bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competing Endogenous RNA Network in Non-Keloid-Prone Individuals During Wound Healing
Authors: Han Bing , Xu Shuqia , Liu Xiangxia , Shi Jun , Liu Zheng , Zhang Yujing , Deng Yu , Li Zequan , Xu Yangbin , Zhu Zhaowei 
Published: December 2021

Abstract
To study the interaction between differentially expressed long non-coding RNAs (lncRNAs), microRNAs, and messenger RNAs during wound healing in normal individuals. The GSE113621 dataset was downloaded from gene expression matrix, specimens regarding non-keloid-prone individuals were selected, including items before and 6 weeks after injury. A Pearson correlation coefficient of > 0.95 was selected as the index to screen targeting relationships among different RNAs. Cytoscape was used to construct a network diagram. The expression of 2547 lncRNAs was changed during the wound healing process—1479 were upregulated and 1068 were downregulated. After analyzing competitive endogenous RNA network, 4 upregulated (MEG8, MEG3, MIR181A1HG, MIR4435-2HG) lncRNAs were found expressed during wound healing. MEG8/MEG3 may regulate fibroblast proliferation, differentiation, and apoptosis through hsa-miR-296-3p/miR-6763-5p. In-depth mining of gene expression matrix data indicated that lncRNAs and a competitive endogenous RNA regulatory network participate in the wound healing process, possibly providing novel intervention targets and treatment options for delayed wound healing.
A Percutaneous Portal Vein Puncture Under Artificial Ascites for Intraoperative Hepatic Segmentation Using Indocyanine Green Fluorescence: A Technical Report of Laparoscopic Anatomic Liver Resection
Authors: Kasai Meidai , Aihara Tukasa , Ikuta Shinichi , Nakajima Takayoshi , Yamanaka Naoki 
Published: December 2021

Background:
Laparoscopic liver resection have developed and is widely spread as standard procedure in these days, however, laparoscopic anatomic liver resection is still challenging, especially for posterosuperior lesions because of difficulties in segmental mapping and surgical techniques. Recently, the positive staining and negative staining method using fluorescent imaging techniques have been reported from experienced Asian centers, allowing to identify the tumor-bearing portal territory to be resected including the posterosuperior segment in laparoscopy. Those techniques are applicable in some cases; hence, it remains the room for improvement to establish as a feasible approach. Herein, we describe a percutaneous tumor-bearing portal vein puncture method under artificial ascites after the pneumoperitoneum for laparoscopic segmentectomy for segment 8.

Case Presentation and Surgical Procedure:
A male patient in his 60s was admitted for an incidentally diagnosed hepatic mass in segment 8. Findings of the computed tomography scan showed a 2.5-cm-sized hepatocellular carcinoma lesion. Then, laparoscopic anatomic liver resection for segment 8 was planned. The segmentation of the segment 8 was performed through a percutaneous tumor-bearing portal vein puncture using indocyanine green injection with extracorporeal ultrasound guidance under artificial ascites. According to indocyanine green fluorescence navigation, anatomic liver resection was completed. Operative time was recorded as 375 minutes. The estimated intraoperative blood loss was 50 mL without the requirement for an intraoperative transfusion. The planned resections were successful with histologically negative surgical margins. The patient was discharged on the 19th postoperative day with normal liver function test results. There was no operation-related complication during hospitalization.

Conclusion:
The intraoperative percutaneous portal vein puncture method under artificial ascites was useful for the identification of posterosuperior segment in laparoscopic anatomic segmentectomy.
Pancreatic Cystic Neoplasms and Pregnancy: A Systematic Review of Surgical Cases and a Case Report of a Fully Laparoscopic Distal Pancreatectomy
Authors: Fogliati Alessandro , Garancini Mattia , Uggeri Fabio , Braga Marco , Gianotti Luca 
Published: December 2021

Background:
Mucinous cystic neoplasms and solid pseudopapillary neoplasms are the most common pancreatic tumors occurring in women of fertile age and in pregnant women. The aim of this study is to provide an updated literature review on this association and to present a fully laparoscopic resection of a pregnancy-associated pancreatic cystic neoplasm.

Materials and Methods:
A systematic literature review was performed using PubMed (MEDLINE), Scopus, Ovid, ISI Web of Science, and Google Scholar for searching. The syntax was (pancr*) AND (cyst*) AND (pregn*) AND (tumor). Only English-language articles describing pancreatic surgical resections were included.

Results:
Forty-seven case reports were included. The mean age of the patients was 29.6±5.3. Nine patients (20%) required emergency surgery, 4 (9%) due to cyst rupture, and 5 (11%) due to hemorrhage. Four patients (9%) suffered a miscarriage, and 2 (5%) opted for pregnancy termination; the rest of the women delivered a healthy newborn (86%, n=36). Thirty percent (n=14) of the resected neoplasms were malignant, and among mucinous cystic lesions, this raised to 45% (n=11). All patients diagnosed during the third trimester were resected postpartum, whereas 26/34 (76%) of patients diagnosed during the first 2 trimesters underwent surgery before delivery.

Conclusions:
The most worrisome complications in pregnancy-associated pancreatic cysts are bleeding or rupture. Mucinous cystic neoplasm has a tendency to grow during pregnancy. A postpartum resection was generally preferred when the cystic neoplasm was diagnosed during the third trimester. This report is the first to describe a fully laparoscopic pancreatic resection.
Resource utilization and secondary overtriage for patients with traumatic renal injuries in a regional trauma system
Authors: Iyer Vishnu , Hagedorn Judith C. , Vavilala Monica S. , Rivara Frederick P. , Johnsen Niels V. 
Published: December 2021

BACKGROUND
While renal trauma management has shifted to conservative nonoperative management, insufficient data exist to guide interhospital renal trauma transfer protocols. Secondary overtriage is defined as the potentially avoidable transfer of patients from a lower to a higher-level trauma center despite the lack of need for higher-level care. The goal of this study was to determine the prevalence and predictors of secondary overtriage in renal trauma patients to a level 1 trauma center.

METHODS
A retrospective cohort study was performed of all renal trauma patients transferred to a level 1 institution between 2005 and 2017. Secondary overtriage was defined as a potentially avoidable transfer that consisted of hospital stay <72 hours with survival, no surgical or interventional radiology procedure, and all nonabdominal Abbreviated Injury Scale scores of <3 after transfer. Multivariate logistic regression was performed to estimate odds of secondary overtriage based on predefined clinical criteria.

RESULTS
Of the 612 renal trauma patients transferred between 2005 and 2017, 71 (11.6%) met the criteria for secondary overtriage. Female patients and patients coming from level IV/V trauma centers were more likely to have potentially avoidable transfers (p = 0.01 and p < 0.001, respectively). Mean (SD) Injury Severity Score was 10 (4.2) and 30.7 (14.3) in overtriaged and appropriately triaged patients, respectively (p < 0.001). Of the 71 overtriaged patients, 70.4% had isolated renal injuries. Patients with isolated renal injuries (odds ratio, 39.0; 95% confidence interval, 16.44–105.39) and those transferred from a level IV/V trauma center (odds ratio, 3.85; 95% confidence interval, 1.64–9.61) had a higher likelihood of secondary overtriage.

CONCLUSION
Within our regional trauma system, the majority of secondary overtriage was due to potentially avoidable transfers from level IV/V centers and of patients with isolated renal injuries. By implementing strategies to reduce the secondary overtriage burden on major trauma centers, regional trauma systems can avoid unnecessary costs while maintaining patient safety and ensuring appropriate care.

LEVEL OF EVIDENCE
Therapeutic/care management, Level III.
The tight rope act: A multicenter regional experience of tourniquets in acute trauma resuscitation
Authors: Tatebe Leah Carey , Schlanser Victoria , Hampton David , Chang Grace , Hanson Isaac , Doherty James , Issa Nabil , Ghandour Hani , Kingsley Samuel , Stewart Amy , Anstadt Michael , Dennis Andrew 
Published: December 2021

BACKGROUND
As tourniquets have become more prevalent, device use has been questioned. This study sought to characterize the incidence, indication, and efficacy of tourniquet placement in acute trauma resuscitation.

METHODS
Nine regional level 1 trauma centers prospectively enrolled for 12 months adult patients (18 years or older) who had a tourniquet placed. Age, sex, mechanism, tourniquet type, indication, applying personnel, location placed, level of occlusion, and degree of hemostasis were collected. Major vascular injury, imaging and operations performed, and outcomes were assessed. Analyses were performed with significance at p < 0.05.

RESULTS
A total of 216 tourniquet applications were reported on 209 patients. There were significantly more male patients (183 [88%]) and penetrating injuries (186 [89%]) with gunshots being most common (127 [61%]). Commercial tourniquets were most often used (205 [95%]). Ninety-two percent were placed in the prehospital setting (by fire/paramedics, 56%; police, 33%; bystanders, 2%). The most common indications were pooling (47%) and pulsatile (32%) hemorrhage. Only 2% were for amputation. The most frequent location was high proximal extremity (70%). Four percent were placed over the wound, and 0.5% were distal to the wound. Only 61% of applications were arterial occlusive. Median application time was 30 minutes (interquartile range, 20–40 minutes). Imaging was performed in 54% of patients. Overall, 36% had a named arterial injury. Tourniquet application failed to achieve hemostasis in 22% of patients with a named vascular injury. There was no difference in hemostasis between those with and without vascular injury (p = 0.12) or between who placed the tourniquet (p = 0.07). Seventy patients (34%) required vascular operations. Thirty-four percent of patients were discharged home without admission.

CONCLUSION
Discerning which injuries require tourniquets over pressure dressings remains elusive. Trained responders had high rates of superfluous and inadequate deployments. As tourniquets continue to be disseminated, emphasis should be placed on improving education, device development, and quality control.

LEVEL OF EVIDENCE
Prognostic/Epidemiologic, Level III.
From fruit growth to ripening in plantain: a careful balance between carbohydrate synthesis and breakdown
Authors: Campos N.A. , Colombie S. , Moing Annick , Cassan C. , Amah D. , Swennen R. , Gibon Y. , Carpentier S.C. 
Published: December 2021

AbstractWe investigated the fruit development in two plantain banana cultivars from two weeks after bunch emergence till twelve weeks through high-throughput proteomics, major metabolite quantification and metabolic flux analyses. We give for the first time an insight at early stages of starch synthesis and breakdown. Starch and sugar synthesis and breakdown are processes that take place simultaneously. During the first eight to ten weeks the balance between synthesis and breakdown is clearly in favour of sugar breakdown and a net starch synthesis occurs. During this period, plantain fruit accumulates up to 48% of starch. The initiation of the ripening process is accompanied with a shift in balance towards net starch breakdown. The key enzymes related to this are phosphoglucan water dikinase (PWD), phosphoglucan phosphatase, α-1,6-glucosidase starch debranching enzyme (DBE), alpha glucan phosphorylase (PHS) and 4-alpha glucanotransferase disproportioning enzyme (DPE). The highest correlations with sucrose have been observed for PHS and DPE. There is also a significant correlation between the enzymes involved in ethylene biosynthesis, starch breakdown, pulp softening and ascorbate biosynthesis. The faster ending of maturation and starting of ripening in the Agbagba cultivar are linked to the key enzymes 1-aminocyclopropane-1-carboxylate oxidase and DPE. This knowledge of the mechanisms that regulate starch and sugar metabolisms during maturation and ripening is fundamental to determine the harvest moment, reduce postharvest losses and improve final product quality of breeding programs.
C/EBPδ-induced epigenetic changes control the dynamic gene transcription of S100A8 and S100A9
Authors: Jauch-Speer Saskia-L. , Wolf Jonas , Herrera-Rivero Marisol , Martens Leonie , Chasan Achmet Imam , Witten Anika , Markus Birgit , Schieffer Bernhard , Vogl Thomas , Stoll Monika , Roth Johannes , Fehler Olesja 
Published: December 2021

SUMMARYThe proinflammatory alarmins S100A8 and S100A9 are among the most abundant proteins in neutrophils and monocytes but completely silenced after differentiation to macrophages. The molecular mechanisms of the extraordinarily dynamic transcriptional regulation of s100a8 and s100a9 genes, however, are only barely understood. Using an unbiased genome-wide CRISPR/Cas9 knockout based screening approach in immortalized murine monocytes we identified the transcription factor C/EBPδ as a central regulator of S100A8 and S100A9 expression. S100a8 and S100a9 expression was further controlled by the C/EBPδ-antagonists ATF3 and FBXW7. We confirmed the clinical relevance of this regulatory network in subpopulations of human monocytes in a clinical cohort of cardiovascular patients. Moreover, we identified specific C/EBPδ-binding sites within s100a8 and s100a9 promoter regions, and demonstrated that C/EBPδ-dependent JMJD3-mediated demethylation of H3K27me3 is indispensable for their expression. Overall, our work uncovered C/EBPδ as a novel regulator of S100A8 and S100A9 expression. Therefore, C/EBPδ represents a promising target for modulation of inflammatory conditions that are characterised by S100A8 and S100A9 overexpression.
Microdomain protein Nce102 is a local sensor of plasma membrane sphingolipid balance
Authors: Zahumenský Jakub , Fernandes Caroline Mota , Veselá Petra , Poeta Maurizio Del , Konopka James B. , Malínský Jan 
Published: December 2021

ABSTRACTSphingolipids are essential building blocks of eukaryotic membranes and important signalling molecules, tightly regulated in response to environmental and physiological inputs. Mechanism of sphingolipid level perception at the plasma membrane remains unclear. In Saccharomyces cerevisiae, Nce102 protein has been proposed to function as sphingolipid sensor as it changes its plasma membrane distribution in response to sphingolipid biosynthesis inhibition. We show that Nce102 redistributes specifically in regions of increased sphingolipid demand, e.g., membranes of nascent buds. Furthermore, we report that production of Nce102 increases following sphingolipid biosynthesis inhibition and Nce102 is internalized when excess sphingolipid precursors are supplied. This suggests that the total amount of Nce102 in the plasma membrane is a measure of the current need for sphingolipids, whereas its local distribution marks sites of high sphingolipid demand. Physiological role of Nce102 in regulation of sphingolipid synthesis is demonstrated by mass spectrometry analysis showing reduced levels of complex sphingolipids and long-chain bases in nce102Δ deletion mutant. Nce102 behaves analogously in human fungal pathogen Candida albicans, suggesting a conserved principle of local sphingolipid control across species.
Game of Theories: An Agent-Based Model of How Variation in Contest Cost-Benefits Determines the Evolution of Contest Resolution Rules
Authors: Pinto Nelson Silva 
Published: December 2021

ABSTRACTGame-theory based models are used to understand rules that animals use to settle contests over indivisible resources. However, the empirical literature of contests indicates controversial support to models, with some species supporting different models and other species showing no support to any model. Since strategies used to resolve contests may have different associated costs, it is possible that different conditions have determined the evolution of distinct assessment strategies used by animals. We used an agent-based model to explore the importance of the following conditions: resource availability, probability of reproduction with resource, and damage costs on evolution of assessment strategies. We used self- and mutual-assessment models as a heurist framework to build agents with different assessment strategies. In our model, agents competed for resources in scenarios with different combinations of resource availability, probability of reproduction with resource, and damage costs. We found that agents following the self-assessment with damage strategy were prevalent in scenarios with no probability of reproduction without the resource, independently of other variables. We also found that agents following the non-aggressive strategy occurred in all scenarios. However, agents using the non-aggressive strategy were prevalent only in scenarios with probability of reproduction with the resource. Finally, we observed that agents using mutual-assessment occurred only in a scenario with high risk of damage, low availability of resources, and with probability of reproduction without the resource. These results indicate that agents following the self-assessment with damage and non-aggressive strategies may be able to stay at most scenarios.
Metabolic dysregulation induces impaired lymphocyte memory formation during severe SARS-CoV-2 infection
Authors: Gurshaney Sanjeev , Alvarez Anamaria Morales , Ezhakunnel Kevin , Manalo Andrew , Huynh Thien-Huong , Le Nhat-Tu , Lupu Daniel S. , Gardell Stephen J. , Nguyen Hung 
Published: December 2021

AbstractCellular metabolic dysregulation is a consequence of COVID-19 infection that is a key determinant of disease severity. To understand the mechanisms underlying these cellular changes, we performed high-dimensional immune cell profiling of PBMCs from COVID-19-infected patients, in combination with single cell transcriptomic analysis of COVID-19 BALFs. Hypoxia, a hallmark of COVID-19 ARDS, was found to elicit a global metabolic reprogramming in effector lymphocytes. In response to oxygen and nutrient-deprived microenvironments, these cells shift from aerobic respiration to increase their dependence on anaerobic processes including glycolysis, mitophagy, and glutaminolysis to fulfill their bioenergetic demands. We also demonstrate metabolic dysregulation of ciliated lung epithelial cells is linked to significant increase of proinflammatory cytokine secretion and upregulation of HLA class 1 machinery. Augmented HLA class-1 antigen stimulation by epithelial cells leads to cellular exhaustion of metabolically dysregulated CD8 and NK cells, impairing their memory cell differentiation. Unsupervised clustering techniques revealed multiple distinct, differentially abundant CD8 and NK memory cell states that are marked by high glycolytic flux, mitochondrial dysfunction, and cellular exhaustion, further highlighting the connection between disrupted metabolism and impaired memory cell function in COVID-19. Our findings provide novel insight on how SARS-CoV-2 infection affects host immunometabolism and anti-viral response during COVID-19.Graphical AbstractHighlightsHypoxia and anaerobic glycolysis drive CD8, NK, NKT dysfunctionHypoxia and anaerobic glycolysis impair memory differentiation in CD8 and NK cellsHypoxia and anaerobic glycolysis cause mitochondrial dysfunction in CD8, NK, NKT cells
Characterization of the interaction between SARS-CoV-2 Membrane Protein and Proliferating Cell Nuclear Antigen (PCNA) as a Potential Therapeutic Target
Authors: Zambalde Érika Pereira , Betim Pavan Isadora Carolina , Silva Mancini Mariana Camargo , Severino Matheus Brandemarte , Scudero Orlando Bonito , Morelli Ana Paula , Amorim Mariene Ribeiro , dos Santos Karina Bispo , Góis Mariana Marcela , de Toledo-Teixeira Daniel Augusto , Parise Pierina Lorencini , Mauad Thais , Dolhnikoff Marisa , Saldiva Paulo Hilário Nascimento , Marques-Souza Henrique , Proenca-Modena José Luiz , Ventura Armando Morais , Simabuco Fernando Moreira 
Published: December 2021

ABSTRACTSARS-CoV-2 is an emerging virus from the Coronaviridae family and is responsible for the ongoing COVID-19 pandemic. In this work, we explored the previously reported SARS-CoV-2 structural membrane protein (M) interaction with human Proliferating Cell Nuclear Antigen (PCNA). The M protein is responsible for maintaining virion shape, and PCNA is a marker of DNA damage which is essential for DNA replication and repair. We validated the M PCNA interaction through immunoprecipitation, immunofluorescence co-localization, and a PLA assay. In cells infected with SARS-CoV-2 or transfected with M protein, using immunofluorescence and cell fractioning, we documented a reallocation of PCNA from the nucleus to the cytoplasm and the increase of PCNA and γH2AX (another DNA damage marker) expression. We also observed an increase of PCNA and γH2AX expression in the lung of a COVID-19 patient by immunohistochemistry. In addition, the inhibition of PCNA translocation by PCNA I1 and Verdinexor led to a reduction of plaque formation in an in vitro assay. We, therefore, propose that the transport of PCNA to the cytoplasm and its association with M could be a virus strategy to manipulate cell functions and may be considered a target for COVID-19 therapy.
Insights on the mutational landscape of the SARS-CoV-2 Omicron variant
Authors: Miller Nathaniel L. , Clark Thomas , Raman Rahul , Sasisekharan Ram 
Published: December 2021

AbstractThe SARS-COV2 Omicron variant has sparked global concern due to the possibility of enhanced transmissibility and escape from vaccines and therapeutics. In this study, we describe the mutational landscape of the Omicron variant using amino acid interaction (AAI) networks. AAI network analysis is particularly well suited for interrogating the impact of constellations of mutations as occur on Omicron that may function in an epistatic manner. Our analyses suggest that as compared to previous variants of concern, the Omicron variant has increased antibody escapebreadthdue to mutations in class 3 and 4 antibody epitopes as well as increased escapedepthdue to accumulated mutations in class 1 antibody epitopes. We note certain RBD mutations that might further enhance Omicron’s escape, and in particular advise careful surveillance of two subclades bearing R346S/K mutations with relevance for certain therapeutic antibodies. Further, AAI network analysis suggests that the function of certain therapeutic monoclonal antibodies may be disrupted by Omicron mutations as a result of the cumulative indirect perturbations to the epitope surface properties, despite point-mutation analyses suggesting these antibodies are tolerant of the set of Omicron mutations in isolation. Finally, for several Omicron mutations that do not appear to contribute meaningfully to antibody escape, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBD-RBD interface.