bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

AbstractCoastal 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

AbstractBackgroundThymoma 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.MethodsFour 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.ResultsA 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.ConclusionsThis 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

AbstractBackgroundPatients 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.MethodsTo 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.ResultsWith 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.ConclusionsThe 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

AbstractObjectiveThe objective of this study was to determine the impact of a new salaried medical officer position on health service provision and organisational performance.DesignHealth 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.SettingMedium size rural health service in Victoria, Australia.ParticipantsAll general practitioner, nursing and allied health staff employed by, or who provide services to, the health service.Main outcome measuresSatisfaction with the salaried medical officer position, ability to address patient concerns, themes from interviews, organisational performance data.ResultsForty 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.ConclusionHealth 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

AbstractBackgroundIn the literature, there is not sufficient data on factors affecting the development of complications in patients with penile fracture after early surgical intervention.ObjectivesTo investigate the predictors of long‐term complications in patients who underwent immediate surgical repair for penile fracture.Materials/methodsThis 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.ResultsThe 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 conclusionWe 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

AbstractAimThis 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.MethodsAn 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.ResultsBy 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.ConclusionThe 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

AbstractAimOur 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.MethodsThis 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.ResultsEOS 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.ConclusionUsing 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

AbstractEffects 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.
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

AbstractCervical 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

AbstractIn 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.