sampling identified respondents for interviews to further explore the experiences of health service staff. Financial, administrative and quality information was extracted for analysis.

Setting

Medium size rural health service in Victoria, Australia.

Participants

All general practitioner, nursing and allied health staff employed by, or who provide services to, the health service.

Main outcome measures

Satisfaction with the salaried medical officer position, ability to address patient concerns, themes from interviews, organisational performance data.

Results

Forty surveys (general practitioner, nursing and allied health) were returned and 10 interviews completed. The mean rating for satisfaction with the salaried medical officer position was 8.4 out of 10. Addressing patient care concerns was rated significantly easier by nursing and allied health staff when the salaried medical officer was working. The interviews identified three broad themes: improved efficiency, increased accessibility and eliminated service gaps.

Conclusion

Health service staff reported that a salaried medical officer position at a rural health service improved work efficiency, increased accessibility to timely medical advice and improved quality of care, particularly patients at risk of sudden deterioration.
Penile fracture: Tertiary care center experience and long‐term complications after immediate repair
Authors: Bulbul Emre , Gultekin Mehmet Hamza , Citgez Sinharib , Derekoylu Engin , Demirbilek Muhammet , Akkus Emre , Ozkara Hamdi
Published: December 2021

Background

In the literature, there is not sufficient data on factors affecting the development of complications in patients with penile fracture after early surgical intervention.

Objectives

To investigate the predictors of long‐term complications in patients who underwent immediate surgical repair for penile fracture.

Materials/methods

This clinical study included a total of 31 cases of penile fracture in which surgical treatment was performed within the first 24 h and penile fracture was confirmed during the operation. The patients with and without late complications were compared in terms of parameters such as age, tear size of the tunica albuginea of the penis, bilateral involvement of the corpora cavernosa involvement, urethral injuries, and duration from penile fracture to surgery.

Results

The median age of the patients was 42 years (interquartile range: 34–51 years). The median time from penile fracture to surgery was 13 h (8–18 h). The median tear size was 16 mm (11–21 mm). Late complications were seen in 13 (41.9%) patients in the post‐operative period. Erectile dysfunction developed in five (16.1%) patients in the post‐operative period. There was no statistically significant relationship between age, tear size, time from penile fracture to surgery, and bilateral corporeal involvement in terms of erectile dysfunction development. Painful erections, penile deviations, urethral strictures, tunical scars, and re‐fracture were the other late complications. There was a significant relationship between the development of any complication and time from penile fracture to surgery (p = 0.028) and tear size (p = 0.031). In the receiver operating characteristic analysis of complication development, the cut‐off value for the time from penile fracture to surgery was 13.5 h.

Discussion and conclusion

We found that the longer time interval between penile fracture and surgery worsened the patient outcomes. In addition, tear size was determined to be a predictor for long‐term complications. In our opinion, early treatment of penile fracture can prevent severe complications in these cases.
How compassionate use enabled Israel to deliver the Pfizer‐BioNTech COVID‐19 vaccination to vulnerable children aged 12–15 years before regulatory approval
Authors: Stein Michal , Grossman Zachi , Brosh‐Nissimov Tal , Gottesman Bat‐Sheva , Shahar Arnon , Wechsler Efrat , Matz Eran , Cohen Orna , Alroy‐Preis Sharon , Anis Emilia ,   the Israeli Pediatric Association Task Force
Published: December 2021

Aim

This paper describes the emergency, compassionate use of the COVID‐19 vaccination for high‐risk adolescents aged 12–15 years prior to approval by the American Food and Drugs Administration in May 2021. The target audience had underlying health conditions associated with severe disease and multisystem inflammatory syndrome in children (MIS‐C) or severely immunosuppressed household members.

Methods

An orderly approval system was established in Israel for adolescents aged 12–15 years, based on a professional position paper and compassionate treatment regulations. From 12 February 2021, eligible adolescents were referred to the Israeli Ministry of Health for permission to vaccinate, via four health maintenance organisations. Data were collected about adverse events after vaccinations and the incidence of any cases of COVID‐19.

Results

By 15 March 2021, the vaccine had been approved for 607 adolescents: 333 had received one dose, and 92 had received two doses. The median age was 14.6 years, and the major indication was obesity. Only one child tested positive for the virus, 4 days after vaccination, and no adverse effects were recorded.

Conclusion

The emergency use of COVID‐19 vaccination for 333 adolescents aged 12–15, 92 of them with 2 doses, based on a position paper and compassionate treatment regulations, did not result in any adverse effects. Since 27 July 2021, the same process was further applied in Israel among younger children, aged 5–11, preceding formal release of the clinical trial.
Centers for disease control and prevention guidelines identified more neonates at risk of early‐onset sepsis than the Kaiser‐Permanente calculator
Authors: Hershkovich–Shporen Calanit , Guri Alex , Gluskina Tatiana , Flidel‐Rimon Orna
Published: December 2021

Aim

Our aim was to retrospectively compare how many cases of early‐onset sepsis (EOS) would have been predicted by the the Kaiser‐Permanente (KP) calculator and the United States Centers for Disease Control and Prevention (CDC) guidelines.

Methods

This observational retrospective cohort study comprised 50 newborn infants with documented EOS who were born at the Kaplan Medical Centre, Israel, between 2001 and 2018. We retrospectively evaluated whether the KP calculator and the CDC recommendations would have recommended antibiotic treatment if they had been implemented within four hours of birth.

Results

EOS was diagnosed in 50 of the 109 877 infants born from 34 weeks of gestation. By four hours of birth, 18 were symptomatic, five had an equivocal clinical status, and 27 were asymptomatic. The KP calculator would have recommended antibiotic treatment for 19 (38%) neonates: 18 who were symptomatic and one who was initially asymptomatic. The CDC guidelines would have recommended antibiotic treatment for 27 (54%) nenonates: those 19 plus all 5 with equivocal status and other 3 who were asymptomatic.

Conclusion

Using the CDC guidelines would have identified more equivocal and asymptomatic EOS cases within four hours of birth than the KP calculator. Enhanced observation is recommended when using the KP calculator.
Effects of body condition at far‐off dry period on blood biochemistry, liver triacylglycerol and muscular monocarboxylate transporter‐1 mRNA expression in tropical Holstein dairy cows during peripartum period
Authors: Triwutanon Supawit , Rukkwamsuk Theera
Published: December 2021

Effects of body condition score (BCS) at far‐off dry period on blood biochemistry, liver triacylglycerol, and muscular monocarboxylate transporter‐1 mRNA expression in tropical Holstein dairy cows during peripartum period were studied. Eight dry cows were divided into two groups of four cows based on their BCS at 8 weeks prepartum: high BCS (HBS) and low BCS (LBS). Blood samples were collected weekly from 8 weeks before expected calving date until 8 weeks postpartum for determination of serum glucose, non‐esterified fatty acid (NEFA), and β‐hydroxybutyrate (BHBA). Muscle and liver samples were biopsied at 2 weeks before expected calving date and at 2 weeks postpartum for determination of muscular monocarboxylate transporter‐1 (MCT‐1) mRNA expression and liver triacylglycerol concentrations. Decreased BCS and elevated serum NEFA and BHBA indicated that LBS cows entered to the NEB period earlier than did HBS cows. LBS cows showed lower liver TAG and higher muscular MCT‐1 mRNA expression than did HBS cows. The MCT‐1 mRNA expression at 2 weeks prepartum was negatively correlated with BCSs at 2–3 weeks prepartum and at 1–2 weeks postpartum. In conclusion, LBS cows most likely adapted to NEB by upregulation of muscular MCT‐1 expression and had lower NEB consequences during postpartum period.
On Meditation and the Development of the Internal Analytic Setting
Authors: Ross Alexander
Published: December 2021

This paper proposes meditation as an adjunct to psychoanalytic training by adapting meditation techniques to support the development of specific internal analytic settings to fulfil established training requirements (Hinze, 2015). Previous research has suggested how established meditation techniques engender some similar states of mind to those in various psychoanalytic theories (Cooper, 1999, 2014; Epstein, 1984; Hoffer, 2020; Pelled, 2007; Rubin, 2009). Building on this work, the author develops a novel framework to describe meditation using early Buddhist principles as a foundation (Thanissaro, 2012). This framework defines how different types of concentration and discernment can be developed by using mindfulness, alertness and ardency through meditation. As far as the author is aware, this is the first time these links have been explicitly made. This is followed by the analysis of the mental qualities required for evenly suspended attention, and the development and use of a greater awareness of countertransference, chosen as they point towards the analyst's functions of external listening and internal listening respectively (Parsons, 2007). Two meditation techniques are then described within the framework, to support development of these two internal analytic settings. A clinical example shows how these techniques can be utilized in the consultation room.
Development of an in vitro carcinogenesis model of human papillomavirus‐induced cervical adenocarcinoma
Authors: Zhang Mengzhu , Kiyono Tohru , Aoki Kazunori , Goshima Naoki , Kobayashi Shin , Hiranuma Kengo , Shiraishi Kouya , Saya Hideyuki , Nakahara Tomomi
Published: December 2021

Cervical adenocarcinoma (ADC) is the second most common pathological subtype of cervical cancer after squamous cell carcinoma. It accounts for approximately 20% of cervical cancers, and the incidence has increased in the past few decades, particularly among young patients. The persistent infection of high‐risk human papillomavirus (HPV) is responsible for most cervical ADC. However, almost all available in vitro models are designed to study the carcinogenesis of cervical squamous cell carcinoma. To gain better insights into molecular background of ADC, we aimed to establish an in vitro carcinogenesis model of ADC. We previously reported the establishment of an in vitro model for cervical squamous cell carcinoma by introducing defined viral and cellular oncogenes, HPV16 E6 and E7, c‐MYC, and activated RAS to human cervical keratinocytes. In this study, the expression of potential lineage‐specifying factors and/or SMAD4 reduction was introduced in addition to the defined four oncogenes to direct carcinogenesis toward ADC. The cell properties associated with the cell lineage were analyzed in monolayer and organoid cultures and the tumors in mouse xenografts. In the cells expressing Forkhead box A2 (FOXA2), apparent changes in cell properties were observed, such as elevated expression of columnar cell markers and decreased expression of squamous cell markers. Strikingly, the histopathology of tumors expressing FOXA2 resembled cervical ADC, proposing that FOXA2 plays a vital role in dictating the histopathology of cervical cancers.
An empirical test of the relationship between the bootstrap and likelihood ratio support in maximum likelihood phylogenetic analysis
Authors: Jacob Machado Denis , Portella de Luna Marques Fernando , Jiménez‐Ferbans Larry , Grant Taran
Published: December 2021

In maximum likelihood (ML), the support for a clade can be calculated directly as the likelihood ratio (LR) or log‐likelihood difference (S, LLD) of the best trees with and without the clade of interest. However, bootstrap (BS) clade frequencies are more pervasive in ML phylogenetics and are almost universally interpreted as measuring support. In addition to theoretical arguments against that interpretation, BS has several undesirable attributes for a support measure. For example, it does not vary in proportion to optimality or identify clades that are rejected by the evidence and can be overestimated due to missing data. Nevertheless, if BS is a reliable predictor of S, then it might be an efficient indirect method of measuring support—an attractive possibility, given the speed of many BS implementations. To assess the relationship between S and BS, we analyzed 106 empirical datasets retrieved from TreeBASE. Also, to evaluate the degree to which S and BS are affected by the number of replicates during suboptimal tree searches for S and pseudoreplicates during BS estimation, we randomly selected 5 of the 106 datasets and analyzed them using variable numbers of replicates and pseudoreplicates, respectively. The correlation between S and BS was extremely weak in the datasets we analyzed. Increasing the number of replicates during tree search decreased the estimated values of S for most clades, but the magnitude of change was small. In contrast, although increasing pseudoreplicates affected BS values for only approximately 40% of clades, values both increased and decreased, and they did so at much greater magnitudes. Increasing replicates/pseudoreplicates affected the rank order of clades in each tree for both S and BS. Our findings show decisively that BS is not an efficient indirect method of measuring support and suggest that even quite superficial searches to calculate S provide better estimates of support.
Justice and Doxastic Handicaps
Authors: Fabre Cécile
Published: December 2021

It is tempting to suppose that the reason why the world remains profoundly unjust is that not enough of us hold the correct beliefs about the demands of justice and/or are motivated to bring it about. As Allen Buchanan shows, however, this is to miss a crucially important part of the picture: agents' mistaken beliefs about what it takes to achieve justice can seriously hamper prospects for such achievements. In this article, I expand on Buchanan's taxonomy of mistaken beliefs about what it takes to achieve justice, and I bring his account (so expanded) to bear on the notion of epistemic justice.
Of three sharks and one chimaera: varied habitat preferences across a latitudinal range revealed by coastal and offshore surveys
Authors: Jac Romaric , Höffle Hannes , Albretsen Jon , Jakobsdóttir Klara , Staby Arved , Søvik Guldborg , Junge Claudia
Published: December 2021

Using national and international research survey data and applying a combination of models and mapping tools, this study revealed temperature and depth as the crucial environmental drivers of both the distribution and the abundance of four benthopelagic chondrichthyans inhabiting Norwegian and Icelandic waters: rabbitfish (Chimaera monstrosa), velvet‐belly lanternshark (Etmopterus spinax), blackmouth catshark (Galeus melastomus) and spurdog (Squalus acanthias). C. monstrosa and E. spinax seem to prefer similar spatial and ecological habitats, that is deep and cold waters. In contrast, G. melastomus and S. acanthias both prefer similar ecological habitats, that is warmer and shallower waters; nonetheless, they exhibit a different spatial distribution pattern. The species' varied habitat and spatial preferences may lead to different levels of exposure to fishing activities and associated by‐catch risks. Findings of the species' spatial distributions and their driving forces are expected to inform the sustainable management of these species and the ecosystems they inhabit.
Now you see me: “first” records of the greater amberjack Seriola dumerili at Rapa Nui range extension or increased scientific effort?
Authors: Morales Naití A. , Coghlan Amy Rose , Easton Erin E. , Friedlander Alan M. , Herlan James , Gaymer Carlos F.
Published: December 2021

We report new records of the fisheries‐harvested subtropical greater amberjack Seriola dumerili for the south‐east Pacific Ocean. Despite local fishers' asserting that three Seriola morphotypes exist in the region, only one species (the yellowtail amberjack Seriola lalandi) was previously scientifically recorded for Rapa Nui (also known as Easter Island). Whilst we present the first “scientific record”, S. dumerili, traditional ecological knowledge suggests that this is likely a pre‐existing (albeit transient) species of the Rapa Nui ecoregion. Establishing the existing/historic distributional limits of commercially and ecologically valuable species is key for observing climate‐driven distribution shifts, and the inclusion of traditional ecological knowledge is particularly important in areas with relatively lower scientific effort.