bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression and gene regulatory network of SNHG1 in hepatocellular carcinoma
Authors: Zheng Chaoran , Yu Shicheng 
Published: January 2021

Abstract
Background
Small nucleolar RNA host gene 1 (SNHG1), a long noncoding RNA (lncRNA), is a transcript that negatively regulates tumour suppressor genes, such as p53. Abnormal SNHG1 expression is associated with cell proliferation and cancer. We used sequencing data downloaded from Genomic Data Commons to analyse the expression and interaction networks of SNHG1 in hepatocellular carcinoma (HCC).

Methods
Expression was examined using the limma package of R and verified by Gene Expression Profiling Interactive Analysis. We also obtained miRNA expression data from StarBase to determine the lncRNA-miRNA-mRNA–related RNA regulatory network in HCC. Kaplan–Meier (KM) analysis was performed using the survival package of R. Gene Ontology annotation of genes was carried out using Metascape.

Results
We found that SNHG1 was overexpressed and often amplified in HCC patients. In addition, SNHG1 upregulation was associated with the promotion of several primary biological functions, including cell proliferation, transcription and protein binding. Moreover, we found similar trends of small nucleolar RNA host gene 1 (SNHG1), E2F8 (E2F transcription factor 8), FANCE (FA complementation group E) and LMNB2 (encodes lamin B2) expression. In the SNHG1-associated network, high expression levels of SNHG1 (log-rank P value = 0.0643), E2F8 (log-rank P value = 0.000048), FANCE (log-rank P value = 0.00125) and LMNB2 (log-rank P value = 0.0392) were significantly associated with poor survival. Single-cell analysis showed that E2F8 may play an important role in tumorigenesis or cancer development.

Conclusions
Our results highlight the benefit of utilizing multiple datasets to understand the functional potential regulatory networks of SNHG1 and the role of SNHG1 in tumours.
Establishment of a regression model of bone metabolism markers for the diagnosis of bone metastases in lung cancer
Authors: Zhu Zhongliang , Yang Guangyu , Pang Zhenzhen , Liang Jiawei , Wang Weizhong , Zhou Yonglie 
Published: January 2021

AbstractBackgroundThe aim of this study was to establish a regression equation model of serum bone metabolism markers. We analyzed the diagnostic value of bone metastases in lung cancer and provided laboratory evidence for the early clinical treatment of bone metastases in lung cancer.MethodsA total of 339 patients with non-metastatic lung cancer, patients with lung cancer with bone metastasis, and patients with benign lung disease who were treated in our hospital from July 2012 to October 2015 were included. A total of 103 patients with lung cancer in the non-metastatic group, 128 patients with lung cancer combined with bone metastasis group, and 108 patients with benign lung diseases who had nontumor and nonbone metabolism-related diseases were selected as the control group. Detection and analysis of type I collagen carboxyl terminal peptide β-special sequence (β-CTX), total type I procollagen amino terminal propeptide (TPINP), N-terminal-mid fragment of osteocalcin (N-MID), parathyroid hormone (PTH), vitamin D (VitD3), alkaline phosphatase (ALP), calcium (CA), phosphorus (P), cytokeratin 19 fragment (F211), and other indicators were performed. Four multiple regression models were established to determine the best diagnostic model for lung cancer with bone metastasis.ResultsAnalysis of single indicators of bone metabolism markers in lung cancer was performed, among which F211, β-CTX, TPINP, and ALP were significantly different (P< 0.05). The ROC curve of each indicator was less than 0.712. Based on the multiple regression models, the fourth model was the best and was much better than a single indicator with an AUC of 0.856, a sensitivity of 70.0%, a specificity of 91.0%, a positive predictive value of 82.5%, and a negative predictive value of 72.0%.ConclusionMultiple regression models of bone metabolism markers were established. These models can be used to evaluate the progression of lung cancer and provide a basis for the early treatment of bone metastases.
Clinicopathological features of fibrosarcomatous dermatofibrosarcoma protuberans and the construction of a back-propagation neural network recognition model
Authors: Li Yanan , Liang Jiaqi , Xu Xuewen , Jiang Xian , Wang Chuan , Chen Siyuan , Xiang Bo , Ji Yi 
Published: January 2021

AbstractBackgroundFibrosarcomatous dermatofibrosarcoma protuberans (FS-DFSP) is a form of tumor progression of dermatofibrosarcoma protuberans (DFSP) with an increased risk of metastasis and recurrence. Few studies have compared the clinicopathological features of FS-DFSP and conventional DFSP (C-DFSP).ObjectivesTo better understand the epidemiological and clinicopathological characteristics of FS-DFSP.MethodsWe conducted a cohort study of 221 patients diagnosed with DFSP and built a recognition model with a back-propagation (BP) neural network for FS-DFSP.ResultsTwenty-six patients with FS-DFSP and 195 patients with C-DFSP were included. There were no differences between FS-DFSP and C-DFSP regarding age at presentation, age at diagnosis, sex, size at diagnosis, size at presentation, and tumor growth. The negative ratio of CD34 in FS-DFSP (11.5%) was significantly lower than that in C-DFSP (5.1%) (P = 0.005). The average Ki-67 index of FS-DFSP (18.1%) cases was significantly higher than that of C-DFSP (8.1%) cases (P < 0.001). The classification accuracy of the BP neural network model training samples was 100%. The correct rates of classification and misdiagnosis were 84.1% and 15.9%.ConclusionsThe clinical manifestations of FS-DFSP and C-DFSP are similar but have large differences in immunohistochemistry. The classification accuracy and feasibility of the BP neural network model are high in FS-DFSP.
Co‐administration of 2’3’-cGAMP STING activator and CpG-C adjuvants with a mutated form of HPV 16 E7 protein leads to tumor growth inhibition in the mouse model
Authors: Dorostkar Fariba , Arashkia Arash , Roohvand Farzin , Shoja Zabihollah , Navari Mohsen , Mashhadi Abolghasem Shirazi Maryam , Shahosseini Zahra , Farahmand Mohammad , Shams nosrati Mohammad Sadegh , Jalilvand Somayeh 
Published: January 2021

AbstractPersistent infection with high-risk genotypes of human papillomavirus (HPV) is the leading cause of cervical cancer. The HPV oncoprotein E7 is constitutively expressed in cervical cancer and considered as an essential target for tumor-specific immunity. The goal of this study was to develop a candidate therapeutic vaccine based on the mutated E7 protein that had possibly reduced transformation capacity while was able to elicit a robust immune response. Therefore, the mutant type of HPV 16 E7 (E7GRG) protein was recombinantly expressed in E. coli. The protein was then purified and formulated with 2’-3’cGAMP CDN and/or CpG-C ODN adjuvants and subcutaneously injected to female C57BL/6 mice. To evaluate the immunogenic response, lymphocyte proliferation, secretion levels of IFN-γ and IL-4 cytokines, granzyme B level, and total IgG and subclasses of IgG antibody were measured. The anti-tumor activity was evaluated in tumor-harboring C57BL/6 mice. The highest rate of cell proliferation, IFN-γ and granzyme B levels, and amount of IgG antibody were found in mice group that were injected by E7GRG + 2′-3′cGAMP + CpG-C. Therapeutic immunization with E7GRG + 2′-3′cGAMP + CpG-C also significantly suppressed TC-1 tumor growth in mice. In conclusion, the results demonstrated that E7GRG + 2′-3′cGAMP + CpG-C induced strong cell-mediated and humoral immune responses that resulted in inhibition of tumor in mouse model.
Barriers and drivers to service delivery in global mental health projects
Authors: Qureshi Onaiza , Endale Tarik , Ryan Grace , Miguel-Esponda Georgina , Iyer Srividya N. , Eaton Julian , De Silva Mary , Murphy Jill 
Published: January 2021

Abstract
Background
Research in global mental health (GMH) has previously documented how contextual factors like political instability, poverty and poorly-funded health infrastructure continue to compromise effective and equitable mental health service delivery. There is a need to develop more feasible and evidence-based solutions through implementation research. This paper, one in a series pertaining to implementation in GMH projects worldwide, focuses on implementation factors influencing mental health service delivery.

Methods
This is a qualitative study carried out as part of a Theory of Change-driven evaluation of Grand Challenges Canada’s (GCC’s) Global Mental Health portfolio. Purposive sampling was used to recruit twenty-nine GCC grantees for interviews. A semi-structured interview schedule was used to guide the interviews which were recorded and subsequently transcribed. Transcripts were double-coded and analyzed in NVivo 11 using framework analysis. This paper reports results related to detection and treatment of mental illness, mental health promotion and prevention of mental illness.

Results

Key barriers included: lack of appropriate human resources and expertise for service delivery; lack of culturally appropriate screening tools and interventions; and difficulties integrating services with the existing mental health system. Formative research was a key driver facilitating the cultural adaptation of mental health detection, treatment, promotion and preventative approaches. Recruiting local providers and utilizing mHealth for improving screening, monitoring and data management were also found to be successful approaches in reducing workforce burden, improving sustainability, mental health literacy, participant engagement and uptake.

Conclusions
The study identifies a number of key barriers to and drivers of successful service delivery from the perspective of grantees implementing GMH projects. Findings highlight several opportunities to mitigate common challenges, providing recommendations for strengthening systems- and project-level approaches for delivering mental health services. Further, more inclusive research is required to inform guidance around service delivery for successful implementation, better utilization of funding and improving mental health outcomes among vulnerable populations in low-resource settings.
Successful treatment with Cinryze® replacement therapy of a pregnant patient with hereditary angioedema: a case report
Authors: Kardum Željka , Prus Višnja , Milas Ahić Jasminka , Kardum Darjan 
Published: January 2021

Abstract
Background
Hereditary angioedema (HAE) is a rare disease characterized with recurrent swelling of subcutaneous or mucosal tissue that resolves in approximately 3 days. It can be presented with peripheral edema, abdominal and life-threatening laryngeal angioedema. A variety of triggers are known to cause episodes of angioedema including estrogen exposure. There are different reports regarding the effect of pregnancy on HAE attacks, and in some patients, the pregnancy is a recognized triggering factor.

Case presentation
We present a female Caucasian patient with pre-existing HAE and disease exacerbations during pregnancy, requiring prophylactic use of plasma-derived C1 inhibitor concentrate. She was treated with Cinryze® replacement therapy throughout the pregnancy 1000 IU i.v. 48 times. She gave birth to a healthy male infant, via C-section. After the delivery, the patient was symptom-free for 6 months and required no treatment for HAE.

Conclusions
In the case presented, the angioedema attacks worsened as the pregnancy progressed. The treatment with Cinryze® replacement therapy was effective and safe during pregnancy, with no adverse effects on the infant.
A rapid, simultaneous and quantitative analysis of 26 ginsenosides in white and red Panax ginseng using LC–MS/MS
Authors: Lee Junghak , Han Heeju , Yuan Xiu , Park Eunyoung , Lee Jonghwa , Kim Jeong-Han 
Published: January 2021

AbstractA quantitative analysis of ginsenoside is very important for ginseng studies because each ginsenoside shows different medical activity and metabolic pathway. In this study, a rapid, simultaneous, and quantitative analysis of 26 ginsenosides (Rb1, Rb2, Rc, Rd, Re, Rf, Rg1, Rg2(R), Rg2(S), Rg3(S), Rg3(R), Rg5, Rg6, Rh1(R), Rh1(S), Rh2(R), Rh2(S), F1, F2, F3, F4, K, Mc, PPT(S), XVII, and Y) in white, and red Panax ginseng was established using multiple reaction monitoring (MRM) mode on ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC–MS/MS). The mobile phase of water and methanol containing 0.1% formic acid and HSS T3 C18 analytical column was used for the chromatographic separation. The four sets of stereoisomers were successfully separated within a 26-min run time, eluting the S-isomer faster than the R-isomer with higher concentration. The ginseng extract was diluted by 100, 400 and 8000 times to fit in the calibration range and quantitated by the standard addition method. Matrix matched calibration by mixing 64 µL of the ginseng extract with 16 µL of the standard solution was used for compensating the matrix effect. Such quantitation methodology using dilution, standard addition and matrix matching resulted in precise and unambiguous quantitation of 26 ginsenosides in ginseng products. Major ginsenosides were observed at relatively higher concentrations in red Panax ginseng and the Mc was detected and quantitated for the first time in this study. The comprehensive quantitation system established in this study will contribute to quality evaluation, breeding and culturing, and quantitative metabolomics study of ginseng.
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease
Authors: Zanella M. C. , Cordey S. , Laubscher F. , Docquier M. , Vieille G. , Van Delden C. , Braunersreuther V. , TA Mc Kee , Lobrinus J. A. , Masouridi-Levrat S. , Chalandon Y. , Kaiser L. , Vu D. L. 
Published: January 2021

AbstractBackgroundViral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated pipeline and de novo analysis on pooled routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal, and unexpected viruses.ResultsMedian duration of intensive immunosuppression was 5.1 months (IQR 5.5). GvHD-related mortality rate was 36%. mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥ 3 distinct viruses were detected in 16/25 patients;Anelloviridae(24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7 patients with fatal outcomes, viral sequences not assessed by routine investigations were identified with mNGS and confirmed by RT-PCR. These cases included Usutu virus (1), rubella virus (1 vaccine strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1).ConclusionsClinically unrecognized viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid-refractory/dependent GvHD in consecutive samples. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations, or re-infection.
Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth
Authors: Mahnert Alexander , Verseux Cyprien , Schwendner Petra , Koskinen Kaisa , Kumpitsch Christina , Blohs Marcus , Wink Lisa , Brunner Daniela , Goessler Theodora , Billi Daniela , Moissl-Eichinger Christine 
Published: January 2021

Abstract
Background
Human health is closely interconnected with its microbiome. Resilient microbiomes in, on, and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein, we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a 1 year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars.

Results
Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance, and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crew members were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crew members within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility.

Conclusions
This study highlights main routes of microbial transfer, interaction of the crew, and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors.
Bridging mapping and simulation modelling in the ecosystem service assessments of boreal forests: effects of bioenergy production on carbon dynamics
Authors: Akujärvi Anu , Repo Anna , Akujärvi Altti M. , Liski Jari 
Published: January 2021

Abstract
Background
Increasing the use of forest harvest residues for bioenergy production reduces greenhouse emissions from the use of fossil fuels. However, it may also reduce carbon stocks and habitats for deadwood dependent species. Consequently, simple tools for assessing the trade-offs of alternative management practices on forest dynamics and their services to people are needed. The objectives of this study were to combine mapping and simulation modelling to investigate the effects of forest management on ecosystem services related to carbon cycle in the case of bioenergy production; and to evaluate the suitability of this approach for assessing ecosystem services at the landscape level. Stand level simulations of forest growth and carbon budget were combined with extensive multi-source forest inventory data across a southern boreal landscape in Finland. Stochastic changes in the stand age class distribution over the study region were simulated to mimic variation in management regimes.

Results
The mapping framework produced reasonable estimates of the effects of forest management on a set of key ecosystem service indicators: the annual carbon stocks and fluxes of forest biomass and soil, timber and energy-wood production and the coarse woody litter production over a simulation period 2012–2100. Regular harvesting, affecting the stand age class distribution, was a key driver of the carbon stock changes at a landscape level. Extracting forest harvest residues in the final felling caused carbon loss from litter and soil, particularly with combined aboveground residue and stump harvesting. It also reduced the annual coarse woody litter production, demonstrating negative impacts on deadwood abundance and, consequently, forest biodiversity.

Conclusions
The refined mapping framework was suitable for assessing ecosystem services at the landscape level. The procedure contributes to bridging the gap between ecosystem service mapping and detailed simulation modelling in boreal forests. It allows for visualizing ecosystem services as fine resolution maps to support sustainable land use planning. In the future, more detailed models and a wider variety of ecosystem service indicators could be added to develop the method.
A practical approach to imaging characteristics and standardized reporting of COVID-19: a radiologic review
Authors: Sanli Deniz Esin Tekcan , Yildirim Duzgun , Sanli Ahmet Necati , Turkmen Suha , Erozan Neval , Husmen Guray , Altundag Aytug , Tuzuner Filiz 
Published: January 2021

AbstractNovel coronavirus (2019-nCoV), also known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a pathogen that has caused a rapidly spreading pandemic all over the world. The primary mean of transmission is inhalation with a predilection for respiratory system involvement, especially in the distal airways. The disease that arises from this novel coronavirus is named coronavirus disease 2019 (COVID-19). COVID-19 may have a rapid and devastating course in some cases leading to severe complications and death. Radiological imaging methods have an invaluable role in diagnosis, follow-up, and treatment. In this review, radiological imaging findings of COVID-19 have been systematically reviewed based on the published literature so far. Radiologic reporting templates are also emphasized from a different point of view, considering specific distinctive patterns of involvement.
The effect of reduced scan time on response assessment FDG-PET/CT imaging using Deauville score in patients with lymphoma
Authors: Hornnes Charlotte , Loft Annika , Højgaard Liselotte , Andersen Flemming Littrup 
Published: January 2021

Abstract
Purpose
[18F]Fluoro-deoxy-glucose positron emission tomography/computed tomography (FDG-PET/CT) is used for response assessment during therapy in Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL). Clinicians report the scans visually using Deauville criteria. Improved performance in modern PET/CT scanners could allow for a reduction in scan time without compromising diagnostic image quality. Additionally, patient throughput can be increased with increasing cost-effectiveness. We investigated the effects of reducing scan time of response assessment FDG-PET/CT in HL and NHL patients on Deauville score (DS) and image quality.

Methods
Twenty patients diagnosed with HL/NHL referred to a response assessment FDG-PET/CT were included. PET scans were performed in list-mode with an acquisition time of 120 s per bed position(s/bp). From PET list-mode data images with full acquisition time of 120 s/bp and shorter acquisition times (90, 60, 45, and 30 s/bp) were reconstructed. All images were assessed by two specialists and assigned a DS. We estimated the possible savings when reducing scan time using a simplified model based on assumed values/costs for our hospital.

Results
There were no significant changes in the visually assessed DS when reducing scan time to 90 s/bp, 60 s/bp, 45 s/bp, and 30 s/bp. Image quality of 90 s/bp images were rated equal to 120 s/bp images. Coefficient of variance values for 120 s/bp and 90 s/bp images was significantly < 15%. The estimated annual savings to the hospital when reducing scan time was 8000-16,000 €/scanner.

Conclusion
Acquisition time can be reduced to 90 s/bp in response assessment FDG-PET/CT without compromising Deauville score or image quality. Reducing acquisition time can reduce costs to the clinic.