bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrences of self-administered antibiotics, culture diagnostic challenges and multi-drug resistant S. aureus among Ethiopian pyogenic/bacterial meningitis patients: 2020-2021
Authors: Mihret Wude , Alemu Ashenafi , Hussein Ekram , Merid Yared , Asres Mezgebu Silamsaw , Ayele Samuel , Mola Kasse , Yeshitela Biruk , Beyene Getachew Tesfaye , Mekuria Biruktawit Amdemariam , Yimer Marechign , Mihret Adane 
Published: July 2022

Abstract
Introduction: Bacterial meningitis (BM) is a serious life-threatening disease affecting the central nervous system. Less focus is given to uncommon causes of BM etiologic agents such as Staphylococcus aureus (S. aureus) and their magnitude of antimicrobial resistance (AMR). The disease burden caused by S. aureus is also poorly understood in developing countries such as Ethiopia. Culture based diagnosis of BM is the gold standard method for detection of the etiologic agents of the disease. Use of self-administered antibiotics results in development of AMR of bacterial agents and in culture based diagnostic challenges.Purpose: This study is exploring the status of uncommon cause of BM, the magnitude of antimicrobial resistance and challenges in culture based diagnosis.Patient and Methods:One hundred thirty-seven patients clinically diagnosed with pyogenic meningitis were recruited from the year 2020 to 2021 from four referral level hospitals located in Ethiopia. Cerebrospinal fluid samples transported in Trans-isolate media (T-IM) was inoculated into blood and culture media plates. Colony morphology and biochemical tests were used for identifying the grown bacterial agents. Patient clinical, socio-demographic and laboratory data were entered into SPSS version 20. Analysis was done using Pearson chi-square test and Graph data set chart builder. Non-parametric test was used to analyze statistical significance of P value < 0.05. Results obtained:A total of seven out of 137 culture media plates have shown growths of colonies on chocolate and blood culture media. Five out of the seven isolates were drug resistant S. aureus while two isolates were Neisseria species which are not drug resistant. Conclusion: Use of self-administered antibiotics prior to hospital visitation may be the reason for culture negative results which are challenges for culture based diagnosis. Wider scope of such studies using sensitive diagnostic approaches such as PCR is recommended to analyze the magnitude of uncommon causes of BM. AMR is occurring even in uncommon BM etiologic agents. Further analysis should be made using PCR amplification of drug resistant genes to bring the issue to public health attention.
ESR2 polymorphisms on prostate cancer risk: A systematic review and meta-analysis
Authors: Chang Xueliang , Yang Zhan , Wang Hu , Wang Yaxuan , Li Jingdong , Han Zhenwei 
Published: July 2022

Abstract
Purpose
This meta-analysis was performed to address the association of two ESR2 gene polymorphisms (rs1256049 and rs4986938) with susceptibility to cancer.
Methods
Extensive literature retrieve for eligible candidate gene studies published before May 10, 2022 was conducted in the PubMed, Medline and Web of Science. The search strategy is as follows: (ESR2 OR ERβ OR ER beta OR estrogen receptor beta) AND (polymorphism OR mutation OR variation OR SNP OR genotype) AND (PCa OR PC OR prostate cancer). Potential sources of heterogeneity were sought out via trial sequential analysis, subgroup and sensitivity analysis.
Results
Overall, a total of 10 articles involving 18,064 cases and 19,556 controls for two polymorphisms of ESR2 gene were enrolled. In the stratified analysis of rs1256049, we found that Caucasians might be correlated with an increased risk of prostate cancer, while less susceptibility was found in Asians. We observed that rs4986938 was not associated with prostate cancer risk.
Conclusion
ESR2 rs1256049 polymorphism is associated with a higher risk of prostate cancer in Caucasian population and a lower risk of prostate cancer in Asian population.
Genomic and epigenomic re-categorization of congenital glioblastoma and desmoplastic infantile ganglioglioma
Authors: Gilani Ahmed , Siddiq Zainab , Kleinschmidt-DeMasters BK 
Published: July 2022

Abstract
The recently updated World Health Organization classification of Central Nervous System (CNS) tumors, 5th edition, (CNS5) reclassifies pediatric tumors according to their distinct molecular drivers, recognizing a new entity - infant-type hemispheric glioma (IHG). Defined by its unique epigenetic signature, and/or genomic fusions in ALK, ROS1, NTRK or MET gene, IHG subsumes many cases previously classified as congenital glioblastoma (cGBM). Histologic features of IHG are still poorly defined with known overlap with a clinic-radiologically similar entity- desmoplastic infantile ganglioglioma / astrocytoma (DIG). We revisited our cohort of cGBMs and DIGs, now reclassifying them according to CNS5 and compared the clinical, radiologic and histologic features between the two. 3/6 cases of cGBM that underwent targeted NGS fusion mutation panel were positive for ALK fusions (involving MAP4, MZT2Bex2 and EML4 genes as fusion partners), and 1/6 showed GOPC:ROS1 fusion. Interestingly, GOPC:ROS1 fusion was also shared by 1/5 cases of histologically defined DIG. DNA methylation profiling using the Heidelberg classifier (v12.3) recategorized 2/5 DIG cases as IHG (including the case with ROS1 alteration). In conclusion, histology alone is insufficient to distinguish IHG from DIG, necessitating epigenomic and genomic testing for diagnosis of early-life gliomas.
Tree soil carbon, nitrogen and associated bacterial community compositions, stability, evenness and diversity are enhanced along an age gradient of planted Inga punctata trees.
Authors: Eaton William , Hamilton Debra A. 
Published: July 2022

Abstract
Aims
This study was designed to determine if planting the leguminous tree Inga punctata in formerly cleared former tropical premontane wet forests changed the Nitrogen (N)-fixer and Lignin Degrader community compositions resulting in increased accumulation of soil carbon (C) and N components.
Methods
Soils were collected from old growth (> 50 years old), 4, 8 and 11-year-old I. punctata trees, and assessed for differences in various soil C and N metrics, and the mean proportion of sequences (MPS, as “relative abundance” via 16S rRNA V3, V4 sequencing), composition, stability and evenness of the community of N-fixer and Lignin Degrader genera.
Results
The N-fixer MPS decreased, and Lignin Degraders increased, while evenness and stability of both increased along the tree soil age gradient. The Lignin Degrader MPS were positively correlated with TN, NO3−, TOC, and Biomass C, and negatively correlated with N-fixer MPS and soil NH4+. The N-fixer MPS were negatively correlated with TN, NO3−, TOC, Biomass C and Lignin Degrader MPS, and positively correlated with NH4+. Evenness, stability, and diversity increased for both groups along the tree soil age gradient.
Conclusions
This is the first evidence that I. punctata facilitates changes the tree soil N-fixer and Lignin Degrader communities over time by increasing the diversity, evenness and stability of both groups, and increases the accumulation of tree soil C and N. This suggests I. punctata facilitates soil recovery such that it can serve as C and N sinks, and support its future use in reforestation management strategy.
Enhancing image resolution of fluorescence microscopy with deep learning
Authors: Huang Boyi , Li Jia , Yao Bowen , Yang Zhigang , Lam Edmund Y. , Zhang Jia , Yan Wei , Qu Junle 
Published: July 2022

Abstract
Super-resolution optical imaging is crucial to the study of cellular processes. Current super-resolution fluorescence microscopy is restricted by the need of special fluorophores or sophisticated optical systems, or long acquisition and computational times. In this work, we present a deep-learning-based super-resolution technique of confocal microscopy. We devise a two-channel attention network (TCAN), which takes advantage of both spatial representations and frequency contents to learn a more precise mapping from low-resolution images to high-resolution ones. This scheme is robust against changes in the pixel size and the imaging setup, enabling the optimal model to generalize to different fluorescence microscopy modalities unseen in the training set. Our algorithm shows comparable or better performance in comparison with super-resolution method of stimulated emission depletion (STED) microscopy, which is validated on diverse biological structures and dual-color confocal images of actin-microtubules, where we can observe better image quality and higher resolution. Last but not least, we demonstrate live-cell super-resolution imaging by revealing the detailed structures and dynamic instability of microtubules.
A drug-like molecule engages a nuclear hormone receptor to regulate mitophagy and promote mitochondrial mediated lifespan extension
Authors: Chamoli Manish , Rane Anand , Chinta Shankar , Shahmirzadi Azar , Kumsta Caroline , Nambiar Dhanya , Hall David , Foulger Anna , Angeli Suzanne , Schmidt Minna , Pitteri Sharon , Hansen Malene , Lithgow Gordon , Andersen Julie 
Published: July 2022

Abstract
Autophagy-lysosomal function maintains healthy lifespan and ameliorates disease pathologies in diverse model organisms. An important master regulator of the autophagy-lysosomal pathway is an evolutionary conserved transcription factor EB (TFEB). Decline in TFEB expression or activity is linked to many age-related diseases. As a consequence, TFEB has emerged as an important therapeutic target of interest for these diverse disorders. To identify novel pharmacological inducers of HLH-30/TFEB transcription, we screened a natural product library in mammalian cells. We identified a novel benzocoumarin compound (MIC) that enhances HLH-30/TFEB expression and lysosomal function. MIC robustly increase the lifespan of Caenorhabditis elegans in an HLH-30/TFEB and mitophagy-dependent (dct-1/BNIP3) manner as well as prevents mitochondrial dysfunction in mammalian cells. Mechanistically, MIC acts by reducing binding of the nuclear hormone receptor, DAF-12/FXR, to its ligand in turn inducing HLH-30/TFEB and extending lifespan. A clinically relevant, structurally related mitophagy inducer, urolithin A, was found to also engage DAF-12/FXR signaling in a similar manner. In summary, we have identified DAF-12/FXR as a novel upstream regulator of HLH-30/TFEB, and identified a novel drug-like molecule that acts on DAF-12/FXR to enhance mitochondrial function and extend lifespan.
A Novel MWKF-LSTM Based Intrusion Detection System for the IoT-Cloud Platform with Efficient User Authentication and Data Encryption Models
Authors: P Krishna Kumar , Retnaswamy Bharathi 
Published: July 2022

Abstract
During the past decade, the Internet of Things (IoT) integrated Cloud (IoT-Cloud) has gotten a lot of attention. Security turns out to be an important issue in the IoT-Cloud scenario as millions of devices is connected via the internet. Developing an intrusion detection system (IDS) along with a prevention model to improve IoT-Cloud security, with considered delay, detection rate, as well as false-positive rate are the most important research problems. Here, a new deep learning (DL) model, Morlet Wavelet Kernel Function included Long Short Term Memory (MWKF-LSTM) classifier is proposed to recognize the intrusions in the IoT-Cloud environment. Initially, to maintain a user’s privacy in the network, the SHA-512 hashing mechanism incorporated blockchain authentication (SHABA) model is developed that checks the authenticity of every device/user in the network for data uploading in the cloud. After successful authentication, the data is transmitted to the cloud through various gateways. Then the IDS using MWKF-LSTM is implemented for identifying the type of intrusions present in the received IoT data. The MWKF-LSTM classifier comes up with the Differential Evaluation based Dragonfly Algorithm (DEDFA) optimal feature selection (FS) model for increasing the performance of the classification. After intrusion detection (ID), the non-attacked data is encrypted as well as stored in the cloud securely utilizing Enhanced Elliptical Curve Cryptography (E2CC) mechanism. Finally, in the data retrieval phase, the authentication of the user is again checked for ensuring user privacy and preventing the encrypted data in the cloud from intruders. To show the efficacy of the proposed research model, simulations are performed and the outcomes prove the superior performance of the presented approach over existing models.
A retrospective study of 92 patients with IgG4 related diseases
Authors: Sun Jie , Zhong Yanyan , Yu Hongyun , Xu Jing , Xie Jianye , Wen Dawei , Zhao Lei , Wang Kunyu , Wang Jibo 
Published: July 2022

Abstract
Background: To analyze the clinical characteristics of IgG4 related diseases (IgG4-RD), identify the most commonly used therapeutic drugs, and explore the potential tumor markers of IgG4-RD. Methods: 92 patients with IgG4 related diseases hospitalized in the Affiliated Hospital of Qingdao University from January 1, 2017 to December 31, 2021 were selected as the research object through the Yidu cloud system. Their clinical data were summarized and analyzed to summarize the clinical characteristics of IgG4-RD.Results: The age of diagnosis of IgG4 related diseases in this group was 31-84 years old, and the average age of diagnosis was (58.098 ± 11.344) years old, including 65 males (70.65%) and 27 females (29.35%). The most frequently involved organs and tissues were lymph nodes (37 cases, accounting for 40.2%), pancreas (33 cases, accounting for 35.9%), and salivary glands (31 cases, accounting for 33.7%). In this group, 28 cases (30.4%) were involved in single organ tissue, 32 cases (34.8%) were involved in double organ and multiple organ, respectively. 91 patients were treated with hormone for IgG4 related diseases, and 71 patients were treated with immunosuppressive agents, of which 45 cases were treated with cyclophosphamide (63.38%). In this group, the proportion of IgG4 level greater than 40g / L in tumor patients (18.18%) was significantly higher than that in non tumor patients (1.23%) (P < 0.05). Conclusion: The incidence of IgG4 related diseases is more common in middle-aged and elderly men, and the patients with lymph node, salivary gland and pancreas are more common. About 2 / 3 of the patients are double organ and multi organ patients. The most common rheumatic complications in patients with IgG4-RD are primary biliary cirrhosis, rheumatoid arthritis and Sjogren's syndrome. The most common tumor in patients with IgG4-RD is malignant tumor of digestive system. IgG4 levels greater than 40g/l in patients with IgG4 related diseases may be a potential indicator for predicting IgG4-RD associated tumors.
Anatomical Study of Variations in the Branching Patterns of Neurovascular Pedicle of Latissimus Dorsi
Authors: Naik Kshitij , D’Souza Ashel Chelsea , Ranganath Priya , Parthasarathi Meenakshi 
Published: July 2022

Abstract
Introduction: Variations in the branching and position of the dominant pedicle of the Latissimus Dorsi (LD) muscle has been noted during dissection of the posterior aspect of the cadaver. Knowledge about the point of branching of the pedicle is highly valuable for the surgeon while performing various reconstructive surgeries.Aims and Objectives: To analyze and study the insertion and branching of the dominant neurovascular pedicle of LD.Material and Methods: A total 40 LD muscles were excised from the point of origin and retracted superior-laterally towards its insertion. The pedicle was then cleared of any unwanted fascia by strip dissection and the point of branching was identified with respect to the level of the inferior scapular angle (ISA) .Results: An anatomical variation was observed in the study of the branching of the neurovascular pedicle. Upon consideration via statistical calculations, the following levels of branching locations were noted. ~12.5% - 2.0 inch superior to level of ISA ~37.5% - 1.0 inch superior to level of ISA ~25.0% - 1.5 inch superior to level of ISA ~25.0% - 0.4 inch inferior to level of ISAThe first three types were considered as early branching whereas the last type was considered as late branching of LD.Conclusion: This study shows the variations in the branching in the pedicle of the LD at various points that were considered. This is hence of surgical importance that must be noted to prevent surgical vascular damage that may occur during procedures and also increase the methodology of pre-operative planning.
An Augmented Reality Maintenance Assistant with Real-time Quality Inspection on Handheld Mobile Devices
Authors: Frandsen James T , Tenny Joe , Frandsen Walter , Hovanski Yuri 
Published: July 2022

Abstract
With the advances of industry 4.0, augmented reality (AR) devices are being deployed across the manufacturing sector to enhance worker perception and efficiency. AR is often used to deliver spatially relevant work instructions on mobile devices for maintenance procedures on the factory floor. In these situations, workers use their mobile devices to view instructions in the form of 3D animations and annotations that directly overlay the equipment being maintained. Workers then follow the AR instructions and must ultimately rely on their own judgement and knowledge of the procedure as they progress from step to step. An AR assistant that could validate each stage of the procedure in real time and provide the worker with feedback on any observed errors would ensure that each maintenance procedure is completed successfully. This work presents a mobile, quality inspection system for AR maintenance procedures that is capable of assessing the maintenance task in real time. The system is designed for deployment on handheld mobile devices and can thus manage the challenges inherent to performing quality inspection with a non-fixed vision system. This work enumerates four essential qualities of mobile quality inspection tools and outlines some of the challenges encountered during the development of such a system. In the end, testing established that the system could provide adequate assistance for capturing inspection images, accurately process the captured images using machine vision, and generate detailed feedback from the quality inspection in a timely manner.
Construction and Validation of a Metabolic-Related Genes Prognostic Model for Oral Squamous Cell Carcinoma Based on Bioinformatics
Authors: Zhang Jingfei , Ma Chenxi , Qin Han , Wang Zhi , Zhu Chao , Liu Xiujuan , Hao Xiuyan , Liu Jinghua , Li Ling , Cai Zhen 
Published: July 2022

Abstract
Background: Oral squamous cell carcinoma (OSCC) accounts for a frequently-occurring head and neck cancer, which is characterized by high rates of morbidity and mortality. Metabolism-related genes (MRGs) show close association with OSCC development, metastasis and progression, so we constructed an MRGs-based OSCC prognosis model for evaluating OSCC prognostic outcome.Methods: This work obtained gene expression profile as well as the relevant clinical information from the The Cancer Genome Atlas (TCGA) database, determined the MRGs related to OSCC by difference analysis, screened the prognosis-related MRGs by performing univariate Cox analysis, and used such identified MRGs for constructing the OSCC prognosis prediction model through Lasso-Cox regression. Besides, we validated the model with the GSE41613 dataset based on Gene Expression Omnibus (GEO) database.Results: The present work screened 317 differentially expressed MRGs from the database, identified 12 OSCC prognostic MRGs through univariate Cox regression, and then established a clinical prognostic model composed of 11 MRGs by LASSO Cox analysis. Based on the optimal risk score threshold, cases were classified as low- or high-risk group. As suggested by Kaplan–Meier (KM) analysis, survival rate was obviously different between the two groups in the TCGA training set (P < 0.001). According to subsequent univariate and multivariate Cox regression, risk score served as the factor to predict prognosis relative to additional clinical features (P < 0.001). Besides, area under ROC curve (AUC) values for patient survival at 1, 3 and 5 years were determined as 0.63, 0.70, and 0.76, separately, indicating that the prognostic model has good predictive accuracy. Then, we validated this clinical prognostic model using GSE41613. To enhance our model prediction accuracy, age, gender, risk score together with TNM stage were incorporated in a nomogram. As indicated by results of ROC curve and calibration curve analyses, the as-constructed nomogram had enhanced prediction accuracy compared with clinicopathological features alone, besides, combining clinicopathological characteristics with risk score contributed to predicting patient prognosis and guiding clinical decision-making.Conclusion: In this study, 11 MRGs prognostic models based on TCGA database showed superior predictive performance and had a certain clinical application prospect in guiding individualized.
Preliminary Study on Volumetric 3D Printing Using Visible Light
Authors: JAMES SAGIL , Zarate Joel 
Published: July 2022

Abstract
The realm of 3D printing has been a valuable aspect of manufacturing and mechanical engineering to which complex geometries have been made that might be otherwise highly costly or not feasible by other manufacturing methods. This is where volumetric 3D printing has been advantageous by generating complex geometry with no defects on the surface. The problem with the research done so far is the material used uses photoinitiators that photo-synthesize using ultraviolet (UV) light. The problem with this material is that it is attached to the destructive issues brought on by interacting with UV light, making some additives useless. To solve part of this problem, a solution to the material problem must be shown that a resin can be cured using visible light. This study has investigated the feasibility of novel manufacturing process termed, Visible Light Induced – Volumetric 3D Printing (VLI-V3DP) process, that resulted in successfully finding resin that can be cured using visible light in the 470 & 530 nm range. By curing simple geometry using visible light, one can formulate a resin that can sustain just about any additives that can meet any goal, whether it is organic or not.
High LRRC1 expression indicates poor prognosis of hepatocellular carcinoma
Authors: Cai Qingshan , Wu Dongyang , Shen Yueling , Li Shudong , Liu Liyou , Liu Dong , Zheng Jianxing 
Published: July 2022

Abstract
Objective: This study aimed to elucidate the prognostic value of the leucine rich repeat containing 1 (LRRC1) gene in hepatocellular carcinoma (HCC) and to determine the effects of high and low LRRC1 expression on mutation and immune cell infiltration.Methods: We downloaded HCC mRNA-seq expression and clinical data from UCSC Xena. The expression of LRRC1 was compared between HCC tumor and normal samples. Tumor samples were divided according to high and low LRRC1 expression. Differentially expressed genes between the two groups were identified, and function, mutation, and immune cell infiltration were analyzed. Genes associated with immune cells were identified using weighted gene co-expression network analysis (WGCNA), and transcription factors (TFs) of these genes were predicted.Results: The expression of LRRC1 was upregulated in HCC tissues, and this indicated a poor prognosis for patients with HCC. Differentially expressed genes between tumors with high and low LRRC1 expression were significantly enriched in pathways associated with cancer, amino acid metabolism, carbohydrate metabolism, and the immune system. We identified 15 differentially infiltrated immune cells between tumors with high and low LRRC1 expression and 14 of them correlated with LRRC1 gene expression. We also identified 83 genes that were associated with immune cells. Cyclic AMP-response element binding protein (CREB1) regulated ANXA5, MMP9, and LRRC1 in the TF regulatory network.Conclusion: The LRRC1 gene might serve as a potential immune-associated prognostic biomarker for HCC.