bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasma miRNAs and the risk of cancer: Data mining model in lung cancer
Authors: Duan Xiaoran , Huang Tao , Feng Xiaolei , Qu Xiaoping , Ge Minghui , Yan Linlin , Guo Hao , Liu Xiaohua , Ding Mingcui , Wang Pengpeng , Yang Yongli , Wang Wei , Zhao Jie
Published: January 2023

Data mining(DM) has been widely used in researching the auxiliary diagnosis of cancer. Circulating miRNAs are related to the occurrence and development of various cancer types. For this reason, they have the potential to be used as biomarkers for early tumor diagnosis. Previously, we found that SVM model combined with plasma miRNAs biomarkers could be a method for lung cancer prediction; However, it still has some limitations. So this study further enlarges the analysis to other DM techniques, and explores more accurate methods for auxiliary diagnosis of lung cancer. Univariate analysis showed the differences had statistical significance in the smoking, fever, chest tightness or pain, cough, bloody phlegm, haemoptysis, and 10 plasma miRNAs (miR-21, miR-20a, miR-210, miR-145, miR-126, miR-223, miR-197, miR-30a, miR-30d, and miR-25) between the lung cancer group and normal control group (P < 0.05); Logistic regression analysis showed that fever, chest pain or tightness, cough, miR-21, and miR-223 could be considered as indicators of the presence of cancer (P < 0.05). According to the univariate and multivariate analysis results, two sets of models were constructed using data mining models. The results showed that the sensitivity was 88.6%, the specificity reached 86.7%, the accuracy value was also the highest, and AUC was 0.877 for the GBDT (Gradient Boosting Decision Tree) 16-model, indicating that its predictive effect was the best. Conclusively, this study was to further explore the high accuracy data mining model of lung cancer prediction using plasma miRNAs.
Genomic profiles of IDH-mutant gliomas: MYCN amplified IDH-mutant astrocytoma had the worst prognosis
Authors: Lee Kwanghoon , Kim Seong-Ik , Kim Eric Eunshik , Shim Yu-Mi , Won Jae-Kyung , Park Chul-Kee , Choi Seung Hong , Yun Hongseok , Lee Hyunju , Park Sung-Hye
Published: January 2023

This studyprogression-freene the genetic landscape and prognostic factor of IDH-mutant gliomas. Next-generation sequencing (NGS) using a brain tumor-targeted gene panel, methylation profiles, and clinicopathological features were analyzed for O_IDH_mut (n = 74) in 70 patients and for A_IDH_mut (n = 95) in 90 patients. 97.3% of O_IDH_mut and 98.9% of A_IDH_mut displayed a classic genomic landscape. CIC and/or FUBP1 mutations were detected in 93.2% and MGMTp methylation in 95.9% of O_IDH_mut patients. In A_IDH-mut, TP53 mutations were found in 86.3% and combined ATRX (82.1%) and TERTp (6.3%) mtations in 88.4%. Although there were 3 confusing cases, NOS (not otherwise specified) category, based on genetic profiles, but they were clearly classified by combining histopathology and DKFZ methylation classifier algorithms. The patients with MYCN amplification and/or CDKN2A/2B homozygous deletion in the A_IDH_mut category had a worse prognosis than those without these gene alterations. However, there was no prognostic genetic marker in O_IDH_mut. In histopathologically or genetically ambiguous cases, methylation profiles can be used as an objective tool to avoid a diagnosis of NOS or NEC (not elsewhere classified), as well as for tumor classification. The authors have not encountered a case of true mixed oligoastrocytoma using an integrated diagnosis of genetic and methylation profiles. MYCN amplification, in addition to CDKN2A/2B homozygous deletion, should be included in the genetic criteria for WHO grade 4 A_IDH_mut.
Semi-Supervised Interlayer Intelligent Recognition Method
Authors: Jiao Shixiang , Zhao Jun , He Yufei , Wu Zhenguan , Chen Yan , Zeng Tianyi , Zhang Rui
Published: January 2023

The development and distribution of interlayers in sandstones can lead to increased formation heterogeneity within the reservoir, whichand further affects the movement of fluids in the formation. Therefore, it is mandatory to evaluate the interlayers accurately the fine evaluation of interlayers in sandstones is of great significance for identifying the distribution of underground the fluid systems. The logging data of interlayers are inappropriate for traditional Machine Learning training due to their low measurement proportion compared to the conventional layers. In logging data, the amount of data in interlayers is small compared to conventional reservoirs. Traditional machine learning models are mostly based on samples with balanced distribution,. By contrast, while semi-supervised learning uses requires small labeled samples for learning, and thenby Ccombineing a large number of unlabeled samples for modeling. In order to verify the effect feasibility of semi-supervised learning in the identification of interlayers, the Donghe sandstone section of H oilfield was taken as an example. First, the core analysis results were used to label the logging data; then, in order to dig out more response information that can characterize the interlayers on the logging curve, multiple features were extracted to construct cross features. Finally, an improved model based on autoencoders—probabilistic autoencoder (PAE)—is proposed to solve the problem of interlayers recognition for imbalanced samples. The PAE model can calculate a probability of belonging to a different class for unlabeled samples, and classify new samples according to the maximum probability. Experiments Results show that, compared with traditional machine learning methods and ensemble learning methods, PAE achieves higher recognition accuracy and better generalization performance by updating the algorithm, and can be used as a simple and fast method for interlayers recognition. The algorithm results prove that the semi-supervised method is of great significance for the exploration and development of complex heterogeneous oil reservoirs.The research results are of great significance for the exploration and development of complex heterogeneous oil reservoirs.
Circulating miRNA Signatures in Early-Stage Huntington’s Disease
Authors: Tao Yiran , Mercaldo Nathaniel , Duffy Alexandra , Dayananthan Ashok , Wheelock Vicki L. , Rosas Herminia Diana
Published: January 2023

Huntington’s Disease (HD) is a neurodegenerative disorder caused by the expansion of CAG repeats on exon 1 of the huntingtin (htt) gene. This mutation results in the expression of an aberrant protein, mutant HTT, which sets in place a cascade of events that eventually leads to neuronal death within the basal ganglia and cerebral cortex. MicroRNAs (miRNAs) are a class of small non-coding RNAs of 18 - 22 nucleotides long that play important roles in post-transcriptional regulation due to their abilities to interact with the 3'-UTR regions of mRNAs. Though generated in the nucleus, a significant portion of miRNAs are secreted into the plasma as free molecules or in vesicles for intercellular signaling. Those circulating miRNAs may provide a unique opportunity to study important pathophysiological mechanisms in HD in a non-invasive manner due to their resistance to degradation, ease of detection, and their known regulatory roles in response to inflammation and neurodevelopmental disorders. More recent studies have suggested that miRNA could be used in therapeutic applications. In this study, we sought to identify the aberrant expression of specific miRNAs extracted from the plasma of early-stage HD patients.
Clinical Trial Registration number: NCT01937923
Assessment of resources for physical activity and understanding people’s perception and practices regarding physical activity in an Indian city
Authors: Gautam Susheel , N Kruthika B , . Akashanand , Roy Aaheli , Banandur Pradeep , Banavaram Arvind Anniappan
Published: January 2023

Background
Promoting physical activity in urban India is imperative considering the burden of non-communicable diseases in the country. Planning for improving population level physical activity needs sound understanding of availability and quality of resources/facilities for physical activity and knowing people’s perception and practices regarding the physical activity.
Methods
A cross-sectional study was undertaken in Kolar city of Karnataka state in India. All the resources/facilities required for supporting physical activity were mapped and their quality was assessed utilizing adapted version of physical activity resource assessment questionnaire. The information regarding latitude, longitude and approximate size of the resource was obtained using a hand-held GPS tracker. 495 individuals aged ≥ 18 years, selected by two stage cluster random sampling with probability proportionate to population size technique, were interviewed to assess their perception and practices regarding physical activity using semi-structured questionnaire and global physical activity questionnaire.
Results
Kolar city has 36.3 physical activity resources per lakh population and per person availability of park and playground area was 0.4 Sq. meters. Available resources were concentrated in the center of the city. Half of the sports facilities and 14 of the 17 recreational facilities in the city were of poor to mediocre quality. 38.2% of adults in Kolar city were found to be physically active. Only 19.2% of the study participants had accessed sports/fitness facilities/playgrounds in past 3 months and only 18.8% of the study participants accessed parks in the previous 3 months. 28.6–59.1% of the participants preferred ‘walking’ as a mode of transport for work, college and shopping. Less than 5% of the participants preferred and used cycle as a mode of transport. 1/3rd of the study participants felt that Kolar city is safe of walking and 44.6% felt that the city is safe for cycling.
Conclusion
Creating enabling environment by increasing the number and quality of resources/facilities for physical activity along with their equitable distribution is required to promote and improve population level physical activity in Kolar city. Urban planning with a focus on non-motorized transport including walking would contribute to improved people’s perception and practices regarding physical activity in the city.
Study on Determination and Prediction Method of ultra-micro-volume Adhesive Droplet Volume Parametres
Authors: Zhao Dingrui , Liu Huifang , Chen Xi , Chang Yunlong , Yu Xingfu , Li An
Published: January 2023

Nowadays, in the actual microelectronic packaging process, the requirements for packaging quality and accuracy are becoming higher and higher. The research and prediction of the corresponding parameters of the transfer droplet according to the actual requirements before packaging can not only accurately adjust the relevant configuration parameters of the transfer droplet, but also judge the actual packaging effect preliminarily, and to improve the packaging efficiency and accuracy. Therefore, it is of practical significance to carry out the research on the distribution law and prediction method of transfer droplet parameters. In this paper, based on the needle transfer ultra-micro-volume transfer droplet method, a transfer droplet device that meets the packaging requirements is built, and the reasonable configuration of device parameters is realized through the control system. The pixel method suitable for practical application was found to determine the volume of transfer droplet, and the average deviation of the volume of transfer droplet measured by this method was about 1.85%. By changing the initial distance of the adhesive distribution experiment, it is concluded that the larger the initial distance, the smaller the volume of the transfer droplet, and the smaller the contact area of the transfer droplet. According to the data obtained from the adhesive distribution experiment, the prediction formula of the relationship between the initial distance, the volume of the transfer droplet and the contact area of the transfer droplet is derived. It is found that the average difference rate between the predicted volume and the actual volume is 0.51%, and the average difference rate between the predicted contact area and the actual contact area is 0.56%.
IRAK4 inhibition: an effective strategy for immunomodulating peri-implant osseointegration via reciprocally-shifted polarization in the monocyte-macrophage lineage cells
Authors: Zhao Juan , Li Jia , Xu Antian , Xu Yangbo , Mao Yingjie , He Fuming
Published: January 2023

Background: The biomaterial integration depends on its interaction with the host immune system. Monocyte-macrophage lineage cells are immediately recruited to the implant site, polarized into different phenotypes, and fused into multinucleated cells, thus playing roles in tissue regeneration. IL-1R-associated kinase 4 (IRAK4) inhibition was reported to antagonize inflammatory osteolysis and reciprocally regulate osteoclasts and foreign body giant cells (FBGCs), which may be a potential target in implant osseointegration.
Methods:In in-vitro experiments, we established simulated physiological and inflammatory circumstances in which bone-marrow-derived macrophages were cultured on sand-blasted and acid-etched (SLA) titanium surfaces to evaluate the induced macrophage polarization, multinucleated cells formation, and biological behaviors in the presence or absence of IRAK4i. Then, bone marrow stromal stem cells (BMSCs) were cultured in the conditioned media collected from the aforementioned induced osteoclasts or FBGCs cultures to clarify the indirect coupling effect of multinucleated cells on BMSCs. We further established a rat implantation model, which integrates IRAK4i treatment with implant placement, to verify the positive effect of IRAK4 inhibition on the macrophage polarization, osteoclast differentiation, and ultimately the early peri-implant osseointegration in vivo.
Results: Under inflammatory conditions, by transforming the monocyte-macrophage lineage cells from M1 to M2, IRAK4i treatment could down-regulate the formation and activity of osteoclast and relieve the inhibition of FBGC generation, thus promoting osteogenic differentiation in BMSCs and improve the osseointegration.
Conclusions: This study may improve our understanding of the function of multinucleated cells and offer IRAK4i as a therapeutic strategy to improve early implant osseointegration and help to eliminate the initial implant failure.
A mobile car monitoring system as a supplementary tool for air quality monitoring in urban and rural environments. The case study from Poland
Authors: Maslouski Mikita , Jarosz-Krzemińska Elżbieta , Jagoda Paweł , Adamiec Ewa
Published: January 2023

Living in healthy environment should be regarded as a primary human right and not a privilege rendered to chosen ones. For that reason, a national air monitoring grid should be as extensive as possible. Unfortunately, small towns and villages, which are also exposed to air pollution episodes are not commonly covered by monitoring grid. Fixed air monitoring systems have their limitations, which can be overcome by e.g., properly validated, reliable but cheaper mobile monitoring systems. The aim of this study was to assess the use of a car mobile PM10 monitoring system to study ambient air quality in rural communities surrounding Kraków, not covered by fixed monitoring grid. A monitoring dataset was collected during 6 winter car campaigns conducted between December 2021 and March 2022. Except for providing multiple monitoring data, the main goal pertain to methodological aspect of the mobile system, including its validation, indicating its advantages, limitations as well as providing recommendations for the future mobile studies. Our car mobile monitoring system was useful in identifying a local hot-spots with good spatial and temporal resolution, thus giving the local government decision-making tool for taking appropriate action in places not included in national monitoring grid.
Safety Profile of Intravitreal Injections in the Injection Cabinet: No Cases of Endophthalmitis Seen After 7,238 Injections
Authors: Ozgur Gokhan , Gokmen Onur
Published: January 2023

Aim: The present study evaluates the rate of endophthalmitis in intra vitreal injections (IVI) performed in a modular injection cabin that could be easily sited in a closet in an office environment, and the performance tests of the cabin in terms of heating, ventilation and air conditioning (HVAC).
Method: The injections given over approximately 18 months in the cabin and the demographics of the patients were screened retrospectively, and the cabin was subjected to HVAC tests.
Results: A total of 7,238 injections were performed in the defined period, and no cases of endophthalmitis were encountered (0%). The results of the air flow and flow rate, particle count, pressure difference, decontamination time, light, moisture and heat tests were all found to be above the standard defined by the International Organization for Standardization (ISO).
Conclusion: An injection cabin is a practical modular construction that can be easily sited in any space without the need for special climatization, and provides a sterile and safe environment for IVI.
A novel approach for the analysis of single-cell RNA sequencing identifies TMEM14B as a novel poor prognostic marker in hepatocellular carcinoma
Authors: Ma Ding , Liu Shuwen , He Qinyu , Kong Lingkai , Liu Kua , Xiao Lingjun , Xin Qilei , Bi Yanyu , Wu Junhua , Jiang chunping
Published: January 2023

Background
A fundamental goal in cancer-associated genome sequencing is to identify the key genes. Protein-protein interactions (PPIs) play a crucially important role in this goal. Here, human reference interactome (HuRI) map was generated and 64006 PPIs involving 9094 proteins were identified.
Methods
Here, we developed a physical link and co-expression combinatory network construction (PLACE) method for genes of interest, which provides a rapid way to analyze genome sequencingdatasets.Next, Kaplan‒Meier survival analysis, CCK8 assays,scratch wound assays and Transwell assays were applied to confirm the results.
Results
In this study, we selected single-cell sequencing data from patients with hepatocellular carcinoma (HCC) in GSE149614. The PLACE method constructs a protein connection network for genes of interest, and a large fraction (80%) of the genes (screened by the PLACE method) were associated with survival.Then,PLACE discovered that transmembrane protein 14B (TMEM14B) was the most significant prognostic key gene, and target genes of TMEM14B were predicted. The TMEM14B-target generegulatory network was constructed by PLACE. We also detected that TMEM14B-knockdown inhibited proliferation and migration.
Conclusions
The results demonstrate that we proposed a new effective method for identifying key genes. The PLACE method can be used widely and make outstanding contributions to the tumor research field.
Formal Analysis of Reconfigurable and Autonomous Robotic Arm]{Formal Analysis of Reconfigurable and Autonomous Robotic Arm
Authors: Rahim Muhammad Abdul Basit Ur , Raheem Muhammad Ahsan Ur , Sohail Muhammad Khalid , Farid Mohammad Atif , Mufti Muhammad Rafiq
Published: January 2023

Automation is one of the foremost technological trends in mining. Automation empowers mining companies to work around the clock and maximize productivity. Robotics brings a new degree of security to mines, from mechanical drills to self-driving ore trucks. The safety of these robots is also essential to ensure they should not damage themselves.
In this paper, we have formally modeled a robotic mining arm mechatronic system that could damage itself if a sensor were to fail. This report demonstrates how the damage caused by sensor failure can be prevented by formally modeling the system and verifiable properties to test that it would not damage itself during a sensor failure. The models and properties developed showed that the system would fail safely in such a scenario. Moreover, it is reconfigurable to deal with hazardous situations. We use the model-checking tool UPPAAL to model the robotic arm and verify it for safety, liveness, and deadlock-freeness properties.
Metagenomic analysis of oral plaques and aortic valve tissues reveals oral bacteria associated with aortic stenosis
Authors: Yoshiba Sayaka , Nakagawa Hirofumi , Kuwata Hirotaka , Nabuchi Akihiro , Yaso Atsutoshi , Shirota Tatsuo
Published: January 2023

Objectives
Endotoxins derived from bacteria in the oral cavity enter the bloodstream, leading to the onset of various systemic diseases, including heart valve disease. However, information on the oral bacteria involved in aortic stenosis is limited.
Materials and Methods
We comprehensively analyzed the microbiota in aortic valve tissues collected from patients with aortic stenosis using metagenomic sequencing and investigated the relationships between the valve microbiota and the oral microbiota and oral cavity conditions.
Results
Metagenomic analysis revealed the presence of 629 bacterial species in five oral plaque and 15 aortic valve clinical specimens. Patients were classified into two groups according to their aortic valve microbiota composition using principal coordinate analysis. Examination of the oral conditions of the patients showed no difference in the decayed/missing/filled teeth index; however, patients were divided into two groups (A and B) based on the aortic valve microbiota composition. Bacteria in group B tended to be associated with severe disease, and the number of bacteria on the dorsum of the tongue and the positive rate of bleeding during probing were significantly higher in this group than in group A. The pathophysiology of aortic stenosis may be related to the presence of oral bacteria such as Streptococcus oralis and Streptococcus sanguinis following bacteremia.
Conclusions
Systemic inflammation in severe periodontitis may be driven by the oral microbiota, supporting the indirect (inflammatory) association between oral bacteria and aortic stenosis.
Clinical Relevance:
Appropriate oral hygiene management may contribute to the prevention and treatment of aortic stenosis.
A functional electrochemical sensing platform for the detection of lead ions
Authors: Khaleel Mustafa , Soylu Pervin Deveci
Published: January 2023

A novel electrochemical sensor for the detection of lead ions was constructed by using electrodeposition of gold nanoparticles (GNPs) and glutathione (GSH) onto reduced graphene oxide (rGO) to form a GSH@GNP@rGO nanocomposite on a glassy carbon electrode (GSH@GNP@rGO@GCE). The sensing properties of the obtained sensor were tested by Cyclic Voltammetry (CV) and Differential Pulse Voltammetry (DPV). Under optimized experimental conditions, the voltammetry response gradually raises by increasing the concentration (2-20 μΜ). The result showed that the GSH@GNP@rGO@GCE sensor exhibited high sensitivity towards Pb(II) with a low detection limit of 0.43 μMby DPV. Our studies suggest that the GSH@GNP@rGO nanocomposite could potentially be used for detecting Pb(II).
Preoperative magnetic resonance imaging of anal fistulas with scrotal extension
Authors: Vo Duc , Nguyen Nam , Nguyen Linh , Nguyen Thien , Phan Chien , Nguyen Truc
Published: January 2023

The aim of this study was to elucidate the magnetic resonance (MR) characteristics of anal fistulas extending to the scrotum, the rules applicable to them, and to correlate MR features with surgical findings. We conducted a retrospective study in 150 consecutive patients with anal fistulas extending into the scrotum, who were diagnosed and underwent surgery at University Medical Center Ho Chi Minh City between January 2017 and April 2022. MR findings were evaluated and compared with surgical findings using the Cohen’s kappa coefficient (k) with a 95% confidence interval. 150 patients (mean age 37.6 ± 10.9 years) with 166 fistulas, including 150 anal fistulas with scrotal extension. Most fistulas were low transsphincteric (80.0%, 120/150 patients). There was strong agreement for primary tract classification and detecting the location of internal openings between MRI and surgical findings with k = 0.83 (0.78–0.87) and k = 0.89 (0.85 – 0.93) (p<0.001), respectively. There is a significant correlation between the location of internal openings and the type of fistula (p<0.05). Low transsphincteric fistulas were predominant in the anterior group (103/122 patients vs. 10/19 patients), while in the posterior group it was more common in the high transsphincteric fistulas (7/19 patients vs. 14/122 patients), and the intersphincteric fistulas (1/19 patients vs. 5/122 patients); and the suprasphincteric fistulas were only seen in posterior group (1 patient). Anal fistulas with scrotal extension are exceptions to Goodsall’s rule. Albeit being long-tract fistulas, most of them are low transsphincteric and have anterior internal openings.
Evolvable Design of Network-oriented Services based on Core/Periphery Structure
Authors: Takagi Shiori , Arakawa Shin'ichi , Murata Masayuki
Published: January 2023

In the recent years, many new network-oriented services have emerged, and such services will need to be virtualized in the multi-access edge computing (MEC) environment, which is currently being standardized along with fifth generation (5G). The service design should be adaptable to user requirements and environmental changes for accommodating a large number of services at low cost. In addition, it is required not only to assume environmental changes when initially designing the service functions network, but also to enable the network to continue to change its structure to adapt to new environmental changes in the future. We have been investigated a core/periphery structure that allows service to effectively adapt to each user request and environmental variation. The advantage of the core/periphery structure is that it helps reduce the costs for maintaining or changing services by distinguishing the service functions into core and periphery functions. In this paper, we propose a method to evolve service functions network based on a core/periphery structure. Adapting to environmental changes requires the addition of interfaces between service functions or the development of new service functions. Our method evolves the structure of the service function network at low cost by keeping the core and peripheral functions at the appropriate scale. Our simulation results reveal that the structure of the service function networks can continue to evolve for a low cost and can maintain a high service accommodation ratio.
Social Determinants of Health: A Need for Evidence-Based Guidelines on How to Capture Data on Underserved Patients
Authors: Tran Nguyen H. , Almodallal Yahya , Batheja Mashal , Martin Nicole , Le-Rademacher Jennifer , Ridgeway Jennifer , Sia Irene G. , Jatoi Aminah
Published: January 2023

Background. Social determinants of health lead to better cancer care. This multi-site, single-institution study sought to capture data on social determinants of health data in Asian Americans with hepatocellular carcinoma; this group constitutes 60% of patients with this malignancy and are often undertreated or not treated at all.
Methods. This study took advantage of an institutional initiative designed to capture and integrate social determinants of health data into the electronic medical record for all patients. Medical records of Asian Americans with hepatocellular cancer were reviewed to acquire data on housing instability, lack of transportation, financial concerns, and social isolation; a score of 1 indicated poor social determinants of health.
Results. Of 112 adult Asian American patients with hepatocellular cancer, 22 (20%) were Southeast Asian, and 74 (67%) described English proficiency. A score of 1 (highest risk) was observed in 1 patient (0.9%) for housing instability; 1 (0.9%) lack of transportation; no patient for financial hardship; and 1 (0.9%) for social isolation. However – and importantly -- total noncompletion per domain (no question answered within that domain) was observed in 90 patients (80%) for housing instability; 90 (80%) for lack of transportation; 92 (82%) for financial hardship; and 90 (80%) for social isolation. Of note, institution-wide benchmark total noncompletion rates were 0.3%, 0.3%, 47%, and 39% for these respective domains.
Conclusion. High total noncompletion rates make social determinants of health data challenging to interpret and underscore the need for evidence-based guidelines on how best to capture such data in underserved patients.
Open water dreissenid mussel control projects: lessons learned from a retrospective analysis
Authors: Dahlberg Angelique D , Waller Diane L , Hammond David , Lund Keegan , Phelps Nicholas BD
Published: January 2023

Dreissenid mussels are one of the most problematic aquatic invasive species (AIS) in North America, causing significant ecological and economic impacts. To date, dreissenid mussel control efforts in open water have included physical, biological, and chemical methods. The feasibility of successful dreissenid mussel management or eradication in lakes is relatively undocumented in the freshwater management literature. This review presents information on 33 open water dreissenid mussel control projects in 23 North America lakes. We reviewed data from past dreissenid mussel control projects and identified patterns and knowledge gaps to help inform adaptive management strategies. The three key lessons learned include 1) pre- and post-treatment survey methods should be designed to meet management objectives, e.g., by sampling for all life stages and taking into account that no survey method is completely comprehensive; 2) defining the treatment area – particularly ensuring it is sufficiently large to capture all life stages present – is critical to meeting management objectives; and 3) control projects provide an opportunity to collect mortality, depth, water chemistry, eDNA, effects on non-target organisms, and other efficacy-related data that can inform safe and effective adaptive management.
Reactivity properties of the HOSO and HSO2 isomers in liquid medium: A sequential Monte-Carlo/Quantum-Mechanics Study
Authors: Junqueira Geórgia M.A. , Ballester Maikel Y. , Nascimento Marcos A. C.
Published: January 2023

Understanding the atmospheric sulfur cycle is fundamental in developing actions to mitigate its effects on acid rain formation. Solvation of HOSO and HSO2 species has been indicated as a possible pathway in sulfur acid formation. To observe differences in the behavior of these isomers in the water medium, electrical and reactivity properties - electronic chemical potential (μ), chemical hardness (η), and electrophilicity (ϵ)- have been obtained. Once the respective first solvation shells (15H2O for HSO2 and 23 H2O for HOSO) are considered, an increase of 25% in the dipole moment of HSO2 was observed, while the dipole moment of HOSO decreases in 11%. Both solvated isomers become softer (η decreases) compared to gas phase.
Methods: HOSO and HSO2 radicals in the presence of water are investigated through a sequential Monte Carlo/ Quantum Mechanics methodology. There, the intermolecular interactions are described by the Lennard-Jones plus the Coulomb potentials. For this, the DICE program was employed. The quantum calculations were performed at CASPT2/aug−cc− pV(T+d)Z level of theory through MOLPRO computational package.
Identification of key genes related to immune cells in patients with COVID-19 via Integrated Bioinformatics-Based Analysis
Authors: Chen Zhao-jun , Chen Hai-hua
Published: January 2023

Background
COVID-19 has spread all over the world which poses a serious threat to social economic development and public health. Despite enormous progress has been made in the prevention and treatment of COVID-19, the specific mechanism and biomarker related to disease severity or prognosis have not been clarified yet. Our study intended to further explore the diagnostic markers of COVID-19 and their relationship with serum immunology by bioinformatics analysis.
Methods
The datasets about COVID-19 were downloaded from the Gene Expression Omnibus (GEO) dataset. The differentially expressed genes (DEGs) were selected via the limma package. Then, weighted gene co-expression network analysis (WGCNA) was conducted to identify the critical module associated with the clinic status. The intersection DEGs were processed for further enrichment analysis. The final diagnostic genes for COVID-19 were selected and verified through special bioinformatics algorithms.
Results
There were significant DEGs between the normal and COVID-19 patients. These genes were mainly enriched in cell cycle, complement and coagulation cascade, extracellular matrix (ECM) receptor interaction, and the P53 signalling pathway. As much as 358 common intersected DEGs were selected in the end. These DEGs were enriched in organelle fission, mitotic cell cycle phase transition, DNA helicase activity, cell cycle, cellular senescence, and P53 signalling pathway. Our study also identified CDC25A, PDCD6, and YWAHE were potential diagnostic markers of COVID-19 with the AUC (area under curve), 0.958 (95% CI: 0.920–0.988), 0.941(95% CI: 0.892 − 0.980), and 0.929(95% CI: 0.880 − 0.971). Moreover, CDC25A, PDCD6, and YWAHE were correlated with plasma cells, macrophages M0, T cells CD4 memory resting, T cells CD8, dendritic cells, and NK cells.
Conclusions
Our study discovered that CDC25A, PDCD6 and YWAHE can be used as diagnostic markers for COVID-19. Moreover, these biomarkers were also closely associated with immune cell infiltration, which plays a pivotal role in the diagnosis and progression of COVID-19.
Rare gene mutations of wild-type gastrointestinal stromal tumors
Authors: Liu Qiuyu , Li Chunxiao , Li Zhen , Fu Fangfang , Han Qian , Zhu Haohui , Bai Xiaoyun , Gao Xuejuan , Kong Lingfei
Published: January 2023

Background
Wild-type (WT) gastrointestinal stromal tumors (GISTs) are a subgroup of GISTs lacking KIT and PDGFRA mutations. Further gene and clinical characterization of WT GISTs will help determining patient prognosis and developing targeted therapy.
Methods
A total of 105 patients with GISTs were enrolled, and 15 were WT GISTs. Immunohistochemistry (IHC) staining, Sanger sequencing (SS) and next generation sequencing (NGS) approach were used to analyze WT GISTs.
Results
The 15 WT GISTs (median age, 50 [range, 9–82] years; 66.6% female; 73.3% stomach) showed the following gene mutations. SDH-deficient WT GISTs (n = 7) had mutations in SDHA, CCND1, RB1, FLT3, TP53 and SDHD. Patient with SDHA (c.G1690A), CCND1, RB1, and FLT3 (c.C2917T) mutations was a middle-aged women, stomach tumor location and high proliferative activity. Patients with TP53 ( c.300_308delGAAAACCTA; c.G841T) mutation or coexisting mutation of SDHD (c.336de1T) were showed high p53 expression, middle-aged women, stomach tumor location. Non-SDH-deficient WT GISTs (n = 8) had mutations in BRAF, TERT, and CDH1. Two patients harbored BRAF (V600E) mutation: one was a micro-GISTs, elderly female, stomach location, and low risk, the other was accompany TERT mutation, elderly male, small intestine location, and high risk. Patient with CDH1 (c.G2356A) mutation was a middle-aged male, duodenum tumor location and high risk.
Conclusions
We identified rare gene mutations of CCND1, RB1, FLT3, TERT, and CDH1 in WT GISTs. what's more, mutations of CCND1, RB1, TP53, BRAF, and CDH1 were likely to show high risk and malignant behavior which will provided new insights into the biology and mutations in WT GISTs.
Knowledge of, and factors associated with current use of modern contraceptives among young people 10 - 24years in central and western Uganda: A cross-sectional study
Authors: Bunani Nelson , Tweheyo Raymond , Beavaline Evelyne Nyachwo , Kabagenyi Allen , Neema Stella , Rutebemberwa Elizeus
Published: January 2023

Background
Although modern contraceptives are the most effective way for averting unintended pregnancies and related adverse reproductive events for the mother and baby, their use in Uganda remains low compared to the national target for the year 2020. Adolescents and young people start using modern contraceptives at 23.8 years, yet most of them have had sexual intercourse by age 16. The objective of the study was to determine the knowledge of, and factors associated with the current use of modern contraceptives among young people 10–24 years in central and western Uganda.
Methods
This was a cross cross-sectional study. Data was collected from 289 in- and out-of-school young people aged 10–24 years in five districts of western and central Uganda between July and August 2020. Digital questionnaires designed in Census and Survey Processing System (CSPro) version 7.5.1 were used. Data was transferred to Stata 15.1 for analysis. Modified Poisson regression at bivariable and multivariable analysis was used to determine the factors associated with modern contraceptive use.
Results
About 62.6% of the respondents had high knowledge of modern contraceptives. Most respondents were highly knowledgeable on injectable contraceptives 278 (96.2%) and male condoms (96.5%). Emergency contraceptives were known by only 138 (47.8%) of the respondents. In addition, the current use of modern contraceptives was 58.5% (169). Modern contraceptive use was significantly associated with being aged 20–24 years (Adj. PRR = 0.69, 95%CI; 0.52–0.90), p = 0.007; not residing with someone as a sexual partner (Adj. PRR = 0.71, 95%CI; 0.57–0.88), p = 0.002; and being a student (Adj. PRR = 1.37, 95% CI; 1.04–1.79), p = 0.023.
Conclusion
Young people 10–24 years in central and western Uganda were highly knowledgeable about modern contraceptives, particularly injectables, and condoms, but least knowledgeable about emergency contraceptives. Respondents who were students compared to non-students were more likely to be using modern contraceptives, while those aged 20–24 years and those not staying with their sexual partners were less likely to use modern contraceptives. Awareness campaigns among young people aged 20–24 years and those co-residing with a sexual partner will be necessary to improve modern contraceptive use among young people aged 10–24 years.
Growth and adaptability of provenances and progenies of Pinus maximinoi h. E. Moore in northern Mozambique
Authors: Dias Cremildo Riba Gouveia , Guacha Laurina Adriano , Mbanze Aires Afonso
Published: January 2023

The aim of this study was to evaluate the growth and adaptability of Pinus maximinoi provenances and progenies and to estimate the genetic variation that could be exploited in future breeding work. The company Floresta de Niassa Lda established a trial with four provenances and nineteen progenies in the Chimbonila district of northern Mozambique. The field trial was set up in a randomized block design with four repetitions and six-plant linear plots. At two, four and eight years of age, performance in total height, diameter at breast height (DBH) and survival were analysed. The results at eight years of age showed no significant variation between provenances for all variables analysed, and any of these provenances can be used for reforestation in northern Mozambique. The first group was composed of 9 (45%) of the best performing progenies, mostly from Yuscaran and San Jeronimo, and the second (last) group was composed of 11 (55%) of the worst performing progenies, mostly from Tatumbla and Coban. Most of the nine best classified progenies based on the predicted additive genetic effect and genetic gain belonged to Yuscaran and Tatumbla. On the other hand, most of the progenies at the level of the seventeen best classified individuals belonged to San Jeronimo and can be used for future breeding projects in northern Mozambique.
Formal Regional Delineation A case study on water availability scenario on overall Bangladesh
Authors: das Prosenjit , Anika Anika tahasin.
Published: January 2023

Water is an essential element for the existence of human being. A huge portion of people in the whole world is dependent on the access of water. Bangladesh is a developing country with high population and land ratio in the whole world. The availability of water varies in different administrative area due to their different geographical characteristics and topographical characteristics. In this study, the 64 administrative areas of Bangladesh is delineated into different regions on the basis of five main criteria such as rainfall, temperature, population density, no of water bodies available, total cultivable lands has been selected to identify the condition of water availability in the whole Bangladesh. The required database has been collected from Bangladesh Bureau of Statistics (BBS 2011) and has been analyzed through composite index method to categorize the whole Bangladesh according to the availability of water. The data reliability is checked through the level of skewness. Then the acquired data is classified by using the equal class interval method and the arithmetic mean method. According to the value of skewness the equal class interval method has been accepted for the study.
Identification of potential crucial genes associated with breast cancer using bioinformatics analysis and experimental verification
Authors: Ni Xiaoyu , Yang Haibing , Liu Chao
Published: January 2023

In this study, we identified a total of 492 DEGs, including 176 up-regulated and 316 down-regulated DEGs. GO analysis showed that the up-regulated DEGs are mainly involved in cell division, nucleus and protein binding. The down-regulated DEGs mainly involve immune response, extracellular exosome and calcium ion binding. Top five enriched pathways obtained in the KEGG pathway analysis are pathways in cancer, cytokine-cytokine receptor interaction, focal adhesion, the PI3K-akt signaling pathway and ECM-receptor interaction. Top 10 up-regulated hub genes identified from the PPI network are AURKA, CDC6, CCNA2, CDCA8, NUSAP1, CDK1, CCNB1, CCNB2, UBE2C, HMMR. The top 10 down-regulated hub genes are IGF1, JUN, FGF2, CXCL12, KIT, PTGS2, LEP, EGF, EGR1, FOS. Survival analysis showed that the expression levels of WIF1 (P = 0.019) and HMMR (P = 0.027) were correlated with the prognosis of patients with breast cancer. In addition, gene expression and methylation analysis showed that COL11A1 is highly expressed and hyper-methylation. MMP1 is highly expressed and hypo-methylation. SFRP1, WIF1 is low expressed and hyper-methylation in breast cancer. In terms of tumor purity and immune cell infiltration analysis, Interestingly, it is found that HMMR makes a strong connection with B Cell, CD8+T Cell, neutrophil, dendritic cell (P <0.05). MMP1 was negtively associated with tumor purity. The use of bioinformatics can effectively analyze the data of the gene chip, obtain the inherent information of the organism, and provide the basis for the next experiment. This study identifies key genes and pathways in breast cancer that will advance our understanding of molecular mechanisms.
Dissemination of the high-risk clone ST147 carbapenem-resistant Klebsiella pneumoniae from a local tertiary care hospital in the Republic of Korea
Authors: Park Jungsun , Shin Eunkyung , Kim Min-Kyeong , Joo Seongjae , Jeong Hyun Ju , Kim Jin Seok , Yoo Jaeil , Kim Junyoung
Published: January 2023

Background : The emergence of carbapenem-resistant Enterobacterales (CRE) infections is rapidly increasing and represents a serious public threat. In 2020, a total of 16,883 carbapenemase-producing Enterobacterales strains were collected; among these isolates, 21 strains were repeatedly isolated in a local tertiary care hospital.
Methods : Antimicrobial susceptibility testing was performed using the broth microdilution method. All 21 strains of CRKP were analyzed by PFGE after XbaI digestion. The 21 CRKP strains were sequenced on the Illumina Miseq and Oxford Nanopore GridION platforms.
Results : These 21 CRKP isolates showed an identical antimicrobial resistance profile, such as resistance to ampicillin, carbapenems, cephems, chloramphenicol, fluoroquinolone, macrolides and trimethoprim/sulfamethoxazole. Based on whole-genome analysis, these 21 CRKP isolates shared a common genetic structure (ISAba125-IS630-blaNDM-1-bleMBL) and harbored additional resistance determinants (blaOXA-1, blaCTX-M-15, blaSHV-11, blaSHV-67, aac(6')-Ib-cr, qnrS1, OqxA, OqxB, catB3, mph(A), sul1, and dfrA12) and mutations in the quinolone resistance-determining regions of gyrA (S83I) and parC (S80I). These isolates belonged to the ST147 and KL64 capsular types, which were carried on IncFIB replicon plasmids. The 21 CRKP strains collected from one hospital were divided into five PFGE patterns, and they were closely related with a minimum similarity value of 95.2%. These isolates were found to be highly related based on the presence of between 2 and 27 SNPs.
Conclusions : These findings indicate that NDM-1-producing K. pneumoniae ST147 may have been introduced via a common source, implying nosocomial transmission; furthermore, continuous monitoring is necessary to prevent endemic transmission.
Classification of FLT3 Inhibitors and SAR Analysis by Machine Learning Methods
Authors: Zhao Yunyang , Tian Yujia , Pang Xiaoyang , Li Guo , Yan Aixia , Shi Shenghui
Published: January 2023

FMS-like tyrosine kinase 3 (FLT3) is a type III receptor tyrosine kinase, which is an important target for anti-cancer therapy. In this work, we conducted a structure-activity relationship (SAR) study on 3867 FLT3 inhibitors we collected. MACCS fingerprints, ECFP4 fingerprints, and TT fingerprints were used to represent the inhibitors in the dataset. A total of 36 classification models were built based on support vector machine (SVM), random forest (RF), eXtreme Gradient Boosting (XGBoost), and deep neural networks (DNN) algorithms. Model 3D_3 built by deep neural networks (DNN) and TT fingerprints performed best on the test set with the highest prediction accuracy of 85.83% and Matthews correlation coefficient (MCC) of 0.72 and also performed well on the external test set.
In addition, we clustered 3867 inhibitors into 11 subsets by K-Means algorithm to figure out the structural characteristics of the reported FLT3 inhibitors. Finally, we analyzed the SAR of FLT3 inhibitors by RF algorithm based on ECFP4 fingerprints. The results showed that 2-aminopyrimidine, 1-ethylpiperidine, 2,4-bis(methylamino)pyrimidine, amino-aromatic heterocycle, [(2E)-but-2-enyl]dimethylamine, but-2-enyl, and alkynyl were typical fragments among highly active inhibitors. Besides, three scaffolds in Subset_A (Subset 4), Subset_B, and Subset_C showed a significant relationship to inhibition activity targeting FLT3.
Natural Amenities and Neo-Hobbesian Local Public Finance
Authors: Petach Luke
Published: January 2023

A revenue maximizing local government must obey a migration constraint when levying taxes. Using this insight, I develop a simple theory of taxation that suggests natural amenities are a key factor influencing local tax rates. Natural amenities confer rents to residents which governments and interest groups compete to extract. Revenue maximizing local tax rates are increasing in the level of natural amenities, increasing in moving costs, and decreasing in households’ reservation utility. Using data on natural amenities and taxation for US counties, I find that local tax rates are in-fact increasing the level of natural amenities. Finally, I suggest an alternative interpretation of the “tax revolts” of the late 1970’s. Rather than an attempt to constrain Leviathan, local property tax reform (such as California’s Proposition 13) and restrictions on housing supply are the outcome of competition over amenity rents in which property owners successfully capture a monopoly position at the expense of other social groups including renters and local government.
JEL Codes: H21, H71, D72