bluuebunny/crossref_metadata_2025_split huggingface dataset:
Individual‐based simulations of genome evolution with ancestry: The GenomeAdmixR R package
Authors: Janzen Thijs , Diaz Fernando 
Published: April 2021

Abstract

Hybridization between populations or species results in a mosaic of the two parental genomes. This and other types of genome admixture have received increasing attention for their implications in speciation, human evolution, Evolve and Resequence (E&R) and genetic mapping. However, a thorough understanding of how local ancestry changes after admixture and how selection affects patterns of local ancestry remains elusive. The complexity of these questions limits analytical treatment, but these scenarios are specifically suitable for simulation.

Here, we present the R package GenomeAdmixR, which uses an individual‐based model to simulate genomic patterns following admixture forward in time. GenomeAdmixR provides user‐friendly functions to set up and analyse simulations under evolutionary scenarios with selection, linkage and migration.

We show the flexible functionality of the GenomeAdmixR workflow by demonstrating (a) how to design an E&R simulation using GenomeAdmixR and (b) how to use GenomeAdmixR to verify analytical expectations following from the theory of junctions.

GenomeAdmixR provides a mechanistic approach to explore expected genome responses to realistic admixture scenarios. With this package, we aim to aid researchers in testing specific hypotheses based on empirical findings involving admixing populations.
Iron deficiency anaemia and early childhood caries: a cross‐sectional study
Authors: Mohamed WE , Abou El Fadl RK , Thabet RA , Helmi M , Kamal SH 
Published: April 2021

AbstractBackgroundThis study aimed to assess the association between iron deficiency anaemia (IDA) and dental caries in early childhood.MethodsA total of 40 children with proven IDA and another 40 healthy age and sex‐matched children were enrolled in this cross‐sectional study. Legal guardians were interviewed to collect data on oral hygiene measures and dietary habits. Anthropometric measurements were performed for all participants, and blood samples were collected to assess complete blood count and body iron status. Patients were confirmed to have IDA based on haemoglobin level (Hb), red blood cells indices and body iron status. Caries experience was determined based on the number of decayed, missing and filled primary teeth using dmft index.ResultsA statistically significant negative correlation between dmft index scores and haemoglobin level (r = −0.454, P < 0.001) and mean corpuscular haemoglobin (MCH) level (r = −0.380, P = 0.001) was detected, and in accordance there was a positive statistically significant correlation between caries experience and the presence of anaemia (r = −0.60, P < 0.001).ConclusionIn early childhood, dental caries might coexist with IDA even in its mildest form. All children exhibiting severe early childhood caries should be investigated for IDA and anaemia should be managed if present.
Elective node dissection versus observation for management of patients with early‐stage cT1/T2N0 tongue carcinoma: A systematic review and meta‐analysis of prospective studies
Authors: Alsini Albaraa Y. , Alsubaie Hemail M. , Marzouki Hani Z. , Abu‐Zaid Ahmed , Al‐Qahtani Khalid 
Published: April 2021

AbstractObjectiveTo carry out a meta‐analysis of prospective literature comparing the clinical efficacy of elective neck dissection (END) vs observation (OBS) in patients with early‐stage cT1/T2N0 tongue carcinoma.Design/Setting/Participants/Outcome MeasuresWe systematically reviewed four databases from inception to 30‐October‐2020. We considered all studies meeting the following PICOS conditions: (a) Patients: early‐stage cT1/T2N0 tongue carcinoma, (b) Intervention: END, (c) Comparator: OBS, (d) Outcomes: local tongue recurrence, cervical nodal recurrence, disease‐specific survival (DSS) rate, and disease‐free survival (DFS) rate and (e) Study design: prospective reports. We pooled dichotomous data as relative risks (RRs) with 95% confidence intervals (CIs).ResultsFour studies (one case‐control study and three randomised controlled trials) met our inclusion criteria. There were 448 eligible patients (225 and 223 patients were treated with END and OBS, respectively). END significantly correlated with improved DSS rate (RR = 1.15, 95% CI: 1.04‐1.27, P = .007). Nonetheless, there were no significant differences between END and OBS groups regarding the rates of local tongue recurrence (RR = 1.23, 95% CI: 0.50‐3.03, P = .65), cervical nodal recurrence (RR = 0.45, 95% CI: 0.16‐1.27, P = .13) and DFS rate (RR = 1.08, 95% CI: 0.91‐1.27, P = .38). Pooled analysis for cervical nodal recurrence was heterogeneous, and sensitivity analysis revealed a significantly lower cervical nodal recurrence rate in favour of END group (RR = 0.30, 95% CI: 0.13‐0.67, P = .004).ConclusionEND correlated with a significant decrease in cervical nodal recurrence and improved DSS rate. END might be superior to OBS in patients with early‐stage cT1/T2N0 tongue cancer.
Hippocampal glucocorticoid target genes associated with enhancement of memory consolidation
Authors: Buurstede Jacobus C. , van Weert Lisa T.C.M. , Colucci Paola , Gentenaar Max , Viho Eva M.G. , Koorneef Lisa L. , Schoonderwoerd Robin A. , Lanooij Suzanne D. , Moustakas Ioannis , Balog Judit , Mei Hailiang , Kielbasa Szymon M. , Campolongo Patrizia , Roozendaal Benno , Meijer Onno C. 
Published: April 2021

AbstractGlucocorticoids enhance memory consolidation of emotionally arousing events via largely unknown molecular mechanisms. This glucocorticoid effect on the consolidation process also requires central noradrenergic neurotransmission. The intracellular pathways of these two stress mediators converge on two transcription factors: the glucocorticoid receptor (GR) and phosphorylated cAMP response element‐binding protein (pCREB). We therefore investigated, in male rats, whether glucocorticoid effects on memory are associated with genomic interactions between the GR and pCREB in the hippocampus. In a two‐by‐two design, object exploration training or no training was combined with post‐training administration of a memory‐enhancing dose of corticosterone or vehicle. Genomic effects were studied by chromatin immunoprecipitation followed by sequencing (ChIP‐seq) of GR and pCREB 45 min after training and transcriptome analysis after 3 hr. Corticosterone administration induced differential GR DNA‐binding and regulation of target genes within the hippocampus, largely independent of training. Training alone did not result in long‐term memory nor did it affect GR or pCREB DNA‐binding and gene expression. No strong evidence was found for an interaction between GR and pCREB. Combination of the GR DNA‐binding and transcriptome data identified a set of novel, likely direct, GR target genes that are candidate mediators of corticosterone effects on memory consolidation. Cell‐specific expression of the identified target genes using single‐cell expression data suggests that the effects of corticosterone reflect in part non‐neuronal cells. Together, our data identified new GR targets associated with memory consolidation that reflect effects in both neuronal and non‐neuronal cells.
How does the affordable care act Medicaid expansion affect cigarette consumption?—The mechanism and heterogeneity
Authors: Wang Lingxiao , Zheng Yuqing , Buck Steven C. 
Published: April 2021

AbstractWe examine the average effect of the affordable care act (ACA) Medicaid expansion on cigarette consumption as well as heterogeneous effects by consumer types, depending on whether they use anti‐smoking products and their baseline level of cigarette consumption. Using the Nielsen homescan consumer panel and generalized difference‐in‐differences (GDD) method, we find that anti‐smoking products can induce cigarette smoking among moderate and heavy smokers. However, the ACA Medicaid expansion reduces cigarette smoking through channels other than anti‐smoking products. As a net result, the ACA Medicaid expansion leads to a reduction in smoking. Light smokers are the main beneficiaries of ACA Medicaid expansion—their average cigarette consumption reduces by over one pack per month.
Clinical Performance of CAD/CAM Monolithic Lithium Disilicate Implant‐Supported Single Crowns Using Solid or Predrilled Blocks in a Fully Digital Workflow: A Retrospective Cohort Study With Up To 33 Months of Follow Up
Authors: Bompolaki Despoina , Punj Amit , Fellows Christopher , Truong Christina , Ferracane Jack L. 
Published: April 2021

AbstractPurposeTo assess the clinical performance of CAD/CAM monolithic implant‐supported restorations manufactured using a fully digital workflow and two different types of ceramic blocks.Materials and MethodsOne hundred and one patients received single‐unit implant‐supported restorations at a University predoctoral clinic. All restorations were designed and fabricated using either a predrilled LS2 block (group P, n = 59) or a conventional solid LS2 block with an occlusal opening drilled manually prior to crystallization (group M, n = 42). The mean follow‐up time after restoration delivery was 18.4 ± 4.8 months (range 12 to 33 months). Patients with less than a 12‐month follow‐up were excluded. Electronic health records were reviewed to identify number and type of complications during the follow‐up time. Clinical outcomes were classified as success, survival, and failure of the restoration. Chi‐square tests were used to identify differences in success and survival rates between the groups. Nonparametric Mann‐Whitney U tests were used to identify differences in the number of major and minor complications as well as the total number of complications that were observed among groups.ResultsOverall success and survival rates were 80.2% and 97%, respectively. Seventy one restorations (70.3%) were complication‐free. There were no significant differences between the groups with regards to the number of complications or success and survival rates.ConclusionsSingle‐unit CAD/CAM monolithic implant‐supported restorations that are fabricated in a fully digital workflow present relatively high complication rates and moderate short‐term clinical outcomes. Clinical studies with longer follow‐up times are needed to evaluate long‐term outcomes of these restorations.
Characterization of fosfomycin resistance and molecular epidemiology among carbapenem-resistant Klebsiella pneumoniae strains from two tertiary hospitals in China
Authors: Wang Haichen , Min Changhang , Li Jun , Yu Ting , Hu Yongmei , Dou Qingya , Zou Mingxiang 
Published: April 2021

Abstract
Background
Fosfomycin has been proven to be a vital choice to treat infection caused by multidrug resistance bacteria, especially carbapenem-resistant Klebsiella pneumoniae (CRKP). However, fosfomycin resistant cases has been reported gradually. In this study, we reported the fosfomycin-resistant rate in CRKP strains and further revealed the molecular mechanisms in resistance gene dissemination.

Results
A total of 294 non-duplicated CRKP strains were collected. And 55 fosfomyin-resistant strains were detected, 94.5% of which were clustered to sequence type (ST) 11 by PCR followed up sequencing. PFGE further revealed two major groups and four singletons. The positive rates of genes responsible to fosfomycin and carbapenem resistance were 81.8% (fosA3), 12.7% (fosA5) and 94.5% (blaKPC-2), respectively. Genomic analysis confirmed insertion sequence (IS) 26 was the predominant structure surrounding fosA3. The fosA3 genes in six isolates were located on plasmids which were able to transfer to E. coli J53 recipient cells by means of conjugation.

Conclusions
Although the resistant rate of CRKP to fosfomycin is relatively low in our area, considering its gene is located on transferrable plasmid and inserted in IS structure, continuous monitoring is still needed.
Posterior reversible encephalopathy syndrome in a patient with Richter's syndrome on combination DA-R-EPOCH chemotherapy regimen: a case report
Authors: Egoryan Goar , Murguia-Fuentes Ricardo , Agab Mohamed , Abou-Ghanem Nagwa , Yanez-Bello Maria Adriana , Pyakuryal Bimatshu , Trelles-Garcia Daniela Patricia , Ibrahim Rami , Filipiuk Dorota , Gidron Adi , Rodriguez-Nava Guillermo 
Published: April 2021

Abstract
Background
Posterior reversible encephalopathy syndrome (PRES) is a clinical-radiologic entity characterized by headaches, altered mental status, seizures, visual loss, and a characteristic imaging pattern in brain magnetic resonance images. The exact etiology and pathogenesis of this condition are not yet fully elucidated.

Case presentation
A 72-year-old White man presented with 2 weeks of low-grade fever and chills, night sweats, fatigue, dysphagia, and new-onset rapidly increasing cervical lymphadenopathy. He had a history of chronic lymphocytic leukemia with transformation to diffuse large B-cell lymphoma for which he was started on dose-adjusted rituximab, etoposide, prednisone vincristine, cyclophosphamide, and doxorubicin (DA-R-EPOCH). Shortly after treatment initiation, the patient developed severe airway obstruction due to cervical lymphadenopathy that required emergency intubation. A few days later, the cervical lymphadenopathy and the status of the airway improved, and sedation was consequently weaned off to plan for extubation. However, the patient did not recover consciousness and developed generalized refractory seizures. Brain magnetic resonance imaging revealed edema in the cortical gray and subcortical white matter of the bilateral occipital and inferior temporal lobes, consistent with PRES.

Conclusions
Posterior reversible encephalopathy syndrome refers to a neurological disorder and imaging entity characterized by subcortical vasogenic edema in patients who develop acute neurological signs and symptoms of a usually reversible nature in different settings, including chemotherapy. Despite its name, PRES is not always fully reversible, and permanent sequelae can persist in some patients. Clinicians should be aware of the possible association between chemotherapy and PRES to ensure early recognition and timely treatment.
Deep learning elements in maritime simulation programmes: a pedagogical exploration of learner experiences
Authors: Jamil Md Golam , Bhuiyan Zakirul 
Published: April 2021

AbstractIn this paper, we explore the learning and teaching of a maritime simulation programme to understand its deep learning elements. We followed the mixed methods approach and collected student perception data from a maritime school, situated within a UK university, using reflection-based survey (n = 112) and three focus groups with eleven students. Findings include the needs for defining clear learning outcomes, improving the learning content to enable exploration and second-chance learning, minimising theory–practice gaps by ensuring skills-knowledge balance and in-depth scholarship building, facilitating tasks for learning preparation and learning extension, and repositioning simulation components and their assessment schemes across the academic programme. Overall, the paper provides evidence on the importance of deep learning activities in maritime simulation and suggests guidelines on improving the existing practice. Although the findings are derived from a maritime education programme, they can be considered and applied in other academic disciplines which use simulation in their teaching and learning.
Assessment of lymphovascular invasion in early stage endometrial carcinoma -a retrospective study
Authors: Moatasim Ambreen , Hameed Zujajah , Ahmad Imran 
Published: April 2021

Abstract
Introduction
Endometrial carcinoma is associated with several known prognostic factors. Recently, lymphovascular invasion (LVI) has gained a prominent position in the risk assessment of early endometrioid endometrial carcinoma, in identifying patients who can benefit from adjuvant radiation therapy. This study aims to assess LVI in early-stage endometrioid endometrial carcinoma accurately with emphasis on its extent /grading. We also propose a few local recommendations for improving LVI reproducibility in endometrial carcinoma to guide future studies.

Methods
The duration of this retrospective study was 2 years. Early-stage I (Ia and Ib), and grade 1 and 2 endometrioid endometrial carcinomas were included. 03 reviewers independently recorded their findings on H&E stained slides. LVI was graded as none, focal and substantial. In discordant cases, immunohistochemical stain CD 31 was used.
All the data was entered in the statistical software SPSS version 26 and analyzed for frequencies. The relationships between various histological parameters assessed and the degree of reproducibility for LVI amongst various observers were also determined.

Results
Out of a total of 70 cases of endometrioid carcinoma diagnosed on hysterectomy specimen, only 32 met our inclusion criteria. The rate of LVI positivity was 6.3 %, 34.4 %, and 37.5 % respectively for reviewers 1, 2, and 3. The degree of reproducibility in LVI assessment and LVI grading was significant amongst reviewers 2 and 3. Also, a significant association was drawn between tumor grade and LVI.

Conclusion
Despite limitations in our study we recommend including both LVI assessment and grading in routine reporting formats locally. By adding a second reviewer in LVI assessment and using CD31 in discrepant cases LVI positivity can be significantly increased.
A retroperitoneal supra-adrenal non-communicating gastric duplication cyst: a case report and comprehensive literature review
Authors: Al Awfi Mahmood Masud , Al Balushi Zainab Nasser , Al Jahdhami Suad Rashid , Sherif Mahmoud Hatem , Al Sibai Sareyah 
Published: April 2021

Abstract
Background
Gastric duplication cyst is a rare congenital anomaly. It is usually located in close proximity to the stomach. Nevertheless, there have been seldom reports in the literature that describe unusual locations. Retroperitoneal gastric duplications cysts are extremely rare and are usually confused with renal or adrenal cysts.

Case presentation
In this case report, we are presenting a 2-year-old girl with a complaint of bouts of abdominal pain, found to have a retroperitoneal supra-adrenal cyst on imaging. She underwent laparoscopic resection of the cyst with uneventful post-operative course. The histopathological diagnosis was surprisingly gastric duplication cyst.

Conclusion
In our review of the literature, the variability of this condition and its clinical manifestation are apparent. We also conclude that this diagnostic entity should be part of the differential diagnosis of intraperitoneal or retroperitoneal cysts and that laparoscopic resection of retroperitoneal cysts is the preferred approach.
Dosing Recommendations for Vancomycin in Children and Adolescents with Varying Levels of Obesity and Renal Dysfunction: a Population Pharmacokinetic Study in 1892 Children Aged 1–18 Years
Authors: Smit Cornelis , Goulooze Sebastiaan C. , Brüggemann Roger J. M. , Sherwin Catherine M. , Knibbe Catherijne A. J. 
Published: April 2021

AbstractVancomycin is an effective but potentially nephrotoxic antibiotic commonly used for severe infections. Dosing guidelines for vancomycin in obese children and adolescents with or without renal impairment are currently lacking. This study describes the pharmacokinetics of vancomycin in a large pediatric cohort with varying degrees of obesity and renal function to design practical dosing guidelines for this population. A multi-center retrospective population pharmacokinetic study was conducted using data from patients aged 1−18 years who received >1 dose of vancomycin and had ≥1 vancomycin concentration measured between January 2006 and December 2012. Besides pharmacokinetic data, age, gender, body weight, creatinine clearance (CLcr, bedside Schwartz equation), ward, race, and neutropenic status were collected. Population pharmacokinetic analysis and simulations were performed using NONMEM7.4. A total of 1892 patients (5524 samples) were included, with total body weight (TBW) ranging 6−188 kg (1344 normal weight, 247 overweight, and 301 obese patients) and CLcr down to 8.6 mL/min/1.73 m2. The two-compartment model, with clearance (CL) significantly increasing with TBW and CLcr, central and peripheral volume of distribution and inter-compartmental clearance increasing with TBW, performed well for all age, weight, and renal function ranges. A dosing guideline is proposed that integrates body weight and CLcr resulting in effective and safe exposures across all ages, body weight, and renal functions in the pediatric population. We have characterized the full pharmacokinetic profile of vancomycin in obese children and adolescents aged 1−18 years and propose a practical dosing guideline that integrates both body weight and renal function.
Dynamics of snow cover in Kirovohrad region at the end of the XX and the beginning of the XXI centuries
Authors: Nedostrelova Larysa V. 
Published: April 2021

Snow cover significantly affects the formation of climate in winter. The snow over has low thermal conductivity, which protects the soil from freezing. In the spring, the snow cover significantly moistens the soil and plays an important role in the surface water regime and in the economic activity of the country. It should be noted that the lack or insufficient height of snow cover can be the cause of freezing of winter crops and their death, which leads to a decrease and even loss of yield. Accordingly, the increase in crop yields depends on the proper use of snow cover. The purpose of the research is to determine the characteristics of the snow cover and analyze their changes in Kirovohrad region in the late twentieth and early twenty-first centuries. Data of daily observations of snow cover at meteorological stations of Kirovohrad region for the period from 1996 to 2018 were used as primary information in the work. It is established that the appearance of snow cover at the stations of Kirovohrad region coincides in two periods (1961-1990 and 1996-2018) and was observed in the third decade of October at almost all stations, except for the area of data distribution of Dolynska weather station, where the first appearance of snow cover during 1961-1990 occurred in the first decade of October. The disappearance of snow in this period was observed in the third decade of April, in contrast to data from the climate cadaster, where 75% of stations observed snowmelt in the second decade of April, while at Dolynska station in the south of the region snowmelt occurred in the third decade of March. At Kropyvnytskyi station, located in the central part of Kirovohrad region, the appearance and disappearance of snow cover was observed in both periods on the same dates. In the period 1996-2018, the values of the highest decadal peaks for the winter were lower than in the climatic norm. The frequency of winters with the highest decadal height of snow cover in different gradations varies greatly in the study periods. For 1996-2018, the maximum was observed in the gradation of 1-5 cm; in the climatic norm the greatest recurrence is recorded in the gradation of 11-20 cm, significant indicators are observed in the gradation of 21-30 cm. The maximum recurrences of the decadal height of the snow cover are 100% and are determined in the gradation of 0-5 cm in both periods of snow cover.
Les routines discursives dans les débats du Parlement européen
Authors: Rouski Margarita 
Published: April 2021

L’existence d’associations lexicales redondantes plus ou moins figées caractérise les discours spécialisés et s’articule avec la théorie des genres discursifs. En nous positionnant dans la perspective de la phraséologie étendue, notre objectif est d’analyser et d’étudier les séquences préfabriquées (sur l’exemple de « à titre », « à ce titre ») dans un genre institué, celui des débats au sein du Parlement européen. Analyser ces routines paraît un défi intéressant à cause des particularités que présente ce genre discursif qui se construit au carrefour de l’oral et de l’écrit. La forte présence de l’interdiscours juridique détermine toute la fonctionnalité des débats.