bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning a confidence score and the latent space of a new Supervised Autoencoder for diagnosis and prognosis in clinical metabolomic studies
Authors: Barlaud Michel , Chardin David , Gille Cyprien , Pourcher Thierry 
Published: March 2022

Abstract
Background: Presently, there is a wide variety of classification methods and deep neural networks approaches in bioinformatics. Deep neural networks have proven their effectiveness for classification tasks, and have outperformed classical methods, but they suffer from a lack of interpretability. Therefore, these innovative methods are not appropriate for decision support systems in healthcare. The algorithm should provide the main pieces of information allowing computed diagnosis and prognosis for the final decision by the clinician. To address this lack of interpretability, we used a new supervised autoencoder (SAE). The main advantage of our supervised autoencoder is its ability to provide a diagnosis with a confidence score for each patient thanks to a softmax classifier, and a meaningful latent space visualization. This confidence score and visual evaluation are crucial for clinical interpretability. Moreover, we used a new efficient feature selection method with a structured constraint for biologically interpretable results. Experimental results on three metabolomics datasets of clinical samples illustrate the effectiveness of our confidence score diagnostic method: Results: The supervised autoencoder provides an accurate localization of the patients in the latent space, and an efficient confidence score. Experiments show that the SAE outperforms classical methods (PLS-DA, Random Forests, SVM, and neural networks (NN)). Furthermore, the metabolites selected by the SAE were found to be relevant. Conclusion: In this paper, we have proposed a new efficient method for diagnosis or prognosis support using clinical metabolomics analyses.
Comparative Investigation on the Effect of Fiber Additives with Different Characteristics on the Mechanical Strength of Heat-cured PMMA Denture Base Resins
Authors: Yerliyurt Kaan , Taşdelen Taha B. , Eğri Özlem , Eğri Sinan 
Published: March 2022

Abstract
Background:
To determine and compare effects on mechanical properties using glass, polypropylene and carbon fibers with 3, 6- and 12-mm lengths, and 0.25, 0.50 and 1.0% concentrations (v/v) as reinforcement of PMMA denture base resins.
Methods:
In order to enhance mechanical properties glass fibers, polypropylene fibers and carbon fibers with 3, 6 and 12mm lengths were added to the resin in different fiber volume to resin volume ratios (0.25, 0.50 and 1.0% v/v). Mechanical properties (flexural strength, modulus of elasticity and ultimate tensile strength) were comparatively investigated using three-way ANOVA tests on the results of three point bending and tensile tests. Morphologies of the fracture surfaces were analyzed using scanning electron microscopy.
Results:
All three fibers exhibited reinforcement in flexural strength (P < 0.05) regardless of their length (P > 0.05) but concentration had significant effect. Denture base resin reinforced by glass fibers or carbon fibers exhibited increase in modulus of elasticity, using polypropylene fibers for reinforcement decreased the modulus of elasticity. Carbon fiber reinforced resin at 0.25% concentrations showed greater ultimate tensile values.
Conclusions:
Reinforcement with glass fibers, polypropylene fibers and carbon fibers resulted with enhanced mechanical properties. Fiber type and fiber concentration had significant effect on both flexural and tensile properties, while fiber length did not exhibit significance on mechanical properties.
A New Dual-peak Fluorescent Probe for Water Content Detection Made from Taxus
Authors: Wang Gang , Wang Gang , Li Yaping , Chen Haipeng , Tang Shuqin , Cheng Yiyang , Yu Yuhong , Abdul Qayoom Majeedano , Pu Shangrao 
Published: March 2022

Abstract
In this paper, the leaves of Taxus were used as the sole carbon source, and two kinds of carbon dots blue and red, with different properties, were synthesized by hydrothermal method under different conditions. The red carbon dots were quenched in water, and the blue carbon dots had stable fluorescence properties in water environment. The bimodal fluorescence probe formed by mixing, could accurately and stably measure the water content in ethanol, which was the range of 82.5%-100%, is highly correlated with the fluorescence intensity ratio (I481/I678) of mixed carbon dots under 390 nm excitation light, with R2 = 0.995 and the detection limit as low as 0.31%. The experimental materials are environmentally friendly, low in cost, simple to operate, and the water content measured by proportional fluorescence has high accuracy, which is provides a new method for measuring moisture in ethanol.
Predictive model for the preoperative assessment and prognostic modeling of lymph node metastasis in endometrial cancer
Authors: Asami Yuka , Hiranuma Kengo , Takayanagi Daisuke , Matsuda Maiko , Shimada Yoko , Kato Mayumi Kobayashi , Kuno Ikumi , Murakami Naoya , Komatsu Masaaki , Hamamoto Ryuji , Kohno Takashi , Sekizawa Akihiko , Matsumoto Koji , Kato Tomoyasu , Yoshida Hiroshi , Shiraishi Kouya 
Published: March 2022

Abstract
Lymph node metastasis (LNM) is a well-established prognostic factor in endometrial cancer (EC). We aimed to construct a model that predicts LNM and prognosis using preoperative factors such as myometrial invasion (MI), enlarged lymph nodes (LNs), histological grade determined by endometrial biopsy, and serum cancer antigen 125 (CA125) level using two independent cohorts consisting of 254 EC patients. The area under the receiver operating characteristic curve (AUC) of the constructed model was 0.80 regardless of the machine learning techniques. Enlarged LNs and higher serum CA125 levels were more significant in patients with low-grade EC (LGEC) and LNM than patients without LNM, whereas deep MI and higher CA125 levels were more significant in patients with high-grade EC (HGEC) and LNM than patients without LNM. The predictive performance of LNM in the HGEC group was higher than that in the LGEC group (AUC = 0.84 and 0.75, respectively). Patients in the group without postoperative pathological LNM and positive LNM prediction had significantly worse relapse-free and overall survival than patients with negative LNM prediction (log-rank test, P < 0.01). This study showed that preoperative clinicopathological factors can predict LNM with high precision and detect patients with poor prognosis. Furthermore, clinicopathological factors associated with LNM were different between HGEC and LGEC patients.
WITHDRAWN: Salvianolic acid B alleviates the injury of HK-2 cells induced by iopromide through inhibiting the activation of NLRP3 inflammasome
Authors: Pei Ming-Xin , Dong Shu-Jun , Gao Xin-Yue , Luo Ting , Fan Dong , Jin Jun-Feng , Zhao Xiao-Duo , Chen Yan-Ling 
Published: March 2022

Abstract
Purpose
In this study, we conducted to explore whether the protective effect of Salvianolic acid B (Sal B) on iopromide-induced human proximal tubular epithelial cells (HK-2 cells) injury is related to the inhibition of NLRP3 inflammasome (TRN: NL8582, registration date: 2020-05-01).
Methods
HK-2 cells were treated with several concentrations of iopromide or Sal B for 3 h, the cell viability was detected by Cell Counting Kit-8 (CCK-8) assay. The levels of reactive oxygen species and the mitochondrial membrane potential were evaluated by DCFH-DA and rhodamine 123 staining, separately. The nucleus morphology of apoptotic cells was observed by DAPI staining. The expression levels of inflammation and apoptosis related proteins were detected by Western blot. In addition, after the introduction of TLR4 inhibitor (TAK-242) to pretreat the cells, the above indicators were detected. The free energy and the docking amino acid residues between Sal B and TLR4 or NLRP3 were analyzed.
Results
Sal B can stably bind to TLR4 or NLRP3, counteract the decrease of cell viability and MMP, the increase of ROS, the number of apoptotic cells, and the expression levels of the above proteins which induced by iopromide. The effect of TAK-242 is similar to that of 100 µmol/L Sal B. However, the pre-treatment group with TAK-242 and Sal B at the same time had no significant difference in cell viability and apoptosis rate compared with the pre-treatment group with TAK-242 or Sal B alone.
Conclusions
Sal B can reduce iopromide-induced HK-2 cells damage through inhibiting NLRP3 inflammasome.
Pharmacokinetic of new analgetic tridecapeptide with an octaarginine vector investigated after original analytical approach
Authors: Kosman Vera , Faustova Natalya , Karlina Marina , Makarov Valery , Makarova Marina 
Published: March 2022

Abstract
New analgetic tridecapeptide (TDP) with an octaarginine vector was proposed for clinical use in chronic pain syndrome. The aim of the work was to investigate pharmacokinetic properties of TDP in the form for oral administration. Special analytical approach was proposed because classical chromatographic methods are low powerful for peptides quantification in biological matrices. The study was carried out on male rats and rabbits with a single oral administration of the drug in three doses, a single intravenous administration in one dose and multiple administrations to rats in one dose. To determine TDP concentration in blood plasma, tissues, and excretes, enzyme immunoassay with commercially available reagent kit for similar target analyte (Elisa kit for 1-Deamino 8D-Arginine Vasopressin (DDAVP), Cloud Clone Corp., USA) have been developed and validated. Pharmacokinetic parameters were calculated by noncompartment method of statistical moments.The pharmacokinetics of TDP was found to be linear after single administration in the dose range 10-50 mg/kg for rats and 5-25 mg/kg for rabbits. The absolute bioavailability of the TDP after oral (intragastrical) via intravenous administration for rats and rabbits was about 8-16%.The active substance was intensively distributed into muscles, liver, spleen, the lowest tissue distribution was detected for kidneys. TDP was excreted with urine in trace amounts (about 0.2%), with feces – about 1.2%; repeated administration did not lead to its cumulation. Pharmacokinetics parameters of new analgetic tridecapeptide with an octaarginine vector were evaluated after original analytical approach. Final study included all main areas necessary to characterize the original drug pharmacokinetic.
Healing of ROS-induced cerebral ischemia/reperfusion injury by sustainable drug “chiral gold nanoclusters”
Authors: Yu Yang , Zhuang Peng-fei , Shen Xiao-lei , Ge Ming-hao , Zou Zhi-ru , Li Dao-yong , Zhang Zhen-xing , Liu Chang , Mei Xi-fan , Li Dan 
Published: March 2022

Abstract
Background
Excessive reactive oxygen species (ROS) is produced by Ischemia-reperfusion (IR) injury that results in serious neurological disruption. Even though many antioxidant drugs can scavenge ROS, there has not been a sustainable drug for brain IR injury due to the limitation of blood-brain barrier (BBB) penetration, insufficient drug efficiency, unexpected side effects. Nanomaterials can improve these problems by delivering organic drugs, but the release of environmental hazards is still a concern.
Results
We used a simple one-pot synthesis method for the fabrication of IR-targeted nanomedicine, i.e., D-glutathione stabilized gold nanoclusters (GSH-AuNCs) for the treatment of brain IR injury. Though no additional drug was delivered, GSH-AuNCs themselves were found to penetrate BBB, suppressing ROS and neuroinflammation. GSH-AuNCs also exhibited excellent renal clearance efficiency due to the ultra-small sizes. This drug neither remains in the body nor pollutes the environment.
Conclusion
With high clearance ability, insignificant environmental concerns, GSH-AuNCs are promising for treating IR injury and can be used as a sustainable drug for practical applications.
Advantages of Deep Learning with Convolutional Neural Network in Detecting Disc Displacement of the Temporomandibular Joint in Magnetic Resonance Imaging
Authors: Lee Yeon-Hee , Won Jong Hyun , Kim Seunghyeon , Auh Q-Schick , Noh Yung-Kyun 
Published: March 2022

Abstract
Aim: This study aimed to investigate the usefulness of deep-learning-based automatic detection of anterior disc displacement (ADD) in patients with temporomandibular joint disorder (TMD) using magnetic resonance imaging (MRI). Methods: Sagittal MRI images of 2520 TMJs were collected from the study population (861 men, 399 women; average age 37.33±18.83 years). A deep learning algorithm with a convolutional neural network (CNN) was performed. Data augmentation and the Adam optimizer were applied to reduce the risk of overfitting the deep learning model. The prediction performance of the models and human experts was compared using area under the curve (AUC). Results: The prediction performance of the fine-tuning model was excellent with an AUC of 0.8775, with acceptable accuracy (0.83%). On comparing the AUC values of the from-scratch (0.8269) and freeze models (0.5858), the performances of the other models were lower than that of the fine-tuning model. Through Grad-CAM visualizations, the fine-tuning scheme focused more on the TMJ disc when judging ADD, and the sparsity was higher than that of the from-scratch scheme (84.69% vs. 55.61%, p-value <0.05). In the three fine-tuning ensembled models using different data augmentation techniques, the prediction accuracy was 0.8333. Moreover, the AUC values of ADD were higher when patients with TMD were divided by age group (0.8549–0.9275) and sex (male: 0.8483, female: 0.9276). The accuracy of the ensemble model was higher than that of the human experts; however, this difference was not significant (p-value: 0.1633–0.0519). Conclusion: Our CNN model had excellent and outstanding accuracy in detecting ADD and could potentially be used by clinicians to evaluate ADD on MR images of TMD patients and improve treatment outcomes.
Removal of arsenic contaminants from water using iron oxide nanoparticles by inductively coupled plasma mass spectrometery
Authors: Hassan Syeda Sara , Zehra Syed Shane , Ahmed Zubair , TALPUR MOHAMMAD YOUNIS Younis , Panhwar Sallahuddin 
Published: March 2022

Abstract
⎫ The adsorption capacity of arsenic on the prepared novel iron oxide nanoparticles was 1.96 mg/g having higher surface area with excellent catalytic degradation property. ⎫ The adsorption dataset best fits in the Langmuir model (pseudo-second-order model). ⎫ To check the removal efficiency of arsenic by iron oxide magnetite nano catalyst (adsorbent) on real water samples was 81.09% and synthetic water prepared on laboratory was 99.8% tested by Inductively couple plasma mass spectrometry (ICP-MS) instrument.
Full-length chloroplast genome of Dongxiang wild rice reveals single-copy region switching in cpDNAs
Authors: Jianguang Liang , Rui Chen , Fantao Zhang , Qian Wang , Yingxia Yang , Mingjie Lv , Shuangyong Yan , Gao Shan 
Published: March 2022

Abstract
Background: Plant chloroplast DNA (cpDNA) typically has a circular structure, including a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (IR1 and IR2). The organization of these four elementary regions LSC-IR1-SSC-IR2 is highly conserved across all plant cpDNAs. Only very a few structural variations (SVs) occurring at the elementary-region level have been reported.
Results: In the present study, we assembled the full-length cpDNA of Dongxiang wild rice line 159 (DXWR159). Using the long PacBio subreads, we discovered a large inversion of SSC and a large duplication of IR in DXWR159 cpDNAs. The large inversion of SSC results in a reverse orientation of SSC. According to the orientation of SSC, the structures of rice cpDNAs can be classified into the forward SSC (SSC-F) and reverse SSC (SSC-R) types. As the most significant finding, both SSC-F and SSC-R type cpDNAs were detected in several seedlings of DXWR159. The inversion of SSC was named as SSC switching.
Conclusions: The frequencies of short tandem repeats (STRs) and large SVs were under-estimated in plant cpDNAs. STRs may not be useful as molecular markers in phylogenetic studies, particularly at low taxonomic levels. SSC switching is not a rarely occurring event and is active in cell growth. We propose that SSC switching ubiquitous occurs in plant cpDNAs and further investigation may reveal novel and important functions associated with SSC switching.
Four decades of experience with cluster headache: description of a series in a University Hospital of Spain
Authors: Pascual Julio , Madera Jorge , Pérez-Pereda Sara , González-Quintanilla Vicente , Suárez Andrea González , Benito Estíbaliz 
Published: March 2022

Abstract
Background: There are few published series of cluster headache. Our aim was to longitudinally describe the epidemiological and clinical features of cluster headache patients in our region since 1980.Methods: Retrospective analysis of the clinical charts of patients diagnosed as cluster headache in a Spanish tertiary hospital.Results: 153 patients were included. 137 (89,5%) were males. Mean age at the beginning of symptoms and diagnosis was 32.8 years (mean deviation 11.3) and 39.5 years (mean deviation 11.4) respectively. 128 had episodic cluster headache (92.2% males) and 25 chronic cluster headache (76% males). Mean age at the beginning was delayed in chronic cluster headache versus episodic cluster headache (37.6 vs 31.8 years; p= 0.023). Four patients (2.6%) had familial antecedents. 3 (2%) referred to visual aura. At diagnosis, 66% were smokers and 15% heavy alcohol drinkers. Median duration of cluster period and median frequency was 60 days every 2 years. 16 (10.5%) had only one cluster period during follow-up.Conclusion: Theoretical prevalence of cluster headache in our area was 0.05%. The diagnostic delay close to 7 years indicates an insufficient recognition of this entity. A late beginning and being a woman were associated with chronic cluster headache, while one out of ten patients only experienced one cluster period.
FIMICS: a panel of long noncoding RNAs for cardiovascular conditions
Authors: Firat Huseyin , Zhang Lu , Baksi Shounak , Leszek Przemyslaw , Schordan Eric , Ounzain Samir , Kottwitz Jan , Heidecker Bettina , Lüscher Thomas F , Pedrazzini Thierry , Devaux Yvan 
Published: March 2022

Abstract

Cardiovascular disorders such as heart failure are leading causes of mortality. Patient stratification via identification of novel biomarkers could improve management of cardiovascular diseases of complex etiologies. Long-noncoding RNAs (lncRNAs) are highly tissue-specific in nature and have emerged as important biomarkers in human diseases. In this study, we aimed to identify cardiac-enriched lncRNAs as potential biomarkers for cardiovascular conditions.
Deep RNA sequencing and quantitative PCR identified differentially expressed lncRNAs between failing and non-failing hearts. An independent dataset was used to evaluate the enrichment of lncRNAs in normal hearts.
We identified a panel of 3233 lncRNAs, named FIMICS, that were either cardiac-enriched or differentially expressed between failing and non-failing hearts. Expression of lncRNAs in blood samples differentiated patients with myocarditis and acute myocardial infarction.
We hereby present the FIMICS panel, a readily available tool to provide insights into cardiovascular pathologies and which could be helpful for diagnosis, monitoring and prognosis purposes.
Dry season prevalence of Plasmodium falciparum in asymptomatic Gambian children, with a comparative evaluation of diagnostic methods
Authors: Mooney Jason P. , DonVito Sophia M. , Jahateh Maimuna , Bittaye Haddy , Bottomley Christian , D'Alessandro Umberto , Riley Eleanor M. 
Published: March 2022

Abstract
Background
Subclinical infection with Plasmodium falciparum remains highly prevalent, yet diagnosing these often low density infections remains a challenge. Infections can be subpatent, falling below the limit of detection for conventional thick-film microscopy and rapid diagnostic testing (RDT). In this study, we characterised the prevalence of subclinical P. falciparum infections in school-aged children at the start of the dry season in the Upper River Region of The Gambia in 2017/2018, with a goal to also compare the utility of different diagnostic tools.
Methods
In a cross-sectional survey of children living in 29 villages on the south bank of the Gambia river (median age of 10 years), matched microscopy, RDT (detecting histidine-rich protein II) and polymerase chain reaction (targeting either 18S rRNA or var gene acidic terminal sequence and (varATS)) were used to determine the prevalence of patent and subpatent infections and to compare the performance of the different diagnostic methods.
Results
The prevalence of varATS qPCR-detectable infections was 10.2% (141/1381) with a median density of 3.12 parasites/µL. Malaria prevalence was highly heterogeneous across the region, ranging from < 1% to ~ 40% prevalence in different village clusters. Compared to varATS, 18S rRNA PCR detected fewer low density infections, with an assay sensitivity of 50% and specificity of 98.8%. Parasite prevalence in the cohort was 2.9% by microscopy and 1.5% by RDT. Compared to varATS qPCR, microscopy and RDT had sensitivities of 11.5% and 9.2%, respectively, although both methods were highly specific (> 98%). Samples that were positive by all three tests (varATS qPCR, RDT and microscopy) had significantly higher parasite densities (median = 1705 parasites/µL) than samples that were positive by varATS qPCR only (median = 2.4 parasites/µL).
Conclusions
The majority of subclinical malaria infections in school-aged children were of extremely low parasite density and detectable only by ultra-sensitive PCR analysis. Understanding the duration of these low density infections, their physiological impact and their contribution to sustained parasite transmission is necessary to inform malaria elimination strategies.
NMR Dipolar Cross-Relaxation Interaction Between Nanoconfined Fluids and Matrix Solids
Authors: Chen Jinhong , Liu Chao , Althaus Stacey , Boudjatit Mohammed 
Published: March 2022

Abstract
Many different methods have been developed to investigate fluid-solid interactions in nanoporous systems. These methods either only work in the liquid phase or provide an indirect measurement by probing the fluid-solid interaction based on a measured property change of the fluid or solid under different sample conditions. Here, we report a direct measurement technique using NMR dipolar cross-relaxation between the nanoconfined fluids and the matrix solids. The method was tested using a methyl functionalized mesostructured silica saturated with methanol as a model sample. A formal theory was established to describe the enhanced dipolar cross-relaxation interaction between the nanoconfined fluids and the matrix solids. Both the experiment and theory showed that nanoconfinement of the fluids enhances the dipolar cross-relaxation interaction between the fluid and the matrix solids, which can be applied to investigate the fluid-solid interaction for various materials of similar nanostructure.