bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic factors for persistent symptoms in adults with mild traumatic brain injury: an overview of systematic reviews
Authors: Déry Julien , Ouellet Béatrice , de Guise Élaine , Bussières Ève-Line , Lamontagne Marie-Eve 
Published: July 2023

Abstract
Background
Mild traumatic brain injury (mTBI) is an increasing public health problem, because of its persistent symptoms and several functional consequences. Understanding the prognosis of a condition is an important component of clinical decision-making and can help to guide the prevention of persistent symptoms following mTBI. The prognosis of mTBI has stimulated several empirical primary research papers and many systematic reviews leading to the identification of a wide range of factors. We aim to synthesize these factors to get a better understanding of their breadth and scope.

Methods
We conducted an overview of systematic reviews. We searched in databases systematic reviews synthesizing evidence about the prognosis of persistent symptoms after mTBI in the adult population. Two reviewers independently screened all references and selected eligible reviews based on eligibility criteria. They extracted relevant information using an extraction grid. They also rated independently the risk of bias using the ROBIS tool. We synthesized evidence into a comprehensive conceptual map to facilitate the understanding of prognostic factors that have an impact on persistent post-concussion symptoms.

Results
From the 3857 references retrieved in a database search, we included 25 systematic reviews integrating the results of 312 primary articles published between 1957 and 2019. We examined 35 prognostic factors from the systematics reviews. No single prognostic factor demonstrated convincing and conclusive results. However, age, sex, and multiple concussions showed an affirmatory association with persistent post-concussion outcomes in systematic reviews.

Conclusion
We highlighted the need for a comprehensive picture of prognostic factors related to persistent post-concussion symptoms. We believe that these prognostic factors would guide clinical decisions and research related to prevention and intervention regarding persistent post-concussion symptoms.

Systematic review registration
PROSPERO CRD42020176676
A distributional regression approach to modeling the impact of structural and intermediary social determinants on communities burdened by tuberculosis in Eastern Amazonia – Brazil
Authors: Giacomet Clóvis Luciano , Ramos Antônio Carlos Vieira , Moura Heriederson Sávio Dias , Berra Thaís Zamboni , Alves Yan Mathias , Delpino Felipe Mendes , Farley Jason E. , Reynolds Nancy R. , Alonso Jonas Bodini , Teibo Titilade Kehinde Ayandeyi , Arcêncio Ricardo Alexandre 
Published: July 2023

Abstract
Background
Tuberculosis (TB) is a disease that is influenced by social determinants of health. However, the specific structural and intermediary determinants of TB in Eastern Amazonia remain unclear. Despite being rich in natural resources, the region faces significant challenges related to poverty, inequality, and neglected diseases. The objective of this study was to use mathematical modeling to evaluate the influence of structural and intermediary determinants of health on TB in Eastern Amazonia, Brazil.

Methods
This cross-sectional included all TB cases diagnosed and registered in the Notifiable Diseases Information System (SINAN) from 2001 to 2017. Data on social determinants were collected at the census tract level. The generalized additive model for location, scale, and shape (GAMLSS) framework was employed to identify the effect of social determinants on communities with a high TB prevalence. The Double Poisson distribution (DPO) was chosen, and inclusion of quadratic effects was tested.

Results
A total of 1730 individuals were diagnosed with TB and reported in SINAN during the analyzed period. The majority were female (59.3%), aged 31 to 59 years (47.6%), identified as blacks (67.9%), and had incomplete elementary education (46.6%). The prevalence of alcoholism was 8.6% and mental illness was 0.7%. GAMLSS analyses demonstrated that the risk of community incidence of TB is associated with the proportion of the population lacking basic sanitation, as well as with the age groups of 16–31 years and > 61 years.

Conclusions
The study highlights the strategic utility of GAMLSS in identifying high-risk areas for TB. Models should encompass a broader range of social determinants to inform policies aimed at reducing inequality and achieving the goals of the End TB strategy.
Designing and psychometric analysis of an instrument to assess learning process in a virtual environment
Authors: Ahmady Soleiman , Kohan Noushin , Mirmoghtadaie Zohreh Sadat , Hamidi Hadi , Sabet Divshali Babak , Rakhshani Tayebeh , Khani Jeihooni Ali 
Published: July 2023

AbstractBackgroundToday, methods that enable students to benefit from online programs to the fullest and learn independently and self-directed are of critical importance. Many scales have been developed to measure self-directed learning in the physical classroom. This study was conducted to design and assess the psychometric properties of an instrument to assess learning process in a virtual environment.Materials and methodsA questionnaire for assessing s learning process in a virtual environment was developed following six steps. The process began with a systematic search for related articles. A qualitative study was then conducted to identify self-directed learning strategies and processes in virtual environments. The identified strategies were then compared with those from a literature review, and the scale items were developed accordingly. Expert validation, exploratory factor analysis, and reliability analysis were conducted to ensure questionnaire validity and reliability. This study included online postgraduate students from Iranian medical science universities in 2019.ResultsThe scale consisted of 5 factors and 44 items. In exploratory factor analysis, five subscales explained 90% of the total variance. Cronbach’s alpha was 0.91 for the total scale. The interclass correlation coefficient between the test and retest was 0.77.ConclusionA questionnaire designed to assess learning process in a virtual environment for postgraduate virtual students has reasonable psychometric properties, including reasonable internal reliability and construct validity.
Strong coupling in plasmonic metal nanoparticles
Authors: Lee Yoon-Min , Kim Seong-Eun , Park Jeong-Eun 
Published: July 2023

AbstractThe study of strong coupling between light and matter has gained significant attention in recent years due to its potential applications in diverse fields, including artificial light harvesting, ultraefficient polariton lasing, and quantum information processing. Plasmonic cavities are a compelling alternative of conventional photonic resonators, enabling ultracompact polaritonic systems to operate at room temperature. This review focuses on colloidal metal nanoparticles, highlighting their advantages as plasmonic cavities in terms of their facile synthesis, tunable plasmonic properties, and easy integration with excitonic materials. We explore recent examples of strong coupling in single nanoparticles, dimers, nanoparticle-on-a-mirror configurations, and other types of nanoparticle-based resonators. These systems are coupled with an array of excitonic materials, including atomic emitters, semiconductor quantum dots, two-dimensional materials, and perovskites. In the concluding section, we offer perspectives on the future of strong coupling research in nanoparticle systems, emphasizing the challenges and potentials that lie ahead. By offering a thorough understanding of the current state of research in this field, we aim to inspire further investigations and advances in the study of strongly coupled nanoparticle systems, ultimately unlocking new avenues in nanophotonic applications.
Fluid management strategies and their interaction with mechanical ventilation: from experimental studies to clinical practice
Authors: de Carvalho Eduardo Butturini , Battaglini Denise , Robba Chiara , Malbrain Manu L. N. G. , Pelosi Paolo , Rocco Patricia Rieken Macedo , Silva Pedro Leme 
Published: July 2023

AbstractPatients on mechanical ventilation may receive intravenous fluids via restrictive or liberal fluid management. A clear and objective differentiation between restrictive and liberal fluid management strategies is lacking in the literature. The liberal approach has been described as involving fluid rates ranging from 1.2 to 12 times higher than the restrictive approach. A restrictive fluid management may lead to hypoperfusion and distal organ damage, and a liberal fluid strategy may result in endothelial shear stress and glycocalyx damage, cardiovascular complications, lung edema, and distal organ dysfunction. The association between fluid and mechanical ventilation strategies and how they interact toward ventilator-induced lung injury (VILI) could potentiate the damage. For instance, the combination of a liberal fluids and pressure-support ventilation, but not pressure control ventilation, may lead to further lung damage in experimental models of acute lung injury. Moreover, under liberal fluid management, the application of high positive end-expiratory pressure (PEEP) or an abrupt decrease in PEEP yielded higher endothelial cell damage in the lungs. Nevertheless, the translational aspects of these findings are scarce. The aim of this narrative review is to provide better understanding of the interaction between different fluid and ventilation strategies and how these interactions may affect lung and distal organs. The weaning phase of mechanical ventilation and the deresuscitation phase are not explored in this review.
Does human milk composition predict later risk of obesity? A systematic review
Authors: Vieira Queiroz De Paula Mayara , Grant Maude , Lanigan Julie , Singhal Atul 
Published: July 2023

Abstract
Background
Possible mechanisms behind the association of breastfeeding with a lower risk of later obesity are unknown but one possibility is the unique composition of human milk. Here, we systematically reviewed the evidence linking breast-milk macronutrient and hormonal composition with later obesity.

Methods
We searched 7 databases for studies that included infants predominantly breast-fed for the first 3 months and which analysed associations between a measure of breast-milk composition and later (> 6 months) measures of obesity or body composition.

Results
47 publications were identified for full-text screening, of which 10 were eligible and only 3 found significant associations. Higher leptin concentration in breast milk at age 1 month was associated with lower infant BMI at 12, 18 and 24 months of age (1 study). Higher breast-milk adiponectin concentration at 6 weeks and 4 months were associated with adiposity at age 12 and 24 months (1 study). In 1 study, breast-milk carbohydrate content was positively associated, and fat content negatively associated, with adiposity at age 12 months. No significant associations were found between other hormones or macronutrients in human milk and later risk of obesity or body composition.

Conclusions
The evidence linking breast-milk composition with later obesity was inconsistent and confined to single, individual studies. Our review highlights the methodological limitations of previous studies and the need for further research in this area.
G9a inactivation in progenitor cells with Isl1-Cre with reduced recombinase activity models aspects of Dandy-Walker complex
Authors: Chi Lijun , Zhong Ling , Lee Dorothy , Yu Xinwen , Caballero Amalia , Nieman Brian , Delgado-Olguin Paul 
Published: July 2023

ABSTRACT
G9a, also known as EHMT2, is essential for embryogenesis and has specific functions in multiple developmental processes. G9a inactivation affects development of the nervous system, which is formed with contribution of descendants of progenitor cells expressing the transcription factor Isl1. However, the function of G9a in Isl1-expressing progenitors is unknown. Here, we show that G9a is required for proper development of multiple structures formed with contribution of Isl1-expressing progenitors. A Cre-dependent GFP reporter revealed that the recombinase activity of the Isl1-Cre used in this study to inactivate G9a was reduced to a subset of Isl1-expressing progenitor cells. G9a mutants reached endpoint by 7 weeks of age with cardiac hypertrophy, hydrocephalus, underdeveloped cerebellum and hind limb paralysis, modeling aspects of Dandy-Walker complex. Moreover, neuroepithelium of the lateral ventricle derived from Isl1-expressing progenitors was thinner and disorganized, potentially compromising cerebrospinal fluid dynamics in G9a mutants. Micro-computed tomography after iodine staining revealed increased volume of the heart, eye lens and brain structures in G9a mutant fetuses. Thus, altered development of descendants of the second heart field and the neural crest could contribute to multicomponent malformation like Dandy-Walker.
A functional sgRNA-CRISPR screening method for generating murine RET and NTRK1 rearranged oncogenes
Authors: Schubert Laura , Le Anh T. , Hinz Trista K. , Navarro Andre C. , Nelson-Taylor Sarah K. , Nemenoff Raphael A. , Heasley Lynn E. , Doebele Robert C. 
Published: July 2023

ABSTRACT
CRISPR/Cas9 gene editing represents a powerful tool for investigating fusion oncogenes in cancer biology. Successful experiments require that sgRNAs correctly associate with their target sequence and initiate double stranded breaks which are subsequently repaired by endogenous DNA repair systems yielding fusion chromosomes. Simple tests to ensure sgRNAs are functional are not generally available and often require single cell cloning to identify successful CRISPR-editing events. Here, we describe a novel method relying on acquisition of IL3-independence in Ba/F3 cells to identify sgRNA pairs that generate oncogenic gene rearrangements of the Ret and Ntrk1 tyrosine kinases. The rearrangements were confirmed with PCR, RT-PCR and sequencing and Ba/F3 cells harboring Ret or Ntrk1 rearrangements acquired sensitivity to RET and TRK inhibitors, respectively. Adenoviruses encoding Cas9 and sgRNA pairs inducing the Kif5b-Ret and Trim24-Ret rearrangements were intratracheally instilled into mice and yielded lung adenocarcinomas. A cell line (TR.1) established from a Trim24-Ret positive tumor exhibited high in vitro sensitivity to the RET inhibitors LOXO-292 and BLU-667 and orthotopic TR.1 cell-derived tumors underwent marked shrinkage upon LOXO-292 treatment. Thus, the method offers an efficient means to validate sgRNAs that successfully target their intended loci for the generation of novel, syngeneic murine oncogene-driven tumor models.
Flat mount preparation for whole-mount fluorescent imaging of zebrafish embryos
Authors: Frommelt Joseph , Liu Emily , Bhaidani Afraz , Hu Bo , Gao Yuanyuan , Ye Ding , Lin Fang 
Published: July 2023

ABSTRACT
The zebrafish is a widely used model organism for biomedical research due to its ease of maintenance, external fertilization of embryos, rapid embryonic development, and availability of established genetic tools. One notable advantage of using zebrafish is the transparency of the embryos, which enables high-resolution imaging of specific cells, tissues, and structures through the use of transgenic and knock-in lines. However, as the embryo develops, multiple layers of tissue wrap around the lipid-enriched yolk, which can create a challenge to image tissues located deep within the embryo. While various methods are available, such as two-photon imaging, cryosectioning, vibratome sectioning, and micro-surgery, each of these has limitations. In this study, we present a novel deyolking method that allows for high-quality imaging of tissues that are obscured by other tissues and the yolk. Embryos are lightly fixed in 1% PFA to remove the yolk without damaging embryonic tissues and are then refixed in 4% PFA and mounted on custom-made bridged slides. This method offers a simple way to prepare imaging samples that can be subjected to further preparation, such as immunostaining. Furthermore, the bridged slides described in this study can be used for imaging tissue and organ preparations from various model organisms.
All ions must serve: The role of various regimes of data acquisition in joint classifier for intraoperative mass spectrometry-based glial tumour identification
Authors: Pekov Stanislav I. , Zavorotnyuk Denis S. , Sorokin Anatoly A. , Bormotov Denis S. , Derkach Mariya M. , Starkov Dmitrii N. , Popov Igor A. 
Published: July 2023

Background: Ambient ionisation mass spectrometry, in combination with machine learning techniques, provides a promising tool for rapid intraoperative tumour tissue identification. However, deficiency of non-tumour control samples leads to the classifiers overfitting, especially in neurosurgical applications. Ensemble learning approaches based on the analysis of multimodal mass spectrometry data are able to overcome the overfitting problem through the extended time of data acquisition. In this work, the contribution of each regime of the data acquisition and the requirements for the metrics for further mass spectrometry set-up optimisation are evaluated. Methods: Two independent datasets of the multimodal molecular profiles, a total of 81 glial tumour and non-tumour pathological tissues, were analysed in a cross-validation set-up. The XGboost algorithm was used to build classifiers, and their performance was evaluated using different testing and validating sets. The individual classifiers for each mass spectrometry regime were aggregated into joint classifiers. The impact of each regime was evaluated by the exclusion of specific regimes from the aggregation. Results: The aggregated classifiers with excluded regimes show lower accuracy for most, but not all, excluded regimes. False positive rates have been found to be increased in most cases proving the strong effect of the ensemble learning approach on the overcoming of the “small sample size” problem. Conclusions: The impact of each group of regimes – with different ion polarity, resolution or mass range of spectra was found to be non-linear. It might be attributed to biochemical reasons as well as to the physical limitation of mass analysers. The required metrics for the evaluation of each regime contribution to the classification efficiency should be a numerical estimation of how the classifier depends on any given regime and could not be estimated only by excluding any group of regimes at all.
Worldwide prevalence of carpal tunnel syndrome among dental health care personnel - A systematic review and meta-analysis
Authors: Chenna Deepika , Madi Medhini , Kumar Mathangi , Kumar Vijay , Chopperla Sitaram , Tadikonda Abhinav , Pentapati Kalyana 
Published: July 2023

Background: Carpal Tunnel Syndrome (CTS) is one such common disorder among dental health care personnel caused due to the entrapment neuropathy of the median nerve in the carpal tunnel. We aimed to evaluate the pooled estimates of the CTS among dental healthcare personnel. Methods: We systematically reviewed the existing literature from six databases till January 1st, 2022. Studies reported in English along with the prevalence of CTS or where prevalence could be calculated were included. Independent screening of title and abstracts, and the full text was done by two examiners. Information collected was authors, year of publication, geographic location, type of dental healthcare personnel, sample size, distribution of age, sex, CTS, method of diagnosis, and risk of bias. The random effect model was used to estimate the pooled estimates. Results: Thirty-seven studies yielded 38 estimates. A total of 17,152 dental health care personnel were included of which 2717 had CTS. The overall pooled prevalence of CTS among the included studies was 15%, with a high heterogeneity. Meta-analysis showed no significant difference in the pooled estimates of CTS between male and female dental healthcare personnel (OR: 0.73; 95% CI: 0.52 -1.02; I2= 69.71). The pooled estimates among the dentist and dental auxiliaries were 20% and 10%, respectively. The pooled prevalence of CTS with self-reported measures, clinical examination and NCS were 21%, 13% and 8% respectively. Meta-regression showed that the prevalence estimates were significantly associated with publication year (coefficient: 0.006; 95% CI= 0.002-0.01). Conclusion: One out of seven dental health care personnel may be affected by CTS. No significant difference was seen in the prevalence of CTS between male and female dental healthcare personnel.
Single-cell transcriptional uncertainty landscape of cell differentiation
Authors: Gao Nan Papili , Gandrillon Olivier , Páldi András , Herbach Ulysse , Gunawan Rudiyanto 
Published: July 2023

Background: Single-cell studies have demonstrated the presence of significant cell-to-cell heterogeneity in gene expression. Whether such heterogeneity is only a bystander or has a functional role in the cell differentiation process is still hotly debated. Methods: In this study, we quantified and followed single-cell transcriptional uncertainty – a measure of gene transcriptional stochasticity in single cells – in 10 cell differentiation systems of varying cell lineage progressions, from single to multi-branching trajectories, using the stochastic two-state gene transcription model. Results: By visualizing the transcriptional uncertainty as a landscape over a two-dimensional representation of the single-cell gene expression data, we observed universal features in the cell differentiation trajectories that include: (i) a peak in single-cell uncertainty during transition states, and in systems with bifurcating differentiation trajectories, each branching point represents a state of high transcriptional uncertainty; (ii) a positive correlation of transcriptional uncertainty with transcriptional burst size and frequency; (iii) an increase in RNA velocity preceding the increase in the cell transcriptional uncertainty. Conclusions: Our findings suggest a possible universal mechanism during the cell differentiation process, in which stem cells engage stochastic exploratory dynamics of gene expression at the start of the cell differentiation by increasing gene transcriptional bursts, and disengage such dynamics once cells have decided on a particular terminal cell identity. Notably, the peak of single-cell transcriptional uncertainty signifies the decision-making point in the cell differentiation process.