bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond Plan-Do-Study-Act cycle – staff perceptions on facilitators and barriers to the implementation of telepresence robots in long-term care
Authors: Wong Joey , Young Erika , Hung Lillian , Mann Jim , Jackson Lynn 
Published: July 2023

AbstractBackgroundQuality improvement (QI) programs with technology implementations have been introduced to long-term care (LTC) to improve residents’ quality of life. Plan-Do-Study-Act (PDSA) cycle is commonly adopted in QI projects. There should be an appropriate investment of resources to enhance learning from iterative PDSA cycles. Recently, scholars explored possibilities of implementation science (IS) with QI methods to increase QI projects’ generalisability and make them more widely applicable in other healthcare contexts. To date, scant examples demonstrate the complementary use of the two methods in QI projects involving technology implementation. This qualitative study explores staff and leadership teams’ perspectives on facilitators and barriers of a QI project to implement telepresence robots in LTC guided by the Consolidated Framework for Implementation Research (CFIR).MethodsWe employed purposive and snowballing methods to recruit 22 participants from two LTC in British Columbia, Canada: operational and unit leaders and interdisciplinary staff, including nursing staff, care aides, and allied health practitioners. CFIR was used to guide data collection and analysis. Semi-structured interviews and focus groups were conducted through in-person and virtual meetings. Thematic analysis was employed to generate insights into participants’ perspectives.ResultsOur analysis identified three themes: (a) The essential needs for family-resident connections, (b) Meaningful engagement builds partnership, and (c) Training and timely support gives confidence. Based on the findings and CFIR guidance, we demonstrate how to plan strategies in upcoming PDSA cycles and offer an easy-to-use tool ‘START’ to encourage the practical application of evidence-based strategies in technology implementation:Share benefits and failures;Tailor planning with staff partners;Acknowledge staff concerns;Recruit opinion leaders early; andTarget residents’ needs.ConclusionsOur study offers pragmatic insights into the complementary application of CFIR with PDSA methods in QI projects on implementing technologies in LTC. Healthcare leaders should consider evidence-based strategies in implementing innovations beyond PDSA cycles.
Identification of cell subpopulations associated with disease phenotypes from scRNA-seq data using PACSI
Authors: Liu Chonghui , Zhang Yan , Gao Xin , Wang Guohua 
Published: July 2023

AbstractBackgroundSingle-cell RNA sequencing (scRNA-seq) has revolutionized the transcriptomics field by advancing analyses from tissue-level to cell-level resolution. Despite the great advances in the development of computational methods for various steps of scRNA-seq analyses, one major bottleneck of the existing technologies remains in identifying the molecular relationship between disease phenotype and cell subpopulations, where “disease phenotype” refers to the clinical characteristics of each patient sample, and subpopulation refer to groups of single cells, which often do not correspond to clusters identified by standard single-cell clustering analysis. Here, we present PACSI, a method aimed at distinguishing cell subpopulations associated with disease phenotypes at the single-cell level.ResultsPACSI takes advantage of the topological properties of biological networks to introduce a proximity-based measure that quantifies the correlation between each cell and the disease phenotype of interest. Applied to simulated data and four case studies, PACSI accurately identified cells associated with disease phenotypes such as diagnosis, prognosis, and response to immunotherapy. In addition, we demonstrated that PACSI can also be applied to spatial transcriptomics data and successfully label spots that are associated with poor survival of breast carcinoma.ConclusionsPACSI is an efficient method to identify cell subpopulations associated with disease phenotypes. Our research shows that it has a broad range of applications in revealing mechanistic and clinical insights of diseases.
Random capillary glucose levels throughout pregnancy, obstetric and neonatal outcomes, and long-term neurodevelopmental conditions in children: a group-based trajectory analysis
Authors: Chen Shuyun , Persson Margareta , Wang Rui , Dalman Christina , Lee Brian K. , Karlsson Håkan , Gardner Renee M. 
Published: July 2023

AbstractBackgroundGestational diabetes mellitus (GDM) is associated with both short- and long-term risks, although it is unknown if risks vary by severity, timing, and duration of gestational hyperglycemia. We aimed to identify trajectories of random capillary glucose (RCG) levels throughout pregnancy and assess their associations with both obstetric/neonatal outcomes and children’s risk of neurodevelopmental conditions (NDCs) (i.e., autism, intellectual disability, and attention-deficit/hyperactivity disorders [ADHD]).MethodsA population-based cohort study was conducted involving 76,228 children born to 68,768 mothers without pregestational diabetes. Group-based trajectory modeling was utilized to identify distinct glucose trajectories across RCG values throughout the course of pregnancy. The associations between these trajectory groups and obstetric/neonatal outcomes as well as children’s NDCs were then assessed using generalized estimating equation models with a logit link. The Benjamini-Hochberg (BH) procedure was employed to adjustP-values for multiple comparisons, controlling the false discovery rate (FDR).ResultsFive distinct glucose trajectory groups were identified, each with varying percentages diagnosed with GDM. Their associations with obstetric/neonatal outcomes as well as children’s NDCs varied. For example, when compared to the “Persistently Low” group, other groups exhibited varying degrees of increased risk for large-for-gestational-age babies, with the exception of the “High in Early Pregnancy” group. Compared to the “Persistently Low” group, all other trajectory groups were associated with NDC outcomes, except the “High in Mid-Pregnancy” group. However, none of the associations with offspring NDCs remained significant after accounting for the FDR correction.ConclusionsPersistent high glucose levels or moderately elevated glucose levels throughout pregnancy, as well as transient states of hyperglycemia in early or mid-pregnancy, were found to be associated with increased risks of specific obstetric and neonatal complications, and potentially offspring NDCs. These risks varied depending on the severity, timing, duration, and management of hyperglycemia. The findings underscore the need for continuous surveillance and individualized management strategies for women displaying different glucose trajectories during pregnancy. Limitations such as potential residual confounding, the role of mediators, and small sample size should be addressed in future studies.
Early non-response as a predictor of later non-response to antipsychotics in schizophrenia: a randomized trial
Authors: Long Yujun , Wu Qiongqiong , Yang Ye , Cai Jingda , Xiao Jingmei , Liu Zhaoqian , Xu Yifeng , Chen Ying , Huang Manli , Zhang Ruiguo , Xu Xijia , Hu Jian , Liu Zhifen , Liu Fang , Zheng Yingjun , Meng Huaqing , Wang Zhimin , Tang Yanqing , Song Xueqin , Chen Yunchun , Wang Xueyi , Liu Tiebang , Wu Xiaoli , Fang Maosheng , Wan Chunling , Zhao Jingping , Wu Renrong 
Published: July 2023

Abstract
Background
It remains a challenge to predict the long-term response to antipsychotics in patients with schizophrenia who do not respond at an early stage. This study aimed to investigate the optimal predictive cut-off value for early non-response that would better predict later non-response to antipsychotics in patients with schizophrenia.

Methods
This multicenter, 8-week, open-label, randomized trial was conducted at 19 psychiatric centers throughout China. All enrolled participants were assigned to olanzapine, risperidone, amisulpride, or aripiprazole monotherapy for 8 weeks. The positive and negative syndrome scale (PANSS) was evaluated at baseline, week 2, week 4, and week 8. The main outcome was the prediction of nonresponse. Nonresponse is defined as a < 20% reduction in the total scores of PANSS from baseline to endpoint. Severity ratings of mild, moderate, and severe illness corresponded to baseline PANSS total scores of 58, 75, and 95, respectively.

Results
At week 2, a reduction of < 5% in the PANSS total score showed the highest total accuracy in the severe and mild schizophrenia patients (total accuracy, 75.0% and 80.8%, respectively), and patients who were treated with the risperidone and amisulpride groups (total accuracy, 82.4%, and 78.2%, respectively). A 10% decrease exhibited the best overall accuracy in the moderate schizophrenia patients (total accuracy, 84.0%), olanzapine (total accuracy, 79.2%), and aripiprazole group (total accuracy, 77.4%). At week 4, the best predictive cut-off value was < 20%, regardless of the antipsychotic or severity of illness (total accuracy ranging from 89.8 to 92.1%).

Conclusions
Symptom reduction at week 2 has acceptable discrimination in predicting later non-response to antipsychotics in schizophrenia, and a more accurate predictive cut-off value should be determined according to the medication regimen and baseline illness severity. The response to treatment during the next 2 weeks after week 2 could be further assessed to determine whether there is a need to change antipsychotic medication during the first four weeks.

Trial registration
This study was registered on Clinicaltrials.gov (NCT03451734).
Cell-growth phase-dependent promoter replacement approach for improved poly(lactate-co-3-hydroxybutyrate) production in Escherichia coli
Authors: Nagao Yuki , Koh Sangho , Taguchi Seiichi , Shimada Tomohiro 
Published: July 2023

AbstractEscherichia coli is a useful platform for producing valuable materials through the implementation of synthetic gene(s) derived from other organisms. The production of lactate (LA)-based polyester poly[LA-co-3-hydroxybutyrate (3HB)] was carried out in E. coli using a set of five other species-derived genes: Pseudomonas sp. 61-3-derived phaC1STQK (for polymerization), Cupriavidus necator-derived phaAB (for 3HB-CoA generation), and Megasphaera elsdenii-derived pct (for LA-CoA generation) cloned into pTV118NpctphaC1ps(ST/QK)AB. Here, we aimed to optimize the expression level and timing of these genes to improve the production of P(LA-co-3HB) and to manipulate the LA fraction by replacing the promoters with various promoters in E. coli. Evaluation of the effects of 21 promoter replacement plasmids revealed that the phaC1STQK-AB operon is critical for the stationary phase for P(LA-co-3HB) production. Interestingly, the effects of the promoters depended on the composition of the medium. In glucose-supplemented LB medium, the dps promoter replacement plasmid resulted in the greatest effect, increasing the accumulation to 8.8 g/L and an LA fraction of 14.1 mol% of P(LA-co-3HB), compared to 2.7 g/L and 8.1 mol% with the original plasmid. In xylose-supplemented LB medium, the yliH promoter replacement plasmid resulted in the greatest effect, with production of 5.6 g/L and an LA fraction of 40.2 mol% compared to 3.6 g/L and 22.6 mol% with the original plasmid. These results suggest that the selection of an appropriate promoter for expression of the phaC1STQK-AB operon could improve the production and LA fraction of P(LA-co-3HB). Here, we propose that the selection of cell-growth phase-dependent promoters is a versatile biotechnological strategy for effective intracellular production of polymeric materials such as P(LA-co-3HB), in combination with the selection of sugar-based carbon sources.
Integrative analysis of the ST6GALNAC family identifies GATA2-upregulated ST6GALNAC5 as an adverse prognostic biomarker promoting prostate cancer cell invasion
Authors: Li Meiqian , Ma Zhihui , Zhang Yuqing , Feng Hanyi , Li Yang , Sang Weicong , Zhu Rujian , Huang Ruimin , Yan Jun 
Published: July 2023

Abstract
Background
ST6GALNAC family members function as sialyltransferases and have been implicated in cancer progression. However, their aberrant expression levels, prognostic values and specific roles in metastatic prostate cancer (PCa) remain largely unclear.

Methods
Two independent public datasets (TCGA-PRAD and GSE21032), containing 648 PCa samples in total, were employed to comprehensively examine the mRNA expression changes of ST6GALNAC family members in PCa, as well as their associations with clinicopathological parameters and prognosis. The dysregulation of ST6GALNAC5 was further validated in a mouse PCa model and human PCa samples from our cohort (n = 64) by immunohistochemistry (IHC). Gene Set Enrichment Analysis, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and drug sensitivity analyses were performed to enrich the biological processes most related to ST6GALNAC5. Sulforhodamine B, transwell, luciferase reporter and chromatin immunoprecipitation (ChIP) assays were used to examine the PCa cell proliferation, invasion and transcriptional regulation, respectively.

Results
Systematical investigation of six ST6GALNAC family members in public datasets revealed that ST6GALNAC5 was the only gene consistently and significantly upregulated in metastatic PCa, and ST6GALNAC5 overexpression was also positively associated with Gleason score and predicted poor prognosis in PCa patients. IHC results showed that (1) ST6GALNAC5 protein expression was increased in prostatic intraepithelial neoplasia and further elevated in PCa from a PbCre;PtenF/F mouse model; (2) overexpressed ST6GALNAC5 protein was confirmed in human PCa samples comparing with benign prostatic hyperplasia samples from our cohort (p < 0.001); (3) ST6GALNAC5 overexpression was significantly correlated with perineural invasion of PCa. Moreover, we first found transcription factor GATA2 positively and directly regulated ST6GALNAC5 expression at transcriptional level. ST6GALNAC5 overexpression could partially reverse GATA2-depletion-induced inhibition of PCa cell invasion. The GATA2-ST6GALNAC5 signature exhibited better prediction on the poor prognosis in PCa patients than GATA2 or ST6GALNAC5 alone.

Conclusions
Our results indicated that GATA2-upregulated ST6GALNAC5 might serve as an adverse prognostic biomarker promoting prostate cancer cell invasion.
Quasi-dendritic sulfonate-based organic small molecule for high-quality NIR-II bone-targeted imaging
Authors: Chen Pengfei , Qu Fan , He Liuliang , Li Mingfei , Sun Pengfei , Fan Quli , Zhang Chi , Li Daifeng 
Published: July 2023

AbstractThe visualization of bone imaging in vivo is of great significance for the understanding of some bone-related diseases or physiological processes. Herein, a bone-targeted NIR-II small molecule (TTQF-SO3), which was modified with multiple sulfonate groups, was successfully fabricated for the second near-infrared (NIR-II) bone imaging. In vitro studies revealed that TTQF-SO3 showed high affinity for hydroxyapatite and excellent macrophage accumulation ability. In in vivo assays, TTQF-SO3 displayed high bone uptake ability and high NIR-II bone imaging quality, demonstrating the specific bone-targeting ability of the sulfonate-containing probe. In addition, the noninvasive NIR-II imaging detection in bone calcium loss was successfully verified in osteoporosis mice models. Moreover, the negative charge characteristic of TTQF-SO3 showed efficient lymphoid enrichment in living mice by intravenous injection. Overall, these warrant that our TTQF-SO3 is an optimal bone-targeted diagnostic agent for high-quality NIR-II imaging, highlighting its potential promise for clinical translation.
Graphical Abstract
Exploring the relationship between North Star Ambulatory Assessment and Health Utilities Index scores in Duchenne muscular dystrophy
Authors: Audhya Ivana , Rogula Basia , Szabo Shelagh M. , Feeny David , Bolatova Talshyn , Gooch Katherine 
Published: July 2023

AbstractBackgroundThe North Star Ambulatory Assessment (NSAA) documents motor performance in ambulatory individuals with Duchenne muscular dystrophy (DMD). Health Utilities Index (HUI) scores, reflecting preferences for health-related quality-of-life (HRQoL) implications of health states, are commonly estimated within trials. This study sought to characterize the relationship between the NSAA score and utility in DMD.MethodsFamily members serving as proxy respondents for placebo-treated ambulatory individuals with DMD (NCT01254019; BioMarin Pharmaceuticals Inc) completed the HUI and the NSAA (score range, 0–34). Mean change over time on these measures was estimated, and the correlation between changes in NSAA score and a) HUI utility; b) HUI3 ambulation and HUI2 mobility attribute scores, over 48 weeks was calculated.ResultsBaseline mean (range) age was 8.0 years (5–16;n = 61) and mean (standard deviation [SD]) scores were 0.87 (0.13; HUI2), 0.82 (0.19; HUI3), and 21.0 (8.1; NSAA). Mean (SD) change over 48 weeks was –0.05 (0.14; HUI2), –0.06 (0.19; HUI3), and –2.9 (4.7; NSAA). Weak positive correlations were observed between baseline NSAA score and HUI utility (HUI2:r = 0.29; HUI3:r = 0.17) and for change over 48 weeks (HUI2:r = 0.16; HUI3:r = 0.15). Stronger correlations were observed between change in NSAA score and the HUI3 ambulation (r = 0.41) and HUI2 mobility (r = 0.41) attributes.ConclusionsAmong ambulatory individuals with DMD, NSAA score is weakly correlated with HUI utility, suggesting that motor performance alone does not fully explain HRQoL. Stronger relationships were observed between HUI ambulation and mobility attributes, and NSAA. Although unidimensional measures like the NSAA are informative for documenting disease-specific health impacts, they may not correlate well with measures of overall health status; requiring use in conjunction with other patient-reported and preference-based outcomes.
Single-cell transcriptome sequencing–based analysis: probing the mechanisms of glycoprotein NMB regulation of epithelial cells involved in silicosis
Authors: Yang Shaoqi , Sun Yuheng , Long Min , Zhou Xinbei , Yuan Mengqin , Yang Liliang , Luo Wei , Cheng Yusi , Zhang Xinxin , Jiang Wei , Chao Jie 
Published: July 2023

AbstractChronic exposure to silica can lead to silicosis, one of the most serious occupational lung diseases worldwide, for which there is a lack of effective therapeutic drugs and tools. Epithelial mesenchymal transition plays an important role in several diseases; however, data on the specific mechanisms in silicosis models are scarce. We elucidated the pathogenesis of pulmonary fibrosis via single-cell transcriptome sequencing and constructed an experimental silicosis mouse model to explore the specific molecular mechanisms affecting epithelial mesenchymal transition at the single-cell level. Notably, as silicosis progressed, glycoprotein non-metastatic melanoma protein B (GPNMB) exerted a sustained amplification effect on alveolar type II epithelial cells, inducing epithelial-to-mesenchymal transition by accelerating cell proliferation and migration and increasing mesenchymal markers, ultimately leading to persistent pulmonary pathological changes. GPNMB participates in the epithelial-mesenchymal transition in distant lung epithelial cells by releasing extracellular vesicles to accelerate silicosis. These vesicles are involved in abnormal changes in the composition of the extracellular matrix and collagen structure. Our results suggest that GPNMB is a potential target for fibrosis prevention.
Weighted ASTRID: fast and accurate species trees from weighted internode distances
Authors: Liu Baqiao , Warnow Tandy 
Published: July 2023

Abstract
Background
Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., “gene tree heterogeneity”). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing “gene trees”) and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance.

Results
Our experimental study evaluating weighted ASTRID typically shows improvements in accuracy compared to the original (unweighted) ASTRID, and shows competitive accuracy against weighted ASTRAL, the state of the art. Our re-implementation of ASTRID also improves the runtime, with marked improvements on large datasets.

Conclusions
Weighted ASTRID is a new and very fast method for species tree estimation that typically improves upon ASTRID and has comparable accuracy to weighted ASTRAL, while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode.
Analysis of JS-contractions with applications to fractional boundary value problems
Authors: Mehmood Nayyar , Nisar Zubair , Mukheimer Aiman , Abdeljawad Thabet 
Published: July 2023

AbstractIn this article, we modify JS-contractions by weakening the conditions on the function θ, where $\theta : ( 0,\infty ) \rightarrow ( 1,\infty ) $
θ
:
(
0
,
∞
)
→
(
1
,
∞
)
is a strictly increasing function. We prove fixed-point results for obtained contractions. Some examples are given to validate the results and modifications. We use our main theorem to establish the existence results for the solutions of the Atangana–Baleanu–Caputo fractional boundary value problem with integral boundary conditions. We also present a new definition of θ-Ulam stability and find the stability of our fractional boundary value problem.