bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of 18F-FDG PET/CT in predicting the pathological response to neoadjuvant PD-1 blockade in combination with chemotherapy for resectable esophageal squamous cell carcinoma
Authors: Wang Xiaoyan , Yang Weixiong , Zhou Qian , Luo Hui , Chen Wenfang , Yeung Sai-Ching Jim , Zhang Shuishen , Gan Yi , Zeng Bo , Liu Zhenguo , Feng Shiting , Zhang Xiangsong , Cheng Chao 
Published: May 2022

Abstract
Purpose Accurate assessment of residual disease of tumor and lymph nodes after neoadjuvant immunochemotherapy is crucial in the active surveillance for patients with pathological complete response (pCR) and the optimal extent of lymphadenectomy for patients with non-pCR. This post-hoc analysis aimed to evaluate the performance of 18F-FDG PET/CT to predict the pathological response to neoadjuvant immunochemotherapy for esophageal squamous cell carcinoma (ESCC).Methods Fifty-eight resectable ESCC patients, received two cycles of camrelizumab in combination with chemotherapy were enrolled in the final analysis. The 18F-FDG PET/CT scans were acquired at baseline (scan-1) and after immunochemotherapy but prior to surgery (scan-2). Maximum standardized uptake value (SUVmax), mean standardized uptake value (SUVmean), tumor-to-blood pool SUVmax ratio (SUVTBR), metabolic tumor volume (MTV) and total lesion glycolysis (TLG) were evaluated for their association with the pathological response to immunochemotherapy.Results Nineteen patients (32.8%, 19/58) had pCR and thirty-nine patients (67.2%, 39/58) had non-pCR after two doses of camrelizumab and chemotherapy. At scan-2, the SUVmax, SUVmean, SUVTBR, TLG and MTV were significantly lower in pCR than that in non-pCR patients. Decrease in TLG and MTV between scan-2 and scan-1 of the same patient were significantly higher in the pCR than in the non-pCR group. In the receiver operating characteristic curve analysis, SUVmax, SUVmean, SUVTBR, TLG and MTV in scan-2 showed excellent predictive value for the pCR of primary tumors. Furthermore, SUVmax in scan-2 were higher in positive lymph nodes than that in negative ones, suggesting a high negative predictive ability (98.6%) with a cut-off value at 1.4.Conclusion The parameters of 18F-FDG PET/CT have the excellent performance for predicting pCR after the combined neoadjuvant immunochemotherapy in resectable ESCC.Trial registration: ChiCTR ChiCTR2000028900. Registered 6 January 2020.
A survey on attention mechanisms for medical applications: are we moving towards better algorithms?
Authors: Gonçalves Tiago , Rio-Torto Isabel , Teixeira Luís F. , Cardoso Jaime S. 
Published: May 2022

Abstract
The increasing popularity of attention mechanisms in deep learning algorithms for computer vision and natural language processing made these models attractive to other research domains. In healthcare, there is a strong need for tools that may improve the routines of the clinicians and the patients. Naturally, the use of attention-based algorithms for medical applications occurred smoothly. However, being healthcare a domain that depends on high-stake decisions, the scientific community must ponder if these high-performing algorithms fit the needs of medical applications. With this motto, this paper extensively reviews the use of attention mechanisms in machine learning (including Transformers) for several medical applications. This work distinguishes itself from its predecessors by proposing a critical analysis of the claims and potentialities of attention mechanisms presented in the literature through an experimental case study on medical image classification with three different use cases. These experiments focus on the integrating process of attention mechanisms into established deep learning architectures, the analysis of their predictive power, and a visual assessment of their saliency maps generated by post-hoc explanation methods. This paper concludes with a critical analysis of the claims and potentialities presented in the literature about attention mechanisms and proposes future research lines in medical applications that may benefit from these frameworks.
Combinatorial algorithms guide economic deliberation
Authors: Hong Tao , Stauffer William 
Published: May 2022

Abstract
Economic deliberations often require sophisticated analysis, but the behavioral algorithms and neurobiological mechanisms for complex deliberations remain unknown. We asked nonhuman primates (NHPs) to select optimal, or suboptimal, item subsets in a modified optimization problem. Surprisingly, the NHP behavior reflected computational algorithms – some that rely on combinatorial reasoning – and the deliberation times reflected the number of operations the best-matching algorithms used. Artificial neural networks revealed that constructing combinatorial solutions required greater computational resources than their greedy counterparts. These results provide mechanistic insights into the sophisticated reasoning skills that support economic deliberation.
Fine mapping of a reduced height gene Rht22 in Jianyangailanmai (Ttiticum turgidum L., 2n=4x=28, AABB)
Authors: Wang Chao , Bao Yunjing , Yao Qin , Long Dan , Xiao Xue , Fan Xing , Kang Houyang , Zeng Jian , Sha Lina , Zhang Haiqin , Wu Dandan , Zhou Yonghong , Zhou Qiang , Wang Yi , Cheng Yiran 
Published: May 2022

Abstract
As the valuable germplasm resources of wheat genetic improvement, tetraploid wheat has several reduced height (Rht) genes that reduced plant height and enhanced harvest index. Rht22 discovered from Jianyangailanmai (JAM, Ttiticum turgidum L., 2n = 4x = 28, AABB), significantly increases in spikelet number per spike, while its accurate position was still unknown. In this study, a high-density genetic map was constructed by specific-length amplified fragment sequencing (SLAF-seq) in F7 RIL_DJ population derived from a cross between dwarf Polish wheat (DPW, Ttiticum polonicum L., 2n = 4x = 28, AABB) and JAM. Two plant height loci, Qph.sicau-4B and Qph.sicau-7A, were mapped on 4BS and 7AS, respectively. Qph.sicau-7A on 7AS with the interval of 0.33-4.46Mb was recommended as the candidate region of Rht22. Fine mapping confirmed and narrowed Rht22 on 7AS between xbag295.s53 and xb295.191 in three different populations. The physical region ranged from 0.53 to 1.48 Mb and included 18 candidate genes. Transcriptome analysis of two pairs of NILs found 135 differentially expressed genes (DEGs) associated with semi-dwarfism. Out of 135 DEGs, 83 annotated DEGs participated in hormones synthesis and signal transduction, cell wall composition, DNA replication, microtubules and phragmoplast arrays were significant down-regulation in semi-dwarf line. Thus, Rht22 disturbs these processes to impair the cell proliferation, and then reduces cell number of internode to cause semi-dwarfism in JAM.
Selection pressure dominates the use of synonymous codons in genes linked to epilepsy
Authors: Chaudhary Kaustubh Pramod , Sophiarani Yengkhom , Nath Anupam , Tiwari Rahul , Bordoloi Hemashree , Gupta Suruchi , Hanjabam Joykishan Sharma , Singh Ashish , Malakar Arup Kumar , Paul Prosenjit 
Published: May 2022

Abstract
Bioinformatic approaches were utilized to investigate the pattern of codon usage in 109 epilepsy-related genes. The genes were found to be rich in G and C nucleotides, with GC usage 7% higher than AT. Preferred codon analysis confirmed the dominance of G and C at the wobble position of codons. CAG is the most frequently used codon. The ENc analysis, on the other hand, did not reveal any exceptional codon usage bias. Correlation of GC content at the first and second codon positions with the third codon position (neutrality plot) suggested the impact of selection pressure in shaping the GC enriched compositional pattern observed in epilepsy-related genes. It was further confirmed by correspondence analysis. Altogether, our findings imply that the pattern of evolutionary processes (especially selection pressure) operating on epilepsy-related genes, might aid in the development of novel therapies.
Effects of Cardiac Rehabilitation in Cardiopulmonary Fitness with High Risk Myocardial Infarction
Authors: Choi Seok Yeon , Kim Ji Hee 
Published: May 2022

Abstract
BackgroundTo compare the effects of cardiac rehabilitation on the degree of improvement in cardiopulmonary fitness (CPF) in patients at high risk of myocardial infarction (MI).MethodsPatients commissioned for cardiac rehabilitation between January 2016 and December 2020 were screened for risk stratification based on the American Association of Cardiovascular and Pulmonary Rehabilitation guidelines. We retrospectively reviewed patients who underwent both an initial and 3 months after the onset exercise tolerance test (ETT). During this period, 42 subjects were included of which 26 underwent at least one CR program and 16 did not. The results of CPF improvement were measured as VO2 peak, VEpeak, and METs values derived through ETT.ResultsPrior to ETT, all demographic features, including ejection fraction, showed no significant differences between the two groups. The initial CPF values were the same. However, after three months, the VO2 peak and MET values showed significant differences between the two groups. Contrary to our expectations, the VEpeak did not show the same results; however, when compared within each group, the CR participants showed a significant change, whereas the CR non-participants did not, suggesting that CR affects VE peak enhancement. Additionally, exercise time differed significantly between the two groups.ConclusionsCPF values and exercise time increased significantly after 3 months in CR participants. Although the VEpeak showed no significant change between the two groups, the CR participants showed a significant increase after three months, whereas the CR non-participants did not.
Prognostic models for short-term annual risk of severe acute complications and mortality in patients living with type 2 diabetes using a national medical claim database
Authors: Vimont Alexandre , Béliard Sophie , Valéro René , Leleu Henri , Durand-Zaleski Isabelle 
Published: May 2022

Abstract
ObjectivePrognostic models in patients living with diabetes allow physicians to estimate individual risk based on medical records and biological results. Clinical risk factors are not always all available to evaluate these models so that they may be complemented with models from claims databases. The objective of this study was to develop, validate and compare models predicting the annual risk of acute severe complications and mortality in patients living with type 2 diabetes (T2D) from a national claims data.Research design and methodsAdult patients with T2D were identified in a national medical claims database through their history of treatments or hospitalizations. Prognostic models were developed using logistic regression (LR), random forest (RF) and neural network (NN) to predict annual risk of outcome: (1) severe acute cardiovascular (CV) complications, (2) other severe acute T2D-related complications, and (3) all-cause mortality. Risk factors included demographics, comorbidities, the adjusted Diabetes Severity and Comorbidity Index (aDSCI) and diabetes medications. Model performance was assessed using discrimination (C-statistics), balanced accuracy, sensibility and specificity.ResultsA total of 22,708 patients with T2D were identified, with mean age of 68 years and average duration of T2D of 9.7 years. Age, aDSCI, disease duration, diabetes medications and chronic cardiovascular disease were the most important predictors for all outcomes. Discrimination with C-statistic ranged from 0.715 to 0.786 for severe acute CV complications, from 0.670 to 0.847 for other severe complications and from 0.814 to 0.860 for all-cause mortality, with RF having consistently the highest discrimination.ConclusionThe proposed models reliably predict acute severe complications and mortality in patients with T2D, without requiring medical records or biological measures. These predictions could be used by payers to alert primary care providers and high-risk patients living with T2D.
MVDroid: an Android malicious VPN detector using neural networks
Authors: Seraj Saeed , Khodambashi Siavash , Pavlidis Michalis , Polatidis Nikolaos 
Published: May 2022

Abstract
When it comes to protecting our privacy, most Virtual Private Networks (VPNs) fail. Many of the popular VPNs are not safe to use specially if we are using a VPN to protect our privacy online. VPNs can look perfect on the surface, yet still be an absolute privacy and security disaster when we take a closer look. Some VPNs will infect our computer with malware, install hidden tracking libraries on our devices, steal private information, leave our data exposed to third parties, and even steal our bandwidth. In general, we should be cautious when downloading any VPN app on our mobile device. Hence, there is a need for detection of malicious VPNs before installing them on our Android mobile device. This article delivers a dataset of Android VPNs, including malicious or benign, and an optimized multi-layer perceptron neural network for detecting VPNs infected by malwares based on the permissions of the apps. Experimental results show that the pro[1]posed methodology is both practical and effective while it out performs other standard classifiers in terms of accuracy, precision, and recall.
Manipulating coordination geometry dependent electron coupling for
high-current-density electrocatalytic water oxidation
Authors: Zhao Sheng , Hu Feng , Yin Lijie , Li Linlin , Chang Yu-Ming , Chen Han-Yi , Peng Shengjie 
Published: May 2022

Abstract
Understanding the structure-activity relationship between the coordination geometry of metal sites and electron structure is a crucial pathway to analyze the activity origin of electrocatalytic oxygen evolution (OER). Herein, we report a conceptual advance, which presents the correlation between coordination geometry distortion of active sites and effect of oxygen atom mediated electron interactions on OER. Ni2+ ions are introduced into FeWO4 on Ni foam via self-substitution to form Fe–O–Ni unity and manipulate the coordination geometry as well as d-electron of the Fe sites. Structural regulation optimizes the adsorption energy of OER intermediates on the Fe sites. Fe0.53Ni0.47WO4/NF with the optimized coordination geometry can achieve an ultra-low overpotential of 203 mV@100 mA cm− 2 and 240 mV@1000 mA cm− 2 with robust stability for 500 hours in alkaline conditions. The research develops novel electrocatalysts with impressive OER performance and provides new insights into the design of highly active catalytic systems.
Development and Validation of the Ayurvedic Nutritional Assessment Scale
Authors: Mukta  , Harti Shivakumar 
Published: May 2022

Abstract
IntroductionThe bodies as well as the diseases are formed by the food; happiness and misery are dependent on the wholesome and unwholesome foods and hence an adequate nutritional level is an essential pillar for the well being. Before prescribing any form of dietary or lifestyle changes it is essential to understand the condition and requirement of the person, hence an assessment beforehand helps in better prescription. The aim of the current study was to develop and validate a nutritional assessment scale , with an applicability in Ayurvedic facilities for research and clinical practice.MATERIALS AND METHODS The development and validation of the Ayurvedic nutritional assessment scale was done in 3 phases. First phase included literature review for item selection and consensus with experts, second phase tool development and validation and final phase the empirical evaluation was done in which the tool was applied in the field trial. RESULTS Total items in the questionnaire were 74 , the scale was found valid in content validity and construct validity and reliable for internal consistency
Energy storage performance of nitrogen doped reduced graphene oxide/co-doped polyaniline nanocomposites
Authors: Altınışık Hasan , Getiren Bengü , Çıplak Zafer , Soysal Furkan , Yildiz Nuray 
Published: May 2022

Abstract
The design and exploration of carbon-based electrode materials have become highly significant for developing supercapacitor technology, which has attracted considerable attention in energy storage systems. Here, nitrogen-doped reduced graphene oxide (N-rGO) – Polyaniline (PANI) nanocomposites were synthesized by a facile two-step method in which in situ polymerization of aniline monomer was performed on hydrothermally synthesized N-rGO nanosheets in DBSA and H2SO4 medium for co-doping of PANI chains. The effects of acid concentrations (DBSA:H2SO4 0.5 − 0.25:1 n/n) and N-rGO:aniline ratio (N-rGO:aniline 1:4–10 m/m) used in the preparation of the electrode material on the capacitive properties were investigated. It is found that the co-doped N-rGO-PANI nanocomposites exhibit a high specific capacitance of 346.3 Fg− 1 at 1 Ag− 1, remarkable rate capacity (99.9%, 1–10 Ag− 1) and excellent cycling stability at 5 Ag− 1 (81.3%, 5000 cycles) in a two-electrode system. As a result, constructing co-doped PANI chains and N-doped rGO provided a viable and simple way to improve the capacitive performances of supercapacitors.
Functional Subsets of Plasma Cells Associated with Amyloid Production and Venetoclax Sensitivity in Light Chain Amyloidosis
Authors: Wang Xuezhu , Han Hongxiao , Sun Jian , Wang Qi , Gao Xue-min , Shen Kai-ni , Zhang Lu , Zhao Yushan , Cao Xin-xin , Qian Minping , Chen Yang , Li Jian 
Published: May 2022

Abstract
Light-chain amyloidosis (AL) is characterised by a systematic deposition of amyloidogenic immunoglobulin light chains produced by pathogenic bone marrow plasma cells (BMPCs), the features of which remain elusive. Herein, we conducted a single-cell RNA-seq and image flow cytometry analysis of BMPCs in AL in comparison with those in healthy controls and their precursors: monoclonal gammopathy of undetermined significance (MGUS). We identified seven BMPC subsets with overlapping but distinct functions such as DNA repair, cell proliferation, osteoclast differentiation, chromatin organisation, and immunoglobulin production. The subsets enriched in AL overexpressed amyloid-beta binding protein-encoding genes, such as apolipoprotein E (APOE) and cystatin 3 (CST3), and exhibited plasmablastic morphology. The subsets related to aberrant light-chain production in AL upregulated pathways of neutrophil degranulation and transportation to as well as modifications in the Golgi apparatus, especially that of N-linked protein glycosylation. The predominant subset was most susceptible to glucocorticoid and proteasome inhibitors and highly expressed venetoclax sensitivity-associated genes in t(11;14) AL. We further validated a patient subgroup featuring a larger proportion of the predominant subset and a higher expression of cyclin D1 (CCND1) and venetoclax sensitivity-associated genes. Our findings provide insights into the mechanisms underlying the functional heterogeneity of BMPCs in AL.
Isotretinoin treatment upregulates the expression of p53 in the skin and sebaceous glands of patients with acne vulgaris
Authors: Agamia Naglaa F. , Mulla K. F. El , Elsayed N. , Ghazala R. A. , Maksoud R. Abdel El , Elmonem E. Abdel , Talat E. , Zaki I. I. , Sabah R. , Melnik B. C. 
Published: May 2022

Abstract
The transcriptomic regulation induced by isotretinoin (13-cis retinoic acid) is still a matter of debate as short-term exposures of immortalized sebocytes with isotretinoin produced conflicting results. Based on translational evidence, it has been hypothesized that oral isotretinoin treatment upregulates the expression of the transcription factor p53. Twenty-five patients suffering from acne vulgaris were treated with isotretinoin (0.6 mg/kg body weight) for 6 weeks. Biopsies from back skin were taken before and after isotretinoin treatment for the determination of p53 expression by immunohistochemical staining, quantification of p53 protein concentration by enzyme-linked immunosorbent assay and TP53 gene expression by quantitative reverse transcription real time PCR. Fifteen socio-demographically cross-matched healthy volunteers served as controls. Isotretinoin treatment significantly increased the nuclear expression of p53 in sebaceous glands of treated patients compared to pre-treatment levels and p53 levels of untreated controls. Furthermore, the p53 protein and gene expression significantly increased in the skin after treatment. The magnitude of p53 expression showed an inverse correlation to acne severity score and body mass index. Under clinical conditions, isotretinoin induced the expression of p53, which controls multiple transcription factors involved in the pathogenesis of acne vulgaris including FoxO1, androgen receptor and critical genes involved in the induction of autophagy and apoptosis. Increased p53-FoxO1 signalling enhanced by systemic isotretinoin treatment explains the underlying transcriptomic changes causing sebum suppression but also the adverse effects associated with systemic isotretinoin therapy.
Development and characterization of EST-SSR markers in Rhodomyrtus tomentosa based on transcriptome
Authors: Sun Lina , Li Jinhua , Sun Kaidao , Wang Huaxin , Yang Kaitai , Chen Qi , Lin Mao 
Published: May 2022

Abstract
Rhodomyrtus tomentosa (Ait.) Hassk is a flowering evergreen plant with traditional medicine and ornamental usages. This study aimed to develop a set of EST-SSRs markers for genetic diversity analysis of R. tomentosa. Transcriptome sequencing was performed to obtain the expressed sequence tags in different plant tissues. A total of 51,486 unigenes with a mean length of 1,173 bp were achieved. 18,879 SSRs were identified in 14,132 unigenes, in which 3,541 unigenes contained more than one SSR. The top three SSR repeat types were mononucleotide (8,126, 43.04%), dinucleotide (5,846, 31.06%) and trinucleotide (4,610, 24.42%). The most abundance motifs were A/T (7,816, 41.40%), followed by AG/CT (5,002, 26.50%) and AAG/CTT (934, 4.95%). Of these SSRs, 11,726 SSRs were eligible for designing of flanking primers. Among the 100 randomly selected primers, 50 primers generated corresponding PCR products, whereas 23 primers were polymorphic. Thirteen primers with good reproducibility were used to characterize the genetic relationship of sixteen natural R. tomentosa plants. The mean value of observed heterozygosity (Ho), expected heterozygosity (He), fixation index (Fst), and Shannon information index (I) were 0.240, 0.414, 0.413, and 0.641, respectively. UPGMA (unweighted pair-group method with arithmetic averages) dendrogram divided the sixteen R. tomentosa plants into five groups, which were able to distinguish the plants according to geographical origin. This study presented a set of EST-SSRs that could be useful for population genetic relationship analysis in R. tomentosa.