bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fusion data of digital olfation devises for the evaluation of the quality of fresh coffee beans
Authors: Cascos Gema , Lozano Jesús , Arroyo Patricia , Ruiz-Canales Antonio , Oates Martin John , Martín-Vertedor Daniel 
Published: January 2023

Abstract
The aim of this work is to discriminate the volatile organic compounds (VOCs) that are characteristic of different qualities of fresh coffee beans, with two electronic devises that allows one to classify the fresh product. Coffea arabica at red stage of ripeness were harvested in the Choluteca region (Honduras). Sensory analysis classification, volatile compound profile and electronic nose analysis were done. Samples were classiffied as high, medium and low-quality coffee. The tasting panel could discriminate samples based on their pleasant or unpleasant attributes. The high-quality coffee presented the highest values of the positive attributes with the highest scores in the fruity, herbal and sweet attribute. Low-quality samples showed negative attributes related to roasted, smokey and abnormal fermentation. Alcohols and aromatic compounds were highest in high-quality samples, while carboxylic acids, pyrazines and pyridines in low-quality ones. The VOC with positive attribute were phenylethyl alcohol, nonanal and 2-methyl-propanoic acid, octyl ester, while the compounds with negative attribute were pyridine, octanoic acid and dimethyl sulfide. The aroma of fresh coffee beans qualities were also discriminated by the E-nose instruments. PLS-DA model obtained from the E-nose data was able to classify the different qualities of fresh coffee beans and explained 96.9% of the total variance. A PLS chemometric approach was assed for quantifying the fruity aroma of the fresh coffee beans, obtaining an RP2 of 0.88. Thus, the E-nose is concluded to be an acurate, inexpensive and non-destrutive device for discriminating between different coffee qualities during the processing.
Model Selection for Deep Learning with Gradient Norms: An Empirical Study
Authors: Xiong Haoyi , An Haozhe , Li Xuhong , Li Xingjian , Zhu Zhanxing , Ma Yingying , Sun Zeyi 
Published: January 2023

Abstract
Recent theoretical works [1–3] propose to exploit the loss gradient norm averaged across training samples as a measure of overfitting and generalization performance of DNNs, to investigate the upper bound of generalization error of deep neural networks (DNNs). However, the extremely high computational cost makes such gradient norms infeasible to obtain in practice. In this work, we carry out empirical studies by proposing a formulated mean empirical gradient norms (MEGAN), where we use a fast implementation of Fully-Connected (FC) Layer gradient norms [4] to compute MEGAN. Our empirical studies find that the sum of MEGAN over the optimization path of deep learning (i.e. epochs) could accurately predict the generalization performance of DNNs. Our empirical studies also include extensive experiments to demonstrate the potential of MEGAN for model selection of DNNs in hyper-parameter search settings. Our in-depth analyses interpret the behavior of MEGAN during training epochs and confirm MEGAN as an efficient and effective way to measuring the generalization performance of DNN with the training set only.
PhyloBench: a Benchmark for Evaluating Phylogenetic Programs
Authors: Spirin Sergey , Sigorskikh Andrey , Efremov Aleksei , Penzar Dmitry , Karyagina Anna 
Published: January 2023

Abstract

Motivation. Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options.Choosing a program, options, and parameters can be a nontrivial task.No benchmark for comparison of phylogenetic programs on real protein sequences is publicly available.
Results. We have developed PhyloBench, a benchmark for evaluating the quality of phylogenetic inference, and used it to test a number of popular phylogenetic programs. PhyloBench is based on natural, not simulated, protein sequences of orthologous evolutionary domains. The measure of accuracy of an inferred tree is its distance to the corresponding species tree. A number of tree-to-tree distance measures were tested. The most reliable results were obtained using the Robinson–Foulds distance. Our results confirmed recent findings that distance methods are more accurate than maximum likelihood and maximum parsimony. We tested the bayesian program MrBayes on natural protein sequences and found that it is superior to maximum likelihood, but inferior to distance methods. Of the methods we tested, the Balanced Minimum Evolution method implemented in FastME yielded the best results.
Availability. Benchmark alignments and reference trees are available at https://mouse.belozersky.msu.ru/tools/phylobench/ together with a web-interface that allows for a semi-automatic comparison of a user's method with a number of popular programs.
Clinical Application of the Global Leadership Initiative on Malnutrition Using a Combination of Different Muscle Mass Indices in Patients with Gastric Cancer: A Multicenter, Cross-Sectional, Observational Cohort Study
Authors: Zheng Jingxian , Wang Xiaojie , Yu Jiami , Hu Qiaoting , Zhan Zhouwei , Zhou Sijing , Xu Jingjie , Li Qifei , Wang Chang , Zhao Qingchuan , Xu Hongxia , Shi Hanping , Guo Zengqing 
Published: January 2023

Abstract
Background: Malnutrition is associated with poor prognosis and prevalent in gastric cancer patients. However, there is no standardized method for evaluating malnutrition; the Global Leadership Initiative on Malnutrition (GLIM) aimed to establish a standard criteria for evaluating malnutrition. However, the cutoff point for muscle reduction remains unclear, and its clinical value has not yet been verified. Hence, we aimed to examine the relationship between combinations of different muscle measurement indices and the survival of gastric cancer patients to determine the accurate method for diagnosing sarcopenia, establish the standard GLIM criteria, and explore its clinical value.
Methods: This multicenter and observational cohort study included 1,406 gastric cancer patients. The accurate prediction combination was determined using the cutoff point for muscle loss by predicting the survival risk according to the GLIM criteria established using a combination of muscle mass indicators. Least absolute shrinkage and selection operator regression analysis was used to screen the independent risk factors for survival with the construction of a Cox regression model. The R software was used to establish the nomogram of individual survival prediction and to verify the clinical significance of malnutrition diagnosed based on the GLIM criteria.
Results: The risk ratio of patients with malnutrition based on the leg circumference and weight-corrected grip strength was the highest (hazard ratio [HR]=2.159, 95% confidence interval [CI]=1.800, 2.588 in severely malnourished patients). Malnutrition occurred in 54.5% of patients diagnosed with gastric cancer based on the GLIM criteria. Malnutrition is an independent risk factor for unfavorable survival in gastric cancer patients; its nomogram model can accurately predict the survival of gastric cancer.
Conclusion: Muscle loss is one of the components of the GLIM criteria and is determined by measuring the leg circumference and weight-corrected grip strength. The GLIM criteria are effective in diagnosing malnutrition and predicting the survival in gastric cancer patients.
Differences in molecular characteristics and overall survival between incidental and symptomatic lower grade gliomas
Authors: Demetz Matthias , Krigers Aleksandrs , Moser Patrizia , Kerschbaumer Johannes , Thomé Claudius , Freyschlag Christian F. 
Published: January 2023

Abstract
Purpose:
Data on differences in overall survival and molecular characteristics between incidental (iLGG) and symptomatic lower grade Glioma (sLGG) are limited. The aim of this study was to investigate differences between patients with iLGG and sLGG.
Methods:
All adult patients with a histologically proven diffuse (WHO°II) or anaplastic (WHO°III) glioma who underwent their first surgery at the authors’ institution between 2010 and 2019 were retrospectively included. Tumor volume on pre- and postoperative MRI scans was determined. Clinical and routine neuropathological data were gained from patients’ charts.
Results:
Out of 161 patients included, 23 (14%) were diagnosed as incidental findings. Main reasons for obtaining MRI were: headache(n=12), trauma(n=2), MRI indicated by other departments(n=7), staging examination for cancer(n=1), volunteering for MRI sequence testing(n=1).
The asymptomatic patients were significantly younger with a median age of 38 years (IqR28-48) vs. 50 years (IqR38-61), p=0.011. Incidental LGG showed significantly lower preoperative tumor volumes in T1 CE (p=0.008), FLAIR (p=0.038) and DWI (p=0.028).
Incidental LGG demonstrated significantly lower anaplasia levels (p=0.004) and lower expression of MIB-1 (p=0.008) compared to sLGG. IDH1-mutation was significantly more common in iLGG (p=0.024).
Incidental LGG showed a significantly longer OS (mean 212 vs 70 months, p=0.005) and PFS (mean 201 vs 61 months, p=0.001) compared to sLGG.
Conclusion:
Our study is the first to depict a significant difference in molecular characteristics between iLGG and sLGG. The findings of this study confirmed and extended the results of previous studies showing a better outcome and more favorable radiological, volumetric and neuropathological features of iLGG.
Compressive and Tensile Strength Anisotropy of Friable Sandstone and Thin-bed Shale of the Pleistocene Erin Formation – Insights for safe operating mud weight windows for vertical and horizontal wells
Authors: Harrypersad-Daniel A. M. , Blake O. O. , Ramsook R. 
Published: January 2023

Abstract
The compressive and tensile strengths are essential parameters used for determining the safe mud weight window (SMWW) during borehole drilling, especially in friable rocks where the SMWW tends to be narrow and therefore, the margin for wellbore instability issues is high. However, these parameters are seldomly reported for friable rocks due to the difficulties and challenges faced while recovering and preparing friable cores and outcrop samples for strength testing. This study evaluates the compressive and tensile strengths of friable rocks under dry and saturated conditions, and investigates how strength anisotropy affect the SMWW. Unconfined compressive strength, confined compressive strength (up to 130 MPa effective pressure), and Brazilian (tensile strength) measurements were made perpendicular and parallel to the outcrop bedding of the friable sandstone and thin-bed shale lithofacies of the Erin Formation, Southern Trinidad. In spite of this Formation being one of the main petroleum reservoirs, there are no published data on the rock strength. The results show that strength anisotropy exist, which is larger under saturated conditions. Under confinement, the friable rocks accumulated large strain (an average of 20% strain) and experienced significant strain hardening causing the strength to be high. The ratio of the yield strength to failure strength is less than 0.2, under dry conditions. Thin section analysis of tested specimens shows intragranular fracturing across quartz grains, which led to grain crushing and pore collapse. Catalastic flow within the specimens and no stress drop after the peak stress suggest the friable rocks failed in a ductile manner. The effect of the strength anisotropy on the SMWW for the sandstone and thin-bed shale was determined for wells that are orientated in the principal stress directions (Sv, Shnmi and SHmax), of a normal faulting stress regime, at depths of 3400 to 6900 ft. The upper mud weight limit of the SMWW is not influenced by the tensile strength anisotropy. However, the lower mud weight of the SMWW was influenced by the compressive strength anisotropy, predominantly for Sv and Shnmi aligned wells that are penetrating through the saturated friable sandstone. Since the rocks are friable, drilling outside of the SMWW by 5% to 8%, if forecasted using the strongest compressive strength, can result in wellbore instability.
An intelligent radiation frost forecasting and warning system for agricultural environments
Authors: Bagheri Nikrooz , bagheri meisam , Sepahvand Movahed 
Published: January 2023

Abstract
Every year, radiation frost causes the loss of a large number of agricultural products. Currently, there is numerous equipment to protect plants against frost. Turning on the equipment late causes inefficiency in raising the air temperature in time, and turning them on early increases energy consumption and costs. Therefore, accurately forecasting frost is very important for turning on the equipment in time. Therefore, in this research, an intelligent radiation frost forecasting and warning system was designed and constructed. This system is composed of a wireless sensor, computing and intelligent forecasting based on deep learning methods and warning announcements to the farmer by the SMS. Intelligent forecasting is based on forecasting dew point temperature for the next three hours according to the in-situ measurement of temperature and relative humidity of the air. The meteorological data of the studied regain from 2011–2021 were used to train the network. The Performance evaluation of the IFFS was carried out. Based on the obtained results, the system accuracy in measuring temperature and relative humidity of the air was 99% and 98%, respectively. The F-score of the IFFS obtained 96%, and the system accuracy in the announcement of the warning obtained 100%. Due to the high accuracy of the IFFS for forecasting radiation frost, the application of this system is recommended for better protection of plants.
Effect of argon to oxygen ratio on the properties of tungsten oxide films prepared by DC magnetron sputtering
Authors: 史 泽 , Li Yuechan , Xie An , Sun Dongya 
Published: January 2023

Abstract
In this paper, tungsten oxide films were deposited on ITO-coated glass by DC magnetron sputtering at different argon to oxygen ratio (30:10, 40:10, 50:10, 60:10, 70:10, 80:10). The microstructure was analyzed by means of XRD and SEM. The electro-chromic properties were analyzed by UV-Vis and electrochemical workstation. The results show that the electrochromic properties of tungsten oxide films can be con-trolled by changing the ratio of argon to oxygen. When the ratio of argon to oxygen is 50:10, the electrochromic property is the best. The optical modulation amplitude of the films prepared under this process reached 56.92%, the response time from the colored state to the bleached state was the shortest (tc=5.8s, tb=3.4s), and there was a maximum coloring efficiency (CE=52.5 cm2/C). After 600 cycles, the attenuation degree of cyclic voltammetry curve is the smallest, indicating that its cyclic stability effect is the best. This work offers an important reference value for the development of high-performance electrochromic films via magnetron sputtering engineering techniques.
Metabolomic analysis for the unique profile and novel biomarkers of neuropsychiatric systemic lupus erythematosus
Authors: Li Xue , Guo Yixue , Lu Huaqing , Pei Wenwen , Wang Yifan , He Jing , Sun Xiaolin 
Published: January 2023

Abstract
Background: Neuropsychiatric systemic lupus erythematosus (NPSLE) is a common manifestation of systemic lupus erythematosus (SLE), with high mortality and disability rate. The lack of effective diagnostic methods, such as biomarkers, makes it difficult to diagnose and treat NPSLE. Metabolomics studies in autoimmune diseases shed new light on the identification of biomarkers beyond autoantibodies and cytokine profiling. This research aimed to explore the unique metabolomic profile, and discover novel molecular biomarkers and pathways for NPSLE.
Methods: Cerebrospinal fluid samples from 26 NPSLE patients, 9 SLE controls, 7 connective tissue disease (CTD) controls and 9 nervous system disorder (NSD) controls were analysed to identify metabolomic signatures, significant pathways and biomarkers in the discovery cohort, using ultra performance liquid chromatography–tandem mass spectrometry (UPLC–MS). Next, the potential biomarkers were verified in an independent validation cohort including 22 NPSLE patients, 11 SLE controls and 4 NSD controls.
Results: The metabolite profiles of cerebrospinal fluid (CSF) samples allowed significant differentiation of NPSLE patients from other disease controls. β-alanine metabolism and inositol phosphate metabolism pathways were significantly perturbed in NPSLE group. In the discovery cohort, 44 CSF metabolites with variable importance in projection (VIP) scores >1.5 and p < 0.05 were considered as the most differential metabolic biomarkers, including β-alanine amino acid and inositol. The diagnostic value of inositol was verified in the validation cohort, with the greatest specificity of 95.45% and the sensitivity of 60.00% for NPSLE. The CSF inositol level was higher in NPSLE patients with neuropsychiatric damage, cranial neuropathy and cerebrovascular disease.
Conclusion: CSF metabolomic profile of NPSLE patients is unique from other disease controls. The pathway perturbations are involved in β-alanine metabolism and inositol phosphate metabolism. Inositol is a promising biomarker for the diagnosis and neuropsychiatric damage evaluation of NPSLE, and has potential relationships with specific NPSLE manifestations.
Validate your white matter tractography algorithms with a reappraised ISMRM 2015 Tractography Challenge scoring system
Authors: Renauld Emmanuelle , Théberge Antoine , Petit Laurent , Houde Jean-Christophe , Descoteaux Maxime 
Published: January 2023

Abstract
Since 2015, research groups seek to produce the nec-plus-ultra tractography algorithms using the ISMRM 2015 Tractography Challenge as evaluation. In particular, since 2017, machine learning has made its entrance into the tractography world. The ISMRM 2015 Tractography Challenge is the most used phantom during tractography validation, although it contains limitations. We offer, here, a new Tractometer scoring system for this phantom, where segmentation of the bundles is now based on manually-defined regions of interest rather than on bundle recognition. Bundles are now more reliably segmented, offering more stable metrics with higher precision for future users. New code is available online. Scores of the initial 96 submissions to the challenge are updated. Overall, conclusions from the 2015 challenge are confirmed with the new scoring, but individual tractograms scores have changed, and the data is much improved at the bundle- and streamline-level. This work also led to the production of a ground truth tractogram with less noisy streamlines and an example of processed data, all available on the Tractometer website. This enhanced Tractometer scoring system and new data should continue to help researchers develop and evaluate the next generation of tractography techniques.
Utility of monocyte distribution width for diagnosing colonic diverticulitis in the emergency department: a retrospective cohort study
Authors: Chang Chang-Yuan , Hsu Tai-Yi , He Guan-Yi , Shih Hong-Mo , Wu Shih-Hao , Huang Fen-Wei , Chen Pei-Chun , Tsai Wen-Chen 
Published: January 2023

Abstract
Background
Colonic diverticulitis is a leading cause of abdominal pain. The monocyte distribution width (MDW) is a novel inflammatory biomarker with prognostic significance for coronavirus disease and pancreatitis; however, no study has assessed its correlation with the severity of colonic diverticulitis.
Methods
This single-center retrospective cohort study included patients older than 18 years who presented to the emergency department between November 1, 2020, and May 31, 2021, and received a diagnosis of acute colonic diverticulitis after abdominal computed tomography. The characteristics and laboratory parameters of patients with simple versus complicated diverticulitis were compared. The significance of categorical data was assessed using the chi-square or Fisher’s exact test. The Mann–Whitney U test was used for continuous variables. Multivariate regression analysis was performed to identify predictors of complicated colonic diverticulitis. Receiver operator characteristic (ROC) curves were used to test the efficacy of inflammatory biomarkers in distinguishing simple from complicated cases.
Results
Of the 160 patients enrolled, 21 (13.125%) had complicated diverticulitis. Although right-sided was more prevalent than left-sided colonic diverticulitis (70% versus 30%), complicated diverticulitis was more common in those with left-sided colonic diverticulitis (61.905%, p = 0.001). Age, white blood cell (WBC) count, neutrophil count, C-reactive protein (CRP) level, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and MDW were significantly higher in the complicated diverticulitis group (p < 0.05). Logistic regression analysis indicated that the left-sided location and the MDW were significant and independent predictors of complicated diverticulitis. The area under the ROC curve (AUC) was as follows: MDW, 0.870 (95% confidence interval [CI], 0.784–0.956); CRP, 0.800 (95% CI, 0.707–0.892); NLR, 0.724 (95% CI, 0.616–0.832); PLR, 0.662 (95% CI, 0.525–0.798); and WBC, 0.679 (95% CI, 0.563–0.795). The MDW had the largest AUC for diagnosing complicated diverticulitis; when the MDW cutoff was 20.38, the sensitivity and specificity were maximized to 90.5% and 80.6%, respectively.
Conclusions
Patients with complicated diverticulitis were significantly older and predominantly had left-sided colonic diverticulitis. A large MDW was a significant and independent predictor of complicated diverticulitis. The MDW may aid in planning antibiotic therapy for patients with colonic diverticulitis in the emergency department.
Surface Water Quality Trends in the Tarkwa Mining Area: 1993 – 2013
Authors: Seshie Vivian Isabella , Kuma Jerry Samuel Yao , Lasidzi Nikao Adziman 
Published: January 2023

Abstract
Tarkwa is characterised by a tropical and humid climate, as well as Birimian quartzites, sandstones, schists, phyllites, and conglomerates. The mining area is located in the Ankobra River Basin, bounded to the west, north, and south by the Ankobra, Huni, and Bonsa Rivers. Huni and Bonsa tributaries include Ahumabru, Teberebie, Bediabewu, Achofe, Awonabeng, Abekoase, Esumang, and Subri. This study presents 1993, 2002 and 2013 data. From 1993–2013, pH, conductivity, TDS, Alk, Ca, Mg, Na, K, Cl, SO₄², NO₃, Fe, Cu, Hg, Pb, Cr, Al, and Mn were studied. This paper compares early 1990s baseline data from Ghana Australian Gold (GAG), now AngloGold Ashanti Iduapriem Limited (AAIL), and Gold Fields Ghana Limited (GF), to recent data from the Tarkwa Nsuaem Municipality (TNM) mining area. Descriptive statistics and paired t-tests were used to calculate K-values and 20-year trends. For 20 years, pH, TDS, Cl, Mg, Na, SO₄², and NO₃ did not change significantly; Cu, Pb, and Conductivity did. Between 1993 and 2002, Fe, Ca, K, Alkalinity, and Mn increased, but not between 2002 and 2013. From 1993–2013, the pH, Cond, TDS, Cl, SO₄², NO₃, Ca, Al, Na, Fe, Cu, and Pb were all lower than the EPA's maximum mine effluent discharge limit.