bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cells in Silico – introducing a high-performance framework for large-scale tissue modeling
Authors: Berghoff Marco , Rosenbauer Jakob , Hoffmann Felix , Schug Alexander 
Published: October 2020

Abstract
Background
Discoveries in cellular dynamics and tissue development constantly reshape our understanding of fundamental biological processes such as embryogenesis, wound-healing, and tumorigenesis. High-quality microscopy data and ever-improving understanding of single-cell effects rapidly accelerate new discoveries. Still, many computational models either describe few cells highly detailed or larger cell ensembles and tissues more coarsely. Here, we connect these two scales in a joint theoretical model.

Results
We developed a highly parallel version of the cellular Potts model that can be flexibly applied and provides an agent-based model driving cellular events. The model can be modular extended to a multi-model simulation on both scales. Based on the NAStJA framework, a scaling implementation running efficiently on high-performance computing systems was realized. We demonstrate independence of bias in our approach as well as excellent scaling behavior.

Conclusions
Our model scales approximately linear beyond 10,000 cores and thus enables the simulation of large-scale three-dimensional tissues only confined by available computational resources. The strict modular design allows arbitrary models to be configured flexibly and enables applications in a wide range of research questions. Cells in Silico (CiS) can be easily molded to different model assumptions and help push computational scientists to expand their simulations to a new area in tissue simulations. As an example we highlight a 10003 voxel-sized cancerous tissue simulation at sub-cellular resolution.
Construction of an 11-microRNA-based signature and a prognostic nomogram to predict the overall survival of head and neck squamous cell carcinoma patients
Authors: Huang Yusheng , Liu Zhiguo , Zhong Limei , Wen Yi , Ye Qixiang , Cao Donglin , Li Peiwu , Liu Yufeng 
Published: October 2020

AbstractBackgroundHead and neck squamous cell carcinoma (HNSCC) is a fatal malignancy owing to the lack of effective tools to predict overall survival (OS). MicroRNAs (miRNAs) play an important role in HNSCC occurrence, development, invasion and metastasis, significantly affecting the OS of patients. Thus, the construction of miRNA-based risk signatures and nomograms is desirable to predict the OS of patients with HNSCC. Accordingly, in the present study, miRNA sequencing data of 71 HNSCC and 13 normal samples downloaded from The Cancer Genome Atlas (TCGA) were screened to identify differentially expressed miRNAs (DEMs) between HNSCC patients and normal controls. Based on the exclusion criteria, the clinical information and miRNA sequencing data of 67 HNSCC samples were selected and used to establish a miRNA-based signature and a prognostic nomogram. Forty-three HNSCC samples were assigned to an internal validation cohort for verifying the credibility and accuracy of the primary cohort. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to explore the functions of 11 miRNA target genes.ResultsIn total, 11 DEMs were successfully identified. An 11-miRNA risk signature and a prognostic nomogram were constructed based on the expression levels of these 11 DEMs and clinical information. The signature and nomogram were further validated by calculating the C-index, area under the curve (AUC) in receiver-operating characteristic curve analysis, and calibration curves, which revealed their promising performance. The results of the internal validation cohort shown the reliable predictive accuracy both of the miRNA-based signature and the prognostic nomogram. GO and KEGG analyses revealed that a mass of signal pathways participated in HNSCC proliferation and metastasis.ConclusionOverall, we constructed an 11-miRNA-based signature and a prognostic nomogram with excellent accuracy for predicting the OS of patients with HNSCC.
Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement
Authors: Sonnenberg Cecilie Bækkedal , Kahlke Tim , Haugen Peik 
Published: October 2020

Abstract
Background
The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.

Results
We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.

Conclusion
The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.
Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus
Authors: Sahraei Shadi Eshghi , Cleary Michelle , Stenlid Jan , Brandström Durling Mikael , Elfstrand Malin 
Published: October 2020

Abstract
Background
With the expanding ash dieback epidemic that has spread across the European continent, an improved functional understanding of the disease development in afflicted hosts is needed. The study investigated whether differences in necrosis extension between common ash (Fraxinus excelsior) trees with different levels of susceptibility to the fungus Hymenoscyphus fraxineus are associated with, and can be explained by, the differences in gene expression patterns. We inoculated seemingly healthy branches of each of two resistant and susceptible ash genotypes with H. fraxineus grown in a common garden.

Results
Ten months after the inoculation, the length of necrosis on the resistant genotypes were shorter than on the susceptible genotypes. RNA sequencing of bark samples collected at the border of necrotic lesions and from healthy tissues distal to the lesion revealed relatively limited differences in gene expression patterns between susceptible and resistant genotypes. At the necrosis front, only 138 transcripts were differentially expressed between the genotype categories while 1082 were differentially expressed in distal, non-symptomatic tissues. Among these differentially expressed genes, several genes in the mevalonate (MVA) and iridoid pathways were found to be co-regulated, possibly indicating increased fluxes through these pathways in response to H. fraxineus.
Comparison of transcriptional responses of symptomatic and non-symptomatic ash in a controlled greenhouse experiment revealed a relatively small set of genes that were differentially and concordantly expressed in both studies. This gene-set included the rate-limiting enzyme in the MVA pathway and a number of transcription factors. Furthermore, several of the concordantly expressed candidate genes show significant similarity to genes encoding players in the abscisic acid- or Jasmonate-signalling pathways.

Conclusions
A set of candidate genes, concordantly expressed between field and greenhouse experiments, was identified. The candidates are associated with hormone signalling and specialized metabolite biosynthesis pathways indicating the involvement of these pathways in the response of the host to infection by H. fraxineus.
Pre-purification of diatom pigment protein complexes provides insight into the heterogeneity of FCP complexes
Authors: Kansy Marcel , Volke Daniela , Sturm Line , Wilhelm Christian , Hoffmann Ralf , Goss Reimund 
Published: October 2020

Abstract
Background
Although our knowledge about diatom photosynthesis has made huge progress over the last years, many aspects about their photosynthetic apparatus are still enigmatic. According to published data, the spatial organization as well as the biochemical composition of diatom thylakoid membranes is significantly different from that of higher plants.

Results
In this study the pigment protein complexes of the diatom Thalassiosira pseudonana were isolated by anion exchange chromatography. A step gradient was used for the elution process, yielding five well-separated pigment protein fractions which were characterized in detail. The isolation of photosystem (PS) core complex fractions, which contained fucoxanthin chlorophyll proteins (FCPs), enabled the differentiation between different FCP complexes: FCP complexes which were more closely associated with the PSI and PSII core complexes and FCP complexes which built-up the peripheral antenna. Analysis by mass spectrometry showed that the FCP complexes associated with the PSI and PSII core complexes contained various Lhcf proteins, including Lhcf1, Lhcf2, Lhcf4, Lhcf5, Lhcf6, Lhcf8 and Lhcf9 proteins, while the peripheral FCP complexes were exclusively composed of Lhcf8 and Lhcf9. Lhcr proteins, namely Lhcr1, Lhcr3 and Lhcr14, were identified in fractions containing subunits of the PSI core complex. Lhcx1, Lhcx2 and Lhcx5 proteins co-eluted with PSII protein subunits. The first fraction contained an additional Lhcx protein, Lhcx6_1, and was furthermore characterized by high concentrations of photoprotective xanthophyll cycle pigments.

Conclusion
The results of the present study corroborate existing data, like the observation of a PSI-specific antenna complex in diatoms composed of Lhcr proteins. They complement other data, like e.g. on the protein composition of the 21 kDa FCP band or the Lhcf composition of FCPa and FCPb complexes. They also provide interesting new information, like the presence of the enzyme diadinoxanthin de-epoxidase in the Lhcx-containing PSII fraction, which might be relevant for the process of non-photochemical quenching. Finally, the high negative charge of the main FCP fraction may play a role in the organization and structure of the native diatom thylakoid membrane. Thus, the results present an important contribution to our understanding of the complex nature of the diatom antenna system.
A combination of genome-wide association study and transcriptome analysis in leaf epidermis identifies candidate genes involved in cuticular wax biosynthesis in Brassica napus
Authors: Jin Shurong , Zhang Shuangjuan , Liu Yuhua , Jiang Youwei , Wang Yanmei , Li Jiana , Ni Yu 
Published: October 2020

Abstract
Background
Brassica napus L. is one of the most important oil crops in the world. However, climate-change-induced environmental stresses negatively impact on its yield and quality. Cuticular waxes are known to protect plants from various abiotic/biotic stresses. Dissecting the genetic and biochemical basis underlying cuticular waxes is important to breed cultivars with improved stress tolerance.

Results
Here a genome-wide association study (GWAS) of 192 B. napus cultivars and inbred lines was used to identify single-nucleotide polymorphisms (SNPs) associated with leaf waxes. A total of 202 SNPs was found to be significantly associated with 31 wax traits including total wax coverage and the amounts of wax classes and wax compounds. Next, epidermal peels from leaves of both high-wax load (HW) and low-wax load (LW) lines were isolated and used to analyze transcript profiles of all GWAS-identified genes. Consequently, 147 SNPs were revealed to have differential expressions between HW and LW lines, among which 344 SNP corresponding genes exhibited up-regulated while 448 exhibited down-regulated expressions in LW when compared to those in HW. According to the gene annotation information, some differentially expressed genes were classified into plant acyl lipid metabolism, including fatty acid-related pathways, wax and cutin biosynthesis pathway and wax secretion. Some genes involved in cell wall formation and stress responses have also been identified.

Conclusions
Combination of GWAS with transcriptomic analysis revealed a number of directly or indirectly wax-related genes and their associated SNPs. These results could provide clues for further validation of SNPs for marker-assisted breeding and provide new insights into the genetic control of wax biosynthesis and improving stress tolerance of B. napus.
Ropivacaine infiltration analgesia of the drainage exit site enhanced analgesic effects after breast Cancer surgery: a randomized controlled trial
Authors: Wang Baona , Yan Tao , Kong Xiangyi , Sun Li , Zheng Hui , Zhang Guohua 
Published: October 2020

Abstract
Background
Postoperative pain after breast cancer surgery remains a major challenge in patient care. Local infiltration analgesia is a standard analgesic technique used for pain relief after surgery. Its application in patients who underwent mastectomy requires more clear elucidation. This study aimed to investigate the effect of ropivacaine infiltration of drainage exit site in ameliorating the postoperative pain after mastectomy.

Methods
A prospective randomized controlled study was conducted in 74 patients who were scheduled for unilateral mastectomy by standardized general anesthesia. Both intervention group and control group were given infiltration of the two entry points of drainage catheters with 10 ml 0.5% ropivacaine (Group A) (n = 37) or 10 ml normal saline (Group B) (n = 37). Pain scores were recorded in post-anesthesia care unit (PACU), at 6 h, 12 h, 24 h and 36 h after operation by using a visual analogue scale (VAS). Postoperative nausea and vomiting (PONV) incidence, postoperative analgesic and antiemetic requirements, the incidence of chronic pain, as well as the quality of recovery were recorded.

Results
The patients in Group A showed a significant reduction in postoperative pain in PACU (p < 0.0005), at 6 h (p < 0.0005), 12 h (p < 0.0005), and 24 h after surgery (p < 0.05) when compared to those in Group B. There were more postoperative analgesic requirements in Group B (p < 0.05). With regard to the quality of recovery, Group A was shown to be much superior over Group B (p < 0.05).

Conclusions
Ropivacaine infiltration of the two drainage exit sites decreased the degree of postoperative acute pain after mastectomy, and this approach improved patients’ quality of recovery.

Trial registration
retrospectively registered in Chictr.org.cn registry system on 24 February 2020 (ChiCTR2000030139).
A retrospective study of sepsis-associated encephalopathy: epidemiology, clinical features and adverse outcomes
Authors: Chen Jiayi , Shi Xiaobei , Diao Mengyuan , Jin Guangyong , Zhu Ying , Hu Wei , Xi Shaosong 
Published: October 2020

Abstract
Background
Sepsis-associated encephalopathy (SAE) is a common complication of sepsis that may result in worse outcomes. This study was designed to determine the epidemiology, clinical features, and risk factors of SAE.

Methods
This was a retrospective study of all patients with sepsis who were admitted to the Critical Care Medicine Department of Hangzhou First People’s Hospital Affiliated with Zhejiang University School of Medicine from January 2015 to December 2019.

Results
A total of 291 sepsis patients were screened, and 127 (43.6%) were diagnosed with SAE. There were significant differences in median age, proportion of underlying diseases such as hypertension, Sequential Organ Failure Assessment (SOFA) score, Acute Physiology and Chronic Health Evaluation II (APACHE II) score, gastrointestinal infections, detection rate of Enterococcus, and 28-day mortality between the SAE and non-SAE groups. Both the SOFA score and APACHE II score were independent risk factors for SAE in patients with sepsis. All 127 SAE patients were divided into survival and non-survival groups. The age, SOFA score, and APACHE II score were independently associated with 28-day mortality in SAE patients.

Conclusion
In the present retrospective study, nearly half of patients with sepsis developed SAE, which was closely related to poor outcomes. Both the SOFA score and APACHE II score were independent risk factors for predicting the occurrence and adverse outcome of SAE.
Increasing the uptake of vitamin D supplement use in Australian residential aged care facilities: results from the vitamin D implementation (ViDAus) study
Authors: Walker Pippy , Kifley Annette , Kurrle Susan , Cameron Ian D. 
Published: October 2020

Abstract
Background
Adequate (≥800 IU/day) vitamin D supplement use in Australian residential aged care facilities (RACFs) is variable and non-optimal. The vitamin D implementation (ViDAus) study aimed to employ a range of strategies to support the uptake of this best practice in participating facilities. The aim of this paper is to report on facility level prevalence outcomes and factors associated with vitamin D supplement use.

Methods
This trial followed a stepped wedge cluster, non-randomised design with 41 individual facilities serving as clusters pragmatically allocated into two wedges that commenced the intervention six months apart. This multifaceted, interdisciplinary knowledge translation intervention was led by a project officer, who worked with nominated champions at participating facilities to provide education and undertake quality improvement (QI) planning. Local barriers and responsive strategies were identified to engage stakeholders and promote widespread uptake of vitamin D supplement use.

Results
This study found no significant difference in the change of vitamin D supplement use between the intervention (17 facilities with approx. 1500 residents) and control group (24 facilities with approx. 1900 residents) at six months (difference in prevalence change between groups was 1.10, 95% CI − 3.8 to 6.0, p = 0.6). The average overall facility change in adequate (≥800 IU/day) vitamin D supplement use over 12 months was 3.86% (95% CI 0.6 to 7.2, p = 0.02), which achieved a facility level average prevalence of 59.6%. The variation in uptake at 12 months ranged from 25 to 88% of residents at each facility. In terms of the types of strategies employed for implementation, there were no statistical differences between facilities that achieved a clinically meaningful improvement (≥10%) or a desired prevalence of vitamin D supplement use (80% of residents) compared to those that did not.

Conclusions
This work confirms the complex nature of implementation of best practice in the RACF setting and indicates that more needs to be done to ensure best practice is translated into action. Whilst some strategies appeared to be associated with better outcomes, the statistical insignificance of these findings and the overall limited impact of the intervention suggests that the role of broader organisational and governmental support for implementation should be investigated further.

Trial registration
Retrospectively registered (ANZCTR ID: ACTRN12616000782437).
The effects of neostigmine on postoperative cognitive function and inflammatory factors in elderly patients – a randomized trial
Authors: Zhu Bao , Sun Defeng , Yang Lin , Sun Zhongliang , Feng Yan , Deng Chengcheng 
Published: October 2020

Abstract
Background
Postoperative cognitive dysfunction is a common postoperative complication in elderly patients. In elderly patients, the decline of organ function and neuromuscular junction function make them more sensitive to muscle relaxants. They are more likely to experience residual muscle relaxation after surgery, which may cause various adverse events. Neostigmine, a commonly used muscle relaxant antagonist, can reduce the expression of inflammatory factors, thereby reducing the pro-inflammatory response and neurodegeneration of the cerebral cortex and hippocampus after surgery. The study aimed at observing the effect of different doses of neostigmine on postoperative cognitive function and peripheral inflammatory factors in elderly patients.

Methods
One hundred thirty-two elderly patients who underwent a radical section of gastrointestinal cancer at First Affiliated Hospital of Dalian Medical University were divided into neostigmine and saline groups at a 2:1 ratio. Neostigmine was intravenously injected in the post-anesthesia care unit (PACU) according to the train-of-four ratio (TOFR) T4/T1. When TOFR was ≤0.5, 0.04 mg/kg neostigmine was administered, whereas when TOFR was > 0.5, 0.02 mg/kg neostigmine was injected. The main observation indexes were cognitive function, interleukin 1 beta (IL-1β), tumor necrosis factor-alpha (TNF-α), and interleukin 6 (IL-6) in peripheral blood at the different times before and after the surgery. Secondary observation indicators include the number of atropine injection, extubating time, PACU residence time, incidence of hypoxemia, hypercapnia, and postoperative nausea and vomiting in PACU, time of exhaustion, and length of hospitalization.

Results
The extubating and PACU times in 0.04 mg/kg and 0.02 mg/kg groups were significantly shorter than those in the control group (P < 0.001). The incidence of early postoperative cognitive decline in 0.04 mg/kg and 0.02 mg/kg groups was 10 and 15.7%, respectively, which were significantly lower than those in the control group (P = 0.013).

Conclusion
In elderly patients, 0.02–0.04 mg/kg neostigmine could significantly reduce the incidence of early postoperative cognitive decline without affecting peripheral inflammatory factors.

Trial registration
Trial registration: Chinese Clinical Trial Registry, ChiCTR2000031739. Registered 8 April 2020 - Retrospectively registered, http://www.medresman.org.cn.