bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust Rank Aggregation Based Analysis of Hub Genes and Correlation with Immune Infiltration in Aortic Dissection
Authors: Zhang Weizong , Yuan Hong , Sun Jindong , Yu Huamin , Shi Minjuan , Hu Haiqiang , Zhang Huihui , Bai Xinhua , Shen Chaofeng , Tu Sijia , Wang Gang 
Published: May 2023

Abstract
Background
Aortic dissection (AD) is an acute critical disease of the cardiovascular system characterized by high mortality and morbidity. According to reports, immune cell infiltration is associated to AD. However, the intrinsic molecular mechanisms underlying the pathogenesis of AD still need to be clarified.
Methods
Four datasets (GSE52093, GSE98770, GSE153434 and GSE190635) were download through the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) of each dataset were screened by robust rank aggregation (RRA) algorithms. Gene ontology (GO) functional enrichment analysis and Kyto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to DEGs. Using the Search Tool for Retrieval of Interacting Genes/Proteins (STRING) database, a protein–protein interaction (PPI) network was constructed, and the hub genes were identified by Cytoscape. And, after correcting for nonbiological effects between four datasets by Rank-In algorithm, we obtained a merged matrix. Furthermore, we adopted this merged matrix to evaluate immune infiltration by using CIBERSORT and single sample gene set enrichment analysis (ssGSEA). Finally, we calculated the correlation between hub genes and immune cells.
Results
Sixty-two integrated DEGs were identified. These DEGs were mainly enriched in 69 biological process (BP) terms and the ATP-binding cassette (ABC) transporters pathways. By applying 12 methods from Cytoscape plugin CytoHubba respectively, we selected final hub genes. The final hub genes consist of angiotensin Ⅰ converting enzyme (ACE), angiotensin converting enzyme 2 (ACE2), calsequestrin 2 (CASQ2) and TIMP metallopeptidase inhibitor 1 (TIMP1). CIBERSORT showed that monocytes (P < 0.001) and activated mast cells (P < 0.05) were higher fraction in AD group. ssGSEA showed that regulatory T cell (P < 0.05), CD56 bright natural killer (NK) cell (P < 0.01), central memory CD4 T cell (P < 0.01), T follicular helper cell (P < 0.01), activated dendritic cell (P < 0.001), myeloid derived suppressor cells (MDSC) (P < 0.001), monocytes (P < 0.001), NK T cell (P < 0.001), type 1 T helper cell (Th1) (P < 0.001) and Th17 cell (P < 0.001) were higher fraction in AD group.
Conclusion
ACE, ACE2, CASQ2 and TIMP1 are engaged in the process of AD, which can be used as molecular biomarkers for the screening and diagnosis of AD. Immune cell infiltration plays a major role in the development of AD.
Predation risk, foraging and reproduction of an insectivore fish species associated with two estuarine habitats
Authors: Guedes Éden , Pereira Juan , Brito Gitá , Pessanha Andre , Júnior Alexandre 
Published: May 2023

Abstract
Pneumatophore fringes and mudflats are extremely valuable habitats and provide structures on which many fish species benefit in terms of food and reduced predation risk. We analysed the spatiotemporal patterns in feeding habits, reproductive aspects and effects of predatory fish presence to assess the ecological drivers of the common halfbeak, Hyporhamphus unifasciatus, in a Brazilian estuary. Sampling was conducted in the rainy (January to July 2016) and dry (August to December 2016) periods. Fish were collected in the two estuarine habitats using a beach seine. In summary, the results demonstrated that the number of predatory fishes was a strong predictor of population abundance and biomass, followed by pneumatophore complexity. The abundance and biomass values tended to increase with increasing habitat structural complexity towards the upper estuary. There was evidence that fish exhibited movement during the rainy season related to spawning events and subsequent juvenile recruitment in this area. Hymnoptera was the item most frequently ingested and made the greatest contributions to the volume of diet in habitat types throughout the year. There was an increase in the condition factor in the rainy season and thus was associated with energy reserves, reproduction and growth (fitness). We concluded that predation is an important ecological process that operates at local spatial scales and that together with the density of pneumatophores, predation is considered an important attractiveness that could affect the abundance of common halfbeak populations associated with estuarine habitats.
A case report of a continuous ambulatory drug delivery (CADD) pump to deliver opioid agonist treatment in an acute care setting
Authors: Wigg Casey , Nolen Amy , Jauhal Lisa , Sharma Malika 
Published: May 2023

Abstract
Background:
People with substance use disorder (SUD) are at risk of complications of drug use and frequent hospitalization, and may continue to use substances during admission to acute care. Acute care harm reduction strategies including oral or injectable prescription opioids may aid in care retention and improve health outcomes in this patient population.
Case Presentation:
A 58 year-old woman with refractory opioid use disorder was admitted to hospital for management of dysphagia secondary to esophageal stricture. She received injectable opioid agonist therapy using a continuous ambulatory drug delivery (CADD) pump in order to facilitate completion of her hospital admission.
Conclusions:
The patient successfully received acute medical care with the use of a CADD pump for consistent, patient-controlled opioid administration, with the support of an interdisciplinary team and by respecting the patient’s own substance use goals.
Effects of Certified Perioperative Nurses on the Establishment of Preoperative Outpatient and Rate of Preoperative Assessment in Japan: A Cross-Sectional Study
Authors: Hara Kentaro , Yamamoto Chie , Mills Shigeko , Osaki Kengo , Tokuyama Kaoru , Inoue Takahiro 
Published: May 2023

Abstract
Background
In patients undergoing surgery, nurse-led preoperative assessments include preoperative outpatient and preoperative visits. Certified perioperative nurses are expected to intervene pre- and post-operatively in patients undergoing surgery. This study aimed to investigate the effects of certified perioperative nurses on preoperative outpatient and preoperative assessments.
Methods
The study period ranged from February 2021 to September 2022, and data were collected and analyzed using a questionnaire at 247 facilities that administer more than 800 general anesthetics annually. The primary outcome measure was the preoperative assessment rate of preoperative and outpatient visits. To analyze the factors affecting the rate of preoperative assessment with the primary endpoint of preoperative outpatient and preoperative visits, we performed multivariate analysis of facility characteristics, medical staff background, and the presence or absence of certified perioperative nurses. The datasets generated and analyzed during the current study are available from the corresponding author on reasonable request.
Results
Sixty-eight and forty-one institutions in the enrolled and non-enrolled groups underwent a preoperative assessment, respectively, and the enrolled group underwent a significantly higher number of preoperative assessments than did the non-enrolled group. The medians of the enrolled and non-enrolled groups were 90.0 and 83.0, respectively, indicating a significantly higher preoperative assessment rate in the enrolled group than in the non-enrolled group. Multivariate analysis of factors influencing the preoperative assessment rate revealed a significant association with certified perioperative nurse attendance.
Conclusions
Facilities where certified perioperative nurses are enrolled have a significantly higher prevalence of preoperative outpatient visits and significantly higher rates of preoperative assessments than do facilities where certified perioperative nurses are not enrolled. Enrollment of certified perioperative nurses will lead to the improvement of the quality of preoperative nursing interventions.
Changes in periphyton communities with land use in tropical mountain streams from Loja (Ecuador)
Authors: Cartuche Alonso , Manoylov Kalina , Ibelings Bastiaan W. , Venail Patrick , Aguirre Nikolay 
Published: May 2023

Abstract

Riparian vegetation along a stream regulates the flow of sediments and nutrients. It also provides stability to the riverbanks and controls the watershed microclimate that ultimately influences the primary production of lotic environments. The degradation of terrestrial vegetation can also have an impact on the biotic component of rivers. Periphyton communities are altered in their composition, abundance, and diversity when the natural conditions in the watershed are modified. While widely studied in Europe and North America, studies on changes in periphyton community structure in mountainous tropical ecosystems are rare. In this study, we investigated if and how alteration of the riparian vegetation results in changes in the diatom community composition of seven streams in southern Ecuador. Streams were sampled in one or 2 zones, with 5 sub-samples each. The sampled streams show different levels of degradation within their watersheds. Temperature was higher in open (i.e. deforested) areas within a stream and open areas, e.g. pastures, had higher abundance of cyanobacteria filaments. Total algal cell abundances increased from forested to open and more fully degraded zones. Species richness was lowest in the forested areas. Microbial diversity was low across all habitats, but the highest values were documented in the degraded habitats. Diatom communities dominated at all sites, followed by filamentous bacteria. Gomphonema minutum (Agardh) Agardh, G. parvulum (Kütz.) Kütz., and Achnanthidium minutissimum (Kütz.) Czarnacki were the most common and abundant species. Diatom communities from zones with different land use within a stream were as different from each other as communities from different watershed streams.
Perivascular epithelioid cell tumors (PEComas) of the bone and soft tissue: A Japanese Musculoskeletal Oncology Group (JMOG) multi-institutional study
Authors: Izubuchi Yuya , Hamada Shunsuke , Tanzawa Yoshikazu , Fujita Ikuo , Imanishi Jungo , Koyanagi Hirotaka , Shimatani Akiyoshi , Komatsubara Tadashi , Tanaka Takaaki , Fukushima Mana , Imamura Yoshiaki , Ueda Takafumi , Kawano Hirotaka , Matsumine Akihiko 
Published: May 2023

Abstract
Purpose: Perivascular epithelioid cell tumors (PEComas) of the bone and soft tissues are rare mesenchymal neoplasms, some of which are malignant. However, their clinical and pathological characteristics remain unclear. This study was performed to investigate the clinical and pathological characteristics of PEComas in bone and soft tissues by leveraging information from the Japanese Musculoskeletal Oncology Group.
Methods: Ten patients, including four male and six female patients with a median age of 49 years, were retrospectively reviewed. PEComas of the visceral organs, including the uterus and retroperitoneum, were excluded.
Results: Nine tumors arose in the soft tissue and one in the bone, with a mean size of 9.3 cm. Four patients showed local recurrence or distant metastasis. The 1-year survival rate was 77%. Pathologically, eight tumors were classified as malignant and two as having uncertain malignancy potential. Half of the tumors showed high MIB-1 index values of >30%. Immunohistochemically, the melanocyte marker HMB45 was expressed in 90% cases, and muscle-specific markers were expressed only in 30–50% cases. Transcription factor binding to IGHM enhancer 3 (TFE3) expression was positive in 89% of the patients. Tumors with high expression of TFE3 were classified as PEComas with malignant potential according to Folpe’s classification.
Conclusions: Bone and soft tissue PEComas may have a higher malignancy potential than other visceral PEComas and are more likely to develop as TFE3-rearranged PEComas.
Evaluation of temporal changes in fracture transmissivity in an excavation damaged zone after backfilling a gallery excavated in mudstone
Authors: Aoyagi Kazuhei , Ishii Eiichi 
Published: May 2023

Abstract
The long-term geological disposal of high-level radioactive waste relies on predictions of future changes in a disposal facility’s hydro-mechanical characteristics in order to assess potential leakage through fractures in the excavation damaged zone (EDZ) after backfilling the facility. This study evaluated the transmissivity of EDZ fractures using in situ hydraulic tests around the area of a full-scale, experimental, engineered barrier system in the Horonobe Underground Research Laboratory, Hokkaido, Japan. After their installation, the buffer blocks swelled, altering the stresses within the EDZ fractures. The effects of these changing stresses on the fractures’ transmissivity were assessed over a period of four years. The transmissivity continuously decreased in this period to about 26% of its value measured prior to the swelling. Using the Barton–Bandis normal-stress-dependent fracture-closure model, the decrease in transmissivity is quantitatively attributed to closure of the EDZ fractures, which was caused by the swelling pressure increasing up to 0.88 MPa. Evidence of fracture closure came from seismic tomography surveying, which revealed a slight increase in seismic velocity in the study area with increasing swelling pressure. The results show that EDZ fractures were closed by swelling of the full-scale buffer material. They also demonstrate the applicability of the Barton–Bandis model to preliminary estimation of the long-term transmissivity of EDZ fractures in facilities for the geological disposal of radioactive waste.
Verifying and Refining Early Statuses in Alzheimer’s Disease Progression: A Possibility from Deep Feature Comparison
Authors: Liu Mianxin , Cui Liang , Zhao Zixiao , Ren Shuhua , Huang Lin , Guan Yihui , Guo Qihao , Xie Fang , Huang Qi , Shen Dinggang 
Published: May 2023

Abstract
Background: Defining effective early status of Alzheimer’s disease (AD) could be challenging, due to complexity in linking early and late stages in the progression and the internal biological heterogeneity within same status. We explore whether it is possible to verify and refine candidature early statuses in the AD progressions by comparing the neurological features learned by deep learning models.
Methods: We collect functional magnetic resonance imaging (fMRI) data from 432 subjects, including 79 healthy controls (HCs), 109 amnestic mild cognitive impairments (aMCIs), 39 non-amnestic MCIs (naMCIs), 98 subjective cognitive declines (SCDs) and 107 ADs. We train graph convolutional networks (GCNs) based on multiscale functional networks to accurately classify aMCI from naMCI and HC from MCIs. The trained models are applied to AD and SCD groups to suggest the neural feature similarity (as the ratio of predictions) among the statuses and identify clinically informative subpopulations. The corresponding demographics, cognitive assessments, T1, and PET images are used to provide supportive evidences for sub-divided populations based on the model decisions.
Results: The GCN model achieves 89.2±1.9% and 83.7±3.1% accuracies in aMCI-vs-naMCI and HC-vs-MCI classifications. The aMCI-vs-naMCI classification model identifies 71.8% of the AD subjects as aMCI. The HC-vs-MCI classification model suggests that 73.5% of the SCDs are MCI, in which 88.8% are further diagnosed as “aMCI” by the aMCI-vs-naMCI classifier. The analyses based on T1 and PET images suggests that the aMCI-like AD exhibits more globally elaborated Aβ depositions, severer glucose metabolism reduction and grey matter atrophy than naMCI-like AD after contrasted with clinical HCs. MCI-like SCD shows more reduction of glucose metabolism than HC-like SCD, baselined by clinical HCs. Further, aMCI-like SCD exhibits slightly elaborated Aβ while naMCI-like SCD shows none when compared to clinical HCs. MCI-like SCD has lower executive ability than HC-like SCD. aMCI-like SCD shows lower memory ability than naMCI-like SCD.
Conclusions: This study suggests an overall neurological similarity among SCD, aMCI and AD from perspective of brain dynamics, and verifies the position of SCD and aMCI in the AD progression. Further, it offers a potentially refined progression progress, consisting of aMCI-like SCD, aMCI, and aMCI-like AD dementia.
Clinical Trials Registration: The data collection has been registered as “ChiCTR2000036842”.
Effectiveness of Intra-thecal Methotrexate in Refractory Anti-N-methyl-d-aspartate Receptor Encephalitis
Authors: Hommady Raid , Alsohaibani Abdullah , Alayed Ruba , Alshehri Abdulaziz , AbuMelha Ahlam , Aljomah Lama , Hundallah Khalid , Almuqbil Mohammed , Altuwaijri Waleed , Alrumayyan Ahmad , Alrifai Muhammed Talal , Baarmah Duaa Mohammed 
Published: May 2023

Abstract
Background
Anti-N-methyl-d-aspartate receptor encephalitis is one of the most common autoimmune encephalitis for which first- and second-line therapies have been recommended following international consensus. However, some refractory cases do not respond to the first- and second-line therapy and require further immune-modulatory therapies such as intra-thecal methotrexate. In this study, we reviewed six confirmed cases of refractory anti-N-methyl-d-aspartate receptor encephalitis from two tertiary centers in Saudi Arabia that required escalation of treatment and received a six-month course of intra-thecal methotrexate. The aim of this study was to evaluate the effectiveness of intra-thecal methotrexate as immunomodulatory therapy for refractory anti-N-methyl-d-aspartate receptor encephalitis.
Methods:
We retrospectively evaluated six confirmed cases of refractory anti N-methyl-d-aspartate receptor encephalitis who did not improve after first- and second-line therapy and received monthly intra-thecal methotrexate treatment course for six consecutive months. We reviewed patient demography, underlying etiologies, and compared their modified Rankin score prior to receiving intra-thecal methotrexate and six months after completing the treatment.
Results:
Three of the six patients showed a marked response to intra-thecal methotrexate with a modified Rankin scale of 0–1 at 6-month follow-up. None of the patients experienced any side effects during or after intra-thecal methotrexate treatment, and no flareups were observed.
Conclusion:
Intra-thecal methotrexate may be a potentially effective and relatively safe escalation option for immunomodulatory therapy of refractory anti- N-methyl-d-aspartate receptor encephalitis. Future studies on intra-thecal methotrexate -specific treatment regimens may further support its utility, efficacy, and safety in treating refractory anti- N-methyl-d-aspartate receptor encephalitis.
The M6A Methyltransferase METTL3 drives thyroid cancer progression and lymph node metastasis by targeting LINC00894
Authors: Zhou Xiang , Yu Leitao , Chang Lihsa , Liang Qiaoqiao , Zhao Rongjie , Xiao Yong , Xu Zheng 
Published: May 2023

Abstract
Background：Long non-coding RNAs (lncRNAs) are significant contributors to various human malignancies. The aberrant expression of lncRNA LINC00894 has been referred to in various human malignancies. Consequently, our aim is to illustrate the role of LINC00894 and its underlying mechanism in the development of papillary thyroid carcinoma (PTC).
Method：Bioinformatics analysis of differentially expressed RNA from TCGA and GEO datasets and selected the target lncRNA LINC00894.The analysis of SRAMP found that there are abundant M6A methylation sites in LINC00894. And further analysis from StarBase, GEPIA, and TCGA datasets to find related differentially expressed genes METTL3. The Colony formation and CCK8 assay confirmed the relationship between LINC00894, METTL3, and the proliferative capacity of PTC cells. The analysis of AnnoLnc2, Starbase datasets, and meRIP-PCR, qRT-PCR confirmed the influence of Mettl3-mediated modification of M6A on LINC00894. The study employed KEGG enrichment analysis as well as Western blotting to investigate the impact of LINC00894 on the expression of proteins related to the Hippo signaling pathway.
Results：LINC00894 hypoexpression was detected in PTC tissues and cells and even lower in PTC with lymphatic metastasis. LINC00894 inhibits the lymphangiogenesis of vascular endothelial cells and the proliferation of cancer cells. METTL3 enhances PTC progression by upregulating LINC00894, which relies on enhancing the LINC00894 mRNA stability through the M6A-YTHDC2-dependent pathway.LINC00894 may inhibit PTC malignant phenotypes through the Hippo signaling pathway.
Conclusion： The METTL3-YTHDC2 axis stabilizes LINC00894 mRNA in an M6A-dependent manner and subsequently inhibits tumor malignancy through the Hippo signaling pathway.
Comparative study between Enhanced Recovery After Surgery versus conventional peri-operative care in elective gastrointestinal surgery and compliance to ERAS protocols at an Indian tertiary care public hospital
Authors: Shukla Pragati , Jhaveri Rupen , Yadav Anurag , Kacheriwala Samir 
Published: May 2023

Abstract
Introduction: The benefits of fast track surgery protocols have been well established for abdominal surgeries. They are now being used for other surgeries also including urology and even neurosurgery. However very few Indian public hospitals implement these protocols. There is difficulty in complying to the stated protocols.
Materials and Methods:A prospective randomized control study carried out from September, 2021 to October, 2022 at the Department of General Surgery, Sir Sayajirao General Hospital, Vadodara amongst all patients undergoing elective abdominal surgeries. Patients were divided into two groups (ERAS and Control) by closed envelope technique, each having 30 patients. ERAS group patients received peri-operative care defined by ERAS criteria while the control group patients received conventional care.
Results: Stoma closure was the most commonly performed surgery among both groups. The mean time of starting liquids was 1.2 ± 0.4 days in the ERAS group compared to 4.4 ± 0.8 days in the control group. Soft diet was also started early in the ERAS group (2.2 ± 0.4 days vs 5.7 ± 1.2 days.) The mean time of first defecation was 2.4 ± 0.6 days in the ERAS group and 4.7 ± 0.9 days in the control group. Foley’s catheter inserted intra-operatively was removed after a mean 1.3 ± 0.7 days in the ERAS group compared to 1.7 ± 0.9 days in the control group. The patients in ERAS group needed an average of 3.3 days of post op IV opioid analgesia as compared to 4.5 days of control group. The mean length of hospital stay was 13.2 ± 6.2 days for the ERAS group compared to 19.3 ± 8.8 days in the control group. Total number of patients who developed complications were 7 in ERAS group and 18 in control group. The compliance to pre-, peri-, and post-operative components was 80%, 65% and 88.3% respectively.
Conclusion: Due to the significantly decreased length of stay and lesser complications, ERAS protocols, or at least some elements of the ERAS protocols can be implemented even in the public hospital setup. Higher bed turnover ratio can help in maximizing the benefits of the existing resources to help more number of patients.