bluuebunny/crossref_metadata_2025_split huggingface dataset:
A key molecular driver of tumor-infiltrating lymphocytes in invasive breast cancer on machine learning–based meta-mining research
Authors: Honda Chikako , Kurozumi Sasagu , Ball Graham , Katayama Ayaka , Yokobori Takehiko , Oyama Tetsunari , Horiguchi Jun , Shirabe Ken , Fujii Takaaki 
Published: October 2023

Abstract
Background: The immune system affects all phases of tumor growth, from initiation to progression and dissemination. However, molecular mechanisms of tumor immunity remain unclear. Therefore, this study aimed to identify targets significantly associated with tumor-infiltrating lymphocytes (TILs) in early-stage breast cancer (BC) using a novel machine learning (ML) approach.
Method: We identified 719 patients with early-stage BC from The Cancer Genome Atlas datasets having the available digital hematoxylin and eosin-stained whole slide images (WSIs) and transcriptomic data from tumor sites. The grades of stromal TILs in WSIs were evaluated using the criteria of the International Working Group for TILs in BC: low, intermediate, and high. Using our own artificial neural network ML methods, key genes were identified based on the differential mRNA expression between stromal-TIL grades.
Results: In this study, the ML system identified 49 genes that demonstrated significantly different expressions between stromal-TIL grades. Clustering analysis with this gene set further divided patients into two molecular subtypes (subtypes 1 and 2), which were significantly associated with tumor aggressiveness. The 10-year overall survival of subtype 1 was significantly poorer than that of subtype 2 (hazard ratio: 2.27, 95% confidence interval: 1.11-4.64, p = 0.025). We also found that these 49 genes are strongly associated with inducible T-cell co-stimulator (ICOS).
Conclusion: our findings suggest that TIL-related gene sets (ICOS-related genes) could interpret the complex molecular gene networks controlling tumor immunity in early-stage BC.
Single-cell RNA sequencing suggests plasmids constrain bacterial heterogeneity and conjugation is subpopulation specific
Authors: Cyriaque Valentine , Ibarra-Chávez Rodrigo , Kuchina Anna , Seelig Georg , Nesme Joseph , Madsen Jonas 
Published: October 2023

Abstract

Transcriptional heterogeneity is common within isogenic bacterial populations. Nonetheless, the interplay between conjugative plasmids and host subpopulation dynamics remains elusive. Here, the efficacy of microbial split-pool ligation transcriptomics in unraveling plasmid-host interactions was demonstrated through the generation of high-quality single-cell transcriptomic data. We found that transcription was impacted by growth state but also by plasmid carriage at the single-cell level, resulting in a reduction in subpopulations. Transcriptional heterogeneity among plasmid-encoded genes was also uncovered. This included core plasmid functions such as replication and maintenance fluctuations, likely associated with the cell cycle. Other key heterogeneously transcribed functions included tra genes revealing a subpopulation not engaging in conjugation and representing a possible plasmid strategy decreasing its burden at the population level. In sum, this study advances the understanding of plasmid-mediated subpopulation dynamics through a comprehensive single-cell transcriptomics approach, providing valuable insights into the intricate interplay between plasmids and bacteria.
Impedance Changes of the Li-ion Cell in the Course of Discharge
Authors: Křivík Petr 
Published: October 2023

Abstract
The paper deals with the measurement of the cell impedance parameters during discharging of the Li-ion NCR18650B cell. Re (Z) and Im (Z) of the battery were measured by PEIS method. Results of the impedance changes during discharging and charging were plot to Nyquist diagrams. Important values Rs, Rsei, Rct, Csei, Qsei, Cdl α and σ were found during discharging of the Li-ion cell with and without using CPE element.
Expression of key unfolded protein response genes predicts patient survival and an immunosuppressive microenvironment in glioblastoma
Authors: Oliveira Fernanda Dittrich , de Campos Rafael Paschoal , Pereira Luiza Cherobini , Meira Lisiane , Lenz Guido 
Published: October 2023

Abstract
Background
Dysregulation of cellular processes related to protein folding and trafficking leads to the accumulation of misfolded proteins in the endoplasmic reticulum (ER), triggering ER stress. Cells cope with ER stress by activating the unfolded protein response (UPR), a signaling pathway that has been implicated in a variety of diseases, including cancer. However, the role of the UPR in cancer initiation and progression is still unclear.
Methods
Here we used bulk and single cell RNA sequencing data to investigate ER stress-related gene expression in glioblastoma, as well as the impact key UPR genes have on patient survival.
Results
ER stress-related genes are highly expressed in both cancer cells and tumor-associated macrophages, with evidence of high intra- and inter-tumor heterogeneity. Elevated levels of the UPR-related genes, namely HSPA5, P4HB, and PDIA4, have been identified as risk factors, while high MAPK8 (JNK1) expression emerges as a protective factor in glioblastoma patients, underscoring the prognostic relevance of UPR genes in this cancer type. Finally, the expression patterns of XBP1 and MAPK8, crucial downstream targets of the ER sentinel IRE1α, show significant correlation with the presence of immune cell subtypes associated with immunosuppression and a worse patient outcome. These findings suggest a link between the expression of these genes, the immunosuppressive tumor microenvironment, and the overall survival of individuals with glioblastoma.
Conclusions
We performed a comprehensive transcriptional characterization of the unfolded protein response in glioblastoma patients and identified UPR-related genes associated with glioblastoma patient survival. These findings hold promise for the development of valuable prognostic and predictive biomarkers, offering insights into potential targets for the advancement of therapeutic approaches in glioblastoma treatment.
Molecular detection and analysis of a Enzootic Nasal Tumor Virus 2 in china
Authors: Li Pengfei , Li Lingxia , DU Guoyu , Wu Jinyan , Liu Xiaobo , Mao Shouhui , Shang Youjun , Yuan Ligang 
Published: October 2023

Abstract
Enzootic nasal tumor virus (ENTV) is a Betaretrovirus, which is associated with the neoplastic transformation of epithelial cells of the ethmoid turbinates. It has two types, ENTV-1 in sheep and ENTV-2 in goats, respectively. As we know, the incidence rate of ENTV-2 related diseases in China and even the world has increased in recent years. In this study, an infection of ENTV-2 was detected by RT-PCR in a goat flock in Chongqing City, and a full-length genome of ENTV-2 (named ENTV-2-CQ) with 7469 nucleotides (nt) was sequenced. Comparing with full-length genome sequences revealed that ENTV-2-CQ strain has high identity to the reference complete genomes (86.63–99.41%) at the nucleotide level. ENTV-2-CQ shared the highest nucleotide identity with a ENTV-2FJ isolate (GenBank accession number MK559457.1). Phylogenetic analysis shows that ENTV-2-CQ and ENTV-2 are located in the same major branch, mainly related to isolates from China from 2015 to 2022. Our research will contribute to a deeper understanding of the epidemiology and pathogenesis of this important retrovirus.
Recurrent Paradoxical Embolism and Manganese Deposition in the Basal Ganglia in a Patient with Hereditary Haemorrhagic Telangiectasias: A Case Report and Literature Review
Authors: Tang Qiwen , Xia Ping , Hu Xingyue , Shao Yuquan 
Published: October 2023

Abstract

Background
Hereditary hemorrhagic telangiectasia (HHT) is a rare autosomal dominant inherited vascular disorder that can involve multiple organs, thus can be associated with so many clinical departments that proper screening and diagnosis of HHT are needed for providing better management of both patients and their family members.
Case presentation:
we present a 58-year-old female patient with recurrent paradoxical brain embolism due to HHT. Though ischemic stroke caused by HHT-induced vascular disorders has been reported, our patient presented with two neurological complications at the same time: recurrent paradoxical brain embolisms and bilateral globus pallidus manganese deposition, which is rarely reported. We also review the literature on the clinical features and management of HHT for prompt diagnosis of this genetic disease behind paradoxical embolism.
Conclusions
When patients with ischemic stroke, especially recurrent ischemic stroke, have combined AVMs in single or multiple organs, or clues for AVMs like manganese deposition in globus pallidus, genetic diseases such as HHT may be the reason for ischemic stroke and shouldn't be missed in the evaluation of embolic sources.
Skimming the Achieved? – Quantifying the Fiscal Incentives of the German Fiscal Equalization Scheme and its Reforms since 1970
Authors: Bury Yannick , Feld Lars P. , Burret Heiko T. 
Published: October 2023

Abstract

Marginal rates of contribution (MRC), i.e., the rates at which additional revenues are skimmed via larger contributions or lower transfer receipts, quantify the incentives of a fiscal equalization scheme. The present paper is the first to calculate the marginal rates of contribution for the Laender (states) in the German fiscal equalization scheme for each of the 51 years since its establishment in 1970 and over five major reforms, taking into account all relevant revenues. Our results show that MRC have been at a consistently high level. Until 2019 the scheme induced an almost full skimming of additional tax revenues of recipient states. With the system’s latest reform in 2020, MRC increased further. Recipient states now face an over-skimming of additional tax revenues and thus, massive fiscal disincentives to maintain their own tax base. While these findings have been widely expected, comprehensive evidence has been missing so far.
JEL Codes: H71, H73, H77, H11
Contouring practices and artefact management within a synthetic CT-based radiotherapy workflow for the central nervous system.
Authors: Rossi Elia , Emin Sevgi , Gubanski Michael , Gagliardi Giovanna , Hedman Mattias , Villegas Fernanda 
Published: October 2023

Abstract
Background: The incorporation of magnetic resonance (MR) imaging in radiotherapy (RT) workflows improves contouring precision, yet it introduces geometrical uncertainties when registered with computed tomography (CT) scans. Synthetic CT (sCT) images could minimize these uncertainties and streamline the RT workflow. This study aims to compare the contouring capabilities of sCT images with conventional CT-based/MR-assisted RT workflows, with an emphasis on managing artefacts caused by surgical fixation devices (SFDs).
Methods: The study comprised a commissioning cohort of 100 patients with cranial tumors treated using a conventional CT-based/MR-assisted RT workflow and a validation cohort of 30 patients with grade IV glioblastomas treated using an MR-only workflow. A CE-marked artificial-intelligence-based sCT product was utilized. The delineation accuracy comparison was performed using Dice Similarity Coefficient (DSC) and Average Hausdorff Distance (AHD). Artefacts within the commissioning cohort were visually inspected, classified and an estimation of thickness was derived using Hausdorff Distance (HD). For the validation cohort, boolean operators were used to extract artefact volumes adjacent to the target and contrasted to the planning treatment volume (PTV).
Results: The combination of high DSC (0.94) and low AHD (0.04 mm) indicates equal target delineation capacity between sCT images and conventional CT scans. However, the results for organs at risk delineation were less consistent, likely because of voxel size differences between sCT images and CT scans and absence of standardized delineation routines. Artefacts observed in sCT images appeared as enhancements of cranial bone. When close to the target, they could affect its definition. Therefore, in the validation cohort the clinical target volume (CTV) was expanded towards the bone by 3.5 mm, as estimated by HD analysis. Subsequent analysis on Cone-Beam CT (CBCT) scans showed that the CTV adjustment was enough to provide acceptable target coverage.
Conclusion: The tested sCT product performed on par with conventional CT in terms of contouring capability. Additionally, this study provides both the first comprehensive classification of metal artefacts on a sCT product and a novel method to assess the clinical impact of artefacts caused by SFDs on target delineation. This methodology encourages similar analysis for other sCT products.
Selective digestive tract decontamination in critically ill adults with acute brain injuries: a Post-Hoc analysis of a Randomized Clinical Trial.
Authors: Young Paul , Devaux Anthony , Li Qiang , Billot Laurent , Davis Joshua , Delaney Anthony , Finfer Simon , Hammond Naomi , Micallef Sharon , Seppelt Ian , Venkatesh Balasubramanian , Myburgh John A 
Published: October 2023

Abstract
Purpose: To determine whether Selective Decontamination of the Digestive Tract (SDD) reduces in-hospital mortality in mechanically ventilated critically ill adults admitted to the Intensive Care Unit (ICU) with acute brain injuries or conditions.
Methods: A post-hoc analysis from a crossover, cluster-randomized clinical trial. ICUs were randomly assigned to adopt or not to adopt a SDD strategy for two alternating 12-month periods, separated by a 3-month inter-period gap. Patients in the SDD group (n=2791; 968 admitted to the ICU with an acute brain injury) received a 6-hourly application of an oral paste and administration of a gastric suspension containing colistin, tobramycin, and nystatin for the duration of mechanical ventilation, plus a 4-day course of an intravenous antibiotic with a suitable antimicrobial spectrum. Patients in the control group (n=3191; 1093 admitted to the ICU with an acute brain injury) received standard care. The primary outcome was in-hospital mortality within 90 days. There were four secondary clinical outcomes: death in ICU, ventilator-, ICU- and hospital-free days to day 90.
Results Of 2061 patients with acute brain injuries (mean age, 55.8 years; 36.4% women), all completed the trial. In patients with acute brain injuries, there were 313/968 (32.3%) and 415/1093 (38.0%) in-hospital deaths in the SDD and standard care groups (unadjusted odds ratio [OR], 0.76, 95% confidence interval [CI] 0.63 to 0.92; p = 0.004). The use of SDD was associated with statistically significant improvements in the four clinical secondary outcomes compared to standard care. There was no statistical difference in the heterogeneity of treatment effect between patients with and without acute brain injuries (interaction p=0.22).
Conclusions: In this post-hoc analysis of a randomized clinical trial in critically ill patients with acute brain injuries receiving mechanical ventilation, the use of SDD significantly reduced in-hospital mortality in patients compared to standard care without SDD. These findings require confirmation.
Trial Registration: Clinical Trials.gov registration number: NCT02389036
Gender differences in the development of conduct problems: trajectories, predictors, and outcomes through childhood
Authors: Álvarez-Voces María , Romero Estrella 
Published: October 2023

Abstract
Gender differences in the trajectories of conduct problems (CP) have received very little attention in the literature. The present four-year longitudinal study explores gender differences in CP trajectories through early childhood, assessing gender-specific predictors and outcomes. Gender-separated CP trajectories were identified in a sample of 2,246 young children (Mage=4.25; 48.53% girls) using latent class growth analyses (LCGA). Five trajectories were found in girls (i.e., low, average, downward, upward, and stable high) and four in boys (i.e., low, average, stable high, and upward). Low socioeconomic status was related to the most problematic trajectories only in boys, whereas the interpersonal psychopathic trait (grandiose-deceitful) was more pronounced in girls with higher CP scores relative to other psychopathic traits. Meanwhile, boys’ trajectories were more varied in terms of negative outcomes (e.g., bullying, victimization) than those of girls. This study contributes to the body of work on heterogeneity in CP by identifying different trajectories according to gender, and shows the relevance of gender in understanding the predictors, development, and outcomes of CP.
Identification and genetic diversity analysis of broomrape in Xinjiang, China
Authors: Zhang Xuekun , Du Juan , Wang Panpan , Wang Peng , Liu Zheng , Yao Zhaoqun , Zhao Sifeng , Xi Hui 
Published: October 2023

Abstract
Background: As a holoparasitic weed, broomrape has seriously threatened the production of economically important crops, such as melon, watermelon, processed tomato, and sunflower, in the Xinjiang Province in recent years. However, the distribution and genetic diversity of broomrape populations in Xinjiang are not clear at present, which hinders their prevention and control process. The purpose of this study is to identify the main species and the genetic differentiation structure of the broomrape population in Xinjiang province.
Methods and Results In the present study, 93 samples from different geographic regions of Xinjiang were collected to identify the species based on ITS and plastid rps2 regions, and the samples were also used to analyze the genetic diversity based on ISSR markers. The results showed that broomrape is not monophyletic in Xinjiang and consists of two major clades (Orobanche cf. aegyptiaca and O. cernua) and three subclades (O. cf. aegyptiaca var. tch, O. cf. aegyptiaca var. klz, O. cernua.var. alt) by phylogenetic analysis based on ITS and rps2. Furthermore, the results of the genetic diversity analysis indicated that the 11 selected primers produced 154 repeatable polymorphic bands, of which 150 were polymorphic. The genetic diversity of the samples was 37.19% within populations and 62.81% among the populations, indicating that the main genetic differentiation occurred among the populations. There was less gene exchange between populations, with a gene flow index (Nm) of 0.2961 (<1). The UPGMA dendrogram indicated that most populations with similar geographical conditions and hosts were clustered first, and then all samples were separated into two major groups and seven subclusters.
Conclusion
The broomrapes are mainly O. cf. aegyptiacaand O. cernua in Xinjiang province, which were separated into two major groups and seven subclusters furtherly based on ISSR markers. This is the first study to clarify genetic diversity and population distribution of broomrape in Xinjiang. Our results provide a theoretical basis for the prevention, control, and breeding of broomrape-resistant varieties.
Kidney volume normative values in Central European children aged 0-19 years – a multicenter study
Authors: Obrycki Łukasz , Sarnecki Jędrzej , Pac Michal , Lichosik Marianna , Sopińska Małgorzata , Placzyńska Małgorzata , Milart Joanna , Stańczyk Małgorzata , Mirecka Julia , Wasilewska Agnieszka , Michalski Maciej , Lewandowska Weronika , Dereziński Tadeusz , Šuláková Terezie , Šupík David , Čekuolis Andrius , Vitkevič Renata , Wierzbicka Aldona , Koziej Jan , Skoczyński Krzysztof , Horubała Jan , Jankauskiene Augustina , Kalicki Bolesław , Jobs Katarzyna , Tkaczyk Marcin , Feber Janusz , Litwin Mieczysław 
Published: October 2023

Abstract
Background and Objecitves: The currently available kidney volume normative values in children are restricted to small populations from single-centre studies not assessing kidney function and including none or only a small number of adolescents. This study aimed to obtain ultrasound-based kidney volume normative values derived from a large European Caucasian paediatric population with normal kidney function.
Methods: After recruitment of 1427 children aged 0–19 years, 1396 individuals with no history of kidney disease and normal estimated glomerular filtration rate were selected for the sonographic evaluation of kidney volume. Kidney volume was correlated with age, height, weight, body surface area and body mass index. Kidney volume curves and tables related to anthropometric parameters were generated using the LMS method. Kidney volume predictors were evaluated using multivariate regression analysis with collinearity checks.
Results: No clinically significant differences in kidney volume in relation to height were found between males and females, between supine and prone position and between left and right kidneys. Males had, however, larger age-related kidney volumes than females in most age categories. For the prediction of kidney volume, the highest coefficient correlation was observed for body surface area (r = 0.94), followed by weight (r = 0.92), height (r = 0.91), age (r = 0.91), and body mass index (r = 0.67; p < 0.001 for all).
Conclusions: This study presents LMS-percentile curves and tables for kidney volume which can be used as reference values for children aged 0–19 years.
Comparative Chloroplast Genome Analysis of Two Deciduous Phalaenopsis species, Phylogenetic Relationships, and Development of Indel markers
Authors: Liu Hailin , Ye Guangying , Wang Zaihua , Li Mingzhi , Li Dongmei 
Published: October 2023

Abstract
Background: Phalaenopsisis a taxonomically controversial genus and the most horticulturally valuable group in the family Orchidaceae. Inconsistencies among morphological characteristics and the lack of genomic resources have greatly impeded studies of the taxonomy and evolutionary relationships of this particular genus. The chloroplast genomes of Phalaenopsis wilsonii f. wilsonii and Phalaenopsis braceanum remains pending.
Results: Here, we successfully obtained the entire chloroplast genome sequences of P. wilsonii f. wilsonii and P. braceanumand subsequently compared them with chloroplast genomes of various other species. Our aim was to enhance our understanding of the taxonomy of Phalaenopsis, as well as aid the utilization of wild orchid resources. The chloroplast genomes of Phalaenopsis wilsonii f. wilsonii and Phalaenopsis braceanum exhibited similar lengths, measuring 145,874 bp and 145,935 bp, respectively. These genomes comprised a total of 128 genes, which consisted of 75 protein-coding genes, 38 transfer RNA genes, 8 ribosomal RNA genes, and 7 pseudogenes. The GC content was 36.79%. By conducting a comparative analysis of these two chloroplast genomes, we observed a significant resemblance in their structural properties, amino acids frequencies, and codon usage bias. The biased usage of certain amino acid codons in deciduous orchids might be associated with their resistance to various types of adverse conditions (e.g., drought and nutrient deficiency). Among the four types simple sequence repeats (SSRs) that have been identified, A/T repeats constituted the highest occurrence. Seven protein-coding genes, including petN,psaI, psbH, psbM, rpl33, rpl23, and rps16, were under positive selection.Ten InDel markers greater than 10 bp were developed and used to distinguish between these two species. Phylogenetic analysis revealed that P. braceanum was sister to P. stobariana; the combined P. braceanum + P. stobariana clade was sister to P. wilsonii.
Conclusions: Our study provided novel findings concerning the chloroplast genomes of P. wilsonii f. wilsonii and P. braceanum. Our data provide key molecular resources for Phalaenopsisspecies that will aid future studies of the genetic evolution and environmental adaptation of orchids. The divergent hotspots identified could be serve as valuable resources for the creation of molecular markers, enabling the identification of Phalaenopsis species and facilitating phylogenetic investigations between closely related species or individuals with morphological traits similar to those of Phalaenopsis.