bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seiches and the slide/seiche dynamics; subcritical and supercritical subaquous mass flows and their deposits. Examples from Swiss Lakes
Authors: Siegenthaler Christoph 
Published: October 2021

AbstractFour historically documented large and potentially dangerous lacustrine waves in Swiss lakes show that these waves have been seiches (standing waves) triggered by sublacustrine slides; a statement which is in accordance with the experience of seismologists who see earthquakes triggering seiches in lakes. Nevertheless, large historical waves in Switzerland have recently been modeled as progressive shallow water waves (tsunamis), probably because the slide/seiche dynamics are not known, and experiments with subaquatic slides fail to generate seiches in test–flumes. It appears that these tests exhibit a small shear–energy/slide–energy ratio ε, if compared with the situation in lakes. These facts incite a shear–stress lemma that states that ε is the constituent factor for the slide/seiche coupling. The structure of the subaqueous mass flow deposit (MFD) in lakes Lucerne and Geneva suggests the occurrence of subcritical and of supercritical slide flows. The former would generate a contortite, a MFD with contorted bedding, the latter a debrite (mudclast conglomerate). Potential slide energy considerations are used for an estimation of the amplitudes of large seiches produced by subaquatic slides, a proceeding that yields partly similar and partly very different results, as compared with numerical tsunami simulations.
Depression of lncRNA MINCR antagonizes LPS-evoked acute injury and inflammatory response via miR-146b-5p and the TRAF6-NFkB signaling
Authors: Gao Wei , Zhang Ying 
Published: October 2021

AbstractBackgroundInflammation plays an important role in the development of acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). The long non-coding RNA (lncRNA) MINCR is closely related to inflammation injury. This study was performed to explore the protective effects and mechanisms of MINCR in lipopolysaccharide (LPS)-induced lung injury and inflammation.MethodsThe expression levels of MINCR and miR-146b-5p in lung tissue status were detected by using quantitative real-time polymerase chain reaction (qRT-PCR), hematoxylin and eosin staining, immunohistochemical staining, and terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Enzyme-linked immunosorbent assay and Western blotting analysis were used to detect the expression of inflammatory factors such as tumor necrosis factor (TNF)-α, interleukin (IL)-6, and IL-10 in lung tissue. The relationship between MINCR, miR-146b-5p, and TRAF6 was explored using bioinformatics analysis and luciferase assay.ResultsThe expression levels of MINCR were increased in a mouse model of LPS-induced ALI and small airway epithelial cells (SAECs). shMINCR resulted in increased cell viability and decreased apoptosis, which protected against LPS-induced cell damage. shMINCR can inhibit the formation of neutrophil extracellular traps, neutrophil numbers, myeloperoxidase activity, and the production of inflammatory cytokines IL-6, IL-1β, and TNF-α induced by LPS. The silencing of miR-146b-5p reversed the effects of MINCR on LPS-induced lung damage. Sh-MINCR decreased the expression levels of TRAF6 and p-P65 in LPS-induced SAECs and lung tissues. Co-transfection of sh-MINCR with miR-146b-5p inhibitor reversed the effect of sh-MINCR on the expression of TRAF6 and p-P65.ConclusionsMINCR may induce alveolar epithelial cell injury and inflammation and aggravate the progression of ALI/ARDS through miR-146b-5p and TRAF6/NF-κB pathways, which would provide a promising target for the treatment of ALI/ARDS.
The collagen structure of C1q induces wound healing by engaging discoidin domain receptor 2
Authors: Hayuningtyas Ria Aryani , Han Myeonggil , Choi Seoyeon , Kwak Man Sup , Park In Ho , Lee Ji-Hyun , Choi Ji Eun , Kim Dae Ki , Son Myoungsun , Shin Jeon-Soo 
Published: October 2021

Abstract
Background
C1q has been reported to reveal complement-independent roles in immune and non-immune cells. C1q binds to its specific receptors to regulate distinct functions that rely on the environment and cell types. Discoidin domain receptor 2 (DDR2) is activated by collagen and functions in wound healing by controlling matrix metalloproteinase (MMP) expression. Since C1q exhibits a collagen-like structure, we hypothesized that C1q might engage DDR2 to regulate wound healing and extracellular matrix (ECM) remodeling.

Methods
Cell-based assay, proximity ligation assay, ELISA, and surface plasmon analysis were utilized to investigate DDR2 and C1q binding. We also investigate the C1q-mediated in vitro wound healing ability using the human fibrosarcoma cell line, HT1080.

Results
C1q induced the phosphorylation of DDR2, p38 kinase, and ERK1/2. C1q and DDR2 binding improved cell migration and induced MMP2 and MMP9 expression. DDR2-specific shRNA reduced C1q-mediated cell migration for wound healing.

Conclusions
C1q is a new DDR2 ligand that promotes wound healing. These findings have therapeutic implications in wound healing-related diseases.
Evaluation of candidate reference genes for quantitative real-time PCR analysis in a male rat model of dietary iron deficiency
Authors: Fiddler Joanna L. , Clarke Stephen L. 
Published: October 2021

Abstract
Background
Quantitative real-time polymerase chain reaction (qPCR) is a reliable and efficient method for quantitation of gene expression. Due to the increased use of qPCR in examining nutrient-gene interactions, it is important to examine, develop, and utilize standardized approaches for data analyses and interpretation. A common method used to normalize expression data involves the use of reference genes (RG) to determine relative mRNA abundance. When calculating the relative abundance, the selection of RG can influence experimental results and has the potential to skew data interpretation. Although common RG may be used for normalization, often little consideration is given to the suitability of RG selection for an experimental condition or between various tissue or cell types. In the current study, we examined the stability of gene expression using BestKeeper, comparative delta quantitation cycle, NormFinder, and RefFinder in a variety of tissues obtained from iron-deficient and pair-fed iron-replete rats to determine the optimal selection among ten candidate RG.

Results
Our results suggest that several commonly used RG (e.g., Actb and Gapdh) exhibit less stability compared to other candidate RG (e.g., Rpl19 and Rps29) in both iron-deficient and iron-replete pair-fed conditions. For all evaluated RG, Tfrc expression significantly increased in iron-deficient animal livers compared to the iron-replete pair-fed controls; however, the relative induction varied nearly 4-fold between the most suitable (Rpl19) and least suitable (Gapdh) RG.

Conclusion
These results indicate the selection and use of RG should be empirically determined and RG selection may vary across experimental conditions and biological tissues.
A laminar augmented cascading flexible neural forest model for classification of cancer subtypes based on gene expression data
Authors: Zhong Lianxin , Meng Qingfang , Chen Yuehui , Du Lei , Wu Peng 
Published: October 2021

Abstract
Background
Correctly classifying the subtypes of cancer is of great significance for the in-depth study of cancer pathogenesis and the realization of personalized treatment for cancer patients. In recent years, classification of cancer subtypes using deep neural networks and gene expression data has gradually become a research hotspot. However, most classifiers may face overfitting and low classification accuracy when dealing with small sample size and high-dimensional biology data.

Results
In this paper, a laminar augmented cascading flexible neural forest (LACFNForest) model was proposed to complete the classification of cancer subtypes. This model is a cascading flexible neural forest using deep flexible neural forest (DFNForest) as the base classifier. A hierarchical broadening ensemble method was proposed, which ensures the robustness of classification results and avoids the waste of model structure and function as much as possible. We also introduced an output judgment mechanism to each layer of the forest to reduce the computational complexity of the model. The deep neural forest was extended to the densely connected deep neural forest to improve the prediction results. The experiments on RNA-seq gene expression data showed that LACFNForest has better performance in the classification of cancer subtypes compared to the conventional methods.

Conclusion
The LACFNForest model effectively improves the accuracy of cancer subtype classification with good robustness. It provides a new approach for the ensemble learning of classifiers in terms of structural design.
SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations
Authors: Rosário-Ferreira Nícia , Guimarães Victor , Costa Vítor S. , Moreira Irina S. 
Published: October 2021

AbstractBackgroundBlood cancers (BCs) are responsible for over 720 K yearly deaths worldwide. Their prevalence and mortality-rate uphold the relevance of research related to BCs. Despite the availability of different resources establishing Disease-Disease Associations (DDAs), the knowledge is scattered and not accessible in a straightforward way to the scientific community. Here, we propose SicknessMiner, a biomedical Text-Mining (TM) approach towards the centralization of DDAs. Our methodology encompasses Named Entity Recognition (NER) and Named Entity Normalization (NEN) steps, and the DDAs retrieved were compared to the DisGeNET resource for qualitative and quantitative comparison.ResultsWe obtained the DDAs via co-mention using our SicknessMiner or gene- or variant-disease similarity on DisGeNET. SicknessMiner was able to retrieve around 92% of the DisGeNET results and nearly 15% of the SicknessMiner results were specific to our pipeline.ConclusionsSicknessMiner is a valuable tool to extract disease-disease relationship from RAW input corpus.
On the robustness of generalization of drug–drug interaction models
Authors: Kpanou Rogia , Osseni Mazid Abiodoun , Tossou Prudencio , Laviolette Francois , Corbeil Jacques 
Published: October 2021

Abstract
Background
Deep learning methods are a proven commodity in many fields and endeavors. One of these endeavors is predicting the presence of adverse drug–drug interactions (DDIs). The models generated can predict, with reasonable accuracy, the phenotypes arising from the drug interactions using their molecular structures. Nevertheless, this task requires improvement to be truly useful. Given the complexity of the predictive task, an extensive benchmarking on structure-based models for DDIs prediction was performed to evaluate their drawbacks and advantages.

Results
We rigorously tested various structure-based models that predict drug interactions using different splitting strategies to simulate different real-world scenarios. In addition to the effects of different training and testing setups on the robustness and generalizability of the models, we then explore the contribution of traditional approaches such as multitask learning and data augmentation.

Conclusion
Structure-based models tend to generalize poorly to unseen drugs despite their ability to identify new DDIs among drugs seen during training accurately. Indeed, they efficiently propagate information between known drugs and could be valuable for discovering new DDIs in a database. However, these models will most probably fail when exposed to unknown drugs. While multitask learning does not help in our case to solve the problem, the use of data augmentation does at least mitigate it. Therefore, researchers must be cautious of the bias of the random evaluation scheme, especially if their goal is to discover new DDIs.
Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris)
Authors: Ospina Oscar E. , Lemmon Alan R. , Dye Mysia , Zdyrski Christopher , Holland Sean , Stribling Daniel , Kortyna Michelle L. , Lemmon Emily Moriarty 
Published: October 2021

AbstractBackgroundSpecies interactions can promote mating behavior divergence, particularly when these interactions are costly due to maladaptive hybridization. Selection against hybridization can indirectly cause evolution of reproductive isolation within species, a process termed cascade reinforcement. This process can drive incipient speciation by generating divergent selection pressures among populations that interact with different species assemblages. Theoretical and empirical studies indicate that divergent selection on gene expression networks has the potential to increase reproductive isolation among populations. After identifying candidate synaptic transmission genes derived from neurophysiological studies in anurans, we test for divergence of gene expression in a system undergoing cascade reinforcement, the Upland Chorus Frog (Pseudacris feriarum).ResultsOur analyses identified seven candidate synaptic transmission genes that have diverged between ancestral and reinforced populations ofP. feriarum, including five that encode synaptic vesicle proteins. Our gene correlation network analyses revealed four genetic modules that have diverged between these populations, two possessing a significant concentration of neurotransmission enrichment terms: one for synaptic membrane components and the other for metabolism of the neurotransmitter nitric oxide. We also ascertained that a greater number of genes have diverged in expression by geography than by sex. Moreover, we found that more genes have diverged within females as compared to males between populations. Conversely, we observed no difference in the number of differentially-expressed genes within the ancestral compared to the reinforced population between the sexes.ConclusionsThis work is consistent with the idea that divergent selection on mating behaviors via cascade reinforcement contributed to evolution of gene expression inP. feriarum. Although our study design does not allow us to fully rule out the influence of environment and demography, the fact that more genes diverged in females than males points to a role for cascade reinforcement. Our discoveries of divergent candidate genes and gene networks related to neurotransmission support the idea that neural mechanisms of acoustic mating behaviors have diverged between populations, and agree with previous neurophysiological studies in frogs. Increasing support for this hypothesis, however, will require additional experiments under common garden conditions. Our work points to the importance of future replicated and tissue-specific studies to elucidate the relative contribution of gene expression divergence to the evolution of reproductive isolation during incipient speciation.
Two target genes based multiple cross displacement amplification combined with a lateral flow biosensor for the detection of Mycobacterium tuberculosis complex
Authors: Huang Junfei , Xiao Ziyu , Yang Xinggui , Chen Xu , Wang Xiaojuan , Chen Yijiang , Zheng Wenlin , Chen Wei , Chen Huijuan , Li Shijun 
Published: October 2021

Abstract
Background
Tuberculosis (TB) is a serious chronic infectious disease caused by Mycobacterium tuberculosis complex (MTBC). Hence, the development of a novel, simple, rapid and sensitive method to detect MTBC is of great significance for the prevention and treatment of TB.

Results
In this study, multiple cross displacement amplification (MCDA) combined with a nanoparticle-based lateral flow biosensor (LFB) was developed to simultaneously detect two target genes (IS6110 and mpb64) of MTBC (MCDA-LFB). One suite of specific MCDA primers designed for the IS6110 and mpb64 genes was validated using genomic DNA extracted from the reference strain H37Rv. The MCDA amplicons were analyzed using a real-time turbidimeter, colorimetric indicator (malachite green, MG) and LFBs. The optimal amplification temperature and time were confirmed, and the MCDA-LFB method established in the current report was evaluated by detecting various pathogens (i.e., reference strains, isolates and clinical sputum samples). The results showed that the two sets of MCDA primers targeting the IS6110 and mpb64 genes could effectively detect MTBC strains. The optimal reaction conditions for the MCDA assay were determined to be 67 °C for 35 min. The MCDA assay limit of detection (LoD) was 100 fg per reaction for pure genomic DNA. The specificity of the MCDA-LFB assay was 100%, and there were no cross-reactions for non-MTBC strains. For sputum samples and MTBC strain detection, the positive rate of MCDA-LFB for the detection of MTBC strains was consistent with seminested automatic real-time PCR (Xpert MTB/RIF) and higher than acid-fast staining (AFS) and culture assays when used for sputum samples. The MCDA-LFB assay was a rapid tool, and the whole procedure for MCDA-LFB, including DNA template preparation, MCDA reaction and amplification product analysis, was completed within 70 min.

Conclusion
The MCDA-LFB assay targeting the IS6110 and mpb64 genes is a simple, rapid, sensitive and reliable detection method, and it has potential significance for the prevention and treatment of TB.
Factors associated with hospital outcomes of patients with penetrating craniocerebral injuries in armed conflict areas of the Democratic Republic of the Congo: a retrospective series
Authors: Mudekereza Paterne Safari , Murhula Gauthier Bahizire , Kachungunu Charles , Mudekereza Amani , Cikomola Fabrice , Mubenga Leon-Emmanuel Mukengeshai , Balungwe Patrick Birindwa , Budema Paul Munguakonkwa , Molima Christian , Mugabo Erick Namegabe , Lekuya Hervé Monka 
Published: October 2021

Abstract
Introduction
Penetrating craniocerebral injuries (PCCI) are types of open head injuries caused by sharp objects or missiles, resulting in communication between the cranial cavity and the external environment. This condition is deemed to be more prevalent in armed conflict regions where both civilians and military are frequently assaulted on the head, but paradoxically their hospital outcomes are under-reported. We aimed to identify factors associated with poor hospital outcomes of patients with PCCI.

Methods
This was a retrospective series of patients admitted at the Regional Hospital of Bukavu, DRC, from 2010 to 2020. We retrieved medical records of patients with PCCI operated in the surgical departments. A multivariate logistic regression model was performed to find associations between patients’ admission clinico-radiological parameters and hospital outcomes. Poor outcome was defined as a Glasgow Outcomes Score below 4.

Results
The prevalence of PCCI was 9.1% (91/858 cases) among admitted TBI patients. More than one-third (36.2%) of patients were admitted with GCS < 13, and 40.6% of them were unstable hemodynamic. Hemiplegia was found in 23.1% on admission. Eight patients had an intracerebral hemorrhage. Among the 69 operated patients, complications, mainly infectious, occurred in half (50.7%) of patients. Poor hospital outcomes were observed in 30.4% and associated with an admission GCS < 13, hemodynamic instability, intracerebral hemorrhage, and hemiplegia (p < 0.05).

Conclusion
The hospital poor outcomes are observed when patients present with hemodynamic instability, an admission GCS < 13, intracerebral hemorrhage, and hemiplegia. There is a need for optimizing the initial care of patients with PCCI in armed conflict regions.
Sodium nitroprusside protects HFD induced gut dysfunction via activating AMPKα/SIRT1 signaling
Authors: Li Xiaomei , Li Chen , Li Yuanqi , Liu Cong , Liang Xue , Liu Ting , Liu Zhihua 
Published: October 2021

Abstract
Background
Activation of Adenosine 5′-monophosphate-activated protein kinase/Sirtuin1 (AMPK/SIRT1) exerts an effect in alleviating obesity and gut damage. Sodium nitroprusside (SNP), a nitric oxide (NO) donor, has been reported to activate AMPK. This study was to investigate the effect of SNP on HFD induced gut dysfunction and the mechanism.

Methods
SNP was applied on lipopolysaccharide (LPS) stimulated Caco-2 cell monolayers which mimicked intestinal epithelial barrier dysfunction and HFD-fed mice which were complicated by gut dysfunction. Then AMPKα/SIRT1 pathway and gut barrier indicators were investigated.

Results
SNP rescued the loss of tight junction proteins ZO-1 and occludin, the inhibition of AMPKα/SIRT1 in LPS stimulated Caco-2 cell monolayers, and the effects were not shown when AMPKa1 was knocked-down by siRNA. SNP also alleviated HFD induced obesity and gut dysfunction in mice, as indicated by the decreasing of intestinal permeability, the increasing expression of ZO-1 and occludin, the decreasing levels of pro-inflammatory cytokine IL-6, and the repairing of gut microbiota dysbiosis. These effects were complicated by the increased colonic NO content and the activated AMPKα/SIRT1 signaling.

Conclusions
The results may imply that SNP, as a NO donor, alleviates HFD induced gut dysfunction probably by activating the AMPKα/SIRT1 signaling pathway.
Genomic profiling of a patient with quadruple synchronous colorectal cancer: a case report
Authors: Jia Xiongjie , Peng Xinyu , Sun Junjie , Zhang Tao , Lin Hengxue , Bai Tianliang , Zhang Aimin 
Published: October 2021

Abstract
Background
Synchronous colorectal cancer (SCRC) is featured by the presence of multiple primary tumor lesions in a single patient at initial diagnosis. It is less common with the prevalence of approximately 3.5% among colorectal cancer (CRC). Some studies of SCRC have been performed in patients with two tumor lesions. However, SCRC cases with three or more tumor lesions were rare and remained to be investigated.

Case presentation
In this case report, we presented a 56-year-old male SCRC case with quadruple tumor lesions which is rarely seen in clinical practice. After laparoscopic radical resection of sigmoid carcinoma and partial rectum resection, the four tumor samples were subjected to pathological evaluation and next-generation sequencing (NGS) based genetic profiling. The four tumor lesions included two adenocarcinomas with moderate differentiation at sigmoid colon and rectum respectively, a grade 1 neuroendocrine tumor (NET) at rectum and a high-grade intraepithelial neoplasia at ascending colon. Each tumor exhibited distinct histology types and mutation profiles. After surgical resection, the patient remained disease-free after four cycles of chemotherapy with oxaliplatin and capecitabine (XELOX).

Conclusions
The tumor lesions in this case showed different pathological and genetic features which indicats the heterogeneity of SCRC. The genomic profilling might provide novel insights to understand SCRC at molecular level.