bluuebunny/crossref_metadata_2025_split huggingface dataset:
R&amp;D intensity and its influence on renewable energy consumption: Evidence from selected Asian economies
Authors: Li Wei , Ullah Sana 
Published: January 2022

Abstract
The main objective of this study is to investigate the impact of research and development (R&D) intensity on renewable energy consumption in Asian economies. We have relied on the autoregressive distributive lag (ARDL) model to get empirical estimates. The results show that the short and long-run estimates attached to R&D intensity are significantly positive in China and Japan, signifying that a rise in R&D intensity increases the renewable energy consumption in China and Japan. Conversely, the short-run estimated coefficients of energy intensity are significantly negative in India and positive in Japan. In the long run, the estimates of energy intensity are positive and significant in India and Japan only. Among the control variables, the rise in CO2 emissions causes renewable energy consumption to rise in all three economies in the long run. However, the long-run effects of an increase in trade also positively affect renewable energy consumption in China and Japan. Lastly, a rise in financial development gives rise to renewable energy consumption in the long run in China only. On the policy front, policymakers should promote investment in R&D to minimize the costs of conventional energy consumption.
Solitary Fibrous Tumor: A Rare Differential for Submandibular Gland Swelling
Authors: kushwaha naveen kumar 
Published: January 2022

Abstract
INTRODUCTION-

Solitary fibrous tumour is a spindle cell neoplasm that commonly arise in the pleura and other serosal regions with more than 50% of these tumours located in the thoracic cavity, however extrathoracic tumours have been reported in various sites such as the liver, skin and the head and neck. Solitary fibrous tumours (SFTs) of the head and neck region are extremely rare with oral cavity being the most common site
MATERIALS AND METHODS-

A 60 yr. old lady presented with a painless right submandibular swelling that had increased in size during the previous 8 months with no constitutional symptoms. Clinically, there was a firm, mobile,6x5 cm right submandibular swelling with no palpable cervical lymph nodes, calculi and the submandibular duct opening was patent. MRI showed a well-defined heterogeneously enhancing lesion involving the right submandibular gland likely neoplastic. FNAC and USG guided core needle biopsy failed to yield any conclusive results. The patient then underwent complete removal of the tumour.
RESULTS-

Since SFT are rare and share many histological features with other spindle cell neoplasms of the salivary gland, immunohistochemistry is an essential tool to correctly diagnose SFT. NAB2-STAT6 gene fusion product is a highly sensitive and specific marker for SFT and is considered the molecular hallmark. In our case, the resection specimen showed the characteristic histopathological findings for SFT and stained positive for STAT6, CD34, CD99, and BCL-2.
CONCLUSION-

Clinicians should include SFT in the differential diagnosis of tumours that arise from soft tissues of the head and neck. Immunohistochemical staining is essential to diagnose SFT. Management is complete excision of the mass with long term follow up, because of the potential for recurrence and malignant transformation.
The Effectiveness And Safety of Gemcitabine Plus Nab-Paclitaxel In Elderly Patients With Advanced Pancreatic Cancer: A Single-Center Retrospective Cohort Study
Authors: Ohwada Sae , Todaka Akiko , Nakase Hiroshi , Shirasu Hiromichi , Kawakami Takeshi , Hamauchi Satoshi , Tsushima Takahiro , Yokota Tomoya , Onozawa Yusuke , Yasui Hirofumi , Yamazaki Kentaro 
Published: January 2022

Abstract
Purpose: This study aimed to evaluate the effectiveness and safety of gemcitabine (GEM) plus nab-paclitaxel (GnP) in patients aged ≥75 years with advanced pancreatic cancer and compare it with monotherapy (GEM or S-1).Methods: We retrospectively reviewed the data of patients with advanced pancreatic cancer aged ≥75 years who received either GnP or monotherapy (GEM or S-1) between January 2014 and May 2020. The primary efficacy outcome was overall survival (OS).Results: A total of 96 patients were included in this study; 51 were treated with GnP and 45 with monotherapy (31 with GEM and 14 with S-1). The median OS and progression-free survival were 10.8 and 6.7 months in the GnP group and 10.7 and 4.3 months in the monotherapy group, respectively. The treatment effect on OS was consistently favorable in the GnP group across most subgroups, particularly in patients with locally advanced cancer, modified Glasgow prognostic score of 0 or 1, and neutrophil/lymphocyte ratio <3.1. The disease control rates were 76% and 48% in the GnP and monotherapy groups, respectively, and grade 3 or 4 neutropenia occurred in 23 (45%) and 11 (24%) patients of the GnP and monotherapy groups, respectively.Conclusions: This study demonstrated that GnP was not superior to monotherapy with regard to OS. However, multivariate analysis showed that GnP treatment positively affected the OS and could be considered a treatment option, even for elderly patients.
Cytokines and Vascular Mediators Fingerprints Based on Interaction Networks in Kidney Transplanted and Non-Transplanted Moderately Ill COVID-19 Patients
Authors: Brunialti Milena Karina Coló , Leite Giuseppe Gianini Figueirêdo , Araújo Orlei Ribeiro , Eburneo Gabriela Strafolino , Peçanha-Pietrobom Paula M , Ferreira Paulo Roberto Abrão , Bellei Nancy Junqueira , Arakaki Jaquelina Sonoe Ota , Requião-Moura Lúcio R. , Salomao Reinaldo 
Published: January 2022

Abstract
This prospective study enrolled 68 hospitalized COVID-19 patients (including 20 kidney transplant recipients, KTRs) and 29 controls, and a panel comprising 23 circulating cytokines and vascular mediators was run at different time points. The associations between in-hospital mortality and mediators were determined using logistic regression and correlation-based network (CBN) analysis. In total, 17.6% of patients died, and the in-hospital mortality was associated with early and over-time levels of several mediators. Death was predicted by sVCAM, IL-9, and KTR in the multivariable model (AUC-ROC=0.94). Overall, circulating mediator levels were similar in the non-KTR and KTR COVID-19 patients. Compared to their respective controls, the number of interactions in the networks increased more in non-KTRs (14–55) than in KTRs (16–26), with a higher positive/negative edges (pe/ne) ratio in non-KTRs than in KTRs patients. The correlation network was also more connected in survivors than in non-survivors. Changing the pe/ne ratio from the first to the third day of hospitalization seems to be associated with survival: from 12 to 21.5 among survivors and from 4.0 to 2.37 among non-survivors. In conclusion, in-hospital mortality was associated with increased levels of cytokines and vascular mediators, but survivors and non-KTR patients showed more densely connected CBNs.
DeepPVC: Prediction of A Partial Volume-Corrected Map for Brain Positron Emission Tomography Studies Via a Deep Convolutional Neural Network
Authors: Matsubara Keisuke , Ibaraki Masanobu , Kinoshita Toshibumi 
Published: January 2022

Abstract
Background

Partial volume correction with anatomical magnetic resonance (MR) images (MR-PVC) is useful for accurately quantifying tracer uptake on brain positron emission tomography (PET) images. However, MR segmentation processes for MR-PVC are time-consuming and prevent the widespread clinical use of MR-PVC. Here we aimed to develop a deep learning model to directly predict PV-corrected maps from PET and MR images, ultimately improving the MR-PVC throughput.
Methods

We used MR T1-weighted and [11C]PiB PET images as training input data from 156 participants from the Alzheimer’s Disease Neuroimaging Initiative database using the U-Net model. We calculated PV-corrected maps as the training target using the region-based voxel-wise PVC method. The trained deepPVC model was validated by six-fold cross-validation and then tested using MR T1-weighted and [11C]PiB PET images from 36 participants acquired at sites other than the training dataset. We calculated the structural similarity index (SSIM) of the PV-corrected maps and intraclass correlation (ICC) of the PV-corrected standardized uptake value (SUV) between the RBV PVC and deepPVC as indicators for validation and testing.
Results

A high SSIM (0.810 ± 0.042) and ICC (0.867 ± 0.086) were observed in the validation and test data (SSIM, 0.828 ± 0.032; ICC, 0.910 ± 0.053). The computation time required to predict a PV-corrected map for a participant (48 s without a graphics processing unit) was much shorter than that for the RBV PVC and MR segmentation processes.
Conclusion

These results suggest that the deepPVC model directly predicts PV-corrected maps from MR and PET images and improves the throughput of MR-PVC by skipping the MR segmentation processes.
Determination of ERG(+), EZH2, NKX3.1, and SPINK-1 Subtypes to Evaluate Their Association With Clonal Origin and Disease Progression in Multifocal Prostate Cancer
Authors: SEGURA-MORENO Yenifer Yamile , SANABRIA-SALAS María Carolina , de Mesa Jorge Andrés Mesa-López , VARELA-RAMIREZ Rodolfo , ACOSTA-VEGA Natalia Lizeth , Serrano Martha Lucía 
Published: January 2022

Abstract
BackgroundThe prognostic relevance of prostate cancer (PCa) molecular subtypes remains controversial, given the presence of multiple foci, with the possibility of different subtypes, in the same PCa patient. To help elucidate the clonal origin of heterogeneity in PCa and its association with disease progression, SPOP, ERG(+), EZH2, NKX3.1, and SPINK-1 subtypes were analyzed.MethodsEighty-three samples of different foci (n=50) and positive lymph nodes (LN) (n=13) from 20 PCa patients were used to analyze the presence of the TMPRSS2-ERG fusion and expression levels of ERG, EZH2, NKX3.1, and SPINK-1, using RT-PCR. Mutations in exons 6 and 7 of the SPOP gene were searched by sequencing. The presence of subtypes and molecular patterns were established, combining the presence of all subtypes analyzed. To establish the clonal origin of multifocal PCa, the molecular concordance between different foci of the same patient was determined. Association of these subtypes with histopathological groups and time to biochemical recurrence (BCR) was assessed. ResultsNo mutation in SPOP was found in any sample. The ERG(+) subtype was the most frequent. The molecular pattern with the four PCa subtypes was detected only in 3 samples (4%), all LN, but it was the most frequent (40%) in patients. Molecular discordance was the predominant status (55%) when all the analyzed molecular characteristics were considered. All the subtypes could be found starting from preneoplastic lesion, and all but one LN molecular subtype were ERG(+) and NKX3.1 subtypes. Only the expression of the NKX3.1 gene was significantly different among the histopathological groups. No association was found between BCR time in patients, and molecular subtypes or molecular concordance, or between clinicopathological characteristics and molecular subtype with ERG, EZH2, and SPINK-1 subtypes.ConclusionThe predominance of molecular discordance in prostatic foci per patient, which reflects the multifocal origin of PCa foci, highlights the importance of analyzing multiple samples, to establish the prognostic and therapeutic relevance of molecular subtypes in a patient. All the subtypes analyzed here are of early onset, starting from preneoplastic lesions. NKX3.1 gene expression is the only molecular characteristic that shows a progression pattern by sample.
Prognostic Value and Possible Mechanism of m6A Methyltransferase METTL3 in Prostate Cancer
Authors: Li Huifeng , Fei Xiawei , Shen Yanting , Wu Zhenqi 
Published: January 2022

Abstract
Background: The N6-methyladenosine (m6A) methyltransferase METTL3 has been reported to be closely related to prostate cancer (PCa). Thus, we aimed to explore its prognostic value and possible mechanism in PCa.Methods: The METTL3 gene and protein expression status in between the PCa and normal tissues as well as the correlation between METTL3 and Gleason score (GS) were evaluated using The Cancer Genome Atlas Project (TCGA) dataset and the tissue microarray (TMA) dataset. The prognostic value of METTL3 was evaluated using 490 PCa patients from TCGA cohort followed by the verification using 515 PCa patients from the dataset integrated by TCGA cohort and International Cancer Genome Consortium (ICGC) cohort. The machine learning methods were used for the possible mechanism of METTL3 which was closely related to the prognosis of PCa. A nomogram was constructed to provide a quantitative approach to predict the prognosis of PCa. Results: The gene and protein expression levels of METTL3 in the PCa tissues were significantly higher than those in the normal tissues, and the gene and protein expression levels of METTL3 in the high (GS>7) risk PCa tissues were significantly higher than those in the low-moderate risk PCa (GS≤7) tissues. The PCa patients with high expression level of METTL3 had higher risk for the progression-free survival (PFS) events and poorer short-term and long-term PFS than those with low expression level of METTL3. Through using machine learning, a METTL3 related risk model (M-RM) consisted of seven m6A methyltransferase METTL3 target genes was obtained. The high M-RM score was revealed to be significantly related to the poor PFS of PCa as well as the high activity of the KEGG pathways closely related to the process of cell cycle. Conclusion: METTL3 has the potential to be the prognostic predictor of PCa. Its coded protein may affect the prognosis of PCa mainly through regulating the expression of their target genes closely related to the process of cell cycle. These outcomes will be benefit to improve the prognosis of patients, as well as reduce the mortality of PCa.
Relationship of N6-Methyladenosine-Related lncRNAs With Tumor Microenvironment and Clinical Prognosis in Osteosarcoma
Authors: Chen Wen-Kang , Zhang Han-Jing , Jiang Yong-Hui , Liu An-Song , Yin Ke , Xie Pei-Han , Chen Ying-Ying , Dai Zhu , Zhan Xin-Li 
Published: January 2022

Abstract
Background: The aberrant expression of long non-coding RNAs (lncRNAs) can affect the occurrence and progression of various cancers, including osteosarcoma (OS), by regulation of N6-methyladenosine (m6A) modification. However, their interaction involved in the prognostic value of OS and tumor microenvironment remains unclear.Methods: We collected data from TCGA and GEO datasets. Using Pearson correlation, univariate, multivariate, LASSO Cox regression analyses, we identified the prognostic m6A-related lncRNAs and conducted the prognostic cluster and model. Survival analyses were used to analyze different clusters and models, respectively. The receiver operating characteristic (ROC) curve and independent prognosis analysis was used to evaluate the performance of the risk model. We also examined the relationship of the risk model and cluster with immune checkpoint (PD1 and CTLA-4) and tumor microenvironment (TME).Results: A total of 43 m6A-related lncRNAs have significant prognostic significance for OS patients. Patients of cluster 2 have a longer survival time than cluster 1. CD8+ T cells, resting NK cells, and Monocytes were highly inflamed tissues in cluster 2, while gamma delta T cells and M0 macrophages were lowly in cluster 1. Meantime, OS patients with lower prognosis scores had better overall survival status, and ROC curves proved that the risk model had better prognostic abilities with the area under the curve (AUC) of 0.938 and 0.924 in train and test datasets, respectively. The risk score of 17 m6A-related lncRNAs was identified as an independent risk factor for OS. Both PD1 and CTLA-4 were closely associated with m6A-related lncRNAs and prognostic scores. The risk score was higher in cluster 2, while cluster 1 had a lower purity of tumor cells and a higher density of immune-related cells in the TME. Conclusions: We established a new m6A-related lncRNAs prognostic biomarker that can predict the prognostic risk of OS was significantly linked with the OS tumor microenvironment.
Mining Metagenomes Reveals Diverse Antibiotic Biosynthetic Genes in Uncultured Microbial Communities
Authors: Amin Dina H. , Nageeb Wedad M. , Elkelish Amr , Makharita Rabab R. 
Published: January 2022

Abstract
Background: Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing non-ribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. Bioinformatics analysis were conducted to detect predict NRPS domains and their substrate specificity.Results: Successfully, 17 NRPS positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrates specificity has no hits with the known ones hence they are more likely to use different substrates to produce new diverse antimicrobials. Conclusions: We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.
Influences of Induction Time and Additional LacI on the Growth Rate and Yield of the T7 Expression System in Three Escherichia Coli Strains
Authors: Arias-Vaccari Nicolás , Guerra Daniel Giraldez 
Published: January 2022

Abstract
The T7 expression system is commonly used to obtain high yields of heterologous proteins in Escherichia coli. Still, laboratories empirically optimize its use, frequently with little information for rationally choosing the change of settings in each case. Here, we monitored the expression of green fluorescent protein (GFP) as a function of growth in three strains, with and without additional LacI repressor and IPTG added at different times. BL21(DE3) strain showed the best yield; however, its inability to repress T7 harmed the culture unless additional LacI was provided. The BLR(DE3) and MG1655 strains suppressed T7 leaking by themselves but differed in the outcomes of additional LacI. While LacI overexpression improved BLR’s growth and yield, it severely harmed the MG1655 culture. In all cases, early induction with IPTG offered a better outcome than adding it too late. MG1655 was least sensitive to this timing thanks to its capability of keeping a high growth rate for longer. Notably, the GFP production rate was linear to growth rates throughout the culture, meaning that the ribosomal fraction allocated to GFP production was constant at all the analyzed time points. This observation is consistent with a general, time-resolved regulation function and supports the interpretation of our data through a proteome allocation model (PAM). A simple PAM simulated correctly the carbon overflow triggered by heterologous overexpression, indicating that if any anabolic fraction is added to compete for proteome allocation, the rate of precursors consumption will decrease, thus leading to said overflow. This model proposes that a LacI promiscuous repression activity can explain its observed opposite effects on BLR(DE3) and MG1655 strains. Through different levels of downregulation, the carbon fixating proteome fraction would reach a state closer or farther from optimum in each host.
Developmental Independence of Median Fins From the larval Fin Fold Revises Their Evolutionary Origin
Authors: Miyamoto Kazuhide , Kawakami Koichi , Tamura Koji , Abe Gembu 
Published: January 2022

Abstract
The median fins in modern fish that show separated forms (dorsal, anal, and caudal fins) are derived from a continuous fold-like structure, both in ontogeny and phylogeny. The median fin fold (MFF) hypothesis assumes that the median fins evolved by reducing some positions in the continuous fin fold of basal chordates, based on the classical morphological observation of developmental reduction in the larval fin folds of living fish. However, the developmental processes of median fins are still unclear at the cellular and molecular levels. Here, we describe the transition from the larval fin fold into the median fins in zebrafish at the cellar and molecular developmental level. We demonstrate that reduction does not play a role in the emergence of the dorsal fin primordium: the reduction occurs passively after the primordium formation, rather than actively scrapping the non-fin forming region by inducing cell death. We also report that the emergence of specific mesenchymal cells and their proliferation promote the dorsal fin primordium formation. Based on these results, we propose a revised hypothesis of median fin evolution in which acquisition of de novo developmental mechanisms is a crucial evolutionary component of the separated forms of median fins.
Predictors of Recurrence and Survival in Malignant Triton Tumours: A Case Report and Systematic Review
Authors: Pumputis Allison E. , Callan Laura , Branch Anna , Boldt R. Gabriel , Warner Andrew , Logan Diane , Read Nancy , Siddiqi Fawaz , Ross Douglas , Dubois Luc , Fortin Dalilah , Palma David A. , Nichols Anthony C. 
Published: January 2022

Abstract
1.1 Introduction: Malignant triton tumours (MTTs) are a rare and aggressive subset of malignant peripheral nerve sheath tumours (MPNSTs). A systematic review was conducted to better understand the prognosis and prognostic factors of MTTs in adult patients, and provide treatment guidance for clinicians encountering this rare tumour. 1.2 Methods: A PubMed search was conducted using keywords: “rhabdomyoblastic,” “rhabdomyosarcomatous,” “triton,” “case series” and “case report”. Reference list search was also completed. Two independent investigators completed abstract and full-text reviews. Articles were restricted to peer-reviewed articles in English language only containing adult MTT cases (≥ 18 years), and excluding articles with insufficient treatment/outcome data. Univariable and multivariable Cox proportional hazards regression was performed to identify significant predictors of overall survival (OS) and progression-free survival (PFS). 1.3 Results: A total of 123 cases from the literature and 1 case from our institution were included in the final analysis. The 2-year and 5-year OS was 46.2% and 32.2%, and the 2-year and 5-year PFS was 27.1% and 21.3%, respectively. On multivariable analysis for OS, prior radiation exposure (hazard ratio [HR]: 3.99, p = 0.027), central nervous system or spine disease site (HR: 5.86, p < 0.001) and positive neurofibromatosis 1 (NF1) status (HR: 3.42, p < 0.001) were associated with worse survival. Adjuvant radiotherapy (HR: 0.58, p = 0.038) was associated with improved survival. Positive NF1 status (HR: 2.34, p < 0.001) and positive margins (HR: 3.28, p < 0.001) were associated with worse PFS. 1.4 Conclusions: MTTs are rare and have poor long-term survival. Negative surgical margins and adjuvant radiation were found to be associated with improved outcomes.