bluuebunny/crossref_metadata_2025_split huggingface dataset:
Average capacity of quantum entanglement
Authors: Wei Lu 
Published: January 2023

Abstract
As an alternative to entanglement entropies, the capacity of entanglement becomes a promising candidate to probe and estimate the degree of entanglement of quantum bipartite systems. In this work, we study the statistical behavior of entanglement capacity over major models of random states. In particular, the exact and asymptotic formulas of average capacity have been derived under the Hilbert–Schmidt and Bures-Hall ensembles. The obtained formulas generalize some partial results of average capacity computed recently in the literature. As a key ingredient in deriving the results, we make use of techniques in random matrix theory and our previous results pertaining to the underlying orthogonal polynomials and special functions. Simulations have been performed to numerically verify the derived formulas.
Constructing high-strength nano-micro fibrous woven scaffolds with native-like anisotropic structure and immunoregulatory function for tendon repair and regeneration
Authors: Cai Jiangyu , Liu Jiao , Xu Junjie , Li Yufeng , Zheng Ting , Zhang Tianlun , Han Kang , Chen Shaojuan , Jiang Jia , Wu Shaohua , Zhao Jinzhong 
Published: January 2023

Abstract
Tendon injuries are common debilitating musculoskeletal diseases with high treatment expenditure in sports medicine. The development of tendon-biomimetic scaffolds may be promising for improving the unsatisfactory clinical outcomes of traditional therapies. In this study, we combined an advanced electrospun nanofiber yarn-generating technique with a traditional textile manufacturing strategy to fabricate innovative nano-micro fibrous woven scaffolds with tendon-like anisotropic structure and high-strength mechanical properties for the treatment of large-size tendon injury. Electrospun nanofiber yarns made from pure poly L-lactic acid (PLLA) or silk fibroin (SF)/PLLA blend were fabricated, and their mechanical properties matched and even exceeded those of commercial PLLA microfiber yarns. The PLLA or SF/PLLA nanofiber yarns were then employed as weft yarns interlaced with commercial PLLA microfiber yarns as warp yarns to generate two new types of nanofibrous scaffolds (nmPLLA and nmSF/PLLA) with a plain-weaving structure. Woven scaffolds made from pure PLLA microfiber yarns (both weft and warp directions) (mmPLLA) were used as controls. In vitro experiments showed that the nmSF/PLLA woven scaffold with aligned fibrous topography significantly promoted cell adhesion, elongation, proliferation, and phenotypic maintenance of tenocytes compared with mmPLLA and nmPLLA woven scaffolds. Moreover, the nmSF/PLLA woven scaffold exhibited the strongest immunoregulatory functions and effectively modulated macrophages towards the M2 phenotype. In vivo experiments revealed that the nmSF/PLLA woven scaffold notably facilitated Achilles tendon regeneration with improved structure by macroscopic, histological, and ultrastructural observations six months after surgery, compared with the other two groups. More importantly, the regenerated tissue in the nmSF/PLLA group had excellent biomechanical properties comparable to those of the native tendon. Overall, our study provides an innovative biological-free strategy with ready-to-use features, which presents great potential for clinical translation for damaged tendon repair.
Numerical simulation of the dolomite in-situ desulfurization in molten iron
Authors: Qiao-kun Shen , Qing-chun Yu , Jia-hao Zhang , Xiao-fei Yao , Wei-jin Yu 
Published: January 2023

Abstract
With the growing need for high-quality steel, the requirement for efficient deep desulfurization technologies is growing, and lots of research have be conducted. The desulfurization in hot iron with Mg produced in situ by the aluminothermic reduction of decomposed dolomite was simulated. The magnesium generated at the molten matte-slag interface is dissolved in the molten iron and desulfurizing while spread downwards The process has been studied by experiment and computational fluid dynamics simulation. Some analysis and assumptions were made for the simulation conditions and the simulated data are in good agreement with the experimental results. The rate of desulfurization depended mainly on the reaction rate and is almost independent of the rate of diffusion of Al, S and Mg according to the results. Under the present experimental conditions, the desulfurization rate increased with the increase in temperature and the amount of reactants. However, the effect is not obvious when the temperature is higher than 1623K. The adjustment in diffusion coefficient has minimal influence on the desulfurization efficiency. The desulfurization reaction is mainly in the homogeneous phase, and the proportion of magnesium bubble desulfurization could be ignored when the temperature is between 1523 K–1723 K.
The hitchhikers’ guide to RNA sequencing and functional analysis
Authors: Chen Jiung-Wen , Shrestha Lisa , Green George , Leier André , Marquez-Lago Tatiana T 
Published: January 2023

Abstract
DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantification, but once sequencing has concluded researchers can be easily overwhelmed with questions such as how to go from raw data to differential expression (DE), pathway analysis and interpretation. Several pipelines and procedures have been developed to this effect. Even though there is no unique way to perform RNA-Seq analysis, it usually follows these steps: 1) raw reads quality check, 2) alignment of reads to a reference genome, 3) aligned reads’ summarization according to an annotation file, 4) DE analysis and 5) gene set analysis and/or functional enrichment analysis. Each step requires researchers to make decisions, and the wide variety of options and resulting large volumes of data often lead to interpretation challenges. There also seems to be insufficient guidance on how best to obtain relevant information and derive actionable knowledge from transcription experiments. In this paper, we explain RNA-Seq steps in detail and outline differences and similarities of different popular options, as well as advantages and disadvantages. We also discuss non-coding RNA analysis, multi-omics, meta-transcriptomics and the use of artificial intelligence methods complementing the arsenal of tools available to researchers. Lastly, we perform a complete analysis from raw reads to DE and functional enrichment analysis, visually illustrating how results are not absolute truths and how algorithmic decisions can greatly impact results and interpretation.
Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources
Authors: Wong Edith D , Miyasato Stuart R , Aleksander Suzi , Karra Kalpana , Nash Robert S , Skrzypek Marek S , Weng Shuai , Engel Stacia R , Cherry J Michael 
Published: January 2023

Abstract
As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architecture, to curation of novel data types, to incorporation of data from, and collaboration with, other knowledgebases. We are continuing to make steps toward providing the community with an S. cerevisiae pan-genome. Here, we describe software upgrades, a new nomenclature system for genes not found in the reference strain, and additions to gene pages. With these improvements, we aim to remain a leading resource for students, researchers, and the broader scientific community.
The future of carbon neutrality from a scientific research perspective: an interview with Jing-Hai Li
Authors: Chen Li-Hua 
Published: January 2023

ABSTRACT
Since China announced that it will strive to achieve carbon peak by 2030 and carbon neutrality by 2060, it has become the focus of the whole society. The implementation of carbon peaking and carbon neutrality goals requires a range of revolutionary technologies and involves an array of key scientific questions. A great deal of research has focused on the development of new concepts and innovative technologies on carbon science and sustainable development.
NSR recently interviewed Professor Jing-Hai Li about the topic of the future of carbon neutrality science and technology from a scientific research perspective. Professor Li is an academician of the Chinese Academy of Sciences (CAS) at the Institute of Process Engineering, CAS. He is a scientist who has been working on exploring complex systems in chemical engineering by multi-scale methodology for more than 30 years. He proposed the concept of Mesoscience, a new interdisciplinary discipline.
DUOX2 regulates secreted factors in virus‐infected respiratory epithelial cells that contribute to neutrophil attraction and activation
Authors: Kasumba Dacquin M. , Huot Sandrine , Caron Elise , Fortin Audray , Laflamme Cynthia , Zamorano Cuervo Natalia , Lamontagne Felix , Pouliot Marc , Grandvaux Nathalie 
Published: January 2023

AbstractThe first line of defense against respiratory viruses relies on the antiviral and proinflammatory cytokine response initiated in infected respiratory epithelial cells. The cytokine response not only restricts virus replication and spreading, but also orchestrates the subsequent immune response. The epithelial Dual Oxidase 2 (DUOX2) has recently emerged as a regulator of the interferon antiviral response. Here, we investigated the role of DUOX2 in the inflammatory cytokine response using a model of A549 cells deficient in DUOX2 generated using Crispr‐Cas9 and infected by Sendai virus. We found that the absence of DUOX2 selectively reduced the induction of a restricted panel of 14 cytokines and chemokines secreted in response to Sendai virus by 20 to 89%. The secreted factors produced by epithelial cells upon virus infection promoted the migration, adhesion, and degranulation of primary human neutrophils, in part through the DUOX2‐dependent secretion of TNF and chemokines. In contrast, DUOX2 expression did not impact neutrophil viability or NETosis, thereby highlighting a selective impact of DUOX2 in neutrophil functions. Overall, this study unveils previously unrecognized roles of epithelial DUOX2 in the epithelial‐immune cells crosstalk during respiratory virus infection.
Long‐term cell fate and functional maintenance of human hepatocyte through stepwise culture configuration
Authors: Sugahara Go , Ishida Yuji , Lee Jae Jin , Li Meng , Tanaka Yasuhito , Eoh Hyungjin , Higuchi Yusuke , Saito Takeshi 
Published: January 2023

AbstractHuman hepatocyte culture system represents by far the most physiologically relevant model for our understanding of liver biology and diseases; however, its versatility has been limited due to the rapid and progressive loss of genuine characteristics, indicating the inadequacy of in vitro milieu for fate maintenance. This study, therefore, is designed to define environmental requirements necessary to sustain the homeostasis of terminally differentiated hepatocytes. Our study reveals that the supplementation of dimethyl sulfoxide (DMSO) is indispensable in mitigating fate deterioration and promoting adaptation to the in vitro environment, resulting in the restoration of tight cell–cell contact, cellular architecture, and polarity. The morphological recovery was overall accompanied by the restoration of hepatocyte marker gene expression, highlighting the interdependence between the cellular architecture and the maintenance of cell fate. However, beyond the recovery phase culture, DMSO supplementation is deemed detrimental due to the potent inhibitory effect on a multitude of hepatocyte functionalities while its withdrawal results in the loss of cell fate. In search of DMSO substitute, our screening of organic substances led to the identification of dimethyl sulfone (DMSO2), which supports the long‐term maintenance of proper morphology, marker gene expression, and hepatocytic functions. Moreover, hepatocytes maintained DMSO2 exhibited clinically relevant toxicity in response to prolonged exposure to xenobiotics as well as alcohol. These observations suggest that the stepwise culture configuration consisting of the consecutive supplementation of DMSO and DMSO2 confers the microenvironment essential for the fate and functional maintenance of terminally differentiated human hepatocytes.
A genome‐wide CRISPR screen identifies the CCT chaperonin as a critical regulator of vesicle trafficking
Authors: Chen Yongtian , Kang Jing , Zhen Ru , Zhang Liyang , Chen Caiyong 
Published: January 2023

AbstractVesicle trafficking is a fundamental cellular process that controls the transport of various proteins and cargos between cellular compartments in eukaryotes. Using a combination of genome‐wide CRISPR screening in mammalian cells and RNAi screening in Caenorhabditis elegans, we identify chaperonin containing TCP‐1 subunit 4 (CCT4) as a critical regulator of protein secretion and vesicle trafficking. In C. elegans, deficiency of cct‐4 as well as other CCT subunits impairs the trafficking of endocytic markers in intestinal cells, and this defect resembles that of dyn‐1 RNAi worms. Consistent with these findings, the silencing of CCT4 in human cells leads to defective endosomal trafficking, and this defect can be rescued by the dynamin activator Ryngo 1–23. These results suggest that the cytosolic chaperonin CCT may regulate vesicle trafficking by promoting the folding of dynamin in addition to its known substrate tubulin. Our findings establish an essential role for the CCT chaperonin in regulating vesicle trafficking, and provide new insights into the regulation of vesicle trafficking and the cellular function of the cytosolic chaperonin.
Delirium in trauma ICUs: a review of incidence, risk factors, outcomes, and management
Authors: Williams Elliot C. , Estime Stephen , Kuza Catherine M. 
Published: January 2023

Purpose of review
This article reviews the impact and importance of delirium on patients admitted to the ICU after trauma, including the latest work on prevention and treatment of this condition. As the population ages, the incidence of geriatric trauma will continue to increase with a concomitant rise in the patient and healthcare costs of delirium in this population.

Recent findings
Recent studies have further defined the risk factors for delirium in the trauma ICU patient population, as well as better demonstrated the poor outcomes associated with the diagnosis of delirium in these patients. Recent trials and meta-analysis offer some new evidence for the use of dexmedetomidine and quetiapine as preferred agents for prevention and treatment of delirium and add music interventions as a promising part of nonpharmacologic bundles.

Summary
Trauma patients requiring admission to the ICU are at significant risk of developing delirium, an acute neuropsychiatric disorder associated with increased healthcare costs and worse outcomes including increased mortality. Ideal methods for prevention and treatment of delirium are not well established, especially in this population, but recent research helps to clarify optimal prevention and treatment strategies.
Hip Displacement Does Not Change After Pelvic Obliquity Correction During Spinal Fusion in Children With Cerebral Palsy
Authors: Asma Ali , Cobanoglu Mutlu , Ulusaloglu Armagan Can , Rogers Kenneth J. , Miller Freeman , Howard Jason J. , Shah Suken A. , Shrader M. Wade 
Published: January 2023

Background:
Children with cerebral palsy (CP) frequently develop both neuromuscular hip dysplasia and scoliosis, and occasionally, the timing of the worsening of both of these pathologies is concurrent. The question as to whether the hip or spine should be addressed first in CP remains controversial, with the majority of evidence being “expert opinion.” The purpose of this project was to determine the impact of posterior spinal fusion (PSF) on the change in hip displacement for children with CP without previous reconstructive hip surgery.

Methods:
This was an Institutional Review Board-approved study that observed 67 patients from 2004 to 2018. Inclusion criteria included children with CP, 18 years of age and younger, Gross Motor Function Classification System IV and V, undergoing PSF at a single tertiary care children’s hospital with a minimum 2-year follow-up. The primary outcome was the change in hip displacement as quantified by the migration percentage (MP). The hip with the highest MP (worst hip) at the spine preoperative analysis were included for analysis. Triradiate cartilage (TRC) status and pelvic obliquity correction were analyzed with multivariate analysis.

Results:
Sixty-seven patients were included for analysis, with a mean age of 12.5±2.3 years. The mean major curve angle of the major curve was 77±23 degrees and the mean preoperative pelvic obliquity was 21±12 degrees. There was no statistically significant change in MP after PSF from a mean preoperative value of 41±27%, to a mean postoperative value of 41±29% at the last follow-up, (P=0.76) The mean follow-up time was 4.1±2.7 years. TRC status (P=0.52) and the severity of pelvic obliquity (P=0.10) did not statistically impact the change in MP after PSF.

Conclusion:
PSF did not influence—either negatively or positively—the progression of hip displacement in children with CP, regardless of pelvic obliquity correction or TRC status. The lack of deterioration in hip displacement post-PSF, however, may suggest a protective effect of spine surgery.

Level of Evidence:
Level III—retrospective cohort study.
What is New in Pediatric Orthopaedic: Basic Science
Authors: Lynch Brian , Botros Daniel , Halanski Matthew , Barsi James 
Published: January 2023

Background:
An understanding of musculoskeletal basic science underpins most advancements in the field of orthopaedic surgery. Knowledge of biomechanics, genetics, and molecular pathways is integral to the understanding of the pathophysiology of disease and guides novel treatment options to improve patient outcomes. The purpose of this review is to provide a comprehensive and current overview of musculoskeletal basic science relevant to pediatric orthopaedic surgery.

Methods:
Comprehensive Pubmed database searches were performed for all English language articles published between January 2016 and November 2021 using the following search terms: basic science, pediatric orthopaedics, fracture, trauma, spine, scoliosis, DDH, hip dysplasia, Perthes, Legg-Calve-Perthes, clubfoot, and sports medicine. Inclusion criteria focused on basic science studies of pediatric orthopaedic conditions. Clinical studies or case reports were excluded. A total of 3855 articles were retrieved. After removing duplicates and those failing to meet our inclusion criteria, 49 articles were included in the final review.

Results:
A total of 49 papers were selected for review based on the date of publication and updated findings. Findings are discussed in the subheadings below. Articles were then sorted into the following sub-disciplines of pediatric orthopaedics: spine, trauma, sports medicine, hip, and foot.

Conclusions:
With this review, we have identified many exciting developments in pediatric orthopaedic trauma, spine, hip, foot, and sports medicine that could potentially lead to changes in disease management and how we think of these processes.

Level of Evidence:
Level V
A Comprehensive Assessment of Psychosocial Well-being Among Growing Rod Graduates: A Preliminary Investigation
Authors: Yildiz Mevhibe İrem , Goker Barlas , Demirsöz Talat , Aslan Cihan , Demirkiran Halil Gokhan , Karahan Sevilay , Yazici Mumin Kazim , Yazici Müharrem 
Published: January 2023

Background:
Traditional growing rods (TGR) encompass a long process, in which patients experience physical and psychosocial difficulties. However, the effect of repeating surgeries on the overall psychological functioning of graduated patients has not been thoroughly investigated in the literature. The aim of this study is to evaluate the psychological well-being of graduated idiopathic early-onset scoliosis patients in terms of psychopathology, neurocognition, and psychosocial functioning, and determine the accuracy of scoliosis outcome questionnaires in these regards.

Methods:
TGR graduates with idiopathic early-onset scoliosis without known intellectual disabilities or neuromuscular impairments were included. Patients were thoroughly evaluated using psychological instruments [Wechsler Adult Intelligence Scale, Auditory Consonant Trigram Test, Verbal Fluency Test, Beck Depression Inventory, Beck Anxiety Inventory, Rosenberg Self-Esteem Scale, Symptom Checklist-90, Post-Traumatic Growth Inventory, Strengths and Difficulties Questionnaire, Spinal Appearance Questionnaire, Scoliosis Research Society 22-item questionnaire (SRS-22)]. Results were compared with normative data when available. Spearman correlations were performed between the results of these tests, the total treatment duration, and the number of spinal surgeries.

Results:
Of the 15 patients included in the study, 9 were females, and the mean age was 18.73 (16 to 23). The mean age at index surgery was 6.38 (3 to 10) whereas that of graduation was 14.00 (12 to 16). The average number of spinal surgeries was 14.28 (7 to 20). Two patients performed below the range of adult intellectual functioning. Auditory Consonant Trigram Test showed normal verbal working memory and attention control. Six patients had abnormal Verbal Fluency Test performance. Eight patients had abnormal ratings on at least one of the assessment scales of psychopathology (Symptom Checklist-90, Beck Depression Inventory, and Beck Anxiety Inventory). Eight patients had low-to-moderate self-esteem (Rosenberg self-esteem scale). The median spinal appearance questionnaire and SRS-22 scores were 34 and 4.18, respectively. Pain and function subdomains of SRS-22 scored higher than self-image and mental health. No correlation was found between the treatment duration and number of surgeries and test scores. SRS-22 showed correlations with multiple psychological tests.

Conclusion:
Completed TGR treatment yields acceptable correction of deformities and surgical outcomes, however, may fail to improve psychological well-being. This is the first study to find various psychosocial abnormalities in two-thirds of cases.

Level of Evidence:
Level IV; cross-sectional study.