bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supervised machine learning for predicting shear sonic log (DTS) and volumes of petrophysical and elastic attributes, Kadanwari Gas Field, Pakistan
Authors: Ahmed Syed Adnan , MonaLisa  , Hussain Muyyassar , Khan Zahid Ullah 
Published: August 2022

Shear sonic log (DTS) availability is vital for litho-fluid discrimination within reservoirs, which is critical for field development and production. For certain reasons, most of the wells in the Lower Indus Basin (LIB) lack DTS logs, which are modeled using conventional techniques based on empirical relations and rock physics modeling. However, in their extensive computation, these approaches need assumptions and multiple prerequisites, which can compromise the true reservoir characteristics. Machine learning (ML) has recently emerged as a robust and optimized technique for predicting precise DTS with fewer input data sets. To predict the best DTS log that adheres to the geology, a comparison was made between three supervised machine learning (SML) algorithms: random forest (RF), decision tree regression (DTR), and support vector regression (SVR). Based on qualitative statistical measures, the RF stands out as the best algorithm, with maximum determination of correlation (R2) values of 0.68, 0.86, 0.56, and 0.71 and lower mean absolute percentage error (MAPE) values of 4.5, 2.01, 4.79, and 4.65 between the modeled and measured DTS logs in Kadanwari-01, -03, -10, and -11 wells, respectively. For detailed reservoir characterization, the RF algorithm is further employed to generate elastic attributes such as P-impedance (Zp), S-impedance (Zs), lambda-rho (λρ), mu-rho (μρ), as well as petrophysical attributes such as effective porosity (PHIE) and clay volumetric (Vcl) utilizing seismic and well data. The resultant attributes helped to establish a petro-elastic relationship delineated at the reservoir level. Possible gas zones were determined by zones with high PHIE (8%–10%) and low values of other attributes like Vcl (30%–40%), Zp (10,400–10,800 gm/cc*m/s), and Zs (6,300–6,600 gm/cc*m/s). The potential bodies are also validated by low λρ (27–30 GPa*g/cc) cross ponding to higher μρ (38–44 GPa*g/cc).
A High-Quality Genome Assembly of Sorghum dochna
Authors: Chen Yu , Zhang Yongbai , Wang Hongjie , Sun Juan , Ma Lichao , Miao Fuhong , Zhang Zixin , Cheng Yang , Huang Jianwei , Yang Guofeng , Wang Zengyu 
Published: August 2022

Sweet sorghum (Sorghum dochna) is a high-quality bio-energy crop that also serves as food for humans and animals. However, there is little information on the genomic characteristics of S. dochna. In this study, we presented a high-quality assembly of S. dochna with PacBio long reads, Illumina short reads, high-throughput chromosome capture technology (Hi-C) sequencing data, gene annotation, and a comparative genome analysis. The results showed that the genome of S. dochna was assembled to 777 Mb with a contig N50 of 553.47 kb and a scaffold N50 of 727.11 kb. In addition, the gene annotation predicted 37,971 genes and 39,937 transcripts in the genome of S. dochna. A Venn analysis revealed a set of 7,988 common gene annotations by integrating five databases. A Cafe software analysis showed that 191 gene families were significantly expanded, while 3,794 were significantly contracted in S. dochna. A GO enrichment analysis showed that the expanded gene families were primarily clustered in the metabolic process, DNA reconstruction, and DNA binding among others. The high-quality genome map constructed in this study provides a biological basis for the future analysis of the biological characteristics of S. dochna, which is crucial for its breeding.
Changes in the composition of gut and vaginal microbiota in patients with postmenopausal osteoporosis
Authors: Yang Xueli , Chang Tian , Yuan Qian , Wei Wei , Wang Pingping , Song Xiaojian , Yuan Huijuan 
Published: August 2022

BackgroundPostmenopausal osteoporosis (PMO) is influenced by estrogen metabolism and immune response, which are modulated by several factors including the microbiome and inflammation. Therefore, there is increasing interest in understanding the role of microbiota in PMO.ObjectivesTo investigate variations in gut microbiota (GM) and vaginal microbiota (VM) in postmenopausal women with osteoporosis.MethodsA total of 132 postmenopausal women were recruited for the study and divided into osteoporosis (n = 34), osteopenia (n = 47), and control (n = 51) groups based on their T score. The serum levels of interleukin (IL)-10, tumor necrosis factor (TNF)-α, and lipopolysaccharide-binding protein were determined via enzyme-linked immunosorbent assay. Additionally, 16S rRNA gene V3-V4 region sequencing was performed to investigate the GM and VM of the participants.ResultsSignificant differences were observed in the microbial compositions of fecal and vaginal samples between groups (p &lt; 0.05). It was noted that for GM, Romboutsia, unclassified_Mollicutes, and Weissella spp. were enriched in the control group, whereas the abundances of Fusicatenibacter, Lachnoclostridium, and Megamonas spp. were higher in the osteoporosis group than in the other groups. Additionally, for VM, Lactobacillus was enriched in the control group, whereas the abundances of Peptoniphilus, Propionimicrobium, and Gallicola spp. were higher in the osteoporosis group than in the other groups. The predicted functional capacities of GM and VM were different in the various groups. We also found that the serum level of IL-10 in the osteoporosis group was significantly lower than that in the control group and osteopenia group, while TNF-α was significantly higher in the osteoporosis group than that in the control group (p &lt; 0.05).ConclusionThe results show that changes in BMD in postmenopausal women are associated with the changes in GM and VM; however, changes in GM are more closely correlated with PMO than VM.
Association between thyroid function and disease severity in restless legs syndrome
Authors: Geng Chaofan , Yang Zhenzhen , Kong Xiumei , Xu Pengfei , Zhang Hongju 
Published: August 2022

BackgroundRestless Legs Syndrome (RLS) is a common neurological disorder. Growing evidence shows that dopaminergic dysfunction and iron deficiency are associated with the pathogenesis of RLS. Additionally, the dopaminergic system is linked with the hypothalamic-pituitary-thyroid (HPT) axis. Thus, the current study aimed to compare thyroid function between RLS patients and healthy subjects and investigate the associations with clinical characteristics of RLS.MethodsSerum levels of thyroid hormones were investigated in 102 first-episode drug-naïve RLS patients and 80 matched healthy controls (HCs). Baseline data and clinical characteristics were performed by professional personnel. In addition, multivariate regression was used to analyze the relationship between thyroid function and RLS.ResultsCompared with control group, RLS patients had significantly higher serum thyroid-stimulating hormone (TSH) levels (p &lt; 0.001), and higher prevalence of subclinical hypothyroidism [Odds ratio (OR) 8.00; 95% confidence interval (CI) = 3.50–18.30; p &lt; 0.001]. The Subclinical hypothyroidism rate (47.1 vs. 10%, p &lt; 0.001) in RLS patients was higher than the HCs group. Regression analysis revealed that serum TSH (OR = 1.77; 95% CI = 1.41–2.23; p &lt; 0.001) was independently associated with RLS. There was a statistically significant positive correlation between TSH and the Pittsburgh sleep quality index (PSQI) scores (r = 0.728, p &lt; 0.001), and the International Restless Legs Scales (IRLS) points (r = 0.627, p &lt; 0.001). Spearman correlation analysis showed that FT3 was positive correlated with HAMA14 score (r = 0.239, p = 0.015). In addition, compared with the good-sleeper group, poor-sleeper patients had significantly higher serum TSH levels (p &lt; 0.001).ConclusionSerum levels of TSH and the prevalence of subclinical hypothyroidism were higher in RLS patients, indicating the imbalance between thyroid hormones (TH) and the dopaminergic system may contribute to the development of primary RLS. Additionally, the TH axis may influence the quality of sleep in RLS patients.
Advanced diffusion MRI and image texture analysis detect widespread brain structural differences between relapsing-remitting and secondary progressive multiple sclerosis
Authors: Oladosu Olayinka , Liu Wei-Qiao , Brown Lenora , Pike Bruce G. , Metz Luanne M. , Zhang Yunyan 
Published: August 2022

IntroductionDisease development in multiple sclerosis (MS) causes dramatic structural changes, but the exact changing patterns are unclear. Our objective is to investigate the differences in brain structure locally and spatially between relapsing-remitting MS (RRMS) and its advanced form, secondary progressive MS (SPMS), through advanced analysis of diffusion magnetic resonance imaging (MRI) and image texture.MethodsA total of 20 patients with RRMS and nine patients with SPMS from two datasets underwent 3T anatomical and diffusion tensor imaging (DTI). The DTI was harmonized, augmented, and then modeled, which generated six voxel- and sub-voxel-scale measures. Texture analysis focused on T2 and FLAIR MRI, which produced two phase-based measures, namely, phase congruency and weighted mean phase. Data analysis was 3-fold, i.e., histogram analysis of whole-brain normal appearing white matter (NAWM); region of interest (ROI) analysis of NAWM and lesions within three critical white matter tracts, namely, corpus callosum, corticospinal tract, and optic radiation; and along-tract statistics. Furthermore, by calculating the z-score of core-rim pathology within lesions based on diffusion measures, we developed a novel method to define chronic active lesions and compared them between cohorts.ResultsHistogram features from diffusion and all but one texture measure differentiated between RRMS and SPMS. Within-tract ROI analysis detected cohort differences in both NAWM and lesions of the corpus callosum body in three measures of neurite orientation and anisotropy. Along-tract statistics detected cohort differences from multiple measures, particularly lesion extent, which increased significantly in SPMS in posterior corpus callosum and optic radiations. The number of chronic active lesions were also significantly higher (by 5–20% over z-scores 0.5 and 1.0) in SPMS than RRMS based on diffusion anisotropy, neurite content, and diameter.ConclusionAdvanced diffusion MRI and texture analysis may be promising approaches for thorough understanding of brain structural changes from RRMS to SPMS, thereby providing new insight into disease development mechanisms in MS.
Source localization and functional network analysis in emotion cognitive reappraisal with EEG-fMRI integration
Authors: Li Wenjie , Zhang Wei , Jiang Zhongyi , Zhou Tiantong , Xu Shoukun , Zou Ling 
Published: August 2022

BackgroundThe neural activity and functional networks of emotion-based cognitive reappraisal have been widely investigated using electroencephalography (EEG) and functional magnetic resonance imaging (fMRI). However, single-mode neuroimaging techniques are limited in exploring the regulation process with high temporal and spatial resolution.ObjectivesWe proposed a source localization method with multimodal integration of EEG and fMRI and tested it in the source-level functional network analysis of emotion cognitive reappraisal.MethodsEEG and fMRI data were simultaneously recorded when 15 subjects were performing the emotional cognitive reappraisal task. Fused priori weighted minimum norm estimation (FWMNE) with sliding windows was proposed to trace the dynamics of EEG source activities, and the phase lag index (PLI) was used to construct the functional brain network associated with the process of downregulating negative affect using the reappraisal strategy.ResultsThe functional networks were constructed with the measure of PLI, in which the important regions were indicated. In the gamma band source-level network analysis, the cuneus, the lateral orbitofrontal cortex, the superior parietal cortex, the postcentral gyrus, and the pars opercularis were identified as important regions in reappraisal with high betweenness centrality.ConclusionThe proposed multimodal integration method for source localization identified the key cortices involved in emotion regulation, and the network analysis demonstrated the important brain regions involved in the cognitive control of reappraisal. It shows promise in the utility in the clinical setting for affective disorders.
The association between weight-adjusted-waist index and increased urinary albumin excretion in adults: A population-based study
Authors: Qin Zheng , Chang Kaixi , Yang Qinbo , Yu Qiao , Liao Ruoxi , Su Baihai 
Published: August 2022

AimsThe negative effect of obesity on kidney health has been reported. The association between weight-adjusted-waist index (WWI, a newly developed adiposity index) and albuminuria has not been reported earlier.MethodsThis cross-sectional study was conducted among adults with complete data about WWI and urinary albumin-to-creatinine ratio (ACR) in 2005–2018 National Health and Nutrition Examination Survey (NHANES). WWI was calculated as waist circumference (WC) divided by the square root of weight. Weighted multivariable logistic regression and generalized additive model were employed to explore the independent relationship between WWI with albuminuria and its non-linearity. A two-piecewise linear regression model was used to calculate the threshold effect. Subgroup analysis and interaction tests were also performed.ResultsA total of 36,921 participants were enrolled with a prevalence of albuminuria of 9.32%. The prevalence of albuminuria increased with the higher WWI tertiles (Tertile 1: 5.31%, Tertile 2: 8.23%, Tertile 3: 15.65%). WWI was positively associated with a higher likelihood of albuminuria (OR = 1.28, 95% CI: 1.15–1.43), and this relationship remains stable in subgroups (all P for trend &gt; 0.05). Non-linear positive relationships were detected in females with a breakpoint of 10.93. A positive association between WWI and albuminuria (OR = 1.39, 95% CI: 1.20–1.61) was observed on the right of the breakpoint, while the association on the left was of no statistical significance. WWI showed a stronger correlation with albuminuria (OR = 1.28) than other markers of obesity including body mass index (BMI, OR = 1.02) and WC (OR = 1.01).ConclusionWeight-adjusted-waist index levels were positively related to an increased likelihood of albuminuria in United States adults and showed a stronger relationship than BMI and WC. Our findings indicated that WWI may serve as a simple anthropometric index to predict albuminuria.
Risk of secondary malignant neoplasms in children following proton therapy vs. photon therapy for primary CNS tumors: A systematic review and meta-analysis
Authors: Upadhyay Rituraj , Yadav Divya , Venkatesulu Bhanu P. , Singh Raj , Baliga Sujith , Raval Raju R. , Lazow Margot A. , Salloum Ralph , Fouladi Maryam , Mardis Elaine R. , Zaorsky Nicholas G. , Trifiletti Daniel M. , Paulino Arnold C. , Palmer Joshua D. 
Published: August 2022

BackgroundCentral nervous system tumors are now the most common primary neoplasms seen in children, and radiation therapy is a key component in management. Secondary malignant neoplasms (SMNs) are rare, but dreaded complications. Proton beam therapy (PBT) can potentially minimize the risk of SMNs compared to conventional photon radiation therapy (RT), and multiple recent studies with mature data have reported the risk of SMNs after PBT. We performed this systematic review and meta-analysis to characterize and compare the incidence of SMNs after proton and photon-based radiation for pediatric CNS tumors.MethodsA systematic search of literature on electronic (PubMed, Cochrane Central, and Embase) databases was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) method. We included studies reporting the incidence and nature of SMNs in pediatric patients with primary CNS tumors. The crude incidence of SMNs and all secondary neoplasms were separately extracted, and the random-effects model was used for pooled analysis and subgroup comparison was performed between studies using photons vs. protons.ResultsTwenty-four studies were included for analysis. A total of 418 SMNs were seen in 38,163 patients. The most common SMN were gliomas (40.6%) followed by meningiomas (38.7%), sarcomas (4.8%), and thyroid cancers (4.2%). The median follow-up was 8.8 years [3.3–23.2].The median latency to SMN for photons and protons were 11.9 years [5-23] and 5.9 years [5-6.7], respectively. The pooled incidence of SMNs was 1.8% (95% CI: 1.1%–2.6%, I2 = 94%) with photons and 1.5% (95% CI: 0%–4.5%, I2 = 81%) with protons. The pooled incidence of all SNs was not different [photons: 3.6% (95% CI: 2.5%–4.8%, I2 = 96%) vs. protons: 1.5% (95% CI: 0–4.5%, I2 = 80%); p = 0.21].ConclusionWe observed similar rates of SMN with PBT at 1.5% compared to 1.8% with photon-based RT for pediatric CNS tumors. We observed a shorter latency to SMN with PBT compared to RT. With increasing use of pencil beam scanning PBT and VMAT, further studies are warranted to evaluate the risk of secondary cancers in patients treated with these newer modalities.
Continuous subcortical language mapping in awake glioma surgery
Authors: Axelson Hans W. , Latini Francesco , Jemstedt Malin , Ryttlefors Mats , Zetterling Maria 
Published: August 2022

Repetitive monopolar short-train stimulation (STS) delivered from a suction probe enables continuous mapping and distance assessment of corticospinal tracts during asleep glioma resection. In this study, we explored this stimulation technique in awake glioma surgery. Fourteen patients with glioma involving language-related tracts were prospectively included. Continuous (3-Hz) cathodal monopolar STS (five pulses, 250 Hz) was delivered via the tip of a suction probe throughout tumor resection while testing language performance. At 70 subcortical locations, surgery was paused to deliver STS in a steady suction probe position. Monopolar STS influence on language performance at different subcortical locations was separated into three groups. Group 1 represented locations where STS did not produce language disturbance. Groups 2 and 3 represented subcortical locations where STS produced language interference at different threshold intensities (≥7.5 and ≤5 mA, respectively). For validation, bipolar Penfield stimulation (PS; 60 Hz for 3 s) was used as a “gold standard” comparison method to detect close proximity to language-related tracts and classified as positive or negative regarding language interference. There was no language interference from STS in 28 locations (Group 1), and PS was negative for all sites. In Group 2 (STS threshold ≥ 7.5 mA; median, 10 mA), there was language interference at 18 locations, and PS (median, 4 mA) was positive in only one location. In Group 3 (STS threshold ≤ 5 mA; median, 5 mA), there was language interference at 24 locations, and positive PS (median 4 mA) was significantly (p &lt; 0.01) more common (15 out of 24 locations) compared with Groups 1 and 2. Despite the continuous stimulation throughout tumor resection, there were no seizures in any of the patients. In five patients, temporary current spread to the facial nerve was observed. We conclude that continuous subcortical STS is feasibly also in awake glioma surgery and that no language interference from STS or interference at ≥7.5 mA seems to indicate safe distance to language tracts as judged by PS comparisons. STS language interference at STS ≤ 5 mA was not consistently confirmed by PS, which needs to be addressed.
Combined SUVmax and localized colonic wall thickening parameters to identify high-risk lesions from incidental focal colorectal 18F-FDG uptake foci
Authors: Xu Wenmin , Li Hansen , Guo Ziqian , Zhang Linqi , Zhang Rusen , Zhang Long 
Published: August 2022

ObjectiveTo evaluate the detection ability of 18F-FDG PET/CT for identifying high-risk lesions (high-risk adenomas and adenocarcinoma) from incidental focal colorectal 18F-FDG uptake foci combining maximum standard uptake value (SUVmax) and localized colonic wall thickening (CWT). The secondary objective was to investigate the factors of missed detection of high-risk adenomas by 18F-FDG PET/CT.Patients and methodsA total of 6394 patients who underwent 18F-FDG PET/CT in our hospital from August 2019 to December 2021 were retrospectively analysed, and 145 patients with incidental focal colorectal 18F-FDG uptake foci were identified. The optimal cut-off value of SUVmax for 18F-FDG PET/CT diagnosis of high-risk lesions was determined by receiver operating characteristic (ROC) curves. SUVmax and localized CWT were combined to identify high-risk lesions from incidental focal colorectal 18F-FDG uptake foci. The characteristics of incidental adenomas detected and high-risk adenomas missed by 18F-FDG PET/CT were compared.ResultsOf the 6394 patients, 145 patients were found to have incidental focal colorectal FDG uptake foci (2.3%), and 44 patients underwent colonoscopy and pathological examination at the same time. In fact, 45 lesions, including 12 low-risk lesions and 33 high-risk lesions (22 high-risk adenomas, 11 adenocarcinoma), were found by colonoscopy. The area under the ROC curve of SUVmax for low-risk lesions and high-risk lesions was 0.737, and the optimal cut-off value was 6.45 (with a sensitivity of 87.9% and specificity of 58.3%). When SUVmax ≥6.45, the combination of localized CWT parameters has little influence on the sensitivity and specificity of detection; when SUVmax &lt;6.45, the combination of localized CWT parameters can improve the specificity of detection of high-risk lesions, but the sensitivity has little change. In addition, the size of high-risk adenomas discovered incidentally by 18F-FDG PET/CT was larger than that of high-risk adenomas missed, but there was no significant difference in lesion location, pathological type or intraepithelial neoplasia between the two groups.ConclusionsThe combination of SUVmax and localized CWT parameters of 18F-FDG PET/CT helped identify high-risk lesions from incidental focal colorectal 18F-FDG uptake foci, especially for lesions with SUVmax &lt;6.45. Lesion size may be the only factor in 18F-FDG PET/CT missing high-risk adenomas.