bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measles pneumonitis, an important cause to recognize in the era of COVID-19: a case report
Authors: Alawad Mouhammad J. , Nauman Areej , Ahmed Farheen S. , Kaul Ridhima , Neffati Nedia 
Published: April 2023

Introduction and Importance:
Measles is an acute febrile viral illness with a characteristic rash. It is usually present in children. Due to the vaccine’s development and wide use, serious complications are quite infrequent in vaccine-covered areas.

Case Presentation:
A 36-year-old immunocompetent woman presented with a fever and a macular rash affecting the face and upper trunk. She was found to have transaminitis and later developed bilateral pulmonary infiltrates with decreased oxygen saturation. After extensive work, the measles PCR returned positive results. The patient was treated conservatively until she recovered.

Discussion:
Measles pneumonitis is a rare complication that usually occurs in immunosuppressed patients. Due to the coronavirus disease pandemic, diagnosis can be difficult, especially if the presentation is not classic.

Conclusion:
We report this case to emphasize the importance of correct diagnosis and proper management.
Displaced varus proximal humerus fracture with conservative treatment: a case report
Authors: Asavanapakas Panpaporn , Klabklay Prapakorn , Maliwankul Korakot , Chuaychoosakoon Chaiwat 
Published: April 2023

Introduction and importance:
The authors report a case of an elderly female with a displaced varus misalignment of a proximal humerus fracture which met the indications for surgery, but the patient was treated conservatively with an arm sling due to the wishes of the patient and her relatives. The clinical outcome was nearly full function compared with the right shoulder.

Presentation of case:
A 65-year-old Thai female presented with right shoulder pain 1 h after a fall during which her right shoulder hit the floor. Radiographs of the right shoulder in anteroposterior and lateral transcapular views showed a proximal humerus fracture with varus misalignment. The patient and her relatives decided on conservative treatment with an arm sling. At 12 weeks following the fall she was able to move her right shoulder nearly equally to the left shoulder.

Intervention and outcome:
The authors discussed the treatment options with the patient and her relatives and recommended open reduction and internal fixation with a locking plate and screw, but they decided on conservative treatment with an arm sling. At 12 weeks following the fall she was able to move her right shoulder nearly equally to the left shoulder. She had no pain and could do normal life activities with the right shoulder.

Relevance and impact:
Patients with severe varus deformity are usually treated with surgery. If there are contraindications for surgery, the stability of the fracture should first be evaluated through radiographs of the fracture in various arm positions.
Kidney stone management in the era of miniaturized percutaneous nephrolithotomy: does it improve safety? a prospective cohort study
Authors: Sakly Aymen , Zakhama Walid , Jleli Nejm , Chafik Anas , Binous Yassine 
Published: April 2023

Objective:
to compare the safety and the efficacy of standard percutaneous nephrolithotomy (sPCNL) vs. mini PCNL (mPCNL).

Methods:
The authors conducted a prospective single-centre cohort study over a 2-year period of all consecutive patients who underwent sPCNL or mPCNL for 2–4 cm renal stones. Patients with active urinary tract infection, abnormal coagulopathy state, malformative uropathies and multitract-access procedures were excluded. In total, 90 patients underwent sPCNL using a 30 Fr access sheath with 24 Fr nephroscope while 52 patients underwent mPCNL using a mPCNL system: 12 Fr nephroscope and a 16.5/17.5F access sheath. Blood loss estimation was assessed postoperatively after 6 h by considering haemoglobin drop and blood transfusion if required. Stone free rate at 1 month was defined by the absence of stone or residual fragments less than or equal to 3 mm on computed tomography scan.

Results:
Stone characteristics were comparable in both treatment arms. The mean stone size was comparable for sPCNL and mPCNL groups (32.6±10.8 mm vs. 29.4±11.8 mm). Operative time was longer in the mPCNL group (124±40.4 min vs. 95.8±32.3 min, P<0.001). According to the Clavien–Dindo classification, no statistical difference was found between the groups in terms of complication rate (P=0.092). However, the mean of haemoglobin drop and transfusion rate were significantly in favour of mPCNL (1.43±1.5 vs. 0.88±1.4 g/dcl, P=0.04). Hospital stay was found to be significantly shorter for patients undergoing mPCNL (4.4±3.9 vs. 2.7±1.7 days, P<0.001). The success rate in the sPCNL group was higher than mPCNL group in terms of stone clearance at one month (69.4% vs. 62.7%, P=0.06).

Conclusion:
Both sPCNL and mPCNL have shown good outcomes in this indication. Although the stone free rate was equal for both techniques, hospital stay, bleeding and transfusion rate are much lower with the use of mPCNL.
Descriptive Analysis of Newly Hired Academic Nurse Educator Onboarding Practices
Authors: Hansbrough Wendy , Dunker Kimberly , Duprey Melissa , Lawrence April 
Published: April 2023

Background:
Prelicensure nursing programs often hire clinical experts who are novice educators to teach integration of nursing clinical judgment within the context of patient care experiences.

Purpose:
To describe practices of schools of nursing to onboard, orient, and mentor newly hired faculty.

Methods:
Faculty (n = 174) and leaders (n = 51) replied to an online survey.

Results:
The majority (81.63%) of leaders hire novice nurse educators; 58.14% require a minimum bachelor of science in nursing degree; 54.72% have an orientation plan consisting of a mean of 13.86 hours, which was mostly asynchronous learning. Of the 77.08% of leaders with an onboarding plan, 84.13% assign a preceptor; 51.35% of them are compensated.

Conclusions:
Most schools of nursing hire experienced clinical nurses who are novice nurse educators, without organizational structures to support acquisition of teaching expertise. Academic institutions are called on to support clinical nurse educator professional development. Evidence is needed to design effective and fiscally pragmatic onboarding programs based on the certified nurse educator competencies.
A Comparative Evaluation of Iliac Crest Cortical-Cancellous Bone Blocks Graft With and Without Concentrated Growth Factors (CGFs) in Secondary Alveolar Bone Grafting: A Retrospective Study
Authors: Lai Yongzhen , Jiang Xiao xian , Lu Meng , Mao Chuanqing , Cai Zhiyu , Wang Chengyong , Liu Jing , Chen Weihui 
Published: April 2023

Background:
The purpose of this study was to investigate the clinical effect and bone resorption of iliac crest cortical-cancellous bone block grafts combined with concentrated growth factor (CGF) compared with iliac crest cortical-cancellous bone block grafts only in secondary alveolar bone grafting.

Materials and Methods:
Eighty-six patients (43 in the CGF group and 43 in the non-CGF group) with unilateral alveolar clefts were examined. Patients (17 in the CGF group and 17 in the non-CGF group) were randomly chosen for radiologic evaluation. Quantitative evaluation of the bone resorption rate was made with cone-beam computed tomography and Mimics 19.0 software at 1 week and 12 months after surgery.

Results:
The success rate of bone grafting was 95.3% and 79.1% in the CGF and non-CGF groups, respectively (P=0.025). The mean bone resorption rate at 12 months postoperatively was 35.66±15.80% and 41.39±19.57% in the CGF and non-CGF groups, respectively (P=0.355). The bone resorption patterns of the 2 groups were similar on the labial, alveolar process, and palatal sides, and there was no obvious bone resorption on the labial side in either group. Nasal side bone resorption in the CGF group was significantly less than that in the non-CGF group (P=0.047).

Conclusions:
Cortical-cancellous bone block grafts reduce labial bone resorption, while CGF reduces nasal bone resorption and improves the success rate. The combination of bone block and CGF in secondary alveolar bone grafting is worthy of further clinical application.
A tractable physical model for the yeast polarity predicts epistasis and fitness
Authors: Daalman Werner Karl-Gustav , Sweep Els , Laan Liedewij 
Published: April 2023

Accurate phenotype prediction based on genetic information has numerous societal applications, such as crop design or cellular factories. Epistasis, when biological components interact, complicates modelling phenotypes from genotypes. Here we show an approach to mitigate this complication for polarity establishment in budding yeast, where mechanistic information is abundant. We coarse-grain molecular interactions into a so-called mesotype, which we combine with gene expression noise into a physical cell cycle model. First, we show with computer simulations that the mesotype allows validation of the most current biochemical polarity models by quantitatively matching doubling times. Second, the mesotype elucidates epistasis emergence as exemplified by evaluating the predicted mutational effect of key polarity protein Bem1p when combined with known interactors or under different growth conditions. This example also illustrates how unlikely evolutionary trajectories can become more accessible. The tractability of our biophysically justifiable approach inspires a road-map towards bottom-up modelling complementary to statistical inferences.This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
Global epistasis on fitness landscapes
Authors: Diaz-Colunga Juan , Skwara Abigail , Gowda Karna , Diaz-Uriarte Ramon , Tikhonov Mikhail , Bajic Djordje , Sanchez Alvaro 
Published: April 2023

Epistatic interactions between mutations add substantial complexity to adaptive landscapes and are often thought of as detrimental to our ability to predict evolution. Yet, patterns of global epistasis, in which the fitness effect of a mutation is well-predicted by the fitness of its genetic background, may actually be of help in our efforts to reconstruct fitness landscapes and infer adaptive trajectories. Microscopic interactions between mutations, or inherent nonlinearities in the fitness landscape, may cause global epistasis patterns to emerge. In this brief review, we provide a succinct overview of recent work about global epistasis, with an emphasis on building intuition about why it is often observed. To this end, we reconcile simple geometric reasoning with recent mathematical analyses, using these to explain why different mutations in an empirical landscape may exhibit different global epistasis patterns—ranging from diminishing to increasing returns. Finally, we highlight open questions and research directions.
This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
Mutation bias and the predictability of evolution
Authors: Cano Alejandro V. , Gitschlag Bryan L. , Rozhoňová Hana , Stoltzfus Arlin , McCandlish David M. , Payne Joshua L. 
Published: April 2023

Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. We argue that empirical knowledge of mutational biases is likely to improve in the near future, and that this knowledge is readily applicable to the challenges of short-term prediction.
This article is part of the theme issue ‘Interdisciplinary approaches to predicting evolutionary biology’.
Alcanivorax xiamenensis sp. nov., a novel marine hydrocarbonoclastic bacterium isolated from surface seawater
Authors: Lai Qiliang , Fu Xiaoteng , Wang Jianning , Dong Chunming , Wang Liping , Wang Wanpeng , Shao Zongze 
Published: April 2023

A novel

Alcanivorax

-related strain, designated 6-D-6T, was isolated from the surface seawater collected around Xiamen Island. The novel strain is Gram-stain-negative, rod-shaped and motile, and grows at 10–45 °C, pH 6.0–9.0 and in the presence of 0.5–15.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that it belongs to the genus

Alcanivorax

, with the highest sequence similarity to

Alcanivorax dieselolei

B5T (99.9 %), followed by

Alcanivorax xenomutans

JC109T (99.5 %),

Alcanivorax balearicus

MACL04T (99.3 %) and other 13 species of the genus

Alcanivorax

(93.8 %–95.6 %). The digital DNA–DNA hybridization and average nucleotide identity values between strain 6-D-6T and three close type strains were 40.1–42.9/90.6–91.4 %, and others were below 22.9/85.1 %, respectively. The novel strain contained major cellular fatty acids of C16 : 0 (31.0 %), C19 : 0
ω8c cyclo (23.5 %), C17 : 0 cyclo (9.7 %), C12 : 0 3OH (8.6 %), summed feature 8 (7.6 %) and C12 : 0 (5.4 %). The genomic G+C content of strain 6-D-6T was 61.38 %. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified phospholipids and one amino-group-containing phospholipid were detected. On the basis of phenotypic and genotypic characteristics, strain 6-D-6T represents a novel species within the genus

Alcanivorax

, for which the name Alcanivorax xiamenensis sp. nov. is proposed. The type strain is 6-D-6T (=MCCC 1A01359T=KCTC 92480T).
Single nuclei multiomic analyses identify human cardiac lymphatic endothelial cells associated with coronary arteries in the epicardium
Authors: Travisano Stanislao Igor , Harrison Michael R M , Thornton Matthew E. , Grubbs Brendan H. , Quertermous Thomas , Lien Ching-Ling 
Published: April 2023

SummaryCardiac lymphatic vessels play important roles in fluid homeostasis, inflammation, disease, and regeneration of the heart. The developing cardiac lymphatics in human fetal hearts are closely associated with coronary arteries, similar to those in zebrafish hearts. We identified a population of cardiac lymphatic endothelial cells that reside in the epicardium. Single nuclei multiomic analysis of the human fetal heart revealed the plasticity and heterogeneity of the cardiac endothelium. Furthermore, we found that VEGFC is highly expressed in arterial endothelial cells, providing a molecular basis for the arterial association of cardiac lymphatic development. Using a cell-type-specific integrative analysis, we identified a novel population of cardiac lymphatic endothelial cells marked by the PROX1, the lymphangiocrine RELN, and enriched in binding motifs of ETV transcriptional factors. We report the first in vivo molecular characterization of human cardiac lymphatics and provide a valuable resource to understand fetal heart development.
Retention time and fragmentation predictors increase confidence in variant peptide identification
Authors: Skiadopoulou Dafni , Vašíček Jakub , Kuznetsova Ksenia , Käll Lukas , Vaudel Marc 
Published: April 2023

AbstractPrecision medicine focuses on adapting care to the individual profile of patients, e.g. accounting for their unique genetic makeup. Being able to account for the effect of genetic variation on the proteome holds great promises towards this goal. However, identifying the protein products of genetic variation using mass spectrometry has proven very challenging. Here we show that the identification of variant peptides can be improved by the integration of retention time and fragmentation predictors into a unified proteogenomic pipeline. By combining these intrinsic peptide characteristics using the search-engine post-processor Percolator, we demonstrate improved discrimination power between correct and incorrect peptide-spectrum matches. Our results demonstrate that the drop in performance that is induced when expanding a protein sequence database can be compensated, and hence enabling efficient identification of genetic variation products in proteomics data. We anticipate that this enhancement of proteogenomic pipelines can provide a more refined picture of the unique proteome of patients, and thereby contribute to improving patient care.
Role of pioneer neurons and neuroblast behaviors on otic ganglion assembly
Authors: Bañón A , Alsina B 
Published: April 2023

AbstractCranial ganglia are aggregates of sensory neurons that mediate distinct types of sensation. It is little understood how individual neurons coalesce, distribute and shape the ganglion. The statoacoustic ganglion (SAG) displays several lobes spatially arranged to properly connect with hair cells of the inner ear. To investigate the cellular behaviors involved in the 3D organization of the SAG, we use high resolution confocal imaging of single cell labeled zebrafish neuroblasts (NB), photoconversion, photoablation and genetic perturbations. We find that otic NB delaminate out of the otic epithelium in an EMT-like manner, rearranging apical polarity and primary cilia proteins. We also show that, once delaminated, NB migrate directionally and actively, requiring RhoGTPases. Interestingly, cell tracking of individual delaminated NB reveals that NB migrate and coalesce around a small population of pioneer SAG neurons. These pioneer SAG neurons are not from otic placode origin and populate the coalescence region before otic neurogenesis begins. Upon ablation of these cells, migratory pathways of delaminated NB are disrupted and, consequently, SAG shape is affected. Altogether, this work shows for the first time the role of pioneer SAG neurons in orchestrating SAG development.Summary StatementLittle is known how cranial sensory ganglia organize in 3D. We unveil the repertoire of cellular behaviours underlying statoacoustic morphogenesis and its dependence on relevant pioneer neurons.
Microtomographic investigation of a large corpus of cichlids
Authors: Haberthür David , Law Mikki , Ford Kassandra , Häsler Marcel , Seehausen Ole , Hlushchuk Ruslan 
Published: April 2023

AbstractA large collection of cichlids (N=133) from Lake Victoria in Africa spanning a length range of 6 to 18 cm was nondestructively imaged using micro-computed tomography. We describe our method to efficiently obtain three-dimensional tomographic datasets of the oral and pharyngeal jaws and the whole skull of these fishes for accurately describing their morphology. The tomographic data we acquired (9.8 TB of projection images) yielded 1.5 TB of three-dimensional image stacks used for extracting the relevant features of interest. Herein we present our method and an outlook on analyzing the acquired data; a morphological description of the oral and pharyngeal jaws of the fishes, a three-dimensional geometric morphometrics analysis of landmark features on the fish skulls, and a robust method to automatically extract the otoliths of the fishes from the tomographic data.
PanGraphViewer: A Versatile Tool to Visualize Pangenome Graphs
Authors: Yuan Yuxuan , Ma Ricky Ka-Kui , Chan Ting-Fung 
Published: April 2023

AbstractPangenome graphs provide a powerful way to present both sequence and structural features in a given genome relative to the typical features of a population. There are different methods of building pangenome graphs, but few tools are available to visualize them. To address this problem, we developed PanGraphViewer, which is written in Python 3 and runs on all major operating systems. The PanGraphViewer package contains two separate versions: a desktop-based application and a web-based application. Compared to other graph viewers that are initially designed to visualize individual genome graphs, PanGraphViewer targets pangenome graphs and allows the viewing of pangenome graphs built from multiple genomes in either the (reference) graphical fragment assembly format or the variant call format (VCF). Apart from visualization of different types of structural variations (SV), PanGraphViewer also integrates genome annotations with graph nodes to analyze insertions or deletions in a particular gene model. The graph node shapes in PanGraphViewer can represent different types of genomic variations when a VCF file is used. Notably, PanGraphViewer displays subgraphs from a chromosome or sequence segment based on any given coordinates. This function is absent from most genome graph viewers. PanGraphViewer is freely available athttps://github.com/TF-Chan-Lab/panGraphViewerto facilitate pangenome analysis.
Cell-derived ECM loaded electrospun Polycaprolactone/Chitosan nanofibrous scaffolds for periodontal regeneration
Authors: Santos Mafalda S. , Cordeiro Rachel , Moura Carla S. , Cabral Joaquim M. S. , Ferreira Frederico Castelo , Silva João C. , Carvalho Marta S. 
Published: April 2023

ABSTRACTPeriodontitis is an inflammatory infection caused by bacterial plaque accumulation that affects the periodontium, a complex structure of different tissues (cementum, periodontal ligament and alveolar bone) that surrounds and supports the teeth. Current treatments lack bioactive signals to induce tissue repair and coordinated regeneration of the periodontium, thus alternative strategies are needed to improve clinical outcomes. Cell-derived extracellular matrix (ECM) has been combined with biomaterials to enhance their biofunctionality for various tissue engineering (TE) applications. In this work, bioactive cell-derived ECM loaded electrospun polycaprolactone/chitosan (PCL/CTS) nanofibrous scaffolds were developed combining polymer solutions with lyophilized decellularized ECM (dECM) derived from human Periodontal Ligament Stem/Stromal Cells (PDLSCs). The work’s aims were to fabricate and characterize cell-derived ECM electrospun PCL/CTS scaffolds in terms of morphology, physico-chemical, thermal and mechanical properties and assess their ability to enhance the osteogenic differentiation of PDLSCs, envisaging periodontal TE applications. PDLSCs were cultured and used for dECM production. PDLSCs-derived dECM was characterized regarding morphology, protein expression, DNA removal efficiency, and glycosaminoglycans and collagen contents. Osteogenic differentiation of PDLSCs was performed on PCL, PCL/CTS and PCL/CTS/ECM electrospun scaffolds for 21 days. The obtained results demonstrate that PCL/CTS/ECM scaffolds promoted cell proliferation compared to PCL and PCL/CTS scaffolds, while maintaining similar physical and mechanical properties of PCL/CTS scaffolds. PCL/CTS/ECM scaffolds enhanced the osteogenic differentiation of PDLSCs, confirmed by increased alkaline phosphatase activity, calcium deposition, and bone-specific marker genes expression. Moreover, PCL/CTS scaffolds showed higher levels of cell mineralization than PCL scaffolds. Overall, this work describes the first use of lyophilized cell-derived ECM loaded electrospun scaffolds for periodontal TE applications and highlights its potential as a promising therapeutic strategy for periodontitis treatment.