bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time breath analysis towards a healthy human breath profile
Authors: Sasiene Zachary Joseph , LeBrun Erick Scott , Schaller Eric , Mach Phillip Michael , Taylor Robert , Candelaria Lionel , Glaros Trevor Griffiths , Baca Justin , McBride Ethan Matthew 
Published: January 2024

AbstractThe direct analysis of molecules contained within human breath has had significant implications for clinical and diagnostic applications in recent decades. However, attempts to compare one study to another or to reproduce previous work are hampered by: variability between sampling methodologies, human phenotypic variability, complex interactions between compounds within breath, and confounding signals from comorbidities. Towards this end, we have endeavored to create an averaged healthy human ‘profile’ against which follow-on studies might be compared. Through the use of direct secondary electrospray ionization combined with a high-resolution mass spectrometry and in-house bioinformatics pipeline, we seek to curate an average healthy human profile for breath and use this model to distinguish differences inter- and intra-day for human volunteers. Breath samples were significantly different in PERMANOVA analysis and ANOSIM analysis based on Time of Day, Participant ID, Date of Sample, Sex of Participant, and Age of Participant (p< 0.001). Optimal binning analysis identify strong associations between specific features and variables. These include 227 breath features identified as unique identifiers for 28 of the 31 participants. Four signals were identified to be strongly associated with female participants and one with male participants. A total of 37 signals were identified to be strongly associated with the time-of-day samples were taken. Threshold indicator taxa analysis indicated a shift in significant breath features across the age gradient of participants with peak disruption of breath metabolites occurring at around age 32. Forty-eight features were identified after filtering from which a healthy human breath profile for all participants was created.
Application of NDVI Sentinel-2Ac Imagery for Agricultural Land Development in Food Buffer Area of New Capital City Indonesia
Authors: Ramadhani D. , Susanto S. , Setyawan C. , Khoiruzaki M. , Abdilah M. R. W. 
Published: January 2024

Abstract
Paser Regency is one of the food buffer areas for the New Capital City (IKN) of Indonesia in East Kalimantan Province. The relocation of the capital to IKN increases the number of populations and food demand as well. To meet food needs in IKN in the future, the development of agricultural land is needed. This study aimed to identify the type and direction of land use in Paser Regency to ensure food self-sufficiency. Sentinel-2 satellite Imagery with the Maximum Likelihood Classification (MLC) method was used in this study. The sentinel data from 2018 to 2022 was analyzed to identify the existing land use types over the past five years. The land use direction was determined based on the existing land use type, soil type, and land slope class. The results with an accuracy value for the overall test of 91.68% and kappa accuracy of 0.86 showed a change in land use from 2018 to 2022. Eight types of main land used were identified such as non-swamp rice fields, swamp rice fields, oil palm plantations, moors, shrubs, forests, settlements, and water bodies. The application of NDVI Sentinel-2Ac Imagery can identify a potential area of 13,249.7 hectares for rice field development and can significantly increase rice production to ensure food self-sufficiency in IKN.
Effect of microwave heating on sensory quality assessment of butterfly pea (Clitoria ternatea L.) flower using simple additive weighting
Authors: Juanda  , Hartuti S , Agustina R 
Published: January 2024

Abstract
Drying of butterfly pea flowers is necessary to extend its shelf life and to use it in various functional food products, such as various types of drinks and foods, as well as natural colouring materials. Currently, the use of butterfly pea flowers in functional drinks is growing in various regions, including Indonesia. This research aims to determine butterfly pea flowers’ microwave power and drying time based on sensory analysis using the SAW (simple additive weighting) method. The hedonic test was also conducted to assess the level of preference of panellists for steeping butterfly pea flower tea based on pre-set parameters to obtain the tea preferences. Panellists perform sensory assessments determined based on a numerical scale of 1-7, where value 7 is strongly like, value 6 is like, value 5 is somewhat like, value 4 is neutral, value 3 is somewhat dislike, value 2 is dislike, and value 1 is strongly dislike. The results showed that the level of preference for alternative treatment to sensory quality, consisting of criteria of colour, flavour, taste, and aftertaste, it was known that alternative treatment with rank 1 was obtained at 180 watts microwave power treatment and drying time for 17 minutes.
The Use of EVI Algorithm in Predicting Rice Productivity, Harau District, Lima Puluh Kota Regency, West Sumatra
Authors: Yanti D. , Permata D.A , Safitri I. , Irfan M. , Harahap F.L. 
Published: January 2024

Abstract
Using remote sensing data in predicting rice productivity can provide information quickly and easily for relatively large areas. Harau District is a rice center in Lima Puluh Kota Regency and is one of the many rice-producing areas in West Sumatra Province. This study aims to determine a mathematical model to estimate rice productivity in Harau District, Lima Puluh Kota Regency, using the EVI (Enhanced Vegetation Index) algorithm. This study used two methods, field observation and MODIS image data processing (MOD13A1 v006). The results of the analysis obtained a mathematical model to predict rice productivity in Harau District, namely y = 5393.3x4 - 8140.7x3 + 4518.9x2 - 1121.6x + 113.55 where y is the productivity value (tons/ha) and x as the EVI value. The percentage of errors in observation and estimation data was 15.284%, and the results of the observation and estimation data validation test (NSE) were 0.734, a good category.
Mutagenesis of soybean var. Kipas Putih
Authors: Zuyasna  , Zuraida  , Hayati E. , Marliah A. , Basyah B. , Nura  , Ghufrani Y. , Gunawan  
Published: January 2024

Abstract
The low availability of superior soybean varieties that can adapt to Indonesia’s diverse environment and agroecosystem is the cause of low soybean production. On November 3, 1992, the Kipas Putih variety from Aceh was released as a National variety. This variety is not popular and does not meet the tempe industry criteria because the seed size is relatively small when compared to other superior varieties such as the Dega1, Biosoy, and Grobogan varieties. The Kipas Putih soybean variety weighs 12 g for 100 seeds an average dry weight production capacity of 1.69 tons ha-1, and a protein and fat content of 35% and 20.5%. To improve the quality of the Kipas Putih soybean variety, mutations carried out using gamma ray radiation at Patir Batan, Pasar Minggu – Jakarta. Research results from the mass selection process to the 8th generation (M8) produces several lines that weigh 100 grains between 14 - 18 g and a protein content of between 40 - 48%, which exceeds the characteristics of the Kipas Putih. The seed weight per plant of the M8 Kipas Putih soybean mutant line was higher than that of the Kipas Putih (parent) variety and the Dega1 variety. Most of the qualitative characters of the mutant lines were no different from their parent Kipas Putih variety. Most of the qualitative characters of the mutant lines were no different from their parents the Kipas Putih variety. This shows that mutation using gamma ray radiation can change quantitative characters such as the number of seeds per plant and the weight of 100 seeds.
Application of ultrasound-assisted extraction of anthocyanin from Syzygium cumini Fruit
Authors: Safriani N , Husna N E , Tamamy M M 
Published: January 2024

Abstract
This research investigated the effect of extraction temperature and duration on the total anthocyanin (TA) yield from Syzygium cumini fruit through the application of ultrasound-assisted solvent extraction. The research used a Randomized Block Design with two variables: the extraction temperature, i.e., 30, 40, and 50 °C, and the extraction duration, i.e., 30, 45, and 60 minutes. The finding demonstrated that the temperature of extraction significantly affected the TA and vitamin C levels. Still, they did not affect the antioxidant activity of Syzygium cumini fruit extract. The TA extract rose as the extraction temperature increased, but the vitamin C content decreased. The extraction duration significantly affected the resulting extract’s TA and antioxidant activity. Increasing the extractionduration was in line with the TA and antioxidant activity of Syzygium cumini fruit extract. Considering the TA and antioxidant activity, the best treatment was attained when the extraction process was conducted at 50 °C for 60 minutes, with the characteristics of the Syzygium cumini fruit extract obtained, which had a TA of 176.73 mg/L, vitamin C content of 33.27 mg/100g of material, antioxidant activity of 45.49%. The TA value and antioxidant activity were higher than the maceration method extraction extraction.
Integrated bulk and single-cell transcriptomes reveal pyroptotic signature in prognosis and therapeutic options of hepatocellular carcinoma by combining deep learning
Authors: Liu Yang , Li Hanlin , Zeng Tianyu , Wang Yang , Zhang Hongqi , Wan Ying , Shi Zheng , Cao Renzhi , Tang Hua 
Published: January 2024

AbstractAlthough some pyroptosis-related (PR) prognostic models for cancers have been reported, pyroptosis-based features have not been fully discovered at the single-cell level in hepatocellular carcinoma (HCC). In this study, by deeply integrating single-cell and bulk transcriptome data, we systematically investigated significance of the shared pyroptotic signature at both single-cell and bulk levels in HCC prognosis. Based on the pyroptotic signature, a robust PR risk system was constructed to quantify the prognostic risk of individual patient. To further verify capacity of the pyroptotic signature on predicting patients’ prognosis, an attention mechanism-based deep neural network classification model was constructed. The mechanisms of prognostic difference in the patients with distinct PR risk were dissected on tumor stemness, cancer pathways, transcriptional regulation, immune infiltration and cell communications. A nomogram model combining PR risk with clinicopathologic data was constructed to evaluate the prognosis of individual patients in clinic. The PR risk could also evaluate therapeutic response to neoadjuvant therapies in HCC patients. In conclusion, the constructed PR risk system enables a comprehensive assessment of tumor microenvironment characteristics, accurate prognosis prediction and rational therapeutic options in HCC.
The sialic acid–Siglec immune checkpoint: an opportunity to enhance immune responses and therapy effectiveness in melanoma
Authors: Coccimiglio Magali , Chiodo Fabrizio , van Kooyk Yvette 
Published: January 2024

Abstract
Modulation of immune responses through immune checkpoint blockade has revolutionized cutaneous melanoma treatment. However, it is still the case that not all patients respond successfully to these therapies, indicating the presence of as yet unknown resistance mechanisms. Hence, it is crucial to find novel targets to improve therapy efficacy. One of the described resistance mechanisms is regulated by immune inhibitory Siglec receptors, which are engaged by the carbohydrates sialic acids expressed on tumour cells, contributing to programmed cell death protein-1 (PD1)-like immune suppression mechanisms. In this review, we provide an overview on the regulation of sialic acid synthesis, its expression in melanoma, and the contribution of the sialic acid–Siglec axis to tumour development and immune suppressive mechanisms in the tumour microenvironment. Finally, we highlight potential sialic acid–Siglec axis-related therapeutics to improve the treatment of melanoma.
Prevalence and odds of anxiety and depression in cutaneous malignant melanoma: a proportional meta-analysis and regression
Authors: Kungwengwe Garikai , Gowthorpe Chloe , Ali Stephen R , Warren Harry , Drury Damien J , Ang Ky-Leigh , Gibson John A G , Dobbs Thomas D , Whitaker Iain S 
Published: January 2024

Abstract

Background
The psychological burden of cutaneous malignant melanoma (CM) is all-encompassing, affecting treatment adherence, recurrence and mortality. However, the prevalence and risk factors of anxiety and depression in CM remain unclear.

Objectives
To establish a benchmark pooled prevalence of anxiety and depression in CM, to provide magnitudes of association for clinical, therapeutic and demographic correlates, and to elucidate temporal trends in anxiety and depression from the time of diagnosis.

Methods
This review followed the MOOSE guidelines. MEDLINE, Embase, PsychINFO, Web of Science and the Cochrane Library were queried from database inception to 24 August 2023. Study selection, data extraction and quality assessment were performed by two independent authors, utilizing both the Joanna Briggs Institute (JBI) and National Institutes of Health risk-of-bias tools for the latter. The GRADE approach was used to rate the certainty of evidence. Prevalence rates, 95% confidence intervals (CIs) and prediction intervals (PIs) were derived using a random-effects model and estimating between- and within-study variance.

Results
Nine longitudinal and 29 cross-sectional studies were included (7995 patients). Based on the JBI and NIH tools, respectively, quality assessment found 20 and 17 to be at low risk of bias, 12 and 15 to be at moderate risk and 6 and 5 to be at high risk of bias. The prevalence of anxiety [30.6% (95% CI 24.6–37.0; PI 18–47%)] and depression [18.4% (95% CI 13.4–23.9; PI 10–33%)] peaked during treatment, declining to pretreatment levels after 1 year [anxiety: 48% vs. 20% (P = 0.005); depression: 28% vs. 13% (P = 0.03)]. Female sex [odds ratio (OR) 1.8, 95% CI 1.4–2.3; P &lt; 0.001], age &lt; 60 years (OR 1.5, 95% CI 1.2–2.0; P = 0.002) and low educational level (OR 1.5, 95% CI 1.2–2.0; P &lt; 0.001) were likely to result in a large increase in the odds of anxiety. Depression was 12.3% higher in those with stage IV vs. those with stage I CM (P = 0.05). Relative to immune checkpoint inhibition, the rates of depression were 22% (P = 0.002) and 34% (P &lt; 0.001) higher among patients with advanced-stage CM receiving interferon-α and chemotherapy, respectively. A significant reduction in self-reported depression scores was demonstrated over time (P = 0.003).

Conclusions
Notably, anxiety and depression in CM affect women, those younger than 60 years of age and the less educated, with up to 80% higher odds of anxiety in these groups. Anxiety and depression surge during chemotherapy and interferon treatment, especially in advanced CM. Our findings facilitate risk stratification and underscore the need for multidisciplinary vigilance.
Investigation of clear cell renal cell carcinoma grades using diffusion-relaxation correlation spectroscopic imaging with optimized spatial-spectrum analysis
Authors: Luo Yuansheng , Zhu Mengying , Wei Xiaobin , Xu Jianrong , Pan Shihang , Liu Guiqin , Song Yang , Hu Wentao , Dai Yongming , Wu Guangyu 
Published: January 2024

Abstract

Objectives
To differentiate high-grade from low-grade clear cell renal cell carcinoma (ccRCC) using diffusion-relaxation correlation spectroscopic imaging (DR-CSI) spectra in an equal separating analysis.

Methods
Eighty patients with 86 pathologically confirmed ccRCCs who underwent DR-CSI were enrolled. Two radiologists delineated the region of interest. The spectrum was derived based on DR-CSI and was further segmented into multiple equal subregions from 2*2 to 9*9. The agreement between the 2 radiologists was assessed by the intraclass correlation coefficient (ICC). Logistic regression was used to establish the regression model for differentiation, and 5-fold cross-validation was used to evaluate its accuracy. McNemar’s test was used to compare the diagnostic performance between equipartition models and the traditional parameters, including the apparent diffusion coefficient (ADC) and T2 value.

Results
The inter-reader agreement decreased as the divisions in the equipartition model increased (overall ICC ranged from 0.859 to 0.920). The accuracy increased from the 2*2 to 9*9 equipartition model (0.68 for 2*2, 0.69 for 3*3 and 4*4, 0.70 for 5*5, 0.71 for 6*6, 0.78 for 7*7, and 0.75 for 8*8 and 9*9). The equipartition models with divisions &gt;7*7 were significantly better than ADC and T2 (vs ADC: P = .002-.008; vs T2: P = .001-.004).

Conclusions
The equipartition method has the potential to analyse the DR-CSI spectrum and discriminate between low-grade and high-grade ccRCC.

Advances in knowledge
The evaluation of DR-CSI relies on prior knowledge, and how to assess the spectrum derived from DR-CSI without prior knowledge has not been well studied.
Sclerotherapy with intralesional bleomycin injection under guidance of multi-slice CT for retrobulbar orbital low-flow vascular lesions—single-center experience
Authors: Lin Shin-Nan , Wu Yi-Ming , Siow Tiing-Yee , Yeh Chih-Hua , Toh Cheng-Hong , Tseng Ti-Yung , Wong Ho-Fai 
Published: January 2024

Abstract

Objective
This study investigated the safety and efficacy of sclerotherapy with intralesional bleomycin injection (IBI) for retrobulbar orbital low-flow vascular lesions under multi-slice computed tomography (CT) guidance.

Methods
Between January 2010 and September 2021, consecutive patients with retrobulbar orbital low-flow vascular lesions who underwent CT-guided IBI at a tertiary centre in Taiwan were enrolled. Their medical records and imaging data were retrospectively collected.

Results
This study enrolled 13 patients (7 male and 6 female patients; age range: 1-57 years; mean age: 25.9 years) with lymphatic malformation (LM, n = 4), venolymphatic malformation (n = 1), and venous malformation (VM, n = 8). The overall radiological response rate was 76.9% (10 of 13); the radiological response rate was 75.0% in the VM group (6 of 8) and 75.0% in the LM group (3 of 4). Moreover, 3 patients (23.1%) had minor complications and 1 (7.7%) had a major complication. The mean clinical and radiological follow-up was 8.3 months and no recurrence or progression was reported.

Conclusion
CT-guided IBI is an effective and relatively safe minimally invasive treatment for retrobulbar orbital low-flow vascular lesions, with an overall radiological response rate of 76.9% in a mean of 1.5 sessions and a low complication rate.

Advances in knowledge
CT-guided sclerotherapy with IBI is a relatively safe, effective, and feasible alternative treatment option for retrobulbar orbital low-flow vascular lesions.
Role of non-contrast CT component of prostate-specific membrane antigen PET/CT scan in the detection of peripheral zone prostate cancer
Authors: Aggarwal Piyush , Krishna Kumar R G , Das Chandan J , Kubihal Vijay , Subudhi T Kishan , Khan M A , Kumar Rakesh 
Published: January 2024

Abstract

Objective
The aim of this study was to look for feasibility of non-contrast CT (NCCT) in detecting peripheral zone prostate cancer (PCa).

Methods
A retrospective analysis included 50 biopsy-proven PCa patients between April 2019 and March 2022 who underwent staging whole body prostate-specific membrane antigen (PSMA)/CT prior to treatment. The control subjects were 50 randomly selected adult male patients who underwent PET/CT for non-prostate malignancy during the same time period. Two readers independently calculated the Hounsfield unit (HU) of normal peripheral zone, central zone, and corresponding PSMA avid focus in cases.

Results
No significant difference was seen in the mean HU value of normal peripheral zone between cases and controls. Significant difference in the mean HU was seen between the PSMA avid focus in cases (40.1 ± 6.2) and normal peripheral zone of cases (28.2 ± 7.0) and controls (27.7 ± 5.8). No significant difference was found between the mean HU values of high-grade PCa and non-high-grade PCa. Receiver operating characteristic (ROC) curve analysis revealed a mean HU cut-off of ≥35 for detecting PCa with a sensitivity and specificity of 86% and 90%, respectively, between cases and controls (AUC 0.88).

Conclusion
Detection of clinically significant PCa is possible on routinely performed NCCT scans. Radiologists should routinely look for and convey these findings to facilitate further work-up and early detection of PCa.

Advances in knowledge
Our study adds to the knowledge that NCCT scans performed for unrelated indications can serve as a screening tool for clinically significant PCa.
Elevated splenic 18F-fluorodeoxyglucose positron emission tomography/computed tomography activity is associated with 5-year risk of recurrence in non-metastatic invasive ductal carcinoma of the breast
Authors: Wang Yiting , Li Yuchao , Jiang Hongyuan , Zuo Changjing , Xu Wengui 
Published: January 2024

Abstract

Objective
To construct prediction models including baseline 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) metabolic parameters of tumoural lesions and non-tumour lymphoid tissue for recurrence-free survival within 5 years (5y-RFS) after imaging examination in patients with invasive ductal carcinomas (IDCs) of the breast.

Methods
The study included 101 consecutive female patients. Univariable and multivariable Cox regression were used to identify clinicopathological and metabolic parameters associated with risk of recurrence. Four prediction models based on the results of multivariable analysis were constructed and visualized as nomograms. Performance of each nomogram was evaluated using the concordance index (C-index), integrated discrimination improvement, decision curve analysis (DCA), and calibration curve.

Results
N3 status, total metabolic tumour volume, the maximum standardized uptake value of spleen, and spleen-to-liver ratio were significant predictors of 5y-RFS. The nomogram including all significant predictors demonstrated superior predictive performance for 5y-RFS, with a C-index of 0.907 (95% CI, 0.833-0.981), greatest net benefit on DCA, good accuracy on calibration curves, and excellent risk stratification on Kaplan-Meier curves.

Conclusions
The model that included metabolic parameters of the spleen had the best performance for predicting 5y-RFS in patients with IDCs of the breast. This model may guide personalized treatment decisions and inform patients and clinicians about prognosis.

Advances in knowledge
This research identifies 18F-FDG PET/CT metabolic parameters of non-tumour lymphoid tissue as predictors of recurrence in breast cancer.
Deep learning for automated segmentation in radiotherapy: a narrative review
Authors: Bibault Jean-Emmanuel , Giraud Paul 
Published: January 2024

Abstract
The segmentation of organs and structures is a critical component of radiation therapy planning, with manual segmentation being a laborious and time-consuming task. Interobserver variability can also impact the outcomes of radiation therapy. Deep neural networks have recently gained attention for their ability to automate segmentation tasks, with convolutional neural networks (CNNs) being a popular approach. This article provides a descriptive review of the literature on deep learning (DL) techniques for segmentation in radiation therapy planning. This review focuses on five clinical sub-sites and finds that U-net is the most commonly used CNN architecture. The studies using DL for image segmentation were included in brain, head and neck, lung, abdominal, and pelvic cancers. The majority of DL segmentation articles in radiation therapy planning have concentrated on normal tissue structures. N-fold cross-validation was commonly employed, without external validation. This research area is expanding quickly, and standardization of metrics and independent validation are critical to benchmarking and comparing proposed methods.