bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of T-POD and SAM Pelvic Sling II and the influence of attachment level in the initial management of unstable pelvic type C injuries – a cadaveric study
Authors: Privalov Maxim , Junge Malte , Jung Matthias Karl , Vetter Sven Yves , Franke Jochen , Hetjens Svetlana , Grützner Paul Alfred , Stadthalter Holger 
Published: March 2024

Abstract
Background
Type C pelvic fractures (AO/OTA) are severe injuries that frequently lead to bleeding and hemodynamic instability. Pelvic binders play a crucial role in their initial management. Placement at the correct level in the prehospital setting is challenging. The aim of this study was to compare two pelvic binders regarding their effectiveness in reducing intrapelvic volume and increasing intrapelvic pressure in patients with type C pelvic fractures (AO/OTA) when applied at three different levels.

Methods
Rotationally and vertically unstable pelvic injuries (AO/OTA classification 61-C1.1) were produced in five fresh-frozen human cadaveric specimens. Intrapelvic volume, vesical pressure and compression pressure within the pubic symphysis and the sacroiliac joint were measured when applying a SAM Pelvic Sling II and a T-POD at the level of the greater trochanter as well as levels higher and lower than recommended.

Results
Comparison of the two pelvic binders positioned at the recommended level (greater trochanter) showed no significant difference in volume reduction (13.85 ± 31.37 cm3, p = 0.442), however, increase in vesical pressure was significantly higher when using the T-POD (5.80 ± 3.27 cmH2O, p = 0.017). When positioned at the level of the iliac crest, vesical pressure increase and intrapelvic volume reduction were significantly greater with the T-POD (14.00 ± 8.57 cmH2O, p = 0.022 and 10.45 ± 5.45 cm3, p = 0.031 respectively). Application of the SAM Pelvic Sling II below the greater trochanter led to a significantly greater decrease in volume (-32.26 ± 7.52 cm3, p = 0.003) than the T-POD. Comparison of the recommended attachment level with incorrect positioning led to no significant differences for the T-POD, while the SAM Pelvic Sling II achieved a significantly lower volume reduction when placed at the iliac crest (40.15 ± 14.57 cm3, p = 0.012) and a significantly lower increase in vesical pressure when applied below the greater trochanter (3.40 ± 1.52 cmH2O, p = 0.007).

Conclusion
Direct comparison of the two pelvic binders showed that the T-POD achieved significantly greater results when applied at the recommended level and was less susceptible to incorrect positioning. These outcomes support the preferred use of the T-POD for prehospital emergency pelvic stabilisation.
Determining the environmental effect of Chinese FDI on the Belt and Road countries CO2 emissions: an EKC-based assessment in the context of pollution haven and halo hypotheses
Authors: Liu Peiqian , Ur Rahman Zia , Jóźwik Bartosz , Doğan Mesut 
Published: March 2024

AbstractThis work aims to examines the effect of Chinese outward foreign direct investment (CoFDI), renewable energy, and energy intensity on CO2 emissions in 46 Belt and Road Initiative (BRI) nations divided into: Panel A, consisting of 16 European countries, and Panel B, comprising 30 Asian and MENA countries. This analysis used data from 2005 to 2018, applying second-generation econometric techniques. The empirical outcomes, obtained using Driscoll–Kraay methods, confirmed the pollution halo effect in Panel A, suggesting that FDI flows in these countries are environmentally friendly. In contrast, the results indicated a positive impact of CoFDI on CO2e in Panel B, supporting the pollution haven hypothesis that FDI may add to pollution. In addition, the study found an inverted-U-shaped association between per capita income and CO2e, validating the environmental Kuznets curve (EKC) hypothesis in both panels. The findings also revealed that energy intensity positively affects CO2e, whereas renewable energy has a significant negative effect in both panels, while the interaction terms of renewable and energy intensity are heterogenous in both panels. Based on these findings, the study recommends policy makers of these countries to attract clean FDI, particularly in renewable sectors, and shift from fossil fuel-based energy to renewable sources to control pollution by enacting energy-saving initiatives via lowering energy intensity.
BSXplorer: analytical framework for exploratory analysis of BS-seq data
Authors: Yuditskiy Konstantin , Bezdvornykh Igor , Kazantseva Anastasiya , Kanapin Alexander , Samsonova Anastasia 
Published: March 2024

Abstract
Background
Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily.

Results
BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication.

Conclusions
BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research.
Evaluation of aphid resistance on different rose cultivars and transcriptome analysis in response to aphid infestation
Authors: Dong Wenqi , Sun Lei , Jiao Bo , Zhao Pu , Ma Chunhong , Gao Junping , Zhou Shuo 
Published: March 2024

Abstract
Background
The rose is one of the most important ornamental flowers in the world for its aesthetic beauty but can be attacked by many pests such as aphids. Aphid infestation causes tremendous damage on plant tissues leading to harmed petals and leaves. Rose cultivars express different levels of resistance to aphid infestation yet the information remains unclear. Not only that, studies about the transcriptional analysis on defending mechanisms against aphids in rose are limited so far.

Results
In this study, the aphid resistance of 20 rose cultivars was evaluated, and they could be sorted into six levels based on the number ratio of aphids. And then, a transcriptome analysis was conducted after aphid infestation in one high resistance (R, Harmonie) and one highly susceptibility (S, Carefree Wonder) rose cultivar. In open environment the majority of rose cultivars had the highest aphid number at May 6th or May 15th in 2020 and the resistance to infestation could be classified into six levels. Differential expression analysis revealed that there were 1,626 upregulated and 767 downregulated genes in the R cultivar and 481 upregulated and 63 downregulated genes in the S cultivar after aphid infestation. Pathway enrichment analysis of the differentially expressed genes revealed that upregulated genes in R and S cultivars were both enriched in defense response, biosynthesis of secondary metabolites (phenylpropanoid, alkaloid, and flavonoid), carbohydrate metabolism (galactose, starch, and sucrose metabolism) and lipid processing (alpha-linolenic acid and linolenic acid metabolism) pathways. In the jasmonic acid metabolic pathway, linoleate 13S-lipoxygenase was specifically upregulated in the R cultivar, while genes encoding other crucial enzymes, allene oxide synthase, allene oxide cyclase, and 12-oxophytodienoate reductase were upregulated in both cultivars. Transcription factor analysis and transcription factor binding search showed that WRKY transcription factors play a pivotal role during aphid infestation in the R cultivar.

Conclusions
Our study indicated the potential roles of jasmonic acid metabolism and WRKY transcription factors during aphid resistance in rose, providing clues for future research.
De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome
Authors: Ryder David , Stone David , Minardi Diana , Riley Ainsley , Avant Justin , Cross Lisa , Soeffker Marta , Davidson Deborah , Newman Andrew , Thomson Peter , Darby Chris , van Aerle Ronny 
Published: March 2024

Abstract
Background
Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited.

Results
A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome.

Conclusions
We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.
Identification and validation of RNA-binding protein SLC3A2 regulates melanocyte ferroptosis in vitiligo by integrated analysis of single-cell and bulk RNA-sequencing
Authors: Zhang Jingzhan , Xiang Fang , Ding Yuan , Hu Wen , Wang Hongjuan , Zhang Xiangyue , Lei Zixian , Li Tingting , Wang Peng , Kang Xiaojing 
Published: March 2024

Abstract
Background
The pathogenesis of vitiligo remains unclear. The genes encoding vitiligo-related RNA-binding proteins (RBPs) and their underlying pathogenic mechanism have not been determined.

Results
Single-cell transcriptome sequencing (scRNA-seq) data from the CNCB database was obtained to identify distinct cell types and subpopulations and the relative proportion changes in vitiligo and healthy samples. We identified 14 different cell types and 28 cell subpopulations. The proportion of each cell subpopulation significantly differed between the patients with vitiligo and healthy groups. Using RBP genes for unsupervised clustering, we obtained the specific RBP genes of different cell types in vitiligo and healthy groups. The RBP gene expression was highly heterogeneous; there were significant differences in some cell types, such as keratinocytes, Langerhans, and melanocytes, while there were no significant differences in other cells, such as T cells and fibroblasts, in the two groups. The melanocyte-specific RBP genes were enriched in the apoptosis and immune-related pathways in the patients with vitiligo. Combined with the bulk RNA-seq data of melanocytes, key RBP genes related to melanocytes were identified, including eight upregulated RBP genes (CDKN2A, HLA-A, RPL12, RPL29, RPL31, RPS19, RPS21, and RPS28) and one downregulated RBP gene (SLC3A2). Cell experiments were conducted to explore the role of the key RBP gene SLC3A2 in vitiligo. Cell experiments confirmed that melanocyte proliferation decreased, whereas apoptosis increased, after SLC3A2 knockdown. SLC3A2 knockdown in melanocytes also decreased the SOD activity and melanin content; increased the Fe2+, ROS, and MDA content; significantly increased the expression levels of TYR and COX2; and decreased the expression levels of glutathione and GPX4.

Conclusion
We identified the RBP genes of different cell subsets in patients with vitiligo and confirmed that downregulating SLC3A2 can promote ferroptosis in melanocytes. These findings provide new insights into the pathogenesis of vitiligo.
Defined co-cultures of glutamatergic and GABAergic neurons with a mutation in DISC1 reveal aberrant phenotypes in GABAergic neurons
Authors: Heider Johanna , Stahl Aaron , Sperlich Denise , Hartmann Sophia-Marie , Vogel Sabrina , Breitmeyer Ricarda , Templin Markus , Volkmer Hansjürgen 
Published: March 2024

Abstract
Background
Mutations in the gene DISC1 are associated with increased risk for schizophrenia, bipolar disorder and major depression. The study of mutated DISC1 represents a well-known and comprehensively characterized approach to understand neuropsychiatric disease mechanisms. However, previous studies have mainly used animal models or rather heterogeneous populations of iPSC-derived neurons, generated by undirected differentiation, to study the effects of DISC1 disruption. Since major hypotheses to explain neurodevelopmental, psychiatric disorders rely on altered neuronal connectivity observed in patients, an ideal iPSC-based model requires accurate representation of the structure and complexity of neuronal circuitries. In this study, we made use of an isogenic cell line with a mutation in DISC1 to study neuronal synaptic phenotypes in a culture system comprising a defined ratio of NGN2 and ASCL1/DLX2 (AD2)-transduced neurons, enriched for glutamatergic and GABAergic neurons, respectively, to mimic properties of the cortical microcircuitry.

Results
In heterozygous DISC1 mutant neurons, we replicated the expected phenotypes including altered neural progenitor proliferation as well as neurite outgrowth, deregulated DISC1-associated signaling pathways, and reduced synaptic densities in cultures composed of glutamatergic neurons. Cultures comprising a defined ratio of NGN2 and AD2 neurons then revealed considerably increased GABAergic synapse densities, which have not been observed in any iPSC-derived model so far. Increased inhibitory synapse densities could be associated with an increased efficiency of GABAergic differentiation, which we observed in AD2-transduced cultures of mutant neurons. Additionally, we found increased neuronal activity in GABAergic neurons through calcium imaging while the activity pattern of glutamatergic neurons remained unchanged.

Conclusions
In conclusion, our results demonstrate phenotypic differences in a co-culture comprising a defined ratio of DISC1 mutant NGN2 and AD2 neurons, as compared to culture models comprising only one neuronal cell type. Altered synapse numbers and neuronal activity imply that DISC1 impacts the excitatory/inhibitory balance in NGN2/AD2 co-cultures, mainly through increased GABAergic input.
Preventive and therapeutic effects of rifaximin on hepatic encephalopathy with differential application dosages and strategies: a network meta-analysis
Authors: Fang Guihua , Liu Shuna , Liu Bin 
Published: March 2024

Abstract
Background
Hepatic encephalopathy (HE) is a neuropsychiatric syndrome that affects the prognosis of patients with liver disease and is considered an independent risk factor for hospitalization and death. Rifaximin has been approved for HE treatment. This review will analyze the effect of rifaximin on different stages of HE with differential application dosages and strategies by traditional and network meta-analyses.

Methods
We performed a systematic search of PubMed, EmBase, and Cochrane Library databases up to February 26, 2023, to identify randomized controlled trials (RCTs) about rifaximin for the prevention and treatment of HE. The outcomes included incidence of HE and HE progression, HE reversal, mortality, and adverse effects.

Results
A total of 21 studies were included. In the primary prevention of HE, rifaximin significantly reduced the incidence of HE (OR: 0.66; 95% CI: 0.45, 0.96; p = 0.032). In secondary prevention, rifaximin significantly reduced the risk of recurrence in patients who were in remission (OR: 0.38; 95% CI: 0.28, 0.52; p < 0.001). In the treatment of minimal HE, rifaximin significantly reduced the breakthrough of MHE to OHE (OR: 0.17; 95% CI: 0.04,0.63; p = 0.008). Rifaximin also significantly improved the clinical symptoms of MHE and OHE patients (OR: 3.76; 95% CI: 2.69, 5.25; p < 0.001). However, rifaximin did not reduce mortality at any stage in HE patients (OR: 0.79; 95% CI: 0.58, 1.08; p = 0.133). Additionally, rifaximin did not increase the risk of adverse effects (OR: 0.96; 95% CI: 0.74, 1.24; p = 0.749). In the network meta-analysis, the 400 mg T.I.D. intervention had a relative advantage for HE risks in primary and secondary prevention. In the treatment of MHE, 600 mg b.i.d. was superior in preventing the breakthrough from MHE to OHE.

Conclusion
Rifaximin prevented HE risks and progression and improved clinical symptoms in patients with MHE but did not reduce mortality. For primary and secondary prevention, 400 mg t.i.d. could be considered. 600 mg b.i.d. could be considered in patients with MHE.
Prediction of survival and analysis of prognostic factors for patients with AFP negative hepatocellular carcinoma: a population-based study
Authors: Liu Chengyu , Li Zikang , Zhang Zhilei , Li Jinlong , Xu Congxi , Jia Yuming , Zhang Chong , Yang Wuhan , Wang Wenchuan , Wang Xiaojuan , Liang Kuopeng , Peng Li , Wang Jitao 
Published: March 2024

Abstract
Purpose
Hepatocellular carcinoma (HCC) has a poor prognosis, and alpha-fetoprotein (AFP) is widely used to evaluate HCC. However, the proportion of AFP-negative individuals cannot be disregarded. This study aimed to establish a nomogram of risk factors affecting the prognosis of patients with AFP-negative HCC and to evaluate its diagnostic efficiency.

Patients and methods
Data from patients with AFP-negative initial diagnosis of HCC (ANHC) between 2004 and 2015 were collected from the Surveillance, Epidemiology, and End Results database for model establishment and validation. We randomly divided overall cohort into the training or validation cohort (7:3). Univariate and multivariate Cox regression analysis were used to identify the risk factors. We constructed nomograms with overall survival (OS) and cancer-specific survival (CSS) as clinical endpoint events and constructed survival analysis by using Kaplan-Meier curve. Also, we conducted internal validation with Receiver Operating Characteristic (ROC) analysis and Decision curve analysis (DCA) to validate the clinical value of the model.

Results
This study included 1811 patients (1409 men; 64.7% were Caucasian; the average age was 64 years; 60.7% were married). In the multivariate analysis, the independent risk factors affecting prognosis were age, ethnicity, year of diagnosis, tumor size, tumor grade, surgery, chemotherapy, and radiotherapy. The nomogram-based model related C-indexes were 0.762 (95% confidence interval (CI): 0.752–0.772) and 0.752 (95% CI: 0.740–0.769) for predicting OS, and 0.785 (95% CI: 0.774–0.795) and 0.779 (95% CI: 0.762–0.795) for predicting CSS. The nomogram model showed that the predicted death was consistent with the actual value. The ROC analysis and DCA showed that the nomogram had good clinical value compared with TNM staging.

Conclusion
The age(HR:1.012, 95% CI: 1.006–1.018, P-value < 0.001), ethnicity(African-American: HR:0.946, 95% CI: 0.783–1.212, P-value: 0.66; Others: HR:0.737, 95% CI: 0.613–0.887, P-value: 0.001), tumor diameter(HR:1.006, 95% CI: 1.004–1.008, P-value < 0.001), year of diagnosis (HR:0.852, 95% CI: 0.729–0.997, P-value: 0.046), tumor grade(Grade 2: HR:1.124, 95% CI: 0.953–1.326, P-value: 0.164; Grade 3: HR:1.984, 95% CI: 1.574–2.501, P-value < 0.001; Grade 4: HR:2.119, 95% CI: 1.115–4.027, P-value: 0.022), surgery(Liver Resection: HR:0.193, 95% CI: 0.160–0.234, P-value < 0.001; Liver Transplant: HR:0.102, 95% CI: 0.072–0.145, P-value < 0.001), chemotherapy(HR:0.561, 95% CI: 0.471–0.668, P-value < 0.001), and radiotherapy(HR:0.641, 95% CI: 0.463–0.887, P-value:0.007) were independent prognostic factors for patients with ANHC. We developed a nomogram model for predicting the OS and CSS of patients with ANHC, with a good predictive performance.
Age- and sex-specific associations of frailty with mortality and healthcare utilization in community-dwelling adults from Ontario, Canada
Authors: Verschoor Chris P. , Theou Olga , Ma Jinhui , Montgomery Phyllis , Mossey Sharolyn , Nangia Parveen , Saskin Refik , Savage David W. 
Published: March 2024

Abstract
Background
Understanding how health trajectories are related to the likelihood of adverse outcomes and healthcare utilization is key to planning effective strategies for improving health span and the delivery of care to older adults. Frailty measures are useful tools for risk stratification in community-based and primary care settings, although their effectiveness in adults younger than 60 is not well described.

Methods
We performed a 10-year retrospective analysis of secondary data from the Ontario Health Study, which included 161,149 adults aged ≥ 18. Outcomes including all-cause mortality and hospital admissions were obtained through linkage to ICES administrative databases with a median follow-up of 7.1-years. Frailty was characterized using a 30-item frailty index.

Results
Frailty increased linearly with age and was higher for women at all ages. A 0.1-increase in frailty was significantly associated with mortality (HR = 1.47), the total number of outpatient (IRR = 1.35) and inpatient (IRR = 1.60) admissions over time, and length of stay (IRR = 1.12). However, with exception to length of stay, these estimates differed depending on age and sex. The hazard of death associated with frailty was greater at younger ages, particularly in women. Associations with admissions also decreased with age, similarly between sexes for outpatient visits and more so in men for inpatient.

Conclusions
These findings suggest that frailty is an important health construct for both younger and older adults. Hence targeted interventions to reduce the impact of frailty before the age of 60 would likely have important economic and social implications in both the short- and long-term.