bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inter-assay variability of next-generation sequencing-based gene panels
Authors: Quy Pham Nguyen , Fukuyama Keita , Kanai Masashi , Kou Tadayuki , Kondo Tomohiro , Yoshioka Masahiro , Matsubara Junichi , Sakuma Tomohiro , Minamiguchi Sachiko , Matsumoto Shigemi , Muto Manabu 
Published: April 2022

Abstract
Background
Tumor heterogeneity has been known to cause inter-assay discordance among next-generation sequencing (NGS) results. However, whether preclinical factors such as sample type, sample quality and analytical features of gene panel can affect the concordance between two different assays remains largely unexplored.

Methods
Replicate sets of DNA samples extracted from formalin-fixed paraffin-embedded tissues (FFPE) (n = 20) and fresh frozen (FF) tissues (n = 10) were herein analyzed using a tumor-only (TO) and paired tumor–normal (TN) gene panel in laboratories certified by the Clinical Laboratory Improvement Amendment. Reported variants from the TO and TN panels were then compared. Furthermore, additional FFPE samples were sequentially sliced from the same FFPE block and submitted to another TN panel assay.

Results
Substantial discordance (71.8%) was observed between the results of the two panels despite using identical DNA samples, with the discordance rate being significantly higher for FFPE samples (p < 0.05). Among the 99 variants reported only in the TO panel, 32.3% were consistent with germline variants, which were excluded in the TN panel, while 30.3% had an allele frequency of less than 5%, some of which were highly likely to be artificial calls. The comparison of two independent TN panel assay results from the same FFPE block also showed substantial discordance rate (55.3%).

Conclusions
In the context of clinical settings, our comparative analysis revealed that inter-NGS assay discordance commonly occurred due to sample types and the different analytical features of each panel.
Distinct lipid membrane interaction and uptake of differentially charged nanoplastics in bacteria
Authors: Dai Shang , Ye Rui , Huang Jianxiang , Wang Binqiang , Xie Zhenming , Ou Xinwen , Yu Ning , Huang Cheng , Hua Yuejin , Zhou Ruhong , Tian Bing 
Published: April 2022

Abstract
Background
Nanoplastics have been recently found widely distributed in our natural environment where ubiquitously bacteria are major participants in various material cycles. Understanding how nanoplastics interact with bacterial cell membrane is critical to grasp their uptake processes as well as to analyze their associated risks in ecosystems and human microflora. However, little is known about the detailed interaction of differentially charged nanoplastics with bacteria. The present work experimentally and theoretically demonstrated that nanoplastics enter into bacteria depending on the surface charges and cell envelope structural features, and proved the shielding role of membrane lipids against nanoplastics.

Results
Positively charged polystyrene nanoplastics (PS-NH2, 80 nm) can efficiently translocate across cell membranes, while negatively charged PS (PS-COOH) and neutral PS show almost no or much less efficacy in translocation. Molecular dynamics simulations revealed that the PS-NH2 displayed more favourable electrostatic interactions with bacterial membranes and was subjected to internalisation through membrane penetration. The positively charged nanoplastics destroy cell envelope of Gram-positive B. subtilis by forming membrane pore, while enter into the Gram-negative E. coli with a relatively intact envelope. The accumulated positively charged nanoplastics conveyed more cell stress by inducing a higher level of reactive oxygen species (ROS). However, the subsequently released membrane lipid-coated nanoplastics were nearly nontoxic to cells, and like wise, stealthy bacteria wrapped up with artifical lipid layers became less sensitive to the positively charged nanoplastics, thereby illustrating that the membrane lipid can shield the strong interaction between the positively charged nanoplastics and cells.

Conclusions
Our findings elucidated the molecular mechanism of nanoplastics’ interaction and accumulation within bacteria, and implied the shielding and internalization effect of membrane lipid on toxic nanoplastics could promote bacteria for potential plastic bioremediation.

Graphical Abstract
Early and strong antibody responses to SARS-CoV-2 predict disease severity in COVID-19 patients
Authors: Plūme Jānis , Galvanovskis Artis , Šmite Sindija , Romanchikova Nadezhda , Zayakin Pawel , Linē Aija 
Published: April 2022

Abstract
Background
Antibody response to SARS-CoV-2 is a valuable biomarker for the assessment of the spread of the virus in a population and evaluation of the vaccine candidates. Recent data suggest that antibody levels also may have a prognostic significance in COVID-19. Most of the serological studies so far rely on testing antibodies against spike (S) or nucleocapsid (N) protein, however antibodies can be directed against other structural and nonstructural proteins of the virus, whereas their frequency, biological and clinical significance is unknown.

Methods
A novel antigen array comprising 30 SARS-CoV-2 antigens or their fragments was developed and used to examine IgG, IgA, IgE and IgM responses to SARS-CoV-2 in sera from 103 patients with COVID-19 including 34 patients for whom sequential samples were available, and 20 pre-pandemic healthy controls.

Results
Antibody responses to various antigens are highly correlated and the frequencies and peak levels of antibodies are higher in patients with severe/moderate disease than in those with mild disease. This finding supports the idea that antibodies against SARS-CoV-2 may exacerbate the severity of the disease via antibody-dependent enhancement. Moreover, early IgG and IgA responses to full length S protein may be used as an additional biomarker for the identification of patients who are at risk of developing severe disease. Importantly, this is the first study reporting that SARS-CoV-2 elicits IgE responses and their serum levels positively correlate with the severity of the disease thus suggesting a link between high levels of antibodies and mast cell activation.

Conclusions
This is the first study assessing the prevalence and dynamics IgG, IgA, IgE and IgM responses to multiple SARS-CoV-2 antigens simultaneously. Results provide important insights into the pathogenesis of COVID-19 and have implications in planning and interpreting antibody-based epidemiological studies.
Comparison of the effects of different calorie amounts of enteral nutrition in hypercatabolism associated with ghrelin-POMC in endotoxemic rats
Authors: Duan Jianfeng , Cheng Minhua , Xu Yali , Tang Shaoqiu , Li Xiaoyao , Chen Yan , Lu Huimin , Gao Tao , Yu Wenkui 
Published: April 2022

Abstract
Background
Hypercatabolism often occurs in critically ill patients, and it increases infection rates and mortality in these patients. Enteral nutrition (EN) is commonly used in case of hypercatabolism. However, the effect of amount of calories in EN on hypercatabolism remains unexplored.

Objective
Here, we compared the effect of low-calorie, medium-calorie and high-calorie EN on hypercatabolism in the acute phase of endotoxemia, which is associated with gastrointestinal hormones and hypothalamic neuropeptide proopiomelanocortin (POMC).

Methods
Overall 84 adult male Sprague–Dawley rats were used for research. A set of rats were divided into 5 groups, Control (NS) and lipopolysaccharide (LPS) groups were fed a standard chow diet; LPS + L (LPS + 40 kcal/kg/day EN), LPS + M (LPS + 80 kcal/kg/day EN) and LPS + H (LPS + 120 kcal/kg/day EN) groups received EN through a gastric tube for 3 days. Another set of rats were used for parallel control experiment and divided into 5 groups: NS + F (saline + fasting) and LPS + F (LPS + fasting) groups were given no food, NS + L (saline + 40 kcal/kg/day EN), NS + M (saline + 80 kcal/kg/day EN) and NS + H (saline + 120 kcal/kg/day EN) groups received EN through a gastric tube for 3 days. Hypercatabolism was evaluated by assessing skeletal muscle protein synthesis and atrophy, insulin resistance, and corticosterone levels. Moreover, serum inflammatory factors, gastrointestinal hormones, hypothalamic ghrelin, growth hormone secretagogue receptor-1α, hypothalamic neuropeptide, and intestinal injury indicators were detected.

Results
Low-calorie EN effectively increased serum and hypothalamic ghrelin possibly due to slight intestinal barrier damage, thereby decreasing hypothalamic POMC expression; consequently, it alleviated rat insulin resistance, reduced blood cortisol levels and muscle atrophy, and improved the survival rate of rats in the acute phase of endotoxemia. Interestingly, with an increase in calories in enteral nutrition, the aforementioned effects did not increase.

Conclusions
Low-calorie EN could effectively increase gastrointestinal hormone ghrelin by reducing intestinal damage and suppressing POMC expression to ameliorate hypercatabolism when compared with medium-calorie and high-calorie EN. Therefore Low-calorie EN may be preferred for providing EN in the acute stage of endotoxemia.
L-theanine prevents progression of nonalcoholic hepatic steatosis by regulating hepatocyte lipid metabolic pathways via the CaMKKβ-AMPK signaling pathway
Authors: Liang Juanjuan , Gu Lili , Liu Xianli , Yan Xintong , Bi Xiaowen , Fan Xirui , Zhou Jinyi , Lu Shuai , Luo Lan , Yin Zhimin 
Published: April 2022

Abstract
Background
L-theanine, a non-protein amino acid was found principally in the green tea, has been previously shown to exhibit potent anti-obesity property and hepatoprotective effect. Herein, we investigated the effects of L-theanine on alleviating nonalcoholic hepatic steatosis in vitro and in vivo, and explored the underlying molecular mechanism.

Methods
In vitro, HepG2 and AML12 cells were treated with 500 μM oleic acid (OA) or treated with OA accompanied by L-theanine. In vivo, C57BL/6J mice were fed with normal control diet (NCD), high‐fat diet (HFD), or HFD along with L-theanine for 16 weeks. The levels of triglycerides (TG), accumulation of lipid droplets and the expression of genes related to hepatocyte lipid metabolic pathways were detected in vitro and in vivo.

Results
Our data indicated that, in vivo, L-theanine significantly reduced body weight, hepatic steatosis, serum levels of alanine transaminase (ALT), aspartate transaminase (AST), TG and LDL cholesterol (LDL-C) in HFD-induced nonalcoholic fatty liver disease (NAFLD) mice. In vitro, L-theanine also significantly alleviated OA induced hepatocytes steatosis. Mechanic studies showed that L-theanine significantly inhibited the nucleus translocation of sterol regulatory element binding protein 1c (SREBP-1c) through AMPK-mTOR signaling pathway, thereby contributing to the reduction of fatty acid synthesis. We also identified that L-theanine enhanced fatty acid β-oxidation by increasing the expression of peroxisome proliferator–activated receptor α (PPARα) and carnitine palmitoyltransferase-1 A (CPT1A) through AMP-activated protein kinase (AMPK). Furthermore, our study indicated that L-theanine can active AMPK through its upstream kinase Calmodulin-dependent protein kinase kinase-β (CaMKKβ).

Conclusions
Taken together, our findings suggested that L-theanine alleviates nonalcoholic hepatic steatosis by regulating hepatocyte lipid metabolic pathways via the CaMKKβ-AMPK signaling pathway.
Rice bacterial blight resistant cultivar selection based on visible/near-infrared spectrum and deep learning
Authors: Zhang Jinnuo , Feng Xuping , Wu Qingguan , Yang Guofeng , Tao Mingzhu , Yang Yong , He Yong 
Published: April 2022

Abstract
Background
Rice bacterial blight (BB) has caused serious damage in rice yield and quality leading to huge economic loss and food safety problems. Breeding disease resistant cultivar becomes the eco-friendliest and most effective alternative to regulate its outburst, since the propagation of pathogenic bacteria is restrained. However, the BB resistance cultivar selection suffers tremendous labor cost, low efficiency, and subjective human error. And dynamic rice BB phenotyping study is absent from exploring the pattern of BB growth with different genotypes.

Results
In this paper, with the aim of alleviating the labor burden of plant breeding experts in the resistant cultivar screening processing and exploring the disease resistance phenotyping variation pattern, visible/near-infrared (VIS–NIR) hyperspectral images of rice leaves from three varieties after inoculation were collected and sent into a self-built deep learning model LPnet for disease severity assessment. The growth status of BB lesion at the time scale was fully revealed. On the strength of the attention mechanism inside LPnet, the most informative spectral features related to lesion proportion were further extracted and combined into a novel and refined leaf spectral index. The effectiveness and feasibility of the proposed wavelength combination were verified by identifying the resistant cultivar, assessing the resistant ability, and spectral image visualization.

Conclusions
This study illustrated that informative VIS–NIR spectrums coupled with attention deep learning had great potential to not only directly assess disease severity but also excavate spectral characteristics for rapid screening disease resistant cultivars in high-throughput phenotyping.
Retrospective evaluation of a robust hybrid planning technique established for irradiation of breast cancer patients with included mammary internal lymph nodes
Authors: Hennet Marina , Radonic Stephan , Schneider Uwe , Hartmann Matthias 
Published: April 2022

Abstract
Background
The irradiation of breast cancer patients with included internal mammary lymph nodes challenges radiation planning with regard to robustness and protection of OARs. In this publication, a feasible hybrid radiation technique is presented with a retrospective dosimetric and radiobiological analysis of patient data of our institute from 2016 to 2020 and robustness analysis.

Methods
The proposed hybrid irradiation technique consists of two IMRT tangents and two partial VMAT fields. The retrospective dosimetric and radiobiological evaluation are made for 217 patient treatments (right- and left-sided). The robustness is evaluated regarding an artificial swelling from 0.4 to 1.5 cm for a random example patient and compared to a pure VMAT planning technique with use of a virtual bolus. The out of field stray dose is calculated for a selected patient plan and compared to alternative radiation techniques.

Results
The coverage D95% of the PTVEval (with breast swelling of 1.5 cm) changes for the hybrid plan from 96.1 to 92.1% of prescribed dose and for the pure VMAT plan from 94.3 to 87%. The retrospective dosimetric evaluation of patient irradiations reveals a Dmean for total lung 6.5 ± 0.9 Gy (NTCP[Semenenko 2008] 2.8 ± 0.5%), ipsilateral lung 10.9 ± 1.5 Gy, contralateral lung 2.2 ± 0.6 Gy, heart 2.1 ± 1.1 Gy (ERR[Schneider 2017] 0.02 ± 0.17%) and contralateral breast 1.7 ± 0.6 Gy. The scatter dose of the hybrid irradiation technique is higher than for pure VMAT and lower than for pure IMRT irradiation.

Conclusions
The feasibility of the proposed planning technique is shown by treating many patients with this technique at our radiotherapy department. The hybrid radiation technique shows a good sparing of the OARs in the retrospective analysis and is robust with regards to a breast swelling of up to 1.5 cm. The slightly higher stray dose of the hybrid technique compared to a pure VMAT technique originates from higher number of MUs and lower conformity.
Applicability of a pathological complete response magnetic resonance-based radiomics model for locally advanced rectal cancer in intercontinental cohort
Authors: Boldrini Luca , Lenkowicz Jacopo , Orlandini Lucia Clara , Yin Gang , Cusumano Davide , Chiloiro Giuditta , Dinapoli Nicola , Peng Qian , Casà Calogero , Gambacorta Maria Antonietta , Valentini Vincenzo , Lang Jinyi 
Published: April 2022

Abstract
Background
Predicting pathological complete response (pCR) in patients affected by locally advanced rectal cancer (LARC) who undergo neoadjuvant chemoradiotherapy (nCRT) is a challenging field of investigation, but many of the published models are burdened by a lack of reliable external validation. Aim of this study was to evaluate the applicability of a magnetic resonance imaging (MRI) radiomic-based pCR model developed and validated in Europe, to a different cohort of patients from an intercontinental cancer center.

Methods
The original model was based on two clinical and two radiomics features extracted from T2-weighted 1.5 T MRI of 161 LARC patients acquired before nCRT, considered as training set. Such model is here validated using the T2-w 1.5 and 3 T staging MRI of 59 LARC patients with different clinical characteristics consecutively treated in mainland Chinese cancer center from March 2017 to January 2018. Model performance were evaluated in terms of area under the receiver operator characteristics curve (AUC) and relative parameters, such as accuracy, specificity, negative and positive predictive value (NPV and PPV).

Results
An AUC of 0.83 (CI 95%, 0.71–0.96) was achieved for the intercontinental cohort versus a value of 0.75 (CI 95%, 0.61–0.88) at the external validation step reported in the original experience. Considering the best cut-off threshold identified in the first experience (0.26), the following predictive performance were obtained: 0.65 as accuracy, 0.64 as specificity, 0.70 as sensitivity, 0.91 as NPV and 0.28 as PPV.

Conclusions
Despite the introduction of significant different factors, the proposed model appeared to be replicable on a real-world data extra-European patients’ cohort, achieving a TRIPOD 4 level.
Translating, contextually adapting, and pilot testing of psychosocial and mental health assessment instruments for Congolese refugees in Rwanda and Uganda
Authors: Kasujja Rosco , Bangirana Paul , Chiumento Anna , Hasan Tasdik , Jansen Stefan , Kagabo Daniel M. , Popa Maria , Ventevogel Peter , White Ross G. 
Published: April 2022

Abstract
Background
Forcibly displaced people are at elevated risk of experiencing circumstances that can adversely impact on mental health. Culturally and contextually relevant tools to assess their mental health and psychosocial needs are essential to inform the development of appropriate interventions and investigate the effectiveness of such interventions.

Methods
We conducted two related studies: (1) to translate and contextually adapt the Patient Health Questionnaire (PHQ-9), a measure of depressive symptomatology, along with assessment instruments measuring levels of daily stress (Checklist for Daily & Environmental Stressors; CDES), social capital (Shortened and Adapted Social Capital Assessment Tool; SASCAT) and perceived social support (Multidimensional Scale of Perceived Social Support; MSPSS) for use with Congolese refugees; (2) to conduct pilot testing of the assessment instruments (including cognitive interviewing about participants’ views of completing them) and a validation of the adapted PHQ-9 using a ‘known group’ approach by recruiting Congolese refugees from refugee settings in Rwanda (n = 100) and Uganda (n = 100).

Results
Study 1 resulted in the translation and adaptation of the assessment instruments. No substantive adaptations were made to the SASCAT or MSPSS, while notable linguistic and contextual adaptations were made in both sites to the CDES and the PHQ-9. The cognitive interviewing conducted in Study 2 indicated that the adapted assessment instruments were generally well received by members of the refugee communities. Participants recruited on the basis that local informants adjudged them to have high levels of depressive symptoms had significantly higher PHQ-9 scores (M = 11.02; SD = 5.84) compared to those in the group adjudged to have low levels of depressive symptoms (M = 5.66; SD = 5.04). In both sites, the adapted versions of the PHQ-9 demonstrated concurrent validity via significant positive correlations with levels of daily stressors. Each of the four adapted assessment instruments demonstrated at least adequate levels of internal consistency in both sites.

Conclusions
The adapted versions of the PHQ-9, CDES, SASCAT and MSPSS are appropriate for use amongst Congolese refugees in Rwanda and Uganda. We recommend further application of the approaches used in the current studies for contextually adapting other assessment instruments in humanitarian settings.
Oncometabolites drive tumorigenesis by enhancing protein acylation: from chromosomal remodelling to nonhistone modification
Authors: Fu Yidian , Yu Jie , Li Fang , Ge Shengfang 
Published: April 2022

AbstractMetabolites are intermediate products of cellular metabolism catalysed by various enzymes. Metabolic remodelling, as a biochemical fingerprint of cancer cells, causes abnormal metabolite accumulation. These metabolites mainly generate energy or serve as signal transduction mediators via noncovalent interactions. After the development of highly sensitive mass spectrometry technology, various metabolites were shown to covalently modify proteins via forms of lysine acylation, including lysine acetylation, crotonylation, lactylation, succinylation, propionylation, butyrylation, malonylation, glutarylation, 2-hydroxyisobutyrylation and β-hydroxybutyrylation. These modifications can regulate gene expression and intracellular signalling pathways, highlighting the extensive roles of metabolites. Lysine acetylation is not discussed in detail in this review since it has been broadly investigated. We focus on the nine aforementioned novel lysine acylations beyond acetylation, which can be classified into two categories: histone acylations and nonhistone acylations. We summarize the characteristics and common functions of these acylation types and, most importantly, provide a glimpse into their fine-tuned control of tumorigenesis and potential value in tumour diagnosis, monitoring and therapy.
Extracellular vesicle IL-32 promotes the M2 macrophage polarization and metastasis of esophageal squamous cell carcinoma via FAK/STAT3 pathway
Authors: Sun Yixuan , Qian Yuzhen , Chen Chunxia , Wang Hongfei , Zhou Xiuman , Zhai Wenjie , Qiu Lu , Zhou Xiaowen , Ning Haoming , Zhao Yumiao , Shi Chao , Han Lu , Qi Yuanming , Wu Yahong , Gao Yanfeng 
Published: April 2022

Abstract
Background
Metastasis is the leading cause of mortality in human cancers, including esophageal squamous cell carcinoma (ESCC). As a pro-inflammatory cytokine, IL-32 was reported to be a poor prognostic factor in many cancers. However, the role of IL-32 in ESCC metastasis remains unknown.

Methods
ESCC cells with ectopic expression or knockdown of IL-32 were established and their effects on cell motility were detected. Ultracentrifugation, Transmission electron microscopy and Western blot were used to verify the existence of extracellular vesicle IL-32 (EV-IL-32). Coculture assay, immunofluorescence, flow cytometry, and in vivo lung metastasis model were performed to identify how EV-IL-32 regulated the crosstalk between ESCC cells and macrophages.

Results
Here, we found that IL-32 was overexpressed and positively correlated to lymph node metastasis of ESCC. IL-32 was significantly higher in the tumor nest compared with the non-cancerous tissue. We found that IL-32β was the main isoform and loaded in EV derived from ESCC cells. The shuttling of EV-IL-32 derived from ESCC cells into macrophages could promote the polarization of M2 macrophages via FAK-STAT3 pathway. IL-32 overexpression facilitated lung metastasis and was positively correlated with the proportion of M2 macrophages in tumor microenvironment.

Conclusions
Taken together, our results indicated that EV-IL-32 derived from ESCC cell line could be internalized by macrophages and lead to M2 macrophage polarization via FAK-STAT3 pathway, thus promoting the metastasis of ESCC. These findings indicated that IL-32 could serve as a potential therapeutic target in patients with ESCC.