bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward MR protocol-agnostic, bias-corrected brain age predicted from clinical-grade MRIs
Authors: Valdes-Hernandez Pedro , Nodarse Chavier Laffitte , Peraza Julio , Cole James , Cruz-Almeida Yenisel 
Published: August 2023

Abstract
The predicted brain age minus the chronological age (‘brain-PAD’) could become a clinical biomarker. However, most brain age methods were developed to use research-grade high-resolution T1-weighted MRIs, limiting their applicability to clinical-grade MRIs from multiple protocols. To overcome this, we adopted a double transfer learning approach to develop a brain age model agnostic to modality, resolution, or slice orientation. Using 6,224 clinical MRIs among 7 modalities, scanned from 1,540 patients using 8 scanners among 15 + facilities of the University of Florida’s Health System, we retrained a convolutional neural network (CNN) to predict brain age from synthetic research-grade magnetization-prepared rapid gradient-echo MRIs (MPRAGEs) generated by a deep learning-trained ‘super-resolution’ method. We also modeled the “regression dilution bias”, a typical overestimation of younger ages and underestimation of older ages, which correction is paramount for personalized brain age-based biomarkers. This bias was independent of modality or scanner and generalizable to new samples, allowing us to add a bias-correction layer to the CNN. The mean absolute error in test samples was 4.67–6.47 years across modalities, with similar accuracy between original MPRAGEs and their synthetic counterparts. Brain-PAD was also reliable across modalities. We demonstrate the feasibility of clinical-grade brain age predictions, contributing to personalized medicine.
Revisiting the Nexus of Taxes vis-à-vis Inequality: New Insights from Wavelet Coherence Approach Using Top Decile’s Income Share in Australia
Authors: Gangopadhyay Partha , Das Narasingha 
Published: August 2023

Abstract
We examine the nexus between taxes and income inequality in Australia – using per capita GDP as a control variable over the period 1972-2019. We apply the bi, partial and vector wavelet coherence methodologies to investigate the nature and the direction of coherences between chosen variables to marshal evidence of a complex relationship between taxes and inequality. Our findings are three-fold: first, from 2000 to 2019, per capita GDP significantly leads inequality in higher frequencies (long-run), while in the middle frequency, only after 2015, significant coherence is observed between these two variables. In lower frequencies, or short-run, from 1972 to 1985 and from 2017 onward, significant coherence is observed with the same lead-lag relationship between per capita GDP and inequality. Both partial wavelet and vector wavelet models confirm the time-varying effect of GDP on inequality, which also fluctuated across frequencies. For checking the robustness of our findings, we then extended the analysis to incorporate the effect of resource booms on Australian inequality. Even with resource booms, the central messages of our findings on the nexus between taxes and inequality in Australia remain unaltered, which indicates that Australia enjoys a strong taxation base to fund quality public services and targeted transfers for controlling inequality.
JEL Classification: H20; H25; A14; B23; C32
Establishment and characterization of a recurrent MPNST primary cell line:RsNF
Authors: Zhang Xingnan , Hu Chenhao , Li Dezhi , Liu Song 
Published: August 2023

Abstract
Malignant peripheral schwannoma (MPNST) is a highly aggressive and recurrent soft tissue sarcoma. It most commonly occurs secondary to neurofibromatosis type I, and it has a 5-year survival rate of only 8%-13%. In order to better study the tumor heterogeneity of MPNST and to develop diverse treatment options, more tumor-derived cell lines are needed to obtain richer biological information. Here, we established a patient-derived primary cell line of relapsed MPNST-RsNF cells with a genetic background of NF1 mutation. Through tumor molecular marker targeted sequencing and single-cell transcriptome sequencing, it was found that chromosome 7 copy number variation (CNV) was amplified in this cell line, and ZNF804B, EGFR, etc., were overexpressed on chromosome 7. Therefore, RsNF cells can be used as a useful tool in NF1 associated-MPNST genomic amplification studies and to develop new therapeutic strategies.
Breathing in Virtual Reality for Promoting Mental Health: A Scoping Review
Authors: Pancini Elisa , Natale Anna Flavia Di , Villani Daniela 
Published: August 2023

Abstract

Breathing techniques have long been recognized as effective strategies for promoting mental health-related outcomes such as relaxation and emotional regulation. Virtual reality (VR), with its immersion and interactivity, offers the possibility to amplify the effectiveness of breathing techniques in promoting mental health. Recently, there has been an increasing use of VR to support breathing, although a formal summary of this integration is lacking. Following the PRISMA-ScR reporting guidelines, this scoping review aims to investigate the integration of breathing techniques and VR experiences and examine their potential effects on mental health-related outcomes. The synthesis of the reviewed studies (n = 14) reveals that different VR experiences can be used to strengthen breathing techniques. VR can, for example, reduce distractions and enhance focus during breathing exercises, provide direct, real-time feedback on the practice, and be used to create personalized environments, allowing users to train their breathing techniques in various contexts, from calming virtual nature settings to safe environments for practicing breathing skills that can be applied to real-life situations. Furthermore, this scoping review reveals the positive effects of VR-based breathing interventions on reducing clinical symptoms and increasing well-being and physical health outcomes. Overall, while acknowledging some methodological heterogeneity in the existing studies, the findings demonstrate the unique and promising potential of integrating breathing techniques with VR experiences. Future research is recommended to understand long-term effects, user experience, and the potential customization of interventions for diverse clinical and well-being contexts.
Antimicrobial resistance pattern of anaerobic bacteria causing lower respiratory tract infections.
Authors: Shariff Malini , Khawung Elizabeth 
Published: August 2023

Abstract
Background
Anaerobes are indigenous flora of the human body but have the potential to cause serious diseases. Anaerobic bacteria are involved in all morbid conditions of respiratory infections, and the frequencies of isolation are high in pneumonia and at the time of acute exacerbation of chronic lower airway infection. These are often missed due to the complexity of their isolation and identification. Hence, this study aimed to study anaerobes causing respiratory tract infections and determine their antibiotic susceptibility.
Materials & Methods
Clinical specimens such as bronchial aspirates and pleural aspirates collected from patients with respiratory diseases attending Vallabhbhai Patel Chest Institute were processed, the anaerobes isolated were identified, and their susceptibilities to various groups of antimicrobials were studied using standard microbiological methods.
Results
Three hundred forty-four patients were included in the study, 124 males and 147 females. Of these 344 patients, 165 yielded anaerobes in their clinical samples. Ninety patients had more than one type of anaerobic organism. Hence, a total of 271 isolates were recovered belonging to as many as 16 genera. The MIC of seven antibiotics on 154 isolates was tested. The isolates belonged to the genera Bacteroides, Prevotella, Veillonella, and Actinomyces, among others. Variable resistance was observed to most classes of antibiotics by many genera.
Conclusions
Metronidazole is commonly used against anaerobes, but the study showed that the isolates were 20–30% resistant to the antibiotic. Starting this as an empirical therapy might lead to treatment failure.
Plasma Proteomic Characterization of Colorectal Cancer Patients with FOLFOX Chemotherapy by Integrated Proteomics Technology
Authors: Wang Xi , Zhang Keren , He Wan , Zhang Luobin , Gao Biwei , Xu Ruilian , Tian Ruijun 
Published: August 2023

Abstract
Background Colorectal Cancer (CRC) is a prevalent form of cancer, and the effectiveness of the main postoperative chemotherapy treatment, FOLFOX, varies among patients. In this study, we aimed to identify potential biomarkers for predicting the prognosis of CRC patients treated with FOLFOX through plasma proteomic characterization.Methods Using a fully integrated sample preparation technology SISPROT-based proteomics workflow, we achieved deep proteome coverage and trained a machine learning model from a discovery cohort of 90 CRC patients to differentiate FOLFOX-sensitive and FOLFOX-resistant patients. The model was then validated by targeted proteomics on an independent test cohort of 26 patients.Results We achieved deep proteome coverage of 831 protein groups in total and 536 protein groups in average for non-depleted plasma from CRC patients by using a Orbitrap Exploris 240 with moderate sensitivity. Our results revealed distinct molecular changes in FOLFOX-sensitive and FOLFOX-resistant patients. We confidently identified known prognostic biomarkers for colorectal cancer, such as S100A4, LGALS1, and FABP5. The classifier based on the biomarker panel demonstrated a promised AUC value of 0.908 with 93% accuracy. Additionally, we established a protein panel to predict FOLFOX effectiveness, and several proteins within the panel were validated using targeted proteomic methods.Conclusions Our study sheds light on the pathways affected in CRC patients treated with FOLFOX chemotherapy and identifies potential biomarkers that could be valuable for prognosis prediction. Our findings showed the potential of mass spectrometry-based proteomics and machine learning as an unbiased and systematic approach for discovering biomarkers in CRC.
Generation of porcine circovirus type 4 virus-like particles and their use to detect serum antibodies
Authors: Fang Zheng , Sun Mingxia , Wang Shanghui , Cai Xuehui , An Tongqing , Wang Haiwei , Tu Yabin 
Published: August 2023

Abstract
Porcine Circovirus type 4 (PCV4), first identified in 2019 as a newly emerging pathogen, has been found in several provinces of China, as well as in Korea and Thailand. Since PCV4 is not included in immunization programs, epidemiological investigations should be conducted for PCV4-positive antibodies detection. Virus-like particles (VLPs) are commonly employed for serological analysis of pathogen infections. However, there are no reports on using PCV4 VLPs in PCV4 infection investigation. In this study, we successfully generated self-assembled PCV4 VLPs using an E.coli expression system and purified the PCV4 VLPs through a two-step purification process. Subsequently, we utilized the purified VLPs as encapsulated antigens to develop an indirect ELISA. The established ELISA method showed high specificity, sensitivity, and repeatability, making it suitable for PCV4 antibodies investigation of serum samples. Finally, the ELISA was applied to detect 422 serum samples from regions in China, of which 134 tested positive. Therefore, PCV4-VLPs-based ELISA could effectively detect antibodies against PCV4 in serum samples, contributing to a better understanding of PCV4 epidemiology.
Testing the Validity of Philips Curve in Nigeria
Authors: Lawal Jamiu Oluwatosin 
Published: August 2023

Abstract
The study tested for the validity of Philips curve in Nigeria. The study utilizes time series data covering the periods between 1986 and 2021. Prior to the estimation procedures, the stochastic properties of the time series data were examined using Augmented Dickey Fuller (ADF) and Philip-Perron (PP). The results of the time series properties indicate that the variables are combination of both I(0) and I(1) in the same specification which prompt the use of autoregressive distributive lags (ARDL) developed by Pesaran et al (2001). In addition, granger causality was performed to test for causal relationship. Both in the short run and long run, the results show a significant positive impact of unemployment on inflation. This implies that Philips curve that shows trade-off between inflation and unemployment rate does not hold in Nigeria both in the short-run and long-run. The granger causality test revealed no causation relationship between inflation and unemployment rate in Nigeria. The recommendations include among others the following: Government should create more job opportunities. This can be done by investing in other sectors of the economy such as the agricultural and industrial sectors. The monetary authority should moderate its current policy stance, lower interest rates, and control the growth of money in order to boost investment and economic growth. This would encourage small-scale businesses to emerge and thus reduce the unemployment rate in the country.
A semiempirical method optimized for modeling proteins
Authors: Stewart James J. P. 
Published: August 2023

Abstract
Context In recent years, semiempirical methods such as PM6, PM6-D3H4, and PM7 have been increasingly used for modeling proteins, in particular enzymes. These methods were designed for more general use, and consequently were not optimized for studying proteins. Because of this, various specific errors have been found that could potentially cast doubt on the validity of these methods for modeling phenomena of biochemical interest such as enzyme catalytic mechanisms and protein-ligand interactions. To correct these and other errors, a new method specifically designed for use in organic and biochemical modeling has been developed.Methods Two alterations were made to the procedures used in developing the earlier PMx methods. A minor change was made to the theoretical framework, which affected only the nonquantum theory interatomic interaction function, while the major change involved changing the training set for optimizing parameters, moving the focus to systems of biochemical significance. This involved both the selection of reference data and the weighting factors, i.e., the relative importance that the various data were given. As a result of this change of focus, the accuracy in prediction of heats of formation, hydrogen bonding, and geometric quantities relating to noncovalent interactions in proteins was improved significantly.
Oblivious Network Intrusion Detection Systems
Authors: Sayed Mahmoud AbdelHafeez , Taha Mostafa 
Published: August 2023

Abstract
A main function of network Intrusion Detection Systems (NIDSs) is to monitor network traffic and match it against rules. Oblivious NIDSs (O-NIDS) perform the same tasks of NIDSs but they use encrypted rules and produce encrypted results without being able to decrypt the rules or the results. Current implementations of O-NIDS suffer from slow searching speeds and/or lack of generality. In this paper we present a generic approach to implement a privacy-preserving O-NIDS based on hybrid binary gates. We also present two resources-flexible algorithm bundles built upon the hybrid binary gates to perform the NIDS's essential tasks of direct matching and range matching as a proof of concept. Our approach utilizes a Homomorphic Encryption (HE) layer in an abstract fashion, which makes it implementable by many HE schemes compared to the state of the art where the underlying HE scheme is a core part of the approach. This feature allowed using already-existing HE libraries that utilize parallelization techniques in GPUs for faster performance. We achieved a rule encryption time as low as 0.012\% of the state of the art with only 0.047\% of its encrypted rule size. Also, we achieved a rule matching speed that is almost 20,000 times faster than the state of the art.
Nomogram for predicting distant metastasis and prognosis in HR+/HER2- breast cancer patients without lymph node metastasis
Authors: zhang weifang , Liu Bo , Shang Fangjian , Yang Chenhui , liu yunjiang 
Published: August 2023

Abstract
Background
HR+/HER2- breast cancer patients without lymph node metastasis (N0) but with distant metastasis (DM) are rare. This study aims to explore the risk factors of N0 patients with distant metastasis and build nomogram to predict the occurrence and prognosis of distant metastasis.
Methods
Patients with HR+/HER2- N0 breast cancer diagnosed between 2010 and 2017 were retrospectively collected from the Surveillance, Epidemiology, and End Result (SEER) database. Univariate and multivariate logistic analysis were performed to identify risk factors for DM. Nomogram was constructed based on multivariate regression results. Univariate and multivariate Cox regression were used to identify the prognostic factors of DM patients, and Nomogram was constructed to predict 1-year, 3-year, and 5-year BCSS. The performance of nomogram was evaluated by concordance index (C-index), receiver operating characteristic (ROC) curves, calibration curve and decision curve analyses (DCAs).
Results
A total of 63005 patients were enrolled, including 1208 patients (1.3%) with DM. Race, T stage, location, grade and PR were independent risk factors for DM. The area under curve (AUC) values of the development cohort and validation cohort were 0.835 and 0.836, respectively. Seven significant prognostic factors including age, race, grade, ER, PR, surgery, and site of metastasis were included to build nomogram to predict 1-year, 3-year, and 5-year BCSS. The C-index of the development cohort and validation cohort were 0.70 and 0.68, respectively.
Conclusions
Our nomogram can predict the occurrence and prognosis of DM in HR+/HER2- N0 patients, providing guidance for individualized survival assessment and appropriate treatment for the special population.
Pachychoroid Spectrum Diseases: Long-term Visual Outcomes, with a Focus on Risk Factors Affecting Central Serous Chorioretinopathy
Authors: Azuma Keiko , Tanaka Nobuya , Aoki Shuichiro , Kitamoto Kohdai , Ueda Kohei , Inoue Tatsuya , Obata Ryo 
Published: August 2023

Abstract
Purpose: To analyze the long-term visual outcomes of pachychoroid spectrum diseases (PSD).
Design: Retrospective study.
Methods: We reviewed the medical charts of consecutive patients with PSD, including focal choroidal excavation (FCE), pachychoroid pigment epitheliopathy (PPE), central serous chorioretinopathy (CSC), and pachychoroid neovasculopathy (PNV). The patients visited the Tokyo University Hospital from January 2008 to April 2022. Survival analyses were performed, in which loss of vision was defined as visual acuity (VA) of 0.2 logarithm of minimal angle of resolution (logMAR) or worse, 0.5 logMAR or worse, or VA worsening by 0.3 logMAR or greater. Moreover, we further investigated factors associated with visual prognosis, particularly in the CSC group.
Results: A total of 741 eyes of 638 patients were included in this analysis. The CSC or PNV group showed significantly worse visual prognosis than the FCE&PPE group for VA to 0.2 logMAR or worse (P=0.0117 or 0.0001, respectively) and for VA worsening by 0.3 logMAR or greater (P=0.0283 or 0.0037, respectively). In the CSC group, unlike age, sex, or treatment history, the duration of subfoveal fluid existence ≥12 months (continuous or intermittent) was significantly associated with visual prognosis (P<0.0001).
Conclusions: Among PSD, CSC and PNV were associated with a higher risk of vision loss in the long term than FCE and PPE. The duration of subretinal fluid existence was identified as a significant factor affecting long-term visual outcomes in CSC.
Simulation study of the punching forming process and die wear of spur gears
Authors: Chen Zhiyuan , Guo Zenghui , Fang Bin , Gao Liying , Su Guosheng , Liu Bingqiang 
Published: August 2023

Abstract
As an important transmission component, the spur gear has been widely used in automobiles and various mechanical equipment. However, spur gears are produced by the hobbing and shaving, which inevitably reduces the service strength and service life of the gear. In this paper, the punching forming process of spur gear is presented. Compared with the traditional gear machining process, the process not only avoids the destruction of the metal flow line and significantly improves the material utilization rate. The effect of tooth filling and equivalent strain accumulation on gear forming quality were discussed by finite element simulation. The effects of upper die punching speed, lower die preheating temperature and friction coefficient on lower die wear during forming were studied by response surface method. The optimum process parameters of punching of spur gear were lower die preheating temperature of 280℃, friction coefficient of 0.27, upper die feed speed of 8.3 mm/s, respectively.It is predicted that about 110,000 gears can be produced before the wear failure of the lower die. On the basis of the finite element simulation results, the gear punching test is carried out. The experimental results are in good agreement with the simulation results, and the metal flow line at the tooth is uniform and continuous, which verifies the reliability of the punching process. This study provides a feasible way for plastic forming of spur gear.
The Properties of Soilless Culture Substrates Determine the Evolutionary Direction of Rhizosphere Microbial Communities in Potato Breeding, Having Potential Impact on Breeding
Authors: Yan Kan , Ma Yanni , Bao Songming , Li Wandi , Wang Yunjiao , Sun Chao , Lu Xin 
Published: August 2023

Abstract
Background
Coconut bran and vermiculite are commonly used substrates in the process of potato germplasm breeding under soilless cultivation conditions, each possessing distinct physicochemical properties and indigenous microbial reservoirs. In comparison to natural soil, there is a lack of evaluation and limited understanding of the root-associated microbial communities in soilless cultivation environments. As soilless cultivation is increasingly applied in agriculture, the evolution of these microorganisms can significantly impact the breeding environment and the microecological environment within the regions involved in breeding.
Results
The physicochemical characteristics of the substrates significantly influence the composition and evolution of indigenous bacterial communities under similar treatments. Substrate permeability has almost no effect on the microbial community, while WSN (water-stable aggregates), TN (total nitrogen), AK (available potassium), and TOC (total organic carbon) are identified as the most critical influencing factors. They show a positive correlation with bacterial communities but a negative correlation with fungal communities. Coconut bran exhibits higher values for these four indicators. During the two stages of mixed fermentation after basal fertilization and 50 days of potato cultivation, coconut bran consistently maintains higher bacterial diversity and abundance while possessing lower fungal diversity and abundance. Coconut bran substrates exhibit a more complex microbial network and higher bacterial-fungal negative correlations. Each group is enriched with specific functional biomarkers, where coconut bran substrates are associated with polysaccharide degradation and denitrification-related microorganisms, along with an abundance of plant growth-promoting rhizobacteria (PGPRs). In contrast, vermiculite substrates are enriched with Dyella, a microorganism involved in rock weathering, but also contain a higher abundance of plant pathogens, particularly potato pathogenic bacteria and fungi (Pectobacterium and Botryotinia).
Conclusion
Coconut bran and vermiculite, as distinct soilless cultivation substrates, play a crucial role in shaping the microbial community composition during various stages of potato breeding. Higher levels of WSN, TN, AK, and TOC in coconut bran substrates provide a healthier microecological environment. These findings offer potential insights into the selection of soilless cultivation substrates for healthy and sustainable potato breeding and the adjustment of beneficial microbial community composition.